B13A-Evolve-A2.txt ******************************************************************************* Graham L. Kendall Modified 5/30/2009 Email grahamkendall74135@yahoo.com I am found on IRC Efnet, Undernet, Dalnet as glk Files found at http:www.grahamkendall.net/ All are free to use any of this material without limit. ============== The biological synthesis (1930 to 1950) validated Darwinian natural selection. From 1900 to 1930-1950 biology was in disarray, having no universal mechanism to explain the origin of species. During these two decades biologists came to agree that Darwin was correct. Simply miraculous since genetics didn't exist in his life time. == http://uk.news.yahoo.com/18/20090529/tsc-ancient-eruption-killed-off-... A huge volcanic eruption in China some 260 million years ago led to the sudden extermination of marine life clear around the world, British paleontologists announced, in a report being published this week in the journal Science. The researchers were able to pinpoint the exact timing of the massive eruption thanks to a layer of fossilized rock which showed mass extinction of different life forms -- clearly linking the volcanic blasts to a major environmental catastrophe. "The abrupt extinction of marine life we can clearly see in the fossil record firmly links giant volcanic eruptions with global environmental catastrophe," said Paul Wignall, a professor and palaeontologist at the University of Leeds, who was the lead author of the research paper in the May 29 edition of Science. The eruption in southwest China unleashed about a half million cubic kilometers of lava, covering an area five times the size of Wales, according to the research by scientists at the British university. The mass extinction of ocean life came about because of the collision of fast flowing lava with shallow sea water, which caused a violent explosion at the start of the eruptions and threw huge quantities of sulphur dioxide into the stratosphere. == "Ida," the small "missing link" found in Germany that's created a big media splash and will likely continue to make waves among those who study human origins. In a new book, documentary, and promotional Web site, paleontologist Jorn Hurum, who led the team that analyzed the 47-million-year-old fossil seen above, suggests Ida is a critical missing-link species in primate evolution (interactive guide to human evolution from National Geographic magazine). (Among the team members was University of Michigan paleontologist Philip Gingerich, a member of the Committee for Research and Exploration of the National Geographic Society, which owns National Geographic News.) The fossil, he says, bridges the evolutionary split between higher primates such as monkeys, apes, and humans and their more distant relatives such as lemurs. "This is the first link to all humans," Hurum, of the Natural History Museum in Oslo, Norway, said in a statement. Ida represents "the closest thing we can get to a direct ancestor." Ida, properly known as Darwinius masillae, has a unique anatomy. The lemur-like skeleton features primate-like characteristics, including grasping hands, opposable thumbs, clawless digits with nails, and relatively short limbs. "This specimen looks like a really early fossil monkey that belongs to the group that includes us," said Brian Richmond, a biological anthropologist at George Washington University in Washington, D.C., who was not involved in the study, published this week in the journal PLoS ONE. But there's a big gap in the fossil record from this time period, Richmond noted. Researchers are unsure when and where the primate group that includes monkeys, apes, and humans split from the other group of primates that includes lemurs. "[Ida] is one of the important branching points on the evolutionary tree," Richmond said, "but it's not the only branching point." At least one aspect of Ida is unquestionably unique: her incredible preservation, unheard of in specimens from the Eocene era, when early primates underwent a period of rapid evolution. (Explore a prehistoric time line.) "From this time period there are very few fossils, and they tend to be an isolated tooth here or maybe a tailbone there," Richmond explained. "So you can't say a whole lot of what that [type of fossil] represents in terms of evolutionary history or biology." In Ida's case, scientists were able to examine fossil evidence of fur and soft tissue and even picked through the remains of her last meal: fruits, seeds, and leaves. What's more, the newly described "missing link" was found in Germany's Messel Pit. Ida's European origins are intriguing, Richmond said, because they could suggestcontrary to common assumptionsthat the continent was an important area for primate evolution. == Primate Eye Evolution: Small Evolutionary Shifts Make Big Impacts -- Like Developing Night Vision http://www.sciencedaily.com/releases/2009/05/090518213952.htm ScienceDaily (May 24, 2009) In the developing fetus, cell growth follows a very specific schedule. In the eye's retina, for example, cones -- which help distinguish color during the day -- develop before the more light-sensitive rods -- which are needed for night vision. But minor differences in the timing of cell proliferation can explain the large differences found in the eyes of two species -- owl monkeys and capuchin monkeys -- that evolved from a common ancestor. Researchers from Cornell, St. Jude's Children's Research Hospital in Tennessee and the Federal University of Para, Brazil, have found an evolutionary mechanism that provides insight into how important changes in brain structure of primates can evolve. That evolution appears to proceed via simple genetic changes that affect the timing of development of brain regions, they report in a paper published May 18 online and in a future print issue of Proceedings of the National Academy of Sciences. In both monkey species, the specialized eye cells develop in the growing embryo from a single retinal progenitor cell. In their basic design, the eyes of these primates have the capability and necessary architecture to be either nocturnal or diurnal, based on a species' ecological niche and needs, said Cornell neurobiologist and psychologist Barbara Finlay. Finlay and her colleagues compared the developing eyes in fetuses of the two species to better understand how the nocturnal owl monkeys developed retinas with many more rod cells than cones, while capuchin monkeys, which are active during the day (diurnal), developed more cone cells than rods. "These two species evolved about 15 million years ago from a common ancestor that had a diurnal eye," said Finlay, a Cornell professor of psychology and senior author of the paper. "So we believed that comparing how their eyes develop during embryonic growth could help us understand what evolutionary changes would be required to evolve from a diurnal to a nocturnal eye," said Finlay. By comparing the timing of retinal cell proliferation in the two species, the researchers found evidence that an extended period of progenitor cell proliferation in the owl monkey gave rise to an increased number of rod and other associated cells that make its eyes adept at night vision; the eyes also evolved to be large, with bigger light-gathering and light-sensing structures needed for nocturnal sight. "The beauty of the evolutionary mechanism we have identified is that it enables the eye to almost toggle back and forth between a nocturnal and a diurnal structure," said neurobiologist Michael Dyer of St. Jude's hospital. "It is an elegant system that gives the eye a lot of flexibility in terms of specialization." This research was funded by the National Science Foundation and Brazil's NSF equivalent, National Counsel of Technological and Scientific Development. Journal reference: 1. Michael A. Dyer, Rodrigo Martins, Manoel da Silva Filho, Jos Augusto P. C. Muniz, Luiz Carlos L. Silveira, Constance L. Cepko, and Barbara L. Finlay. Developmental sources of conservation and variation in the evolution of the primate eye. Proceedings of the National Academy of Sciences, 2009; DOI: 10.1073/pnas.0901484106 http://www.pnas.org/content/early/2009/05/15/0901484106 Adapted from materials provided by Cornell University. Cornell University (2009, May 24). Primate Eye Evolution: Small Evolutionary Shifts Make Big Impacts -- Like Developing Night Vision. -- Bob. == Waddington, C.H. in The Strategy of the Genes. Allen & Unwin, London, (1957), == Cohen, I.L. in Darwin Was Wrong - A Study in Probabilities. New Research Publications, Inc., New York, NY (1984) Ehrlich, Paul and L.C. Birch. Evolutionary History and Population Biology in Nature, 1967. -- One Man's Junk May Be A Genomic Treasure Scientists have only recently begun to speculate that what's referred to as "junk" DNA -- the 96 percent of the human genome that doesn't encode for proteins and previously seemed to have no useful purpose -- is present in the genome for an important reason. But it wasn't clear what the reason was. Now, researchers at the University of California, San Diego (UCSD) School of Medicine have discovered one important function of so-called junk DNA. Genes, which make up about four percent of the genome, encode for proteins, "the building blocks of life." An international collaboration of scientists led by Michael G. Rosenfeld, M.D., Howard Hughes Medical Investigator and UCSD professor of medicine, found that some of the remaining 96 percent of genomic material might be important in the formation of boundaries that help properly organize these building blocks. Their work will be published in the July 13 issue of the journal Science. "Some of the 'junk' DNA might be considered 'punctuation marks' -- commas and periods that help make sense of the coding portion of the genome," said first author Victoria Lunyak, Ph.D., assistant research scientist at UCSD. In mice, as in humans, only about 4 percent of the genome encodes for protein function; the remainder, or "junk" DNA, represents repetitive and non-coding sequences. The research team studied a repeated genomic sequence called SINE B2, which is located on the growth hormone gene locus, the gene related to the aging process and longevity. The scientists were surprised to find that SINE B2 sequence is critical to formation of the functional domain boundaries for this locus. Functional domains are stretches of DNA within the genome that contain all the regulatory signals and other information necessary to activate or repress a particular gene. Each domain is an entity unto itself that is defined, or bracketed, by a boundary, much as words in a sentence are bracketed by punctuation marks. The researchers' data suggest that repeated genomic sequences might be a widely used strategy used in mammals to organize functional domains. "Without boundary elements, the coding portion of the genome is like a long, run-on sequence of words without punctuation," said Rosenfeld. Decoding the information written in "junk" DNA could open new areas of medical research, particularly in the area of gene therapy. Scientists may find that transferring encoding genes into a patient, without also transferring the surrounding genomic sequences which give structure or meaning to these genes, would render gene therapy ineffective. == what are the 10 greatest inventions of evolution? They are: > 1) Origin of life > 2) DNA+RNA > 3) Photosynthesis > 4) The complex cell > 5) Sex > 6) Movement > 7) Sight > 8) Hot Blood > 9) Consciousness > 10) Death Sex always costs a lot. That's the point of it. If you can't afford it you are selected out, == Biggest Trilobite Sea Beasts Found ... in Swarms Talk about ruining a good beach day. Swarms of up to a thousand giant trilobitesextinct marine arthropods such as this 35-inch-long (90-centimeter-long) fossil specimenroamed shallow prehistoric seas, new fossils show. The 465-million-year-old fossils, found recently in northern Portugal, are of the