B12B-Evolve-A1.txt Graham L. Kendall Modified 10/22/2007 Email grahamkendall74135@yahoo.com I am found on IRC Efnet/Undernet/Dalnet as glk Files on science and religion are found at http://www.grahamkendall.net/ http://snipurl.com/yt8o my url http://tinyurl.com/ydjvt3 my url All are free to use any of this material without limit. Linking to this url is allowed. ******************************************************************************* == With the advent of high-throughput DNA sequencing and whole-genome analysis, it has become clear that the coding portions of the genome are organized hierarchically in gene families and superfamilies. Because the hierarchy of genes, like that of living organisms, reflects an ancient and continuing process of gene duplication and divergence, many of the conceptual and analytical tools used in phylogenetic systematics can and should be used in comparative genomics. Phylogenetic principles and techniques for assessing homology, inferring relationships among genes, and reconstructing evolutionary events provide a powerful way to interpret the ever increasing body of sequence data. In this review, we outline the application of phylogenetic approaches to comparative genomics, beginning with the inference of phylogeny and the assessment of gene orthology and paralogy. We also show how the phylogenetic approach makes possible novel kinds of comparative analysis, including detection of domain shuffling and lateral gene transfer, reconstruction of the evolutionary diversification of gene families, tracing of evolutionary change in protein function at the amino acid level, and prediction of structure-function relationships. A marriage of the principles of phylogenetic systematics with the copious data generated by genomics promises unprecedented insights into the nature of biological organization and the historical processes that created it. === Vietnam houses new plant, animal species HANOI, Vietnam - Scientists have discovered 11 new species of plants and animals in Vietnam, including a snake, two butterflies and five orchid varieties, the World Wildlife Fund said Wednesday. The new species were found in a remote region known as the "Green Corridor" in Thua Thien Hue province in central Vietnam, the international conservation group said. "You only discover so many new species in very special places, and the Green Corridor is one of them," Chris Dickinson, the WWF's chief technical adviser in the region, said in a statement. The new snake species, the white-lipped keelback, generally lives near streams and eats frogs and other small animals, the WWF said. It has a yellow-white stripe along its head, red dots on its body and can grow to more than 30 inches long. The new butterfly species are among eight discovered in Thua Thien Hue since 1996. One is a "skipper," a butterfly that flies in a quick, darting motion. Three of the new orchid species are leafless, which is unusual for orchids, the WWF said. The other new plant species include one in the aspidistra family, which produces a black flower and can subsist in low light, and an arum, which produces yellow flowers surrounded by funnel-shaped leaves. "It's great news for Vietnam," said Bernard O'Callaghan, Vietnam program coordinator for the World Conservation Union. "The jungles and mountains of Vietnam are fascinating places and they continue to surprise scientists." The WWF said all the new species are exclusive to tropical forests in Vietnam's Annamites mountain range. It said all the species in the area are under threat from illegal logging, hunting and development. == The first comprehensive comparison of the genetic blueprints of humans and chimpanzees shows our closest living relatives share perfect identity with 96 percent of our DNA sequence, an international research consortium reported today. http://www.sciam. com/article. cfm?articleID= 9D0DAC2B- E7F2-99DF- 3AA795436FEF8039 A lot more genes may separate humans from their chimp relatives than earlier studies let on. Researchers studying changes in the number of copies of genes in the two species found that their mix of genes is only 94 percent identical. The 6 percent difference is considerably larger than the commonly cited figure of 1.5 percent. http://www.hhmi. org/news/ eichler2. html The traditional comparison cited in textbooks is that the difference is 1.2 percent, based on variations in single base-pairs in gene sequences. "But our data on these duplications shows a 2.7 percent difference, base per base, between chimps and humans," said Eichler. "So when we talk about how similar chimps and humans are, we really need to be careful that we are referring to variation in the whole genome as opposed to just those single-base- pair changes." http://www.scienced aily.com/ releases/ 2007/04/07041214 1025.htm Human-Chimp Differences Uncovered With Analysis Of Rhesus Monkey Genome Science Daily An international consortium of researchers has published the genome sequence of the rhesus macaque monkey and aligned it with the chimpanzee and human genomes. Published April 13 in a special section of the journal Science, the analysis reveals that the three primate species share about 93 percent of their DNA, yet have some significant differences among their genes. == Convergence is found not only in directly observable phenotypic characters, but also at the molecular level. For instance, the protein rhodopsin for color vision is tuned to particular colors by substitutions at key sites, and different species adapting to the same color sometimes use identical substitutions. It can become uncertain whether molecular similarities and identities are due to convergence or common ancestry. Convergence (also called homoplasy) is the independent evolution of similar traits among distantly related organisms such as humans and octopi have similar eye anatomy (although one is inverted, the other verted). Life is replete with examples of convergence on every level: molecular, cellular, even behavioral. Convergence is the key to understanding that evolution, despite its tremendous variety, is fraught with direction == Work of D.M. Raup: the morphospace for the geometry of the shells secreted by the molluscs. Some regions of this morphospace are thickly populated. But other zones are more or less empty. In these, the solutions to the equations that govern the geometry can be used to visualize the hypothetical shapes, but they somehow look wrong. Thus the general morphospace is continuous, but only particular points are realized in the real world determined by evolution. == A Perspective by Leslie Orgel: A simpler nucleic acid, in SCIENCE, 17 Nov 2000, discusses self-replication of the simpler nucleic acid TNA as well as RNA. It seems to me that the self-replicating property of RNA, TNA and similar nucleic acids assures the appearance of life by one route or another == Consider experiments done by Lenski and Travisano with the bacterium Escherichia coli over a large number of generations. It was first separated into several populations. Then they were allowed to diversify, and were separated further. Finally all populations were switched from their customary and agreeable glucose diet to a maltose diet and allowed to try to adapt during 1000 generations. The degree and mode of their adaptation was partly due to convergence, in addition to starting points and chance, and the three could be separated statistically. Over the long term, convergence won. == Dr. Duane Gish (according to AIG, the "foremost creationist debater in the world today"), claimed in 1978 that this transition was impossible because it meant that at one time some ancestral mammal-like reptile had to have had two jaw joints? Gish wrote: "The two most distinguishable osteological differences between reptiles and mammals, however, have never been bridged by a transitional series. All mammals, living or fossil, have a single bone, the dentary, on each side of the lower jaw, and all mammals, living or fossil, have three auditory ossicles or ear bones, the malleus, incus and stapes. In some fossil reptiles the number and size of the lower jaw bones are reduced compared to living reptiles. Every reptile, living or fossil, however, has at least four bones in the lower jaw and only one auditory ossicle, the stapes. . . There are no transitional fossil forms showing, for instance, three or two jawbones, or two ear bones. No one has explained yet, for that matter, how the transitional form would have managed to chew while his jaw was being unhinged and rearticulated, or how he would hear while dragging two of his jaw bones up into his ear." (Gish, 1978, p. 80) Other creationists wrote: "Mammals also have three bones in their ears, while reptiles have only one. Where did the two 'extras' come from? Evolutionary theory attempts to explain it as follows: Reptiles have at least four bones in the lower jaw, whereas mammals have only one; so, when reptiles became mammals, there was supposedly a reshuffling of bones; some from the reptile's lower jaw moved to the mammal's middle ear to make the three bones there and, in the process, left only one for the mammal's lower jaw. However, the problem with this line of reasoning is that there is no fossil evidence whatsoever to support it. It is merely wishful conjecture." (Watchtower and Bible Tract Society, 1985, p. 81)" But, as so often happens, practically no sooner did creationists assert these false claims than the fossils proving science correct were found (although biologists already knew from embryology & genetics that our middle ear bones came from two bones at the rear of the "reptile" jaw, which in mammals is a single bone, the dentary). Another amusing case of this kind was Behe & the walking whale. "Not only is this explanation not "merely wishful conjecture", but it can be clearly seen in a remarkable series of fossils from the Triassic therapsids. The earliest therapsids show the typical reptilian type of jaw joint, with the articular bone in the jaw firmly attached to the quadrate bone in the skull. In later fossils from the same group, however, the quadrate-articular bones have become smaller, and the dentary and squamosal bones have become larger and moved closer together. This trend reaches its apex in a group of therapsids known as cynodonts, of which the genus Probainognathus is a representative. Probainognathus possessed characteristics of both reptile and mammal, and this transitional aspect was shown most clearly by the fact that it had TWO jaw joints--one reptilian, one mammalian: "Probainognathus, a small cynodont reptile from the Triassic sediments of Argentina, shows characters in the skull and jaws far advanced toward the mammalian condition. Thus it had teeth differentiated into incisors, a canine and postcanines, a double occipital condyle and a well-developed secondary palate, all features typical of the mammals, but most significantly the articulation between the skull and the lower jaw was on the very threshhold between the reptilian and mammalian condition. The two bones forming the articulation between skull and mandible. === Palaeolithic hominins (Klein 1994, 1995, 2000). The focus in Europe has centred on Western Europe, and in particular the supposed boundary markers between the Middle and the Upper Palaeolithic at ca. 40 000 BP. These are the time periods in which Neanderthals and Homo sapiens, respectively, occupied Europe. According to this model, the hominins inhabiting Africa between 130 000 and 60 000 BP were physically modern or near-modern, but behaviourally they were very similar to their Neanderthal contemporaries. The Neanderthals are believed to have manufactured a small range of recognisable stone artifact types, with their assemblages varying remarkably little over time and space despite environmental differentiation. It is also suggested that they obtained the raw materials for their stone tools from local sources rather than from afar. This, the model hypothesises, is indicative of small home ranges and/or simple social networks (Klein 1995) . Also, resources such as bone, ivory and shell were rarely intentionally modified with the intention of producing formal artifacts. Although campsites of Neanderthals have been successfully identified, excavations have yielded little or no evidence for either the erection of structures or for any other formal modification of these sites (Klein 1995). It is suggested that the population figures of the Neanderthals were low and they were ineffectual hunter-gatherers who lacked, for example, the ability to fish. Klein (1995) also argues that the Neanderthals left no indisputable evidence for either art or decoration. Whereas the Mousterian Neanderthals produced only small quantities of symbolic artifacts, there are rich bodies of Aurignacian and Gravettian symbolic evidence. These take the form of body ornaments, three dimensional ivory figurines, beads, decorated or engraved or painted slabs, blade and burin technology, bone and ivory and antler tools and projectiles, as well as evidence on these objects for abundant intentional polishing (White 1990). These same Neanderthal-Upper Palaeolithic attributes are applied by Klein (1995) to the African MSA-LSA transition. In this scenario, therefore, the MSA of Africa is equated with the Middle Palaeolithic of Europe in terms of the range of artifacts produced, behavioural patterns and symbolic capacity. An alternative argument has been put forward by Hilary Deacon (1989, 1995; Deacon & Deacon 1999) that, unlike in Africa, Europe was already occupied and in the grips of a glaciation when the first Homo sapiens arrived on the continent during a period of rapid climatic fluctuation with minor interstadials (Palmer 2000). Faced with these challenges, modern homininswould have had to both carve out a niche for themselves as well as find a way of expressing their self-identity. The beginning of the Upper Palaeolithic marks an explosion of archaeological sites, which has been correlated with a significant increase in population numbers; this has usually been the sequence of events upon modern hominins entering vast new territories (Diamond 1998). This would have resulted in the need for innovative ways of hunting and catching more food, and Deacon has suggested that this need manifested itself in specialised fishing and hunting equipment (Deacon & Deacon 1999). Groups would have been in competition with each other both for living space and hunting grounds, and means of identification would have needed to be expressed. Deacon hypothesises this was done via the explosion of art seen in this period, bone and shell ornaments, as well as the innovative stone tool technologies. In other words the Upper Palaeolithic was a regionally distinct phenomenon utilising stylistic symbolic signalling as identity. The summaries of the behavioural implications of the southern African MSA have primarily focused on Klasies River. This is because Klasies River is the most excavated of the southern African MSA sites, with the best understood sequence. Die Kelders hasnt been far behind in Kleins summary of his faunal analysis work and the behavioural implications thereof. As these two sites are, consequently, the most important in the published literature they are included in-depth in this discussions. Southern African sites are amongst the most and best excavated in Africa and it is from here that potentially the best information derives. Other sites apart from Klasies River and Die Kelders have the potential to fill out and broaden our understanding of MSA behaviour when they are considered together as a whole. The literature is a mine of information, but it is also a mix of conflicting ideas. In essence though, unsuitable as it is because of the inherent influence from the European Upper Palaeolithic record, the following are the generally recognised attributes of cognitively modern behaviour (McBrearty & Brooks 2000: 491): Increasing artifact diversity Standardization of artifact types Blade technology Worked bone and other organic materials Personal ornaments and art or images Structured living spaces Ritualistic Economic intensification, reflected in the exploitation of aquatic or other resources that require specialized technology Enlarged geographic range Expanded exchange networks. It can tentatively be proposed that the period of transition from the Acheulian to the MSA stone tool industries also saw the first substantial rise of signs of cognitively modern behaviour. It appears that a mental threshold was broken through. From the evidence presented, when the southern African MSA is looked at as a whole including the unpublished sources of information instead of selective focusing on the better known sites and analyses such as Kleins, then a picture emerges of the behavioural patterns of the MSA humans which is more conclusive than those from the well known published sources alone. Although the hypothesis has its problems, which are detailed above, the weight of evidence appears to be on the side of the MSA humans possessing fully modern human behaviour exhibited through subsistence strategies, distribution on the landscape, and stylistic symbolism in stone and organic artifacts. == Ancestor of the living fossil sheds new light Zoologists called it the find of the century when in 1938, fishermen hoisted ashore a fish thought to have been extinct since the dinosaurs roamed. Called a coelacanth, it was a relative of some of the first landwalking creatures. Now, scientists are reporting a fossil find that helps complete the story: the front fin of an early coelacanth, which is quite different from that of todays coelacanths. It clarifies the evolution of this crucial structure, they say, which in fish descendants evolved into walking limbs and then arms. The fossil reveals connections to even more primitve fish, and shows that the fin bones still had to evolve a fair amount before the first walking creatures arose, according to the scientists. They described the finding in a paper in the July/August issue of the research journal Evolution & Development. People often see coelacanths as living fossils, but thats not quite accurate, said Matt Friedman, a graduate student at the University of Chicago and lead author of the paper. If you look deep in the fossil record to the first members of that group, they are really different and very diverse. Same goes for some other socalled living fossils, he added. The 400 millionyearold coelacanth fossil is the first known of its kind, and fills a shrinking evolutionary gap between fins and limbs, the researchers said. Scientists are interested in early coelacanths because theyre close relatives of the first socalled fleshyfinned fishes. This is the lineage that, with their meaty fins, gave rise to limbed vertebrates that took the first steps onto land. Yet the fossil fin isnt as similar to modern fleshyfinned fish as it is to some primitive members of the other great lineage of bony fishesthe rayfinned fishes, Friedman and colleagues said. These are the largest class of fish, and those whose fins are webs of skin supported by spines. Some living rayfinned fishes such as paddlefishes and sturgeons have a branching arrangement of bones similar to that found in the coelacanth fossil, Friedman and colleagues said. This ends intense debate about the primitive pattern for lobed fins, which involves the ancestry of all limbs, including our own, said the universitys Michael Coates, one the researchers. To understand the developmental evolution of the limbs of tetrapods [fourlimbed vertebrates], we shouldnt be looking at the fins of our nearest living fish relatives lungfishes and coelacanths because theyre far too specialized. Scientists believe another recently discovered fossil is a true missing link between fish and tetrapods. It was a fierce predator dubbed Tiktaalik roseae, which lived 385 million years ago. The early coelacanth fin fossil shows that as far as limbs go, the key difference separating early fleshyfinned fishes and Tiktaalik was in fin bones called radials, Friedman and colleagues wrote. These are widely thought to have evolved into fingers. The fossil coelacanth is named Shoshonia arctopteryx after the Shoshoni people of Wyoming and the Shoshone National Forest in northern Wyoming, where the specimen was found. It was astonishing luck, Friedman said, adding that the fossil had fallen off a cliff about 200 feet high onto some rocks. The fourinch (10 cm) long specimen details the fin of the animal, which the scientists approximate would have been about 18 to 24 inches (45 to 60 cm) long. Zoologists called it the find of the century when in 1938, fishermen hoisted ashore a fish thought to have been extinct since the dinosaurs roamed. Called a coelacanth, it was a relative of some of the first landwalking creatures.Now, scientists are reporting a fossil find that helps complete the story: the front fin of an early coelacanth, which is quite different from that of todays coelacanths. It sheds light on the evolution of this crucial structure, which in the fishs descendants evolved into walking limbs and later arms, scientists say.The fossil reveals connections to even more primitve fish, and shows that the fin bones still had to evolve a fair amount before the first walking creatures arose, according to the scientists. They described the finding in a paper in the July/August issue of the research journal Evolution & Development.People usually think of coelacanths as living fossils, but thats something of a misconception, said Matt Friedman, a graduate student at the University of Chicago and lead author of the paper. If you look deep in the fossil record to the first members of that group, they are really different and very diverse. Same goes for some other socalled living fossils, he added.The 400 millionyearold coelacanth fossil is the first known of its kind, and fills a shrinking evolutionary gap between fins and limbs, the researchers said. Scientists are interested in early coelacanths because theyre close relatives of the first socalled fleshyfinned fishes. This is the lineage that, with their meaty fins, gave rise to limbed animals, which took the first steps onto land.Yet the fossil fin isnt as similar to modern fleshyfinned fish as it is to some primitive members of the other great lineage of bony fishesthe rayfinned fishes, Friedman and colleagues said. These are the largest class of fish, and those whose fins are webs of skin supported by spines. Some living rayfinned fishes such as paddlefishes and sturgeons have a branching arrangement of bones similar to that found in the coelacanth fossil, Friedman and colleagues said.This ends intense debate about the primitive pattern for lobed fins, which involves the ancestry of all limbs, including our own, said the universitys Michael Coates, one the researchers. To understand the developmental evolution of the limbs of tetrapods [fourlimbed vertebrates], we shouldnt be looking at the fins of our nearest living fish relativeslungfishes and coelacanthsbecause theyre far too specialized. Scientists believe another recently discovered fossil is a true missing link between fish and tetrapods. It was a fierce predator dubbed Tiktaalik roseae, which lived 385 million years ago.The early coelacanth fin fossil shows that as far as limbs go, the key difference separating early fleshyfinned fishes and Tiktaalik was in fin bones called radials, Friedman and colleagues wrote. These are widely thought to have evolved into fingers.The fossil coelacanth is named Shoshonia arctopteryx after the Shoshoni people of Wyoming and the Shoshone National Forest in northern Wyoming, where the specimen was found. It was astonishing luck, Friedman said, adding that the fossil had fallen off a cliff about 200 feet high onto some rocks. The fourinch (10 cm) long specimen details the fin of the animal, which the scientists approximate would have been about 18 to 24 inches (45 to 60 cm) long. == http://www.prometheusbooks.com/chapters/Top%20Ten%20Myths.pdf Evolution book with sample pages The Top 10 Myths About Evolution (Paperback) by Cameron M. Smith (Author), Charles Sullivan (Author) Key Phrases: transitionalfossils, olderspecies, sixthextinction, NewYork, GreatChainofBeing, YoungEarthCreationists. === Species Detectives Track Unseen Evolution Date: July 20, 2007 http://www.sciencedaily.com/releases/2007/07/070719011423.htm Science Daily New species are evading detection using a foolproof disguise -- their own unchanged appearance. Research published in the journal, BMC Evolutionary Biology, suggests that the phenomenon of different animal species not being visually distinct despite other significant genetic differences is widespread in the animal kingdom. DNA profiles and distinct mating groups are the only way to spot an evolutionary splinter group from their look-alike cousins, introducing uncertainty to biodiversity estimates globally. Markus Pfenninger and Klaus Schwenk searched the Zoological Record database (1978-2006) to pinpoint reports of hidden (cryptic) species both biogeographically and taxonomically, and found 2207 examples. Pfenninger and Schwenk, who are from Germany based at J.W. Goethe-Universitat in Frankfurt found evidence for cryptic species evenly spread among all major branches of the animal kingdom. They also found that cryptic species were just as likely to be found in all biogeographical regions. The findings go against received wisdom that the insect or reptile branches of the animal kingdom are more likely to harbour cryptic species, and that these are more likely to be found in the tropics than in temperate regions. Zoologists should therefore consider factoring in a degree of cryptic diversity as a random error in all biodiversity assessments. A cryptic species complex is a group of species that is reproductively isolated from each other - but lacking conspicuous differences in outward appearance. Researchers using techniques such as polymerase chain reaction (PCR) and DNA sequencing have increasingly discovered - often unexpectedly - that similar-looking animals within a presumed species are in fact genetically divergent. As well as highlighting hidden biodiversity among creatures zoologists have already catalogued, the findings have implications for conservation efforts. Another possibility is that pathogens, parasites and invasive species disguised as their relatives may yet remain undetected, representing a potential human health threat. Article: Markus Pfenninger and Klaus Schwenk, "Cryptic animal species are homogeneously distributed among taxa and biogeographical regions" BMC Evolutionary Biology (in press) == Dinosaurs shared the Earth for millions of years with the species that were their ancestors, a new study concludes. Dinosaurs arose in the Late Triassic, between 235 million and 200 million years ago, and came to dominate the planet in the Jurassic, 200 million to 120 million years ago. Scientists had thought the dinosaurs rapidly replaced their ancestor species. Indeed, until 2003, when a creature called Silesaurus was discovered in Poland, no dinosaur precursors had been found from the Late Triassic. Now, researchers report in the journal Science they have evidence from northern New Mexico that dinosaurs and their precursor species coexisted for tens of millions of years. Matthew T. Carrano, curator of dinosauria at the Smithsonian's National Museum of Natural History, said there has been a long-standing debate over whether dinosaurs replaced earlier species gradually or suddenly. "What they have is a snapshot of the transition, and it's clear there is a persistent environment with dinosaurs and these other older animals. So, at least in this place in the southwestern U.S., it was not abrupt," said Carrano, who was not part of the research team. "Finding dinosaur precursors ... together with dinosaurs tells us something about the pace of changeover. If there was any competition between the precursors and dinosaurs, then it was a very prolonged competition," Randall Irmis, a graduate student at the University of California, Berkeley and co-author of the report, said in a statement. The team reported finding 1,300 fossil specimens, including several complete bones, at Hayden Quarry at Ghost Ranch, an area made famous through the paintings of Georgia O'Keeffe. There were no complete skeletons, and researchers are continuing to work at the site. Their finds included bones from both early dinosaurs and dinosaur precursors as well as remains of crocodile ancestors, fish and amphibians, all dating between 220 million and 210 million years ago. Included were leg bones of the carnivorous Chindesaurus bryansmalli, a close relative of the Coelophysis, a well-known Triassic dinosaur. They said both walked on two legs, reminiscent of the much later Velociraptor depicted in the film "Jurassic Park." They also found remains of a Dromomeron romeri, a relative of the 235 million-year-old Argentinian middle Triassic precursor called Lagerpeton. Dromomeron was between three and five feet long, the authors concluded. Another discovery was an unnamed, four-footed beaked grazer about three times the size of Dromomeron, they said. == http://afarensis.blogsome.com/ evolution == Giant panda ancestor not so giant Scientists compared the panda skulls from past and present The giant panda's earliest known ancestor was much smaller than its modern-day counterpart, scientists say. A fossilised skull found in south China revealed the ancient animal, known as Ailuropoda microta, was about half the size of today's giant panda. However, the "pygmy" bear, which lived about two million years ago, shows strong similarities to modern pandas and also lived on a bamboo diet. The finding is reported in Proceedings of the National Academy of Sciences. The skull was uncovered in a karst, or limestone, cave in China's Guangxi province; it was in a remarkably intact state. Prior to this discovery, the fossil record of A. microta - the "pigmy giant panda" - was limited to a few isolated teeth and jaw fragments. Russell Ciochon, an anthropologist at the University of Iowa, US, and an author on the PNAS paper, said: "Pandas have very unique skulls, so to have the whole skull with all of the upper dentition means we can see very much what the animal looked like." Strong similarities The team deduced that the species, which lived during the late Pliocence Epoch, was significantly smaller than today's giant panda (A. melanoleuca). It seems that pandas have been eating bamboo for a long time The researchers' estimates put A. microta's body length at about 1m (3ft). Its modern counterpart is more than 1.5m-long (5ft). Despite the size difference, the scientists found strong anatomical similarities between the pandas of past and present. They discovered the pygmy bear had heavy wear patterns on its teeth and defined muscle scars, suggesting it had the very powerful chewing mechanism required for a diet of bamboo shoots. Professor Ciochon told the BBC News website: "What struck us was it was very much like a miniaturised version of the living giant panda, yet it was over two million years old." The team does not know if A. microta carried the same distinctive black and white markings as its relative. Committed vegetarians The skull of the giant panda's earliest known ancestor also provides more clues into its evolution. Professor Ciochon said: "Bears are generally carnivorous or omnivorous, and then you have pandas - they have gone in a completely different direction, they are committed vegetarians. It probably has been exploiting this kind of environment for many millions of years "Early on in the evolutionary history of pandas, they must have invaded this bamboo niche and begun to eat bamboo. "Given the food source they were eating was very prevalent, then they must have become more and more specialised. It probably has been exploiting this kind of environment for many millions of years." A. microta is thought to have lived in a moist lowland tropical forest habitat where bamboo was one of the most dominant plant types. Other creatures that lived in the same area at about the same time were a giant extinct elephant-like creature, Stegodon, and a giant extinct ape Gigantopithecus. Today, the giant panda lives in the upland bamboo forests of Sichuan. However, half of the panda's mountainous bamboo habitat was lost between 1974 and 1988 and the animal is listed as Endangered on the IUCN Red List of Threatened Species. == The most detailed probe yet into the workings of the human genome has led scientists to conclude that a cornerstone concept about the chemical code for life is badly flawed. The ground-breaking study, published in more than two dozen papers in journals on both sides of the Atlantic, takes a small percentage of the genome to pieces to draw up a "parts list," identifying the biological role of every component. For the international team of investigators, the four-year project was the computer-equivalent of passing a fine-toothed comb through a mountain of raw data. Reporting in the British journal Nature and the US journal Genome Research on Thursday, they suggest that an established theory about the genome should be consigned to history. Under this view, the genome is rather like a ribbon studded with some 22,000 "nuggets" in the form of genes, which make proteins, the essential stuff of life. Genes -- deemed so valuable that some discoverers of them have been prompted to file patents over them for commercial gain -- amount to only around a twentieth, or even less, of the genetic code. In between the genes and the sequences known to regulate their activity are long, tedious stretches that appear to do nothing. The term for them is "junk" DNA, reflecting the presumption that they are merely driftwood from our evolutionary past and have no biological function. But the work by the ENCODE (ENCyclopaedia of DNA Elements) consortium implies that this nuggets-and- dross concept of DNA should be, well, junked. The genome turns out to a highly complex, interwoven machine with very few inactive stretches, the researchers report. Genes, it transpires, are just one of many types of DNA sequences that have a functional role. And "junk" DNA turns out to have an essential role in regulating the protein-making business. Previously written off as silent, it emerges as a singer with its own discreet voice, part of a vast, interacting molecular choir. "The majority of the genome is copied, or transcribed, into RNA, which is the active molecule in our cells, relaying information from the archival DNA to the cellular machinery," said Tim Hubbard of the Wellcome Trust Sanger Institute, a British research group that was part of the team. "This is a remarkable finding, since most prior research suggested only a fraction of the genome was transcribed. " Francis Collins, director of the US National Human Genome Research Institute (NHGRI), which coralled 35 scientific groups from around the world into the ENCODE project, said the scientific community "will need to rethink some long-held views about what genes are and what they do." "(...) This could have significant implications for efforts to identify the DNA sequences involved in many human diseases," he said. Another rethink is in offing about how the genome has evolved, said Collins. Until now, researchers had thought that the pressure to survive would relentlessly sculpt the human genome, leaving it with a slim, efficient core of genes that are essential for biological function. But the ENCODE consortium were surprised to find that the genome appears to be stuffed with functional elements that offer no identifiable benefits in terms of survival or reproduction. The researchers speculate that there is a point behind this survival of the evolutionary cull. Humans could share with other animals a large pool of functional elements -- a "warehouse" stuffed with a variety of tools on which each species can draw, enabling it to adapt according to its environmental niche. The ENCODE endeavour flows from the Human Genome Project, which concluded in April 2003 with the publication of a polished draft of the human genetic code. But having the draft is not the same as knowing what is in it or how it works. And this is essential for unlocking knowledge about our evolutionary odyssey, just as it is needed for engineering new treatments for inherited disease. The collaborative study focussed on 44 strategically chosen targets which together account for about one percent of the genome, or about 30 million of the three billion "rungs" in the DNA double-helix ladder. == http://www.talkorigins.org/faqs/comdesc/section1.html macroevolution == Scientists estimate that there were over 2,000 genera of dinosaurs. == First Fossil Hagfish (Myxinoidea): A Record from the Pennsylvanian of Illinois DAVID BARDACK A fossil hagfish (Myxinoidea), a new genus from the Pennsylvanian, shows tentacles, structures of the head skeleton and internal organs. No other fossils of this group have been reported. Although this new hagfish differs from living forms in position of the gills, feeding apparatus, and relatively well developed eyes, it is quite similar to its recent relatives. Thus, hagfishes have a long, conservative geological history. Cladograms showing myxinoids as a sister group to the vertebrates are supported. == How Ancient Whales Lost Their Legs, Got Sleek And Conquered The Oceans Science Daily When ancient whales finally parted company with the last remnants of their legs about 35 million years ago, a relatively sudden genetic event may have crowned an eons-long shrinking process. J.G.M. 'Hans' Thewissen, Ph.D., a member of the department of anatomy at Northeastern Ohio Universities College of Medicine in Rootstown, Ohio, holds a two-month old fetus of a spotted dolphin. A reconstruction of the fossil whale Kutchicetus, which lived about 45 million years ago in India, is behind him. (Credit: Carole Harwood/NEOUCOM) An international group of scientists led by Hans Thewissen, Ph.D., a professor of anatomy at Northeastern Ohio Universities College of Medicine, has used developmental data from contemporary spotted dolphins and fossils of ancient whales to try to pinpoint the genetic changes that could have caused whales, dolphins and porpoises to lose their hind limbs. More than 50 million years ago the ancestors of whales and dolphins were four-footed land animals, not unlike large dogs. They became the sleek swimmers we recognize today during the next 15 million years, losing their hind limbs in a dramatic example of evolutionary change. "We can see from fossils that whales clearly lived on land - they actually share a common ancestor with hippos, camels and deer," said team member Martin Cohn, Ph.D., a developmental biologist and associate professor with the UF departments of zoology and anatomy and cell biology and a member of the UF Genetics Institute. "Their transition to an aquatic lifestyle occurred long before they eliminated their hind limbs. During the transition, their limbs became smaller, but they kept the same number and arrangement of hind limb bones as their terrestrial ancestors." In findings to be published this week in the Proceedings of the National Academy of Sciences, scientists say the gradual shrinkage of the whales' hind limbs over 15 million years was the result of slowly accumulated genetic changes that influenced the size of the limbs and that these changes happened sometime late in development, during the fetal period. However, the actual loss of the hind limb occurred much further along in the evolutionary process, when a drastic change occurred to inactivate a gene essential for limb development. This gene - called Sonic hedgehog - functions during the first quarter of gestation in the embryonic period of the animals' development, before the fetal period. In all limbed vertebrates, Sonic hedgehog is required for normal limbs to develop beyond the knee and elbow joints. Because ancient whales' hind limbs remained perfectly formed all the way to the toes even as they became smaller suggests that Sonic hedgehog was still functioning to pattern the limb skeleton. The new research shows that, near the end of 15 million years, with the hind limbs of ancient whales nonfunctional and all but gone, lack of Sonic hedgehog clearly comes into play. While the animals still may have developed embryonic hind limb buds, as happens in today's spotted dolphins, they didn't have the Sonic hedgehog required to grow a complete or even partial limb, although it is active elsewhere in the embryo. The team also showed why Sonic hedgehog became inactive and all traces of hind limbs vanished at the end of this stage of whale evolution, said Cohn. A gene called Hand2, which normally functions as a switch to turn on Sonic hedgehog, was shown to be inactive in the hind limb buds of dolphins. Without it, limb development grinds to a halt. "By integrating data from fossils with developmental data from embryonic dolphins, we were able to trace these genetic changes to the point in time when they happened," Thewissen said. "Studies on swimming in mammals show that a sleek body is necessary for efficient swimming, because projecting organs such as rudimentary hind limbs cause a lot of drag, and slow a swimmer down," said Thewissen, who spends about a month every year in Pakistan and India collecting fossils that document the land-to-water transition of whales. Researchers say the findings tend to support traditional evolutionary theory, a la Charles Darwin, that says minor changes over vast expanses of time add up to big changes. And while Sonic hedgehog's role in the evolution of hind limbs in ancient whales is becoming apparent, it is still not fully defined. "It's clear when ancient whales lost all vestiges of the limb it was probably triggered by loss of Sonic hedgehog," said Clifford Tabin, Ph.D., a professor of genetics at Harvard Medical School who was not involved in the research. "But it's hard to say for certain because you're looking at events long after they occurred. As they suggest, there could have been a continual decrease in Sonic as the limbs reduced until the modern version of the animal arrived." The study itself, combining fossil and developmental data, is notable, Tabin said. "Whales went through this remarkable transformation to become more like the ancestral fish," Tabin said. "Convergence of evolutionary studies and developmental genetics give us another piece in this growing tapestry of how genetic changes lead to morphological change. It is a remarkable process that was achieved simply and led to profound consequences in how whales were able to survive. Only now in the last five years are we developing this understanding of how the world of evolution is controlled genetically." == The longest human tail on record belonged to a twelve-year-old boy living in what was then French Indochina, which measured nine inches (229 mm). == Gene mutation linked to cognition is found only in humans The human and chimpanzee genomes vary by just 1.2 percent, yet there is a considerable difference in the mental and linguistic capabilities between the two species. A new study showed that a certain form of neuropsin, a protein that plays a role in learning and memory, is expressed only in the central nervous systems of humans and that it originated less than 5 million years ago. The study, which also demonstrated the molecular mechanism that creates this novel protein, will be published online in Human Mutation, the official journal of the Human Genome Variation Society. == Babies' clutch reflex is a vestige of when our ancestors had to cling to their mom's fur safely to be transported. == The oldest dated zircons date from about 4400 Million years - very close to the hypothesized time of the Earth's formation. The Greenland sediments include banded iron beds. They contain possibly organic carbon and quite possibly indicate that photosynthetic life had already emerged at that time. The oldest known fossils (from Australia) date from a few hundred million years later, 3.5 billion years ago. == A speciation example can be found on page 22 of the February, 1989 issue of Scientific American in an article titled "A Breed Apart." That article tells about studies conducted on a fruit fly, Rhagoletis pomonella, that is a parasite of the hawthorn tree and its fruit, commonly called the thorn apple. About 150 years ago, some of these flies began infesting apple trees, as well. In 1989, as documented in the Scientific American article researchers did tests on the fruit flies and found that the two populations are now different species. In other words, speciation had occurred. == Carl Woese, 79 this year, "discoverer" of the Domain Archaea continues to revolutionize biology: He proposes two "communal" microbial evolutionary stages prior to classical Darwinian "vertical" evolution, dominated by horizontal gene transfer between differing organisms, as still happens today. In his model of common descent, there isn't a single first cell but a common, evolving gene pool, starting with translation. The last common universal ancestor was a community of organisms evolving together by sharing innovations. Eukaryotes are descended from archaeans rather than bacteria. == Transitional species The terrestrial tetrapod to modern whale transitional series includes Synonyx, Pakecetus, Ambulocetus, Remingtonocetus, Rhodocetus, Basilosaurus, Durodon and Mysticetus before arriving at the modern toothed whales, Odontoceti. The dinosaur-to-bird series includes Troodontidae, Archeopteryx, Confusiusornis, Enantiornithes, Ichthyornis, and Hesperornis before arriving at Aves, the modern birds. == The cranial capacity of the brains of early human ancestors can now be shown to have increased gradually, and not have been subject to sudden changes. == Mystery fossil turns out to be giant fungus 20-foot-tall organism evaded classification for more than a century A Prototaxites fossil in the desert of Saudi Arabia. Reprinted from Review of Paleobotany and Palynology, Vol. 116, "Rotted Wood-Alga-Fungus: The History and Life of Prototaxites Dawson 1959," by Francis Hueber, p. 146, Smithsonian Institution, Copyright 2001, with permission from Elsevier. CHICAGO - Scientists have identified the Godzilla of fungi, a giant, prehistoric fossil that has evaded classification for more than a century, U.S. researchers said on Monday. A chemical analysis has shown that the 20-foot-tall (6-metre) organism with a tree-like trunk was a fungus that became extinct more than 350 million years ago, according to a study appearing in the May issue of the journal Geology. Known as Prototaxites, the giant fungus originally was thought to be a conifer. Then some believed it was a lichen, or various types of algae. Some suspected it was a fungus. "A 20-foot-fungus doesn't make any sense. Neither does a 20-foot-tall algae make any sense, but here's the fossil," C. Kevin Boyce, a University of Chicago assistant professor of geophysical sciences, said in a statement. Francis Hueber of the National Museum of Natural History first suggested the fungus possibility based on an analysis of the fossil's internal structure, but had no conclusive proof. Boyce and colleagues filled in the blanks, comparing the types of carbon found in the giant fossil with plants that lived about the same time, about 400 million years ago. If Prototaxites were a plant, its carbon structures would resemble similar plants. Instead, Boyce found a much greater diversity in carbon content than would have been expected of a plant. Fungi, which include yeast, mold and mushrooms, represent their own kingdom, neither plant nor animal. Once classified as plants, they are now considered a closer cousin to animals but they absorb rather than eat their food. Samples of the giant fungi have been found all over the world from 420 million to 350 million years ago during a period in which millipedes, bugs and worms were among the first creatures to make their home on dry land. No animals with a backbone had left the oceans yet. The tallest trees stood no more than a couple of feet (a metre) high, offering little competition for the towering fungi. Plant-eating dinosaurs had not yet evolved to trample Prototaxites' to the ground. "It's hard to imagine these things surviving in the modern world," Boyce said. (c) Reuters 2007. All rights reserved. Republication or redistribution of Reuters content, including by caching, framing or similar means, is expressly prohibited without the prior written consent of Reuters. Reuters and the Reuters sphere logo are registered trademarks and trademarks of the Reuters group of companies around the world. == Shark-Eating Dino Fossil Found in Utah A Utah site frozen in Early Jurassic time recently yielded discoveries that include an enormous, previously unknown carnivorous dinosaur, a new shark species, at least three other new fish and three new trees. All of the now-extinct organisms once thrived in or around a giant lake 200 million years ago, according to paleontologists who made the finds. Anatomical features and track marks linked to the dinosaur suggest it specialized in eating and catching fish, including sharks and huge bony fish that, when consumed, would have been "like biting through chain mail," Utah State paleontologist James Kirkland told Discovery News. The fish-loving dino, which the researchers believe was a cousin of the crested dino Dilophosaurus, would have been a formidable adversary to its fearsome prey. "These (dinosaurs) got up to 18-20 feet in length, 6-7 feet high at the hips, and weighed between 750-1,000 pounds," explained Andrew Milner, city paleontologist at the St. George Dinosaur Discovery Site on Johnson Farm, Utah, where the excavations took place. Long, sharp teeth at the front of the dinosaur's mouth helped to keep fish from flying out, said Kirkland, while other, more slender teeth had "steak-knife serration" wear patterns between the tip and the gum line. "The only other meat-eating dinosaurs with teeth worn like that are the spinosaurs Spinosaurus and Suchimimus from North Africa where large...fish dominated," said Kirkland. One of the fish species discovered at the site, now called Lake Dixie, was indeed a semionotid an early type of fish that usually had an elongated body, gills, jaws and scales or bony plates. "Fish in the past were more armored than they are today," Kirkland explained. The new shark species, named Lissodus johnsonorum, would have been an easier dinner, since its skeleton was made of cartilage and not hard bone, but the crunchy fish were more prevalent in the lake and outnumbered sharks 10 to one. The Dilophosaurus relative also possessed nasal openings that retracted back from the end of its snout so, like today's crocodiles and alligators, it could still breath when its mouth was underwater. Perhaps the most dramatic finds at the site are the dinosaur track marks. Milner said these belonged to several creatures including other dinosaur species, other reptiles and early ancestors of mammals. A Utah site frozen in Early Jurassic time recently yielded discoveries that include an enormous, previously unknown carnivorous dinosaur, a new shark species, at least three other new fish and three new trees. All of the now-extinct organisms once thrived in or around a giant lake 200 million years ago, according to paleontologists who made the finds. Anatomical features and track marks linked to the dinosaur suggest it specialized in eating and catching fish, including sharks and huge bony fish that, when consumed, would have been "like biting through chain mail," Utah State paleontologist James Kirkland told Discovery News. The fish-loving dino, which the researchers believe was a cousin of the crested dino Dilophosaurus, would have been a formidable adversary to its fearsome prey. "These (dinosaurs) got up to 18-20 feet in length, 6-7 feet high at the hips, and weighed between 750-1,000 pounds," explained Andrew Milner, city paleontologist at the St. George Dinosaur Discovery Site on Johnson Farm, Utah, where the excavations took place. Long, sharp teeth at the front of the dinosaur's mouth helped to keep fish from flying out, said Kirkland, while other, more slender teeth had "steak-knife serration" wear patterns between the tip and the gum line. "The only other meat-eating dinosaurs with teeth worn like that are the spinosaurs Spinosaurus and Suchimimus from North Africa where large...fish dominated," said Kirkland. One of the fish species discovered at the site, now called Lake Dixie, was indeed a semionotid an early type of fish that usually had an elongated body, gills, jaws and scales or bony plates. "Fish in the past were more armored than they are today," Kirkland explained. The new shark species, named Lissodus johnsonorum, would have been an easier dinner, since its skeleton was made of cartilage and not hard bone, but the crunchy fish were more prevalent in the lake and outnumbered sharks 10 to one. The Dilophosaurus relative also possessed nasal openings that retracted back from the end of its snout so, like today's crocodiles and alligators, it could still breath when its mouth was underwater. Perhaps the most dramatic finds at the site are the dinosaur track marks. Milner said these belonged to several creatures including other dinosaur species, other reptiles and early ancestors of mammals. == The evidence indicates that whales are descended from artiodactyls instead of from mesonychids (Andrewsarchus was a mesonychid). == Good Vibrations: How Termites Know Whats For Dinner Termites may be blind, but they can still tell if your house would make a tasty dinner based on the musical good vibrations wood makes as they chomp on it. Because termites cant smell, taste or even see their food, researchers wondered how they knew what they were eating, especially since they seemed to be fairly sophisticated in their choices. If you give them a large block of wood and a small block of wood, theyll actually be able to tell the difference. And the question is, how do they do that? and the answer came as vibrations, said Ra Inta, an entomologist with the Commonwealth Scientific and Industrial Research Organization (CSIRO). As termites grip and pull wood fibers, the fibers snap and send a small impulse through the entire structure that theyre eating, Inta said in a recorded interview distributed by CSIRO. Those vibrations return to the termites and let them know what theyre eating. The researchers found that they could manipulate the termites tastes by generating false vibrations. When you record their feeding in a large block of wood, which they normally prefer, and you play it through a small block of wood, their feeding preference will actually change, Inta said. It appears to them that the block of wood is actually larger. Inta still has to figure out what exactly the insects are responding to in the vibration signals and how they distinguish between different types of materials. If we can understand what they assess and what they prefer in the vibration signal, then we can make use of whatever is in that signal to manipulate their behavior Inta said. So we can try and get them away from your house to somewhere else, or we can get them away from your house altogether. == Termites Are Actually Social Cockroaches Termites may look like white ants, but new genetic research confirms they are really a social kind of cockroach. Given how relatively solitary regular cockroaches are compared with termites and their complex societies, researchers note these findings could shed light on how social behaviors develop in all insects. Researchers added that the cockroach penchant for coprophagy, or eating feces, could very well have led termites to evolve in the first place. Scientists had long known that cockroaches and termites were related to each other and to praying mantises. Features they all share include specialized cases that enclose their eggs and perforations in the internal parts of their heads. What researchers have debated for decades is whether or not termites evolved from cockroaches. Evidence suggesting this possibility included symbiotic microbes that certain termites and wood roaches had in common, as well as physical similarities between their young. After conducting the most exhaustive genetic analyses yet into the subject, studying 107 different species of termites, cockroaches and mantises from across the globe, entomologist Paul Eggleton at the Natural History Museum in London and his colleagues now conclude termites are indeed a family of cockroaches, findings detailed online April 5 in the journal Biology Letters. "This finally establishes where termites belong within the insects," Eggleton told LiveScience. At first these results might appear unlikely, given the extraordinary differences in behavior and diet between these insects. Although cockroaches are somewhat convivial, they cannot hold a candle to the astonishingly complex societies termites can form, with colonies including up to millions of insects specialized into workers, soldiers, kings and queens. And termites are renowned for eating dead wood, while cockroaches are well-known coprophages, or feces-eaters. Eggleton and his colleagues note, however, that ants and bees, which are likewise social, evolved from solitary wasps. They added that cockroach traits such as their gregariousness and their coprophagy might have set the stage for the evolution of termites. When termite ancestors devoured each other's droppings, they could have shared the microbes that eventually led to a key termite feature, the ability to break down wood. Ensuring such wood-digesting microbes get passed on to offspring requires a close relationship between parents and their young, laying the groundwork for "their whole complex social system to have evolved," == Parasites Eavesdrop on Stink Bug Sex Talk Parasitic wasps eavesdrop on the sex talk of female stink bugs in order to find new prey, researchers have discovered. Thanks to their foul-smelling secretions, stink bugs seem repulsive to humans, but scelionid wasps love themthey infect stink bug eggs and then feed on them in order to survive. However, its not always easy for the wasps to stumble upon the eggs in the first place. So Brazilian biologist Raul Laumann and his colleagues wondered whether the wasps pinpointed eggs by tuning into the sexual signals that stink bugs transmit through plants by vibrating their bodies. These signals, which provide information to other stink bugs about the sender's sex, location and receptiveness to mating, also provide eavesdropping wasps with a clever way to find new host eggs Laumann and his colleagues at Embrapa Recursos Geneticos e Biotecnologia recorded the sexual vibrations emitted by male and female Brazilian stink bugs and played them for parasitic wasps that had been placed either on green bean plants or an artificial substrate that allowed them to easily track the wasps movements. In both cases, wasps moved towards the source of the vibrations from female stink bugs, but not male stink bugseither one particular leaf of the green bean plant or one part of the film substrate. The wasps tended to choose and remain on the leaves and parts of the film that vibrated with the female songs, avoiding the parts that did not vibrate at all. In the presence of the vibrations, the wasps also appeared to be searching around with their antennae as if they knew prey might be nearby. The wasps probably realize that eggs laid by female stink bugs could be close to the source of the vibrations, Laumann told LiveScience. This study, published in the April issue of Animal Behaviour, is the first to show that parasites tune into insects vibratory sexual communication signals, he said. == Ability to Bite Evolved in Fishy Ancestors The ability of ferocious land animals to bite prey evolved in ancient fish, a new study finds. Fish predominantly capture prey with suction, which can be seen by watching a goldfish constantly puckering its mouth. But land animals cant use this technique and instead use jaws that clamp together to catch and grasp a meal. This feeding adaptation is another piece of evidence scientists use to illuminate the evolutionary transition from fish to land vertebrates. To learn more about this, Molly Markey and her colleague Charles Marshall, both of the Museum of Comparative Zoology at Harvard University, analyzed fossil skulls from an extinct amphibian (Phonerpeton) that lived mostly on land, an earlier extinct amphibian (Acanthostega) that lived mostly in the water and a fishy predecessor, Eusthenopteron. In particular, they measured the contours of the seams between adjacent skull bones at the roofs of these skulls. Called sutures, these junctures are lined with stretchy collagen, and the bony plates slide miniscule amounts relative to one another when an organism eats. The scientists then compared the sutures on the extinct creatures to those found on the skull of a living freshwater fish, Polypterus, which they had measured in a previous study. Polypterus uses suction to capture prey, thus its skull sutures gave the researchers a baseline for what a suction-organisms skull should look like. "A biting or chewing motion would result in a faint pushing together of the frontal bones in the skull, while a sucking motion would pull those bones ever so slightly apart, Markey said. By comparing the skull roofs of living fish to those of early amphibians and their fishy ancestors, we were able to determine whether the fossil species fed by suction or by biting, she added. Biters v. suckers The suture patterns from Eusthenopteron, a species of lobe-finned fish that lived about 380 million years ago, matched those of suction feeders. But analysis of the early amphibian Acanthostega showed that, while it had many fish features , it was more likely a biter than a sucker. Even though they spent a lot of time in the water, [the earliest amphibian ancestors] were biting on their prey, which is a prerequisite to capturing prey on land, Markey told LiveScience. Aquatic biting jaws This is interesting, Markey said, because it suggests early amphibians inherited their biting jaws from ancestors who lived solely in the water. The findings, detailed this week in the online edition of the journal Proceedings of the National Academy of Sciences, might help answer an old scientific question: Did fish make the move to land to escape from predators or to exploit new food sources? Our findings do support the idea that they came on land to exploit new food sources, but were not sure, Markey said. == Global Warming Could Doom Male Crocodiles Rising temperatures could force the birth of more female crocodiles and fewer males, an expert said today. The scenario could cause some croc populations to disappear. Crocodile gender is determined by temperature during incubation. Nest temperatures of 89.6 to 91.4 degrees Fahrenheit (32-33 Celsius) result in males. Anything warmer or cooler produces females. Temperatures typically vary from the top of a nest to the bottom, producing both genders. "A difference of 0.5 - 1 [Celsius] in incubation temperature results in markedly different sex ratios," said Alison Leslie, of South Africas University of Stellenbosch. "More female hatchlings due to the cooler or hotter incubation temperatures could lead to eventual extirpation of the species from an area." Scientists generally agree that the planet is warming and will continue to do so for decades