largest trilobites ever discovered. The trilobites may have clustered to mate and moltshedding old exoskeletons as new ones grew inas well as avoid predators, scientists say. The benefits of swarming may explain why these distant relatives of horseshoe crabs were among the most widespread arthropods of the Paleozoic era (542 to 251 million years ago). (Related: "Horseshoe Crabs Remain Mysteries to Biologists.") Even so, finding complete specimens bigger than 12 inches (30 centimeters) is raremaking the new find "remarkable," the study authors write in a recent edition of the journal Geology. The critters lived at high latitudes near Gondwanaa huge southern supercontinentand close to the South Pole during the Ordovician period (map of Earth during the Ordovician period). This oxygen-rich, cold-water habitat may have contributed to these trilobites' gigantic sizes, the authors added. But repeated, sudden, "lethal" influxes of oxygen-starved water may have led to the newfound trilobites' demise millions of years ago. == Scientists Unveil Missing Link In Evolution Scientists have unveiled a 47-million-year- old fossilised skeleton of a monkey hailed as the missing link in human evolution. The search for a direct connection between humans and the rest of the animal kingdom has taken 200 years - but it was presented to the world today at a special news conference in New York. The discovery of the 95%-complete 'lemur monkey' - dubbed Ida - is described by experts as the "eighth wonder of the world". They say its impact on the world of palaeontology will be "somewhat like an asteroid falling down to Earth". Researchers say proof of this transitional species finally confirms Charles Darwin's theory of evolution, and the then radical, outlandish ideas he came up with during his time aboard the Beagle. == Chemist Shows How RNA Can Be the Starting Point for Life An English chemist has found the hidden gateway to the RNA world, the chemical milieu from which the first forms of life are thought to have emerged on earth some 3.8 billion years ago. He has solved a problem that for 20 years has thwarted researchers trying to understand the origin of life how the building blocks of RNA, called nucleotides, could have spontaneously assembled themselves in the conditions of the primitive earth. The discovery, if correct, should set researchers on the right track to solving many other mysteries about the origin of life. It will also mean that for the first time a plausible explanation exists for how an information-carrying biological molecule could have emerged through natural processes from chemicals on the primitive earth. The author, John D. Sutherland, a chemist at the University of Manchester, likened his work to a crossword puzzle in which doing the first clues makes the others easier. Whether weve done one across is an open question, he said. Our worry is that it may not be right. Other researchers say they believe he has made a major advance in prebiotic chemistry, the study of the natural chemical reactions that preceded the first living cells. It is precisely because this work opens up so many new directions for research that it will stand for years as one of the great advances in prebiotic chemistry, Jack Szostak of the Massachusetts General Hospital wrote in a commentary in Nature, where the work is being published on Thursday. Scientists have long suspected that the first forms of life carried their biological information not in DNA but in RNA, its close chemical cousin. Though DNA is better known because of its storage of genetic information, RNA performs many of the trickiest operations in living cells. RNA seems to have delegated the chore of data storage to the chemically more stable DNA eons ago. If the first forms of life were based on RNA, then the issue is to explain how the first RNA molecules were formed. For more than 20 years researchers have been working on this problem. The building blocks of RNA, known as nucleotides, each consist of a chemical base, a sugar molecule called ribose and a phosphate group. Chemists quickly found plausible natural ways for each of these constituents to form from natural chemicals. But there was no natural way for them all to join together. The spontaneous appearance of such nucleotides on the primitive earth would have been a near miracle, two leading researchers, Gerald Joyce and Leslie Orgel, wrote in 1999. Others were so despairing that they believed some other molecule must have preceded RNA and started looking for a pre-RNA world. The miracle seems now to have been explained. In the article in Nature, Dr. Sutherland and his colleagues Matthew W. Powner and Batrice Gerland report that they have taken the same starting chemicals used by others but have caused them to react in a different order and in different combinations than in previous experiments. they discovered their recipe, which is far from intuitive, after 10 years of working through every possible combination of starting chemicals. Instead of making the starting chemicals form a sugar and a base, they mixed them in a different order, in which the chemicals naturally formed a compound that is half-sugar and half-base. When another half-sugar and half-base are added, the RNA nucleotide called ribocytidine phosphate emerges. A second nucleotide is created if ultraviolet light is shined on the mixture. Dr. Sutherland said he had not yet found natural ways to generate the other two types of nucleotides found in RNA molecules, but synthesis of the first two was thought to be harder to achieve. If all four nucleotides formed naturally, they would zip together easily to form an RNA molecule with a backbone of alternating sugar and phosphate groups. The bases attached to the sugar constitute a four-letter alphabet in which biological information can be represented. My assumption is that we are here on this planet as a fundamental consequence of organic chemistry, Dr. Sutherland said. So it must be chemistry that wants to work. The reactions he has described look convincing to most other chemists. The chemistry is very robust all the yields are good and the chemistry is simple, said Dr. Joyce, an expert on the chemical origin of life at the Scripps Research Institute in La Jolla, Calif. Dr. Sutherlands proposal has not convinced everyone. Dr. Robert Shapiro, a chemist at New York University, said the recipe definitely does not meet my criteria for a plausible pathway to the RNA world. He said that cyano-acetylene, one of Dr. Sutherlands assumed starting materials, is quickly destroyed by other chemicals and its appearance in pure form on the early earth could be considered a fantasy. Dr. Sutherland replied that the chemical is consumed fastest in the reaction he proposes, and that since it has been detected on Titan there is no reason it should not have been present on the early earth. If Dr. Sutherlands proposal is correct it will set conditions that should help solve the many other problems in reconstructing the origin of life. Darwin, in a famous letter of 1871 to the botanist Joseph Hooker, surmised that life began in some warm little pond, with all sorts of ammonia and phosphoric salts. But the warm little pond has given way in recent years to the belief that life began in some exotic environment like the fissures of a volcano or in the deep sea vents that line the ocean floor. Dr. Sutherlands report supports Darwin. His proposed chemical reaction take place at moderate temperatures, though one goes best at 60 degrees Celsius. Its consistent with a warm pond evaporating as the sun comes out, he said. His scenario would rule out deep sea vents as the place where life originated because it requires ultraviolet light. A serious puzzle about the nature of life is that most of its molecules are right-handed or left-handed, whereas in nature mixtures of both forms exist. Dr. Joyce said he had hoped an explanation for the one-handedness of biological molecules would emerge from prebiotic chemistry, but Dr. Sutherlands reactions do not supply any such explanation. One is certainly required because of what is known to chemists as original syn, referring to a chemical operation that can affect a molecules handedness. Dr. Sutherland said he was working on this problem and on others, including how to enclose the primitive RNA molecules in some kind of membrane as the precursor to the first living cell. == http://www.evolverzone.com/ == RNA can be stabilized - its behaviour in solution is a bit different than when adsorbed onto a mineral surface. Before 2004, formation of ribose sugar (formaldehyde and glyceraldehyde in alkaline solutions with heat) was easy, but degraded quickly. Some thought that meant some other compound had to be the backbone for pre-RNA, since it couldn't accumulate enough to be useful. "Borate minerals stabilize ribose", Ricardo A, Carrigan MA, Olcott AN, Benner SA, Science 2004, 9 January, 303(5655), 196. Without borate minerals, a solution of formaldehyde and glyceraldehyde at alkaline pH at 25 or 45 degrees turned brown (rampant polymerization) within 1 hour (25 deg) or 10 minutes (45 degrees) WITH borate minerals, the solutions did NOT turn brown even after incubating for 2 MONTHS. Analysis of the solution revealed that the majority of the carbon was in the form of pentose sugars - ribose, arabinose, xylose, and lyxose. All it took to go from 'impossible to generate useful amounts' to 'mundane' was the presence of a common mineral. "Theoretical study on the factors controlling the stability of the borate complexes of ribose, arabinose, lyxose and xylose", Sponer JE, et at., Chemistry 2008, 14(32):9990-9998. Ribose is the most stable pentose sugar. == http://www.blackwellpublishing.com/ridley/tutorials/ == 200,000 year old human hair found in dung Strands of hair from a human who lived 200,000 years ago have been found preserved inside fossilised hyena dung from South Africa. Palaeontologists found 40 strands of fossilised hair inside samples of coprolite, or fossilised dung, from a cave in South Africa that was used by brown hyaenas. Until now the oldest samples of human hair were from a 9,000 year old mummy found in northern Chile. It is extremely rare for soft tissue such as hair, skin and muscle to survive more than a few hundred years and only hard tissue like bone is fossilised normally. But scientists believe the new samples of hair are the remains of an early species of human that was scavenged by hyaenas after death, allowing the delicate hairs to be preserved inside the dung as it fossilised. They now hope that future analysis of the hairs could help to shed light on exactly which species it came from, the colour of their hair and even the state of health of the person it came from. Dr Lucinda Backwell, a palaeontologist at the University of Witwatersrand in Johannesburg, South Africa, who led the group that found the hairs, said: "This find is so unusual as the human fossil record at this time is exceedingly poor, and of course hair is relatively fragile and degrades easily. It is the first non-bony material in the early hominid fossil record. "As analytical techniques become more advanced they could shed light on what the person looked like, their state of health, and other aspects that cannot be investigated with current technologies." The researchers, who include archaeologists from York University and University of Bradford, used tweezers to remove 40 hairs from a single piece of dung found in a fossilised hyena latrine near Sterkfontein caves, where other early human remains have been found. They compared the fossilised hairs to samples from modern humans, primates and other animals in an attempt to identify them. They concluded that the width of the hairs is consistent with those of humans and the shape is similar to those found in modern humans. Scales on the hairs were also similar to those found on human hair as opposed to other primates. The researchers, who have published their findings this month in the Journal of Archaeological Science, believe that the hair may have belonged to an early human species known as Homo heidelbergensis, which was living in Africa around 200,000 years ago, or could be from one of the first Homo sapiens, who are thought to have evolved around 195,000 years ago. They could not rule out, however, that it was from another, entirely new human species. Dr Kirsty Penkman from York University attempted to extract DNA and protein from the hair samples but was unable to find any. The scientists hope that as techniques improve it may be possible to extract some in the future or that they may have more luck with other human remains that can be found in fossilised dung. Experts now believe that fossilised dung may help to provide more examples of ancient human remains. Dr Backwell added: "Brown hyaenas are scavengers, not hunters, so the hominid was dead by the time the hyena came upon it. "It would appear that predator dung could be a good source of human hair in the fossil record. "The contents of such dung could shed light on the ancient environments where early humans and their ancestors once lived." == http://www.evolverzone.com/ == Modern Australia lacks big land predators, but until about 30,000 years ago, the continent was ruled by Thylacoleo carnifex, the marsupial "lion." == Piltdown Man >I just checked. Dawson claimed to have found a second skull, >but no physical evidence that he had ever turned up. Um, AFAIK it did. Sort of, at least. Dawson actually came with some pieces he claimed to have found on another property some miles away. Skeptical folks reportedly looked at the bones and concluded that they displayed the same morphology as Piltdown 1. But "Piltdown 2" was never published. Incidentally, just like Piltdown, Dawson was taking care of the second property too... But he was never clear about exactly where "Piltdown 2" actually had been found, and he got sick and died before anyone had time to make him show them. The "Piltdown 2" find consisted of a missing part of the frontal bone of "Piltdown 1" (yes, an articulating piece of the same bone!) and some parts of another cranium most likely also looted from the same museum collection of Fuegian skulls as the first one. == http://roughguidetoevolution.blogspot.com/ == According to Carl Haub, a demographer at the Population Reference Bureau in Washington, D.C., between 50,000 B.C. and A.D. 2002, about 106 billion people were born. == Hobbits 'are a separate species' Scientists have found more evidence that the Indonesian "Hobbit" skeletons belong to a new species of human - and not modern pygmies. The 3ft (one metre) tall, 30kg (65lbs) humans roamed the Indonesian island of Flores, perhaps up to 8,000 years ago. Since the discovery, researchers have argued vehemently as to the identity of these diminutive people. Two papers in the journal Nature now support the idea they were an entirely new species of human. The team, which discovered the tiny remains in Liang Bua cave on Flores, contends that the population belongs to the species Homo floresiensis - separate from our own grouping Homo sapiens . They argue that the "Hobbits" are descended from a prehistoric species of human - perhaps Homo erectus - which reached island South-East Asia more than a million years ago. Over many years, their bodies most likely evolved to be smaller in size, through a natural selection process called island dwarfing, claim the discoverers, and many other scientists. However, some researchers argued that this could not account for the Hobbit's chimp-sized brain of almost 400 cubic cm - a third the size of the modern human brain. Disease theory This was a puzzle, they said, because the individuals seem to have crafted complex stone tools. They said the Hobbits were probably part of a group of modern humans with abnormally small brains. One team led by William Jungers from Stony Brook University in the US analysed remains of the Hobbit foot. They found that, in some ways, it is incredibly human. The big toe is aligned with the others and the joints make it possible to extend the toes as the body's full weight falls on the foot, attributes not found in great apes. But in other respects, it is incredibly primitive. It is far longer than its modern human equivalent, and equipped with a very small big toe, long, curved lateral toes, and a weight-bearing structure that resembles that of a chimpanzee. So unless the Flores Hobbits became more primitive over time - a rather unlikely scenario - they must have branched off the human line at an even earlier date. In another study, Eleanor Weston and Adrian Lister of London's Natural History Museum looked at fossils of several species of ancient hippos. They then compared those found on the island of Madagascar with the mainland ancestors from which they evolved. "It could be that H. floresiensis' skull is that of a Homo erectus that has become dwarfed from living on an island, rather than being an abnormal individual or separately-evolved species, as has been suggested," said Dr Weston, a palaeontologist at the museum. "Looking at pygmy hippos in Madagascar, which possess exceptionally small brains for their size, suggests that the same could be true for H. floresiensis , and that (it could be) the result of being isolated on the island." == The idea of evolution creating intelligence is that it does so a little at a time. First we get bacteria that adjust their enzyme production to changes in their environment, then we get amoebae that change their relationships with other amoebae based on changes in the environment, then we get sponges that differentiate cells to perform specific functions ... skip a bunch of evolution, and we get animals with eyes and limbs and sophisticated nervous systems to sense and record their environment ... and we get fish, who learn from experience, mimic the actions of other fish, care for their young ... and we get social primates, who can use symbolic processing to create constructs of cosmic complexity. == Darwin in a test tube: Scientists make molecules that evolve, compete, mimick behavior of Darwin's finches As described in an article published this week in an advance, online edition of the journal Proceedings of the National Academy of Sciences (PNAS), the work demonstrates some of the classic principles of evolution. For instance, research shows that when different species directly compete for the same finite resource, only the fittest will survive. The work also demonstrates how, when given a variety of resources, the different species will evolve to become increasingly specialized, each filling different niches within their common ecosystem. Conducted by Sarah Voytek, Ph.D., a recent graduate of the Scripps Research Kellogg School of Science and Technology, the work is intended to advance understanding of Darwinian evolution. Using molecules rather than living species offers a robust way to do this because it allows the forces of evolution to work over the course of mere days, with a trillion molecules in a test tube replicating every few minutes. "We can study things very quickly," says Scripps Research Professor Gerald Joyce, M.D., Ph.D., who was Voytek's advisor and her coauthor on the paper. Joyce is the dean of the faculty at Scripps Research, where he is also a professor in the Department of Molecular Biology, the Department of Chemistry, and The Skaggs Institute for Chemical Biology. On the voyage of the HMS Beagle, Darwin collected and studied different species of finches on several of the Galapagos Islands. The finches differed in their beak structure some had thick, strong beaks and others had thin, delicate ones. Darwin observed that the different finches were each adapted for the specific types of seeds that served as their primary food source. The big-beaked birds were indigenous to the places where the big seeds grew; in areas where there were also small seeds, there were also small-beaked birds. Darwin reasoned that the finches had a common ancestor but had separated into different species a classic concept in Darwinian evolution known as "niche partitioning," which holds that when two species are competing for resources within a common environment, they become differentiated so that each species adapts to use different preferred resources. For several years, Joyce has been experimenting with a particular type of enzymatic RNA molecule that can continuously evolve in the test tube. The basis of this evolution comes from the fact that each time one of the molecules replicates, there is a chance it will mutate typically about once per round of replication so the population can acquire new traits over time. Two years ago, Voytek managed to develop a second, unrelated enzymatic RNA molecule that also can continuously evolve. This allowed her to set the two RNAs in evolutionary motion within the same pot, forcing them to compete for common resources, just like two species of finches on an island in the Galapagos. In the new study, the key resource or "food" was a supply of molecules necessary for each RNA's replication. The RNAs will only replicate if they have catalyzed attachment of themselves to these food molecules. So long as the RNAs have ample food, they will replicate, and as they replicate, they will mutate. Over time, as these mutations accumulate, new forms emerge some fitter than others. When Voytek and Joyce pitted the two RNA molecules in a head-to-head competition for a single food source, they found that the molecules that were better adapted to use a particular food won out. The less fit RNA disappeared over time. Then they placed the two RNA molecules together in a pot with five different food sources, none of which they had encountered previously. At the beginning of the experiment each RNA could utilize all five types of food but none of these were utilized particularly well. After hundreds of generations of evolution, however, the two molecules each became independently adapted to use a different one of the five food sources. Their preferences were mutually exclusive each highly preferred its own food source and shunned the other molecule's food source. In the process, the molecules evolved different evolutionary approaches to achieving their ends. One became super efficient at gobbling up its food, doing so at a rate that was about a hundred times faster than the other. The other was slower at acquiring food, but produced about three times more progeny per generation. These are both examples of classic evolutionary strategies for survival, says Joyce. More information: "Niche partitioning in the coevolution of 2 distinct RNA enzymes," Proceedings of the National Academy of Sciences Source: == Dinosaur-Bird Evolution Confirmed: Hadrosaur Dinosaur Sequences Confirm Ancient Protein Is Preserved Over Time http://www.sciencedaily.com/releases/2009/04/090430144528.htm ScienceDaily (Apr. 30, 2009) Ancient protein dating back 80 million years to the Cretaceous geologic period has been preserved in bone fragments and soft tissues of a hadrosaur, or duck-billed dinosaur, according to a study in the May 1 issue of Science. Led by scientists at Beth Israel Deaconess Medical Center (BIDMC) and North Carolina State University (NCSU), the new findings support earlier results from analyses suggesting that collagen protein survived in the bones of a well preserved Tyrannosaurus rex, and offer robust new evidence supporting previous conclusions that birds and dinosaurs are evolutionarily related. In April 2007 John Asara, PhD, Director of the Mass Spectrometry Core at BIDMC, together with NCSU paleontologist Mary Schweitzer, PhD, published two papers in Science describing their discovery that collagen extracted from bone fragments of a 68-million-year-old T. rex closely matched the amino acid sequences of modern day chickens. Not surprisingly, the widely publicized findings created