to come. "If that increase actually takes place it's going to increase the temperature of that incubation," Leslie said. "I think global warming is going to have a huge effect." Leslie is the principal investigator of Earthwatch Institutes Crocodiles of the Okavango Delta project in Botswana [image]. Crocodile populations have dwindled dramatically in Botswana, due to overexploitation by hide hunters and conflicts with nearby communities. "Even though crocodilians have been around for millions of years, and as important as these creatures may be in the systems they occupy, they are a much understudied species," == Warming Climate Reverses Sex of Lizards High temperatures can reverse the sex of dragon lizards before they hatch, turning males into females. The finding, detailed in the April 20 issue of the journal Science, could have implications for the development of life as the planet's climate warms. The research reveals that extreme temperatures could inactivate a gene on the male sex chromosomes of dragon lizards and thus turn male embryos into females. The sex-reversed lizards look female and have female organs but genetically they are male, said lead author Alexander Quinn of the University of Canberra in Australia. Sex 101 Until now, scientists have assumed that the sex of mammalian and reptilian offspring is determined by either genes on sex chromosomes or external factors such as temperature, but not both at once. Genetics was thought to direct the sex of Australian central bearded dragon lizards (Pogona vitticeps). Sexual reproduction involves the joining of sex cells, sperm and egg, each of which carries a set of chromosomes, including a sex-determining chromosome. In most mammals, including humans, females have two X (sex) chromosomes , while males have one X and one Y. For the dragon lizard, the sex chromosomes are labeled as Z or W and females have dissimilar chromosomes (ZW), and males have matching ones (ZZ). So it was thought that the female determined the sex of the offspring, the opposite of the case in humans. Heres why: If a dragon lizard egg cell containing a W chromosome is fertilized, the resulting zygote will be ZW (or female) while if a Z egg cell gets fertilized , the result will be ZZ (or male). What the egg cell brings to the table determines the sex outcome. To test this, Quinn and his colleagues from the Australian National University incubated Pogona vitticeps eggs at constant temperatures, ranging from 68 to 99 degrees Fahrenheit (20 to 37 degrees Celsius). No embryos survived at the coldest temperature. In ideal conditions, between 72 to 90 degrees Fahrenheit (22 and 32 degrees Celsius), an equal mix of male and female lizards developed. However, when the mercury soared to between 93 and 99 degrees Fahrenheit (34 and 37 degrees Celsius), significantly more females resulted, indicating that temperature trumped gene-controlled sex determination. It's a girl The scientists examined the baby lizards' physical features, including their sex organs, to label each as being outwardly, or "phenotypically," female or male. They also analyzed the lizards' DNA for female-specific markers linked to the W chromosome. Nearly 100 percent of the eggs incubated at intermediate temperatures developed into lizards with genes that matched their physical features. However, about half of the lizards from high-temperature incubators had a mismatched make-up, in which genetic males "looked like" females. "High temperature during the development of the embryos prevented the male DNA triggering testis development," Quinn told LiveScience. "By default, they developed instead as females with ovaries." The scientists hypothesize that a gene on the Z chromosomenot the female W chromosometriggers male development. They suggest a protein expressed by this gene is sensitive to temperature. "At most temperatures the protein is working at its best, but high temperatures make it less effective, making it unable to trigger male development," Quinn said. Climate change The results suggest that an interaction between temperature and genetics steers sex development in central bearded lizards. Before now, scientists have been concerned about how global warming will affect sex ratios in species such as alligators and marine turtles, where temperature alone drives the sex of offspring. "But now our study opens up the possibility that many [genetically sex-determined] reptiles might face the same risk as well, if they show reversal to 100 percent of one sex at high temperatures, like the bearded dragon, Quinn said. How these animals will adapt to global warming is a complex and open question. Obviously, reptiles with temperature influences in their sex determination must have persisted through many climatic fluctuations throughout their evolutionary history," he said, "but a concern is that the current rate of climate warming might be too fast for these animals to adapt to it." == The Bizarre Sex Life of an Orchid Scientists have discovered an orchid that never needs to get a dateit can fertilize itself by performing a sexual act never before seen in flowers. The hermaphroditic orchid shuns the sexual practices of other flowers and completes the deed without the help of sticky liquids, birds or even a breath of wind, a new study reveals. Many flowers rely on insects or birds, which they attract with sweet scent or tasty nectar, to help with fertilization. The hungry animals brush against the pollen-producing male bits (anther) of one plant and transfer it to the opening of a neighboring flower's female reproductive organs (stigma). Wind can also help this process along, although it's not as direct. The orchid, Holcoglossum amesianum, performs a tricky, 360-degree, gravity-defying dance to pollinate itself. Here's how it works [Images]: First, the cap covering the male anther pops off, uncovering two pollen-holding pollinia attached to a flexible rod called a stipe. The stipe rises up before curving forward and downwards past the edge of the rostellum, a structure that separates the male and female parts of the orchid. Finally, the stipe curves back up and around the rostellum and inserts the pollinia into the stigma cavity. While most flowers spread their pollen to other plants, the new orchid is extremely exclusive and only mates with itself. The self-pollination act was also successful in flower terms, producing fruit about 50 percent of the time. Of the 1,911 H. amesianum orchids the scientists observed growing on tree trunks in Simao, Yunnan, China, all used the same self-pollination strategy. This method of self-pollination, which comes in handy when winds are gentle or insects are lacking, adds to the variety of mechanisms flowering plants have evolved to ensure success. == Flowers Evolve to Suit Birds and Bats The varying shapes of flowers found in tropical forests, from broadly blooming to delicately narrow, may have to do with what has stuck its nose in there to pollinate in past evolutionary eras. Different species of birds and bats may have encouraged flowers to evolve to fit the shape of their snouts or beaks, new findings suggest. Flowers seem to respond to whatever is available and doing the best job of spreading pollen, said study leader Nathan Muchhala, a University of Miami biologist. Birds and bats have also changed their body shapes over time to adapt to available food sources and flower and plant shapes, but flowers have done so more aggressively, he said. "Basically, the flowers are making an evolutionary decision," he told LiveScience. "Organisms can specialize in something (like having wide or narrow openings), but they have to make the tradeoff to be good at one or the other." The findings are detailed in this month's issue of the American Naturalist. If the snout fits Biologists have long observed that pollinators such as birds and bats seem to favor different shapes and species of flowers. However, there has never been evidence to support the idea that flower diversity is a direct result of the need to "choose" one shape over another depending on the pollinator. To test this, Muchhala and his team captured (and later released) a species of nectar bat and hummingbird in the rainforests of Ecuador and brought them together with a variety of artificial flowersfilled with honey waterlike the ones found locally. Flower-pollinator fit was crucial in successful pollination, the results showed. The hummingbirds, with their long and thin beaks, were better guided by flowers with similarly narrow shapes. On the other hand, the much larger bats made better contact with flowers that had wider openings. Lots of pollen dropped to the ground and was wasted by each animal when the reverse was tested, Muchhala said, and also forced the animals to fly in at oddand probably uncomfortableangles. It has probably been a bit of a give and take relationship over the years, Muchhala said, with the flowers doing most of the evolutionary work. "There is definitely some degree of co-evolution (simultaneously adapting together), which you can see just in the fact that flower visiting bats and birds have longer snouts than other bats and birds," he said. "However, flowers seem to respond faster." There isn't just one flower species per bat or bird, Muchhala clarified. "This is a common misconceptionthat is, that each flower has its bat/bird specialist, and they are tightly interdependent," he said. "The one exception is a bat with an extremely long tongue (140 percent of body length!) that I recently discovered in Ecuadora flower with a matching tube length is exclusively specialized to this bat," he said. == Tree discovery yields clues on ancient forests; why ethanol may not be a pollution solution. Early tree: A 30-foot-tall Wattieza. A fossilized specimen recently found in a New York quarry is some 370 million years old. The tree shed its foliage much the way modern palms do. Tree yields clues on ancient forests Paleontologists combing through a New York State quarry have found the remark-ably well-preserved remains of one of the most ancient trees known. It thrived some 360 to 380 million years ago, stood about 30 feet tall, and sported a feather-duster array of foliage at the top instead of sprouting branches with leaves or needles. In 2004, a team of US and British scientists uncovered a crown from the tree species, known as Wattieza. A year later, the team uncovered a 28-foot trunk nearby. Wattieza is the oldest known example of a shape that appears repeatedly over the evolutionary history of trees and still appears today in modern palms and tree ferns. Fossilized stumps of the trees were first discovered in the 1870s near Gilboa, N.Y. Fossilized crowns appeared in places as diverse as Belgium and Venezuela. The team says the tree holds critical clues to what the forest's ecosystem might have been like. For example, the tree species apparently shed foliage repeatedly as it grew. The large amount of tree litter covering the forest floor would have encouraged the evolution of four-legged foragers, the team speculates. The results appear in today's issue of the journal Nature. == Chimps 'more evolved' than humans It is time to stop thinking we are the pinnacle of evolutionary success chimpanzees are the more highly evolved species, according to new research. Evolutionary geneticist Jianzhi Zhang and colleagues at the University of Michigan in Ann Arbor, US, compared DNA sequences for 13,888 genes shared by human, chimp and rhesus macaques. For each DNA letter at which the human or chimp genes differ from our shared ancestral form inferred from the corresponding gene in macaques researchers noted whether the change led to an altered protein. Genes that have been transformed by natural selection show an unusually high proportion of mutations leading to altered proteins. Zhang's team found that 233 chimp genes, compared with only 154 human ones, have been changed by selection since chimps and humans split from their common ancestor about 6 million years ago. This contradicts what most evolutionary biologists had assumed. We tend to see the differences between us and our common ancestor more easily than the differences between chimps and the common ancestor, observes Zhang. The result makes sense, he says, because until relatively recently the human population has been smaller than that of chimps, leaving us more vulnerable to random fluctuations in gene frequencies. This prevents natural selection from having as strong an effect overall. Now that the macaque genome has been sequenced, biologists will be able to learn more about the differences between the apes. == Varki and colleagues at the University of California, San Diego, reported that humans have an altered form of a molecule called sialic acid on the surface of their cells. This variant is coded for by a single gene, which is damaged in humans. Since sialic acids act in part as a docking site for many pathogens, like malaria and influenza, this may explain why people are more susceptible to these diseases than, say, chimpanzees are. A few years later, a team led by Paabo announced that the human version of a gene called FOXP2, which plays a role in our ability to develop speech and language, evolved within the past 200,000 years--after anatomically modern humans first appeared. By comparing the protein coded by the human FOXP2 gene with the same protein in various great apes and in mice, they discovered that the amino-acid sequence that makes up the human variant differs from that of the chimp in just two locations out of a total of 715--an extraordinarily small change that may nevertheless explain the emergence of all aspects of human speech, from a baby's first words to a Robin Williams monologue. And indeed, humans with a defective FOXP2 gene have trouble articulating words and understanding grammar. Then, in 2004, a team led by Hansell Stedman of the University of Pennsylvania identified a tiny mutation in a gene on chromosome 7 that affects the production of myosin, the protein that enables muscle tissue to contract. The mutant gene prevents the expression of a myosin variant, known as MYH16, in the jaw muscles used in biting and chewing. Since the same mutation occurs in all of the modern human populations the researchers tested--but not in seven species of nonhuman primates, including chimps--the researchers suggest that lack of MYH16 made it possible for our ancestors to evolve smaller jaw muscles some 2 million years ago. That loss in muscle strength, they say, allowed the braincase and brain to grow larger. It's a controversial claim, one disputed by anthropologist C. Owen Lovejoy of Kent State University. "Brains don't expand because they were permitted to do so," he says. "They expand because they were selected"--because they conferred extra reproductive success on their owners, perhaps by allowing them to hunt more effectively than the competition. The publication of a rough draft of the chimp genome in the journal Nature immediately told scientists several important things. First, they learned that overall, the sequences of base pairs that make up both species' genomes differ by 1.23%--a ringing confirmation of the 1970s estimates--and that the most striking divergence between them occurs, intriguingly, in the Y chromosome, present only in males. And when they compared the two species' proteins--the large molecules that cells construct according to blueprints embedded in the genes--they found that 29% of the proteins were identical (most of the proteins that aren't the same differ, on average, by only two amino-acid substitutions). The genetic differences between chimps and humans, therefore, must be relatively subtle. And they can't all be due simply to a slightly different mix of genes. Even before the human genome was sequenced back in 2000, says biologist Sean Carroll of the University of Wisconsin, Madison, "it was estimated that humans had 100,000 genes. When we got the genome, the estimate dropped to 25,000. Now we know the overall number is about 22,000, and it might even come down to 19,000." This shockingly small number made it clear to scientists that genes alone don't dictate the differences between species; the changes, they now know, also depend on molecular switches that tell genes when and where to turn on and off. "Take the genes involved in creating the hand, the penis and the vertebrae," says Lovejoy. "These share some of the same structural genes. The pelvis is another example. Humans have a radically different pelvis from that of apes. It's like having the blueprints for two different brick houses. The bricks are the same, but the results are very different." Those molecular switches lie in the noncoding regions of the genome--once known dismissively as junk DNA but lately rechristened the dark matter of the genome. Much of the genome's dark matter is, in fact, junk--the residue of evolutionary events long forgotten and no longer relevant. But a subset of the dark matter known as functional noncoding DNA, comprising some 3% to 4% of the genome and mostly embedded within and around the genes, is crucial. "Coding regions are much easier for us to study," says Carroll, whose new book, The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution, delves deep into the issue. "But it may be the dark matter that governs a lot of what we actually see." What causes changes in both the dark matter and the genes themselves as one species evolves into another is random mutation, in which individual base pairs--the "letters" of the genetic alphabet--are flipped around like a typographical error. These changes stem from errors that occur during sexual reproduction, as DNA is copied and recombined. Sometimes long strings of letters are duplicated, creating multiple copies in the offspring. Sometimes they're deleted altogether or even picked up, turned around and reinserted backward. A group led by geneticist Stephen Scherer of the Hospital for Sick Children in Toronto has identified 1,576 apparent inversions between the chimp and human genomes; more than half occurred sometime during human evolution. When an inversion, deletion or duplication occurs in an unused portion of the genome, nothing much changes--and indeed, the human, chimp and other genomes are full of such inert stretches of DNA. When it happens in a gene or in a functional noncoding stretch, by contrast, an inversion or a duplication is often harmful. But sometimes, purely by chance, the change gives the new organism some sort of advantage that enables it to produce more offspring, thus perpetuating the change in another generation. WHAT THE APES CAN TEACH US A striking example of how gene duplication may havehelped propel us away from our apelike origins appeared in Science last month. A research team led by James Sikela of the University of Colorado at Denver and Health Sciences Center, in Aurora, Colo., looked at a gene that is believed to code for a piece of protein, called DUF1220, found in areas of the brain associated with higher cognitive function. The gene comes in multiple copies in a wide range of primates--but, the scientists found, humans carry the most copies. African great apes have substantially fewer copies, and the number found in more distant kin--orangutans and Old World monkeys--drops off even more. Another discovery, first published online by Nature two months ago, describes a gene that appears to play a role in human brain development. A team led by biostatistician Katherine Pollard, now at the University of California, Davis, and Sofie Salama, of U.C. Santa Cruz, used a sophisticated computer program to search the genomes of humans, chimps and other vertebrates for segments that have undergone changes at substantially accelerated rates. They eventually homed in on 49 discrete areas they dubbed human accelerated regions, or HARS. The region that changed most dramatically from chimps to humans, known as HAR1, turns out to be part of a gene that is active in fetal brain tissue only between the seventh and 19th weeks of gestation. Although the gene's precise function is unknown, that happens to be the period when a protein called reelin helps the human cerebral cortex develop its characteristic six-layer structure. What makes the team's research especially intriguing is that all but two of the HARs lie in those enigmatic functional noncoding regions of the genome, supporting the idea that much of the difference between species happens there. Comparisons of primitive genomes have also led to an astonishing, controversial and somewhat disquieting assertion about the origin of humanity. Along with several colleagues, David Reich of the Broad Institute in Cambridge, Mass., compared DNA from chimpanzees and humans with genetic material from gorillas, orangutans and macaques. Scientists have long used the average difference between genomes as a sort of evolutionary clock because more closely related species have had less time to evolve in different directions. Reich's team measured how the evolutionary clock varied across chromosomes in the different species. To their surprise, they deduced that chimps and humans split from a common ancestor no more than 6.3 million years ago and probably less than 5.4 million years ago. If they're correct, several hominid species now considered to be among our earliest ancestors--Sahelanthropus tchadensis (7 million years old), Orrorin tugenensis (about 6 million years old) and Ardipithecus kadabba (5.2 to 5.7 million years old)--may have to be re-evaluated. And that's not the most startling finding. Reich's team also found that the entire human X chromosome diverged from the chimp's X chromosome about 1.2 million years later than the other chromosomes. One plausible explanation is that chimps and humans first split but later interbred from time to time before finally going their separate evolutionary ways. That could explain why some of the most ancient fossils now considered human ancestors have such striking mixtures of chimp and human traitssome could actually have been hybrids. Or they might have simply coexisted with, or even predated, the last common ancestor of chimps and humans. All of that depends in part on the accuracy of fossil dating and the reliability of using genetic variation as a clock. Both methods currently carry big margins of error. But the more primate genomes that geneticists can lay side by side, the more questions they will be able to answer. "We have rough sequences for humans, orangutans, chimps, macaques," says Eric Lander, director of the Broad Institute and a leader of the research team that decoded the chimpanzee genome. "But we don't have the entire gorilla genome yet. Lemurs are coming along, and so are gibbons." DECODING NEANDERTHALS Also coming along, thanks to two independentteams ofresearchers, is the genome of the closest relative of all: the Neanderthal. Ancestors of Neanderthals first appeared some 500,000 years ago, and for a long time it was a toss-up whether that lineage would outlive our own species, at least in Europe and western Asia--or whether, bizarre as it seems today, they would both survive indefinitely. The Neanderthals held out for hundreds of thousands of years. A discovery published online by Nature last month suggests Neanderthals may have made their last stand in Gibraltar, on the southern tip of the Iberian Peninsula, surviving until about 28,000 years ago--and possibly even longer. The Neanderthals weren't nearly as primitive as many assume, observes Eddy Rubin, director of the Department of Energy's Joint Genome Institute in Walnut Creek, Calif. "They had fire, burial ceremonies, the rudiments of what we would call art. They were advanced--but nothing like what humans have done in the last 10,000 to 15,000 years." We eventually outcompeted them, and the key to how we did so may well lie in our genes. So two years ago, Svante Paabo, the man who deconstructed the FOXP2 language gene and has done considerable research on ancient DNA, launched an effort to re-create the Neanderthal genome. Rubin, meanwhile, is tackling the same task using a different technique. The job isn't an easy one. Like any complex organic molecule, DNA degrades over time, and bones that lie in the ground for thousands of years become badly contaminated with the DNA of bacteria and fungi. Anyone who handles the fossils can also leave human DNA behind. After probing the remains of about 60 different Neanderthals out of the 400 or so known, Paabo and his team found only two with viable material. Moreover, he estimates, only about 6% of the genetic material his team extracts from the bones turns out to be Neanderthal DNA. As a result, progress is maddeningly slow. And while he can't reveal details, Paabo says he'll soon be announcing in a major scientific journal the sequencing of 1 million base pairs of the Neanderthal genome. And he says he has 4 million more in the bag. Rubin, meanwhile, is also poised to publish his results, but refuses to divulge specifics. "Paabo's team has significantly more of a sequence than we do," he says. "Some of the dates will differ, but the conclusions are largely similar." Although Paabo admits that he still hasn't learned much about what distinguishes us from our closest cousins, simply showing he can reconstruct significant DNA sequences from such long-dead creatures is an important proof of concept. Both he and Rubin agree that within a couple of years a reasonably complete Neanderthal genome should be available. "It will tell us about aspects of biology, like soft tissue, that we can't say anything about right now," Rubin notes. "It could tell us about disease susceptibility and immunity. And in places where the sequence overlaps that of humans, it will enable us to compare a prehistoric creature with chimps." Someday it may even be possible to insert equivalent segments of human and Neanderthal DNA into different laboratory mice in order to see what effects they produce. WHAT IT ALL MEANS Precisely how useful this information will be is hard toassess. Indeed, a few experts are dismissive of the whole project. "I'm not sure what Neanderthals will tell us," says Kent State's Lovejoy. "They're real late [in terms of human evolution]. And they represent, at best, a little environmental isolate in Europe. I can't imagine we're going to learn much about human evolution by studying them." Lovejoy is even more dismissive about claims that ancestors of chimps and humans interbred, arguing that using mutation rates in the genome to time evolutionary changes is extraordinarily imprecise. In fact, even the most ardent proponents of genome-comparison research acknowledge that pretty much everything we know so far is preliminary. "We're interested in traits that really distance us from other organisms," says Wisconsin's Carroll, "such as susceptibility to diseases, big brains, speech, walking upright, opposable thumbs. Based on the biology of other organisms, we have to believe that those are very complex traits. The development of form, the increase in brain size, took place over a long period of time, maybe 50,000 generations. It's a pretty complicated genetic recipe." But even the toughest critics acknowledge that these studies have enormous potential. "We will eventually be able to pinpoint every difference between every animal on the planet," says Lovejoy. "And every time you throw another genome, like the gorilla's, into the mix, you increase the chances even more." Some of the differences could have enormous practical consequences. Since his discovery that human cells lack one specific form of sialic acid, which was accomplished even before the human genome was decoded, Varki and his collaborators have determined that 10 of the 60 or so genes that govern sialic-acid biology show major differences between chimps and humans. "And in every case," says Varki, "it's humans who are the odd one out." Such revelations could probably lead to a better understanding of such devastating diseases as malaria, AIDS and viral hepatitisand likely do so faster than by studying the human genome alone. For most of us, though, it's the grand question about what it is that makes us human that renders comparative genome studies so compelling. As scientists keep reminding us, evolution is a random process in which haphazard genetic changes interact with random environmental conditions to produce an organism somehow fitter than its fellows. After 3.5 billion years of such randomness, a creature emerged that could ponder its own origins--and revel in a Mozart adagio. Within a few short years, we may finally understand precisely when and how that happened. == Yesterday's T. Rex is today's chicken The discovery of traces of flesh in a 68-million-year-old Tyrannosaurus rex bone ties the King of the Dinosaurs to modern-day species and, scientists say, heralds a "milestone" shift in paleontology. "Based on the small sample we've recovered, chickens may be the closest relatives (to T. rex)," says geneticist John Asara of Beth Israel Deaconess Medical Center in Boston, co-leader of a team reporting the discovery of faint traces of chicken-like bone lining preserved inside a dinosaur drumstick. In studies reported in the journal Science, Asara and colleagues conclude that seven traces of proteins detected in purified T. rex bone most closely match those reported in chickens, followed by frogs and newts. The astonishing find of barely detectable tissue from a creature tens of millions of years old, along with similar traces the team found in a mastodon bone at least 160,000 years old, upends the conventional view of fossils and may shift paleontologists' focus from bone hunting to biochemistry, say experts. Until now, scientists thought fossilization replaced every last bit of living tissue with inert mineral. "I'd call it a milestone," says paleontologist Hans Larsson of McGill University in Montreal, who was not part of the studies. "Dinosaurs will enter the field of molecular biology and really slingshot paleontology into the modern world." In the two studies, led by Asara and Mary Schweitzer of North Carolina State University in Raleigh, the team unearthed a T. rex buried underneath 60 feet of cliffside rock in Hell Creek, Mont. Keeping the dinosaur entombed in sandstone to prevent contamination, the scientists extracted a few grams of material from its thick thighbone, and forwarded the bone powder to Asara's lab. There it was ground down to about a billionth of a gram of material, suitable for inspection with a high-tech mass spectrometer generally used to precisely diagnose cancer genes inside tumors. The team suspects the dry sandstone, combined with the thickness of the T. rex bone, allowed some faint measure of preservation, only about 1% of the purified sample's collagen, the ribbonlike tissue found in ligaments, tendons and bone lining inside the thighbone. The protein traces are a far cry from the Jurassic Park vision of genes leading to a re-created dinosaur, Larsson notes. He voiced some caution about the results until independent researchers have ruled out the possibility of contamination in the bone samples. "It wasn't terribly long ago we thought there was no preservation whatsoever in fossils," says paleontologist Thomas Holtz of the University of Maryland in College Park. "We have a lot more to learn about fossilization." "Finding any soft tissues in dinosaur bones greatly surprised us," says Schweitzer, who led a 2005 study that found still-elastic blood vessel remains in a dinosaur bone. Her team plans to embark on a worldwide exploration of dinosaur sites in the next year, looking for more fossil bones to examine. == Pope says evolution can't be proven BERLIN Benedict XVI, in his first extended reflections on evolution published as pope, says that Darwin's theory cannot be finally proven and that science has unnecessarily narrowed humanity's view of creation. In a new book, Creation and Evolution, published Wednesday in German, the pope praised progress gained by science, but cautioned that evolution raises philosophical questions science alone cannot answer. "The question is not to either make a decision for a creationism that fundamentally excludes science, or for an evolutionary theory that covers over its own gaps and does not want to see the questions that reach beyond the methodological possibilities of natural science," the pope said. He stopped short of endorsing intelligent design, but said scientific and philosophical reason must work together in a way that does not exclude faith. "I find it important to underline that the theory of evolution implies questions that must be assigned to philosophy and which themselves lead beyond the realms of science," the pope was quoted as saying in the book, which records a meeting with fellow theologians the pope has known for years. In the book, Benedict reflected on a 1996 comment of his predecessor, John Paul II, who said that Charles Darwin's theories on evolution were sound, as long as they took into account that creation was the work of God, and that Darwin's theory of evolution was "more than a hypothesis." "The pope (John Paul) had his reasons for saying this," Benedict said. "But it is also true that the theory of evolution is not a complete, scientifically proven theory." Benedict added that the immense time span that evolution covers made it impossible to conduct experiments in a controlled environment to finally verify or disprove the theory. "We cannot haul 10,000 generations into the laboratory," he said. Evolution has come under fire in recent years by proponents mostly conservative Protestants of "intelligent design," who believe that living organisms are so complex they must have been created by a higher force rather than evolving from more primitive forms. The book, which was released by the Sankt Ulrich publishing house, includes reflections of the pope and others who attended a meeting of theological scholars at the papal summer estate in Castel Gandolfo in early September. The pope's remarks were consistent with one of his most important themes, that faith and reason are interdependent. "Science has opened up large dimensions of reason ... and thus brought us new insights," the pope wrote. "But in the joy at the extent of its discoveries, it tends to take away from us dimensions of reason that we still need. "Its results lead to questions that go beyond its methodical canon and cannot be answered within it," he said. == Transitional fossils leading from Fish to Amphibians Cheirolepis, Osteolepis, Eusthenopteron, Sterropterygion, Panderichthys, Elpistostege, Hynerpeton, Acanthostega, Ichthyostega, Pholidogaster, Pteroplax == How Lowly Bacteria Froze Earth Solid Earth has been through many cold spells since its birth 4.5 billion years ago. Scientists say some drastic episodes froze the planet all the way to the equator. Yet these "snowball Earth" scenarios expose a gaping lack of understanding: What caused them? Lowly bacteria, according to a new study. In the first and worst snowball episode, 2.3 billion years ago, bacteria suddenly developed the ability to break down water and release oxygen. The influx of oxygen destroyed methane in the atmosphere, which had acted as a blanket to keep the planet warm. The idea is presented in the latest issue of the Proceedings of the National Academy of Sciences by researchers at Caltech. In modelling the scenario, the scientists say Earth's exact position from the Sun is the only thing that saved the planet from a permanent deep-freeze. And, they caution, it could happen again. Before the first snowball event, the Sun was only 85 percent as bright as now. But the planet was temperate, much like today. Scientists believe that's because the atmosphere was loaded with methane, a greenhouse gas. It's the same gas used to heat many homes. Then along came cyanobacteria, which evolved into the first organisms to use water in photosynthesis, releasing oxygen as a byproduct. Scientists had thought the shift might have occured perhaps as far back as 3.8 billion years ago. But the Caltech scientists searched ancient rocks for clues and found no evidence for the change prior to 2.3 billion years ago. Here's what they think happened: A regular old Ice Age set in, and glaciers advanced to middle-latitudes as they would many times in geologic history. When the glaciers retreated back toward the poles, they scoured the land and released abunant nutrients into the oceans. There were no plants or animals back then. The cyanobacteria, with their newly developed ability to make oxygen, fed off the fresh flow of nutrients, the thinking goes, and their numbers exploded. And things, well, they snowballed from there. "Their greater range should have allowed the cyanobacteria to come to dominate life on Earth quickly and start releasing large amounts of oxygen," said study team member Robert Kopp, a Caltech graduate student. Computer modeling shows that most of the atmospheric methane may have been destroyed within 100,000 years, certainly within a several million years. Methane is far more insulating than carbon dioxide, another greenhouse gas. Global temperatures plummeted to minus 58 Fahrenheit (-50 C). Ice at the equator was a mile thick. Most organisms died. Biology clung to hydrothermal vents or survived underground, Kopp and his colleagues say. Even today, life has shown itself to be incredibly resilient, eating rocks, swimming in boiling water and enduring thousands of years in the deep freeze. Then evolution pulled another trick, the scientsits figure. Some of the organisms that did survive adapted to breathe oxygen, now that there was a lot of it. It was this ability to use oxygen that allowed life to evolve to more complex forms, the scientists say. That leaves the question of how we got out of that frozen mess the bacteria got us into. Eventually, the scientists say, the changed biology and chemistry caused carbon dioxide to build up enough to generate another greenhouse period. Temperatures climbed to perhaps 122 Fahrenheit (50 C) around the globe, evidence indicates. "It was a close call to a planetary destruction," says Kopp's supervising professor, Joe Kirschvink. "If Earth had been a bit further from the Sun, the temperature at the poles could have dropped enough to freeze the carbon dioxide into dry ice, robbing us of this greenhouse escape from snowball Earth." Kirschvink sees a lesson for industrial humans. While a snowball Earth could not develop in a generation and probably not even within a few hundred years, it looms as a long-term possibility. "We could still go into snowball if we goof up the environment badly enough," he said today. "We haven't had a snowball in the past 630 million years, and because the Sun is warmer now it may be harder to get into the right condition," Kirschvink said. "But if it ever happens, all life on Earth would likely be destroyed. We could probably get out only by becoming a runaway greenhouse planet like Venus." == Prehistoric whale found in inland Italy ROME - Italian researchers have excavated the skeleton of a 4 million-year-old whale in the Tuscan countryside, a discovery that could help reconstruct the prehistoric environment of the sea that once covered the region, officials said Tuesday. The 33-foot skeleton, dating to the Pliocene epoch, was found in almost perfect order, with only the jaw bones out of place, said paleontologists with the Museum of Natural History in Florence. Nearly all of Italy was once under water, and it is not unusual to find cetacean fossils in Tuscany. But the whale skeleton's discovery, about 6 miles east of the Mediterranean, was extraordinary because it was almost complete, and a wealth of organisms were found around it, officials said. "The finding is spectacular," said Elisabetta Cioppi, the head of the museum's paleontology department and coordinator of the excavation. "The variety of the sea organisms associated with the whale shells, fish and others is extraordinary. It enables us to make a thorough reconstruction of the environment," she told The Associated Press in a telephone interview. Fish and other sea organisms are believed to have lived off the whale's decomposing body for decades. Cioppi said researchers are cataloging the organisms for lab research. Also found among the bones were some shark teeth, leading researchers to believe that the whale was attacked just before it died. Cioppi said it was too soon to tell if the shark killed the whale. Excavations for the whale skeleton began in February after an amateur researcher came across the bones while digging for fossils last year and alerted the museum. The skeleton was found about 100 yards underground in Orciano Pisano, about 50 miles west of Florence, the museum said. The warm waters that covered the Tuscan countryside started receding about 1.5 million years ago, said Alessandro Garassino, a professor with Milan's Museum of Natural History. Now blessed with lavish vegetation and rolling hills, the Tuscan countryside has yielded bones and fragments for centuries. Other whale skeletons have been found, including one under a Tuscan vineyard only weeks ago, according to news reports and officials. == What's So Special About Darwin's Finches? People refer to "Darwin's finches" from time to time as a symbol of evolution in the Galapagos Islands, but the father of evolutionary theory actually dropped the ball on those birds, collecting better details on mockingbirds, tortoises and other species. Charles Darwin's observations, notes and collected organisms from the Galapagos Islands during his 5-year voyage on the Beagle resulted in his theory of evolution by natural selection, one of the best substantiated theories in the history of science. He collected several finch species, including the warbler finch, sharp-beaked finch, ground finch, small tree finch, large tree finch, common cactus finch and large ground finch. But Darwin failed to note which islands each particular finch came from. He tried to make up for the deficit by borrowing some finch notes taken by the Beagle's Captain Robert FitzRoy, but Darwin hardly mentioned the finches in his later writing. Upon Darwin's return to London, experts informed him that many of the specimens he had thought included different birds were all finches that looked different from one another. Nonetheless, this variation helped Darwin arrive at his understanding that the finches and other birds had adapted to the islands and specific environments where they live, leading to the theory that species are not fixed and unchanging; instead, they evolve over time from common ancestors. The moniker "Darwin's finches" was popularized in 1947 as a tribute to Darwin by ornithologist David Lack, who published the first modern biological study of the finches, according to Robert Rothman of the Rochester Institute of Technology. In the past few decades, biologists Peter and Rosemary Grant of Princeton University have studied finch populations and showed that the average beak sizes of successive generations changed to adapt to new food sources on Daphne Major, an island in the Galapagos. == It has long been known that greater variation of DNA in the disease defending regions makes it more likely that an individual can resist attacks by bacteria and viruses. == Autobiography of Charles Darwin, Dover Publications, 1992 The Survival of Charles Darwin: A Biography of a Man and an Idea, by Ronald W. Clark, (published by Weidenfeld & Nicholson, 1985 ), p. 199. Ancient Root's of the Modern World, " Quest for the African Dinosaurs " By Louis Jacobs (with a new introdution by the auther). 1993 new paperback edition 2000. ISBN 0-8018-6481 == http://web.archive.org/web/20021113025459/home.austarnet.com.au/stear/ default.htm anti-creation == Our ability to see the world in glorious colour comes at a price - a diminished sense of smell OUR ability to see the world in glorious colour comes at a price - a diminished sense of smell. So say biologists who have found that two separate lineages of primates, one of which includes humans, independently evolved colour vision while losing much of their sense of smell. Humans, other apes and Old World monkeys have trichromatic vision, with eyes containing three colour receptors, sensitive to blue, green and yellow-red. They allow us and our Old World relatives to distinguish around 2.3 million colours. Most other mammals only have receptors for blue and green, and can distinguish far fewer colours. In common with other apes and Old World monkeys, humans also have a degraded sense of smell. About 60 per cent of the thousand or so mammalian olfactory receptor genes in people don't function or contribute to our sense of smell. In other apes and Old World monkeys == http://gregladen.com/wordpress/?p=553 evolution == Transitional between one extinct form and another This is a 95 million year old creature called Adriosaurus microbrachis. It is a lizard like creature with vestigial rear limbs and no forelimbs, adapted to an aquatic environment. The fossil was originally collected in 19th century Slovenia, and has remained unstudied in an Italian natural history museum until recently rediscovered by Michael Caldwell of the University of Alberta. This is a little unusual because other cases of a lizard de-evolving its limbs (its happened a number of times) involve loss of the hind limbs first, then the forelimbs. This order of loss, however, while rare, is not unprecedented. == Mammals Might Have Soared Before Birds Mammals might have taken to the sky before birds, scientists announced today. A new order of mammals has been named based on a recently discovered fossil of a squirrel-sized Mesozoic-era animal [image] that lived at least 130 million years ago and was capable of gliding flight. The ancient mammal, Volaticotherium antiquus, represents a previously unknown group that bore features adapted for arboreal life. This fossil, found in Inner Mongolia, China, puts the first record of gliding flight for mammals at least 70 million years earlier than had been known, the researchers write in the Dec. 14 issue of the journal Nature. In biological classification every organism fits into a hierarchy: * Kingdom * Phylum * Class * Order * Family * Genus * Species Previously, the earliest record of flight in mammals was found in fossils of bats dating back to 51 million years ago, said lead study author, Jin Meng from the American Museum of Natural History in New York. "Of course the bats at that time already had the ability of flapping flight not just gliding, so proto-bats could have been gliders but we don't have any fossil records of that." Telling teeth The specimen was found in a book-sized slab. Bones, teeth and impressions of the soft tissue were preserved. This allowed the researchers to classify this prehistoric animal. "If you're looking for a mammal, the first thing you will look at is the teeth," Meng told LiveScience. Mammalian teeth have developed into four sets: incisors, canines, premolars and molars. Incisors are in the front and considered cutting teeth. Canines are the sharp stabbing teeth. Premolars and molars stand behind the canines and are used for grinding food. This specimen has all those features. "So we can tell that this is a mammal from the dental formula," Meng said. "Also, we can tell from the teeth morphology, because it's very sharp and very hook-like, that this is an insectivore mammal." Unlike herbivores such as the flying squirrel that eats fruits, leaves, and nuts, this ancient gliding beast fed on insects. Extinct lineage The fossil also preserved a large piece of the animal's skin membrane. "We know this [was skin] because it was covered with dense hair," Meng said. "The fur or body hair is another mammalia characteristic. So by finding that, we know that this animal has this large body skin membrane that is used for gliding. And only gliding mammals have that kind of morphology." The V. antiquus, weighing in at less than a pound, is comparable in size and shape to flying squirrels. However, the mammal is not considered a direct ancestor of these or other flying mammals. Instead, V. antiquus provides evidence for the independent origin of flight in this now-extinct lineage of mammals, the researchers conclude. "It's unusual to find such a unique creature," Meng said. "Establishing a new order probably only happens once, if that, in the lifetime of a lucky paleomammalogist." == First Delta-Wing Fighter Was a Reptile The triangular delta-wing shape found on many modern fighter jets was used by a small reptile to glide between trees 225 million years ago, a new study suggests. Sharovipteryx mirabilis is known from only a single fossil. It was about 8 inches long, weighed less than a tenth of a pound and lived during the late Triassic, a time when the first dinosaurs were still evolving. Scientists knew that S. mirabilis had a membrane stretched across its hind legs, which allowed it to glide, but the exact shape of this membrane and the way it was attached to the animal's body has been debated. In a new study, Gareth Dyke, a paleontologist at the University College Dublin in Ireland, and colleagues used wind-tunnel data from modern flying lizards and computer modeling to propose a new membrane configuration for S. mirabilis, one they say is unique because it is grounded in aerodynamics. The creature was previously the only known flying vertebrate to have a flight system dominated by its hind limbs, but the new study suggests it was also the world's first and only known delta-wing glider. The finding, which will be detailed in an upcoming issue of the Journal of Evolutionary Biology, could also have implications for how flight evolved in a more well-known family of ancient flying reptiles: the pterosaurs. Delta-wing shape The new reconstruction suggests that the flight membrane of S. mirabilis was in the shape of a "delta-wing," the triangular shape used by modern fighter jets to fly at several times the speed of sound. "At low flight speeds, there is no real reason to have a wing this shape, but delta wings work efficiently at fast speeds, especially supersonic," Dyke told LiveScience. The new reconstruction suggests S. mirabilis had not one, but two delta wings. The creature's forelimbs likely supported a triangular membrane as well. Splayed out, the creature would have looked roughly like a drawing of a two-tiered Christmas tree, with a small triangular membrane on top attached to its forelimbs, and a larger one stretched out across its hind limbs. Without the forelimb membrane, S. mirabilis would not have been able to control its "pitch" during flight, the researchers say. Pitch is the up and down orientation of an aircraft during flight: A plane pitches up to climb and down to dive. Strange sight When airborne, S. mirabilis would have been a strange sight. It would have glided in an almost upright position, and its forelimbs would have been relatively free to grab small animals or things from trees. To control speed, the researchers think the reptilian glider varied the spread of its legs. "Chances are, it would needed to have been gliding from higher pieces of land or from trees to get into a passive glide in the first place," Dyke said. The new reconstruction could have implications for theories about how flight evolved in pterosaurs, another ancient flying reptile that some scientists have speculated S. mirabilis was an early ancestor of. Unlike S. mirabilis, however, the wing membranes of pterosaurs attached to their forelimbs and hind limbs. "If [S. mirabilis] was an ancestral form for pterosaurs, then unlike birds and bats, which have a forelimb-dominated flight system, the pterosaur condition may have evolved from a hind-limb dominated flight system," Dyke said. == Ancient Flying Reptiles Discovered Paleontologists have uncovered the remains of two new flying reptile species that shared the skies with early birds 120 million years ago in what is now China. The two species, Feilongus youngi and Nurhachius ignaciobritoi, belong to a family of flying reptiles known as pterosaurs. Both were discovered in Liaoning, a northeastern province of China famous for yielding fossils of bird-like dinosaurs. Feilongus had two crests atop its head running from front to back, one along its foot-long snout and another on the back of its head. It had a slight overbite and its teeth were curved and needle-shaped, while that of Nurhachius were pointed and triangular. Rulers of the sky Both species had wingspans of about 8-feet and belonged to groups previously found only in Europe. Pterosaurs were distant relatives of dinosaurs and ruled the skies for millions of years before birds. The members of their order ranged from that of sparrow-sized Pterodactyls to Quetzalcoatlus, the largest flying creature of all time with a wingspan of up to 40-feet. Some pterosaurs flew by flapping their wings like modern birds. Others, like Feilongus and Nurhachius, used their thin wings of stretched skin to ride the wind like kites. Many pterosaurs were covered in hair similar to that of mammals. Overall, 15 species of pterosaurs have been discovered in Liaoning, including three that have yet to be described. The discovery of many more bird-like species in the region suggests that early birds were more diverse and outnumbered the pterosaurs. The distribution of the fossils also suggests that the birds and pterosaurs inhabited different environments. 'Exceedingly rare' "On the coastal areas pterosaur predominate and birds were exceedingly rare," said Alexander Kellner, a paleontologists from the Federal University in Rio de Janeiro in Brazil. "Now in the continent, despite the presence of pterosaurs, birds were more numerous and diverse," Kellner told LiveScience. The hills of Liaoning are also famous for their bounty of feathered dinosaur fossils that many scientists believe are strong evidence that birds evolved from dinosaurs. == Ancient Lizard Glided on Stretched Ribs An ancient arboreal lizard coasted through the air using a wing-like membrane stretched across elongated ribs, a new fossil reveals. Dubbed Xianglong zhaoi, the gliding lizard [image] lived during the Early Cretaceous period, about 150 million years ago. The specimen, detailed in the March 19 issue of the journal for the Proceedings of the National Academy of Sciences, is about 6 inches long, and its immature features suggest it died at a young age. The fossil [image], described by Xing Xu of Shenyang Normal University in China and his colleagues, was discovered in the Liaoning Province in northeastern China, a site that has yielded a treasure trove of feathered dinosaurs and early bird remains in recent years. Xianglongs gliding membrane, called a patagium, is stretched across eight elongated dorsal ribs. Fully expanded, the layer of stretchy skin would have spanned about 4.5 inches across. Xianglong had curved claws that would have enabled it to dwell in treetops, from whose high perch it could launch into the air. Once airborne, the little lizard could probably glide farther than modern flying lizards, perhaps as far as half a football field at a time, Xu said. The lizards wings share several similarities with the wings of modern fast-flying birds, suggesting it might have been more nimble in the air than other gliding lizards (though not as agile as say a hawk). Most gliding animals, such as flying frogs and squirrels, use a membrane spread between their toes or between their body and legs to stay airborne. A gliding membrane spread between elongated ribs is only known to occur in an ancient lizard-like animal that lived during the Late Triassic era and certain living dragon lizards in Southeast Asia. It is really amazing to see evolution making nearly identical structures in animals of different origins spanning such a long history, === "The universe that we observe has precisely the properties we should expect if there is, at bottom, no design, no purpose, no evil, no good, nothing bu pitiless indifference."Richard Dawkins, "God's Utility Function," published in Scientific American (November, 1995), p. 85 == Fish Capable Of Human-like Logic Fish have the reasoning capacity of a 4- or 5-year-old child when it comes to figuring out who among their peers is "top dog," new research shows. Stanford University scientists made the discoverysaid to be the first demonstration that fish can use logical reasoning to figure out their social pecking orderby studying fights among small, highly territorial, spiny-finned fish called cichlids, common in freshwater in tropical Africa, including in Lake Tanganyika in central Africa. Logan Grosenick, a graduate student in statistics, and his colleagues found that a sixth fish could infer or learn indirectly which were the 1st through 5th strongest simply by observing fights among them in adjacent, transparent tanks, rather than by directly fighting each fish itself or seeing each fish fight all four others. This type of reasoning, called transitive inference (TI), is a developmental milestone for human children, showing up nonverbally as early as ages 4 and 5; it also has been reported in monkeys, rats and birds. It allows thinkers to reason that if A is bigger than B, and B is bigger than C, then A is also bigger than C. Anthropomorphizing animals, or casting human intentions on them, is a mistake, Grosenick said, but it's a philosophical matter as to whether the cichlids' ability to infer rankings is the same as similar reasoning in humans. "They are making correct logical inferences on an abstract representation of their world, which would usually be called 'reasoning' in humans," he said. Biologist Russell D. Fernald, one of Grosenick's colleagues on the study, said that fish thinking is very different from that of humans. "The capacity shown here is a necessary precondition for reasoning, but having this capacity does not mean these fish actually reason or do any other specific logical tasks," he told LiveScience. Male cichlids (Astatotilapia burtoni) regularly fight aggressively to establish real estate from a pool of limited territory, to secure control of scarce food resources and to maintain a location for spawning with females. The ability to know in advance with which peer they could pick and win a fight is an advantage for these fish, Fernald said. To learn about fish learning, Grosenick designed experiments that staged dozens of fights across 11 days among five different fish (known to the scientists as A, B, C, D, and E, with A being the strongest and E the weakest) in a circle of transparent, plastic tanks that allowed a bystander fish in a center tank to observe each fight as it took place. A fought B, B fought C and so on. Later on in an open tank, the bystander got to choose between whether to hang out with either the A fish or the E fish, even though the bystander never saw A fight E. The bystander also was tested to choose between the B fish and the D fish, which had never faced off. Bystander fish in experiments typically chose the weakest fisheither D or E (those that had lost the most fights)as their preferred companion, making the safest choice for their long-term survival and ability to reproduce. This preference shows, the team writes in the Jan. 25 issue of the journal Nature, that the fish used observation and logical reasoning to infer or deduce the relative ranking among the five fighting fish. == NAIROBI, Kenya Deep in the dusty, unlit corridors of Kenya's national museum, locked away in a plain-looking cabinet, is one of mankind's oldest relics: Turkana Boy, as he is known, the most complete skeleton of a prehistoric human ever found. But his first public display later this year is at the heart of a growing storm -- one pitting scientists against Kenya's powerful and popular evangelical Christian movement. The debate over evolution vs. creationism -- once largely confined to the United States -- has arrived in a country known as the cradle of mankind. "I did not evolve from Turkana Boy or anything like it," says Bishop Boniface Adoyo, head of Kenya's 35 evangelical denominations, which he claims have 10 million followers. "These sorts of silly views are killing our faith." He's calling on his flock to boycott the exhibition and has demanded the museum relegate the fossil collection to a back room -- along with some kind of notice saying evolution is not a fact but merely one of a number of theories. Against him is one of the planet's best-known fossil hunters, Richard Leakey, whose team unearthed the bones at Nariokotome in West Turkana, in the desolate, far northern reaches of Kenya in 1984. "Whether the bishop likes it or not, Turkana Boy is a distant relation of his," Leakey, who founded the museum's prehistory department, told The Associated Press. "The bishop is descended from the apes and these fossils tell how he evolved." Among the 160,000 fossils due to go on display is an imprint of a lizard left in sedimentary rock, dating back 200 million years, at a time when the Earth's continents were only beginning to separate. Dinosaur fossils and a bone from an early human ancestor, dating back 7 million years, will also be on show along with the bones of short-necked giraffes and elephants whose tusks protrude from their lower jaws. They provide the clearest and unrivaled record yet of evolution and the origins of man, say scientists. But the highlight will be the 5-foot-3 Turkana Boy, who died at age 12 and whose skeleton had been preserved in marshland before its discovery. It will form the center stage of the exhibition to be launched in July following a $10.5 million renovation of the National Museums of Kenya, financed by the European Union. The EU says it has no concerns over the displays and that the museum was free to exhibit what it wished. Followers of creationism believe in the literal truth of the Genesis account in the Bible that God created the world in six days. Bishop Adoyo believes the world was created 12,000 years ago, with man appearing 6,000 years later. He says each biblical day was equivalent to 1,000 Earth years. Adoyo's evangelical coalition is the only religious group voicing concern about the exhibition. Leakey fears the ideological spat may provoke an attack on the priceless collection, one largely found during the 1920s by his paleontologist parents, Louis and Mary Leakey, who passed their fossil-hunting traditions on to him. The museum, which attracts around 100,000 visitors a year, is taking no chances. Turkana Boy will be displayed in a private room, with limited access and behind a glass screen with 24-hour closed-circuit TV. Security guards will be at the entrance. "There are issues about the security," said Dr. Emma Mbua, the head of paleontology at the museum. "These fossils are irreplaceable and we wouldn't want anything to happen to them." Insurance coverage could run into millions of dollars, she added. Mbua, a Protestant, is a little taken aback at the controversy but has no problems reconciling her own faith to the scientific evidence. "Evolution is a fact," adds Mbua, who has run the department for the last five years. "Turkana Boy is our jewel," she said. "For the first time, we will be taking him out of the strong room and showing our heritage to the world." == Tiny formless particles in water solution take on a well-ordered and functional structure as soon as they come into contact with nanoparticles of silica. A unique breakthrough by researchers at Linkoping University in Sweden creates new potential in medicine and biochemistry and at the same time provides a new piece of the puzzle in theories about the origins of life. Normally, inorganic materials like silica are unwelcome in biological systems, since they disrupt the form and function of proteins. We wanted to reverse the thinking and try to design proteins that take on their function only after encountering an inorganic surface, says Bengt-Harald Jonsson, professor of molecular biotechnology. He directs the research team that is now presenting its findings in Angewandte Chemie. The team designed a peptide (a short protein) with a specific distribution of positive charges. The peptide was mixed into a solution of spherical silica particles, about 9 nanometers (billionths of a meter) across. When the peptide was free in the solution it had no structure whatsoever, but when it connected with the negatively charged silica ball it assumed the form of a helix. The result was a complex of a silica particle and a functional protein. When the researchers added amino acids to their peptide, the complex took on the properties of a catalyst, a function similar to that of enzymes in living cells. The method has several possible fields of application: -- recognition of organic molecules -- catalyzing of chemical reactions with precise control -- target-seeking particles for medical uses But the Linkoping University scientists successful experiment may also shed light on the eternal question of the origin of life. Particles of clay containing silica in the primeval soup may have attracted unstructured peptides with amino acids attached and given rise to the first functional proteins. We know that RNA (which plays a decisive role in the transfer of information in cells) can bind with clay particles whose surfaces have negative charges. The probability of peptides with amino acids having formed well-defined structures with the clay at an early stage of development is considerably greater, since they are more diversified than RNA is, says Bengt-Harald Jonsson. Citation: M. Lundqvist, P. Nygren, B.H. Jonsson, and K. Broo: Introduction of structure and function in a designed peptide upon absorption on a silica nanoparticle, Angewandte Chemie 2006, 45. == The smallest form of life known to science just got smaller. Four million of a newly discovered microbe -- assuming the discovery, reported in the journal Science, is confirmed -- could fit into the period at the end of this sentence. Scientists found the microbes living in a remarkably inhospitable environment -- drainage water, as caustic as battery acid, from a mine in Northern California. The microbes, members of an ancient family of organisms known as Archaea, formed a pink scum on green pools of hot mine water laden with toxic metals, including arsenic. "It was amazing," said Jillian F. Banfield of the University of California, Berkeley, a member of the discovery team. "These were totally new." In their paper, the scientists call the microbes "smaller than any other known cellular life form." Scientists say the discovery could bear on estimates of the pervasiveness of exotic microbial life, which some experts suspect forms a hidden biosphere extending down miles whose total mass may exceed that of all surface life. It also may influence the search for microscopic life forms elsewhere in the solar system, a discovery that would prove that life in the universe is not unique to Earth but an inherent property of matter. The tiny microbes came from an abandoned mine at Iron Mountain in Shasta County, Calif., that produced gold, silver, iron and copper, closing in 1963. Today, rain runs over exposed minerals, producing sulfuric acid. The mine is one of the largest Superfund sites. The microbes are about 200 nanometers wide -- the size of large viruses, which scientists consider lifeless because they cannot reproduce on their own. Bacteria average about five times that size. The scientists must do further tests to confirm that the organisms are the smallest ever found, and that they can reproduce. == Shenzhouraptor sinensis was a transitional form that was able to fly and possessed both bird and dinosaur characteristics. == Brain, B. (ed.) 1992. Swartkrans: A cave's chronicle of early man. Almost 100 hominin craniodental fossils were excavated, deriving from the Member 1 Hanging Remnant breccia, Member 1 Lower Bank, Member 2 and Member 3. Six individuals were attributed to Homo, the remainder 50-60 individuals to Paranthropus (otherwise known as the robust australopiths) . This was from the period 1979 to 1986. The previous excavations, 1948 to 1953 and 1965 to 1979, yielded over 200 craniodental remains attributable to Paranthropus which has been equated to between 85-97 individuals. In addition to the above, 72 individually numbered jaws and teeth and 36 postcranial bones, about 21 craniodental fossils and a partial cervical vertebra that were not described by the time of the 1992 publication (but described as such in Grine's chapter) were recovered by Brain from Member 1 Hanging Remnant rubble. Grine gave detailed descriptions of the following: Member 1 Hanging Remnant: 21 specimens Member 1 Lower Bank: 20 numbered specimens representing 13-16 individuals. Member 1-2 Interface: 9 isolated teeth Member 2: 32 numbered specimens representing 21-24 individuals Member 3: 12 numbered speciments representing 9-11 individuals == The Out of Africa theory was based on thousands of DNA tests on people world wide and arrived at the conclusion that we (Homo Sapiens)were all descended from one woman who lived about 12,000 years ago. Of course this does not apply to people of African origin whose DNA goes back much further. Homo Erectus and Homo Habilus and others all predate Homo Sapiens. == The megaphone should be in the hands of science teachers. That the espousers of "intelligent design" can intimidate educators into silence is appalling. Neither teachers, principals, school board members nor the rest of us should back off in our advocacy of the science of evolution. Silence is dangerous. Over time, undermining such basic knowledge will crumble science as the cornerstone for understanding the universe around us. == A study of 142 twin schizophrenics. The study found that if one of a pair of identical twins is schizophrenic then the odds are 68% that the other twin will also be schizophrenic. But this was only true of 15% of fraternal twins. == "Evolution is a vital, well-supported, unifying principle of the biological sciences, and the scientific evidence is overwhelmingly in favor of the idea that all living things share a common ancestry. Although there are legitimate debates about the patterns and processes of evolution, there is no serious scientific doubt that evolution occurred or that natural selection is a major mechanism in its occurrence. It is scientifically inappropriate and pedagogically irresponsible for creationist pseudoscience, including but not limited to "intelligent design," to be introduced into the science curricula of our nation's public schools." === 40 MYA Primates diverge into suborders Strepsirrhini (wet-nosed primates) and Haplorrhini (dry nosed primates). Strepsirrhini contains most of the prosimians; modern examples include the lemurs and lorises. The prosimian tarsiers, along with the simian monkeys and apes are the haplorrhines. One of the earliest haplorrhines is Teilhardina asiatica, a mouse-sized, diurnal creature with small eyes. == 1. Analysis of variation in the human genome indicates that genes associated with brain size have evolved over approximately the last 37,000 years and 5800 years (Evans, Patrick D. et al. 2005. Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans. Science 309: 1717-1720). 2. Sickle-cell resistance has evolved to be more prevalent in areas where malaria is more common. 3. Lactose tolerance has evolved in conjunction with cultural changes in dairy consumption (Durham, William H. 1992. Coevolution: Genes, Culture, and Human Diversity. Stanford, CA: Stanford University Press). 4. Some humans have recently acquired mutations which confer resistance to AIDS and to heart disease. (Dean, M. et al. 1996. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Science 273: 1856-1862; Long, Patricia. 1994. A town with a golden gene. Health 8(1) (Jan/Feb.): 60-66.) == Whenever the Earth's environment is stable, there is no real need for evolutionary change. But the longer that such stability continues, the more well adapted that animals become and the larger the number of extinctions that will occur when that environment changes. == Of all the world records profiled on Extreme Science this one has proved to be the most elusive and tricky to keep updated. It seems there are a number of different organisms that hold the record for the "longest lived" and their exact ages are still under investigation. In fact, the only thing we can report for certain is that the records listed here will probably be upstaged by a new discovery in the near future. Below is a listing of what is currently in the literature as some of the oldest organisms still living today: October, 1999; 250-million-year-old bacteria were found in ancient sea salt beneath Carlsbad, New Mexico. The microscopic organisms were revived in a laboratory after being in 'suspended animation', encased in a hard-shelled spore, for an estimated 250 million years. The species has not been identified, but is referred to as strain 2-9-3, or B. permians. May, 1995; 40-million-year-old bacteria (Bacillus sphaericus) were found in the stomach of a bee encased in amber. These bacteria were also found in a state of suspended animation and were re-animated in a laboratory. 1997; King's Holly (Lomatia tasmanica) - found in the rainforests of Tasmania. Scientists estimated the age of the plant using a nearby fossil of an identical plant. It was found to be over 43,000 years old! The plants appear to be sterile - incapable of producing flowers and viable seeds. Lomatia is triploid, that is, it has three sets of chromosomes instead of two. Because of this it is unable to sexually reproduce. The clonal thickets reproduce vegetatively by root suckering. Fossil leaves found in a late Pleistocene deposit may be genetically identical to present-day plants. The plant is a rare freak of nature whose origins and age are as yet unknown. == Skull Provides Signs of When Humans Left Africa From a new analysis of a human skull discovered in South Africa more than 50 years ago, scientists say they have obtained the first fossil evidence establishing the relatively recent time for the dispersal of modern Homo sapiens out of Africa. The migrants appeared to have arrived at their new homes in Asia and Europe with the distinct and unmodified heads of Africans. An international team of researchers reported today that the age of the South African skull, which they dated at about 36,000 years old, coincided with the age of and closely resembled the skulls of humans who were then living in Europe and the far eastern parts of Asia, even Australia. The timing, the scientists and other experts said, introduced independent evidence supporting archaeological finds and recent genetic studies showing that modern humans left sub-Saharan Africa for Eurasia between 65,000 and 25,000 years ago, probably closer to 45,000 to 35,000 years ago in Europe. Until now, however, paleontologists had been frustrated by the absence of fossils to test the hypothesis of most geneticists that the people of sub-Saharan Africa and in Eurasia at this time were one and the same modern humans. The human fossil record in Africa from 70,000 to 15,000 years ago had been virtually blank. Some scientists, on the other hand, have contended that the migration could have begun as early as 100,000 years ago and that in the intervening time, contact with more archaic populations like the Neanderthals could have produced recognizable changes in what became the modern humans of Eurasia. But no scientists in the migration controversy have disputed that ancestors of the human species originated in Africa. In a report in Fridays issue of the journal Science, a research team led by Frederick E. Grine of Stony Brook University in New York concluded that the South African skull provided critical corroboration of the archaeological and genetic evidence indicating that humans in fully modern form originated in sub-Saharan Africa and migrated, almost unchanged, to populate Europe and Asia. Dr. Grine and his colleagues said in an announcement by Stony Brook that the skull was the first fossil evidence in agreement with the out-of-Africa theory, which predicts that humans like those that inhabited Eurasia should be found in sub-Saharan Africa around 36,000 years ago. Ted Goebel, an anthropologist at Texas A & M University who was not connected to the research, said the skull opened the way to important insights about the missing years of modern humans. Writing in an accompanying commentary in the journal, Dr. Goebel said, Here is the first skull of an adult modern human from sub-Saharan Africa that dates to the critical period, and one that can speak to the relationship of early moderns from Africa and Europe. The new findings pivoted on fixing the skulls age. When it was uncovered in 1952 near the town of Hofmeyr, South Africa, the cranium was almost complete but the bone degraded. Not enough carbon remained for scientists at the time to extract a radiocarbon date. Using new technology, Richard Bailey and other researchers at the University of Oxford, England, measured the amount of radiation that had been absorbed by sand grains that filled the braincase since its burial. They calculated the yearly rate at which radiation had collected in the sand and checked this with data from a CT scan of the bone. In this way, they determined that the Hofmeyr skull belonged to a human who lived 36,000 years ago, plus or minus 3,000 years. Another member of the team, Katerina Harvati of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, made a detailed examination of the shapes, sizes and contours of all parts of the skull. She compared these three-dimensional measurements with those of early human skulls from Europe and with skulls of living humans in Eurasia and southern Africa, including the Khoe-San, commonly known as the Bushmen. Because the Bushmen are well represented in the more recent archaeological record, Dr. Harvati said, they were expected to bear a close resemblance to the Hofmeyr skull. Instead, the skull was found to be quite distinct from all recent Africans, including the Bushmen, she said, and it has a very close affinity with fossil specimens of Europeans living in the Upper Paleolithic, the period best known for advanced stone tools and cave art. Much to my amazement, Dr. Grine said in an interview, the skull linked very closely with those from Europe at the time and not with South African remains 15,000 years on. Dr. Grine said these modern humans probably originated in East Africa, which is rich in fossils of ancestors of the species, and had then moved into Eurasia and also south to the tip of Africa. It would be nice, he conceded, if we had more than one specimen. Another report in Science described one of the earliest occupation sites of modern humans in Europe, at Kostenki on the Don River 250 miles south of Moscow. Its stone and bone tools and a human figurine appeared to have been made about 45,000 years ago, perhaps a little earlier than human sites to the west in Europe. The lead author of the report was Michael Anikovich of the Russian Academy of Sciences. John Hoffecker of the University of Colorado, a team member, said the small figurine may be the oldest example of figurative art ever discovered. Dr. Goebel said the new research archaeology, genetics and the Hofmeyr skull should help explain when and how modern humans leaving Africa spread out to different environments, which, he added, is one of the greatest untold stories in the history of humankind. === Earliest evidence of modern humans in Europe discovered by international team Stone, bone and ivory artifacts may date back 45,000 years Modern humans who first arose in Africa had moved into Europe as far back as about 45,000 years ago, according to a new study by an international research team led by the Russian Academy of Sciences and the University of Colorado at Boulder. The evidence consists of stone, bone and ivory tools discovered under a layer of ancient volcanic ash on the Don River in Russia some 250 miles south of Moscow, said John Hoffecker, a fellow of CU-Boulder's Institute of Arctic and Alpine Research. Thought to contain the earliest evidence of modern humans in Europe, the site also has yielded perforated shell ornaments and a carved piece of mammoth ivory that appears to be the head of a small human figurine, which may represent the earliest piece of figurative art in the world, he said. "The big surprise here is the very early presence of modern humans in one of the coldest, driest places in Europe," Hoffecker said. "It is one of the last places we would have expected people from Africa to occupy first." A paper by Michael Anikovich and Andrei Sinitsyn of the Russian Academy of Sciences, Hoffecker, and 13 other researchers was published in the Jan. 12 issue of Science. The excavation took place at Kostenki, a group of more than 20 sites along the Don River that have been under study for many decades. Kostenki previously has yielded anatomically modern human bones and artifacts dating between 30,000 and 40,000 years old, including the oldest firmly dated bone and ivory needles with eyelets that indicate the early inhabitants were tailoring animal furs to help them survive the harsh climate. Most of the stone used for artifact construction was imported from between 60 miles and 100 miles away, while the perforated shell ornaments discovered at the lowest levels of the Kostenki dig were imported from the Black Sea more than 300 miles away, he said. "Although human skeletal remains in the earliest level of the excavation are confined to isolated teeth, which are notoriously difficult to assign to specific human types, the artifacts are unmistakably the work of modern humans," Hoffecker said. An assemblage of bone and ivory artifacts from the lowest layer at Kostenki that includes a perforated shell, a probable small human figurine (three views, top center) and several... The sediment overlying the artifacts was dated by several methods, including an analysis of an ash layer deposited by a monumental volcanic eruption in present-day Italy about 40,000 years ago, Hoffecker said. The researchers also used optically stimulated luminescence dating -- which helps them determine how long ago materials were last exposed to daylight -- as well as paleomagnetic dating based on known changes in the orientation and intensity of Earth's magnetic field and radiocarbon calibration. Anatomically modern humans are thought to have arisen in sub-Saharan Africa around 200,000 years ago. Kostenki also contains evidence that modern humans were rapidly broadening their diet to include small mammals and freshwater aquatic foods, an indication they were "remaking themselves technologically," he said. They may have used traps and snares to catch hares and arctic foxes, exploiting large areas of the environment with relatively little energy. "They probably set out their nets and traps and went home for lunch," he said. While there is some evidence Neanderthals once occupied the plains of Eastern Europe, they seem to have been scarce or absent there during the last glacial period when modern humans arrived, he said. The lack of competitors like the Neanderthals might have been the chief attraction to the area and the reason why modern humans first entered this part of Europe, Hoffecker said. "Unlike the Neanderthals, modern humans had the ability to devise new technologies for coping with cold climates and less than abundant food resources," he said. "The Neanderthals, who had occupied Europe for more than 200,000 years, seem to have left the back door open for modern humans. " The ivory artifact believed to be the head of a small figurine, discovered during the 2001 field season, was broken and perhaps never was finished by the person who began crafting it more than 40,000 years ago, said Hoffecker. "This is a really interesting piece," he said. "If confirmed, it will be the oldest example of figurative art ever discovered." Buried under 10 feet to 15 feet of silt, the artifacts at Kostenki include blades, scrapers, drills and awls, as well as sturdy antler digging tools known as mattocks that resemble crude pick-axes, he said. Mattocks have been found at other Old World sites and the arctic and were used to dig large pits for the storage of foods and fuel, although traces of such pits have yet to turn up at the lowest levels of Kostenki, he said. Large animal remains at Kostenki include mammoth, woolly rhinoceros, bison, horses, moose and reindeer. A bone chemistry analysis from 30,000-year-old human remains indicates a high consumption of freshwater aquatic foods -- either water birds, fish, or both -- more evidence for efficient food gathering techniques, he said. Except for some early sites in the Near East, the oldest evidence modern humans outside of Africa comes from the Australian continent roughly 50,000 years ago, said Hoffecker, who was awarded an honorary doctorate from the Russian Academy of Sciences in 2006. Several modern human sites in south-central Europe may be almost as old as Kostenki, he said. The study also included researchers from the University of Arizona, the Kostenki Museum-Preserve in Kostenki, the University of Illinois-Chicago, Boston University, the University College London and the Institute of Environmental Geology, Climate and Geoengineering in Rome. Research at Kostenki has been funded by the Leakey Foundation and the National Science Foundation. == A plasmid encoding enzymes for nylon oligomer degradation: nucleotide sequence and analysis of pOAD2 K Kato, K Ohtsuki, Y Koda, T Maekawa, T Yomo, S Negoro and I Urabe Department of Biotechnology, Osaka University, Japan. The entire nucleotide sequence of nylon oligomer degradative plasmid pOAD2 from Flavobacterium sp. KI723T1 was determined. pOAD2 comprises 45519 bp, with a 66.6 mol% G+C content. The precise loci of the four nylon oligomer degradation genes, namely nylA (6-aminohexanoate-cyclic- dimer hydrolase gene), nylB (6-aminohexanoate-dimer hydrolase), nylB' (a gene having 88% homology to nylB) and nylC (endo-type 6- aminohexanoate oligomer hydrolase), and five IS6100 elements were identified on this plasmid. Comparison of the sequence of pOAD2 with those in the GenBank and EMBL databases revealed that the deduced amino acid sequences from eight regions of pOAD2 had significant similarity with the sequences of gene products such as oppA-F (oligopeptide permeases), ftsX (filamentation temperature sensitive), penDE (isopenicillin N-acyltransferase) and rep (plasmid incompatibility). A functional map of pOAD2 is presented. == 1. A piece of DNA duplicates itself. This happens all of the time. . 2. A mutation occurs in the duplicated DNA. 3. This modified, duplicated DNA causes new proteins. 4. The new protein changes the organism. 5. This is evolution. === New Sucker-footed Bat Discovered In Madagascar Scientists have discovered a new species of bat that has large flat adhesive organs, or suckers, attached to its thumbs and hind feet. This is a remarkable find because the new bat belongs to a Family of bats endemic to Madagascar-- and one that was previously considered to include only one rare species. New species of sucker-footed bat (M. schliemanni) with open wings: Ventral view of the holotype of Myzopoda schliemanni obtained in the Parc National d'Ankarafantsika in the western portion of Madagascar and recently described in Mammalian Biology. Previously, only one species in this endemic Malagasy Family of bats was known to science. Now there are two. The new species, Myzopoda schliemanni, occurs only in the dry western forests of Madagascar, while the previously known species, Myzopoda aurita, occurs only in the humid eastern forests of Madagascar, according to new research recently published online in the journal Mammalian Biology. The new species is obviously different from the known species based on pelage coloration, external measurements and cranial characteristics, according to the researchers. Myzopoda are often found in association with broad-leaf plants, most notably Ravenala madagascariensis or the Travelers' Palm, a plant that is endemic to Madagascar but has been introduced to numerous tropical countries. Myzopoda are found in association with such plants because they can use their suckers to climb and adhere to the leaves' flat, slick surface. They are presumed to roost in the leaves during the day. Myzopoda were considered endangered because of their limited distribution and the notion that the family included only one species. The new research, however, modifies both of these ideas. The researchers determined that Myzopoda is not endangered by the loss of the moist tropical forests because the bat appears to have adapted very well to the large broad-leaf Ravenala that are often pioneering plants in zones where the original forests have been cleared and burned. "For now, we do not have to worry as much about the future of Myzopoda," said Steven M. Goodman, Field Museum field biologist and lead author of the study. "We can put conservation efforts on behalf of this bat on the backburner because it is able to live in areas that have been completely degraded, contrary to what is indicated or inferred in the current literature." This underlines the importance of basic scientific research for establishing the priorities for conservation programs and assessments of presumed rare and possibly endangered animals, the study concludes. Due to the physical similarities between M. schliemanni and M. aurita, the researchers concluded that one species probably evolved from the other, most likely after the bat dispersed across the island from east to west. Bats are the last group of land mammals on Madagascar that have not been intensively studied, Goodman said. "Until a decade ago, these animals remained largely understudied. On the basis of recent surveys and taxonomic research, about one-third of the island's bat species were unknown to scientists until a few years ago, and the majority of these are new to science." Only about eight percent of Madagascar's original forest cover remains, as the forests continue to be cleared by associated subsistence agricultural activities and to provide wood energy for urban zones. The island, which is found off the eastern coast of Africa, remains one of the most critically threatened areas in the world, in terms of biodiversity. Madagascar has a higher level of endemism (with plants and animals found nowhere else) than any other landmass in the world of comparable size. "Still today, you can go out and discover things in Madagascar that have never before been seen by scientists," Goodman said. "The sense of discovery is almost levitating." The other co-authors of the research are Felix Rakotondraparany, lecturer in the Animal Biology Department at the University of Antananarivo, and Amyot Kofoky, graduate student at the University of Mahajanga. == 3.5 million years ago, Australopithecus afarensis foraged for fruit, nuts and seeds in a mixture of savannah and woodland. It may also have obtained animal protein from termites or birds' eggs. Time Scale Australopithecines first walked upright: 3.5+ million years ago. First appearance of Homo: about 2 million years ago. First stone tools/weapons: about 2 million years ago. First handaxes: about 1.6 million years ago. First appearance of Homo sapiens: about 100,000 years ago. First hafted weapons: 25-100,000 years ago. First known migration by boat (Australia colonised): 50,000 years ago. Sungir graves: 22,000+ years ago First colonisation of America: 12,000 years ago (perhaps earlier) Large mammals extinct: mostly by 10,000 years ago. First known agriculture: around 10,000 years ago. http://www.bbc.co.uk/sn/prehistoric_life/human/human_evolution/ mother_of_man1.shtml == http://www.webpages.uidaho.edu/~jacks/Lecture7.pdf jaw -> inner ear == We DO know that fairly small self-replicators can be demonstrated to have the property of evolving by mutation and natural selection. These are small (as organics go) molecules in the under 200-atom size range and experiments show them evolving into things that are very much like the bits that make up RNA and DNA which are the larger replicators found in living things. == Think in terms of constant variations in traits across a population, NOT in terms of a single happy mutation transforming subsequent generations. In reality almost all complex traits such as fur thickness, limb length, visual acuity, etc., are polygenic traits to start with- they are controlled by many different genes. All of these traits will present in the population as a Gaussian distribution- the familiar bell curve. -Some animals will have thick fur, some will have thin fur; most will have an intermediate fur density. This happens in all populations of all animals all the time (just check out the forearm hair density of people the next time you're in a large crowd). When the population comes under some acute stress- such as the Ice Age event in the given example- selection pressure is put on all individuals. In this case thicker fur would be helpful to survival and procreation, so the animals which happen to have a suite of genes for thicker fur do somewhat better than the animals with the gene set which results in sparser fur. The entire population, over generations moves -EVEN WITHOUT A SINGLE MUTATION- toward thicker fur. The mean of the Gaussian curve shifts slowly toward greater fur density. Now, of course, as with any trait, any gene, variation in the suite of genes effecting fur thickness continues as the generations roll on. Recombination, mutation and novel gene interactions generate more animals with more or less dense fur- but the ones with less tend to get weeded out and the ones with more tend to be favored under the new much colder climate. ...The Gaussian curve continues to slide in the direction of greater density." What your definition of `kind' is and how far out you take the process. Let's analogize morphological change in an organism to physical change in location. If you stand in your front yard and take one step have you changed your location? Most folks would answer `no, you're really in the same place- your front yard." As above the creatures with the slightly thicker fur are really the same as the ones with slightly thinner fur. But take another step. Then another. And another. Is there anything at all preventing you from walking all the way to Taos, New Mexico? Nope. Would you then be in a different place? Yes. One thing to keep in mind is that once two populations diverge enough from each other than Reproductive Isolating Mechanisms set up. These can be physical or behavioral, but act to isolate all the genes from one population from all the genes in the other population- then each set is free to drift and undergo independent selection separate from the other. In other words, after a certain point (and yes, it's not really a `point' per se, but a span of time or a range of character differences) then it won't only be hair density which distinguishes one population from the other. Lots of features can change simultaneously, and since no two species can occupy the same ecological niche in the same area, selection will pull the two nascent species apart morphologically and behaviorally as rapidly as possible to reduce competition. This will be, of course, reflected in their genes. The result is two populations (or species, or genera, or families, etc.) which most folks would immediately declare to be `different kinds." == http://www.pnas.org/cgi/reprint/102/5/1273 mutation and evolution == Authors Scaal M. Prols F. Fuchtbauer E-M. Patel K. Hornik C. Kohler T. Christ B. Brand-Saberi B. Institution B. Brand-Saberi, Institute of Anatomy, University of Freiburg, Albertstrasse 17, D-79104 Freiburg; Germany. Title BMPs induce dermal markers and ectopic feather tracts. Source Mechanisms of Development. Vol. 110(1-2)(pp 51-60), 2001. Abstract Bone morphogenetic protein (BMP) signaling is known to be involved in multiple inductive events during embryogenesis including the development of amniote skin. Here, we demonstrate that early application of BMP-2 to the lateral trunk of chick embryos induces the formation of dense dermis, which is competent to participate in feather development. We show that BMPs induce the dermis markers Msx- 1 and cDermo-1 and lead to dermal proliferation, to expression of beta-catenin, and eventually to the formation of ectopic feather tracts in originally featherless regions of chick skin. Moreover, we present a detailed analysis of cDermo-1 expression during early feather development. The data implicate that cDermo-1 is located downstream of BMP in a signaling pathway that leads to condensation of dermal cells. The roles of BMP and cDermo-1 during development of dermis and feather primordia are discussed. Authors Chuong C-M. Hou L. Chen P-J. Wu P. Patel N. Chen Y. Institution C.-M. Chuong, Department of Pathology, Univ. Southern California, Los Angeles, CA; United States. Title Dinosaur's feather and chicken's tooth? Tissue engineering of the integument. Source European Journal of Dermatology. Vol. 11(4)(pp 286-292), 2001. Abstract The integument forms the interface between animals and the environment. During evolution, diverse integument and integument appendages have evolved to adapt animals to different niches. The formation of these different integument forms is based on the acquisition of novel developmental mechanisms. This is the way Nature does her tissue/organ engineering and experiments. To do tissue engineering of the integument in the new century for medical applications, we need to learn more principles from developmental and evolutionary studies, A novel diagram showing the evolution and development of integument complexity is presented, and the molecular pathways involved discussed. We then discuss two examples in which the gain and loss of appendages are modulated: transformation of avian scale epidermis into feathers with mutated beta catenin, and induction of chicken tooth like appendages with FGF, BMP and feather mesenchyme. Authors Ohyama A. Saito F. Ohuchi H. Noji S. Institution S. Noji, Dept. Biological Science/Technology, Faculty of Engineering, University of Tokushima, 2-1 Minami-Jyosanjima-cho, Tokushima 770-8506; Japan. E-Mail: noji@bio.tokushima- u.ac.jp. Title Differential expression of two BMP antagonists, gremlin and Follistatin, during development of the chick feather bud. Source Mechanisms of Development. Vol. 100(2)(pp 331-333), 2001. Abstract Expression of four BMP antagonist genes, noggin, chordin, gremlin and Follistatin, was examined during chick feather development. Although expression of noggin and chordin was not detected, gremlin and Follistatin were expressed differentially in feather buds. The differential expression patterns of gremlin and Follistatin change dynamically from the nascent inter-feather bud region to the posterior domain of the feather bud. Authors Noramly S. Freeman A. Morgan BA. Institution B.A. Morgan, Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129; United States. Title beta-catenin signaling can initiate feather bud development. Source Development. Vol. 126(16)(pp 3509-3521), 1999. Abstract Intercellular signaling by a subset of Wnts is mediated by stabilization of cytoplasmic beta-catenin and its translocation to the nucleus. Immunolocalization of beta-catenin in developing chick skin reveals that this signaling pathway is active in a dynamic pattern from the earliest stages of feather bud development. Forced activation of this pathway by expression of a stabilized beta- catenin in the ectoderm results in the ectopic formation of feather buds. This construct is sufficient to induce bud formation since it does so both within presumptive feather tracts and in normally featherless regions where tract-specific signals are absent. It is also insensitive to the lateral inhibition that mediates the normal spacing of buds and can induce ectopic buds in interfollicular skin. However, additional patterning signals cooperate with this pathway to regulate gene expression within domains of stabilized beta- catenin expression. Localized activation of this pathway within the bud as it develops is required for normal morphogenesis and ectopic activation of the pathway leads to abnormally oriented buds and growths on the feather filaments. These results suggest that activation of the beta-catenin pathway initiates follicle development in embryonic skin and plays important roles in the subsequent morphogenesis of the bud. Authors Widelitz RB. Jiang T-X. Chen C-WJ. Stott NS. Chuong C- M. Institution C.-M. Chuong, Department of Pathology, School of Medicine, University of Southern California, Los Angeles, CA 90033; United States. Title Wnt-7a in feather morphogenesis: Involvement of anterior- posterior asymmetry and proximal-distal elongation demonstrated with an in vitro reconstitution model. Source Development. Vol. 126(12)(pp 2577-2587), 1999. Abstract How do vertebrate epithelial appendages form from the flat epithelia? Following the formation of feather placodes, the previously radially symmetrical primordia become anterior- posterior (A-P) asymmetrical and develop a proximo-distal (P-D) axis. Analysis of the molecular heterogeneity revealed a surprising parallel of molecular profiles in the A-P feather buds and the ventral- dorsal (V-D) Drosophila appendage imaginal discs. The functional significance was tested with an in vitro feather reconstitution model. Wnt-7a expression initiated all over the feather tract epithelium, intensifying as it became restricted first to the primordia domain, then to an accentuated ring pattern within the primordia border, and finally to the posterior bud. In contrast, sonic hedgehog expression was induced later as a dot within the primordia. RCAS was used to overexpress Wnt-7a in reconstituted feather explants derived from stage 29 dorsal skin to further test its function in feather formation. Control skin formed normal elongated, slender buds with A-P orientation, but Wnt-7a overexpression led to plateau-like skin appendages lacking an A-P axis. Feathers in the Wnt-7a overexpressing skin also had inhibited elongation of the P-D axes. This was not due to a lack of cell proliferation, which actually was increased although randomly distributed. While morphogenesis was perturbed, differentiation proceeded as indicated by the formation of barb ridges. Wnt-7a buds have reduced expression of anterior (Tenascin) bud markers. Middle (Notch-1) and posterior bud markers including Delta-1 and Serrate-1 were diffusely expressed. The results showed that ectopic Wnt-7a expression enhanced properties characteristic of the middle and posterior feather buds and suggest that P-D elongation of vertebrate skin appendages requires balanced interactions between the anterior and posterior buds. Authors Meyer W. Baumgartner G. Institution Prof. W. Meyer, Anatomisches Institut, Tierarztliche Hochschule Hannover, Bischofsholer Damm 15, D-30173 Hannover; Germany. Title Embryonal feather growth in the chicken. Source Journal of Anatomy. Vol. 193(4)(pp 611-616), 1998. Abstract Prenatal feather growth development in the chicken was studied in 7 body regions in HH stages 27-45, using direct measurements, specific histological and immunohistochemical methods, and scanning electron microscopy. The results from measurements of absolute length values, and, particularly, growth rate development in each HH stage revealed a distinct phase of most intensive growth in HH stage 40-41, which was preceded by feather follicle insertion and accompanied by the occurrence of alpha-keratins in barbule cells. Specific regional evaluation demonstrated that growth in the feather follicles of abdominal skin generally showed the slowest progression from absolute values and that in the feather filaments of the developing wings the most rapid progression occurred during HH stage 40-41 from growth rate values. Authors Noramly S. Morgan BA. Institution B.A. Morgan, Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129; United States. Title BMPs mediate lateral inhibition at successive stages in feather tract development. Source Development. Vol. 125(19)(pp 3775-3787), 1998. Abstract The spacing of feather buds in a tract is thought to arise from the interaction between an inducing signal from the dermis and an inhibitory signal generated in the nascent buds. Local BMP-2 expression in the ectoderm precedes the formation of the ectodermal placodes, which are the first morphological sign of bud differentiation. We have altered the activity of BMP-2 or BMP-4 in the ectoderm of the feather field by expressing them or their inhibitor noggin using retroviral vectors. These experiments demonstrate that BMP-2 is necessary and sufficient to mediate the lateral inhibition that positions buds in a tract. After buds are initiated, BMP-2 and BMP-4 continue to inhibit the adoption of bud fates and help to specify the size and shape of the bud. They may do so in part by their regulation of Fgf receptor expression in both the ectoderm and dermis. Additional insights into pattern formation in the feather bud can be inferred from the effects of altered BMP activity on bud morphogenesis. Authors Viallet JP. Prin F. Olivera-Martinez I. Hirsinger E. Pourquie O. Dhouailly D. Institution D. Dhouailly, Biol. Differenciation Epitheliale, UMR CNRS 5538, Institut A. Bonniot, Domaine Merci-38706 La Tronche Cedex; Title Chick Delta-1 gene expression and the formation of the feather primordia. Source Mechanisms of Development. Vol. 72(1-2)(pp 159-168), 1998. Abstract The chick dermis is known to control the formation of feathers and interfeathery skin in a hexagonal pattern. The evidence that the segregation of two of fibroblasts involves Delta/Notch signalling is based on three facts. Rings of C-Delta-1- expressing fibroblasts precede and delimit the, forming feather primordia. C-Delta-1 is uniformly expressed in the dermis of the scaleless mutant, which is almost entirely devoid of feathers. Feather development is inhibited by overexpression of C-Delta-1 in wild type dermis using a retroviral construct. We also show that the distribution of C- Delta-1 in the mutant dermis can be rescued by its association with a wild type epidermis, which acts as a permissive inducer, or by epidermal secreted proteins like FGF2. Authors Jung H-S. Francis-West PH. Widelitz RB. Jiang T-X. Ting-Berreth S. Tickle C. Wolpert L. Chuong C-M. Institution C.-M. Chuong, Department of Pathology, School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Angeles, CA 90033; ion of BMPs and their relationships with activators in feather formation: Implications for periodic patterning. Source Developmental Biology. Vol. 196(1)(pp 11-23), 1998. Date of Publication: 01 APR 1998. Abstract The formation of periodic patterns is fundamental in biology. Theoretical models describing these phenomena have been proposed for feather patterning; however, no molecular candidates have been identified. Here we show that the feather tract is initiated by a continuous stripe of Shh, Fgf- 4, and Ptc expression in the epithelium, which then segregates into discrete feather primordia that are more strongly Shh and Fgf-4 positive. The primordia also become Bmp-2 and Bmp-4 positive. Bead-mediated delivery of BMPs inhibits local feather formation in contrast with the activators, SHH and FGF4, which induce feather formation. Both FGF-4 and SHH induce local expression of Bmp-4, while BMP-4 suppresses local expression of both. FGF-4 also induces Shh. Based on these findings, we propose a model that involves (1) homogeneously distributed global activators that define the field, (2) a position-dependent activator of competence that propagates across the field, and (3) local activators and inhibitors triggered in sites of individual primordia that act in a reaction-diffusion mechanism. A computer simulation model for feather pattern formation is also presented. Authors Crowe R. Niswandert L. Institution L. Niswandert, Molecular Biology Program, Memorial Sloan-Kettering Can. Center, Box 73, 1275 York Ave., New York, NY 10021; United States. E-Mail: L-niswander@ ski.mskcc. org. Title Disruption of scale development by Delta-1 misexpression. Source Developmental Biology. Vol. 195(1)(pp 70-74), 1998. Date of Publication: 01 MAR 1998. Abstract Notch and its ligands are molecules known to be involved in many cell fate decisions. Due to the proposed role of this signaling system in the choice between feather and smooth skin fate in the embryonic chick, we sought to test whether Notch signaling may also play a role in determining scale fate. Notch-1 and -2, Serrate-1 and - 2, and Delta 1 are expressed in the scales throughout their development. Misexpression of chick Delta-1 using a replication-competent retrovirus results in regions of scale loss. In addition, feather buds are often observed on some of the scuta scales. These results suggest a model in which Delta can act as an inhibitor of skin appendage fate as well as a promoter of feather fate. Authors Padian K. Chiappe LM. Institution K. Padian, Department of Integrative Biology, University of California, Berkeley, CA 94720-3140; United States. Title The origin and early evolution of birds. Source Biological Reviews of the Cambridge Philosophical Society. Vol. 73(1)(pp 1-42), 1998. Abstract Birds evolved from and are phylogenetically recognized as members of the theropod dinosaurs; their first known member is the Late Jurassic Archaeopteryx, now represented by seven skeletons and a feather, and their closest known non-avian relatives are the dromaeosaurid theropods such as Deinonychus. Bird flight is widely thought to have evolved from the trees down, but Archaeopteryx and its outgroups show no obvious arboreal or tree-climbing characters, and its wing planform and wing loading do not resemble those of gliders. The ancestors of birds were bipedal, terrestrial, agile, cursorial and carnivorous or omnivorous. Apart from a perching foot and some skeletal fusions, a great many characters that are usually considered 'avian' (e.g. the furcula, the elongated forearm, the laterally flexing wrist and apparently feathers) evolved in non-avian theropods for reasons unrelated to birds or to flight. Soon after Archaeopteryx, avian features such as the pygostyle, fusion of the carpometacarpus, and elongated curved pedal claws with a reversed, fully descended and opposable hallux, indicate improved flying ability and arboreal habits. In the further evolution of birds, characters related to the flight apparatus phylogenetically preceded those related to the rest of the skeleton and skull. Mesozoic birds are more diverse and numerous than thought previously and the most diverse known group of Cretaceous birds, the Enantiornithes, was not even recognized until 1981. The vast majority of Mesozoic bird groups have no Tertiary records: Enantiornithes, Hesperornithiformes , Ichthyornithiformes and several other lineages disappeared by the end of the Cretaceous. By that time, a few Linnean 'Orders' of extant birds had appeared, but none of these taxa belongs to extant 'families', and it is not until the Paleocene or (in most cases) the Eocene that the majority of extant bird 'Orders' are known in the fossil record. There is no evidence for a major or mass extinction of birds at the end of the Cretaceous, nor for a sudden 'bottleneck' in diversity that fostered the early Tertiary origination of living bird 'Orders'. Authors Widelitz RB. Jiang T-X. Noveen A. Ting-Berreth SA. Yin E.Jung H- S. Chuong C-M. Institution C.-M. Chuong, Pathology Department School of Med., University of Southern California, HMR 204, 2011 Zonal Ave., Los Angeles, CA 90033; United States. Title Molecular histology in skin appendage morphogenesis. Source Microscopy Research & Technique. Vol. 38(4)(pp 452-465), 1997. Abstract Classical histological studies have demonstrated the cellular organization of skin appendages and helped us appreciate the intricate structures and function of skin appendages. At this juncture, questions can be directed to determine how these cellular organizations are achieved. How do cells rearrange themselves to form the complex cyto-architecture of skin appendages? What are the molecular bases of the morphogenesis and histogenesis of skin appendages? Recently, many new molecules expressed in a spatial and temporal specific manner during the formation of skin appendages were identified by molecular biological approaches. In this review, novel molecular techniques that are useful in skin appendage research are discussed. The distribution of exemplary molecules from different categories including growth factors, intracellular signaling molecules, homeobox genes, adhesion molecules, and extracellular matrix molecules are summarized in a diagram using feather and hair as models. We hope that these results will serve as the ground work for completing the molecular mapping of skin appendages which will refine and re-define our understanding of the developmental process beyond relying on morphological criteria. We also hope that the listed protocols will help those who are interested in this venture. This new molecular histology of skin appendages is the foundation for forming new hypotheses on how molecules are mechanistically involved in skin appendage development and for designing experiments to test them. This may also lead to the modulation of healing and regeneration processes in future treatment modalities. Authors Chen C-WJ. Jung H-S. Jiang T-X. Chuong C-M. Institution C.-M. Chuong, Department of Pathology, School of Medicine, University of Southern California, 2011 Zonal Avenue, Los Angeles, CA 90033; United States. Title Rapid communication asymmetric expression of Notch/Delta/ Serrate is associated with the anterior-posterior axis of feather buds. Source Developmental Biology. Vol. 188(1)(pp 181-187), 1997. Abstract We studied the roles of Notch, Delta, and Serrate in vertebrate epithelial appendage morphogenesis using feather as a model and found the following. (1) C-Notch-1, C-Delta-1, and C- Serrate-1 are not expressed at the early placode stage and are therefore not involved in the determination of bad versus interbud compartments. (2) From symmetric short buds to asymmetric long buds, C-Delta-1 and C-Serrate-1 are expressed in the posterior bud mesenchyme in a nested fashion, while C-Notch-1 is expressed as a stripe perpendicular to the anterior-posterior (A-P) axis and positioned posterior to the midpoint. (3) Epithelial-mesenchymal recombination with rotation led to the disappearance of these genes followed by their reappearance with new positions appearing to predict their new morphological orientation. (4) Conditions leading to branched buds (e.g., recombination of later buds) show polarized staining patterns before branching occurs. (5) Conditions leading to symmetrical round buds (e.g., treated with the protein kinase A agonist forskolin) suppress expression of all three genes. These results lead us to hypothesize that Notch, Delta, and Serrate are involved in establishing the A-P asymmetry of feather buds. Authors Ting-Berreth SA. Chuong C-M. Institution Department of Pathology, HMR 204, University of Southern California, 2011 Zonal Avenue,Los Angeles, CA 90033; United States. Title Sonic hedgehog in feather morphogenesis: Induction of mesenchymal condensation and association with cell death. Source Developmental Dynamics. Vol. 207(2)(pp 157-170), 1996. Abstract Sonic hedgehog is involved in vertebrate tissue interactions during development. During early feather development, Sonic hedgehog appears very early in epithelial placodes. During late feather development, Sonic hedgehog expression precedes the development of the marginal plates and is specifically localized in the marginal plate epithelium, which will later undergo cell death. By using retroviral vectors, exogenous Sonic hedgehog overexpression in developing feathers induced enlarged feather buds that have either lost their anterior-posterior polarity or exhibited reverse orientation. The enlarged dermal condensations may be mediated through broader TGF-beta2 expression and reduced protein kinase C (PKC) expression. Reciprocal mesenchymal interaction is required for the induction and maintenance of Sonic hedgehog in the epithelial placodes. In scaleless mutant, Sonic hedgehog is absent in the apteric region and aberrantly expressed in the mesenchyme of the abnormal feather ridge. These findings suggest that Sonic hedgehog mediates key interactions between the epithelium and mesenchyme during feather morphogenesis. Authors Song H. Wang Y. Goetinck PF. Institution Cutaneous Biology Research Center, MGH East, Massachusetts General Hospital, 13th Street,Charlestown, MA 02129; United States. Title Fibroblast growth factor 2 can replace ectodermal signaling for feather development. Source Proceedings of the National Academy of Sciences of the United States of America. Vol. 93(19)(pp 10246-10249) , 1996. Abstract The initiation and morphogenesis of cutaneous appendages depend on a series of reciprocal signaling events between the epithelium and mesenchyme of the embryonic skin. In the development of feather germs, early dermal signals induce the formation of epidermal placodes that in turn signal the mesoderm to form dermal condensations immediately beneath them. We find a spatially and temporally restricted pattern of transcription for the genes that encode fibroblast growth factor (FGF) 2 and FGF receptor (FGFR) 1 in developing feather germs of the chicken embryo. FGF-2 expression is restricted to the epidermal placodes, whereas FGFR-1 expression is limited to the dermal condensations. Transcription of these genes could not be detected in skins of scaleless (sc/sc) embryos that fail to develop feathers as a result of an ectodermal defect. Treatment of sc/sc skins with FGF-2 results in the formation of feathers at the site of application of the growth factor and the induced feathers express FGFR-1 in their dermal condensations. Thus, we have established FGF-2 as an epidermal signal in early feather germ formation. The observation that FGF-2 can rescue the mutant phenotype of sc/sc embryos suggests that FGF-2 either is, or is downstream from, the signal that the sc/sc mutant ectoderm fails to generate. Authors Zou H. Niswander L. Institution Molecular Biology Program, Memorial Sloan-Kettering Cancer Ctr., 1275 York Avenue,New York, NY 10021; United States. Title Requirement for BMP signaling in interdigital apoptosis and scale formation. Source Science. Vol. 272(5262)(pp 738-741), 1996. Abstract Interdigital cell death leads to regression of soft tissue between embryonic digits in many vertebrates. Although the signals that regulate interdigital apoptosis are not known, BMPs -signaling molecules of the transforming growth factor-beta superfamily -are expressed interdigitally. A dominant negative type I BMP receptor (dnBMPR-IB) was used here to block BMP signaling. Expression of dnBMPR in chicken embryonic hind limbs greatly reduced interdigital apoptosis and resulted in webbed feet. In addition, scales were transformed into feathers. The similarity of the webbing to webbed duck feet led to studies that indicate that BMPs are not expressed in the duck interdigit. These results indicate BMP signaling actively mediates cell death in the embryonic limb. Authors Noveen A. Jiang T-X. Chuong C-M. Institution Department of Pathology, University of Southern California, HMR 204, 2011 Zonal Avenue,Los Angeles, CA 90033; United States. Title cAMP, an activator of protein kinase A, suppresses the expression of Sonic hedgehog. Source Biochemical & Biophysical Research Communications. Vol. 219(1) (pp 180-185), 1996. Abstract In Drosophila, it has been shown that protein kinase A and hedgehog have antagonistic actions during the formation of imaginal disks. In vertebrate skin, sonic hedgehog is expressed specifically in the feather bud epithelia. Using an in vitro explant culture model we showed that dibutyryl cAMP, a protein kinase A (PKA) activator, suppresses the expression of Sonic hedgehog, (Shh) and continuous feather growth. The results suggest that Shh and PKA also have antagonistic action during vertebrate skin morphogenesis. Authors Hee Kyung Song. Sawyer RH. Institution Department of Biological Sciences, University of South Carolina,Columbia, SC 29208; United States. Title Dorsal dermis of the scaleless (sc/sc) embryo directs normal feather pattern formation until day 8 of development. Source Developmental Dynamics. Vol. 205(1)(pp 82-91), 1996. Abstract We have examined the ability of the scaleless (sc/sc) backskin dermis (6 to 16 days of incubation) to regulate pattern formation using the presumptive scutate scale epidermis from 11-day normal embryos as the responding tissue. Prior to 8 days of incubation the sc/sc backskin dermis is able to induce hexagonally patterned and uniformly oriented feather germs in normal epidermis. This ability is lost during day 8 and follows a central to lateral gradient. Such gradients are characteristic of normal feather development in the spinal tract. We discuss the change in the inductive ability of the sc/sc dermis in relation to the stabilization of the feather pattern, which occurs all at once throughout the dorsal dermis at 7.5-8 days of development. After day 8 until day 10, the sc/sc backskin dermis only supports the formation of sporadic, unpatterned feather germs; thereafter it will not support feather formation. USC Scientists Uncover Secrets Of Feather Formation; "Jurassic Chicken" Project May Help Studies Of Human Development And Evolution Of Dinosaurs Scientists from the Keck School of Medicine of the University of Southern California have, for the first time, shown experimentally the steps in the origin and development of feathers, using the techniques of molecular biology. Their findings will have implications for the study of the morphogenesis of various epithelial organs-from hairs to lung tissue to mammary glands-and is already shedding light on the controversy over the evolution of dinosaur scales into avian feathers. A paper describing this work, "The Morphogenesis of Feathers", authored by principal investigator and Keck School pathology professor Cheng-Ming Chuong and his colleagues, was selected for advance online publication in the journal Nature and will be available as of October 30, 2002. "The feather is one of the best research models you can find for understanding the basic molecular pathways used by all epithelial cells," says Chuong. "Scientists agree that whether you're looking at a human mammary gland or a chicken feather, epithelial cells use the same underlying logic, the same grammar, to form an organ. But unlike a gland, a feather really lays everything right out there for you." The question of what makes a feather a feather has become rather heated in the recent past, with the discovery in China in the 1990s of fossilized dinosaurs like the Sinorthosaurus (Chinese-bird-dinosaur), with branching skin appendages on its skin. "Some say these things are feathers, some say they're protofeathers, others say they're not feathers at all," Chuong explains. "Everybody wants to know which one is the real first feather." And they want to know how it came to be, as well. Over the years, Chuong notes, paleontologists trying to trace the evolutionary connection between dinosaurs and birds have looked at the ways in which a reptilian scale might turn into an avian feather. Most adult feathers have a backbone, or stem, called a rachis, off of which the feather's barbs branch; each individual barb then branches again into the feather's smallest unit, the barbule, which is made of a single row of epithelial cells. Downy feathers, like those on a chick, lack a rachis altogether and are made up of just barbs studded with barbules. The standing hypothesis among many paleontologists has long been that the scales on dinosaurs must have lengthened into rachides that then became notched to form barbs and barbules. But there has been no real molecular evidence to either back up or refute that argument. Until now. In their Nature paper, Chuong and his colleagues have demonstrated just how barbs and rachides are formed in a modern chicken, and have at the same time demonstrated that the evolution from scale to feather most likely followed a path in which the barbs form first and fuse to form a rachis-rather than a rachis forming first, and then being sculpted into barbs and barbules. This interaction between evolutionary biology and developmental biology (dubbed Evo-Devo) is a relatively new marriage of two previously disparate fields. To come to their conclusions, Mingke Yu, the postdoctoral fellow and first author on the paper, along with colleagues Ping Wu and Randall B. Widelitz in Chuong's laboratory, developed a novel way to genetically manipulate different genes during feather formation. They plucked feathers from chickens, then prompted the chicken to regenerate those feathers under controlled conditions, raising and lowering the expression levels of the genes in question on an individual basis and observing the effects they had on the organization of epithelial cells into different feather forms. Among others, three genes in particular-noggin, bone morphogenetic protein 4 (BMP4), and the whimsically named sonic hedgehog (Shh)-were found to result in new feathers that were rife with abnormal organization in their rachides and barbs. When Chuong's team increased the expression of noggin, for instance, they found that the rachis began to split into several small, thin rachides, and the barbs increased in number. When they increased the expression of BMP4, with which noggin interacts antagonistically, they found that the feather's rachis became gigantic and its barbs merged and were reduced in numbers. In this way, they were able to essentially manipulate the number and size of the feather's barbs and rachides. Finally, when they suppressed Shh, they found a residual webby membrane between the normally separated barbs. "The cells there were supposed to go through apoptosis, or cell death," says Chuong, "in order to create the space between the barbs. But when we took away the sonic hedgehog signal, cell death no longer occurred. It is a similar process to that which occurs in the web of duck feet." What can these new findings on the morphogenesis of feathers tell us about their evolution? "These results suggest that the barbs form first and later fuse to form a rachis, much like downy feathers are formed before flight feathers when a chicken grows up. Under the general rule of ontogeny repeating phylogeny, downy feather made only of barbs probably appeared before the evolution of feathers with rachides and capable of flight," Chuong says. "However, pinning down the exact moment at which dinosaur scales become chicken feathers is non-realistic. Just like Rome, feathers are not made in one process. It took 50 million years for Nature to refine the process, to transform a scale into a flight machine. There were many, many intermediate stages. "While Darwin's theory has explained the 'why' of evolution, much of the 'how' remains to be learned," Chuong adds. "Evo-Devo research promises a new level of understanding." These findings also have medical applications, notes Chuong. "With this study, we learned more about how nature guides epithelial stem cells to form different organs. For example, BMP, Shh and noggin are also used in different ways in making lungs, limbs and spinal cords. By analyzing these models, scientists may be able to fully understand nature's 'grammar,' and learn to use it in repairing or regenerating tissues and organs, which we call tissue engineering." This research was supported by grants from the National Institute of Arthritis and Musculoskeletal and Skin Diseases of the National Institutes of Health, and from the National Science Foundation. Mingke Yu, Ping Wu, Randall B. Widelitz and Cheng-Ming Chuong, _The Morphogenesis of Feathers._ Nature advance online publication, 30 October 2002 (doi:10.1038/nature01196). == 1) Koder RL and Dutton PL : Intelligent design : the de novo engineering of proteins with specified functions. Dalton Trans. 