a great deal of controversy. "With this new paper, we hoped to show that our T. rex discovery was not a unique occurrence," notes Asara, who is also an Instructor in Pathology at Harvard Medical School. "This is the second dinosaur species we've examined and helps verify that our first discovery was not just a one-hit wonder. Our current study was the collaborative effort of a number of independent laboratories, whose findings collectively add up to a robust conclusion." At the heart of the controversy is the idea that ancient protein can exist at all. When an animal dies, protein immediately begins to degrade and, in the case of fossils, is slowly replaced by mineral, a substitution process assumed to be complete by 1 million years. But with this latest evidence, it appears that some proteins do indeed have real staying power. "We wound up identifying nearly double the number of amino acids we recovered in the T. rex study," says Asara. "The sequences displayed high spectral quality and the interpretations were of high confidence." The two scientists had decided to collaborate again after Schweitzer and paleontologist Jack Horner of Montana State University's Museum of the Rockies recovered the 80-million-year-old Brachylophosaurus canadensis femur bone in the summer of 2007 and observed that it appeared to be even better preserved than the original T. rex fossil. Schweitzer's initial laboratory analyses confirmed this observation: After being subjected to demineralization, the B. canadensis bone fragments showed marked preservation of original tissues and molecules, with microstructures resembling soft, transparent vessels, cells and fibrous matrix even though the fossil was much older than the T. rex sample. "Deep burial in sandstone seems to favor exceptional preservation," notes Schweitzer, explaining that this fossil was found under approximately seven meters of sandstone in the Judith River Formation, in parts of what is now Eastern Montana. Chemical extractions of bone and vessel were subsequently sent to the laboratories of BIDMC scientists Lewis Cantley, PhD, and Raghu Kalluri, PhD, where immunoblots and immunochemistry analyses were conducted to determine the presence of collagen protein in the samples. "Having been a part of the T. rex study, I was curious to be part of this investigation as well," explains Cantley, Chief of the Division of Signal Transduction at BIDMC. "In view of the skepticism about the original findings, it was important to demonstrate that our findings in T. rex could be verified in another dinosaur and in other laboratories." The results confirmed the existence of protein. "Because I am a collagen biochemist, our lab was contacted to perform an independent analysis of this new bone find," explains Kalluri, who is Chief of the Division of Matrix Biology at BIDMC. "We isolated the proteins collagen, laminin and elastin from the bone, and also extracted bone cells and blood vessels from this sample. Our findings demonstrated that it did contain basement membrane matrix." In addition, In situ mass spectrometry studies conducted at Montana State University by Recep Avci and Zhiyong Suo independently verified amino acids in dinosaur tissues, including the collagen signature amino acid, hydroxylated proline. From there, using a combination of two mass spectrometry technologies linear ion trap and hybrid linear ion trap/orbitrap Asara was able to improve upon the techniques he had used in analyzing both the T. rex specimen and specimens from bones of other prehistoric animals including a 300,000-year-old mammoth and mastodon. At the beginning of the study, Asara explains, his lab used an ion trap mass spectrometer, which captures and holds peptides through time so that after the collected peptides are measured for mass they are isolated and fragmented to reveal their amino acid sequence. Then, while the study was in progress, his lab acquired a high-resolution and highly mass-accurate Orbitrap XL mass spectrometer, which was used during the second half of the analysis. "Because it is capable of sub 2 ppm mass accuracy, the Orbitrap allowed us to make more confident sequence calls than we did in the T. rex study," Asara explains. "For example, the mass difference between a hydroxyproline amino acid residue [which is plentiful in collagen] and a leucine or isoleucine residue is only 0.0364 Da. Although this very small measurement proved to be an obstacle for the ion trap, it was not a problem for the Orbitrap." Material for mass spectrometry sequence analysis was also sent to the lab of William Lane at Harvard University and mass spectrometry sequence data were independently verified by John Cottrell, PhD, at Matrix Science in London, UK. The end result was a total of eight collagen peptides and 149 amino acids from four different samples, sequences that held up when multiple validation steps were performed, including comparisons with synthetic peptides using a spectral comparison algorithm and statistical evaluation. In the final portion of the study, coauthor Chris Organ, PhD, a Postdoctoral Fellow in the Department of Organismic and Evolutionary Biology at Harvard University, conducted a rigorous phylogenetic analysis of the identified sequences to determine B. canadensis' place within the evolutionary tree of animals. The B. canadensis collagen sequence data were compared to a database of collagen sequence data from 21 species of living animals and sequences from two other fossils, mastodon and T. rex. The results placed B. canadensis on the same family-tree branch with T. rex, in the same group as chicken and ostrich, and more distantly, to alligator and lizard. "The phylogenetic analysis yielded clear results, but the placement of the extinct dinosaurs still rests on a limited amount of sequence data," notes Organ. "There is not enough sequence data to correctly parse out the relationships within Dinosauria [the group containing B. canadensis, T. rex and the two birds] but the group as a whole is well supported by the analysis, which is consistent with studies based on morphology." Ultimately, notes Asara, "We were able to achieve these results, in part, because the mass spectrometry systems that our lab has set up for cancer research are capable of a similar concentration range low to sub femtomole -- needed for ancient fossil protein sequencing. We hope to meet with similar success when it comes to identifying novel signaling proteins from cancerous tissues." This study was funded, in part, through grants from the National Science Foundation, the David and Lucile Packard Foundation, the Merck Postdoctoral Science Research Fellowship, the National Institutes of Health and the Taplin Funds for Discovery, Harvard Medical School. In addition to Asara and Schweitzer, coauthors include BIDMC investigators Lewis Cantley, Raghu Kalluri, Lisa Freimark, Valerie Lebleu, and Michael Duncan II; Wenxia Zheng of North Carolina State University; Chris Organ, John Neveu and William Lane of Harvard University; Recep Avci, and Zhiyong Suo of Montana State University; John Horner of the Museum of the Rockies (MT); Matthew Vander Heiden of the Dana-Farber Cancer Institute; and John Cottrell of Matrix Science, London, UK. Journal reference: 1. Mary H. Schweitzer et al. Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur Brachylophosaurus canadensis. Science, May 1, 2009 Adapted from materials provided by Beth Israel Deaconess Medical Center. == Ape/human evolution 1. The GULO gene is the same severely damaged pseudogene. Not only is it broken, it's broken in the same heritable fashion. This gene, in mammals where it functions normally is part of a system that enables the synthesis of ascorbates in the liver. 2. Several retroviruses nave made their random insertions at the same points in both genomes. 3. The human number 2 chromosome is very clearly a fusion end-to-end of two of the ape chromosomes, with telomeres still evident at the join (telomeres are only normally found at chromosome ends). == Worcester State College anthropologist Jeremy DeSilva decided filming chimpanzees could advance the debate-an obvious reflection of his evolutionary presuppositions. In Uganda's Kibale National Park, DeSilva recorded chimps' anatomical movements as they climbed around in trees. The chimps flex their ankles by raising their feet some 45 degrees from the resting position-far more than humans could do without suffering serious injury. Instead, humans bend their ankles 15 to 20 degrees at most when attempting the equivalent action. Next, DeSilva examined a variety of ape and human fossils, looking at the main bones that compose the ankle joint (the tibia and talus bones). His study shows that "all of the hominin [i.e., human fossil] ankle joints resembled those of modern humans rather than those of apes." That's no surprise to creationists! . Some, such as Stony Brook University anthropologist William Jungers, point out that modern humans can still climb trees without such ankle-flexing capacity. But DeSilva doesn't think early humans could have been simultaneously good at ground-walking and tree-climbing, instead concluding that "full bipedalism would have evolved relatively rapidly as tree-climbing ability declined," ScienceNOW reports. == Scientists Unravel Genome of the Cow The genomes of man and dog have been joined in the scientific barnyard by the genome of the cow, an animal that walked beside them on the march to modern civilization. A team of hundreds of scientists working in more than a dozen countries yesterday published the entire DNA message -- the genome -- of an 8-year-old female Hereford living at an experimental farm in Montana. Hidden in her roughly 22,000 genes are hints of how natural selection sculpted the bovine body and personality over the past 60 million years, and how man greatly enhanced the job over the past 10,000. As with other species, genes governing the immune system, the metabolism of nutrients and social interaction appear to be where much of the evolutionary action has occurred. The result is an animal that lives peacefully in herds and grows large on low-quality food, thanks to the billions of bacteria it carries around. Selective breeding has exaggerated and spread some of those traits, producing hyper-passive Holsteins and muscle-bound Belgian Blues, and dozens of humpbacked breeds that combine characteristics of both. "Are there signatures of the human hand in the cattle genome? The answer is plainly and clearly yes," said Harris A. Lewin, head of the Institute for Genomic Biology at the University of Illinois at Urbana-Champaign. He is the author of one of three papers on the cow genome appearing today in the journal Science. Although sheep and goats were domesticated earlier, cattle are the most important herd animals in the world. There are about 800 distinct breeds, and together they contribute to the nutrition or income of about 6.6 billion people. The cow is the first livestock animal whose genome has been sequenced, part of an effort to read and analyze the DNA of organisms that have scientific, medical or economic importance. In addition to dozens of microbes and several plants, those sequenced so far include the chimpanzee, mouse, rat, dog, chicken, mosquito, fruit fly, opossum and platypus. Of a cow's 22,000 genes, versions of at least 14,000 have counterparts in other mammals. Cows appear to have about 1,000 genes that they share with dogs and rodents but that are not found in people. The most recently evolved genes tend to be clustered in parts of the cow's 31 chromosomes where stretches of DNA have been duplicated, copied and inserted upside down, or added to by invading viruses. Those events are usually catastrophic and often lead to the fatal breakage of chromosomes. Over evolutionary time, however, a few survive and provide the raw material for new genes -- and new functions. This clear relationship between chromosome instability and gene formation is giving scientists a new view of one way evolutionary change happens at the molecular level. "Instead of having only a very slow and gradual change by mutation, you have the ability for much larger and dramatic changes because of these rearrangements," Lewin said. As a practical matter, having the genome is also going to make cattle breeding faster and cheaper. Traits carried by bulls are important in determining how much milk a cow produces. Because bulls don't make milk, however, a bull's "performance profile" has to be sketched by observing the milk production of his daughters -- a process that takes about six years and costs $25,000 to $50,000. Now, male calves can be tested at birth for milk-enhancing traits using gene-chip technology. "It doesn't take a rocket scientist to see that makes sense both logistically and financially," said Curt P. Van Tassell, a geneticist at the U.S. Department of Agriculture's laboratory in Beltsville, who was one of the leaders of the project. There are two types of cattle -- taurine, which have no humps and predominate in Europe, Africa, the Americas and much of Asia; and indicine, which have humps and are in South Asia and East Africa. Both lineages descended from aurochs, a much larger and more aggressive species. Indicine breeds have much greater genetic diversity than taurine breeds, evidence that they were developed from a larger number of "founder" animals. Cows have a large number of genes devoted to big-gun, nonspecific defenses called "innate immunity," probably reflecting the fact that the animals rely on a huge variety of bacteria and other organisms to digest the roughage they eat. "They need an immune system that can deal with that large microbial population in close proximity all the time," said Kim C. Worley, a geneticist at Baylor College of Medicine and one of the leaders of the project. Both types of cattle show evidence of natural selection in genes that appear to be involved in making the animals -- large, horned and potentially dangerous -- docile. In some breeds, specific variants of behavior-related genes are "fixed," or seen in essentially every animal. Curiously, some of those genes are in regions that in the human genome seem to be involved in autism, brain development and mental retardation. == Seal Ancestry Life reconstruction of Puijila darwini swimming in crater lake. Credit: Mark A. Klingler/Carnegie Museum of Natural History Skeletal illustration of Puijila darwini. Credit: ark A. Klingler/Carnegie Museum of Natural History Reconstruction of skeleton showing preserved bones in dark grey. Credit: ark A. Klingler/Carnegie Museum of Natural History A fossil of a primitive "walking seal" with four legs and webbed feet has been found in the Canadian Arctic and dated to be at least 20 million years old. The newfound species, dubbed Puijila darwini, might be the long-sought missing link in the evolution of pinnipeds a group that includes modern seals, sea lions and walruses explaining how the animal group moved from land-dwellers with legs to the semi-aquatic, flippered swimmers around today. "The land-to-sea transition in pinnipeds has been difficult to study because the fossil evidence has been weak and contentious," said Natalia Rybczynski, a paleontologist with the Canadian Museum of Nature who led the expedition that discovered the skeleton. "Puijila is important because it provides a first glimpse into the earliest stages of this important evolutionary transition." The discovery is detailed in the April 23 issue of the journal Nature. From feet to flippers Modern pinnipeds all have flippers limb adaptations well-suited for gliding through the water in search of a fresh seafood dinner. Paleontologists have long thought that these specialized limbs evolved over time as terrestrial species began testing out life in the water. Charles Darwin himself (for whom the new species was named) predicted this land-to-sea transition in The Origin of Species: "A strictly terrestrial animal, by occasionally hunting for food in shallow water, then in streams or lakes, might at last be converted in an animal so thoroughly aquatic as to brace the open ocean." But until Puijila's discovery, the most primitive pinniped known to science (Enaliarctos) was already fully flippered. Accidental discovery Rybczynski and her team found the skeleton purely by accident during an expedition to the Haughton meteor impact crater on Devon Island, one of Canada's northernmost Arctic islands. The team's vehicle had run out of gas, and the first bone of the animal was found while waiting for team members to return with fuel. The bones found on that trip and a subsequent expedition in 2008 produced a surprisingly complete (almost 65 percent) skeleton. The researchers at first thought that the animal was a prehistoric otter, but when they examined it more closely they found they had a far more exciting specimen that shed light on an important aspect of animal evolution. "The remarkably preserved skeleton of Puijila had heavy limbs, indicative of well developed muscles, and flattened phalanges which suggests that the feet were webbed, but not flippers. This animal was likely adept at both swimming and walking on land," said Mary Dawson, curator emeritus of Carnegie Museum of Natural History in Pittsburgh. "For swimming it paddled with both front and hind limbs. Puijila is the evolutionary evidence we have been lacking for so long." The animal was a four-legged carnivore about 43 inches (110 centimeters) from nose to tail. Along with its webbed feet, it had an elongated, streamlined body that would have allowed it to glide through the water with speed and agility. Its large teeth, short snout and jaw suggest it had a nasty bite. Puijila likely hunted on both land and in the water; possible preserved stomach contents suggest the animal's last meal included a duck and some type of rodent. Puijila itself was not an ancestor of modern seals, but the researchers think that both groups evolved from a common ancestor. Researchers are still working to figure out exactly where Puijila fits in on the pinniped family tree. Arctic evolution Other fossils of fish and pollen indicate that the Arctic location where Puijila was once had a cool, coastal temperature environment, similar to present-day New Jersey. "Puijila is the first fossil evidence that early pinnipeds lived in the Arctic," Rybczynski said. "This discovery supports the hypothesis that the Arctic may have been a geographic center in pinniped evolution." (The name Puijila means "young sea mammal" in Inuktitut, the language of the Inuit people in Nunavut, the territory of Canada where the fossil was found.) The lakebed where the fossil was found suggests that the semi-aquatic mammals also went through a freshwater-to-seawater transition, as freshwater lakes would have frozen in the winter, forcing the animals to travel over land to the sea in search of food. The team is planning to go back to the Devon Island site this year to look for more fossils. The Puijila skeleton will be on display at the Canadian Museum of Nature in Ottawa from April 28 to May 10. A model of the fossil will be included in the "Extreme Mammals" exhibition at the American Museum of Natural History in New York, which opens on May 16. The project was supported by the Canadian Museum of Nature, Carnegie Museum of Natural History, American Museum of Natural History, Polar Continental Shelf Program, Northern Scientific Training Program, Government of Nunavut, Qikiqtani Inuit Association and the hamlet of Frise Fiord, Nunavut. == If anti-evolution activists ever had any intentions of developing their own explanation, they have long stopped trying. The few that actually perform original research obtain results that either support evolution, or at least provide no support whatever to any alternative that would satisfy most evolution deniers. After 150 years it should be clear that not only will the activists never deliver that theory, they expel themselves from even trying. == An Amazonian ant has dispensed with sex and developed into an all-female species, researchers have found. The ants reproduce via cloning - the queen ants copy themselves to produce genetically identical daughters. This species - the first ever to be shown to reproduce entirely without sex - cultivates a garden of fungus, which also reproduces asexually. == Fruit flies (Drosophilidae) are a very large family, including at least the following genera: Acletoxenus - Allopygaea - Amiota - Apenthecia - Apsiphortica - Baeodrosophila - Balara - Bialba - Cacoxenus - Calodrosophila - Celidosoma - Chymomyza - Cladochaeta - Collessia - Colocasiomyia - Crincosia - Dettopsomyia - Diathoneura - Dichaetophora - Dicladochaeta - Drosophila - Electrophortica - Eostegana - Erima - Gitona - Hirtodrosophila - Hyalistata - Hypselothyrea - Jeannelopsis - Laccodrosophila - Leucophenga - Liodrosophila - Lordiphosa - Luzonimyia - Marquesia - Mayagueza - Microdrosophila - Miomyia - Mulgravea - Mycodrosophila - Neorhinoleucophenga - Neotanygastrella - Palmomyia - Palmophila - Paraleucophenga - Paraliodrosophila - Paramycodrosophila - Pararhinoleucophenga - Parastegana - Phortica - Phorticella - Poliocephala - Pseudiastata - Pseudocacoxenus - Pseudostegana - Pyrgometopa - Rhinoleucophenga - Samoaia - Scaptodrosophila - Scaptomyza - Soederbomia - Sphaerogastrella - Sphyrnoceps - Stegana - Styloptera - Tambourella - Trachyleucophenga - Zaprionus - Zapriothrica - Zaropunis - Zygothrica == Genetic evidence has shown that Chimpanzees are more closely related to people than they are to gorillas. == Evolutionary Origin Of Bacterial Chromosomes Revealed Researchers have unveiled the evolutionary origin of the different chromosomal architectures found in three species of Agrobacteria. A comprehensive comparison of the Agrobacterium sequence information with the genome sequences of other bacteria suggests a general model for how second chromosomes are formed in bacteria. Agrobacteria are members of the Rhizobiaceae family, which also includes the benign, nitrogen-fixing organisms Rhizobium and Sinorhizobium. Agrobacterium tumefaciens C58 is the workhorse of the plant biotechnology science and industry, thanks to its ability to insert its own DNA into host plants. Members of the Rhizobiaceae have genetic architectures that span single chromosomes, multiple chromosomes and circular DNA molecules (plasmids) of various sizes. The scientists used the sequence information of the genomes of three types of Agrobacterium (biovars), two of which were recently completed, and compared the sequences with those of different bacteria to shed light on the origin of the different chromosomal arrangements. Most bacteria have only one chromosome. The Rhizobiaceae is an unusual bacterial family in that all of its members have either two chromosomes or one chromosome and very large plasmids. Until this study, it was not clear how such multichromosomal architectures had evolved. Joo Setubal, associate professor at the Virginia Bioinformatics Institute and the Department of Computer Science at Virginia Tech, commented: Thanks to the efforts of the Agrobacterium Genome Sequence Consortium and the wider research community, we have sufficient sequence data available from different bacterial species to allow the inference of a general model for bacterial genome evolution. It appears that the transfer of genes from chromosomes to large plasmids mediates second chromosome formation. Examination of different genome sequences within the Rhizobiales family has revealed that gene migration is rife among the different replication units, said Steve Slater, professor at the University of Wisconsin. Genes are not only migrating between organisms but they are also moving within the cell between chromosomes and plasmids. The genetic organization of even essential genes in bacteria is much more complex and fluid than has