2006 Jul (25) 3045-51 2) Winans SC : Bacterial evolution by intelligent design. ACS Chem Biol. Drew: Here's an abstract of the first one, which seems to do only with *human* design of proteins: "One of the principal successes of de novo protein design has been the creation of small, robust protein-cofactor complexes which can serve as simplified models, or maquettes, of more complicated multicofactor protein complexes commonly found in nature. Different maquettes, generated by us and others, recreate a variety of aspects, or functional elements, recognized as parts of natural enzyme function. The current challenge is to both expand the palette of functional elements and combine and/or integrate them in recreating familiar enzyme activities or generating novel catalysis in the simplest protein scaffolds." And here are some statements from the final paragraph of the Winans paper, which also seems to deal only with *human* design of bacteria: "The creation of a new signal specificity will have interesting and unforeseen applications in synthetic biology. ... Researchers should be able to mix and match the binding domains of AHL and DNA of the various LuxR homologues to construct proteins that bind to new DNA sequences that are chosen by the intelligent bacterial designer." === A single point mutation in chickens will turn their feathers into scales. (See, for example, "Development & Evolutionary Origin of Feathers" by R. Prum, J. Experimental Zoology 285: 291-306, 1999. == Change from invertebrate to vertebrate. For wormlike or sluglike inverts the first step was developing a notochord. This is a somewhat stiff, cartilage-like rod running the length of the body between the dorsal nerve cord and the GI tract. It served as a good attachment for muscles and a stiffener of the body, allowing for stronger and more efficient swimming, among other things. With a notochord when the muscles on one side of the body contract the body bends, rather than crumples. Tunicates are good examples of modern, living animals with only a notochord and no bones yet. But once the notochord was established slowly, to be sure, probably as a gradual thickening of a fibrous sheet where muscles attached along the midline, not in a single mutation- then some animals would be selected for stiffer, more mineralized notochords and also for other modifications, such as lateral flares in each segment (remember, these primitive wormlike critters were segmented) the precursors of ribs, etc. Genes which lead to the mineralization of cartilage in mammals are well known- ank, Sox9, osteocalcin, etc. These genes are very similar to genes from `more primative' species which have no mineralized skeletons. It's easy to see how variations in these genes would have been strongly selected for their ability to make harder, more durable skeletons in their owners. Again, millions of years, many, many steps, all of which are supported by the fossil as well as molecular and genetic evidence, not an overnight mutation. == One Key to Bird Flight Discovered Powerful forces are exerted on the shoulders of birds where muscles converge. So scientists have wondered why the joints don't dislocate. Using CAT scans, scientists at Brown and Harvard universities made a virtual skeleton of a pigeon and then calculated all the forces involved. Neither the shoulder socket nor the muscles could keep the wings stable. The key, they found, is the acrocoracohumeral ligament, a short band of tissue that connects the humerus to the shoulder joint. The ligament balances all of the converging forces, from the pull of the massive pectoralis muscle in the bird's breast to the push of wind under its wings. Curious if the same was true of ancient animals, the researchers put some alligators on a treadmill and studied their gaits and used X-rays to make more computer models. The ancestors of modern alligators were closely related to birds. They found that alligators use muscles, not ligaments, to support their shoulders. A look at fossils of Archaeopteryx, thought to be the first bird, revealed its flight mechanism to be unlike the pigeon, too. "Our work also suggests that when early birds flew, they balanced their shoulders differently than birds do today," said study leader David Baier, a post-doctoral research fellow at Brown. "And so they could have flown differently. Some scientists think they glided down from trees or flapped off the ground. == Origin of kidneys It became an advantage to more rigorously control the influx of water in order to move from salty sea water to brackish to fresh water in order to exploit virgin habitat, the critters who had slightly better equipment for that job were able to move into areas their competion could not- and feed, mate, nest, hide from predation, etc. It would be a great advantage. Fossil evidence suggest that the earliest vertebrates evolved in brackish estuaries or fresh- water rivers. This shift from their ancestral marine environment into fresh water necessitated many morphological and physiological adjustments, foremost among which were provisions for dealing with an osmotic influx of water into their now hypertonic tissues. One adaptation was the of an impermeable outer skin, but the necessarily thin membranes of the gills and alimentary canal still allowed free diffusion of water along with the vital diffusion of respiratory gases and absorption of food nutrients. Means of eliminating excess osmotic water had to be developed before fresh-water habitats could be successfully invaded. The earliest vertebrates had inherited an excretory system similar to those of their marine chordate ancestors: a series of tubules opening into the coelom drained fluid from the body cavity to the exterior, with some resorption of valuable solutes, such as salts, etc., through the tubule walls. This system works well in marine animals, whose body fluids are isotonic with seawater, but cannot eliminate the excess osmotic water that hypertonic tissues attract in fresh-water environments. Early vertebrates adapted to their new environment by evolving a tuft of capillaries at the end of the tubules (called a glomerulus) that became partially enveloped by a cup-shaped outgrowth (renal capsule) of the primitive excretory tubule. The blood pressure in the capillaries more efficiently squeezes the excess fluid through slits between cells and salts and other nutrients are resorbed through the remaining length of the tubule. This arrangement is essentially what we have now packaged in our kidneys. The whole series of this development can still be seen as we look through the series of modern analogs of the creatures from which our ancestors evolved. The lineages which didn't develop these modifications either stayed in their more ancestral habitats, to which they were well adapted or they died out, outcompeted by the variants which did happen to possess the more efficient osmotic regulatory machinery. === http://scidiv.bcc.ctc.edu/rv/103/ppt06/Lec14.103.PCLife.ppt life origins* == Mammals Might Have Soared Before Birds Mammals might have taken to the sky before birds, scientists announced today. A new order of mammals has been named based on a recently discovered fossil of a squirrel-sized Mesozoic-era animal [image] that lived at least 130 million years ago and was capable of gliding flight. The ancient mammal, Volaticotherium antiquus, represents a previously unknown group that bore features adapted for arboreal life. This fossil, found in Inner Mongolia, China, puts the first record of gliding flight for mammals at least 70 million years earlier than had been known, the researchers write in the Dec. 14 issue of the journal Nature. Previously, the earliest record of flight in mammals was found in fossils of bats dating back to 51 million years ago, said lead study author, Jin Meng from the American Museum of Natural History in New York. "Of course the bats at that time already had the ability of flapping flight not just gliding, so proto-bats could have been gliders but we don't have any fossil records of that." Telling teeth The specimen was found in a book-sized slab. Bones, teeth and impressions of the soft tissue were preserved. This allowed the researchers to classify this prehistoric animal. "If you're looking for a mammal, the first thing you will look at is the teeth," Meng told LiveScience. Mammalian teeth have developed into four sets: incisors, canines, premolars and molars. Incisors are in the front and considered cutting teeth. Canines are the sharp stabbing teeth. Premolars and molars stand behind the canines and are used for grinding food. This specimen has all those features. "So we can tell that this is a mammal from the dental formula," Meng said. "Also, we can tell from the teeth morphology, because it's very sharp and very hook-like, that this is an insectivore mammal." Unlike herbivores such as the flying squirrel that eats fruits, leaves, and nuts, this ancient gliding beast fed on insects. Extinct lineage The fossil also preserved a large piece of the animal's skin membrane [image]. "We know this [was skin] because it was covered with dense hair," Meng said. "The fur or body hair is another mammalia characteristic. So by finding that, we know that this animal has this large body skin membrane that is used for gliding. And only gliding mammals have that kind of morphology." The V. antiquus, weighing in at less than a pound, is comparable in size and shape to flying squirrels. However, the mammal is not considered a direct ancestor of these or other flying mammals. Instead, V. antiquus provides evidence for the independent origin of flight in this now-extinct lineage of mammals, the researchers conclude. "It's unusual to find such a unique creature," Meng said. "Establishing a new order probably only happens once, if that, in the lifetime of a lucky paleomammalogist." == http://www.talkorigins.org/ http://www.talkorigins.org/origins/faqs.html http://www.talkorigins.org/origins/outline.html http://www.talkorigins.org/origins/faqs-qa.html http://www.talkorigins.org/origins/faqs-mustread.html http://www.talkorigins.org/faqs/faq-misconceptions.html http://www.talkorigins.org/origins/faqs-evolution.html http://www.talkorigins.org/faqs/faq-intro-to-biology.html http://evolution.mbdojo.com/evolution-for-beginners.html http://www.talkorigins.org/origins/other-links-gensci.html http://www.talkorigins.org/origins/other-links.html#evolution http://evolution.berkeley.edu === "the South African australopithecine was originally *estimated* to be 3 million to 3.5 million years old, making it one of the oldest members of the human family. Other estimates dated Little Foot back as far as 4.1 million years, or as recently as 2.5 million years." (2 million years is a BIG difference) "Now a team of geochronologists ***thinks*** it has finally nailed down the fossil's true age--2.2 million years old--." Science is solely concerned with what is true and is very truthful about what it isn't sure of. You are seeing an example of scientific honesty. All scientific pronouncements are phrased in tentative language because very scientist knows new information could prove them wrong or incomplete. Creationists, indoctrinated with inerrant scripture they are not allowed to question, are always astonished by that. They perceive it as a weakness. After all, creationists have the 100% certain really true truth and scientists don't. It is actually the great strength of science. If 3.5 million years was the inerrant dogmatic pronouncement, then the truth would not have been discovered. People would simply stop doing research. A scientist would rather cut off her arm than do that. All dates for fossils are subject to review and revision as new information comes to light. Who would have it any other way if the truth is all that's important? >> I've gone to the original paper. Here is the Materials and Methods section: Materials and Methods Multiple sub-samples of up to 3g from each hand specimen were ultrasonically cleaned in 18MΩ water and acetone. Surface contamination was removed by etching in 3M HCl. Samples were then dissolved in concentrated HCl and aliquots spiked with a mixed 202Pb-233U- 236U spike whose calibration was cross checked against a gravimetric U-Pb solution from the Geological Survey of Canada (S1). Ca was removed by precipitation with HF (S2) and Pb and U were then separated on anion exchange columns using standard techniques (S3- S5). U and Pb isotopic compositions were analysed on a Thermo-Finnigan Triton TIMS instrument using multidynamic and static routines respectively, except for the preliminary SKA samples which were analysed on a single collector Micromass30. In these young thorium-poor samples, thorogenic 208Pb ingrowth is estimated to be <<0.1%, which is insignificant relative to 206Pb ingrowth. Consequently it is possible to eliminate possible uncertainties associated with measuring very low 204Pb beams by presenting the data as ratios based on 208Pb. Total procedural blanks were 93 34 pg Pb with 206Pb/204Pb = 18.3, 207Pb/204Pb = 15.7 and 208Pb/204Pb = 38.2. Blanks were insignificant for U. Mass spectrometric fractionation was correction of Pb isotopic compositions was based on measurements of SRM 981 which gave a mean bias of 0.80 0.14 . Uranium mass fractionation was internally corrected by use of the double spike. Errors and significant correlations in all measured ratios, spike and blank composition and fractionation values were propagated using a general error propagation procedure based on algorithms originally written by Roger Powell. The validity of the procedure was confirmed by comparison with analytical solutions courtesy of Felix Oberli (ETH, Zurich). The strong correlation between the output values arises from the significant blank corrections to the small amount of Pb in the analysed samples. Excess 234U was determined on 10 subsamples using unspiked aliquots of the same solutions used for U-Pb analysis. Analyses were performed on a Nu- Plasma MC-ICPMS instrument at the University of Bern with an equilibrium uraninite solution as standard, using a standard/sample bracketing procedure. The weighted mean of 31 measurements of 234U/238U of the standard was 54.89 0.03 (x 10-6) in good agreement with recent published values (S6). No significant differences were detected between samples (Table S1) and the weighted average value of 4.3 1.2 was used for all four samples. Isochron slopes and weighted averages were calculated using Isopod-Ex v3.4 (S7) and input to an iterative procedure which corrects for initial 234U/238U disequilibrium. Initial 234U excess was calculated to be around 2. Note that the new, updated age estimate is based on ten samples. The uraninite standard was read 31 times. They've clearly gone to great lengths to perform this work carefully and rigorously and then have been completely open about exactly how they achieved their results, making it simple for anyone to repeat their work for confirmation. It's hardly a game. If only "Creation Scientists" were half this thorough and rigorous In any case, the point I wanted to make is that scientists working in any particular field fully understand how reliable any particular determination is. Anthropologists knew there was a good deal of uncertainty surrounding the previous 3 to 3.5 million year estimate for Little Foot. But the media reports "Scientists think the Little Foot fossil is 3 to 3.5 million years old" and the general public walks away thinking to themselves- "scientists say it's a fact that Little Foot is definitely 3.0 to 3.5 million years old." Then when another, more precise and thorough test is done and the age turns out to be more like 2.2 million the public While in reality, they always had a very realistic idea of the tentative confidence that should have been placed in the 3.0 to 3.5 million year age and the much increased confidence that should be placed on the updated 2.2 million year age. -Because they understood well the reliability of the methods that were used for each estimate and the relative rigor with which each test was performed. That is one major reason why the details are always published in the scientific literature, so that people who understand such things can legitimately and rigorously evaluate what the results actually mean. == A single, gigantic asteroid slammed into Earth 65 million years ago, dooming the dinosaurs and many other species, scientists said on Thursday in a new study rebutting theories that multiple impacts did the deed. An examination of rock sediments drilled from five sites at the bottom of the Atlantic Ocean strongly supports the notion that one massive hunk of space rock caused the mass extinction, a research team led by University of Missouri-Columbia geology professor Ken MacLeod found. "It's a completely straightforward, single-impact scenario," MacLeod, whose findings appear in the Geological Society of America Bulletin, said in an interview. "It was a haymaker that nobody saw coming. One shot, and that's all you need to explain it." Scientists believe that an asteroid about 6 miles wide hurtled to Earth 65.5 million years ago at the end of the Cretaceous Period, plunging into what is now Mexico's Yucatan Peninsula to carve out the Chicxulub (pronounced CHIK-shu-loob) crater measuring about 110 miles across. To put it mildly, it was a bad day to live on Earth. The impact triggered a worldwide environmental catastrophe, many scientists believe, expelling vast quantities of rock and dust into the sky, unleashing giant tsunamis, sparking global wildfires and leaving Earth shrouded in darkness for years. The dinosaurs, which had ruled for 160 million years, were wiped out. So were large marine reptiles like the mosasaurs and the plesiosaurs, the flying reptiles known as pterosaurs, the tentacled ammonites that populated the seas and many species of marine plankton. The birds suffered losses but survived. The mammals made it through as well, allowing these warm-blooded, furry little creatures to eventually dominate the land and ultimately setting the stage for the rise of human beings. Evidence of the single-asteroid calamity, in the form of debris from the impact scattered worldwide, is contained in rocks dating back to 65 million years ago. Scientists 26 years ago found a band of iridium -- a metal rare on Earth but common in meteorites -- dating to the end of the Cretaceous Period that suggested a big space rock had smashed into the Earth and blasted its remains around the globe. The subsequent discovery of the Chicxulub crater, dating to the same time, was hailed by many as the smoking gun. But a group of researchers led by Princeton University's Gerta Keller has advanced a competing theory that the impact that created the Chicxulub crater actually predated the end of the dinosaurs by 300,000 years and did not cause the mass extinction. They propose that one or more additional big hunks of space rock later hit the Earth and finished the job, but the impact craters they would have left behind have not yet been found. MacLeod's team examined sediment drilled far below the sea surface about 2,800 miles from the Yucatan impact site, a location they believed to be ideal. Any rock samples taken too close to the crater may be altered by events that occurred immediately after the impact, like waves, earthquakes and landslides. Samples taken too far away may contain too little debris evidence from the impact. The samples they examined boasted a telltale layer of impact-related material, but there was none on top or below -- indicating, they argued, there were no other impacts. == Graham Bell's "The Masterpiece of Nature", a weighty tome which has all you could care to know about the evolution of sexual reproduction. == All members of the Monera Kingdom reproduce asexually only. == Gendered Division Of Labor Gave Modern Humans Advantage Over Neanderthals Diversified social roles for men, women, and children may have given Homo sapiens an advantage over Neanderthals, says a new study in the December 2006 issue of Current Anthropology. The study argues that division of economic labor by sex and age emerged relatively recently in human evolutionary history and facilitated the spread of modern humans throughout Eurasia. "The competitive advantage enjoyed by modern humans came not just from new weapons and devices but from the ways in which their economic lives were organized around the advantages of cooperation and complementary subsistence roles for men, women, and children," write Steven L. Kuhn and Mary C. Stiner (University of Arizona). Kuhn and Stiner note that the rich archaeological record for Neanderthal diets provides little direct evidence for a reliance on subsistence foods, such as milling stones to grind nuts and seeds. Instead, Neanderthals depended on large game, a high-stakes resource, to fuel their massive body mass and high caloric intake. This lack of food diversity and the presence of healed fractures on Neanderthal skeletons--attestin g to a rough-and-tumble lifestyle--suggest that female and juvenile Neanderthals participated actively in the hunt by serving as game drivers, beating bushes or cutting off escape routes. The Middle Paleolithic Neanderthal record also lacks the artifacts commonly used to make weather-resistant clothing or artificial shelters, such as bone needles. Thus, it was the emergence of "female" roles -- subsistence and skill-intensive craft -- that allowed H. sapiens in ecologically diverse tropical and sub-tropical regions to take advantage of other foods and live at higher population densities. "Earlier hominins pursued more narrowly focused economies, with women's activities more closely aligned with those of men with respect to schedule and ranging patterns," write the authors. "It is impossible to argue that [Neanderthal] females and juveniles were fulfilling the same roles--or even an equally diverse suite of economic roles--as females and juveniles in recent hunter-gatherer groups," they add. While some degree of niche specialization between adult male and females is documented for many large-mammal species, recent humans are remarkable for cooperative economies that combine pervasive sharing and complementary roles for individuals of different ages and sexes. == A new DNA sequencing machine that utilizes the firefly enzyme luciferase as one of its main features is helping scientists reconstruct the Neanderthal genome and tap the surface of unanswered questions about this ancient species. Known as pyrosequencing, it uses flashes of light to determine a DNA sequence. The amount of light equals how many base pairs are incorporated into that sequence. Dr. Clare O'Connor, assistant chair of Boston College's biology department, explained that because pyrosequencing is very rapid, it is only effective for stretches of about 100 base pairs at a time. This makes it perfect for examining Neanderthal DNA, which has experienced fragmentation because it is so ancient. So far about one million units of Neanderthal DNA have been analyzed, according to The New York Times article "New DNA Test is Yielding Clues to Neanderthals" by Nicholas Wade. Dr. Svante Paabo, the leader of this research project, estimates that the draft of the entire genome should be ready within two years. Paabo had been searching for a source of Neanderthal DNA for over a decade. His main obstacle was finding uncontaminated DNA. According to O'Connor, this is not an uncommon problem. Two of the major problems when working with ancient DNA are (1) contamination with modern DNA, and (2) chemical damage and fragmentation. In 1997, Paabo finally successfully analyzed part of the mitochondrial DNA of Neanderthals. His search for uncontaminated DNA involved evaluating 70 bones from various museums all over Europe, and turned up only one bone as a source of DNA that comes from the Vindija cave in Croatia. Paabo hopes to find other Neanderthal bones containing usable DNA. Even if more is not found, he believes that the full Neanderthal genome should be able to be completed. Once the Neanderthal genome is completed, scientists hope to begin other projects. One project that would develop, according to The New York Times article, is to discover if the Neanderthals had language by evaluating FOXP2, their analogous version of the human gene for modern human language. This gene underwent marked differences from when humans and chimps split evolutionarily. If the Neanderthal version of the gene is closer to that of the chimps, then it would be unlikely that their language was similar to humans. David Burgess, a professor in the biology department, and other researchers from Massachusetts' universities collaborated as part of an international conglomerate to sequence the sea urchin genome. Burgess's group was responsible for decoding the genome of Strongylocentrotus purpuratus, a male California purple sea urchin. The Human Genome Sequencing Center of Baylor College of Medicine and scientists at Cal Tech in Pasadena headed The Sea Urchin Genome Sequencing Project (SUGSP) Consortium. For two years, 240 scientists in 11 countries analyzed the genome of this marine species. The SUGSP was divided into teams; Burgess's group was responsible for understanding the sea urchin's cytoskeleton genome, which is in charge of cell division and cell movements. The sea urchin's genome is of particular interest to scientists because of how humans share a common ancestor with the species. Because of their evolutionary proximity to vertebrates, researchers can develop a greater comprehension of the evolution of genes responsible for encoding various cytoskeletal proteins. "Understanding the genome will allow us to develop better experiments. Having sequence of genes of the protein [of interest] will allow us to make probes, such as antibodies, to affect the function of these proteins: with homologous proteins in other species the probes may not work across species," said Burgess. Besides Neanderthals and sea urchins,what other genomic projects are out there? Perhaps the most famous is the International HapMAP project. Started in 2002, the goal of the project is to develop a haplotype (the genetic make-up of an individual chromosome) map of the human genome that will describe patterns of variation in it. == http://www.progress iveu.org/ 155822-blood- clots-panspermia -ediacarn- fauna-and- empty-black- boxes blogs evolutiongeek's blog Blood clots, Panspermia, Ediacarn Fauna, and Empty Black Boxes For those of you that may have missed it, I've been going back and forth with Homunculus about the nature of Intelligent Design over the past few days. He doesn't agree with me, nor do I with him, and rather than keep it buried in the comments section I thought I would drag the thread out into the light. After spending the day at the American Museum of Natural History yesterday, I spent the better part of my evening and this morning re-reading the blood-clotting chapter of Behe's Darwin's Black Box and trying to get a grip on the various scientific papers on the subject. I must admit I am not a biochemist, genetecist, or microbiologist (my main interests being in paleontology, ecology, behavior, functional morphology, etc) but I've done my best to understand what's going on here and cited other sources when I feel I can't do the topic justice myself. In any case, here is my line-by-line response to the latest comment sent to me, and I hope that it proves to be enlightening. It is a bit long, so you may want to grab a drink or read it in parts, but hopefully it doesn't put anyone to sleep. And away we go... "ID is a new line of scientific endeavor. It is science." For reasons I've already mentioned and discussed by both of us, I do not find Intelligent Design to be science or even "new" science. ID advocates throw a lot of complex equations and diagrams around, but the argument comes down to a philosophical one. The advocates of intelligent design may be scientists, but this does not automatically mean that the popular books they right qualify as actual science; rather they are philosophical interpretations of science. Also, ID in one form or another has been around for at least 200 years (if not longer) and only recently has been married to biochemistry and probability in order to give it more credibility. It is about as scientific as the once-held belief that Apollo draws the sun across the sky because there was no other way to explain it. ID advocates also attempt to shield their theory from criticism by accepting evolutionary mechanisms in some places, but not others. For instance Behe wrote; "The production of some biological improvements by mutation and natural selection - by evolution - is quite compatible with intelligent design theory." On this point I agree with Ken Millers assessment of the statement when he wrote in his review of Darwin's Black Box, In other words, any evidence for the evolution of complexity is dismissed in advance as being irrelevant to the problem of design. "Design" exists only when and where evolution cannot explain it! (http://www.ncseweb. org/resources/ articles/ 7738_review_ of_michael_ behe39s__ 5_20_2003. asp) "Biologist Behe examines the blood clotting mechanism and demonstrates, line and verse, with ZERO valid refutation, that it is impossible that it could ever develop under any possible form of "evolution" (random changes and survival of the fittest). By making this determination he is going through all the chemical steps. It makes Microsoft Windows XP look like Tinker-toys, so great is the complexity and so impossible is it to "evolve"." The thing Behe points out is that the blood-clotting cascade is exceedingly complex, but his chapter does not rule out evolution. The origins for many of the proteins in the cascade are millions (even billions) of years old, and blood-clotting cascades are not something that fossilizes. Perhaps future work with "junk DNA" will provide the framework for how such a system came to be, but just because we don't have all the answers as of 1996 or 2006 doesn't mean that there is no way that evolution could have produced the cascade; saying that it must have had an intelligent agent involved because we can't figure it out yet is an argument from ignorance. The main part of Behe's argument is that we don't yet know how the cascade is regulated so that it doesn't clot too much blood or too little, but to say that no work has been done to try to figure this out or how the cascade developed is ignoring the facts. (I also found it interesting that Behe criticized Doolittle for using an analogy to explain how such a cascade could have evolved when Behe uses a silly Foghorn-Leghorn analogy all through his chapter). In any case, Behe's argument is that the blood-clotting cascade is irreducibly complex, and we need to understand what he means by "irreducibly complex" in order to discuss his ideas. Behe's definition is found on page 39 of Darwin's Black Box (he's since revised his definition, which I will discuss later); "By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution." Behe seems to be defining evolution in a particular way that suits his purposes, in that it's suppossed to work at a slow, gradual pace. This leaves out the ideas of punctuated equilibrium, exaptation (finding a new use for an already-existing structure), various mutations (like gene duplication and frame-shifts) , and other important factors. He's essentially setting up a straw man so everyone can be impressed when he knocks it down, but just because Behe says that a particular structure or function can't evolve does not make it so. Behe's discussion of blood-clotting worries me as he leaves out other important mechanisms used to slow or stop bleeding, and the discussion is entirely confined to clotting mechanisms in humans. For instance, he only gives a passing reference to constricting blood vessels and platelets, and although I still have some more reading to do, I wonder if these two features came before the blood clotting cascade even developed. This would mean that creatures could have ways of slowing blood loss first and a cascade would add to the efficiency and effectiveness of blood-clotting, but Behe is right in that it would need to be regulated so that blood did not clot too much, selecting against the organism and not allowing them to pass on their genes. Even so, this would be natural selection in action,n selecting for animals that could stop bleeding a little bit better and allow for scaffolding. In any case, here's a quick overview of the process that stops bleeding: Hemostatic clotting starts when biomolecules from the damaged tissue are released, causing the blood vessel to constrict. At that point platelets bind to the wound and cause a temporary plug called a white thrombus, but this conglomeration of platelets is weak. At this point, the blood clotting cascade is signaled to begin functioning. This next part is the actual blood clotting process (that Behe spends so much attention to) where red blood cells are trapped by fibrin (known as a red thrombus). The actual blood clotting phase starts in two ways; via the instrinsic and extrinsic pathways. Again, I'm not a molecular biologist and some of this is still over my head, but I at least tried to grasp some of the evolutionary history of the blood clotting cascade as seen in other phyla. In looking over the relevant literature on the topic, I came across an interesting paper about clotting mechanisms in an invertebrate. Before I reproduce the abstract, however, its important to know that evolutionary antecedents of other phyla, namely the Poriferans, have amoebocytes and proteases (they "cut" proteins and are a major part of the cascade), so it is possible that other basal organisms had a similar arrangement in which the amoebocytes captured invading cells and the proteases helped break the cells down. To the best of my understanding, this is still a hypothesis, but if shown to be true it would help to illuminate the roots (mechanism and components) of clotting mechanisms in metazoans. In the abstract of the paper New Types of Clotting Factors and Defense Molecules Found in Horseshoe Crab Hemolymph: Their Structures and Functions by Iwanaga, Kawabata, and Muta (http://jb.oxfordjou rnals.org/ cgi/content/ abstract/ 123/1/1), the researches describe an "innate immunity" mechanism that allows for this variety of horseshoe crab to defend itself from harmful "invaders" like bacteria using protease (among other things). This is significant as the proteases essentially clot around the bacteria and may have been later co-opted to clot around damaged tissue, showing exaptation. Also, there is more detail to the topic than I can do justice to, and this web site (http://home. tiac.net/ %7Ecri/1998/ hemostasis. html) was extremely helpful in understanding some of the beginnings of the proteins used in blood-clotting and how such a system could have evolved (references to some more papers are also included). Also, Kenneth Miller's reply to Behe's claims is very informative and easy-to-read (even moreso than Behe's book), and I found the section about signaling pathways very interesting. Remember, we're not starting from nothing. We're starting about 600 million years ago in a small pre-vertebrate. with a low-volume low-pressure circulatory system. Just like any small inverterbate with a circulatory system, our ancestral organism would have had a full compliment of sticky white cells to help plug leaks. In addition, that ancestral system would have had something else. Most of the time, hemorrage starts with cell injury, meaning that cells are broken in the vicinity of a wound and their contents are dumped out. That means, among other things, that all of a cell's internal signalling molecules are suddenly spilled out into the damaged vascular system. Included among the contents are a whole slew of internal signalling molecules, including prominent ones like cyclic adenosine monophosphate (abbreviated: cAMP), all dumped into the tissue surrounding a wound. Why would a sudden gusher of cAMP in a wound be significant? Well, it turns out that vertebrates use cAMP as a signalling molecule to control the contractions of smooth muscle cells, the very sort of muscle cells that surround blood vessels. Therefore, the release of internal cAMP from broken cells would automatically cause smooth muscles around a broken vessel to contract, limiting blood flow and making it more likely that the blood's own sticky white cells would be able to plug the leak. That means that we already have some ability to limit damage and plug leaks in a primitive, low-pressure system. Not a bad place to begin. (reference http://www.milleran dlevine.com/ km/evol/DI/ clot/Clotting. html) Upon some further research, cAMP is an ATP-derived molecule important for various tasks, such as signal transduction (changing one type of stimulus into another), in everything from bacteria to humans. Thus, I see no reason to discount that Millers chordate organism would not have cAMP or utilized it in such a manner. Gene duplication and its role in the evolution of the blood clotting cascade has been hotly debated, and Behe largely discounts that it has any implications for evolution. In a reply to Doolittle and Miller in 2000, Behe wrote the following: The predicament is easily resolved when a critical point is recalled: EVIDENCE OF COMMON DESCENT IS NOT EVIDENCE OF NATURAL SELECTION. Homologies among proteins (or organisms) are the evidence for descent with modification- -that is, for evolution. Natural selection, however, is a proposed explanation for how evolution might take place--its mechanism--and so must be supported by other evidence if the question is not to be begged. This, of course, is a well-known distinction (Mayr 1991). Yet, from reviewers' responses to my book, the distinction is often overlooked. Knowledge of homology is certainly very useful, can give us a good idea of the path of descent, and can constrain our hypotheses. Nonetheless, knowledge of the sequence, structure, and function of relevant proteins is by itself insufficient to justify a claim that evolution of a particular complex system occurred by natural selection. Gene duplication is not a Darwinian explanation because duplication points only to common descent, not to the mechanism of evolution. (http://www.arn. org/docs/ behe/mb_indefens eofbloodclotting cascade.htm) Behe seems to omit a few things here and make some mistakes about homology and what it means. He neglects to mention that when gene duplication occurs (often considered a "neutral" mutation) the gene does not simply sit there, doing nothing. Rather, the copied gene is free to have mutations and have natural selection act upon the result (either in favor of or against it). In fact, a gene duplication coupled with a frame-shift mutation may have created the famous nylon-eating bacteria, which are bacteria that developed an entirely novel enzyme to break down a snythetic product. In any case, the role of gene duplication in evolution is one of extreme interest, and a search for "gene duplication" on PubMed yields thousands of articles related to the subject, including its role in evolution. Also, homology can indeed be tied to natural selection. Look at the tetrapod limb, for example. It is present in everything from the most basal tetrapods to you and I, and it has persisted because it works. Although horses, bats, birds, seals, lizards, etc. all have different variations, they all have the same basis as natural selection has modified the design of the tetrapod limb to different modes of life. Birds are an interesting example as their fingers have fused and some bones in the forearm have even been lost, but nevertheless such modifications are from the homologous tetrapod limb that was inherited from earlier forms. After initial criticism of Behe's blood clotting model, he revised his definition of irreducible complexity. "An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but- unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway" (http://www.arn. org/docs/ behe/mb_indefens eofbloodclotting cascade.htm) Ok, but how do we define unselected steps? What steps were unselected? When? How did the information get there if not by evolution? Who did it (as a designer is implied)? This is also looking at evolution as progress being that we're working from what we have and going backwards, and Behe is implying intention or purpose in the arrangement of the parts. Behe makes no attempt to explain any of this, but rather simply says that intelligence or a designer was involved at some point in some way and evolution could not have produced the system. That's a pretty large assertion to make, especially since we still have a lot to learn; it seems as if Behe is assuming all the votes are in and nothing new will come to light about the process. It is not enough (nor is it scientific) to simply say "It couldn't have happened this way, so a designer did it" but then not provide us with any of the details important to the sytems formation. In short, it is a negative argument against evolution that offers up nothing new at all, and some ID advocates have even gone as far to say that we may never know who the designer is, how they did it, or any of those details. I don't find that convincing at all. I would be remiss, however, if I didn't mention Behe's speculation about IR systems. In his book he writes (pps 227-8) "Suppose that nearly 4 billion years ago the designer made the first cell, already containing all of the irreducibly complex biochemical systems discussed here and many others. (One can postulate that the designs for systems that were to be used later, ushc as blood clotting, were present but not "turned on." In present-day organisms plenty of genes are turned off for a while, sometimes for generations, to be turned on at a later time." This reminds me of the creationist "kinds" argument where the first pair of organisms had all the genetic variation that would later show up due to speciation and variation. If Behe is right, all these instructions to later be turned "on" would have to be stored somewhere, probably as non-coding DNA. Just because it doesn't code, however, doesn't mean it's safe from mutations or the outside world. Over billions of years, the genes to control the IR systems would be mutated and may be destroyed or pick up an entirely different function. To prevent this, some new mechanism to protect the genes would have to be invented, most likely invoking theology rather than any science we have. In fact, there are scientists that are tracing evolutionary change through "fossil genes" that have stopped coding and are being degraded over time, as exemplified in Sean B. Carroll's book Making the Fittest. In any case, this is merely Behe's speculation with no data to back it up and shouldn't be entertained as actual science. If there's any truth to it, then someone should be the effort to uncover such a mechanism to allow for genes to be kept safe without change for billions of years, although at this time I doubt there is one. "Nobel laureate Francis Crick does the math on the odds of DNA self-starting. He gets 1x10x2billion. The odds of anything happening since the Big Bang is 1x10x152." I haven't seen these equations, nor have you provided them. Either way, I don't put too much stock in statistical analysis of this kind because we aren't even 100% certain of all the characteristics of the early earth, so how can we make projections if we're not even entirely sure of the environment in which life appeared? It's similar to Lord Kelvin's equations based on the age of the earth and sun; he based them on assumptions we know to be false today, so even though he was very smart his results were wrong because he made the wrong assumptions. Thus, until we know more about the makeup of early earth I think it's impossible to say what the chances are of life resulting from abiogenesis. "Crick dies believing space aliens seeded the planet 3 billion years ago. Nanu-nanu. (The theory is called Panspermia). In case you can't think through this, Crick acknowledged there had to be a Designer." Apparently you haven't done much research on Crick. There were advocates of Panspermia and similiar ideas long before Crick, dating back to Anaxagoras in the 5th Century BC, although it wasn't mentioned more prominently until much later. In any case, Crick hypothesized about panspermia because he was pessimistic about the origin of life on Earth early on, but he never seemed to actually believe it himself. Later, after the discovery of ribozymes, Crick gave up on panspermia, having it now possible to imagine a world of self-replicating proteins (like RNA) leading up to the origin of life. Regardless, Crick was a staunch atheist and certaintly never recognized a designer (especially with a capital "D"). Crick also criticized blind scientific assertions based upon religious convictions, writing (in reference to creationists) this in The Astonishing Hypothesis "They also usually deny that animals and plants have evolved and changed radically over such long periods, although this is equally well established. This gives one little confidence that what they have to say about the process of natural selection is likely to be unbiased, since their views are predetermined by a slavish adherence to religious dogmas." In any case, Crick's name is often thrown around as ID advocates and the idea of panspermia brought up as a result, but this does not hold with what Crick believed or thought at the time of his death (and for a long time prior). "If you're really a credentialed scientist, read Dembski's answer to the detractors you claim to agree with in The Design Revolution (2004). Also essential is Dembski's collaboration Uncommon Dissent: Intellectuals Who Find Darwinism Unconvincing (2004). Deep water and irrefutable to all but the indoctrinated. Remember, those that are indoctrinated don't know they are..." Both are on my list to read in the near future, and just to clarify, I am not yet a credentialed scientist (I don't count my associate's degree in education as part of my scientific credentials) . I will hopefully be compelting my bachelor's degree in ecology and evolution (minor in geology) next year, and hopefully go into a 6-year PhD program shortly thereafter. I will hold judgement on the books until I've read them, but I doubt that they are "irrefutable" ; few works in any area are, especially over time. I also object to the insinuation that I'm indoctrinated and don't know it, and it would be just as unbecoming of me to say the same about you. We take different viewpoints, but everyone who doesn't agree with you isn't some liberal zombie, parrotting beliefs they've never thought about before. "Speaking of which, you keep bringing up the Cambrian fossil record as though you've got the answer. Well, you better tell Richard Dawkins. I've already covered this on Red State and you say you've read it twice, but I'll repeat myself once and give you the 411:" First, perhaps I've mentioned the Cambrian in passing, but I don't believe I've ever talked about it in detail on here or challenged you on that point. I'm actually reading Gould's Wonderful Life and looking into some of the weird critters like Opabina and Anomalocaris at the moment, but I haven't written anything suggesting I have to answer to that question. I do keep mentioning tetrapod evolution, but that's an entirely different subject dealing with the Devonian transition from water to land involving lobe-finned fish. I've spent most of my day on blood clots so I'm not going to do another long entry, but hopefully tomorrow I'll run down the amazing details from the fossil record involving the transition from fish to tetrapod. "Dawkins calls the appearance of the Cambrian critters "a planting", as though they were planted. He agrees it appears as though they appeared fully formed, without any intermediate precursors; but because we all know evolution is true, it cannot be so. Just not enough fossils survived." You're right in that there are some animals for which we do not have a clue as to their ancestry (i.e. Opabina). If you're suggesting that the Cambrian fauna did appear fully-formed, which ones and when? The Cambrian encompasses the time from 542 million years ago to 488 million years ago; a large span of time. All the creatures don't show up at 542 and then nothing changes, but instead there are more basal forms that appear and grow in complexity as the Cambrian goes on (i.e. trilobites). In any case, we've got the Burgess Shale and some fossils from China as well, but we do not have as complete a record as would be helpful, and given the rarity of fossils to beging with, we're lucky to have what we do have from areas like the Burgess Shale. "The fact is there have been numerous pre-Cambrian fossil finds in recent years. Most notable in China (don't remember the region; I'm doing this in bed all from memory). There were Cambrian rocks and pre-Cambrian, and rocks from the period before the pre-Cambrian. It was perfect; in fact, the older fossils were better than anything Cambrian that have been found." What sort of fossils? How are you defining "better"? The Chinese formation you mentioned is in Yunnan, and Ediacaran fauna (the fossils directly prior to the Cambrian) have become increasingly well known. What's interesting about the Ediacaran fauna is that there are a lot of weird body plans and other characteristics we don't see after that time, suggesting that a mass-extinction took place and some of those groups did not make it to the Cambrian. Mass extinctions, of course, give evolution a kick in the butt and can cause a lot of variations and changes as niches are taken over by survivors. In any case, Ediacaran fauna is largely enigmatic, but there are some potential intermediates (i.e. the worm Spriggina for Trilobites). It's also important to keep in mind that just before the Cambrian (about 570 million years ago) there was a large meteoritic impact in Australia, that could have caused an extinction and radiation pattern leading to the Cambrian "explosion." In any case, we don't have all the answers yet, but the Cambrian is not a "smoking gun" for intelligent design either, and we still have much to learn and discover about what occurred at the base of the Cambrian. "Unfortunately for your paradigm and Dawkin's pipe dream, there were ZERO intermediates in those amazing fossils. Just primitive stuff, soft-bodied stuff (that supposedly wouldn't fossilize), and some worms. No precursors to the Cambrian critters; ZERO intermediates, and if there had been any, they would have surely fossilized. This was widely reported, Time, NY Times, etc. Did not help Darwin's so-called Tree of Life one bit; it fact, it is uprooted and turned upside down." I already discussed at least one of the potential intermediates, and more will likely come to light as more study is done. You're right that we're lucky enough to have some soft-bodied organisms in the Ediacaran fauna as well, but all fossilization doesn't happen the same. Sometimes, minerals entirely replace bones (if present), other times outlines are preserved, other times partial replacement occurs, other times soft-bodied animals can be preserved; it happens differently depending on the circumstances and how long the fossil has been in the ground. I also object your statement of if there were any Cambrian precursors, they would have fossilized surely. Perhaps we have some and have not made the connection yet, but barring that, we don't have a complete fossil record at all, each fossil representing a certain time and ecology. To say that there is no intermediate because we have yet to identify it has no real basis, nor the assumption that Cambrian faunal successors would have fossilized without a doubt. Even large creatures with heavy bones or many hard parts don't preserve well, one example being Andrewsarchus, which was a huge mammalian hoofed-carnivore and we only have one skull and a few bits of bone. Fossils are rare, and even if we could find every single fossil we'd still be missing animals because of the rarity of preservation. "You are exercising in a form of group delusion. You are certain you are right." I could say the same for you. Once again, instead of assuming I'm deluded because I don't agree with you, can you not perhaps think, even for a second, that I've looked at the information and come to my own conclusions? I don't agree with everything someone with a doctorate tells me; it's important to know why someone is saying something just as it is important to know exactly what they're saying. From reading your blogs, you seem to take a hard line against liberalism in a variety of forms, blamining it all on Darwin, and I don't call that being open-minded. "While I think ID has interesting things to say (Dembski's Specified Complexity is genius work according to even the hardest-core ID doubters and evolution believers), I don't fall on the ID sword. The critical thing ID has done is review the literature and demonstrated that evolution is a fraction from being totally IMPOSSIBLE." At least that's what ID-advocates would have you think. From what I've read, they all seem to have a cursory idea of evolution but don't seem up on various factors beyond natural selection. ID does have interesting things to say, but that doesn't mean I have to agree. "All the "great work" you cite is all based on the false starting premise of methodological materialism, something I'm sure you've never heard of because your posts are kindergarten level." I have no problem with naturalism in science. I would rather a scientist say "I don't know" based upon natural processes than appeal to some supernatural designer that can't be identified or described. Sometimes what seems supernatural becomes natural, and such is the endevour of science; to keep pushing forward into what we don't yet understand. According to your statement, that any science based upon methodological materialism is worthless, we'd have to throw out great swaths of physics, chemistry, geology, biology, etc. as well to make it fit. As for your insult, I actually take it as a compliment, because it shows me that you're beyond the point of saying anything constructive and resorting to insults instead. "See my posts on Red State where real PHD professor goes wild because I won't address his evolution "proofs", just like all yours, that are based on flawed, WRONG foundations. " So what's the right foundation, then? A conservative one that allows for us to appeal to the supernatural every time we can't figure something out? No thanks. "But he is a professor and working biologist. You're just citing Panda's Thumb rhetoric (I'm repeating myself, but you are) that is doctrinaire claptrap for the Darwin youth (I'll bet you've got a Darwin intermediate emblem on the back of your car). You claim to be well studied; read Uncommon Dissent. Maybe that will break the straight-jacket loose." Just because I don't yet have a doctorate doesn't mean that what I say is worthless, either. I cited the Panda's Thumb in reference to the new Wells book because I felt they did a good group-effort at pointing out it's misleading statements; I don't parrot everything they say. My posts would be a lot shorter if I just believed whatever I was told and just snipped out professional opinions, but through writing I'm trying to strengthen my own arguments and thoughts on the subject, often in context of what I've seen or read from various sources. As for insult #2 about the Darwin emblem, no, I don't have one. All I've got is a sticker for Fender guitars, one that says "I love my botanist," and one that says "Love God, Love Others, The Rest is Details..." Like I said, I'll check out Uncommon Dissent when I have the chance and comment on it when I do, but I see no need for the straight-jacket comment. Does it make you feel like a big man to go around insulting people when they try to make constructive criticisms and point out the problems with the philosophy you're so venomously advocating? That's all I can assume from the uncalled for assertions and insults you're throwing around, only discrediting yourself and your own position in the end. "Anybody can write a blog, write with cock-surity and find mindless fellow indoctrinees to follow with the AMEN chorus. I'd be much more impressed with original thinking than self-congratulation and ad hoc dismissal of things you know not." Indeed, and (gasp) you have a blog too! I guess we're both just mindless indoctrinees on opposite sides of the spectrum then. Some people agree with me and I go to some effort to articulate my thoughts and work a problem through in my blogs, and if I make a mistake, I'll admit it. I don't have all the answers, but at least I'm trying to understand the position of the other side (ID) and spend quite a lot of time reading blogs and books from ID advocates. I'd be much happier finially finishing the 2,000 page monster that is The Structure of Evolutionary Theory, but I've put it off so I can educate myself on the claims of intelligent design and creationism and think them through. If I dismiss them, it's because I've thought about it and I don't agree with it, not because the PT posters told me to. "As I've had to tell so many before, stop relying on "Evolution for Dummies" or Kool-aid sites you find on Google. Read some real books that do not rely on studies with a priori commitments to a pre-determined outcome; that is what the majority of recent "evolutionary science" amounts to." And as I've said so many times before, I've read quite a few books from ID advocates and creationists in addition to books on evolution. What's the last book about evolution that you read? The last time you read an article from a technical journal? Again, your insults are giving away the shaky footing that you're on, relying on personal attacks than anything of substance. I'm sorry that "young whipper-snappers" like me are making you so angry, and I can't speak for everyone else, but for my own part I've put as much effort into understanding intelligent design as I have evolution and my writing reflects that. I can't say the same for you. "Finally, if you believe God did it, you believe in Intelligent Design. God is intelligent and He designed it if He exists. You cannot have it both ways. The guys you're reading are luke-warm believers with nothing but personal philosophy to back them up. By admitting there is a God, you're a Creationist and believe in ID by default. Better get your story straight." I see no problem with having faith and agreeing with evolution, nor do most people I've personally spoken to about the subject. I have no problem with intelligent design as a philosophy, in that God created or designed, but that isn't science (especially when ID advocates wave their arms and say we can't test who the designer is, why they designed, how they designed, etc.). I don't have all the answers, nor do I profess that I do. I believe God created but in a way that's far beyond my understanding and is the "why", evolution being the "how." This isn't for everyone, and that's fine, but I don't lose any sleep at night over it and you saying that I can't believe that way doesn't change anything at all. Just because you dont' like it doesn't mean I have to suddenly change what I believe. Sure, I have a lot of doubts and a lot of questions, but I keep asking those questions and wanting to understand more. Once again, I have no problem with ID as a philosophy but there is no science to it. What's going for it other than a handful of popular books? In any case, I'm sure we will continue to disagree, but by constantly proclaiming that I'm an insane, brainwashed, deluded, indoctrinated, young idiot doesn't do anything to help your case or make ID any more plausible. That's my take on it, and so far I'm not inclined to change my stance on the subject. == http://africatoday. eh7.co.uk/ cgi-bin/public. cgi?sub=news&action=one&cat=65&id=831 Ethiopia: moving the evolution story forward 11/29/06, Bunmi Akpata-Ohohe Scientists have unearthed 3.3-million- year-old fossilised remains of a little girl, the earliest and most complete skeleton of a juvenile human ancestor to be discovered in a slab of sandstone in the Afar region in the remote part of Ethiopia's Dikika region. The remains of the three-year-old girl are of the species Australopithecus afarensis, the same species as an adult skeleton found in 1974, which was nicknamed "Lucy". The find, by far the oldest remains of a hominin child reported in the science bible Nature journal, could shed light on human evolution and how this early human ancestor blurred the line between apes and humans, scientists said. The skeleton nicknamed Selam, the word for peace in several Ethiopian languages, was found by Tilahun Gebreselassie, a member of Zeresenay Alemseged's team, an Ethiopian paleoanthropologist from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Alemseged said Selam is one of the most important hominin fossils on record: "Her completeness, antiquity and age at death combined, make this find unprecedented in the history of palaeoanthropology, and opens many new research avenues to investigate the childhood of early human ancestors." Unlike Lucy, Selam has fingers, a foot and a complete torso. "But the most impressive difference between them is that this baby has a face," said Alemseged. But her upper body, like Lucy's had ape-like features. The girl's leg and foot bones provide evidence that this ancient species walked upright effectively even at the age of three. But the shape of her shoulder blades resembles a young gorilla's and her fingers are long and curved, suggesting this infant climbed trees, noted researchers. == Nymph Of The Sea Reveals Remarkable Brood Geologists from the UK and US, led by the University of Leicester, have made an unusual discovery from over 425 million years ago hard boiled eggs! The scientists discovered the mother complete with her brood of some 20 eggs and 2 possible juveniles inside, together with other details of her soft part anatomy including legs and eyes. The research team consisted of David Siveter from the University of Leicester, Derek Siveter from Oxford, Mark Sutton from Imperial College London and Derek Briggs from Yale. The team has made a digital image of the fossil - an ostracod (a relative of the shrimps) - which is preserved exceptionally in volcanic ash rocks in Herefordshire. Their findings are published on line in the Proceedings of the Royal Society. Professor David Siveter, of the Department of Geology at the University of Leicester, said : Ostracods are common, pin-head sized crustaceans known from thousands of living species in garden ponds to oceans and from countless fossil shells up to 500 million years old; however, their fossilized soft-parts are exceedingly rare. Supposed examples of fossil invertebrate eggs are also few. The fossil we have found contains soft-part anatomy such as legs and eyes and also includes about twenty eggs, each about half a millimetre in size, and two possible juveniles. The fossil has been christened Nymphatelina gravida, meaning a pregnant young woman of the sea. This remarkable discovery provides an unequivocal and unique view of parental brood care in the invertebrate fossil record, it allows gender to be determined in an animal as old as the Silurian period of geological time, and indicates a remarkably conserved egg brooding reproductive strategy. === Were back in time a little over 50 million years. The dinosaurs have been gone for only 13 or 14 million years. Gone too are the great marine lizards. Along the shoreline of the shallow Tethys Sea, on the south coast of the landmass of Eurasia, mammals are turning their interest to an abundant realm long denied them. In nature, no available resource is ever ignored for long, and a coyote-sized animal named Pakicetus is taking the first tentative steps into the warm waters of streams and deltas in its (uppermost middle) Eocene world. It had a long, narrow snout and brain case, close-set eyes, a robust sagittal crest, and the heavy tail of earlier archaic mammals. It also had fairly long (for the time) legs ending in small hooves. What makes Pakicetus interesting to us here however, cant be seen in my painting. The skull has an ear region that is highly unusual in shape, and resembles the same area only in the skulls of modern and fossil whales. This feature is diagnostic for cetaceans, is found in all cetaceans, and in no other animal. Pakicetus certainly could swim, but not strongly, and perhaps foraged as a wader, or moved along the streambed like a modern hippo, feeding on crustaceans and other aquatic animals using its long vibrissae- covered snout to feel its way through the shallows. Even earlier, lost for now in the mist-shrouded era of the Paleocene, an archaic ungulate ancestor gave rise to animals that would eventually lead to artiodactyls (even-toed hoofed animals with incredible modern diversity including; camels, deer, cattle, goats, sheep, antelope, pigs and hippos), mesonychids (carnivorous, or at least omnivorous, hoofed mammals, all now extinct), and cetaceans. The timing of exactly what diverged when is still being researched and debated. Ill have a number of diagrams, cladograms and trees up in the near future. As an artist and not a scientist, Im going to leave questions of timing up to the molecular biologists and paleontologists involved, and simply supply the illustrations. Ive been fortunate to participate in a peripheral way in a number of projects by portraying many of the creatures in the evolutionary transition back to aquatic life. Youll be seeing most of them here in the next few months. I might even have a guest post or two from the scientists Ive worked with. A note on the restoration of Pakicetus Unless you find that once-in-a-lifetime, fully articulated skeleton with skin, scale, fur or feather impressions, the further back you go in time, the more difficult the process becomes of bringing an extinct animal to life. Hopefully, any guesswork involved is educated guesswork based on comparative anatomy, but Pakicetus, as portrayed here, is based on a skull and non-articulated post-cranial material. That means its a composite. The bones are from a number of individuals. As more fossils are found and described, Pakicetus look will change. My take on any fossil-based animal is just that, my take. You can only be true to the fossil evidence you have presented to you and then try to make informed decisions about surface features and color based on possible relatives (or ecological equivalents) of your subject that are alive today and the type of environment the animal lived in. The one thing I always do, is try to look at each animal as a completely formed individual. What I mean by that in this case, is that I didnt think of Pakicetus as a future whale or an early step toward whaleness - even though it certainly was from our viewpoint. Any naturalist transported into the past would see Pakicetus as a successful creature in the world of its time. Changing conditions, differential survival, and genetic mutation would do their work, but Pakicetus lived and breathed and foraged and mated and died a complete creature. == mutations and other imperfections in the current human genome. a.Chromosome abnormalities associated with diseases Numerical abnormalities (monosomy, trisomy) Structural abnormalities (partial deletions, duplications, translocations, inversions, rings) b.Genes and alleles associated with diseases c.Broken ("fossil") genes (pseudogenes) d.Non-deleterious mutant chromosome conditions E.g., the fusion of two chromosomes to form chromosome 2 == Here is a definition of evolution from Douglas J. Futuyma: "In the broadest sense, evolution is merely change, and so is all-pervasive; galaxies, languages, and political systems all evolve. Biological evolution ... is change in the properties of populations of organisms that transcend the lifetime of a single individual." === Eric Lander, a scientist from the Whitehead Institute who worked on the human genome project, said that 2/3 of the 1000 genes involved in human olefaction are broken. == Nothing in the real world can be proved with absolute certainty. However, high degrees of certainty can be reached. In the case of evolution, we have huge amounts of data from diverse fields. Extensive evidence exists in all of the following different forms (Theobald 2004). Each new piece of evidence tests the rest. * All life shows a fundamental unity in the mechanisms of replication, heritability, catalysis, and metabolism. * Common descent predicts a nested hierarchy pattern, or groups within groups. We see just such an arrangement in a unique, consistent, well-defined hierarchy, the so-called tree of life. * Different lines of evidence give the same arrangement of the tree of life. We get essentially the same results whether we look at morphological, biochemical, or genetic traits. * Fossil animals fit in the same tree of life. We find several cases of transitional forms in the fossil record. * The fossils appear in a chronological order, showing change consistent with common descent over hundreds of millions of years and inconsistent with sudden creation. * Many organisms show rudimentary, vestigial characters, such as sightless eyes or wings useless for flight. * Atavisms sometimes occur. An atavism is the reappearance of a character present in a distant ancestor but lost in the organism's immediate ancestors. We only see atavisms consistent with organisms' evolutionary histories. * Ontogeny (embryology and developmental biology) gives information about the historical pathway of an organism's evolution. For example, as embryos whales and many snakes develop hind limbs that are reabsorbed before birth. * The distribution of species is consistent with their evolutionary history. For example, marsupials are mostly limited to Australia, and the exceptions are explained by continental drift. Remote islands often have species groups that are highly diverse in habits and general appearance but closely related genetically. Squirrel diversity coincides with tectonic and sea level changes (Mercer and Roth 2003). Such consistency still holds when the distribution of fossil species is included. * Evolution predicts that new structures are adapted from other structures that already exist, and thus similarity in structures should reflect evolutionary history rather than function. We see this frequently. For example, human hands, bat wings, horse legs, whale flippers, and mole forelimbs all have similar bone structure despite their different functions. * The same principle applies on a molecular level. Humans share a large percentage of their genes, probably more than 70 percent, with a fruit fly or a nematode worm. * When two organisms evolve the same function independently, different structures are often recruited. For example, wings of birds, bats, pterosaurs, and insects all have different structures. Gliding has been implemented in many additional ways. Again, this applies on a molecular level, too. * The constraints of evolutionary history sometimes lead to suboptimal structures and functions. For example, the human throat and respiratory system make it impossible to breathe and swallow at the same time and make us susceptible to choking. * Suboptimality appears also on the molecular level. For example, much DNA is nonfunctional. * Some nonfunctional DNA, such as certain transposons, pseudogenes, and endogenous viruses, show a pattern of inheritance indicating common ancestry. * Speciation has been observed. * The day-to-day aspects of evolution -- heritable genetic change, morphological variation and change, functional change, and natural selection -- are seen to occur at rates consistent with common descent. Furthermore, the different lines of evidence are consistent; they all point to the same big picture. For example, evidence from gene duplications in the yeast genome shows that its ability to ferment glucose evolved about eighty million years ago. Fossil evidence shows that fermentable fruits became prominent about the same time. Genetic evidence for major change around that time also is found in fruiting plants and fruit flies (Benner et al. 2002). The evidence is extensive and consistent, and it points unambiguously to evolution, including common descent, change over time, and adaptation influenced by natural selection. It would be preposterous to refer to these as anything other than facts. == Neanderthal genome unlocks secrets of human evolution Early humans and Neanderthals, our closest and ill-fated evolutionary cousins, went their separate genetic ways some 500,000 years ago, a more distant divorce than once thought, two pathbreaking studies published Wednesday concluded. And even if the two branches of the hominid family tree shared the same habitat for hundreds of thousands of years, notably on the European continent, they engaged in little or no inter-species hanky-panky, the studies showed, settling another point of controversy. Using distinct techniques of DNA sequencing -- which analyses genetic fragments recovered, in this case, from Neanderthal remains -- the coordinated scientific papers in the journals Nature and Science also predicted that the complete Neanderthal genome will be pieced together within two years. Not long ago, the prospect of sequencing the entire genome of an extinct organism was regarded by many specialists as a simply impossible. The demise of Neanderthals some 30,000 years ago is often blamed on smarter and more adaptable Homo sapiens, but there is still no scientific consensus on the exact cause of extinction. The two studies, one headed by Edward M. Rubins and the other by Svante Paabo, arrived at similar conclusions using cutting-edge but different scientific tools. A commentary in Nature introducing both papers suggested they "are the most significant contributions published in this field since the discovery of Neanderthals 150 years ago." The team of US, German and Croat researchers led by Paabo, Director of the Genetics Department at the Max Planck Institute for Evolutionary Anthropology in Leipzig, used a technique called pyrosequencing to analyze one million base pairs of Neanderthal DNA, removing impurities and matching the fragmentary genetic sequences against the template of human chromosomes. "Our finding that the Neanderthal and human genomes are at least 99.5 percent identical led us to develop and successfully implement a targeted method for recovering specific ancient DNA sequences," the authors wrote. The human genome contains some 3.2 billion chemical nucleotide bases, grouped within some 30,000 genes. The Nature paper concluded estimates that human and Neanderthal DNA diverged between 465,000 and 569,000 years ago, and that Neanderthals -- like humans -- "derived from a very small ancestral population of about 3,000 individuals. " Rubin's study, published in the US journal Science, used what is called a "metagenomic" technique to sequence some 65,000 base pairs of Neanderthal DNA which are amplified through replication in bacteria. The result is then further amplified using enzymes. Rubin works at the Lawrence Berkeley National Laboratory in Berkeley, California, and is director of the US Department of Energy's Joint Genome Institute in Walnut Creek, also in California. His analysis yielded a similar estimate of when Homo sapiens and Neanderthals took different evolutionary paths: between 120,000 and 670,000 years ago. The more we learn about the hominids who didn't cut the evolutionary grade, the scientists concluded, the more we learn about ourselves. "The full Neanderthal genome," they added, will also help resolve a long-standing debate: "In evolution, how important are mutations in genes that result in structural and physiological changes, compared with mutations that affect the regulation of those genes?" The first evidence for the Neanderthals emerged in 1856, when workers at a lime quarry in the Neander Valley, western Germany, came across bones initially thought to be that of a bear. Since then, the remains of about 400 Neanderthals have been found, at sites ranging from southern England to continental Europe and the Middle East. == Abstract: To satisfy the minimal requirements for life, an information carrying molecular structure must be able to convert resources into building block and also be able to adapt to or modify its environment to enhance its own proliferation. Furthermore, new copies of itself must have variable fitness such that evolution is possible. In practical terms a minimal protocell should be characterised by a strong coupling between its metabolism and genetic subsystem which is made possible by the container. There is still no general agreement on how such a complex system might have been naturally selected for in a prebiotic environment. However, the historical details are not important for our investigations as they are related to assembling and evolution of protocells in the laboratory. Here we study three different, minimal protocell models of increasing complexity, all of them incorporating the coupling between a ``genetic template'', a container, and eventually a toy metabolism. We show that, for any local growth law associated with template self-replication, the overall temporal evolution of all protocell's components follows an exponential growth (efficient or uninhibited autocatalysis). Thus, such a system attains exponential growth through coordinated catalytic growth of its component subsystems, independent of the replication efficiency of the involved subsystems. As exponential growth implies the survival of the fittest in a competitive environment, these results suggest that protocell assemblies could be efficient vehicles in terms of evolving through Darwinian selection. http://www.santafe.edu/research/publications/workingpapers/06-09-032.pdf == Scientists suggest a new way to study how biomolecules and minerals combined in Earth's primordial "soup." Provided by the Carnegie Institution Over the last half century, researchers have found that mineral surfaces may have played critical roles organizing, or activating, molecules that would become essential ingredients to all life such as amino acids (the building blocks of proteins) and nucleic acids (the essence of DNA). But which of the countless possible combinations of biomolecules and mineral surfaces were key to this evolution? This vexing question has stumped scientists for years because of the sheer volume of possibilities. Now an interdisciplinary team of researchers led by Robert Hazen, of the Carnegie Institution's Geophysical Laboratory and former president of the Mineralogical Society of America, has developed new protocols and procedures for adapting DNA microarray technology to rapidly identify promising molecule/mineral pairs. Hazen's Presidential Address in the November/December issue of American Mineralogist describes this work. It sets out a first-of-its-kind comprehensive survey into research that has identified processes by which minerals may have prompted the transition from a geochemical world to a biological one almost four billion years ago. Scientists understand several probable steps in the origin of life, notably how the first organic molecules could have formed. In fact, prebiotic synthesis processes are now thought to have been so productive that the ancient Earth must have had far more different kinds of molecules than could have been used by early life. One of the biggest questions in origins research, therefore, is how just the right blend of critical biomolecules was selected, concentrated, and organized from the diverse primordial "soup." Previous research by the Carnegie team and others has shown that many molecules, including amino acids, can adhere to mineral surfaces, prompting further organic reactions. These findings have made surface/molecule interactions the subject of intense study. Scientists suspect that organic material was likely introduced to Earth from many complementary sources. Abundant biomolecules form in molecular clouds in deep space, and these extraterrestrial compounds must have rained down on the early Earth. Other molecular synthesis was driven by lightning and ultraviolet radiation in the atmosphere or volcanic heat and chemical reactions in the deep oceans. Some of these building blocks of life were attracted to specific mineral surfaces, where they collected, concentrated, and underwent further reactions. "Some 20 different amino acids form life-essential proteins," Hazen explained. "In a quirk of nature, amino acids come in two mirror-image forms, dubbed left and right-handed, or chiral molecules. Life, it turns out, uses the left-handed varieties almost exclusively. Non-biological processes, however, do not usually distinguish between left and right variants. For a transition to occur between the chemical and biological eras, some process had to separate and concentrate the left- and right-handed amino acids. This step, called chiral selection, is crucial to forming the molecules of life." Like amino acids, some minerals have pairs of crystal surfaces that have a mirror relationship to each other, called left and right faces. Calcite, one such mineral, is common today and was prevalent during the Archean Era when life first emerged. In 2001 Hazen and colleagues performed the first experiments showing that the left-handed amino acid, aspartic acid, preferentially adhere to left-faced calcite. That study confirmed previous theoretical suggestions of a plausible process by which the mixed right- and left-handed -amino acids in the primordial soup could be concentrated and selected on a readily available mineral surface. The challenge since has been to determine which of the countless biomolecules/surface interactions are the most likely candidates to the first steps to life. "Crystal surfaces are complicated," Hazen continued. "They have crevices and craters, and are seldom flat. We need to find which surface types are the best 'docking stations' for different biomolecules. However, there are hundreds of mineral surface types and thousands of plausible prebiotic molecules, making literally millions of possible biomolecule/mineral pairs. It's an overwhelmingly large number of possibilities." DNA microarrays provide a means to address this problem. Microarrays are produced robotically to spot tens of thousands of microscopic droplets of DNA from as many genes onto a slide, enabling scientists to measure which genes are turned on. This rapidly developing technology can be used to identify, for example, the genes involved in disease. The high-throughput has revolutionized biotechnology research. Hazen, working with Carnegie staff scientist Andrew Steele and his team, has developed modifications of this tool to study molecule/mineral interactions. The scientists have devised protocols for cleaning mineral surfaces, spotting the surfaces with up to 96 different organic species, washing the surfaces to remove molecules that don't adhere to a mineral surface, and locating the remaining adsorbed molecules. To discover "which molecules stick and which don't," as Hazen says, the Carnegie scientists are also collaborating with a team at the Smithsonian Institution led by Edward Vicenzi to employ a workhorse of chemistry called Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS). The instrument effectively blasts a sample with ionized particles and fragments the surface-bound molecules and topmost mineral layer. The mass spectrometer allows the researchers to determine what's there. "ToF-SIMS will also allow us to detect the organic molecules that bind most strongly to mineral surfaces," commented Hazen. "In many ways, Hazen's approach cuts to the chase of addressing this problem," said Patricia Dove, professor of geochemistry at Virginia Tech. "By adapting the microarray approach from molecular biology, his research group can identify up to one million types of biomolecules very quickly to learn which have the strongest interactions with mineral surfaces. It doesn't stop there though-another real advance lies in analyzing their experiments by the ToF-SIMS. This eliminates the need for chemical tags whose own properties could influence the results." David Deamer, professor of chemistry and biochemistry at U.C. Santa Cruz, commented that "Bob Hazen is boldly asking a fundamental question related to the origin of life. We know that organic compounds were present in the early Earth environment, but as dilute solutions of thousands of different species in the global seas. How were specific kinds of organics selected to assemble into the first forms of life, and by what process were they sufficiently concentrated to initiate a primitive version of metabolism? We now know that minerals select specific organic compounds out of solution, and can even distinguish between subtle properties such as chirality, binding a left-handed amino acid in preference to one that is right handed. These are very significant results that are guiding my own research as well as many other investigators in the field." Once Hazen and coworkers have identified molecule/surface pairs of interest with the DNA microarray and ToF-SIMS, an arsenal of other techniques can be used to look at the details of the interactions. == Going back (in time) to the scales, is there much of a relationship between the reptile scales (such as those from which feathers evolved) and the scales of their fish ancestors? They're essentially the same. Actually, the amphibians that reptiles evolved from were just as scaley as the reptiles and fish. It's a quirk of fate that an abberant branch of scaleless amphibians is all that has survived to this day. Imagine how wrong you would be about mammals if the only one you'd ever seen was an armadillo, it's a bit like that. Well, not really a "quirk of fate", as a selection for a rather efficient skin capable of exchanging significant amounts of oxygen and CO2. Nonetheless, ancestral amphibians were scaled. The one modern amphibian with scales is the snake-like Caecillian, which has a few scales embedded in its skin. Interestingly, it's scales are NOT homologous to fish or reptile scales. It's an example of the creature re-adapting scales from a scaleless condition. Anatomically, its scales are quite different. Another fun example of re-adaptation is found in a plant called the Star-bracted sedge. Flowering plants evolved in the Cretaceous, coloring specialized leaves around their reproductive parts to help attract insects. The sedges turned their backs on flowers and re- evolved the ancestral wind-blown polination methods. The white-bracted sedge has turned it's back on that turning of the back and is re- evolving flowers, painting leaves around it's pollen-heads white! Poinsettas and dogwoods have done much similar things, losing their original petals, only to call foul and demand them back! Dandilions are the opposite, they kept the petals, but lost the flower-parts! Dandilions reproduce purely asexually, they do not make pollen. They just keep the big yellow flowers because of ancestral genetics. Nature is pretty silly this way. Look at the sea snakes. Sea snakes evolved from land snakes, which may have evolved from marine lizards, which evolved from terrestrial lizards, which evolved from fish. Make up your mind already, are you in the pool or out of it! == Evolution is the observed change in allele frequencies in populations over time. The Theory of Evolution explains the mechanisms of evolution, including mutation, variation, natural selection, sexual selection, genetic drift, speciation, hybridization, contingency, common descent, etc. The primary areas of evidence are as follows: * The nested hierarchy of extant life. * The nested hierarchy in time of extinct life. * The discovery that heredity is chemistry (Watson & Crick, 1953). * Observation of genetic mutation. * Observation of change in allele frequency in populations over time. * Observation of natural and artificial selection and their effects. * Observation of speciation in the wild and in the lab. * Observation of hybridization in the wild and in the lab. * The recently discovered nested hierarchy of genomes (including viral inserts and pseudo-genes). * Direct manipulation of the genomes. == AFTER a tantalisingly successful run at sequencing parts of the extinct woolly mammoth's genome, the project is now stalled for lack of funds. Hendrik Poinar of the McMaster Ancient DNA Centre at McMaster University in Hamilton, Ontario, and his team hope that sequencing the genomes of extinct animals will reveal otherwise inaccessible data on their evolutionary history, population, diversity and other key traits. Cracking the woolly mammoth genome might help solve the mystery of what killed off these animals as the last ice age waned about 12,000 years ago, and provide hints about the demise of their fellow megafauna. Until recently, only mitochondrial DNA from fossilised remains of mammoths had been sequenced. Nuclear DNA was a much more difficult proposition because the sequence is far longer and there are only two strands per cell. Until this year, only a few nuclear genes had been sequenced from frozen mammoths. Then in January, Poinar, along with Ross MacPhee of the American Museum of Natural History in New York City and colleagues, announced that they had run a gram of mammoth bone through a new machine that sequenced 28 million base pairs from small fragments of DNA. They used computer analysis to match 13 million of those base pairs to the published genome of the African elephant. The overlap between mammoth and elephant was 98.55 per cent, which is consistent with an evolutionary split between the two about 5 million years ago (Science, vol 311, p 392). Last month, Poinar told delegates at a meeting of the Society of Vertebrate Paleontology in Ottawa that his team's results had improved over seven additional runs, with each run yielding 20 million base pairs, adding up to a few per cent of the mammoth genome. The team now needs about $500,000 to pay for 100 more runs on the sequencing machine and is applying for grants, MacPhee says. "We accept cheques in any convertible denomination. " The mammoth is a logical starting point for studying extinct giant animals from the ice age. Its remains are among the most abundant in permafrost, and the fact that its genome is similar to that of the modern elephant is a boon. Comparing the two genomes allows scientists to weed out sequences that belong to contaminants in the fossil remains, such as soil bacteria. Efforts to sequence other extinct species could follow success with the woolly mammoth. French explorer Bernard Buigues has collected and stored remains from more than 1000 frozen ice-age fossils - including those of musk oxen, moose and caribou - in a cave he dug out of the Siberian permafrost, and is cooperating with Poinar's team. The same technique is also being used to sequence the Neanderthal genome (see "The Neander code") == New phylum sheds light on human ancestry A genetic analysis of an obscure, worm-like creature retrieved from the depths of the North Atlantic has led to the discovery of a new phylum. The analysis also appears to shed light on the ancestor of chordates, the backboned animals that include human beings and two small invertebrate groups closely related to one another: lancelets and tunicates. Scientists have long been puzzled by the half-inch-long creature known as Xenoturbella that was first retrieved from the Baltic Sea more than 50 years ago. The Xenoturbella does not seem to have a brain, gut or gonads, making it unique among living animals. Now, modern genomic sequencing has revealed Xenoturbella belongs to its own phylum. The analysis also apparently confirms human beings and other chordates share a common ancestor -- a first in science. == A Flys-Eye View of Evolution Howard Hughes Medical Institute researchers have found that mutations in a single structural protein can determine whether an insect develops the highly organized, light-harvesting eye that flies have, or the optically simpler compound eye of a beetle or bee. In their experiments, the scientists showed that flies without this structural protein develop a more primitive eye. This outcome was reversed in the laboratory when researchers supplied the missing protein to a more primitive eye system, inducing it to evolve into the more advanced eye. Its not unusual to see alterations in regulatory proteins with a profound effect on form and function. This new finding, however, is unique because it illustrates how a change in a single structural protein can lead to such a spectacular change in form and function. Charles S. Zuker These findings help illustrate the beauty and power of evolution how small changes can have such an incredible impact, said HHMI investigator Charles S. Zuker, who led the study. Zuker and his colleagues at the University of California , San Diego reported their findings October 1, 2006, in an advance online publication in the journal Nature. The lead author of the paper was Andrew Zelhof. Robert Hardy and Ann Becker were co-authors. Working with the fruitfly Drosophila, the researchers explored the formation of transparent rod-like structures in the compound eye called rhabdomeres. Rhabdomeres feed light to the bundles of photoreceptors that comprise each of the 800 unit eyes in the flys compound eyes. Rhabdomeres are fused into a single light-gathering structure in the more primitive closed rhabdom compound eyes of beetles, bees, and some mosquitoes. Flies, on the other hand, have evolved a more advanced open rhabdom structure. In the more sophisticated eyes of flies, the rhabdomeres are separated, and as a result, fly eyes have significantly better angular resolution, and can detect smaller moving objects. Zuker, Zelhof, and their colleagues planned their experiments to identify the genes and biological pathway required to assemble the light-harvesting system of photoreceptor neurons. To define those genes, they used a chemical to induce mutations in fruitflies and examined the mutant flies under a microscope in search of any with malformed eyes. Much to our delight, we discovered two mutant lines that looked as if their eyes had been transformed from an open-rhabdom to a closed system, said Zuker. In fact, in looking at the eyes of one of those, you could easily mistake them for the eyes of an insect with a closed-rhabdom system, he said. The researchers genetic analysis of these flies resulted in the identification of three genes, spacemaker, prominin and chaoptin, which together orchestrate the assembly of rhabdomeres into the flys elegant photoreceptor system. Zelhof, the lead author of the study, then compared the _expression of spacemaker, prominin, and chaoptin genes in the housefly and a mosquito, whose eyes have the open structure with that of the honeybee and flour beetle - insects with closed-rhabdom eyes. Although spacemaker was expressed in the body of all the species ofinsect that were studied, the scientists found that the gene was not turned on in the eyes of species with closed rhabdom systems. These findings led us to hypothesize that Spacemaker protein may be a key determinant of the evolutionary transition from closed to open-rhabdom systems, said Zelhof. Validating that proposal required one critical acid test; and that was to introduce the protein into a closed system and see whether we could transform it into an open one, he said. Fortunately, in addition to its open rhabdom eye, the fruitfly itself also possesses a primitive closed version of an eye. This is found in the light sensors called ocelli, which are located on the top of the head, and used for navigation. When the researchers engineered fruitflies that expressed the Spacemaker protein in their ocelli, they found that the ocelli completely reorganized into an open rhabdom system. Zuker said the findings offer an important lesson about the beauty of evolution. Its not unusual to see alterations in regulatory proteins with a profound effect on form and function, he said. For example, altering a single transcription factor that controls a hierarchy of downstream products can cause an insect to grow extra legs or lose wings. This new finding, however, is unique because it illustrates how a change in a single structural protein can lead to such a spectacular change in form and function. == Could Interbreeding Between Humans and Neanderthals Have Led to an Enhanced Human Brain? Might mating between an ancient human and a Neanderthal - perhaps occurring in only a single instance - have introduced a gene variant into the human population that enhanced human brain function? That question is at the heart of a new study by researchers at the Howard Hughes Medical Institute and the University of Chicago . The new research, which was published online during the week of November 6, 2006, in the early edition of the Proceedings of the National Academy of Sciences (PNAS), suggests that human evolution was not just a matter of spontaneous advantageous mutations arising within the human lineage. Human evolution may also have been influenced by interbreeding with other Homo species, which introduced gene variants, known as alleles, that are beneficial to human reproductive fitness, said the study's senior author Bruce T. Lahn, a Howard Hughes Medical Institute researcher at the University of Chicago . By no means do these findings constitute definitive proof that a Neanderthal was the source of the original copy of the D allele. However, our evidence shows that it is one of the best candidates. Bruce T. Lahn The scientists said they have developed the most robust genetic evidence to date that suggests humans and Neanderthals interbred when they existed together thousands of years ago. The interbreeding hypothesis contrasts with at least one prominent theory that posits that no interbreeding occurred when the two species encountered one another. Lahn collaborated on the studies with Patrick D. Evans, Nitzan Mekel-Bobrov, Eric J. Vallender and Richard R. Hudson, all of the University of Chicago . In their studies, Lahn and his colleagues performed a detailed statistical analysis of the DNA sequence structure of the gene microcephalin, which is known to play a role in regulating brain size in humans. Mutations in the human gene cause development of a much smaller brain, a condition called microcephaly. Earlier studies by Lahn's group yielded evidence that the microcephalin gene has two distinct classes of alleles. One class, called the D alleles, is comprised of a group of alleles with rather similar DNA sequences. The other class is called the non-D alleles. Lahn and colleagues previously showed that all modern copies of the D alleles arose from a single progenitor copy about 37,000 years ago, which then increased in frequency rapidly and are now present in about 70 percent of the world's population. This rapid rise in frequency indicates that the D alleles underwent positive selection in the recent history of humans. This means that these alleles conferred a fitness advantage on those who possessed one of them such that these people had slightly higher reproductive success than people who didn't possess the alleles, said Lahn. The estimate that all modern copies of the D alleles descended from a single progenitor copy about 37,000 years ago is based on the measurement of sequence difference between different copies of the D alleles. As a copy of a gene is passed from one generation to the next, mutations are introduced at a steady rate, such that a certain number of generations later, the descendent copies of the gene would on average vary from one another in DNA sequence by a certain amount. The greater the number of the generations, the more DNA sequence difference there would be between two descendent copies, said Lahn. The amount of sequence difference between different copies of a gene can therefore be used to estimate the amount of evolutionary time that has elapsed since the two copies descended from their common progenitor. In the new studies reported in PNAS, the researchers performed detailed sequence comparisons between the D alleles and the non-D alleles of microcephalin. The scientists determined that these two classes of alleles have likely evolved in two separate lineages for about 1.1 million years with the non-D alleles having evolved in the Homo sapiens lineage and the D alleles having evolved in an archaic, and now extinct, Homo lineage. Then, about 37,000 years ago, a copy of the D allele crossed from the archaic Homo lineage into humans, possibly by interbreeding between members of the two populations. This copy subsequently spread in humans from a single copy when it first crossed into humans to an allele that is now present in an estimated 70 percent of the population worldwide today. The estimate of 1.1 million years that separates the two lineages is based on the amount of sequence difference between the D and the non-D alleles. Although the identity of this archaic Homo lineage is yet to be determined, the researchers argue that a likely candidate is the Neanderthals. The 1.1 million year separation between humans and this archaic Homo species is roughly consistent with previous estimates of the amount of evolutionary time separating the Homo sapiens lineage and the Neanderthal lineage, said Lahn. Furthermore, the time of introgression of the D allele into humans about 37,000 years ago is when humans and Neanderthals coexisted in many parts of the world. Lahn said the group's data suggest that the interbreeding was unlikely to be a thorough genetic mixing, but rather a rare - and perhaps even a single event that introduced the ancestral D allele previously present in this other Homo species into the human line. By no means do these findings constitute definitive proof that a Neanderthal was the source of the original copy of the D allele, said Lahn. However, our evidence shows that it is one of the best candidates. The timeline - including the introgression of the allele into humans 37,000 years ago and its origin in a lineage that separated with the human line 1.1 million years ago agrees with the contact between, and the evolutionary history of, Neanderthals and humans. And a third line of evidence, albeit weaker, is that the D alleles are much more prevalent in Eurasia and lower in sub-Saharan Africa, which is consistent with an origin in the former area. And we know that Neanderthals evolved outside of Africa , said Lahn. Lahn also said that although the disruption of the microcephalin gene in humans leads to smaller brains, the role of the D alleles in brain evolution remains unknown. The D alleles may not even change brain size; they may only make the brain a bit more efficient if it indeed affects brain function, he said. For example, someone inheriting the D allele may have only a slightly more efficient brain on average. While that enhancement might confer only a subtle evolutionary advantage on that person, when that effect is propagated over a thousand generations of natural selection, the result will be to drive the D alleles to a very high prevalence. Lahn and his colleagues believe that other genes might well show similar telltale signs of an origin in archaic Homo lineages such as Neanderthals. They are currently using their analytical tool to search for evidence of that origin for other genes in the human genome. Such findings may have broader implications for understanding human evolution than just revealing the possibility of human-Neanderthal interbreeding, he said. In addition to being perhaps the most robust genetic evidence for introgression of genes from archaic Homo species into humans, I think this finding demonstrates that the evolution of our species has been profoundly impacted by gene flow from our relative species, said Lahn. Finding evidence of mixing is not all that surprising. But our study demonstrates the possibility that interbreeding contributed advantageous variants into the human gene pool that subsequently spread. This implies that the evolution of human biology has been affected by the contribution of advantageous genetic variants from archaic relatives that we have replaced or even killed off, he said. Until now, said Lahn, the scientific debate over genetic exchange between humans and other Homo species has led to two prominent competing theories. One holds that anatomically modern humans replaced archaic species, with no interbreeding. And the other states that extensive interbreeding did take place and that modern humans evolved from that interbreeding in many regions of the world. Genetic and fossil evidence for the latter multiregional theory has been inconclusive, said Lahn, so that theory has been largely discredited. However, he said, the newer evidence of gene exchange as well as other genetic evidence that might follow could give rise to a more moderate version holding that some genetic exchange did take place. Furthermore, it will become increasingly appreciated that such genetic exchange might have made our species much more fit. === In 1975 a team of Japanese scientists discovered a strain of Flavobacterium living in ponds containing waste water from a factory producing nylon that was capable of digesting certain byproducts of nylon-6 manufacture, such as, 6-aminohexanoate linear dimer, even though those byproducts had not existed prior to the invention of nylon in 1935. Further study revealed that the three enzymes the bacteria were using to digest the byproducts were novel, significantly different than any other enzymes produced by other Flavobacterium strains (or any other bacteria for that matter), and not effective on any other material other than the man made nylon byproducts. http://en.wikipedia .org/wiki/ Nylonase. A summary of the origtinal scientific paper at http://www.talkorig ins.org/origins/ postmonth/ apr04.html shows that actually a number of genetic changes were required for this to take place. In fact multiple changes to at least four different genes were required for this characteristic to evolve. The most important gene, called nylB, was formed from both a deletion mutation and a frame shift mutation in another gene. And similar mutations were found in other genes. For confirmation, the original paper is probably present, at least in microfiche form at your local library: Kato K, Fujiyama K, Hatanaka HS, Priyambada ID, Negoro S, Urabe I, and Okada H. (1991 Aug 15). Amino acid alterations essential for increasing the catalytic activity of the nylon-oligomer- degradation enzyme of Flavobacterium sp. Eur J Biochem , 200, 165-9. == The evolution of the citric acid (Krebs cycle0 has been heavily studied. A major paper was published in 1996 "The puzzle of the Krebs citric acid cycle: assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution." Melendez-Hevia E, Waddell TG, Cascante M. Departamento de Bioquimica, Facultad de Biologia, Universidad de La Laguna, 38206 Tenerife, Canary Islands, Spain. Abstract available here http://www.ncbi. nlm.nih.gov/ entrez/query. fcgi? cmd=Retrieve& db=PubMed& list_uids= 8703096&dopt= Abstract == Richard Dawkins said - "You cannot be both sane and well educated and disbelieve in evolution. The evidence is so strong that any sane, educated person has got to believe in evolution." == SEX BY SURROGATE A male flour beetle (Tribolium castaneum) can mate and impregnate a female he has never met. No other animal is known to have sex by proxy in this way. Many males often mate with each female. The first male will deposit sperm in the female, then a second will arrive and use its spiny genitalia to scrape out his competitor's sperm, before mating itself. Much of the sperm of the first male is carried unwittingly by the second male on its genitalia. One in eight females are fertilised by proxy. HOW WAS THAT FOR YOU? Female brown trout (Salmo trutta) fake orgasms to encourage males to ejaculate prematurely. By doing so, they dupe their partner into thinking it has successfully mated, before the female fish moves on to find a better male with which to do the real thing. BACH IS BEST Java sparrows (Padda oryzivora) appear to prefer the music of some composers. Sparrows will listen longer to music by Bach than by Schoenberg, and prefer Vivaldi to Elliott Carter. MAKE ME CRY There are moths that drink the tears of elephants. Tears contain salt, water and trace levels of protein. Mabra elephantophila steals the tears without the elephants seeming to notice. Lobocraspis griseifusa does not wait for an animal's eyes to moisten - it sweeps its proboscis across the eye of its host, irritating the eyeball, encouraging it to produce tears. GIVE ME BLOOD, AND MAKE IT FRESH Dracula ants (Adetomyrma venatrix) suck the blood of their young. Queen Dracula ants live in Madagascar, cut holes in their own larvae and feed upon the haemolymph, or insect blood, that oozes out. TASTED GOOD, I THINK The star-nosed mole (Condylura cristata) is the fastest-eating mammal in the world, capable of wolfing down a snack of worms in 227 milliseconds. It uses 22 pink fleshy tentacles that adorn its face, each highly sensitive to touch. DON'T SWIM AND EAT European eels (Anguilla anguilla) will not eat at all during their long migration to the Sargasso Sea. SUPERSIZE ME A female hippopotamus (Hippopotamus amphibious) can eat more food relative to its body size than any other ruminant. Its stomach contents can make up one quarter of its total body weight. THAT FLOATING FEELING Seals hold their breath while sleeping on the surface of the water. SHOOT ME, SEE IF I CARE Tardigrades, eight-legged animals that are nicknamed water bears, are the hardiest creatures on earth. The tiny organisms, up to 1.2mm long, are capable of withstanding the most extreme environments by dehydrating and going into a state of frozen animation. There is anecdotal evidence that some can survive being immersed in liquid helium, just 1C above absolute zero. They can withstand being boiled in water, thrown into pure alcohol, and a pressure of 600 mega-pascals (six times the pressure of sea-water at a depth of 10,000 metres). NATURAL AQUALUNG One species of spider spends its life underwater. Using a dense mat of specialised hairs that covers its body and abdomen, the water spider (Argyroneta aquatica) traps a bubble of air around its body, breathing the trapped air. WHO NEEDS SATNAV? Wandering albatrosses (Diomedea exulans) can pinpoint the specific remote island where their nests are located after making foraging flights of several thousand kilometres of featureless ocean. They do not rely on the earth's magnetic field, and no one knows how the birds acquire such precise and impressive navigation ability. TOOTHSOME FARE The cookie-cutter shark (Isistius brasiliensis) measures only 50cm in length, yet has been recorded taking chunks out of the rubber sonar domes of nuclear submarines with its razor-sharp teeth. HONEY, THEY TOOK THE KIDS Adult emperor penguins (Aptenodytes forsteri) attempt to kidnap the chicks of another breeding pair. They forcibly wrestle the juvenile away from its parents, who try to protect the chick by fighting back. Kidnapping often occurs when a penguin that has failed to breed sees a chick begging its parents to be fed, and interprets the juvenile's behaviour as a cue to parent it. FATAL ATTRACTION? A female house sparrow (Passer domesticus) will often seek out the nest of another female that her partner has also mated with. She will then kill the first female's young, to remove the competition and ensure that the male spends as much time as possible helping to raise her chicks. GRUBBED OUT The caterpillar of the large blue butterfly settles beneath its food plant to await discovery by red ants (Myrmica species). By secreting hydrocarbons that mimic those made by Myrmica, the caterpillar tricks a foraging worker into taking it into the nest, where it is placed among the ant grubs. The caterpillar then moves to safer chambers, returning periodically to binge-feed on ant grubs. SLAVERY ON SIX LEGS Some ant species make slaves of others. Those in the subfamily Formicinae will go out and raid the nests of other species nearby, and steal their eggs and pupae. These are taken home, when the resulting young are raised as slaves, having to do all the foraging, cleaning and babysitting for their masters. TIME TO BALE OUT Certain species of canopy ant jump out of trees to escape being eaten. When Cephalotes atratus is approached by a predator it throws itself into the air, orientating its body to steer into a steep glide and head for the lower reaches of the tree trunk. On average, 85 per cent of all ants that take a leap successfully land back on the tree. MARAUDING MUSSELS Mussels can be voracious cannibals. At certain times of the year, up to 70 per cent of all food eaten by the green-lipped mussel (Perna canaliculus) is the larvae of its own species. TRY THIS ON FOR SIZE Uloboridae spiders wrap their victims to death. An individual small uloborid spider (Philoponella vicina) will weave more than 140 metres of silk to wrap a moth or beetle. It binds the silk shroud so tight that it compresses the prey's body, breaking the insect's legs, buckling its compound eyes inwards, and often killing it outright. Spiders of the family Uloboridae have lost their fangs, forcing them to evolve their vice-like death shroud. MURDEROUS MOGS In the UK alone, domestic cats kill 57 million mammals a year, 27 million birds and 5 million reptiles and amphibians. STOP AND YOU DIE Swarms of Mormon crickets (Anabrus simplex), which in the United States reach up to 10km long, keep on the move not just to find food, but to avoid being eaten by each other. If an individual stops for any reason, it is likely to be devoured by some of the millions of its following brethren. THE HOUDINI CHALLENGE The parasitic gordian worm (Paragordius tricuspidatus) begins its life in water before infecting the body of a larger insect host: a cricket. But the worm has a remarkable ability to survive even if its host is eaten by a larger predator. When the cricket is eaten, and partially digested, the worm escapes by burrowing through the body of the predator, usually a fish or amphibian, until it emerges unscathed in the water, where it continues its life cycle. WOULD YOU LIKE EYES WITH THAT? Animals usually swallow using their tongue and throat. The northern leopard frog (Rana pipiens) uses its eyes. To swallow food such as a small cricket, it closes its eyes and retracts its eyeball into its body. These push into the pharynx and against the prey item, and regular retractions help force the food to the back of the oesophagus. THE BIG CELL The yolk in an unfertilised ostrich's egg is the largest single cell found in nature. WE'RE JUST DOWNSIZING The Galapagos marine iguana (Amblyrhynchus cristatus), the only sea-going lizard, is also the only vertebrate known to shrink in body size regularly when adult, and then to grow larger again. The iguanas shrink up to 15 per cent in body length during El Nino weather events, losing bone mass. The following year the iguanas grow even larger before shrinking again. SEEING IS BELIEVING? Tarsiers, a primitive group of primates, have eyeballs bigger than their brains. CAN'T HELP THE WAY WE FEEL... Some genetically engineered mice have have hearts that glow green every time they beat. SAFE CRYOGENICS The wood frog (Rana sylvatica) freezes solid during the winter before thawing out as the temperature rises in spring. The frog has a unique physiology that prevents damaging ice crystals forming within its cells. COME FLY WITH ME The elusive paradise tree snake (Chrysopelea species) is the only vertebrate that can fly - despite having no limbs. The snake is a true glider, defined as covering a greater horizontal distance than it falls vertically. First the tree snake leaps from a tree into the air, and adopts an S-shape, changing its body shape to that of a biplane. Then the snake undulates its body, and while no one can be sure why it does this, the changing posture might serve to move its centres of gravity and the flow of air pressure in a way that allows controllable flight. It can achieve a glide angle of just 13 per cent to the horizontal (90 per cent constituting free fall) and cover distances of 20 metres. WHALE OF A TIME FOR BABIES For the first month of their lives, newborn killer whales (Orcinus orca) and bottlenose dolphins (Tursiops truncatus) do not sleep but remain mobile for 24 hours a day - as do their mothers. EAT ME, BABY A worm-like amphibian, the caecilian (Boulengerula taitanus) takes parenting to a new level. By elongating specialised stratified epithelial cells, mothers transform their skin until it is twice as thick, and it is then eaten by their offspring. PETER PAN SYNDROME? Many tadpoles of the African clawed frog (Xenopus laevis) never turn into frogs, instead growing into giant, grossly deformed tadpoles with a hunchback, on average four times longer and up to 50 times more massive than normal tadpoles. They can survive for years, although they cannot reproduce. CATCH US IF YOU CAN Cuttlefish (Sepia officinalis) change colour almost instantaneously to mimic the rock or seaweed of the seafloor against which they are hiding. They do so while being completely colour-blind. HOME IS BEST In 25 years of intensive research watching a group of killer whales (Orcinus orca) in the coastal waters of the north-eastern Pacific Ocean, there has not been one documented incidence of a male or female offspring leaving their mother. Each baby grows up and remains within the family group for the rest of their lives. CAN'T SWIM? NO PROBLEM Fire ants (Solenopsis invicta) survive floods by clinging together in huge numbers to form large rafts. Moths that Drink Elephants' Tears and Other Zoological Curiosities, by Matt Walker, is published by Portrait, == In 2002, polio researcher Eckard Wimmer generated a so-called "synthetic" poliovirus. A year later, a team led by J. Craig Venter and Hamilton Smith announced similar work with a virus called PhiX.] === New species Plants; Evening Primrose, Kewensis Primrose, Tragopogon, Raphanobrassica, Hemp Nettle, Madia Citrigracilis, Brassica, Maidenhair Fern, Woodsi Chlorella Vulgaris, Bacteria, Fireweed, Goats beard Mabus: Animals and Insects; Walking sticks {Phasmids}, Grasshoppers, Black flies, Cucurlionid Beetles {Tribolium Castaneum}. Worms {Nereis Acuminata}, Faeroe Island house mouse, Cichlid Fish {5 new species since their isolation in lake Nagubago }, spalax-ehrenbergi. Black-Tailed Gnatcatchers. Silverfish. Ensatina Salamanders, Phylloscopus trochiloides {Greenish Warblers }, Peromyces maniculatus {Deer mouse }, Parus major and Paru == ...To deny that basic concepts of historical method with respect to evolution is worse than just denying science; it is denying simple common sense. Down that road lies only solipsism or schizophrenia, neither of which can be used for examination of the outside world. - Daniel Harper === Gould states: But are these Linnaean species, recognized by indepen- dent cultures, merely temporary configurations of the mo- ment, mere way stations on evolutionary lineages in contin- ual flux? I argue . . . that, contrary to popular belief, evolution does not work this way, and that species have a reality through time to match their distinctness at a moment. An average species of fossil invertebrates lives five to ten million years (terrestrial vertebrates have shorter average durations). During this time, they rarely change in any fundamental way. They become extinct, without issue, looking much as they did when they first appeared. . . . Species are stable entities with very brief periods of fuzziness at their origin (although not at their demise because most species disappear cleanly without changing into anything else). As Edmund Burke said in another context: Though no man can draw a stroke between the confines of day and night, yet light and darkness are upon the whole tolerably distinguishable. In short, this is nothing more than Gould expounding on the implications of Punctuated Equilibria on what we should expect to see in the fossil record. To Gould, Mayr's view has the advantage of corresponding with the common sense view as to the reality of species, at least after an initial period while speciation is underway. Evolution is a theory of organic change, but it does not imply, as many people assume, that ceaseless flux is the irreducible state of nature and that structure is but a tempo- rary incarnation of the moment. Change is more often a rapid transition between stable states than a continuous transformation at slow and steady rates. We live in a world of structure and legitimate distinction. Species are the units of nature's morphology. ism. It takes to task those biologists and anthropologists who argue that species boundaries are artifacts of the human capacity to class- ify, and construct artificial divisions. Gould argues, as Ernst Mayr did years before, that species are real biological entities, but he does not suggest that they are genealogically unrelated to one another or that they cannot give rise to new species. Gould and his colleagues are widely cited by creationists in their effort to establish that the fossil record documents no transitions. To creationists this is taken to mean that there are no evolutionary links between created kinds. But Gould, Eldredge and Stanley are talking about the failure of the fossil record to document fine-scale transitions between pairs of species, and its dramatic documentation of rapid evolutionary bursts involving multiple speciation events -- so-called adaptive radiations. They are not talking about any failure of the fossil record to document the existence of intermediate forms (to the contrary, there are so many intermediates for many well- preserved taxa that it is notoriously difficult to identify true ances- tors even when the fossil record is very complete). Nor are Gould, Eldredge, and Stanley talking about any failure of the fossil record to document large-scale trends, which _do_ exist, however jerky they may be. Furthermore, fine-scale transitions are _not_ absent from the fossil record but are merely underrepresented. Eldredge, Gould. and Stanley reason that this is the unsurprising consequence of known mechanisms of speciation. Additionally, certain ecological condi- tions may favor speciation and rapid evolution, so new taxa may appear abruptly in the fossil record in association with adaptive radiation. Since creationists acknowledge that fine-scale transitions ( including those resulting in reproductive isolation) exist and since the fossil record clearly documents large-scale transitions, it would seem that the creationists have no case. Indeed. they do not. Their case is an artifact of misrepresentation to the lay public of exactly _what_ the fossil record fails to document. http://www.talkorigins.org/faqs/quotes/mine/part1-2.html#quote14 ): they A more complete quote would be as follows (words in square brackets ([]) appear in the Panda's Thumb essay, and not in the original): The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils. Yet Darwin was so wedded to gradualism that he wagered his entire theory on a denial of this literal record: The geological record is extremely imperfect and this fact will to a large extent explain why we do not find interminable varieties, connecting together all the extinct and existing forms of life by the finest graduated steps. He who rejects these views on the nature of the geological record, will rightly reject my whole theory. Darwin's argument still persists as the favored escape of most paleontologists from the embarrassment of a record that seems to show so little of evolution [directly]. In exposing its cultural and methodological roots, I wish in no way to impugn the potential validity of gradualism (for all general views have similar roots). I only wish to point out that it is never seen in the rocks. Paleontologists have paid an exorbitant price for Darwin's argument. We fancy ourselves as the only true students of life's history, yet to preserve our favored account of evolution by natural selection we view our data as so bad that we never see the very process we profess to study. For several years, Niles Eldredge of the American Museum of Natural History and I have been advocating a resolution to this uncomfortable paradox. We believe that Huxley was right in his warning. The modern theory of evolution does not require gradual change. In fact, the operation of Darwinian processes should yield exactly what we see in the fossil record. [It is gradualism we should reject, not Darwinism.] So it would seem that Gould has no problems with the fossil record. But did he believe that transitional forms are lacking? Note that in the quote originally presented, the claim is made that they are rare, not absent. Also, as anyone who is familiar with Gould's writings will know, the text quoted reflects his recognition that, while there is a scarcity of transitional fossils between species, there is no such lack of transitional fossils between major groups. We believe that Huxley was right in his warning. The modern theory of evolution does not require gradual change. In fact, the operation of Darwinian processes should yield exactly what we see in the fossil record. It is gradualism we should reject, not Darwinism. It is best, perhaps, to simply allow Gould defend himself, as he did in his [T]ransitions are often found in the fossil record. Preserved transitions are not common -- and should not be, according to our understanding of evolution (see next section) but they are not entirely wanting, as creationists often claim. [He then discusses two examples: therapsid intermediaries between reptiles and mammals, and the half-dozen human species - found as of 1981 - that appear in an unbroken temporal sequence of progressively more modern features.] Faced with these facts of evolution and the philosophical bankruptcy of their own position, creationists rely upon distortion and innuendo to buttress their rhetorical claim. If I sound sharp or bitter, indeed I am -- for I have become a major target of these practices. I count myself among the evolutionists who argue for a jerky, or episodic, rather than a smoothly gradual, pace of change. In 1972 my colleague Niles Eldredge and I developed the theory of punctuated equilibrium. We argued that two outstanding facts of the fossil record -- geologically sudden origin of new species and failure to change thereafter (stasis)reflect the predictions of evolutionary theory, not the imperfections of the fossil record. In most theories, small isolated populations are the source of new species, and the process of speciation takes thousands or tens of thousands of years. This amount of time, so long when measured against our lives, is a geological microsecond . . . Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists -- whether through design or stupidity, I do not know -- as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups. - Gould, Stephen Jay 1983. Evolution as Fact and Theory _Hens Teeth and Horse's Toes: Further Reflections in Natural History_. New York: W. W. Norton & Co., p. 258-260. consistently and extensively explained his position and the evidence for evolution, *including* transitional forms found in the fossil record. The constant abuse of the body of Gould's life's work in the face of this is not merely dishonest, it is despicable. - [Archaeopteryx is not a transitional fossil] Smooth intermediates between Bauplane [body plans] are almost impossible to construct, even in thought experiments: there is certainly no evidence for them in the fossil record (curious mosaics like Archaeopteryx do not count) - Gould, S.J. and N. Eldredge. Punctuated equilibria: the tempo and mode of evolution reconsidered. Paleobiology, 3 (1977): 115-151. (p. 147) At the higher level of evolutionary transition between basic morphological designs, gradualism has always been in trouble, though it remains the official position of most Western evolutionists. Smooth intermediates between _Baupl.8ane_ are almost impossible to construct, even in thought experiments; there is certainly no evidence for them in the fossil record (curious mosaics like _Archaeopteryx_ do not count). It's now obvious that Gould and Eldredge weren't arguing against _Archaeopteryx_ being a transitional form, but arguing that it wasn't an example of a perfectly smooth change between body plans (or Baupl.8ane). For instance, the wing of _Archaeopteryx_ was in essence the forelimb of a dinosaur covered with feathers. This is what Gould and Eldredge meant by the term mosaic: a creature that is a mixture of both primitive and advanced features. But mosaic forms are exactly what we should expect from evolutionary transitions, since there's no reason to expect every part of the body to evolve at the same rate or at the same time. Evolution has no destination in mind, just as the Wright Brothers didn't envision modern jet fighters when they flew at Kitty Hawk. But did Gould believe that _Archaeopteryx_ was a transitional form? He did 1980). Any claim to the contrary would be a misrepresentation. REFERENCES Gould, S. J. 1980. The Tell-tale Wishbone. In The Panda's Thumb: More Reflections in Natural History, pp 267-277. New York: W. W. Norton & Company, Inc. (Originally published in the November, 1977 edition of Natural History) Gould, S. J., & Eldredge, N. 1977. Punctuated equilibria: the tempo and mode of evolution reconsidered. Paleobiology 3:115-151. - Jon (gen2rev) Barber and John Harshman [Editor's note: see also: Archaeopteryx: Answering the Challenge of the Fossil Record by Chris Nedin [Evolution of the horse has no foundation in the fossil record] The popularly told example of horse evolution, suggesting a gradual sequence of changes from four-toed, or fox-like creatures, living nearly 50 million years ago, to today's much larger one-toe horse, has long been known to be wrong. Instead of gradual change, fossils of each intermediate species appear fully distinct, persist unchanged, and then become extinct. Transitional forms are unknown. Ideas on evolution Going Through a Revolution among Scientists, - Boyce Rensberger: Houston chronicle, 5 Nov. 1980, sec. 4, p. 15. comments. It states, in regard to Gould and Eldridge's ideas, that: As they see it, species remain largely stable for long periods and then suddenly change dramatically. The transition happens so fast, they [Gould and Eldridge] suggest, that the chance of intermediate forms being fossilized and found is nil. Then comes the horse evolution paragraph. There are a couple of immaterial typos in the quote originally supplied. The following is what appears in The popularly told example of horse evolution, suggesting a gradual sequence of changes from four-toed, fox-like creatures, living nearly 50 million years ago to today's much larger one-toe horse, has long been known to be wrong. Instead of gradual change, fossils of each intermediate species appear fully distinct, persist unchanged, and then become extinct. Transitional forms are unknown. The following paragraph reads: Eldridge and Gould represent a school of thought called 'punctuated equilibrium,' and although many paleontologists are adherents, many evolutionists from other backgrounds still consider themselves gradualists closer to the Darwinian mold. Times entitled Recent Studies Spark Revolution in Interpretation of Evolution (page C3). However, this quote isn't in it. But it does include Recent discoveries have only strengthened Darwin's epochal conclusion that all forms of life evolved from a common ancestor. Genetic analysis, for example, has shown that every organism is governed by the same genetic code controlling the same biochemical processes. The quote appears to be more an explanation for the general public that the horse sequence, did not represent an orderly ladder running from primitive forms to modern Equus, as was originally thought as far back as Darwin's time, but, instead, is a particularly prolific bush with many branches that all went extinct, except for Equus. As Kathleen Hunt points As new fossils were discovered, though, it became clear that the old model of horse evolution was a serious oversimplification. The ancestors of the modern horse were roughly what that series showed, and were clear evidence that evolution had occurred. But it was misleading to portray horse evolution in that smooth straight line, for two reasons: First, horse evolution didn't proceed in a straight line. We now know of many other branches of horse evolution. Our familiar Equus is merely one twig on a once-flourishing bush of equine species. We only have the illusion of straight-line evolution because Equus is the only twig that survived. (See Gould's essay Life's Little Joke in Bully for Brontosaurus for more on this topic.) Second, horse evolution was not smooth and gradual. Different traits evolved at different rates, didn't always evolve together, and occasionally reversed direction. Also, horse species did not always come into being by gradual transformation (anagenesis) of their ancestors; instead, sometimes new species split off from ancestors (cladogenesis) and then co-existed with those ancestors for some time. Some species arose gradually, others suddenly. Overall, the horse family demonstrates the diversity of evolutionary mechanisms, and it would be misleading -- and would be a real pity -- to reduce it to an oversimplified straight-line diagram. Finally, it is a sign of the creationists' attitude toward the issues press on a question of science. As good a journalist as Mr. Rensberger may Just made to order for their agenda. About Punctuated Equilibria. While the scientists have been refining the theory of evolution in the past decade, some nonscientists have been spreading anew the gospel of creationism -- and the coincidence has confused many laymen . . . Having opposed Darwin for 120 years, fundamentalists tend to seize on any criticism of his theories as vindication . . . But the new theories are intended to explain how evolution came about -- not to supplant it as a principle. Says Harvard's Stephen Jay Gould, . . . Evolution is a fact, like apples falling out of trees. === DNA of a Poplar tree. Scientists found more than 45,500 genes to understand how they control its growth. They have found 93 genes associated with the production of cellulose and lignin, which form the walls of plant cells. The black cottonwood is the third plant, after rice and a weed called Arabidopsis thaliana, to have its genome sequence published. Comparing their respective genomes is expected to shed light on their separate evolutionary paths === The researchers studied the snails DNA, they found that the differences in shell shape were not just determined by the populations genetic relatedness. The mystery was solved when Dr Schilthuizen and field worker Berjaya Elahan of the Sukau-based Kinabatangan Orangutan Conservation Project started observing the snails at night. They discovered that the Opisthostomaas worst nightmare was a nocturnal slug, a new species of a genus called Atopos that uses its tongue to bore holes in the shells and suck the occupant out. When they compared the predatoras behaviour on different hills, they found that in each place it had different table manners. On the hill of Tandu Batu, for example, the predator likes to attack the bottom of the shell, whereas on Gomantong, it prefers to enter its prey from the tip of the shell. Analysis of the arrangement of the spines, ribs, and flanges on the snail's shell showed that each population adapts its shell to defend against the local predator's behaviour. == A review, coauthored by Nick Matzke, of the evidence for the evolution of bacterial flagella appears in Nature Reviews Microbiology, while in Ohio there is renewed concern about the resurgence of attempts to undermine the treatment of evolution in the state science standards. And there's still time to reserve a spot on the next NCSE excursion to the Grand Canyon! PALLEN AND MATZKE IN NATURE REVIEWS MICROBIOLOGY On September 5, 2006, Nature Reviews Microbiology, one of the leading journals in its field, released "From The Origin of Species to the origin of bacterial flagella" in advance online publication form. The article, by Mark J. Pallen of the University of Birmingham and Nicholas J. Matzke of NCSE, reviews the evidence for the evolution of the bacterial flagellum which proponents of "intelligent design" notoriously adduce as a clear example of a designed rather than evolved structure. In the words of the abstract: In the recent Dover trial, and elsewhere, the 'Intelligent Design' movement has championed the bacterial flagellum as an irreducibly complex system that, it is claimed, could not have evolved through natural selection. Here we explore the arguments in favour of viewing bacterial flagella as evolved, rather than designed, entities. We dismiss the need for any great conceptual leaps in creating a model of flagellar evolution and speculate as to how an experimental programme focused on this topic might look. Pallen and Matzke begin by reminding microbiologists of the way in which their discipline became relevant to the Kitzmiller v. Dover trial, "where the term 'flagellum' and its cognates appeared 385 times in the transcripts of the 6-week trial." Proponents of "intelligent design" such as Michael Behe and Scott Minnich -- both of whom testified for the defense in Kitzmiller -- have contended that "irreducibly complex" systems such as the bacterial flagellum could not have evolved. At the trial, Kenneth R. Miller, testifying for the plaintiffs, effectively countered such contentions. After describing Miller's arguments, Pallen and Matzke note that talk about "the" bacterial flagellum is incorrect: "By even the most conservative estimate, there must therefore be thousands of different bacterial flagellar systems, perhaps even millions. Therefore, there is no point discussing the creation or ID of 'the' bacterial flagellum. Instead, one is faced with two options: either there were thousands or even millions of individual creation events, which strains Occam's razor to breaking point, or one has to accept that all the highly diverse contemporary flagellar systems have evolved from a common ancestor." Evidence for the evolution of bacterial flagella includes the existence of vestigial flagella, intermediate forms of flagella, and, importantly, the pattern of similarities among flagella protein sequences. Pallen and Matzke demonstrate that almost all of the core flagellar proteins have known homologies with non-flagellum proteins -- contrary to repeated claims from the "intelligent design" movement, such as Minnich's claim in his expert report that "the other thirty proteins in the flagellar motor (that are not present in the type III secretion system) are unique to the motor and are not found in any other living system." (Further details are provided by Matzke in a post at The Panda's Thumb blog.) Pallen and Matzke offer a call for continued research on flagellar evolution, citing both the need to debunk "the suspicion among members of the public that maybe there is some mystery here, that maybe the ID proponents do have a point" and the prospect of thereby gaining further understanding of bacterial flagella. After sketching a few avenues for future research, they pointedly comment, "Like Darwin, we have found that careful attention to homology, analogy and diversity yields substantial insights into the origin of even the most complex systems." For Pallen and Matzke's article (PDF; subscription required), visit: http://www.nature. com/nrmicro/ journal/vaop/ ncurrent/ pdf/nrmicro1493. pdf For Matzke's comments on The Panda's Thumb blog, visit: http://www.pandasth umb.org/archives /2006/09/ flagellum_ evolu.html == One hears evolution dismissed as "just a theory", as though all of science weren't based on theory and eternally subject to new evidence to the contrary. In science, gravity is "just a theory" - and if you ever drop something and it falls up, they'll reconsider the whole theory for you. That's just how "theoretical" evolution is - constantly subject to evidence and proof. But creationism cannot be tested and proved against evidence using the scientific method - that is why it is not science, it is faith. Molly Ivans == Changes in fruit fly DNA may reflect climate changes Global warming seems to be changing the genetic code of fruit flies in the Northwest and worldwide, researchers reported Aug. 31 in Science Express. For decades, scientists have known that a species of fruit fly, Drosophila subobscura, has certain genetic variations based on geography. The closer to the equator the flies live, the more often certain sections of their DNA flip around. These "chromosome inversions" seem to help the flies cope with warmer weather. Scientists from the University of Washington and elsewhere measured chromosomal inversions in fruit flies caught at 26 sites worldwide, including Salem and Medford. They compared the rates of inversion to those found in flies caught in prior decades at the same sites. They also checked climate records to find the temperature change at those sites over time. The genetic code shifted toward a more low-latitude pattern at 21 of the 22 sites known to have warmed. The change averaged about 1 degree of latitude, the same as moving 69 miles south. The study gives "a clear signal . . . that climate change is occurring and that genetic change is going along with it," == Small Prehistoric Whale Was Vicious Hunter Paleontologists have uncovered a 25-million-year-old whale fossil with a monstrous set of teeth and enormous eyes on the coast of Australia. The discovery has researchers rethinking whales' evolutionary history. Scientists were surprised to find that the vicious-looking specimen is an ancestor of modern baleen whales, gentle giants of today's seas. The fossil suggests a creature that grew to a little more than 11 feet with teeth about an inch-and-a-half long. Baleen whales, which include the blue and humpback, feed by filtering plankton and small fish from seawater through hair-like fibers in their jaws. Their ferocious forebears, on the other hand, appear to have used their teeth to rip and chew meat, said lead researcher Erich Fitzgerald, a palaeobiologist at the Museum Victoria in Melbourne, Australia. The details of the finding are published online in the Aug. 16 Proceedings of the Royal Society of London B. Strange mix Today there are two groups of whales: Mysticetes, or baleen whales, and odontocetes, or toothed whales such as orcas and dolphins. Some modern baleens do have teeth, but they use them for filtering rather than biting. Scientists believe the two groups diverged about 35 million years ago. The fossil's skull shape tells scientists this is undoubtedly a baleen whale, Fitzgerald said. In many ways it is markedly different from its modern counterparts though. The fossil whale has a more varied set of teeth and extremely long incisors, as you might expect to see on a cat or other terrestrial carnivorous animal, said Alton C. Dooley, Jr., Assistant Curator of Paleontology at the Virginia Museum of Natural History. The animal's huge eyes, which scientists associate with sharp underwater vision, are also adaptive for hunting. The whales probably couldn't produce ultrasonic signals for echolocation or sonar though, as some modern whales can to locate prey. == Scientists Say Theyve Found a Code Beyond Genetics in DNA A Genomic Code for Nucleosome Positioning (Nature.com) The genetic code specifies all the proteins that a cell makes. The second code, superimposed on the first, sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself. The discovery, if confirmed, could open new insights into the higher order control of the genes, like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell. The new code is described in the current issue of Nature by Eran Segal of the Weizmann Institute in Israel and Jonathan Widom of Northwestern University in Illinois and their colleagues. There are about 30 million nucleosomes in each human cell. So many are needed because the DNA strand wraps around each one only 1.65 times, in a twist containing 147 of its units, and the DNA molecule in a single chromosome can be up to 225 million units in length. Biologists have suspected for years that some positions on the DNA, notably those where it bends most easily, might be more favorable for nucleosomes than others, but no overall pattern was apparent. Drs. Segal and Widom analyzed the sequence at some 200 sites in the yeast genome where nucleosomes are known to bind, and discovered that there is indeed a hidden pattern. Knowing the pattern, they were able to predict the placement of about 50 percent of the nucleosomes in other organisms. The pattern is a combination of sequences that makes it easier for the DNA to bend itself and wrap tightly around a nucleosome. But the pattern requires only some of the sequences to be present in each nucleosome binding site, so it is not obvious. The looseness of its requirements is presumably the reason it does not conflict with the genetic code, which also has a little bit of redundancy or wiggle room built into it. Having the sequence of units in DNA determine the placement of nucleosomes would explain a puzzling feature of transcription factors, the proteins that activate genes. The transcription factors recognize short sequences of DNA, about six to eight units in length, which lie just in front of the gene to be transcribed. But these short sequences occur so often in the DNA that the transcription factors, it seemed, must often bind to the wrong ones. Dr. Segal, a computational biologist, believes that the wrong sites are in fact inaccessible because they lie in the part of the DNA wrapped around a nucleosome. The transcription factors can only see sites in the naked DNA that lies between two nucleosomes. The nucleosomes frequently move around, letting the DNA float free when a gene has to be transcribed. Given this constant flux, Dr. Segal said he was surprised they could predict as many as half of the preferred nucleosome positions. But having broken the code, We think that for the first time we have a real quantitative handle on exploring how the nucleosomes and other proteins interact to control the DNA, he said. The other 50 percent of the positions may be determined by competition between the nucleosomes and other proteins, Dr. Segal suggested. Several experts said the new result was plausible because it generalized the longstanding idea that DNA is more bendable at certain sequences, which should therefore favor nucleosome positioning. I think its really interesting, said Bradley Bernstein, a biologist at Massachusetts General Hospital. Jerry Workman of the Stowers Institute in Kansas City said the detection of the nucleosome code was a profound insight if true, because it would explain many aspects of how the DNA is controlled. The nucleosome is made up of proteins known as histones, which are among the most highly conserved in evolution, meaning that they change very little from one species to another. A histone of peas and cows differs in just 2 of its 102 amino acid units. The conservation is usually attributed to the precise fit required between the histones and the DNA wound around them. But another reason, Dr. Segal suggested, could be that any change would interfere with the nucleosomes ability to find their assigned positions on the DNA. In the genetic code, sets of three DNA units specify various kinds of amino acid, the units of proteins. A curious feature of the code is that it is redundant, meaning that a given amino acid can be defined by any of several different triplets. Biologists have long speculated that the redundancy may have been designed so as to coexist with some other kind of code, and this, Dr. Segal said, could be the nucleosome code. == Because you can't get the DNA of an extinct organism, you need to compare the DNA of two related living organisms, estimate when their common ancestor lived and estimate mutation rates based on that. Humans and chimps are the obvious species to use as an example. I will use round numbers to make the calculations easier. DNA is quantified using base pairs. A base pair refers to two organic bases held together by weak hydrogen bonds across strands of DNA or RNA. Purines (represented by adenine and guanine) always pair with pyrimidines (represented by cytosine, thymine and in the case of RNA, uracil). Consequently the configuration is A-T and G-C in DNA, and A-U in RNA. It is this bonding between base pairs that maintains DNAs characteristic double helix. Human and chimpanzee DNA both have about three billion base pairs. Of those base pairs something over 98% are identical. But, since I am using round numbers, let's say that exactly 2% are different (a slight overestimate). That would calculate to 0.02 * 3,000,000,000 or about 60,000,000 base pairs that differ between humans and chimps. Mutations change base pairs. They are caused by radiation and other factors. They can affect one or more base pair. (The largest documentated single mutation that I have personally seen in the literature changed seven base pairs.) There are also documented chromosomal mutations. These are very large scale mutations. They involve whole chromosomes or pieces of them, and can alter or duplicate hundreds or thousands of genes at a time. They are an important source for new genetic material. These are the different types of chromosomal mutations which have been observed: Translocation: Part of a chromosomal arm is removed from that chromosome and attached to another. Fusion: Two chromosomes get fused together, resulting in a single chromosome. There is evidence of such a fusion in the human genome, resulting in one fewer chromosome than is found in great apes. Fission: The opposite of fusion. One chromosome becomes two. Segmental Duplication: This is the duplication of a large segment of a chromosome. Chromosomal Duplication: The duplication of an entire chromosome. Genome Duplication: This is where the entire genome gets duplicated, also known as polyploidy. For example, the organism goes from being diploid (2n) to tetraploid (4n). There is evidence that all vertebrates have descend from an ancestor that underwent either one or two rounds of whole genome duplication. Since humans have 46 chromosomes and chimps have 48 either a fusion mutation took place in a human ancestor or a fission mutation took place in a chimp ancestor. So that counts as one of the mutations that took place. Getting back to the numbers for base pairs, we have calculated that there are a total of about 60 million base pairs that are different. It is reasonable to presume that about half of those took place in the chimpanzee heredity line and half in the human line of heredity. So about 30 million base pairs have changed in each line since the common ancestor existed. Since mutations can affect more than a single base pair, it would seem that possibly something like 15 - 20 million mutations took place during each hereditary line. Of course a related question is this: is such a large number of mutations reasonable? To answer that we have to make some assumptions about the length of time it has been since that common ancestor lived and population size. It is generally held - based on fossil evidence and other factors -that the common ancestor of chimps and humans lived about 5 million years ago. It has also been estimated that the worldwide populations of human and chimps has averaged about 100,000 individuals since then. Obviously that has varied, but with a current human population of about 6,000,000,000 that seems like a reasonably small number. Let us further assume that the average age of a generation is 20 years. That is the current estimate, but was probably smaller in the past. That is therefore a conservative estimate. So if you have a population of 100,000 individuals and new individuals are added every 20 years, on average there are 5,000 individuals born each year. Also since we say that a total of 15 - 20 million mutations have taken place in the human line of descent since the common ancestor of chimps and humans lived, and that this has taken 5 million years, it is easy to calculate that on average about 3 - 4 mutations have been added to the human genome each year. Note that is the number added to the entire human genome. Individuals have mutations. I have heard varying numbers, but typically in humans the average number of mutations seems to be about 5 per person. So about 5000 individuals have been born each year. Each individual has an average of about five mutations. If those estimates are correct then there have been an average of about 25,000 mutations occuring each year. Since only 3-4 of those are estimated to be added to the human genome each year (about 0.014%), there would seem to be no reason to think that the total number of mutations that have been added to the human genome since the common ancestor of humans and chimps lived is unreasonable at all. == http://sciencenow.sciencemag.org/cgi/content/full/2006/816/2 Human Evolution, Genome Style Genomes have proven fertile ground for clues to what makes us different from our primate cousins. Now, geneticists have unearthed a several stretches of DNA that may underlie our evolution. One seems to be involved in the most momentous innovation: the rapid expansion of the human cerebral cortex, the brain region responsible for higher cognition. Yet most of this DNA doesn't encode proteins, providing further evidence that changes in gene regulation have been as important, if not more important, as protein changes have been in helping humans evolve. Over the past 5 years, researchers have sequenced the genomes of dozens of animals, including humans, chimpanzees, mice, fish, and chickens. By lining up comparable sections of these genomes and counting up the differences in the DNA sequences, researchers have begun to reconstruct our genetic history. For the most part, researchers have focused on genetic changes--such as mutations in protein-coding genes, gene duplications, and alterations in gene _expression--as key to the evolution of humans. But with ever more sophisticated computer software and hardware, they have begun to look at the DNA in between genes as well. Katherine Pollard, now a biostatistician at the University of California, Davis, and her colleagues tapped this software, which she developed, to look for genetic novelties in humans. She found 49 regions where the DNA was stable in all the mammalian genomes examined except for the human genome, indicating that the sequences had undergone rapid evolution in the human lineage. One called HAR1 had 18 base changes over a 118-base stretch, where less than one was expected during the normal course of evolution. About 96% of those regions, including HAR1, lack any protein-coding genes. The HAR1 region stretches across part of two genes that code for RNA. University of California, Santa Cruz, cell biologist Sofie Salama, working with Pierre Vanderhaeghen, a neuroscientist at the University of Brussels, Belgium, has found one of these genes, HAR1F, is quite active in the 2-month- to 5-month-old human embryo. The HAR1F RNA is present in cells that help organize the human cortex into layers in conjunction with proteins key to that organization, Pollard and her colleagues report online today in Nature. Because RNA can play a role in gene regulation and protein function, Pollard and her colleagues suspect HAR1F RNA may help control the production of proteins involved in organizing the cerebral cortex. The discovery of the RNA gene "opens up a new area of genomic factors that haven't traditionally been looked at," says James Sikela, a genome researcher at the University of Colorado Health Science Center in Denver. The work "is an example of the utility of these new genome sequences." == The mitochondrial genes entire sequence is about 16,000 base pairs. == Evolutionary Theory: Mathematical and Conceptual Foundations (2004) by Sean H. Rice "The Biotic Message" by Walter ReMine == http://news.yahoo.com/s/nm/20060816/sc_nm/science_evolution_dc Possible key human evolution genes identified They could be the missing links of human genetic evolution -- areas of human DNA that changed dramatically after the evolutionary division from chimpanzees, though they had remained almost unchanged for millennia before. Scientists from the United States, Belgium and France identified 49 "human accelerated regions" (HARs) showing a lot of genetic activity. In the most active, identified as HAR1, they found 18 out of the 118 nucleotides had changed since evolutionary separation from chimps some 6 million years ago, while only two had changed in the 310 million years separating the evolutionary lines of chimps and chickens. "Right now we have very suggestive evidence that it might be involved at a critical step in brain development, but we still need to prove that it really makes a difference," team leader David Haussler from the Howard Hughes Medical Institute and the University of California, Santa Cruz told Reuters. Other members of the team came from the University of Brussels and Universite Claude Bernard in France. "It is very exciting to use evolution to look at regions of our genome that haven't been explored yet," Haussler said. "It is extremely unlikely that the evolution of just one region in the genome made the difference between our brains and the brains of non-human primates," he said. "It is much more likely to be a series of many, many small changes, each very important, but none doing the entire job by itself," he added. HAR1 is part of a novel RNA gene HAR1F that is produced during the key formative period for the human brain from seven to 19 weeks of gestation. Not only that, but the RNA is produced by the Cajal-Retzius neuron that plays a crucial role in the six layers of neurons in the human cortex. "We still can't say much about the function. But it's a very exciting finding because it is expressed in cells that have a fundamental role in the design and development of the mammalian cortex," Haussler said, noting the need to investigate the remaining 48 HARs. The findings were published on Wednesday in the science journal Nature. Chris Ponting of Oxford University wrote in the same issue hailing it as a possible major step forward. "Previously, the hunt for changes in DNA that are causally linked to human-specific biology had concentrated on differences that would alter the amino-acid make-up of the encoded protein," Ponting wrote. "Now it would seem that searches within the functional non-coding 'dark matter' might be more enlightening," he added. ===== Most fish have anterior and posterior external nostrils. In tetrapods, the posterior nostril is replaced by the choana, an internal nostril opening into the roof of the mouth. Kenichthys, a 395-million-year-old fossil from China, is exactly intermediate between the two, having nostrils at the margin of the upper jaw (Zhu and Ahlberg 2004). A fossil shows eight bony fingers in the front fin of a lobed fish, offering evidence that fingers developed before land-going tetrapods (Daeschler and Shubin 1998). A Devonian humerus has features showing that it belonged to an aquatic tetrapod that could push itself up with its forelimbs but could not move it limbs back and forth to walk (Shubin et al. 2004). Sinosauropteryx prima. A dinosaur covered with primitive feathers, but structurally similar to unfeathered dinosaurs Ornitholestes and Compsognathus (Chen et al. 1998; Currie and Chen 2001). Fletch: Ornithomimosaurs, therizinosaurs, and oviraptorosaurs. The oviraptorosaur Caudipteryx had a body covering of tufted feathers and had feathers with a central rachis on its wings and tail (Ji et al. 1998). Feathers are also known from the therizinosaur Beipiaosaurus (Xu et al. 1999a). Ambulocetus natans: Early to Middle Eocene, above Pakicetus. It had short front limbs and hind legs adapted for swimming; undulating its spine up and down helped its swimming. It apparently could walk on land as well as swim (Thewissen et al. 1994). Indocetus ramani: earliest Middle Eocene (Gingerich et al. 1993). Anomalocaris, from the Cambrian and Precambrian, has a pair of segmented appendages, indicating arthropod affinities, but it also seems to have lobopod legs. The related Opabinia also apparently had lobopod legs. Other rare Cambrian and Precambrian fossils show some promise of shedding more light on relationships. For example, Spriggina, another Precambrian animal, has a head shield similar to trilobites (Conway Morris 1998, 184-185). Australopithecus afarensis, from 3.9 to 3.0 million years ago (Mya). Its skull is similar to a chimpanzee's, but with more humanlike teeth. Homo habilis (2.4 to 1.5 Mya), which is similar to australopithecines, but which used tools and had a larger brain (650-cc average) and less projecting face. Fletch: Homo erectus (1.8 to 0.3 Mya); brain size averaged about 900 cc in early H. erectus and 1,100 cc in later ones. (Modern human brains average 1,350 cc.) A Pleistocene Homo sapiens which was "morphologically and chronologically intermediate between archaic African fossils and later anatomically modern Late Pleistocene humans" (White et al. 2003, 742). A hominid combining features of, and possibly ancestral to, Neanderthals and modern humans (Bermudez de Castro et al. 1997). === Seventy percent of evangelical Christians believe that living things have always existed in their current form, compared with 32% of mainline Protestants and 31% of Catholics, according to the Pew Research Center for the People and the Press. == David Quammen in "The Reluctant Mr. Darwin: An Intimate Portrait of Charles Darwin and the Making of His Theory of Evolution." Michael Shermer in "Why Darwin Matters: The Case Against Intelligent Design." Stanford University physicist Leonard Susskind, "Intelligent Thought." === Molecular techniques confirm fin theory Performance on the dance floor may not always show it, but people are rarely born with two left feet. We have genes that instruct our arms and legs to grow in the right places and point in the right directions. They also provide for the spaces between our fingers and toes and every other formative detail of our limbs. Evolutionarily speaking, the genetic instructions used to construct and position our limbs were being perfected more than half a billion years ago in fishes, not along the sides of the body where the fins that preceded human arms and legs sprouted, but at the midline that runs along the backbone and belly. This midline -- think of the dorsal, tail and anal fins of a fish - is where the genetic template to produce fins originated, about 100 million years before paired fins evolved and about 200 million years before paired fins evolved into limbs, according to University of Florida genetics researchers. The findings, published online today in the journal Nature, also provide insight into the evolutionary history of genes involved in human birth defects. "Given that paired fins made their evolutionary debut at a particular location on the sides of the body, intuitively one would think the genetic tools for fin development would be brought together in that place," said developmental biologist Martin Cohn, Ph.D., an associate professor with the UF departments of zoology and anatomy and cell biology and a member of the UF Genetics Institute. "We've discovered that the genetic circuitry for building limbs first appeared in an entirely different place - the midline of the animal." The appearance of paired fins on the sides of early vertebrates was a major evolutionary innovation toward fin - and eventually limb - locomotion, Cohn said. The earliest fishes lacked paired fins, similar to the modern-day lamprey - a species of jawless fish with a dorsal fin and tail but no side fins - considered by biologists to share many features with the ancestor of all vertebrates. "The emergence of paired appendages was a critical event in the evolution of vertebrates," Cohn said. "The fossil record provides clear evidence that the first fins evolved along the midline. The sequence of evolutionary events leading to the origin of limbs has been known for some time, but only now are we deciphering how these events occurred at a molecular genetic level." Researchers isolated genes from the spotted catshark, a type of slow-moving shark from the eastern Atlantic Ocean. By studying the activity of a dozen genes in shark embryos, they determined shark median fin development is associated with the presence of genes such as HoxD, Fgf8 and Tbx18, which are vital in the development of human limbs. They also used molecular markers for different cell types to determine which cells give rise to the median fins, finding that they arise from the same cells that form the vertebrae. These same genes dictate the emergence of symmetrical pairs of fins on the animal sides, showing a shared developmental mechanism in completely different locations, according to Renata Freitas and GuangJun Zhang, co-authors of the paper and graduate students in UF's zoology department. Extending their genetic analysis to the lamprey - a living relic from the time before fish had paired fins - researchers found the same genetic cues in place. "That we see these same mechanisms operating in lamprey fins tells us they must have been assembled in the median fins first, and later in evolution this entire genetic program was simply reutilized in a new position to build the first paired fins," Cohn said. "It tells us our own arms and legs have their evolutionary roots in the dorsal, caudal and anal fins of our fishy ancestors." Many of these genetic mechanisms are involved in human birth defects, which provide insight into the evolutionary history of genes and their functions. "Knowing that many of these genes are responsible for limb defects in humans is intriguing," Cohn said. "What we've done is identify where those developmental pathways originated during our evolutionary past and how they became involved in limb development." Learning the mechanics of development enriches our understanding of evolution, according to Ann Campbell Burke, Ph.D., an associate professor of biology at Wesleyan University who was not connected with the study. "Using modern molecular techniques, this confirms in a lovely way an idea that's been around for over 100 years about how paired fins may have evolved in the first place," Burke said. "To translate a 19th century observation about fin development into modern molecular data is a great thing for science. It has become increasingly important to understand developmental processes in our attempts to understand evolution." __._,_.___ == The present-day "Puget Sound" gulls are crosses between "Western" gulls(Larus occidentalis) and "Glaucous winged" gulls(Larus glaucescens). These gulls commonly hybridize == Scientists Say Theyve Found a Code Beyond Genetics in DNA The genetic code specifies all the proteins that a cell makes. The second code, superimposed on the first, sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself. The discovery, if confirmed, could open new insights into the higher order control of the genes, like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell. The new code is described in the current issue of Nature by Eran Segal of the Weizmann Institute in Israel and Jonathan Widom of Northwestern University in Illinois and their colleagues. There are about 30 million nucleosomes in each human cell. So many are needed because the DNA strand wraps around each one only 1.65 times, in a twist containing 147 of its units, and the DNA molecule in a single chromosome can be up to 225 million units in length. Biologists have suspected for years that some positions on the DNA, notably those where it bends most easily, might be more favorable for nucleosomes than others, but no overall pattern was apparent. Drs. Segal and Widom analyzed the sequence at some 200 sites in the yeast genome where nucleosomes are known to bind, and discovered that there is indeed a hidden pattern. Knowing the pattern, they were able to predict the placement of about 50 percent of the nucleosomes in other organisms. The pattern is a combination of sequences that makes it easier for the DNA to bend itself and wrap tightly around a nucleosome. But the pattern requires only some of the sequences to be present in each nucleosome binding site, so it is not obvious. The looseness of its requirements is presumably the reason it does not conflict with the genetic code, which also has a little bit of redundancy or wiggle room built into it. Having the sequence of units in DNA determine the placement of nucleosomes would explain a puzzling feature of transcription factors, the proteins that activate genes. The transcription factors recognize short sequences of DNA, about six to eight units in length, which lie just in front of the gene to be transcribed. But these short sequences occur so often in the DNA that the transcription factors, it seemed, must often bind to the wrong ones. Dr. Segal, a computational biologist, believes that the wrong sites are in fact inaccessible because they lie in the part of the DNA wrapped around a nucleosome. The transcription factors can only see sites in the naked DNA that lies between two nucleosomes. The nucleosomes frequently move around, letting the DNA float free when a gene has to be transcribed. Given this constant flux, Dr. Segal said he was surprised they could predict as many as half of the preferred nucleosome positions. But having broken the code, We think that for the first time we have a real quantitative handle on exploring how the nucleosomes and other proteins interact to control the DNA, he said. The other 50 percent of the positions may be determined by competition between the nucleosomes and other proteins, Dr. Segal suggested. Several experts said the new result was plausible because it generalized the longstanding idea that DNA is more bendable at certain sequences, which should therefore favor nucleosome positioning. I think its really interesting, said Bradley Bernstein, a biologist at Massachusetts General Hospital. Jerry Workman of the Stowers Institute in Kansas City said the detection of the nucleosome code was a profound insight if true, because it would explain many aspects of how the DNA is controlled. The nucleosome is made up of proteins known as histones, which are among the most highly conserved in evolution, meaning that they change very little from one species to another. A histone of peas and cows differs in just 2 of its 102 amino acid units. The conservation is usually attributed to the precise fit required between the histones and the DNA wound around them. But another reason, Dr. Segal suggested, could be that any change would interfere with the nucleosomes ability to find their assigned positions on the DNA. In the genetic code, sets of three DNA units specify various kinds of amino acid, the units of proteins. A curious feature of the code is that it is redundant, meaning that a given amino acid can be defined by any of several different triplets. Biologists have long speculated that the redundancy may have been designed so as to coexist with some other kind of code, and this, Dr. Segal said, could be the nucleosome code. == There are many different definitions of species -- the one favored by evolutionary biologists who study animals (esp. mammals) is the Biological Species Concept, and that is the one that I use in this case. http://www.talkorigins.org/faqs/comdesc/glossary.html#species Hybrids between any of the Madeiran mouse races carrying robertsonian fusions would be sterile or infertile owing to the complex chromosomal configurations that would be produced at meiosis (7, 8). Our results indicate not only that accelerated rates of radiation can occur without involving adaptive processes, but also that chromosomal evolution can be an efficient mechanism of isolation, as several reproductively isolated chromosomal races have appeared in less than 500 years. Reproductive isolation is reproductive isolation. \Races\ is often used in biology when closely related organisms are geographically isolated. == 1] Pollen types are commonly readily distinguised from one another. We can tell pollen from many different groups of plants apart. 2] Pollen and spore cell walls are next to indestructable; if they existed back then we'd find them as fossils, 3] The pollen/spore fossil record is very extensive. Pollen [and spores in general] do indeed extend back a long, long time, to long before there is any recognizable trace of flowering plant [angiosperm] pollen. 4] There are essentially no angiosperms or their pollen in strata below the Cretaceous. Some very prominent wind-pollinated modern families like grasses aren't found below the Tertiary. == Fossils and DNA evidence also showed that snakes were the first serious predators of modern mammals, which evolved about 100 million years ago. "Fossils of snakes with mouths big enough to eat those mammals appear at about the same time. Other animals that could have eaten our ancestors, such as big cats, and hawks and eagles, evolved much later. Venomous snakes evolved about 60 million years ago, raising the stakes and forcing primates to get better at detecting them," she said. "There's an evolutionary arms race between the predators and prey. Primates get better at spotting and avoiding snakes, so the snakes get better at concealment, or more venomous, and the primates respond," she added. She said that some primate groups less threatened by snakes also showed fewer signs of evolutionary pressure to evolve better vision, for example, the lemurs of Madagascar did not have any venomous snakes in their environment, and in evolutionary terms remained where they were. Elsewhere, in South America, monkeys arrived millions of years before venomous snakes, and showed less specialization in their visual system compared with Old World monkeys and apes, which all have good vision, including color. "Having evolved for one purpose, a good eye for color, detail and movement later became useful for other purposes, such as social interactions in groups," she further said. The study is published in the July issue of the Journal of Human Evolution. (ANI) == Let me mention just a few obvious examples in various families: Pongidae (Gorillas, Chimpanzees, Orangutans) Canidae (Wolves/dogs, Foxes) Camelidae (Llamas, Camels) Falconidae (Eagles, Vultures, Hawks) Ursidae (Pandas, Grizzly) Cervidae (Deer, Moose) Bovidae (Cattle, Antelope, sheep) == There are ant parasites that make ants turn purple and climb grass in late afternoon so goats will eat the ants thinking they are little flowers, and the only place the parasites can reproduce themselves are in goat intestines == Cnidarians first appear in the Vendian. Other Vendian metazoan fossils may or may not represent primitive molluscs, arthropods, or sponges. Several animal phyla do *not* have fossil records starting in the Cambrian strata, like bryozoa. == In birds, the males have double Z chromosomes and the females have ZW. As such, avian females are heterogametic in the same way that mammalian males are, thus errors which occur in either the mammalian Y chromosome or the avian W chromosome cannot be corrected as the result of sexual recombination since they Y and W are always unpaired. This does in fact make both vulnerable to retroviruses, and the endogenization of retroviruses generally appears to occur through the unmatched ("heterozygous") chromosomes - which helps to explain why endogenous retroviral families that entered our germline during primate evolution and get expressed in tissues always get expressed in the testes. == The molecular machinery that starts the process by which a biological cell divides into two identical daughter cells apparently worked so well early on that evolution has conserved it across the eons in all forms of life on Earth. Researchers with the U.S. Department of Energy's Lawrence Berkeley National Laboratory and the University of California at Berkeley have shown that the core machinery for initiating DNA replication is the same for all three domains of life - Archaea, Bacteria and Eukarya. In two papers that will be concurrently published in the August edition of the journal Nature Structural and Molecular Biology (now available on-line), the researchers report the identification of a helical substructure within a superfamily of proteins, called AAA+, as the molecular "initiator" of DNA replication in a bacteria, Escherichia coli (E. coli), and in a eukaryote, Drosophila melanogaster, the fruit fly. Taken with earlier research that identified AAA+ proteins at the heart of the DNA replication initiator in archaea organisms, these new findings indicate that DNA replication is an ancient event that evolved millions of years ago, prior to when Archae, Bacteria and Eukarya split into separate domains of life. "The ability of a cell to replicate its DNA in a timely and faithful manner is fundamental for survival, but, despite decades of study, the structural and molecular basis for initiating DNA replication, and the degree to which these mechanisms have been conserved by evolution have been ill defined and hotly debated," said biophysicist Eva Nogales, a collaborator on the Drosophila study. Said biochemist Michael Botchan, also a collaborator on the Drosophila study, "Our two papers fuse together a number of biophysical research techniques to take our understanding of the mechanics of DNA opening and replisome construction to a new level." Biochemist and structural biologist James Berger, a participant in both studies added, "Our findings of evolutionary kinship between the DNA initiators in all three domains make sense because, to paraphrase Francois Jacob, the one thing a cell wants to do is to become two cells. A cell can't do this if it doesn't replicate its DNA in the right place, at the right time, and in the right manner, while simultaneously avoiding over-replication." The Drosophila results were reported in a paper entitled: Nucleotide-dependent conformational changes in the DnaA-like core of the origin recognition complex. This study was led by Botchan and Nogales, and included Megan Clarey, Jan Erzberger, Patricia Grob, Andres Leschziner and Berger. Nogales and Berger hold appointments with Berkeley Lab's Life Science and Physical Biosciences Divisions, respectively, and with UC Berkeley's Molecular and Cell Biology Department, in which Botchan is a professor. Nogales is also an investigator with the Howard Hughes Medical Institute. The E.coli results were presented in a paper entitled: Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling. Berger led this study and his collaborators included Erzberger and Melissa Mott. While the research studies behind these two papers were not coordinated, they did benefit from "a convenient congruence of timely results," as Berger explained. "We had solved our initiator structures in the E.coli study just as results were being generated from the Botchan and Nogales groups on the Drosophila study. Once we compared notes, we immediately pooled forces. When we subsequently were able to dock our bacterial model into a region of their eukaryotic structure, it solidified the evolutionary and functional similarities between the two mechanisms." For the E.coli study, Berger and his team utilized the exceptionally bright and intense x-rays of Beamline 8.3.1 at Berkeley Lab's Advanced Light Source synchrotron. With the data gathered at this protein crystallography facility, Berger and his team assembled a high-resolution model of the molecular structure of a protein known as DnaA, which is a member of the AAA+ family. While it has long been known that DnaA controls the process of initiating DNA replication in bacteria, the molecular details of its myriad activities have until now been a mystery. Berger's team found that when the DnaA protein binds with adenosine triphosphate or ATP, the nucleotide molecule that supplies energy to all components of a cell, the ring-shaped AAA+ proteins assemble into a right-handed spiraling superstructure. This arrangement was unexpected, because in other functional AAA+ complexes, the ring assemblies are closed. In addition, the architecture indicated that the AAA+ superhelix will wrap coils of the DNA double-helix around its exterior, causing the familiar "spiral staircase" of the DNA to deform as a first step in the separation and unwinding of its two gene-carrying strands. "It is likely that the AAA+ rings of the replication initiators are open to allow others proteins to dock onto the initiator complex," said Berger. "These other proteins can help add layers of complexity, such as assisting with helicase loading or inactivating the initiator after replication has begun.The open rings also probably allow DNA to interact with the interior of the initiator assembly." Bacterial cells, like the cells of Achaeans, are prokaryotes, meaning their DNA is not contained within a defined nucleus. Eukaryotes consist of plants and animals and all other organisms whose DNA is contained within a membrane-bound nucleus. Whereas DNA replication in bacteria is typically initiated at a single sites, DNA replication in eukaryotes can be an immensely complicated multi-event affair, involving the coordinated initiation and regulation of hundreds and even thousands of protein machines at different sites throughout the genome. Furthermore, the highly packaged nature of eukaryotic genomes makes it difficult for these protein machines to access the DNA. Because of this complexity, the mechanism for initiating DNA replication in eukaryotes was presumed to be much different than the prokaryote initiator. Studies over the past decade have demonstrated that all of the multiple events that initiate DNA replication in a eukaryote are directed by a single complex of proteins called the origin recognition complex (ORC). However, until now, models of the ORC proteins have lacked sufficient detail to identify the structure of the initiator. In their Drosophila study, Nogales and Botchan and their collaborators studied fruit fly ORC using single-particle electron microscopy. Their images revealed for the first time how the ORC when bound to ATP forms a AAA+ helical structure much like the DnaA superhelix found by Berger and his team in their E.coli study. "This work provides the first view of the mechanical transitions in ORC driven by ATP in a higher organism," said Nogales. "While our studies have not yet shown the initiator wrapped around the DNA, the structural similarity to the DnaA initiator found in the E.coli study suggests that there are likely to be strong mechanistic commonalities in the ways that initiators engage and remodel replication origins, as well as in how they facilitate replisome assembly." The idea that all three domains of life share the same DNA replication initiator is new and will require some re-thinking on the part of biologists who study eukaryotes. Re-thinking will also be required for models of DNA replication that predicted initiators would have similar structures to the protein "clamps" and "clamp loaders" already identified as key mechanisms in the DNA replication process. Said Berger, "Our work shows that there are major structural distinctions between assembled initiator and clamp loader complexes. This not only has important implications for the respective functions of these different mechanisms, it also calls into question some cherished models in the field." The two studies by Nogales, Berger, Botchan and their colleagues also show how when nature finds a mechanism that works well, such a mechanism is conserved through evolution. Said Nogales, "The specialization of DNA replication initiators took place a long time ago, separating them from other members of the AAA+ superfamily of proteins while maintaining an identity among themselves that reflects the importance of the replication process. Through the millions of years, evolution has added bells and whistles around this highly conserved central engine." == Traits are passed down in the form of genes. Take a look at Hox genes, or Pax-6, or G3PDH. The Hox genes have an identical stretch of ~120 nucleotides (the homeobox) that have been found in organisms ranging from flies to man. In fact, every organism that has front to back polarity has hox genes. The odds of this sequence occurring independently in different organisms is 1 in 4^160. Not only that, these hox genes occur in clusters always in a linear arrangement corresponding to the body segments that they control. === For Tyrannosaurs, Midlife Was Terrible Indeed In the popular imagination, Tyrannosaurus rex has become a symbol of indomitable dinosaur ferocity. But the "tyrant lizard" was vulnerable as a youngster, and at sexual maturity it went through "an honest-to-God midlife crisis," according to Florida State University comparative anatomist Gregory Erickson. Erickson studied the remains of a number of North American tyrannosaurs and found that 70 percent survived from age 2 to sexual maturity between 13 and 16. That helps explain why so few sub-adult tyrannosaur fossils have been found. But before 2 they were vulnerable to disease and predators, and at midlife mortality increased to 23 percent per year. "I think love was a dangerous game for tyrannosaurs," Erickson said. "As they came into sexual maturity there was a good chance they started having antagonistic encounters with each other, fighting over mates, fighting over nesting areas." On top of that, females had to lay eggs at this age and may have had to stay at the nest rather than hunt, further endangering the population. == Feathered dinosaurs from China and the evolution of major avian characters Xing XU Recent discoveries of feathered dinosaurs from Early Cretaceous deposits in Liaoning, China, have not only lent strongest support for the dinosaurian hypothesis of bird origins, but have also provided much-needed information about the origins of feathers and avian flight. Preliminary analysis of character evolution suggests that the major avian osteological characters were acquired during the early evolution of maniraptoran dinosaurs. The available evidence also suggests that the first feathers with a filamentous morphology probably evolved in basal coelurosaurs and pennaceous feathers (including those with aerodynamic features) were developed in non-avian maniraptorans, indicating that feathers evolved before the origin of birds and their flight. An evolutionary model is proposed here to describe the major stages of feather evolution, a process characterized by a combination of both transformational and innovative modifications. This model is different from some recent developmental models, which suggest that feathers are evolutionary novelties without a homologous relationship to reptilian scales. Although non-avian theropods are traditionally regarded as distinctly cursorial animals, recent discoveries suggest that the closest relatives of birds might be arboreal theropods. Many bird features, such as the furcula and pennaceous feathers, evolved in a terrestrial context, whereas others, such as some pedal modifications, may have evolved in an arboreal context. Consequently, arboreality may have also contributed to the origin of avian flight. http://www.blackwell-synergy.com/doi/abs/10.1111/j.1749- 4877.2006.00004.x full article free http://www.blackwell-synergy.com/toc/inz/1/1?cookieSet=1 == The latest tapeworm research suggests a time frame for human migration out of Africa, and also reveals that people gave the parasite to domestic animals such as pigs--not the other way around. According to Eric P. Hoberg, a zoologist with the U.S. Department of Agriculture, and his colleagues, tapeworms probably jumped from predators to humans between 2 and 2.5 million years ago, when hominids inhabited savannah environments in sub-Saharan Africa and were likely hunting or scavenging the same prey favored by hyenas and lions. Of the three tapeworms that infect people today, the researchers linked one, Taenia solium, most closely to a species that uses hyenas and African hunting dogs as its hosts. The other two, T. saginata and T. asiatica, are linked most closely to a species with lions as its host. Because T. solium and the pair T. saginata/T. asiatica are only distantly related, it appears that two tapeworms independently made the jump to hominids: the ancestor of T. solium, and a single parent species of both T. saginata and T. asiatica. The amount of genetic difference between T. saginata and T. asiatica suggests that they split from a single human-adapted species by 160,000 years ago, says Hoberg. Worm-carrying human populations may have migrated out of Africa at or before this time, leading to the separation of parasite populations that evolved into the two species. Cattle eventually became the intermediate host in T. saginata, pigs in T. asiatica. Because domestication took place much later, around 10,000 years ago, and because neither animal comes from a sub-Saharan progenitor, the transmission of tapeworms had to be from humans to