been imagined. The three Agrobacterium biovars for which we now have sequences A. tumefaciens C58, A. radiobacter K84, and A. vitis S4 provide an exciting snapshot of chromosome evolution in progress, said Brad Goodner, associate professor at Hiram College. In Biovars I and III, Agrobacteria gene movements have produced second chromosomes derived from plasmids, while in the biovar II strain K84 the plasmid-based replicon has yet to reach second chromosome status. Derek Wood, associate professor at Seattle Pacific University, remarked: The findings in this work provide substantial new evidence that second chromosomes in all bacteria studied to date have plasmid origins. While other mechanisms leading to second chromosome formation seem possible, it is intriguing that this approach has been most productive. Because of the biotechnological importance of Agrobacterium, the sequence information provided by these strains should be an invaluable resource for Agrobacterium researchers and the wider life sciences research community, said Barry Goldman, Biotechnology Prospecting Lead at Monsanto. The work was supported by the National Science Foundation, the M. J. Murdock Charitable Trust Life Sciences program, an education grant from the Howard Hughes Medical Institute, the Conselho Nacional de Desenvolvimento Cientfico e Tecnolgico, and by the Monsanto Company. More than 450 undergraduate students at Hiram College, Oregon State University, Seattle Pacific University, Arizona State University, University of North Carolina, Washington University in St. Louis, and Williams College contributed to the annotation of the three Agrobacterium genomes between 2004 and 2008. == Archea have flagellar motility and their flagellum is completely different. There are also eukaryotic flagella and they are different still. == UA biologist Todd Blackledge unravels web clues to spider evolution http://www.thesuburbanite.com/news/education/x1402120984/ UA-biologist-Todd-Blackledge-unravels-web-clues-to-spider-evolution Akron, Ohio - Spider webs just dont fossilize. But if they did, they probably would look quite different from those of modern spiders. And thats important, says University of Akron researcher and Akron resident Dr. Todd Blackledge, because it implies that new web constructions and silk types helped the order Araneae evolve into one of the insect worlds superpowers. A modern spiders silk web construction differs significantly from its ancestors and gives a strong indication of the link between spider evolution and web function, according to Blackledge, an associate professor of biology in UAs Integrated Bioscience Program. Blackledge shares these findings in his research, Reconstructing Web Evolution and Spider Diversification in the Molecular Era, published in this months Proceedings of the National Academy of Sciences. Blackledge and his research team determined that the silk architecture of a web relates to spider diversification and is linked to the arachnids success as a predator, as revealed in their study of the araneoid orb and cribellate webs. The araneoid orb, made of stretchy spirals coated with a moist adhesive, provides access to a plentitude of flying insects. Many spiders, however, produce cribellate silk, a radically different dry adhesive that adheres to prey. Some cribellate spiders also construct aerial orb webs, but most spin sheet-like webs or have abandoned capture webs altogether, according to the article. The most diverse families within orb-weavers no longer build orb webs, but instead spin aerial sheet webs or cobwebs, Blackledge says. To understand spider diversification, its essential to examine the pattern of evolution of web-spinning behaviors. Blackledge points out that orb webs arose only once and the evolution of these webs is marked by a dramatic increase in their geometric regularity due to spiders increased spinning. Modern spiders complete orb webs in a fraction of the time required for cribellate orb webs. Our study refutes the idea of evolutionary convergence. Instead of these two types of spiders, which use very different adhesive silks, separately evolving orb-spinning behaviors, Blackledge explains, we show that the behavior arose a single time and that spiders subsequently switched the type of silk that they use to make webs sticky. According to Blackledge, these behavioral shifts in silk and web production by spiders likely played a key role in their evolutionary success. == Gruesome group death of young dinos analyzed A muddy lakeside some 90 million years ago drew a herd of young, birdlike dinosaurs to a terrifying end, say paleontologists who excavated the site in Inner Mongolias Gobi Desert. These animals died a slow death in a mud trap, their flailing only serving to attract a nearby scavenger or predator, said the University of Chicagos Paul Sereno, one of the leaders of the dig. He added that the site provides some of the best evidence to date for any dinosaurs cause of death. A map of Inner Mongolia in northern China showing the site of the discovery of a herd of young Sinornithomimus dinosaurs, a place near the outpost Suhongtu. (Courtesy Project Exploration) Composed of juveniles of the species Sinornithomimus dongi, the find suggests youngsters were left to fend for themselves when adults were busy nesting or brooding; there were no adults or hatchlings, Sereno remarked. One pair of the skeletons, prepared for display in Serenos lab and airlifted back to China in late February, preserve the animals last meals in the stomachs, scientists said. Sereno, along with Tan Lin of the Inner Mongolia Department of Land and Resources and Zhao Xijin of the Chinese Academy of Sciences, led the 2001 expedition that found the fossils. The findings are published in the December 2008 issue of the research journal Acta Palaeontologica Polonica. Finding a mired herd is exceedingly rare among living animals, said team member David Varricchio of Montana State University. The best examples are from hoofed mammals. The first bones from the herd were spotted by a Chinese geologist in 1978 at the base of a small hill in a desolate, windswept region of the Gobi Desert. Some 20 years later, a SinoJapanese team excavated the first skeletons, giving the dinosaur its Latin scientific name, which means Chinese bird mimic. Sereno and associates then opened an expansive dig. They followed one skeleton after another deep into the base of the hill to extract more than 25 individuals, ranging from one to seven years old as calculated by annual growth rings in the bones. The team recorded the position of all of the bones and the details of the rock layers to try to understand the longago events. The skeletons showed similar exquisite preservation and were mostly facing the same direction, the researchers said, suggesting that they died together and rather quickly. The details provided key evidence of an ancient tragedy, the scientists argue. Two skeletons fell one right over the other. Although most of their skeletons lay on a flat horizontal plane, their hind legs were stuck deeply in the mud below. Only their hip bones were missing, the likely handiwork of a scavenger working over the meatiest part of the body bodies shortly after the animals died. Plunging marks in mud surrounding the skeletons recorded their failed attempts to escape. Varricchio said he was both excited and downcast by the grim evidence. I was saddened because I knew how the animals had perished. It was a strange sensation and the only time I had felt that way at a dig, he said. In addition to herd composition and behavior, the site also provides encyclopedic knowledge of even the tiniest bones in the skull and skeleton: we even know the size of its eyeball, Sereno said. Sinornithomimus is destined to become one of the bestunderstood dinosaurs. == Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body (Vintage) (Paperback) by Neil Shubin (Author) == Feathered dinosaur throws bird evolution into a flap Theories about bird evolution have been thrown into confusion by the discovery of a small feathery dinosaur. The creature, found in China, belonged to a large group of dinosaurs previously thought to have no connection with birds or feathers. Yet its fossil remains contain clear signs of feather-like structures, including long tail filaments. It is well known that birds are small dinosaurs with feathers. They are believed to be descended from theropods, carnivorous dinosaurs which stood on two legs such as Tyrannosaurus rex and Velociraptor. A number of theropod fossils have been discovered bearing the remains of primitive feathers, thought to have been used for insulation or display rather than flight. But the newly discovered dinosaur, named Tianyulong confuciusi, was not a theropod. It did not even belong to the vast group called Saurischia which included theropods, early birds and huge plant-eating dinosaurs such as Brachyosaurus. Tianyulong was part of the other large dinosaur group, Orinithischia, which included duck-billed hadrosaurs and the armoured Triceratops and Stegosaurus. The dinosaur dates back to the early Cretaceous period, around 130 million years ago. Its incomplete fossil skeleton was found in Liaoning Province, north-eastern China, the home of many other feathered dinosaurs. Even in its own time, Tianyulong was a "living fossil", bearing features tying it to a group of herbivorous dinosaurs that evolved 70 million years earlier. Discussing the research in Nature, US expert Dr Lawrence Witmer, from Ohio University, wrote: "Perhaps the only conclusion that can be drawn... is that little Tianyulong has made an already confusing picture of feather origins even fuzzier." == Jerry Coyne Why Evolution Is True == Archaeopteryx is a word based on ancient Greek archaios meaning 'ancient' and pteryx meaning wing. In German, Archaeopteryx is also known as the Urvogel, a German word meaning original bird or first bird. Both names originated in Germany, where the first fossils were found though archaeopteryx is the one most used in the English speaking world. == http://tinyurl.com/2000-Homo-sapiens http://tinyurl.com/Late-Pleistocene-human-populat == http://toarchive.org/faqs/comdesc/ The oldest dated zircons date from about 4.4 Billion years ago - 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. == http://en.wikipedia.org/wiki/Evolution_as_theory_and_fact == A list of animals that have traits of both reptiles and birds. Some of them are from side-branches on the way to extant birds, and others are *less* derived than dinosaurs, but still have traits found in the birds of today. It's really just a list to rebut the claim that we don't have any examples from the fossil record. We do, and obviously we have more then just a few. Coelophysis, Coelurus, Compsognathus, Sinosauropteryx, Dilong, Beipiaosaurus, Caudipteryx, Protarchaeopteryx, Epidendrosaurus, Epidexipteryx, Jinfengopteryx, Sinornithosaurus, Bambiraptor, Unenlagia, Velociraptor, Pedopenna, Microraptor, Archaeopteryx, Rahonavis, Shenzhouraptor, Jeholornis, Jixiangornis, Sapeornis, Eoconfuciusornis, Confuciusornis, Aberratiodontus, Boluochia Concornis, Enantiornis, Eoalulavis, Eoenantiornis, Gobipteryx, Halimornis, Iberomesornis, Liaoningornis, Liaoxiornis, Longirostravis, Noguerornis, Protopteryx, Sinornis, Vescornis, Patagopteryx, Hongshanornis, Chaoyangia, Songlingornis, Liaoningornis, Yixianornis, Yanornis, Apsaravis, Gansus, Ambiortus, and Ichthyornis. == A chicken's underlying ability to grow teeth derives from a common ancestor with alligators--archosaurs--that is more recent than the one linking birds and mammals. Nevertheless, the underlying genetic mechanism that produces teeth in mice, alligators and mutant chickens remains the same. == What a dinosaur handprint reveals Dinosaur tracks with hand prints show bird-like inward-facing palms at Johnson Farm, Utah. At right, an artist's reconstruction shows the formation of the tracks by the large meat-eating dinosaur Dilophosaurus some 198 million years ago. The discovery from a 198-million-year-old crouching carnivore indicates that even early dinosaurs had forelimbs similar to those of birds. In his classic 1993 film "Jurassic Park," the director showed Tyrannosaurus rex, Velociraptor and other carnivorous dinosaurs walking with their forearms hanging down like a monkey's and their palms more or less parallel to the ground -- a posture derisively referred to by paleontologists as the "bunny position." A growing body of evidence, however, has suggested that the creatures were physically unable to assume this position because their wrist bones would not turn in such a fashion. Now, the first unequivocal handprint of a 198-million-year-old crouching carnivore confirms the speculation, providing clear evidence that the front limb struck the ground on its side, like a karate chop, and thus would have been of little use for walking. The extremely rare handprint from the St. George Dinosaur Discovery Site in Utah indicates that even early dinosaurs had forelimbs similar to those of birds, reinforcing the now widely held conclusion that birds are the only living descendant of the ancient monsters. "What this seems to imply is that, even from fairly early in their history, dinosaurs were entirely bipedal and weren't using their forearms to support themselves in any way," said paleontologist Tom Holtz of the University of Maryland, who was not involved in the research. "Because of that, the hands could specialize as weapons, to grab on to a struggling animal or to fight with other dinosaurs," he said. The handprints are among more than 1,200 dinosaur tracks deposited in mud along the shores of an ancient lake, then buried and fossilized. Most of the tracks are similar to ones found at other sites, said paleontologist Andrew Milner, lead author of the report published Tuesday in the online journal PLoS One. But one set of tracks shows the trail of a carnivore called a theropod leaving the water and climbing up a low hill on the shore. The tracks clearly show the hind feet and, occasionally, the dragging tail. But at one point, Milner said, the theropod apparently stopped and crouched to rest. At that point, between the footprints, is the clear circular impression of the ischium or pelvis, "basically a butt print," Milner said. And to each side of the tracks are the handprints, which are mirror images of each other. They clearly show the third digit pressed into the ground and traces of the second digit, with the claw curling inward. The hands were positioned as they would be for "holding on to a basketball rather than dribbling it," Holtz said. The dinosaur, whose exact species is not known, sat like an ostrich or emu, Milner said. "Early on in the theropods we're seeing bird-like behavior, and the arrangement of the bones in the arms shows a very bird-like arrangement," he said. Paleontologists have not been entirely certain of the hand positioning of dinosaurs because wrist bones are fragile and not generally well preserved, and much of the positioning is governed by cartilage, which is also not preserved, Holtz said. But "unlike a skeleton, this print was made by a living, breathing dinosaur in its normal operations," he said. "And it clearly doesn't put its palms down, just the edges of its hands." == Dr. Daniel Fairbanks, Associate Dean of Science at Utah Valley University, "Relics of Eden: The Powerful Evidence of Evolution in Human DNA". == Paleontologists Strike Fossil Gold in Colombia Coal Mining Removes Rock Layers to Reveal Mammoth Snakes, Other Finds Carlos Jaramillo is lead paleontologist of a Smithsonian-funded team finding fossils at the Cerrejon site, in an open-pit coal mine in northern Colombia. BOGOTA, Colombia -- Carlos Jaramillo is 39 years old but loves to dig in the dirt -- especially the dry, flaky shale formations of Colombia's Guajira province. "If you talk to a paleontologist," he explained, "you're talking to a kid who never grew up." For the past five years, Jaramillo and his team of paleontologists have been burrowing ground so rich in fossils that they have made the kinds of discoveries that thrill the scientific world. And they still have years of digging ahead of them at this site in the Cerrejon region of northeastern Colombia, a remote and oven-hot place not unaccustomed to drug traffickers and the occasional rebel column. Last month, an international group of scientists revealed in the journal Nature that Jaramillo's team had made a startling discovery -- a species of snake larger than a school bus that ruled northern South America 60 million years ago. Evolving after the extinction of the dinosaurs, Titanoboa cerrejonensis -- or titanic boa from Cerrejon -- might have been the largest vertebrate living on land at that time, the Paleocene era. Indeed, it had an average length of 43 feet -- far longer than any of today's pythons or anacondas -- and it weighed 2,500 pounds, more than a small car. Its diet included giant turtles and crocodiles -- Jaramillo's team also discovered the fossilized remains of those creatures under layers and layers of dirt and shale. In all, Jaramillo and his team have found the remains of 28 snakes that measured between 42 and 49 feet. "What we have is a population of big snakes," said Jaramillo, who is Colombian. "It's not one snake. It's a bunch of them." Funded by the Smithsonian Institution, Jaramillo's team -- the other members are students working on their master's or doctorate degrees -- has been digging in the most unusual of sites, the enormous, open-pit Cerrejon coal mine. Worked by some of the world's biggest mining multinationals, Cerrejon's 270 square miles are filled with moonlike craters 300 feet deep. Excavators and earthmovers work without pause, carting off 32 million metric tons of coal a year. They also remove rock and dirt that the paleontologists would never be able to budge -- making it much easier for Jaramillo's team to reach the valuable fossils that he said are opening a window on the first tropical forests that evolved after the dinosaurs disappeared. "They close a pit, and then they open up a new pit, so we always have possibilities," Jaramillo said. "I think we'll have 10, 15 years to do excavations. We always find new things." Arriving for a dig a few months ago, Jaramillo scanned the horizon. For a first-time visitor accompanying him, it appeared to be anything but ground zero for fossils. Huge trucks roared past carrying mounds of coal to be exported to Europe and the United States, and heavy machinery could be heard in the distance, kicking up clouds of dust. Wearing white work helmets, Jaramillo and two members of his team descended into one of the pits. They carried the tools of their trade -- a light chisel to brush off dirt and a hand lens to examine their discoveries. Perhaps even more important is simply having a sharp eye and a soft touch. "You need to train your eyes and you need to have special skills to do that," Jaramillo explained. "If you don't have the skills, you will come here for a year and never find anything." The team's work has already turned up giant crocodiles and freshwater turtles that weighed 300 pounds. There are also hundreds of fossils of leaves so perfectly preserved that the paleontologists can easily make out the veins and ridges. "Oh my God, you can tell the venation very well!" Jaramillo exclaimed, examining a leaf belonging to the Araceae plant family. "This is 60 million years old. So it's probably one of the oldest Araceaes ever found." He then showed off the remains of a recently discovered anaconda, and then the fossils of fish and crabs, too. "This was like a big delta; it was a tropical rain forest," he said. That may be hard to fathom today because it rarely rains in Guajira province, which is now mostly home to scrub grass and small trees. Jaramillo and other scientists think the forest that once thrived in Cerrejon evolved after a giant meteorite hit Mexico's Yucatan Peninsula. The fossils they are recovering are helping to explain how the forest responded to that environmental catastrophe -- and may provide clues on how the modern world will react to, say, global warming. The team's discoveries are piling up -- 4,000 fossils of plants, fruit, flowers and seeds; 75 turtles, 25 crocodiles, as well as fish, crabs and other creatures. The fossils belong to Colombia but are on loan to the Smithsonian Tropical Research Institute in Panama and at the University of Florida at Gainesville. Still, Jaramillo searches for more. He said each find is like the chapter of a book. Pieced together, they tell a long and complex story, one that he said is not yet complete. "The feeling is amazing, because we don't know if here we're going to have a fantastic flower nobody has seen for the last 60 million years, or perhaps there is nothing," he said, as he took a chisel to a mound he had recovered from the shale. "So you just crack the rock open and hope for the best." == The unusually intact fossilized skull of a giant, bony-toothed seabird that lived up to 10 million years ago was found on Perus arid southern coast, researchers said Friday. The museum said in a statement that the birds had wingspans of up to 20 feet (6 meters) and may have used the toothlike projections on their beaks to prey on slippery fish and squid. But studying members of the Pelagornithidae family has been difficult because their extremely thin bones while helpful for keeping the avian giants aloft tended not to survive as fossils. With fossils discovered in North America, North Africa and even Antarctica, Kepska said, the birds were ubiquitous only a few million years before humans evolved and scientists puzzle over why they died out. Some believe they are related to gannets and pelicans, while other say they are related to ducks. Its not exactly what Comfort had in mind, but close enough, dammit. It had toothlike projections, it flew what else do you need. It also means the scientific name is pelagornithid. == Found: Oldest fossilized brain ever is uncovered in Kansas A 300 million-year-old fossilized fish brain was discovered during a routine computed tomography (CT) scan, according to a study published today in the Proceedings of the National Academy of Sciences. Until now, scientists assumed that brains rarelyif everturned into fossils. Other soft tissue fossils, such as muscles and kidneys, have been found that date back longer than 350 million years ago, but because the brain is delicate and consists mostly of water, it's much less likely to be preserved in fossil form, says study co-author John Maisey, a curator in the paleontology division of the American Museum of Natural History in New York. But "It's more than just a curiosity," he says. "Modern technology has revealed a fossil that we really didn't know about before." High-powered scans using x-ray synchrotron microtomography (which, like a CT, uses x-rays to image cross-sections of an object) allowed scientists to peer into the rock-solid skull to see the 0.06-by-0.28-inch (1.5 by 7 mm) brain. The fossil was from an iniopterygian, an ancient extinct fish that is a relative of sharks, rays and ratfish. What surprised researchers even further is that it showed a brain similar to that of modern-day shark. In the fossilization process, the brain itself was replaced with hard minerals, which preserved the shape of the original organ, and the rest of the cavity was filled with sediment, Maisey says. He notes that researchers found several fossilized craniums, each resembling a little "broken bowl of rock," in rock from the Upper Carboniferous period in Kansas and Oklahoma. But only one has yielded a preserved brain structure. "It's quite possible that brain fossils are actually more common, and we simply haven't been able to find them," says Maisey, who noted that researchers may now try to check out other fossilized