cattle and pigs, not the reverse. It has long been thought that prohibitions on eating pork in some religions stem from their role as tapeworm hosts, hence being "unclean." The new study suggests pigs may have gotten the blame deserved by our own ancestors. http://www.archaeology.org/0203/newsbriefs/africa.html == Molecular Characterization of a Diagnostic DNA Marker for Domesticated Tetraploid Wheat Provides Evidence for Gene Flow from Wild Tetraploid Wheat to Hexaploid Wheat === I hadn't really considered the role that phages play in the evolution of viruses -- and it could be highly significant. There is a great deal of lateral gene transfer which goes on between different "species" of bacteria (prokaryotes and archaea) -- so much that what they are speaking of is a lateral gene transfer network, specifically a scale-free, small world. One would expect the same thing with respect to the viruses ("phages") which infect them, only to a far more significant degree. And of course we know that phages greatly influence the evolution of their prokaryotic hosts. But I am at this point unaware of the extent to which they affect the evolution of single-celled eukaryotic life. Lateral gene transfer will undoubtedly still play a role between viruses which infect a given multicellular host, but to a lesser degree given the defenses which multicellular organisms have put in place and the fact that viruses must become specialized to gain entry into typically only a few specific tissues. One of my central interests is the role that viruses play in the evolution of life -- particularly in terms of lateral gene transfer. So far, what I have seen is that retroviruses are mostly responsible there, and largely one-way, no large packages between different species of eukaryotes -- so at this level, the one of the major questions is the extent to which retroviruses are responsible for reshaping the genomes of such hosts, and the answer of course is: plenty. I would consider retroviruses a major engine in the evolution of multicellular life, although clearly not enough to make the establishment of the identification fairly deep phylogenetic trees of their hosts impossible -- given the relative sizes of the genomes involved and the extent to which we are able to identify the contributions of retroelements. Likewise, when retroviruses become endogenized, the literature gives considerable support to the view that the good majority endogenized retroviruses are the result of duplications of retroviruses which have already gained entry, not new infections from exogenous retroviruses. However, families of endogenous retroviruses are presumably especially active only early on, subject to either methalyzation or deleterious mutations, with deleterious mutations resulting in the loss of the envelope gene early on as what might roughly be considered the point of endogenization. Currently, the only endogenous retrovirus which I am are aware of which may still be subject to some very limited horizontal transmission is HERV-K113, although there may be others. Another central question, at least for me, is the extent to which other viruses may contribute to the evolution of multicellular eukaryotes. For example, are transposons which are involved in either non-replicative or replicative transposition as opposed to retrotransposition derived from DNA viruses? To what extent does replicative transposition play a factor in the evolution of multicellular eukaryotes? Currently I am only aware of phages engaging in replicative transposition, for example, according to the Shapiro rolling model. For quite some time, viruses were viewed as largely non-creative, stealing their genes from their hosts. Now of course this seems quite naive, although some of this no doubt takes place. What is more likely is that they are the source of many of the new genes in their hosts, at least in the prokaryotic and archeal realms. No doubt some of this takes place in the realm of single-celled eukaryotes, but other than retroviruses, such contributions in the realm of multicellular organisms seems less likely -- unless the viruses are passed by means of sexual transmission -- and thus better able to enter the germline -- as has apparently been the case in all endogenized retroviruses which entered the primate-human germline. In mammals this seems to be principally through the Y-chromosome and in birds I believe it will prove to be principally through the female W-chromosome as neither is subject to sexual recombination and thus the associated error-correction mechanisms. I would assume that endogenous retroviruses are much less common to enter the germline in those species which do not have such a chromosome, that is, when sex is determined by temperature, multichromosomal or other means. There are of course a fair number of other mechanisms for larger mutations in multicellular organisms. For example, tandem repeat slippage which as I understand it occurs primarily within microsatellites, non-viral insertions and deletions simply as the result of breakage, chromosomal rearrangements (primarily intrachromosomal rearrangements) due to hairpin and cruciform structures which result from inverse palindromic sequences in H-DNA and Z-DNA, and of course the rarer polyploidy, which is actually quite common in orchids -- but which appears to have taken place only two times in our own lineage, although we are aware of at least one rodent which has undergone polyploidy. It appears that retroviruses have played quite critical roles in the evolution of multicellular life. For example, the core of telomerase is essentially a reverse transcriptase which (while there is still considerable debate), at least in my view, most likely originated in a retroviral infection. Now I am aware of the existence of retrophages, although so far I have found the literature to be somewhat sparse. I am also aware of the fact that bacteria which reproduce by exclusively sexual means have linear chromosomes and telomeres, and thus in the majority of cases I would assume a reverse transcriptase, although there are certainly other possibilities. For example, we are aware of the fact that drosophila doesn't even use telomerase but instead employs two retrotransposons for the lengthening of its telomeres. I would assume that this sort of mechanism is employed by at least some prokaryotes which have linear chromosomes. Likewise, we have recently discovered what appears to be a genome in centrosomes which consists of five RNA chromosomes -- but this is still quite tentative. Moreover, we have discovered that bacteria employ cytoskeletons which are homologous to our own, and probably share the same origin, so I would assume that they too would have an RNA genome -- assuming the above holds up. In terms of the origin of life, I of course recognize that at one point we had an RNA-world -- at this point it is virtually a given. But given the recent three-step metabolism discovered by House and Ferry, their thermodynamic metabolism-first model seems more likely than a replicator-first model -- although I would likewise consider this fairly tentative. I would then be of the view that as the chemistry of a metabolic world became increasingly complex, perhaps as the result of polypetides being formed in volcanic vents, this made possible RNA-viruses, perhaps by a route not that much different from the one discovered by Manfred Eigen. Then, according to the views of some (a view which I share), at one or perhaps several points, RNA-viruses invented retrotransposition and thus DNA as a means of evading the defenses of their RNA hosts which then became incorporated as a permanent resident of their hosts, taking over the cells from their earlier RNA-based counterparts, giving rise to the DNA world. In any case, the study of phages may play a very important role in terms of understanding the evolution of life. == Smallpox belongs to the subfamily chordopoxvirinae (which infect vertebrates) and thus the family poxviridae (which also includes entomopoxvirinae). Two other chordopoxvirinae include cowpox (which have rats as their natural host) and monkeypox. Poxviridae, pycodaviridae and astarviridae all share common structural motifs with SIRV1, an archaeal virus -- suggesting common ancestry. == The Paleontological Society Position Statement: Evolution http://www.paleosoc.org/evolutioncomplete.htm Evolution is both a scientific fact and a scientific theory. Evolution is a fact in the sense that life has changed through time. In nature today, the characteristics of species are changing, and new species are arising. The fossil record is the primary factual evidence for evolution in times past, and evolution is well documented by further evidence from other scientific disciplines, including comparative anatomy, biogeography, genetics, molecular biology, and studies of viral and bacterial diseases. Evolution is also a theory an explanation for the observed changes in life through Earth history that has been tested numerous times and repeatedly confirmed. Evolution is an elegant theory that explains the history of life through geologic time; the diversity of living organisms, including their genetic, molecular, and physical similarities and differences; and the geographic distribution of organisms. Evolutionary principles are the foundation of all basic and applied biology and paleontology, from biodiversity studies to studies on the control of emerging diseases. Because evolution is fundamental to understanding both living and extinct organisms, it must be taught in public school science classes. In contrast, creationism is religion rather than science, as ruled by the Supreme Court, because it invokes supernatural explanations that cannot be tested. Consequently, creationism in any form (including "scientific creationism," "creation science," and "intelligent design") must be excluded from public school science classes. Because science involves testing hypotheses, scientific explanations are restricted to natural causes. This difference between science and religion does not mean that the two fields are incompatible. Many scientists who study evolution are religious, and many religious denominations have issued statements supporting evolution. Science and religion address different questions and employ different ways of knowing. The evolution paradigm has withstood nearly 150 years of scrutiny. Although the existence of evolution has been confirmed many times, as a science evolutionary theory must continue to be open to testing. At this time, however, more fruitful inquiries address the tempo and mode of evolution, various processes involved in evolution, and driving factors for evolution. Through such inquiry, the unifying theory of evolution will become an even more powerful explanation for the history of life on Earth. ---------------------------------------------------------------- The Society of Vertebrate Paleontology Statement on Evolution (1994) http://www.vertpaleo.org/policy/policy_statement_evolution.html Excerpt: | The fossil record of vertebrates unequivocally supports the | hypothesis that vertebrates have evolved through time, from | their first records in the early Paleozoic Era about 500 | million years ago to the great diversity we see in the world | today. The hypothesis has been strengthened by so many | independent observations of fossil sequences that it has come | to be regarded as a confirmed fact, as certain as the drift of | continents through time or the lawful operation of gravity. ---------------------------------------------------------------- National Academy of Sciences Science and Creationism: A View from the National Academy of Sciences, Second Edition (1999) http://www.nap.edu/books/0309064066/html/ Excerpt: | Is evolution a fact or a theory? | | The theory of evolution explains how life on Earth has | changed. In scientific terms, "theory" does not mean "guess" | or "hunch" as it does in everyday usage. Scientific theories | are explanations of natural phenomena built up logically | from testable observations and hypotheses. Biological | evolution is the best scientific explanation we have for the | enormous range of observations about the living world. | | Scientists most often use the word "fact" to describe an | observation. But scientists can also use fact to mean | something that has been tested or observed so many times | that there is no longer a compelling reason to keep testing | or looking for examples. The occurrence of evolution in this | sense is a fact. Scientists no longer question whether | descent with modification occurred because the evidence | supporting the idea is so strong. ---------------------------------------------------------------- American Geological Institute Position on Teaching Evolution http://www.agiweb.org/gapac/evolution_statement.html Excerpt: | Scientific evidence indicates beyond any doubt that life has | existed on Earth for billions of years. This life has evolved | through time producing vast numbers of species of plants and | animals, most of which are extinct. Although scientists debate | the mechanism that produced this change, the evidence for the | change is undeniable. ---------------------------------------------------------------- Geological Society of America Position Statement on Evolution (2001) http://rock.geosociety.org/docs/aboutus/position1.htm Excerpt: | The Geological Society of America recognizes that the | evolution of life stands as one of the central concepts of | modern science. Research in numerous fields of science during | the past two centuries has produced an increasingly detailed | picture of how life has evolved on Earth. ---------------------------------------------------------------- Botanical Society of America Statement on Evolution http://www.botany.org/newsite/announcements/evolution.php | Evolution represents one of the broadest, most inclusive | theories used in pursuit of and in teaching this knowledge, | but it is by no means the only theory involved. Scientific | theories are used in two ways: to explain what we know, and to | pursue new knowledge. Evolution explains observations of | shared characteristics (the result of common ancestry and | descent with modification) and adaptations (the result of | natural selection acting to maximize reproductive success), as | well as explaining pollen:ovule ratios, weeds, deceptive | pollination strategies, differences in sexual expression, | dioecy, and a myriad of other biological phenomena. Far from | being merely a speculative notion, as implied when someone | says, "evolution is just a theory," the core concepts of | evolution are well documented and well confirmed. Natural | selection has been repeatedly demonstrated in both field and | laboratory, and descent with modification is so well | documented that scientists are justified in saying that | evolution is true. ---------------------------------------------------------------- American Association of Physics Teachers Statement on the Teaching of Evolution and Cosmology http://www.aapt.org/Policy/evolutandcosmo.cfm Excerpt: | Evolution and cosmology represent two of the unifying concepts | of modern science. There are few scientific theories more | firmly supported by observations than these: Biological | evolution has occurred and new species have arisen over time, | life on Earth originated more than a billion years ago, and | most stars are at least several billion years old. | Overwhelming evidence comes from diverse sources - the | structure and function of DNA, geological analysis of rocks, | paleontological studies of fossils, telescopic observations of | distant stars and galaxies - and no serious scientist | questions these claims. ---------------------------------------------------------------- The Society of Systematic Biologists Support for the Teaching of Evolution and Scope of Systematic Biology (2001) http://systbiol.org/teachevolution.html Ecological Society of America Position Statement on Evolution (1999) http://www.esa.org/pao/esaPositions/Statements/Evolution.php Genetics Society of America Statement on Evolution and Creationism (2003) http://genetics.faseb.org/genetics/g-gsa/statement_on_evolution.shtml Society for the Study of Evolution Statement on Evolution http://www.evolutionsociety.org/statements.html American Institute of Biological Sciences AIBS Endorsed Statement on Evolution, Science, and Society: Evolutionary Biology and the National Research Agenda (1998) http://www.aibs.org/position-statements/980602_aibs_endorsed_st.html http://evonet.sdsc.edu/evoscisociety/ American Anthropological Association Statement on Evolution and Creationism (2000) http://www.aaanet.org/stmts/evolution.htm American Society of Naturalists Statement on Evolution and Education http://www.journals.uchicago.edu/ASN/evo.html American Geophysical Union Earth History and the Evolution of Life Must Be Taught: Creationism Is Not Science http://www.agu.org/sci_soc/policy/positions/evolution.shtml American Physical Society Statement On The Kansas State Board Of Education Decision (1999) http://www.aps.org/statements/99_5.cfm Society of Physics Students Statement on Evolution and Science Education (2003) http://www.spsnational.org/info/2003_sps_statement.htm American Chemical Society Statement on Teaching of Evolutionary Theory http://www.chemistry.org/portal/a/c/s/1/feature_pol.html?id= c373e904891eddda8f6a17245d830100 [link may be line-wrapped] American Astronomical Society Statement on the Teaching of Evolution http://www.aas.org/governance/council/resolutions.html#teach American Association for the Advancement of Science AAAS Board Resolution on Intelligent Design Theory http://www.aaas.org/news/releases/2002/1106id2.shtml National Association of Biology Teachers Statement on Teaching Evolution http://nabt.org/sub/position_statements/evolution.asp National Science Teachers Association Position Statement on the Teaching of Evolution http://www.nsta.org/positionstatement&psid=10 ---------------------------------------------------------------- American Society of Agronomy Crop Science Society of America Soil Science Society of America Position Statement by ASA, CSSA, and SSSA Executive Committees in Support of Teaching Evolution (8/11/2005) http://www.asa-cssa-sssa.org/pdf/intdesign_050815.pdf | Intelligent design is not a scientific discipline and should | not be taught as part of the K-12 science curriculum. | Intelligent design has neither the substantial research base, | nor the testable hypotheses as a scientific discipline. There | are at least 70 resolutions from a broad array of scientific | societies and institutions that are united on this matter. As | early as 2002, the Board of Directors of the American | Association for the Advancement of Science (AAAS) unanimously | passed a resolution critical of teaching intelligent design in | public schools. | | The intelligent design/creationist movement has adopted the | lamentable strategy of asking our science teachers to "teach | the controversy" in science curriculums, as if there were a | significant debate among biologists about whether evolution | underpins the abundant complexity of the biological world. We | believe there is no such controversy. | | The fundamental tenet of evolution descent with modification | is accepted by the vast majority of biologists. The current | debates within the research community deal with the patterns | and processes of evolution, not whether the evolutionary | principles presented by Darwin in 1859 hold true. These | debates are similar to those surrounding the relativistic | nature of gravitational waves. No one doubts the existence of | gravity just because we are still learning how it works; | evolution is on an equally strong footing. | | The discussion of lifes spirituality is most appropriate for | philosophy or religion classes. It is a mistake to conclude | that reluctance to incorporate spiritual questions in science | classes runs counter to the cherished principle that vigorous | challenge is vital to the scientific method. | | In all scientific fields, including evolutionary biology, | challenge has always been essential and welcomed. Scientific | challenge succeeds if it is methodical and findings are | verified to the satisfaction of the scientific community. This | has not happened with creationism either with or without its | new label intelligent design. President Bush, by suggesting | that we use intelligent design as a scientific counterpoint to | the teaching of evolutionary biology, is unwittingly | undermining the scientific method at its core. This is most | unfortunate in an era when U.S. students are already lagging | behind their international peers in science education. ================================================================ The Imminent Demise of Evolution: The Longest Running Falsehood in Creationism (2002) by Glenn R. Morton http://home.entouch.net/dmd/moreandmore.htm Understanding Evolution http://evolution.berkeley.edu/ Counterbalance Meta Library (views on science, ethics, philosophy, and religion) Evolution Section http://www.counterbalance.org/evolution/ Evolution, Science, and Society http://www.rci.rutgers.edu/~ecolevol/fulldoc.pdf Synthetic Theory of Evolution: An Introduction to Modern Evolutionary Concepts and Theories http://anthro.palomar.edu/synthetic/ == Professional scientific research concerning evolution: PLoS Biology (published by the Public Library of Science) http://biology.plosjournals.org/ PLoS Genetics (published by the Public Library of Science) http://genetics.plosjournals.org/ Science (published by the American Association for the Advancement of Science) http://www.sciencemag.org/ Nature http://www.nature.com/ Journal of Biology (published by BioMed Central) http://jbiol.com/ Journal of Evolutionary Biology http://www.blackwellpublishing.com/journal.asp?ref=1010-061X view online content: http://www.blackwell-synergy.com/rd.asp?code=JEB&goto=journal International Journal of Organic Evolution http://evol.allenpress.com/evolonline/?request=index-html#Evolution_Journal [link may be line-wrapped] Molecular Biology and Evolution (published by the Society for Molecular Biology and Evolution) http://www.mbe.oupjournals.org Evolution & Development http://www.blackwellpublishing.com/journal.asp?ref=1520-541X Trends in Ecology & Evolution http://www.elsevier.com/wps/find/journaldescription.cws_home/30339/description [link may be line-wrapped] Trends in Genetics http://www.elsevier.com/wps/find/journaldescription.cws_home/405918/description [link may be line-wrapped] Integrative and Comparative Biology (Journal of the Society for Integrative and Comparative Biology; published as the American Zoologist from 1961 to 2001) http://www.sicb.org/az/ Invertebrate Biology (Journal of the American Microscopical Society) http://www.invertebratebiology.org/ Proceedings of the National Academy of Sciences (PNAS) Biological Sciences http://www.pnas.org/current.shtml#BIOLOGICAL_SCIENCES Palobiology Journal of Paleontology (both published by The Paleontological Society) http://www.psjournals.org/paleoonline/?request=get-archive The Journal of Vertebrate Paleontology (published by the Society of Vertebrate Paleontology) http://www.vertpaleo.org/jvp/ Paleontologia Electronica http://palaeo-electronica.org/ Cladistics The International Journal of the Willi Hennig Society http://www.blackwellpublishing.com/journal.asp?ref=0748-3007 Evolution International Journal of Organic Evolution http://evol.allenpress.com/evolonline/?request=get-archive Biological Journal of the Linnean Society http://www.blackwellpublishing.com/journal.asp?ref=0024-4066 Zoological Journal of the Linnean Society http://www.blackwellpublishing.com/journal.asp?ref=0024-4082 Botanical Journal of the Linnean Society http://www.blackwellpublishing.com/journal.asp?ref=0024-4074 Evolutionary Ecology (published in the Netherlands) http://www.springer.com/west/home/life+sci?SGWID=4-10027-70-35681186-0 [link may be line-wrapped] Genetics http://www.genetics.org/ Molecular Phylogenetics and Evolution http://www.elsevier.com/wps/find/journaldescription.cws_home/622921/description [link may be line-wrapped] Proceedings of the Royal Society: Biological Sciences http://www.pubs.royalsoc.ac.uk/index.cfm?page=1087 Journal of Zoological Systematics and Evolutionary Research http://www.blackwellpublishing.com/journal.asp?ref=0947-5745 == Prum, R.O. (2005) The evolution of feather diversity and function: Exaptation, functional redundancy and historical contingency. In: Briggs, D.E.G. (ed.) Evolving Form and Function: Fossils and Development. p.245-256. ABSTRACT: "Because of the lack of primitive feather morphologies, for most of the last 150 years, studies of feather evolution had to extrapolate backwards from modern feathers to their unknown morphological antecedents. Most traditional studies adopted functional hypotheses for the evolution of feathers and then hypothesized series of logical functional intermediates. The most popular functional hypothesis was that feathers evolved for flight, but many others were also proposed. During most of the 20th century, research on feather evolution did not focus on development, resulting in many evolutionary theories that were developmentally implausible. The developmental theory of the evolution of feathers hypothesized that feathers evolved through a series of developmental novelties and that stages could be reconstructed from the hierarchical relationships among events in feather development. Since 1998, fossil discoveries from the early Cretaceous Yixian Formation of Liaoning, China, confirm key predictions of the developmental theory, including the hypotheses that that plumulaceous feathers are primitive to pennaceous feathers, and that feathers evolved in a terrestrial context before the evolution of flight. The phylogenetic distribution of fossil feathers in theropods confirms that complex, pennaceous feathers, having evolved for other reasons, were co-opted for use in flight. Thus, feathers are a premier example of exaptation: the evolution of a derived function for a plesiomorphic structure. Feather evolution may have involved periods when a diversity of functionally redundant structures was maintained before the origin of subsequent novelties. Thus, episodes of weak selection on feather variants were likely important in fostering evolutionary exploration of the potential feather morphospace that later gave rise to subsequent novelties." == In the last 10 years, more than 350 new animal and plant species have been discovered on Borneo. == http://www.don-lindsay-archive.org/creation/fossil_series.html fossil record === A savvy handicapper would never have put money on the continued existence of this evolutionary dark horse. Nearly hairless, weak--no sharp claws or slicing teeth here--and slow, with a bumpy bipedal gait, humans might initially appear to be one of the unlikeliest survivors on earth. Except for the oversize brains. As the articles in this special edition collectively underscore, so much of the rise of our ancestors from humble beginnings to today's world-dominant swell of humanity tracked the stunning growth of all that furrowed cortex. From roughly two million years to 250,000 years ago, the brain's total volume expanded by a tablespoonful every 100,000 years, estimates Harvard University biologist E. O. Wilson. If we could stretch a modern person's cortex flat, it would occupy an area the size of four sheets of standard letter-size paper. In contrast, a chimp's would cover one sheet; a monkey's, a postcard; and a rat's, a stamp. . . . == The oldest-known spider web with prey still entrapped has been found preserved in a chunk of amber in Spain. The mesh of silk strands - snaring the remains of a fly, beetle, mite and wasp - dates back 110 million years to the time of the dinosaurs. == Use It or Lose It One of the things I enjoy about studying evolution is that it allows us to make powerful predictions about the natural world. This is because evolution often follows predictable paths. Today I want to talk about one of the most predictable phenomena of all: the evolution of loss or, as it was once called, degeneration. I'll start, as I often do, with a question. Why do so many of the animals that live in the deep sea have eyes? At first, this seems extremely odd. The sun doesn't shine in the vasty deep - it's an ocean of blackness. Animals that live in dark caves, be they millipedes, beetles or fish, reliably lose their eyes and their colors. Why doesn't this happen in the sea? Why do I ask? Well, here is a general law of nature: When organisms no longer use something they have - whether we're talking eyes, brilliant colors, wings or even genes for making energy from sunlight - that something rapidly evolves to become lost. As I mentioned yesterday, birds living on remote islands routinely lose the power of flight. Fruit flies that evolve to be asexual - reproducing by laying eggs that don't need to be fertilized - fast lose the ability to respond to male advances. The soil bacterium Myxococcus xanthus normally has (for a bacterium) an elaborate social life; bacteria hunt together and cooperate to build spores. But if you keep the bacteria in bottles of liquid, you can put an end to their social lives by continually shaking the bottles and interrupting their social discourse. After generations of such treatment, the bacteria evolve antisociality: they just can't work together anymore. And - this is especially striking - full-time parasites lose most of their bodies. They also lose many of their genes. Microsporidians, which are strange single-celled fungi that are parasites of animals, have lost their mitochondria. (Mitochondria are what cells use to make energy from sugar.) Animals that become parasites can even lose their brains. This is how one early evolutionary biologist, Edwin Ray Lankester, put it in 1880: Any new set of conditions occurring to an animal which render its food and safety very easily attained, seem to lead as a rule to Degeneration. . Let the parasitic life once be secured, and away go legs, jaws, eyes, and ears; the active, highly-gifted crab, insect, or annelid may become a mere sac, absorbing nourishment and laying eggs. There are two roads to loss. The first is via something known as "relaxed selection." The idea is simple: If a given trait - say, fin color - no longer affects how well you can survive or reproduce, mutations accumulate in the genes for fin color, thus destroying the ability of those genes to work. Relaxed selection is easy to show in a laboratory. Suppose you have a vial full of fruit flies. You assign a mate to each fly at random - thus rendering irrelevant the ability to seduce - and then choose two offspring from each pair to put into the next generation. This way everyone has the same number of surviving children (which means, as you may recall from one of my earlier columns, that natural selection cannot operate). Furthermore, you give everybody a life of luxury and ease, so finding food isn't a problem. After repeating this for some number of generations, you make life difficult again, and see what happens. One such experiment showed that after just 30 generations, a fly's ability to survive in difficult conditions had dropped sharply. If selection is relaxed in this fashion for a long time, the rate of degeneration may start to accelerate. This is because stopping mutations from happening is itself something that usually falls under natural selection. If there is no penalty for having more mutations, more mutations will start to happen. The second road to loss is when natural selection actively drives it. This is called selected loss. Then, it's not simply that eyes (or whatever) no longer help you; they actually get in your way. For instance, for many parasites, there is a premium on being able to reproduce quickly. This means that losing genes you don't need anymore is actually an advantage because you can copy your genome faster if it is smaller. Or, consider flight in birds. Birds typically live longer than mammals of the same size, in part because they can escape from predators more easily. However, flight can take a lot of energy, and it keeps you small. Thus, if there aren't any predators - as on remote islands - flightlessness quickly evolves. (Whether wings then start to disappear depends on whether they are still useful. Ostriches, for example, don't fly but use their big wings in sexual displays, and in fights. I once saw a pair of fighting male ostriches - they really let fly.) Telling the difference between relaxed selection and selected loss isn't straightforward, especially outside the laboratory. But whichever force predominates, the bottom line is clear. Traits that are not actively maintained by natural selection rapidly disappear. Which brings me back to the question about eyes in the deep sea. The corollary of the argument I've outlined above is that if you see that an organism is devoting a lot of energy to keeping a structure, it is likely to be using it. This suggests that there is more light in the deep sea than we might suspect. And indeed, there is. One source of light is other animals. Many animals of the deep sea make light, either to attract mates, or to lure prey, or to escape from danger. Whereas squid that live at the surface shoot jets of ink to confuse the enemy, squid that live in the deep sea shoot jets of light. More amazing still, some light glows from the deep sea vents, where fountains of super-hot water blast through the earth's crust. Exactly what causes the light isn't completely understood, though it's not due only to heat. The fact it is there surely explains why some of the shrimp that make the deep-sea vents their home do have eyes. And here's something extraordinary: At least one species of bacteria seems to use this light to photosynthesize - the only example so far known of an organism harvesting light from a source other than the sun. == Scientists crack rabies virus' armour Scientists from the European Molecular Biology Laboratory have cracked the protection shield used by the rabies virus to protect itself from the body's immune system. The discovery represents a new potential avenue of attack for drugs against rabies and similar diseases such as Ebola and measles. Although their symptoms are very different, Ebola, measles and rabies all belong to a class of viruses which carry their genetic information on a single RNA (ribonucleic acid) molecule. In contrast, most other living organisms keep their genetic information on double-stranded DNA (deoxyribonucleic acid). The rabies virus spreads by breaking into human cells, and effectively hijacking the cell's own machinery to produce more copies of the virus, which then go on to infect more of the host's cells. Key to the success of this operation is a viral protein called a nucleoprotein, which wraps itself around the rabies virus' RNA like a protection shield. Without the shield, the virus' RNA would quickly be destroyed by the enzymes of the host's immune system. Researchers from the EMBL and the Institute of Molecular and Structural Virology (IVMS) in Grenoble used high-intensity X-rays to examine crystals of nucleoprotein bound to RNA. From this they were able to produce a striking high resolution image of the protein. The image shows that the nucleoprotein has two domains which clasp around the RNA strand like a clamp. Many nucleoproteins bind side-by-side along the whole length of the RNA molecule, protecting it from attack by the host's immune system. However, whilst enclosed in this armour, the virus is also unable to access the host's machinery, which it needs to replicate itself. The picture of the protein suggests that the part of the protein connecting the two domains could act like a hinge. When the time for replication has come, a certain signal causes the hinge to open up. 'This dynamic mechanism makes nucleoproteins an excellent drug target,' said Rob Ruigrok, Head of the IVMS. 'Small agents that bind to the protein in such a way to block its flexibility and keep it in the closed state, would prevent replication of the virus and would stop it from spreading.' The discovery has implications for the treatment of other viruses which use similar protection systems, including Ebola, measles and Borna virus. == Mega-crater linked to mass extinction before dinosaurs Scientists say they have found the Earths biggest known crater, and have linked it to the planets worst mass extinction. If they are right, the crater comes from to a meteor impact far more violent than one thought to have killed off the dinosaurs later. A combined image of gravity fluctuations and airborne radar in the Wilkes Land region of East Antarctica . The edges of the crater are colored red and blue; a concentration of mantle material is colored orange (center). Image courtesy of Ohio State University. The researchers reported finding the crater, 300 miles (482 km) wide, hidden beneath East Antarctic ice. They said it may date back some 250 million years to the so-called Permian-Triassic extinction, when almost all animals died out. The event is thought to have cleared the way for the dinosaurs rise. The crater is more than twice the size of the Yucatan peninsulas Chicxulub crater, tied to an impact that may have killed off the great reptiles 65 million years ago. The bigger crater is estimated to be the result of a striking object some 30 miles (48 km) wide, compared to 6 miles (10 km) for the Chicxulub case. Ralph von Frese and Laramie Potts of Ohio State University led a scientific team that identified the crater in East Antarcticas Wilkes Land region, south of Australia. They reported the finding at the American Geophysical Union Joint Assembly meeting in Baltimore, Md. late last month. They used NASA satellites to peer beneath Antarctic ice based on gravity measurements. The study found a huge plug of material from the Earths mantle, the layer of Earth between the crust and the core, which had risen up into the crust, in a formation about 200 miles (322 km) wide. Such formations, called mass concentrations or mascons, are planetary equivalents of bumps on the head. They form when large objects hit, and the denser mantle bounces up into the crust above. The scientists overlaid an image resulting from gravity measurements with airborne radar images of the ground beneath the ice. They found the mascon was centered in a circular ridge some 300 miles wide, enclosing a space larger than Ohio. The ridge alone wouldnt prove anything. But the addition of the mascon signaled impact to von Frese, who has studied moon craters for years. Such signals are open to interpretation, he admitted. But we compared two completely different data sets taken under different conditions, and they matched. To date the impact, the scientists took a hint from the fact that the mascon is still visible. The Earths active geology normally scrubs away such formations eventually. Based on the regions known geologic history, this Wilkes Land mascon formed recently by geologic standardsprobably about 250 million years ago, von Frese said. In another half-billion years, it will probably vanish, he added. Its immediate effects would have devastated life, he said. All the environmental changes that would have resulted from the impact would have created a highly caustic environment that was really hard to endure, he said. == Deer were introduced to the Shetlands which quickly evolved into a dwarf species of deer.And on Flores in Indonesia, there used to be a miniature elephant hardly bigger than a St. Bernard dog. == Masked variation means is that there is genetic variation within the population, but perhaps due to the adaptation to a fairly stable environment, the genetic variation is essentially hidden at the morphological level through the existence of different alleles at different loci, or what is more likely, through a process of canalization, where, due the existence of largely redundant genetic networks, such hidden (or alternatively, "masked" or "cryptic") remains invisible so long as the environment remains stable. Genetic variations can then build up without necessarily resulting in visible differences in terms of how this genes are expressed at the level of the organism where it interacts with its environment. When such genetic variations build up within a population, they result in a form of "evolutionary capacitance" (i.e., a capacity to evolve), which may then be discharged (or "decanalized") when the environment changes quickly. Moreover, when the environment results in such changes in allele frequencies at a given loci, given the linkages which exist at different loci, one can expect additional alleles at different loci to be selected for. == At a molecular level, a large part of what would seem to be going on involves the promoter regions of genes. Essentially, the upstream promoters (as opposed to the basal promoters) will take input in the form of proteins called transcription factors, then determine how much of a given protein the gene (or oftentimes genes) which they are associated with will produce. This is ability to vary the amount of the protein which is produced is important -- since a given protein may be used in varying amounts in different tissues. But it is also important during an organism's development, and likewise, ability to respond to different environments, or, at the level of the population, to respond to differences in how alleles are combined. But when the environment changes to an environment which then remains stable, earlier plasticity of gene _expression may be lost, and new plasticity of gene _expression may develop as a result of mutations to the promoter region itself. And as I have mentioned before, even if the only mutations which occured were point mutations, for smaller promoter regions, only a few point mutations would be required to radically change its behavior. But larger mutations will occur. In fact, we know of at least one example where a gene became duplicated, the duplicate lost functionality as a gene coding protein, but then became a new promoter region for the original gene. == 100,000 year-old DNA sequence allows new look at Neandertal's genetic diversity By recovering and sequencing intact DNA from an especially ancient Neandertal specimen, researchers have found evidence suggesting that the genetic diversity among Neandertals was higher than previously thought. The findings also suggest that genetic diversity may have been higher in earlier Neandertal periods relative to later periods that approached the arrival of humans in Europe. == "Although analysis of genome rearrangements was pioneered by Dobzhansky and Sturtevant 65 years ago, we still know very little about the rearrangement events that produced the existing varieties of genomic architectures. The genomic sequences of human and mouse provide evidence for a larger number of rearrangements than previously thought and shed some light on previously unknown features of mammalian evolution. In particular, they reveal that a large number of microrearrangements is required to explain the differences in draft human and mouse sequences. Here we describe a new algorithm for constructing synteny blocks, study arrangements of synteny blocks in human and mouse, derive a most parsimonious humanmouse rearrangement scenario, and provide evidence that intrachromosomal rearrangements are more frequent than interchromosomal rearrangements. Our analysis is based on the humanmouse breakpoint graph, which reveals related breakpoints and allows one to find a most parsimonious scenario. Because these graphs provide important insights into rearrangement scenarios, we introduce a new visualization tool that allows one to view breakpoint graphs superimposed with genomic dot-plots. " Genome Rearrangements in Mammalian Evolution: Lessons From Human and Mouse Genomes Pavel Pevzner and Glenn Tesler Genome Research Vol 13, Issue 1, 37-45, January 2003 http://www.genome.org/cgi/content/abstract/13/1/37 "Naturally occurring DNA sequences can form noncanonical structures such as H-DNA, which are abundant and regulate the expression of several disease-linked genes. Here, we show that H-DNA-forming sequences are intrinsically mutagenic in mammalian cells. This finding suggests that DNA is a causative factor in mutagenesis and not just the end product. By using the endogenous H-DNA-forming sequence found in the human c-myc promoter, mutation frequencies in a reporter gene were increased 20-fold over background in COS-7 cells. H-DNA-induced double-strand breaks (DSBs) were detected near the H-DNA locus. The structures of the mutants revealed microhomologies at the breakpoints, consistent with a nonhomologous end-joining repair of the DSBs. These results implicate H-DNA-induced DSBs in c-myc gene translocations indiseases such as Burkitt's lymphoma and t(12;15) BALB/c plasmacytomas, where most breakpoints are found near the H-DNA-forming site. Thus, our findings suggest that H-DNA is a source of genetic instability resulting from DSBs and demonstrate that naturally occurring DNA sequences are mutagenic in mammals, perhaps contributing to genetic evolution and disease. " Naturally occurring H-DNA-forming sequences are mutagenic in mammalian cells Guliang Wang, and Karen M. Vasquez Published online before print September 1, 2004, 10.1073/pnas.0405116101 PNAS | September 14, 2004 | vol. 101 | no. 37 | 13448-13453 http://www.pnas.org/cgi/content/abstract/101/37/13448 "Using paired-end sequences from bacterial artificial chromosomes, we have constructed high-resolution synteny and rearrangement breakpoint maps among human, mouse, and rat genomes. Among the >300 syntenic blocks identified are segments of over 40 Mb without any detected interspecies rearrangements, as well as regions with frequently broken synteny and extensive rearrangements. As closely related species, mouse and rat share the majority of the breakpoints and often have the same types of rearrangements when compared with the human genome. However, the breakpoints not shared between them indicate that mouse rearrangements are more often interchromosomal, whereas intrachromosomal rearrangements are more prominent in rat. Centromeres may have played a significant role in reorganizing a number of chromosomes in all three species. The comparison of the three species indicates that genome rearrangements follow a path that accommodates adelicate balance between maintaining a basic structure underlying all mammalian species and permitting variations that are necessary for speciation." Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation Shaying Zhao, Jyoti Shetty, Lihua Hou, Arthur Delcher, Baoli Zhu, Kazutoyo Osoegawa, Pieter de Jong, William C. Nierman, Robert L. Strausberg and Claire M. Fraser Genome Research 14:1851-1860, 2004 http://www.genome.org/cgi/content/full/14/10a/1851 == There is a phenomenon known as "ring species." This occurs when a single species becomes geographically distributed in a circular pattern over a large area. Immediately adjacent or neighboring populations of the species vary slightly but can interbreed. But at the extremes of the distribution -- the opposite ends of the pattern that link to form a circle -- natural variation has produced so much difference between the populations that they function as though they were two separate, non-interbreeding species. A well-studied example of a ring species is the salamander Ensatina escholtzii of the Pacific Coast region of the United States. In Southern California, naturalists have found what look like two distinct species scrabbling across the ground. One is marked with strong, dark blotches in a cryptic pattern that camouflages it well. The other is more uniform and brighter, with bright yellow eyes, apparently in mimicry of the deadly poisonous western newt. These two populations coexist in some areas but do not interbreed -- and evidently cannot do so. Moving up the state, the two populations are divided geographically, with the dark, cryptic form occupying the inland mountains and the conspicuous mimic living along the coast. Still farther to the north, in northern California and Oregon, the two populations merge, and only one form is found. In this area, it is clear that what looked like two separate species in the south are in fact a single species with several interbreeding subspecies, joined together in one continuous ring. The evolutionary story that scientists have deciphered begins in the north, where the single form is found. This is probably the ancestral population. As it expanded south, the population became split by the San Joaquin Valley in central California, forming two different groups. In the Sierra Nevada the salamanders evolved their cryptic coloration. Along the coast they gradually became brighter and brighter. The division was not absolute: some members of the sub-populations still find each other and interbreed to produce hybrids. The hybrids look healthy and vigorous, but they are neither well-camouflaged nor good mimics, so they are vulnerable to predators. They also seem to have difficulty finding mates, so the hybrids do not reproduce successfully. These two factors keep the two forms from merging, even though they can interbreed. By the time the salamanders reached the southernmost part of California, the separation had caused the two groups to evolve enough differences that they had become reproductively isolated. In some areas the two populations coexist, closing the "ring," but do not interbreed. They are as distinct as though they were two separate species. Yet the entire complex of populations belongs to a single taxonomic species, Ensatina escholtzii. Ring species, says biologist David Wake, who has studied Ensatina for more than 20 years, are a beautiful example of species formation in action. "All of the intermediate steps, normally missing, have been preserved, and that is what makes it so fascinating." Link: http://www.pbs.org/wgbh/evolution/library/05/2/l_052_05.html == The Kipunji monkey is brown, with a long, erect crest of hair on its head, elongated cheek whiskers, an off-white belly and tail, and an unusual call, termed a honk-bark by the scientists who first described it. It stands about 3 feet tall. The monkeys live as high as 8,000 feet where temperatures frequently drop below freezing. So, its long coat probably evolved to protect against the cold. DNA work published in a recent Wildlife Conservation Society (WCS) study revealed that the species is truly unique, marking the first new genus for a living monkey species since a swamp monkey discovery in 1923. The new genus, Rungwecebus, (pronounced rung-way-CEE-bus) refers to Mt. Rungwe, where the monkey was first observed. Only 500 remain in the wild because their habitat is the Highlands region of Tanzania that is illegally logged and hunted. WCS's director, John Robinson, Ph.D., said, "It would be the ultimate irony to lose a species this unique so soon after we have discovered it." For further information, see: www.kipunji.org == Cystic fibrosis is the most common single gene disorder in white Caucasians. == French scientists who explored the Coral Sea reported today they have discovered at 1,312 feet underwater a crustacean that was thought to have become extinct 60 million years ago. The location is the Chesterfield Islands, northwest of New Caledonia. The nearly 5-inch long "living fossil," named Neoglyphea neocaledonica, has huge dark eyes and is compared to "halfway between a shrimp and a mud lobster." == Jeffrey H. Schwartz "The Human Fossil Record" (four volumes), 2002-05; "Sudden Origins: Fossils, Genes and the Emergence of Species" (1999); "The Red Ape" (1987, updated 2005), == What Use is Half a Wing in Evolution of Birds? Biologists have long argued about how birds evolved the ability to fly, because it is not immediately evident what improvement in fitness would result from ancestral, partly evolved wings. Two theories have recently dominated the debate: one postulates that flight evolved in tree-dwelling ancestors that used their forelimbs to help them glide, while the other considers ancestral birds to be terrestrial dinosaurs that developed powered flight from the ground up. An article by Kenneth P. Dial and two co-authors in the May 2006 issue of BioScience summarizes experimental evidence indicating that ancestral protobirds incapable of flight could have used their protowings to improve hindlimb traction and thus better navigate steep slopes and obstructions. By using their protowings in this way, they would presumably have had an advantage when pursuing prey and escaping from predators. Dial and colleagues performed experiments on several species of juvenile galliform (chicken-like) birds, concentrating on chukar partridges. Chukars can run 12 hours after hatching, but they cannot fly until they are about a week old. Even before they are able to fly, however, the birds flap their developing wings in a characteristic way while running, which improves their ability to climb steep slopes and even vertical surfaces. Dial and colleagues have named this form of locomotion "wing-assisted Iincline running" (WAIR). After they are able to fly, chukars often use WAIR in preference to flying to gain elevated terrain, and exhausted birds always resort to WAIR. Dial and colleagues describe experiments showing that if the surface area of chukar wings is reduced by plucking or trimming the feathers, WAIR becomes less effective for climbing slopes. Dial and colleagues propose that incipiently feathered forelimbs of bipedal protobirds may have provided the same advantages for incline running as have now been demonstrated in living juvenile birds. Their work thus supports a new theory about the evolution of flight in birds. WAIR, which the authors believe to be widespread in birds, appears to offer an answer to the question first posed by St. George Jackson Mivart in 1871: "What use is half a wing?" == The development of characteristics is not like conscious selective breeding for a particular trait. A mutation is either advantageous, neutral, or inimical. Inimical traits usually are short-lived within a population. An early death usually prevents an unfavorable characteristic from being passed on. Neutral mutations can hang on forever, and advantageous mutations wind up giving some survival advantage, and can become dominant within a population. But no mutation, even an advantageous one, comes into being to meet a need. Mutation is still a random process. == Monroe W. Strickberger's "Evolution" (3rd edition). == Part of our fascination for fish comes from their amazing diversity, brought about by the need to survive and adapt in a huge range of environments. The ability to breathe air is one such adaptation, which has allowed a vast array of fish to survive and thrive in habitats that would simply not support other species. Many commonly-kept aquarium species have this ability, and so it is of interest to look at the biology of air-breathing. Evolution of Air Breathing Air breathing has evolved in a large number of different fish species, thanks primarily to the limited abundance of oxygen in water. Compared to air, water may hold from 35 to 42 times less oxygen, and in addition it is far more energy consuming to extract it from water. This is because of the high viscosity and density of water when compared to air, making it harder to pass it across the gills. For this reason, oxygen has a far greater influence on the lives of fish than terrestrial animals. Because of the limitations on oxygen availability in water, there is a very real danger that levels may become dangerously low, or even life-threatening. Where such conditions occur regularly, fish have had the opportunity to evolve to cope with them. Whilst not all have developed the ability to breathe air (for example, Carp have instead evolved the physiology to withstand short. periods of very low oxygen), many have gone down this route. The most common environment in which air breathing has evolved (in freshwater species), is in tropical swamps and pools that either experience seasonal or daily periods of low oxygen. Many tropical waters are subject to seasonal drying, which concentrates large numbers of fish in a small volume of water. This increases the oxygen demand substantially, and in addition the resulting smaller volume of water tends to heat up quickly, further depressing oxygen levels. Other swamps and pools may be subject to nightly drops in oxygen levels, due to the abundance of aquatic vegetation and algae. Of the vast majority of freshwater species, routine falls in oxygen levels seem to be the primary force that has driven the evolution of air-breathing. Types of Air-Breathing Because air-breathing has evolved in so many families of fish (49, 32 of which are freshwater), there are not surprisingly a number of variations on the theme. Air-breathing can be broken down into two main categories: 'amphibious' and 'aquatic'. Amphibious air-breathing is that carried out by fish on land, such as Mudskippers. Although the occurrence of amphibious air-breathing in true freshwater fish is limited, there are examples such as the African Lungfish (during aestivation), and Clarias catfish during their overland migrations to find new habitats. However, the latter two only indulge in this type of air-breathing when forced, and do not voluntarily exit the water as part of their routine behaviour. More common in freshwater fish is aquatic air-breathing, i.e. the taking of atmospheric air while the fish is in the water, usually by gulping it at the surface. Aquatic air-breathing can further be subdivided into 'facultative' and 'obligatory'. Facultative air breathers, such as Bristle-nosed Plecs, only breathe air when they need to, in response to falling oxygen levels. Continuous air-breathers generally breathe air all the time, although the regularity of it varies. Continuous air breathers may be 'obligatory', i.e. must have access to atmospheric air to survive (such as Trichogaster trichopterus), or 'non-obligatory', i.e. can survive if denied access (such as Corydoras spp). Air Breathing Organs Very few air-breathing fish use their gills to extract air from the atmosphere, and indeed having a large gill area can impede survival on land, or in heavily de-oxygenated water. This is because as well as diffusing in through the gills, oxygen may also diffuse out of them. In fish that inhabit very poorly oxygenated water, this would be a distinct disadvantage, as much of the oxygen in their blood may be lost. Depending on the extent to which they rely on air-breathing, many such fish have lost much of the gill area, to reduce this problem. In such species, the excretion of ammonia may also be affected, with a greater proportion of it being converted to urea. This is particularly well developed in those fish that spend time out of the water, where ammonia excretion would be impossible. To prevent levels building up and becoming toxic, they convert it to relatively harmless urea which can be stored for excretion later on. Air breathing organs (ABOs) are varied in their structure and position. Wherever they are, they usually consist of a highly vascularised 'respiratory epithelium', which is specially developed for the absorption of oxygen from air. The most primitive forms of ABO include the lungs of Lungfish and Bichirs, and modified gas bladders, as seen in Garfish and Butterfly Fish. Other species have modified areas of the stomach, intestine, buccal and pharyngeal cavities, or even specific organs such as the 'labyrinth' in Gouramis, and the 'arborescent' organ in Walking Catfish. Popular Air Breathers There are a number of popular and well known ornamental species that breathe air, including the following: Lungfish: Although not commonly kept, Lungfish are very well known in the aquarium hobby. They are probably the best known air-breathing fish, having lungs specially evolved for the purpose. Of the Lungfishes, the African (Protopterus spp) and South American (Lepidosiren paradoxa) species are the most reliant on air-breathing, and must do so to survive. Their ability to breathe air is so well developed that they can survive in cocoons during the dry season for years at a time (in a state called 'aestivation'). The Australian Lungfish (Neoceratodus forsteri) is not so reliant on air-breathing, having only one lung and being a facultative air-breather. Bichirs: Representatives of the African Bichirs are kept in captivity, and make fascinating pets when cared for properly. They, like the Lungfish, use lungs to breathe air, and are the only known air breathing fish to practice 'recoil aspiration'. This involves the use of the muscles surrounding the lung to contract it, forcing used air out. As the muscles relax, new air is drawn in through the spiracles to the lungs. Many scientists believe that recoil aspiration formed the basis for the evolution of breathing in humans. Notopteridae: This family of fish includes the popular African Knife Fish, Xenomystus nigri, and the Clown Knife Fish, Notopterus chitala. They are both continuous air-breathers, and use their gas bladders as an ABO. Scientific studies have shown their ability to withstand anoxic water (no oxygen) for long periods. Under normal conditions, Clown Knife Fish will take air every 6 to 8 minutes. The Butterfly Fish: Pantodon bucholzi occurs in small pools, ditches, and backwaters in Africa, and is often seen for sale in aquatics outlets. An obligatory air breather, it must be given access to a warm layer of air above the tank. It uses its gas bladder as an ABO, and it relies heavily on air- breathing to meet its oxygen demand. Weather Loach: Fish of the genus Misgurnus have a modified portion of the intestine that they use for extracting oxygen from air. As new air is gulped in, old air is forced out of the vent, giving the impression that they have 'wind'. They are obligatory air-breathers, and as such must be given access to air. Interestingly, they are one of the few freshwater air-breathers that don't come from tropical regions. Callichthyidae: This family of armoured catfish includes the popular Corydoras and Hoplosternum catfish. In species studied, up to 80% of the intestine may be modified for air-breathing, in a similar manner to the Weather loach. It appears that Corydoras aeneus (and therefore possibly other Corydoras) are facultative air-breathers, whereas Hoplosternum littorale is obligatory. A shoal of Corydoras will often come to the surface in quick succession to take air, in a behaviour known as 'synchronous air-breathing'. This is seen in many other air-breathers, and is designed to minimise the chance of predation during risky migrations to the surface. Loricariidae: While not all Plecostomus breathe air, a number of commonly kept ones certainly do. Both Ancistrus and Hypostomus have been shown to take air, using their stomachs as ABOs. Old air is exhaled via the gill chambers, before new air is gulped in. Around 20 species have been shown to breathe air, and they all appear to be facultative, only doing so when necessary. Anabantoidei: Also called 'labyrinth' fish, this group of fishes are renowned for their air breathing abilities, and include popular species such as Trichogaster trichopterus, Colisa spp, Betta splendens, Ctenopoma spp, and so on. The labyrinth organ is a specially modified structure, situated to the rear of, and just above the gills. The labyrinth is an intricate, bony structure, covered in a respiratory epithelium. It can be sealed off from the rest of the mouth, allowing normal feeding to carry on while oxygen is extracted from the air within it. All labyrinth fish are continuous airbreathers, and most are obligatory , making the provision of a warm layer of air essential. Air-breathing is just one of the many fascinating aspects of fish behaviour that can be observed in an aquarium, and which make fish such remarkable animals. Further reading: Air Breathing Fishes, Evolution, Diversity, and Adaptation. J. B. Graham, 1997. Published by Academic Press. == Many species of snakes and legless lizards (such as the "slow worm") initially develop limb buds in their embryonic development, only to reabsorb them before hatching. Similarly, modern cetaceans (adult whales, dolphins, and porpoises) have no hind legs. Even so, hind legs, complete with various developing leg bones, nerves, and blood vessels, temporarily appear in the cetacean fetus and subsequently degenerate before birth. Evolution has an answer to why these embryonic legs exist: snakes, legless lizards and cetaceans all evolved from organisms that had legs. Why would a "designer" give embryos legs and leg buds only to have those things disappear before the organism is born? == Scientists uncover new clues to limb formation (and loss) in some sea mammals Researchers from the Northeastern Ohio Universities College of Medicine have revealed the genetic basis behind one of the best-documented examples of evolutionary change in the fossil record: how whales lost their hind limbs. Writing in this week's Proceedings of the National Academy of Sciences (PNAS), Hans Thewissen and his colleagues report that ancient whales--four-footed land animals not unlike large modern dogs--evolved into graceful, streamlined swimmers through a series of small genetic changes during the whales' embryonic development. "Their research has implications for how evolution acts to create dramatic changes in an organism's body," said Richard Lane, program director in the National Science Foundation (NSF)'s Division of Earth Sciences, which funded the research. "The findings emphasize the synergistic role traditional paleontology and evolutionary and developmental biology play at the frontiers of the evolutionary sciences," said Lane. Thewissen and his colleagues began by exploring the embryonic development of whales' cousins, the dolphins. These creatures are intriguing because for a brief time during development they do sprout hind limbs, which quickly vanish again as the embryos reach the second month in a gestation period that lasts about 12 months. Why? In most mammals, explains Thewissen, "a series of genes is at work at different times, delicately interacting to form a limb with muscles, bones, and skin. The genes are similar to the runners in a complex relay race, where a new runner cannot start without receiving a sign from a previous runner." In dolphins, however, at least one of the genes drops out early in the race, disrupting the genes that were about to follow it. That causes the entire relay to collapse, ultimately leading to the regression of the animals' hind limbs. By analyzing dolphin embryos, Thewissen showed that the dropout is a gene called "Sonic Hedgehog," which is important at several stages of limb formation. "That's why dolphins lose their 'legs,'" he says. In whales, however, the story is more complex. Between 41 million and 50 million years ago, whales' hind limbs did shrink greatly as the former land animals began a return to the sea. But their legs showed no change in the basic arrangement and number of bones, which proved that Sonic Hedgehog was still functioning. Its loss must have come later. In short, "the dramatic loss of Sonic Hedgehog expression was not the genetic change that drove hind limb loss in whales," Lane said. Instead, Thewissen and his colleagues conclude, whales' hind limbs regressed over millions of years via "Darwinian microevolution": a step-by-step process occurring through small changes in a number of genes relatively late in development. == Source:http://www.boston.com/news/science/articles/2006/05/18/humans_chimps_ may_have_bred_after_split/ Humans, chimps may have bred after split Boston scientists released a provocative report yesterday that challengesthe timeline of human evolution and suggests that human ancestors bred with chimpanzee ancestors long after they had initially separated into two species. The researchers, working at the Cambridge-based Broad Institute ofHarvard and MIT, used a wealth of newly available genetic data toestimate the time when the first human ancestors split from the chimpanzees. The team arrived at an answer that is at least 1 millionyears later than paleontologists had believed, based on fossils of early,humanlike creatures. The lead scientist said that this jarring conflict with the fossil record, combined with a number of other strange genetic patterns the teamuncovered, led him to a startling explanation: that human ancestors evolved apart from the chimpanzees for hundreds of thousands of years,and then started breeding with them again before a final break. ''Something very unusual happened," said David Reich, one of thereport's authors and a geneticist at the Broad and Harvard MedicalSchool. The suggestion of interbreeding was met with skepticism bypaleontologists, who said they had trouble imagining a successful breeding between early human ancestors, which walked upright, and the chimpanzee ancestors, which walked on all fours. But other scientists said the work is impressive and will probably force a reappraisal of thestory of human origins. And one leading paleontologist said he welcomed the research as a sign that new genetic information will yield more clues to our deep history than once thought. ''I find this terrifically exciting and important work," said DavidPilbeam, a Harvard paleontologist who was not part of the Broadteam. Pilbeam helped discover an early human ancestor known as Toumai, whichwalked on two legs and is thought to have lived in present-day Chad 6.5million to 7.4 million years ago. The new report, published in today'sissue of the journal Nature, estimates that final break between the humanand chimpanzee species did not come until 6.3 million years ago at the earliest, and probably less than 5.4 million years ago. This contradiction could be resolved, Reich said, if early creatures likeToumai then interbred with chimpanzee ancestors, leaving a population of hybrids that developed into today's humans. (In this scenario, the lineof Toumai creatures then went extinct.) But it is also possible, he said,that the dating of the early human fossils is wrong, or that the datingof other, older fossils used in his calculations is wrong, which would partially undercut the interbreeding theory. Scientists said that thereport will probably bring intense scrutiny, as researchers look forpotential flaws in the work or other explanations for itsfindings. The work will also probably inspire biologists to devote more attentionto hybrids, the term for offspring with parents of different species, and the role that they may play in fueling evolution. Biologists have long known about hybrids -- a half-grizzly bear, half-polar bear was recently discovered in Canada -- but it has been assumed that these were generallylone animals that had had little impact on the story of evolution. TheNature paper joins a wave of work showing that the lines between species are hazy, according to James Mallet, a biologist who studies hybrids at University College London. As two species evolve, they can develop new abilities. Some hybrids couldcombine the best of both species, Mallet said, though the biologicalbarriers to the creation of hybrids increase the longer the species are apart. It is thought that human ancestors were adapting to life on thesavannah instead of the forest, where chimpanzees still live today. It isnot known why human ancestors would have begun mating with chimpanzee ancestors again, or why they would have stopped. To understand how long ago humans split from chimpanzees, Reich and hiscolleagues did a close study of DNA from the two. This technique rests onthe idea that once the populations separate, the DNA will slowly drift apart as natural mutations accumulate. If they can count the number ofchanges, and determine how quickly the changes happened, then they can calculate how long the two populations have been separate, according to Nick Patterson, a scientist who was part of the Broad team. Previous studies have used this idea and found that the two species splitbetween about 5 million and 8 million years ago. The Broad team sought to get a more precise answer by looking at howdifferent the DNA of chimps and humans is at many locations, instead ofcalculating an average difference. The DNA of humans and chimpanzees isquite similar, meaning that scientists can readily identify many segmentsof DNA that are so similar they must have been handed down by a commonancestor, deep in the past. Scientists can then use a computer to put thesegments of human and chimp DNA into alignment, placing side by side thesegments that are very similar. For each pair of segments, they then calculated how long it would havetaken to accumulate all the differences. The team used sophisticated statistical techniques to calculate these ''divergence times." This analysis brought surprises that the team could explain only by suggesting human ancestors and chimpanzee ancestors interbred. First,they found that the divergence times varied widely. Some parts of the DNA seemed to indicate the human and chimpanzee species had been apart muchlonger than others, by millions of years. If humans split from chimps andthen interbred before splitting again, the more divergent DNA sequences could date to before the first split, while the less divergent sequences could date to just before the second split. The other surprise was that sequences from the X chromosome, one of twochromosomes that determine gender, gave consistently more recent divergence times, instead of the range seen on other chromosomes. This,too, would be explained by the idea of interbreeding, according to thereport. The X chromosome is thought to be the focus of fertility problemsin hybrids, and population models suggest that all of the X chromosomesin a hybrid population would quickly come to match those of one of the parent species. This would explain why the human and chimpanzee Xchromosomes are so similar. Although the idea is controversial, there will soon be a wealth of moreinformation to test it. Part of the Broad team's analysis relied on usingDNA sequences from the gorilla and other primates as a kind of baselineto interpret their results. Only a relatively small amount of DNA has been sequenced from gorillas, limiting the amount of data the team coulduse. By the end of 2007, there should be a full sequence of the gorilla,allowing the scientists to do a much fuller analysis, Reichsaid. The team also plans on looking at genetic data for other groups ofclosely related species to try to determine whether those species split apart fairly abruptly, or whether there is evidence that hybridization is a common part of evolution, bringing together the best of two species. == (Note: This is an abbreviated and much condensed form of information contained with The Antiquity of Man: Artifactual, fossil and gene records explored publication.) Recent reviews of the available anatomical (Shoshani et al. 1996) and genetic evidence (Ruvolo 1995, 1997; Wise et al. 1997) have convincingly re-affirmed yet again the theory that apes and anatomically modern humans share a common ancestry. Geneticists have analysed the differences in the amino acid sequences of protein and in the base sequences of DNA from apes and humans. The results have yielded a divergence time-frame of 5-8 million years ago. The anatomical differences and similarities can be summarised as follows: - Apes have larger and more sexually dimorphic canines. The spacing layout is also different. - Human jaws are less robust and forward projecting. - The foramen magnum is more centrally orientated at the skull base in modern humans than in apes. - Humans have a larger brain capacity with regards to endocranial volume:body mass - The human cranial base is wider and shorter. Apes and humans share a transversely broad thoracic cage, a vertebral column inside the rib cage, a dorsally-placed scapula and laterally-facing shoulder joints. - The human thorax is relatively uniform in width, whereas the ape thorax widens towards the base. These differences are due to their different gut shapes. - Upper human limbs are less robust because they no longer server as weight-bearers. A side-effect is that they now have a greater ability for motion. - The human mobile shoulder joint is an indicator of our arboreal ancestry and has undergone only comparatively minor alterations. - Human limbs are shorter in proportion to body size than in apes. However, this discrepancy occurs in the length of our lower limbs. - "In African apes and humans, the humeral shaft twists from the humeral head, which faces medially, down to the coronally oriented elbow joint." (Wood & Richmond 2000: 12) - The human and ape elbow structures have very few distinctions. - The human wrist has more dexterity, for greater tool manipulation. This is closely linked to the precision grip, the first hominin occurrences of which are in Homo habilis and some of the australopiths. - Apes have longer and more curved phalanges, which are related to their greater arboreal lifestyle. Australopiths display intermediary lengths. - Lower limb morphology differs to a larger degree than upper limb morphology between humans and apes: "The substantial differences between the lower limbs of modern humans and apes are largely attributable to the bipedal locomotion of the former. The most striking difference is the greater absolute and relative length of modern human lower limbs that increases stride length and thus the speed of bipedal walking (Jungers 1982). Because the lower limbs support the body during bipedal gait, the acetabulum, femoral head and other lower limb joints are relatively larger in humans (Jungers 1988). Modern human femora are distinctive in that they show the valgus condition (i.e. they converge towards the knee), thus helping to position the feet closer to the midline (Walmsley 1933; Tardieu & Trinkaus 1994)." (Wood & Richmond 2000) - Bipedalism is evident right back with Ardipthecus ramidus at least 4.4 million years ago. The Laetoli footprints were made by a hominin with a divergent big toe and are attributable to Australopithecus afarensis, whose remains have been found in the same stratigraphic layers in the same time-frame at Laetoli. Wood & Richmond (2000: 23) state it clearly when they say that "the presumption is that the common ancestor and the members of the Pan lineage would have had a locomotor system that is adapted for orthograde arboreality and climbing, and probably knuckle-walking as well (Washburn 1967; Pilbeam 1996; Richmond & Strait 1999). This would have been combined with projecting faces accomodating elongated jaws bearing relatively small chewing teeth, and large, sexually-dimorphic, canine teeth with a honing system. Early hominins, on the other hand, would have been distinguished by at least some skeletal and other adaptations for a locomotor strategy and other adaptations for a locomotor strategy that includes substantial bouts of bipedalism (Rose 1991), linked with a masticatory apparatus that combines relatively larger chewing teeth, and more modest-sized canines that do not project as far above the occlusal plane." These predictions are based upon detailed anatomical evidence. This stands in stark contrast to creationists who take their religious text as their starting point and attempt to force-fit the data into their religious paradigm; this results in much amusing contorted effects. Those who back such religious works thereby display a profound ignorance of basic 1st year scientific methods, which places a huge question mark over the reliability of their own published and presented works. Creationist works, and those who support such efforts, have no basis whatsoever in any scientific procedure and basic plain scientific reality. References Jungers, W.L. 1988. Relative joint size and hominoid locomotor adaptations with implications for the evolution of hominid bipedalism. In, Strasser, E. & Dagosto, M. (eds.) The Primate Postcranial skeleton: Studies in Adaptation and Evolution, pp. 247-265. London: Academic Press Pilbeam, D. 1996. Genetic and morphological records of the Hominoidea and hominid origins: a synthesis. Molecular Phylogenetics and Evolution 5: 155-168 Richmond, B. & Strait, D. 1999. Knuckle-walking traits retained in the wrists of early hominids. American Journal of Physical Anthropology, Suppl. 28: 232 Shoshani, J. et al. 1996. Primate phylogeny: morphological vs molecular results. Molecular Phylogenetic Evolution 5: 101-153 Tardieu, C. & Trinkaus, E. 1994. Early ontogeny of the human femoral bicondylar angle. American Journal of Physical Anthropology 95: 183-195 Walmsley, T. 1933. The vertical axes of the femur and their relations. A contribution to the study of erect posture. Journal of Anatomy 67: 284-300 Washburn, S.L. 1967. Behaviour and the origin of Man. Proceedings of the Royal Anthropological Institute 3: 21-27 Wise, C. et al. 1997. Comparative Nuclear and Mitochrondrial Genome Diversity in Humans and Chimpanzees. Molecular Biology Evolution 14(7): 707-716 Wood, B. & Richmond, B. 2000. Human evolution: taxonomy and paleobiology. Journal of Anatomy 196: 19-60 == "Originally, according to DNA samples, it would appear that the domestic dog is most closely related to the grey wolf. "Point-two-percent is the difference between domestic dog DNA and grey wolf DNA, whereas the difference between coyote DNA and dog DNA is 4%. By about 15,000 years ago, at the time of the last Ice Age, they were probably living alongside humans, perhaps retrieving wild animals felled with axes or bows and arrows. The earliest archaeological evidence of dogs as true pets dates back to 12,000 to 14,000 years ago. That is the estimated age of the remains of an old woman holding a puppy in her hand excavated in what is now Israel. - examples have been found dating back as far as 15,000 years ago, the end of the last Ice Age - it seems that the dog skeletons they are finding are similar to wolf skeletons but much smaller. "As a reduction in size is one of the first signs of domestication, and the fact that it's been found in a human settlement, this shows us pretty clearly that that's what's going on." == What did the first so-called simple life forms eat? http://www.windows.ucar.edu/tour/link=/life/first_life.html&edu=high that said this: "The first beings were probably much like coacervates. As a group, these bacteria are called heterotrophic anaerobes. Because there was virtually no oxygen in the atmosphere at this time, these bacteria were necessarily anaerobic, meaning they did not breathe oxygen. Heterotrophs, meaning 'other feeders', are simply organisms that cannot make their own food. The fossils of some these oldest known forms of life have been found in Australian rocks dating back 3.5 billion years. "To create energy, these early bacteria probably used a chemical process called enzymatic catalysis to consume naturally occurring amino acids, sugars, and other organic compounds that had formed spontaneously in the atmosphere then dissolved in liquid water. Because of this chemical process, scientists sometimes call these beings chemo-heterotrophic anaerobes. Upon digestion of these molecules, early bacteria produced methane and carbon dioxide as waste products. Fermenting bacteria would be today's analog of these early creatures. To make beer, barley or wheat is combined with water to make a carbohydrate mash. Bacteria eat the sugars and produce alcohol and CO2 as waste products. In the early Earth, the alcohol and carbon dioxide became part of the natural environment." == Our closest evolutionary cousins, chimpanzees share more than 99% identity in typical protein sequences with humans. For that reason, the common chimpanzee has long been assumed to be an effective animal model for human diseases. === Heterotachy in Mammalian Promoter Evolution Martin S. Taylor, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Colin A. M. Semple Volume 2 | Issue 4 | APRIL 2006 http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10%2E1371% 2Fjournal%2Epgen%2E0020030 Clusters of Internally Primed Transcripts Reveal Novel Long Noncoding RNAs Masaaki Furuno, Ken C. Pang, Noriko Ninomiya, Shiro Fukuda, Martin C. Frith, Carol Bult, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, John S. Mattick, Harukazu Suzuki Volume 2 | Issue 4 | APRIL 2006 http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/ journal.pgen.0020037 http://tinyurl.com/gdz5m Synopsis The human genome has been sequenced, and, intriguingly, less than 2% specifies the information for the basic protein building blocks of our bodies. So, what does the other 98% do? It now appears that the mammalian genome also specifies the instructions for many previously undiscovered "non protein-coding RNA" (ncRNA) genes. However, what these ncRNAs do is largely unknown. In recent years, strategies have been designed that have successfully identified hundreds of short ncRNAsatermed microRNAsamany of which have since been shown to act as genetic regulators. Also known to be functionally important are a handful of ncRNAs orders of magnitude larger in size than microRNAs. The availability of complete genome and comprehensive transcript sequences allows for the systematic discovery of more large ncRNAs. The authors developed a computational strategy to screen the mouse genome and identify large ncRNAs. They detected existing large ncRNAs, thus validating their approach, but, more importantly, discovered more than 60 other candidates, some of which were subsequently confirmed experimentally. This work opens the door to a virtually unexplored world of large ncRNAs and beckons future experimental work to define the cellular functions of these molecules. * Complex Loci in Human and Mouse Genomes PA?r G. EngstrAm, Harukazu Suzuki, Noriko Ninomiya, Altuna Akalin, Luca Sessa, Giovanni Lavorgna, Alessandro Brozzi, Lucilla Luzi, Sin Lam Tan, Liang Yang, Galih Kunarso, Edwin Lian-Chong Ng, Serge Batalov, Claes Wahlestedt, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Christine Wells, Vladimir B. Bajic, Valerio Orlando, James F. Reid, Boris Lenhard, Leonard Lipovich Volume 2 | Issue 4 | APRIL 2006 http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/ journal.pgen.0020047 http://tinyurl.com/zkgc8 Synopsis In the traditional view, most genes occupy their own distinct territory in mammalian genomes. However, it has become apparent that many genes are in fact located in complex regions (complex loci) where they share territory with other genes by utilizing opposite strands of DNA. Such genes either share regions expressed as mRNA (i.e., form cisaantisense pairs) or start from a genome region (called a bidirectional promoter) at which transcription can initiate in both directions along the DNA. In this paper, researchers present the one of the most comprehensive censuses of complex loci to date and investigate their general properties and humanamouse differences to discover the rules of this type of gene organization and its effect on gene regulation. They found about 25% of known human and mouse genes to be in cisaantisense pairs, and estimate the total fraction to be over 40%. At bidirectional promoters, they demonstrated the existence of mirror DNA sequence composition related to the promoters' ability to initiate transcription in two directions. The researchers found over 2,000 "chains"acomplex arrangements where three or more genes are coupled by cisaantisense pairing and/or bidirectional promoters; among them are many genes whose products control the _expression of other genes. * Mice and Men: Their Promoter Properties Vladimir B. Bajic, Sin Lam Tan, Alan Christoffels, Christian SchAnbach, Leonard Lipovich, Liang Yang, Oliver Hofmann, Adele Kruger, Winston Hide, Chikatoshi Kai, Jun Kawai, David A. Hume, Piero Carninci, Yoshihide Hayashizaki Volume 2 | Issue 4 | APRIL 2006 http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/ journal.pgen.0020054 http://tinyurl.com/hoag7 Synopsis Tens of thousands of mammalian genes are expressed in various cells at different times, controlled mainly at the promoter level through the interaction of transcription factors with cis-elements. The authors analyzed properties of a large collection of experimental mouse (Mus musculus) and human (Homo sapiens) transcription start sites (TSSs). They defined four types of TSSs based on the compositional properties of surrounding regions and showed that (a) the regions surrounding TSSs are much richer in properties than previously thought, (b) the four TSSs types are associated with distinct groups of cis-elements and initiating dinucleotides, (c) the regions upstream of TSSs are distinctly different from the downstream ones in terms of the associated cis-elements, and (d) mouse and human TSS properties relative to CpG islands (CGIs) and TATA box elements suggest species-specific adaptation. The authors linked TSS characteristics to gene _expression through categories defined by the Gene Ontology and eVOC classifications and tissue _expression libraries. They provided examples of the preference of immune response genes for TSS types and specific genomic organization. Their results shed light on the fine compositional properties of TSSs in mammals and could lead to better design of promoter- and gene-finding tools, better annotation of promoters by cis-elements, and better regulatory network reconstructions. These areas represent some of the focal topics of bioinformatics and genomics research that are of interest to a wide range of life scientists. * Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines Jinfeng Liu, Julian Gough, Burkhard Rost Volume 2 | Issue 4 | APRIL 2006 http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10%2E1371% 2Fjournal%2Epgen%2E0020029 http://tinyurl.com/kon9u Synopsis There are two types of RNA: messenger RNAs (mRNAs), which are translated into proteins, and non-coding RNAs (ncRNAs), which function as RNA molecules. Besides textbook examples such as tRNAs and rRNAs, non-coding RNAs have been found to carry out very diverse functions, from mRNA splicing and RNA modification to translational regulation. It has been estimated that non-coding RNAs make up the vast majority of transcription output of higher eukaryotes. Discriminating mRNA from ncRNA has become an important biological and computational problem. The authors describe a computational method based on a machine learning algorithm known as a support vector machine (SVM) that classifies transcripts according to features they would have if they were coding for proteins. These features include peptide length, amino acid composition, secondary structure content, and protein alignment information. The method is applied to the dataset from the FANTOM3 large-scale mouse cDNA sequencing project; it identifies over 14,000 ncRNAs in mouse and estimates the total number of ncRNAs in the FANTOM3 data to be about 28,000. * PseudoaMessenger RNA: Phantoms of the Transcriptome Martin C. Frith, Laurens G. Wilming, Alistair Forrest, Hideya Kawaji, Sin Lam Tan, Claes Wahlestedt, Vladimir B. Bajic, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Timothy L. Bailey, Lukasz Huminiecki Volume 2 | Issue 4 | APRIL 2006 http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10%2E1371% 2Fjournal%2Epgen%2E0020023 http://tinyurl.com/ezf4n Synopsis Our understanding of genetics has been dominated by the so-called central dogma: the theory that DNA is transcribed into RNA, which is translated via the genetic code to produce proteins. Thus, DNA is the inherited store of genetic information, proteins are the end products that carry out cellular functions, and RNA is a kind of passive intermediary, hence termed messenger RNA. However, evidence has been accumulating that RNA plays a much more dynamic role than this. This study provides an unprejudiced survey of "pathological" RNA molecules, which resemble protein-coding RNA except that they contain violations of the genetic code. These pseudoamessenger RNAs constitute a surprisingly large fraction of all transcripts, as much as 10%. These ghostly molecules have always been present in RNA surveys, but have stayed below the radar because they do not cleanly correspond to annotated elements in DNA, i.e., "genes". Their prevalence demonstrates that RNA is a distinct continent that cannot be fully understood as a mirror of DNA or proteins. Heterotachy in Mammalian Promoter Evolution Martin S. Taylor, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Colin A. M. Semple Volume 2 | Issue 4 | APRIL 2006 http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10%2E1371% 2Fjournal%2Epgen%2E0020030 http://tinyurl.com/eposf Synopsis Promoters are crucial to the regulation of gene _expression. They are of considerable interest to molecular biologists from a functional perspective and to a much wider audience, as sequence changes within promoters are likely to be a substantial contributor to disease predisposition and the divergence of species. In mammals, promoters have been extensively studied in a case-by-case manner, but the more general mechanisms of promoter evolution are little understood. The authors have undertaken an extensive study of evolutionary trends across experimentally defined promoters. They have discovered that the relative rate of promoter evolution varies between lineages and is substantially accelerated in primates. The authors conclude that the predominant cause is variation in the mutation rate specifically within promoter regions. This finding has important implications for comparative genomics, in particular the identification of functional sites within promoters. The large datasets in this study have also allowed the pattern of evolution to be considered between different types of promoter, giving new insight into their distinct biology. == Journal of Human Evolution American Journal of Physical Anthropology PLoS Biology (published by the Public Library of Science) http://biology.plosjournals.org/ PLoS Genetics (published by the Public Library of Science) http://genetics.plosjournals.org/ Science (published by the American Association for the Advancement of Science) http://www.sciencemag.org/ Nature http://www.nature.com/ Journal of Biology (published by BioMed Central) http://jbiol.com/ Journal of Evolutionary Biology http://www.blackwellpublishing.com/journal.asp?ref=1010-061X view online content: http://www.blackwell-synergy.com/rd.asp?code=JEB&goto=journal International Journal of Organic Evolution http://evol.allenpress.com/evolonline/?request=index-html#Evolution_Journal Molecular Biology and Evolution (published by the Society for Molecular Biology and Evolution) http://www.mbe.oupjournals.org Evolution & Development http://www.blackwellpublishing.com/journal.asp?ref=1520-541X Trends in Ecology & Evolution http://www.elsevier.com/wps/find/journaldescription.cws_home/30339/description Trends in Genetics http://www.elsevier.com/wps/find/journaldescription.cws_home/405918/description Integrative and Comparative Biology (Journal of the Society for Integrative and Comparative Biology; published as the American Zoologist from 1961 to 2001) http://www.sicb.org/az/ Invertebrate Biology (Journal of the American Microscopical Society) http://www.invertebratebiology.org/ Proceedings of the National Academy of Sciences (PNAS) Biological Sciences http://www.pnas.org/current.shtml#BIOLOGICAL_SCIENCES Palobiology Journal of Paleontology (both published by The Paleontological Society) http://www.psjournals.org/paleoonline/?request=get-archive The Journal of Vertebrate Paleontology (published by the Society of Vertebrate Paleontology) http://www.vertpaleo.org/jvp/ Paleontologia Electronica http://palaeo-electronica.org/ Cladistics The International Journal of the Willi Hennig Society http://www.blackwell-synergy.com/loi/cla Evolution International Journal of Organic Evolution http://evol.allenpress.com/evolonline/?request=get-archive Biological Journal of the Linnean Society http://www.blackwell-synergy.com/loi/bij Evolutionary Ecology (published in the Netherlands) http://www.springer.com/west/home/life+sci?SGWID=4-10027-70-35681186-0 Genetics http://www.genetics.org/ Molecular Phylogenetics and Evolution http://www.elsevier.com/wps/find/journaldescription.cws_home/622921/description Proceedings of the Royal Society: Biological Sciences http://www.pubs.royalsoc.ac.uk/index.cfm?page=1087 == A fossil skull from a site called Gawis in Ethiopia is apparently intermediate in form between Homo erectus and our own species, Homo sapiens. Nearby, in the same stratigraphic level from which the skull came, scientists found stone tools made in the Late Acheulean tradition and fossils representing pigs, zebras, elephants and cats, among other species. The find hails from the Middle Pleistocene, a relatively poorly represented time period as far as human fossils go. The discovery team, led by Sileshi Semaw of Indiana University, is working to determine the age of the skull more precisely. == MITOCHONDRIA MYSTERY SOLVED: Mitochondria are the cell's energy-producing organelles and they contain their own DNA (mtDNA). Scientists have long known that offspring inherit the vast majority of their mitochondria from their mother. They believed this was simply because the egg contains many more of the organelles than the sperm does. But new research in fish reveals that sperm mitochondria are actually completely destroyed within the first two hours of fertilization. This may in fact protect the offspring, the researchers note, because the stresses of sperm production can impair the sperm mtDNA. The mechanism of this elimination of the sperm mitochondria--whether they self-destruct or the egg extinguishes them--has yet to be determined. == SHOCKING CONVERGENCE: Two groups of South American and African electric fish, whose lineages diverged 200 million years ago, independently evolved similar ways to generate electricity, according to a new study. In a paper published online this week by the Proceedings of the National Academy of Sciences, researchers report that both groups converted existing sodium channel proteins Eigenmannia virescens from the Amazon and Brienomyrus vadamans from Africa. === Environmental DNA Damage May Drive Human Mutation Mutations drive evolution. Subtle changes in the pairing of the chemical letters of DNA--adenine, cytosine, guanine and thymine--produce new cells with different traits than their ancestors. The fundamental basis of such change is called a single nucleotide polymorphism, or a copying error in the long, chemical book of DNA. Now Japanese researchers have shown how environmentally damaged letters lead to transcription flaws and, ultimately, human diversity. Ultraviolet light, environmental chemicals, even the by-products of normal cellular metabolism all conspire to continually assault the DNA of humans and every other living thing. Typically, they cause the four chemical precursors to undergo oxidation. For guanine, or G, its oxidized version is called 8-oxoG. When lurking in the area during DNA replication, it bonds with adenine and causes the latter to pair with thymine rather than with its correct partner, unoxidized guanine. This is a permanent change, or mutation. Geneticist Yusaku Nakabeppu of Kyushu University and his colleagues studied the abundance of 8-oxoG in cellular cultures from four subjects, two men and two women. By fluorescently labeling monoclonal antibodies that attach to DNA sites where 8-oxoG has made its changes the researchers revealed that the oxidized guanine does not occur randomly throughout the chromosome but rather clusters in certain areas. In fact, 8-oxoG showed a remarkable preference for areas of the chromosome where genetic material was being exchanged and mutations occurred. This preference remained the same for chromosomes from all four subjects, leading Nakabeppu to suggest that 8-oxoG may be responsible for such exchanges and mutations. After all, the clustering of single nucleotide polymorphisms has been observed before, but its cause remains unknown. And that means Nakabeppu and his colleagues may have shown how environmental damage leads to cellular mutation, for good and for ill. == 1.Despite much recent controversy about the theory of evolution, major changes in our understanding of evolution over the past twenty years have gone virtually unnoticed.[1] At the heart of Darwin's theory of evolution is an explanation of how plants and animals evolved from earlier forms of life that have long since disappeared; but his theory says nothing about the factors that determine the shape, color, and size of a particular fish, whale, or butterfly. Darwin and his contemporaries realized that understanding the evolution of animal forms and understanding how a fertilized egg develops into a whale, cow, or human being must be deeply connected; but they didn't know how to make the connection. Surprising discoveries in the 1980s have begun to tell us how an embryo develops into a mature animal, and these discoveries have radically altered our views of evolution and of the relation of human beings to all other animals. The new field of study in which these breakthroughs have been made is called Evo Devo, short for evolution and development, "development" referring to both how an embryo grows and how the newborn infant matures into an adult. Sean Carroll, author of one of the books under review and a coauthor of another, has made important contributions to the understanding of evolution and development. From DNA to Diversity, written with two other scientists, is the second edition of a book that has become a classic for students of evolution. The title of Carroll's other book, Endless Forms Most Beautiful, comes from the famous final sentence of The Origin of Species: "There is a simple grandeur in this view of life... that from so simple an origin, through the process of gradual selection of infinitesimal changes, endless forms most beautiful and most wonderful have been evolved." In 1830, nearly thirty years before Darwin published his book, two French naturalistsGeorges Cuvier and Etienne Geoffroy St. Hilairedebated the significance of the anatomical similarities between distantly related animals, such as the flippers of whales and the wings of bats. Cuvier held that form was dictated by function: the bat's wing, needed for flying, had a separate origin from the whale's flipper, needed for swimming. Geoffroy St. Hilaire opposed this view, arguing that the underlying skeletal similarities pointed to the existence of a common archetype for both flippers and wings. While neither man claimed that animal forms could change over generations, St. Hilaire's archetypal form foreshadowed some recent discoveries about development and evolution. No doubt this debate was in the mind of Charles Darwin as he formulated his theories in an attempt to account for the origins of animal forms. The contemporary Darwinian theory of evolution is based on three ideas: natural selection, heredity, and variation. Small random changesvariationsoccur in organisms through mutations of genes, and when these changes give an organism a greater chance of survival, they persist from one generation to the next through natural selection. That is, organisms with traits that make them better adapted to the environment they inhabit will have better reproductive success than other members of the same species that do not possess the advantageous traits. In each successive generation, then, an ever-larger proportion of the species in question will possess the mutation that produces the advantageous traits. "Natural selection," Darwin wrote, "acts solely by accumulating successive, favorable variations." Evolution in the Darwinian view was gradual: "it can act only by short and slow steps." And since, in this view, all changes are random, there are no predetermined directions in which organisms evolve. All living organisms, Darwin claimed, are descended from one or a few common ancestors. Neither Darwin nor any of his contemporaries knew about the workings of heredityhow we inherit the eye color of our father or the hair color of our mother. The work of the Czech monk Gregor Mendel, first published in 1865, had gone unnoticed in Darwin's day and was only rediscovered around 1900. Mendel had shown that specific traits, such as the color of a pea, or the smoothness or roughness of its skin, could be inherited independently of one another. The new science of "genetics," the idea that units called "genes" within each cell transmit specific traits, such as hair color, from one generation to the next, began in the first decade of the twentieth century. Studies of inherited traits in fruit flies in the following decades established convincing evidence for genes, but they remained invisible. Scientists still didn't know how the gene made it possible for information to pass from one generation to the next, and how mutations in genes could, over many generations, lead to a new species that had a form different from its distant progenitor. By the 1940s, though the structure of the gene was still unknown, scientists had introduced the idea of the gene into Darwinian theory. They now explained evolution as the consequence of small random changes in genes. This recasting of Darwinian theory was called the Modern Synthesis, following the 1942 publication of Julian Huxley's book Evolution: The Modern Synthesis. The neo-Darwinian theory incorporated the Mendelian idea of genetics, explaining the mechanism of inheritance that was unknown to Darwin. The theory, however, did not account for how particular organisms develop from embryos in the womb to adult forms; that process, known as embryology, was not discussed. The neo-Darwinian view was reinforced in 1953, when the double helix was discovered, showing how genes composed of the nucleic acid DNA transmitted hereditary characteristics. A molecule of DNA is made up of two long strands of chemical building blocks called nucleotides, each containing one of four bases: adenine, thymine, guanine, or cytosine, which are abbreviated A, T, G, and C. The order of the bases in each strand of DNA determines the information in the DNA molecule, information we can think of as providing an overall plan for producing enzymes and other proteins. A gene was now understood to be a specific sequence of DNA bases. Genes vary considerably in size, most of them containing between 10,000 and 20,000 nucleotides, though they can be much longer or shorter. Each of our cells carries all our genes, although most genes remain inactive at any given moment. When a particular gene is activated it is first copied into RNA, a nucleic acid that carries instructions from DNA for assembling proteins. The RNA's instructions are then decoded in a process called "translation," and proteins, including the enzymes essential for cells to function, are produced. Proteins in turn form some 50 percent of all living cells. ------------------------------------------------------------------------------ -- How are particular genes activated? There are, according to recent research, as many as a hundred trillion cells in the human body, and each cell contains thousands of different types of molecules that vary considerably in size; many molecules move about freely inside the cell. All the cells in a given individual have the same DNAit is contained in the largest molecules in each celland hence an identical set of genes. Which specific genes are activated in a particular cell depends, in part, on the cell's location in the embryo or the adult body. Moreover, the activation of one combination of genes will give rise to a liver cell, while the activation of another will produce a brain cell. The structure of the double helix made it apparent how changes, or mutations, in the base sequence of a gene could lead to variations in the characteristics of an organism; such mutations could, if advantageous, accumulate over time. The process appeared to confirm Darwin's view that evolution is gradual. As he wrote in The Origin of Species, nature "can act only by short and slow steps. Hence, the saying Natura non facit saltum," nature doesn't make sudden jumps. The standard view, then, was that variation and selection could account for how the simple organisms of early life evolved into the complex forms of the contemporary biological world. After Mendel's discoveries had been absorbed at the beginning of the twentieth century, it was assumed that as changes accumulated between one species and another, there would be less and less similarity in the kind and number of their genes. More advanced species would have many more genes than lower forms of life; and worms, for example, would have few, if any, genes similar to those of fish, mice, or human beings. Yet it seemed astonishing that random mutations, even over enormous periods of time, could give rise to the remarkable complexity of an organ such as the human eye. "To suppose," Darwin wrote in The Origin of Species, that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree.... Nonetheless, he continued: Reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, as is certainly the case; if further, the eye ever varies and the variations be inherited, as is likewise certainly the case; and if such variations should be useful to any animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, should not be considered as subversive of the theory. The neo-Darwinian belief in small mutational changes in DNA molecules over hundreds of millions of years made the preservation of individual genes over long periods of time highly unlikely. It was thought that the diversity of living forms was the consequence of each animal having evolved its own unique set of genes over millions of years as well. Surely human beings, for example, would not have the same genes as worms. Those assumptions were dramatically overturned when the rough draft of the human genomethe entire set of human geneswas announced in 2001. As it turned out, human beings have far fewer genes than expected about 25,000 rather than the 60,000 or more that had been predicted. This was about the same number as mice have, and even the tiny worms called nematodes have about 14,000 genes. The number of genes in a given species, therefore, is not a measure of its complexity. Why had biologists so overestimated the number of genes in the human genome? Why is it unnecessary for complex animals such as mammals to have ten times as many genes as worms? ------------------------------------------------------------------------------ -- The answers to these questions were already hinted at more than four decades ago. At the time it was known that the bacteria E. coli, which normally live off the sugar glucose, are also capable of producing enzymes that digest other sugars, such as lactose. But biologists noticed that the bacteria only produce the enzyme when lactose is present in their immediate environment. Scientists could not explain how the E. coli somehow "knew" when the lactose-digesting enzyme would be needed. In 1961, Jacques Monod and Francois Jacob discovered that E. coli bacteria actually have a mechanism that controls the production of the enzyme for digesting lactose. As unicellular organisms, E. coli bacteria have only several thousand genes, each of which is made up of a specific sequence of DNA. A single one of these genes, present in all E. coli, carries in its DNA the genetic instructions needed to assemble the enzyme that can digest lactose; the DNA is copied into RNA, which is then "translated" to produce the enzyme itself. When there is no lactose present in the bacteria's immediate environment, the gene is switched off: its DNA is not copied into RNA and the enzyme is not produced. The reason for this, the scientists discovered, is that a protein called a repressor molecule attaches itself to the DNA site where the copying into RNA begins, thus blocking off the DNA and preventing the gene from producing the RNA responsible for the synthesis of the enzyme. On the other hand, when the E. coli bacteria encounter lactose, the lactose binds itself to this repressor molecule, causing the repressor to be detached from the DNA site. This unblocks the DNA, allowing the gene to be copied into RNA, and produce the enzyme that can digest lactose. In other words, the repressor molecule acts as a switch that controls the gene's production of the enzyme. Since only a fraction of the total number of genes present in an organism are expressed, or turned on, at any given time, Monod and Jacob conjectured that other genes must be similarly turned on and off. Although they had not yet found systematic evidence to support these ideas, the discovery of the repressor molecule allowed the two scientists to form a powerful new hypothesis about how genes function. As Jacob recently wrote, in a brief description of the new hypothesis: It proposed a model to explain one of the oldest problems in biology: in organisms made up of millions, even billions of cells, every cell possesses a complete set of genes; how, then, is it that all the genes do not function in the same way in all tissues? That the nerve cells do not use the same genes as the muscle cells or the liver cells? In short, [we] presented a new view of the genetic landscape. The deeper significance of the Monod-Jacob model of gene function, and its implications for the nature of evolution, became apparent with the new field of embryo research that arose almost twenty years later. 2. In 1894, the English biologist William Bateson challenged Darwin's view that evolution was gradual. He published Materials for the Study of Variation, a catalog of abnormalities he had observed in insects and animals in which one body part was replaced with another. He described, for example, a mutant fly with a leg instead of an antenna on its head, and mutant frogs and humans with extra vertebrae. The abnormalities Bateson discovered resisted explanation for much of the twentieth century. But in the late 1970s, studies by Edward Lewis at the California Institute of Technology, Christiana Nusslein-Vollhard and Eric Wieschaus in Germany, and others began to reveal that the abnormalities were caused by mutations of a special set of genes in fruit fly embryos that controlled development of the fly's body and the distribution of its attached appendages. Very similar genes, exercising similar controls, were subsequently found in nematodes, flies, fish, mice, and human beings. What they and others discovered were genes that regulate the development of the embryo and exert control over other genes by mechanisms analogous to that of the repressor molecule studied by Monod and Jacob. Eight of these controlling genes, called Hox genes, are found in virtually all animals worms, mice, and human beings and they have existed for more than half a billion years.[2] Fruit flies and worms have only one set of eight Hox genes; fish and mammals (including mice, elephants, and humans) have four sets. Each set of Hox genes in fish and mammals is remarkably similar to the eight Hox genes found in fruit flies and worms. This discovery showed that very similar genes control both embryological and later development in virtually all insects and animals. (See Figure 1.) To understand what Hox genes do, scientists needed to observe the activity of the genes in the developing embryos of flies and mice. Using new technologies that allowed them to observe under a microscope the locations of the Hox proteins in these embryos, they were able to identify an overall pattern of how Hox genes behave. A newly fertilized fly egg looks like a tiny football: one end, or pole, will eventually become the head region; the other end will become the tail region. These and other divisions of the embryo in later development actually followed the switching on and off of the Hox genes in different parts of the embryo. (See Figure 2.) The mechanism that causes the Hox genes to behave in this way is initiated by the release of proteins from the cells of the mother's body across the newly fertilized embryo. These proteins control the activities of the Hox genes and are released in varying concentrations, causing Hox genes to produce Hox proteins in specific places. As the embryo grows, the production of Hox proteins divides the embryo into a series of segments, or distinct regions, from which subsequent development occurs. Other genes are then activated within each segment, a finer division of the embryo is established, and wings, antennae, and other body parts are formed. In general, scientists reasoned, Hox genes establish the basic division of the embryo into distinct compartments, and each compartment, in turn, establishes the regions of the embryo where development of specific body parts and functions takes place. Still, the details of the mechanisms that a cell uses to establish its position in the embryo remain incomplete. In fact, Nusslein-Vollhard and Wieschaus found that within the fly's embryo there was an overall pattern in which genes were turned on or off; and they saw in this pattern the overall body plan for the full-grown fly. In other words, the activity of the Hox genes, including the formation of compartments within the embryo and the control of other genes that guide development, provided a system of organization that dictated the final adult form of the fly. The presence of a body plan in the genome, whether of a fly, a whale, or a human, was unexpected by embryologists. Previously, most of them did not think that development of embryos was controlled by genes; they had assumed that the different parts of developing embryos were determined by physical interaction between neighboring cells and that there was no overall division of the embryo according to a genetic plan. Experiments had shown, for example, that removing developing wing tissue from one part of an embryo and implanting it elsewhere still gave rise to a wing, although an abnormal one. Scientists attributed the abnormality to the effects of the neighboring cells in the embryo. This was wrong. In fact it was caused by the disruption of the body plan. This new understanding of Hox genes was aided by the discovery that the proteins produced by these genes function in a way that is analogous to Monod and Jacob's repressor molecule. Specifically, although they have different properties, all Hox proteins contain a molecular structure that makes them attach to DNA sites that control genes. This meant that Hox proteins, like the repressor molecule, act as switches that turn neighboring genes on and off.[3] Hox genes, as Carroll explains, are in fact one of many kinds of genes that direct embryo development by a mechanism of switches. One example that is not a Hox gene is the gene that controls the development of the eye in fruit flies. If this gene (called Pax 6) is damaged when it mutates, the fly fails to develop eyes. We now know from the experiments described in Carroll's book that the Pax 6 gene is also found in butterflies, mice, and humans. Indeed, Pax 6 genes are interchangeable. The Pax 6 gene from a fly will turn on genes that make eyes in mice, and the Pax 6 gene from a mouse will turn on genes that make eyes in flies. It had long been assumed that eyes had evolved independently in different species. The structures of mammalian eyes and insect eyes are very different and it would seem most unlikely that they had followed a similar evolutionary path. Mammalian eyes, for example, have a single lens that focuses an image on the retina. Insects have eyes with many tube-like structures, each tube having its own lens and retina. Yet the discovery of the Pax 6 gene gives us reason to believe that the evolution of the eye in all the animals followed related, and to some extent common, paths, though we cannot completely exclude the possibility that each kind of eye evolved following completely independent pathways. In addition to the Pax 6 gene, genes have been found that control the genes responsible for the development of the different kinds of "hearts"or mechanisms that pump bloodwhether in fruit flies or humans, again suggesting similar evolutionary pathways. Indeed the development of legs, wings, arms, fins, and other fish and marine animal appendages are all under the control of virtually identical genes and, as with the Pax genes, in many cases are interchangeable. These findings strongly support the Darwinian view that animals descend from one or a few ancestors. However, contrary to the previously accepted neo-Darwinian view, the same findings showed that different animal forms are not primarily a function of distinct gene pools that have evolved over millions of years. How then do similar collections of genes create the enormous diversity of living forms? In Sean Carroll's view, what creates diversity is the patterns in which genes are turned "on" and "off." The different appendages found in centipedes, fruit flies, lobsters, and brine shrimp are created by varying combinations of Hox gene activity in the developing insect or crustacean embryo. "Switches," Carroll emphasizes, "enable the same...genes to be used differently in different animals" [his italics]. In other words, a Hox gene produces a protein that binds to the DNA's sites where genes copy into RNA and can thus turn genes "on" or "off." This has an important consequence for evolution: mutations in Hox genes will affect the ways in which they act within the embryo, thereby altering the proteins' functions as switches. When the proteins' functions are changed, in turn, this causes them to control genes that are needed for development of a specific physical trait in new ways. In this view, evolution is largely the consequence of random mutations in genetic switches. Genes remain intact, but under new patterns of control. Their function is altered. Complexity and variety are created, at least in part, by combining the activities of old genes in new ways. Carroll's viewwhat we might call the switches hypothesisemphasizes the importance of changes in patterns of turning genes on and off rather than changes in the genes themselves. However, even the most ardent supporter of the switches hypothesis would admit that not only Hox genes but other genes change as well. But the contribution of these changes to evolution is far less than we had previously believed. In fact, vertebratesreptiles, birds, chickens, mice, pythons, and humans do have more genes than insects, though far fewer than had been expected before the human genome was revealed. The increase in the number of genes in these animals is partly responsible for their complexity and diversity. But as Carroll notes, "frogs and snakes, dinosaurs and ostriches, giraffes and whales, have evolved around a similar set of four Hox gene clusters. So again, the mere number of Hox genes does not tell us how these forms evolved." The diversity of these animals comes from changes in the ways genes are turned on and off. For example, though the giraffe has a long neck, it has seven cervical vertebrae, the same number as humans, whales, and all other mammals. Hox genes control this number, but they may also control cell proliferation and consequently the size of the vertebrae. The giraffe's larger vertebrae may have developed because of mutations in the Hox genes controlling the size of vertebrae. Giraffes with large vertebrae and longer necks could feed off tall trees and were consequently selected over other giraffes. Changes in gene regulation, not new genes, gave rise to the long-necked giraffe. Evolution, then, depends on new patterns of gene regulation rather than the creation of new genes. Indeed, it is not meaningful to talk about the function of a single gene in isolation. Genes only function in the context of the organism. There is no single gene for an eye, a limb, or language, much less such tendencies as homosexuality. Genes function in relation to other genes and intercellular signals, much as words vary in meaning and function depending on the way they are used in sentences and the contexts in which they are spoken. It is the combinations of gene activity, which may be different in different species, that create the form of the organism. "We can begin to think of individual groupsinsects, spiders, and centipedes, or birds, mammals, and reptiles, as well as their long extinct fossil relativesnot so much in terms of their uniqueness, but as variations on a common theme," Carroll writes. And surprising, too, is the evidence that all animals, from worms to humans, probably descend from one or a few primitive bacteria. Darwin would have been pleased to discover molecular evidence for his "common descent." 3. A powerful new theory adds considerable weight to this view, putting Carroll's work in a larger perspective. In The Plausibility of Life, Marc W. Kirschner and John C. Gerhart take a broader view than Carroll's on the questions of development and evolutionary biology. They agree that Hox genes make an important contribution to the mechanisms of evolution, but they argue that there are a number of other fundamental properties of organisms that give direction to evolution. The weakness of Darwinian theoryand one that has been seized upon by secular critics of evolutionary theoryis its failure to explain how the gene determines the observable traits of the organism. From an evolutionary point of view, how can complex organs such as eyes, arms, or wings evolve over long periods of time? What about the intermediary forms? The Darwinian view was that early evolutionary forms of arms, legs, or wings might have initially served other purposes (insect legs, for example, might have evolved from gills their ancestors used for respiration). Such transformations of purpose are certainly important in evolution, Kirschner and Gerhart argue, but there must be other mechanisms at work as well. Concerning the human eye, for example: How is it possible for the different parts of an eye to evolve simultaneouslythe lens, the iris, the retina, along with the blood vessels necessary for supplying the eye with oxygen and nutrition as well as the nerves that must receive signals from the retina and send signals to the muscles of the eye? Could these precise nerve and vascular networks be created by gradual random changes in genes over long periods of time, as Darwin claimed? Similarly, how can random mutations and natural selection create not only the necessary muscles and bone that make up the arm, for example, but organize the blood supply and nerves so that, after hundreds of thousands of years, an animal evolves with functioning arms, legs, and eyes? The Darwinian view that developing organs can serve different purposes at different times seems incomplete at best. Darwin thought that at any given time variations in the forms of organisms were purely random. This is true of the neo-Darwinian view as well. However, recent research has shown that even though mutations are random, the effects of a mutation will be restricte