skulls with the high-tech scanners to see if they contain mineralized brains. Of course, this finding also means that paleontologists may have to stretch their own brains a bit to include things other than bones. "Now we have to learn new things about brains," Maisey joked, "that we didn't have to bother with [before]." == Forget Survival of the Fittest: It Is Kindness That Counts A psychologist probes how altruism, Darwinism and neurobiology mean that we can succeed by not being cutthroat. Why do people do good things? Is kindness hard-wired into the brain, or does this tendency arise via experience? Or is goodness some combination of nature and nurture? Dacher Keltner, director of the Berkeley Social Interaction Laboratory, investigates these questions from multiple angles, and often generates results that are both surprising and challenging. In his new book, Born to Be Good: The Science of a Meaningful Life, Keltner weaves together scientific findings with personal narrative to uncover the innate power of human emotion to connect people with each other, which he argues is the path to living the good life. Keltner was kind enough to take some time out to discuss altruism, Darwinism, neurobiology and practical applications of his findings with David DiSalvo. DISALVO: You have a book that was just released called Born to Be Good: The Science of a Meaningful Life. What in a nutshell does the term born to be good mean to you, and what are you hoping people learn from reading the book? KELTNER: Born to be good for me means that our mammalian and hominid evolution have crafted a speciesuswith remarkable tendencies toward kindness, play, generosity, reverence and self-sacrifice, which are vital to the classic tasks of evolutionsurvival, gene replication and smooth functioning groups. These tendencies are felt in the wonderful realm of emotionemotions such as compassion, gratitude, awe, embarrassment and mirth. These emotions were of interest to Darwin, and Darwin-inspired studies have revealed that our capacity for caring, for play, for reverence and modesty are built into our brains, bodies, genes and social practices. My hopes for potential readers are numerous. I hope they learn about the remarkable wisdom of Darwin and the wonders of the study of emotion. I hope they come to look at human nature in a new light, one that is more hopeful and sanguine. I hope they may see the profoundly cooperative nature of much of our daily social living. DISALVO: Youve said that one of the inspirations for your work was Charles Darwins insights into human goodness. Because most people equate his name with survival of the fittest, itll probably be surprising to many that Darwin focused on goodness at all. What were a few of your take aways from Darwins work that really inspired you? KELTNER: What an important question. We so often assume both in the scientific community, and in our culture at large, that Darwin thought humans were violent and competitive and self-interested in their natural state. That is a misrepresentation of what Darwin actually believed, and where the evolutionary study of human goodness is going. My take aways from Darwin are twofold, and as you suggest above, I was surprised as well in arriving at an understanding of Darwins view of human nature. The first take away is found in Descent of Man, where Darwin argues that we are a profoundly social and caring species. This idea is reflected in the two quotes below, where Darwin argues that our tendencies toward sympathy are instinctual and evolved (and not some cultural construct as so many have assumed), and even stronger (or perhaps more ethicalsee his observation about the timid man below) than the instinct for self-preservation: For firstly, the social instincts lead an animal to take pleasure in the society of his fellows, to feel a certain amount of sympathy with them, and to perform various services for them. Such actions as the above appear to be the simple result of the greater strength of the social or maternal instincts than that of any other instinct or motive; for they are performed too instantaneously for reflection, or for pleasure or even misery might be felt. In a timid man, on the other hand, the instinct of self-preservation might be so strong, that he would be unable to force himself to run any such risk, perhaps not even for his own child. The second take away comes from close study of Darwins Expression of Emotion in Man and Animals, published one year after Descent of Man. There, Darwin details descriptions of emotions such as reverence, love, tenderness, laughter, embarrassment and the conceptual tools to document the evolutionary origins of these emotions. That led me to my own work on the physiology and display of these remarkable emotions, and to the science-based conclusion that these emotions lie at the core of our capacities for virtue and cooperation. DISALVO: You recently wrote an article with the provocative title In Defense of Teasing. Because were ostensibly a society set against teasing in any form (school, workplace, and so on), what do you think teasing has to offer that we might be missing? KELTNER: Teasing is the art of playful provocation, of using our playful voices and bodies to provoke others to avoid inappropriate behaviors. Marc Bekoff, a biologist at the University of Colorado, Boulder, has found in remarkable work with coyotes that they sort out leaders from aggressive types in their rough-and-tumble biting. The coyotes that bite too hard in such provocative play are relegated to low status positions. We likewise accomplish so much with the right kind of teasing. Teasing (in the right way, which is what most people do) offers so much. It is a way to play and express affection. It is a way of negotiating conflicts at work and in the family. Teasing exchanges teach children how to use their voices in innumerable wayssuch an important medium of communication. In teasing, children learn boundaries between harm and play. And children learn empathy in teasing, and how to appreciate others feelings (for example, in going too far). And in teasing we have fun. All of this benefit is accomplished in this remarkable modality of play. DISALVO: Your team at U.C. Berkley has done a lot of interesting research on the vagus nerve and its association with altruistic feelings. Tell us a bit about this research and its implications for better understanding the nature of altruism. KELTNER: The vagus nerve is part of the parasympathetic autonomic nervous system. It is a bundle of nerves that originates in the top of the spinal cord, it activates different organs throughout the body (heart, lungs, liver, digestive organs). When active, it is likely to produce that feeling of warm expansion in the chest, for example when we are moved by someones goodness or when we appreciate a beautiful piece of music. University of Illinois, Chicago, psychiatrist Steve Porges long ago argued that the vagus nerve is a care-taking organ in the body (of course, it serves many other functions as well). Several reasons justify this claim. The vagus nerve is thought to stimulate certain muscles in the vocal chamber, enabling communication. It reduces heart rate. Very new science suggests that it may be closely connected to oxytocin receptor networks. And it is unique to mammals. Our research and that of other scientists suggests that the vagus nerve may be a physiological system that supports caretaking and altruism. We have found that activation of the vagus nerve is associated with feelings of compassion and the ethical intuition that humans from different social groups (even adversarial ones) share a common humanity. People who have high vagus nerve activation in a resting state, we have found, are prone to feeling emotions that promote altruismcompassion, gratitude, love, happiness. Arizona State University psychologist Nancy Eisenberg has found that children with elevated vagal tone (high baseline vagus nerve activity) are more cooperative and likely to give. This area of study is the beginning of a fascinating new argument about altruismthat a branch of our nervous system evolved to support such behavior. DISALVO: Oftentimes we learn about intriguing academic work being done on emotions, morality and related areas, but are left asking, OK, but how do we do any of this? Is there anything we can make actual use of here? Looking down the road, what do you want the impact of your work to be out in the world? KELTNER: I have always felt that our science is only as good as the truthful rendition of reality that it provides and the good that it brings to our species. In summarizing the new science of emotion in Born To Be Good, I was struck by how useful this science is. The ancient approaches to ethics and virtuefor example, found in Aristotle or Confuciusprivileged things such as compassion, gratitude and reverence. A new science of virtue and morality is suggesting that our capacities for virtue and cooperation and our moral sense are old in evolutionary terms, and found in emotions that I write about in Born To Be Good. And a new science of happiness is finding that these emotions can be readily cultivated in familiar ways, bringing out the good in others and in oneself. Here are some recent empirical examples: Meditating on a compassionate approach to others shifts resting brain activation to the left hemisphere, a region associated with happiness, and boosts immune functions. Talking about areas of gratitude, in classrooms, at the dinner table or in the diary, boosts happiness and social well-being and health. Experiences of reverence in nature or around morally inspiring others improves peoples sense of connection to others and sense of purpose. Laughing and playing in the face of trauma gives the person perspective upon lifes inevitable difficulties, and improves resilience and adjustment. Devoting resources to others, rather than indulging a materialist desire, brings about lasting well being. This kind of science gives me many hopes for the future. At the broadest level, I hope that our culture shifts from a consumption-based, materialist culture to one that privileges the social joys (play, caring, touch, mirth) that are our older (in the evolutionary sense) sources of the good life. In more specific terms, I see this new science informing practices in almost every realm of life. Here again are some well-founded examples. Medical doctors are now receiving training in the tools of compassionempathetic listening, warm touchthat almost certainly improve basic health outcomes. Teachers now regularly teach the tools of empathy and respect. Executives are learning the wisdom around the country of emotional intelligencerespect, building trustthat there is more to a companys thriving than profit or the bottom line. In prisons and juvenile detention centers, meditation is being taught. == Fish Diversity Tied to Evolution of Diving Ability From clownfish to catfish, grouper to great white, the diversity of fish in the sea is nothing short of astonishing. Now scientists have managed to account for this wide assortment, at least in part, by tracing the evolution of the organ that allows the creatures to swim at different depths. To change their buoyancy and move up and down in the water, fish inflate an internal organ called the swim bladder. Some fish, such as herring, must surface and gulp air in order to fill their swim bladders with oxygen. Other fish, which are able to submerge for much longer periods and thus reach greater depths, are able to use oxygen from their blood in order to inflate the swim bladder, thanks to a specific type of protein known as Root-effect hemoglobin. Michael Berenbrink of the University of Liverpool and his colleagues traced the evolution of this protein in a variety of species, from sharks to dolphinfish, and found that it evolved just once. The emergence of the protein then allowed for the formation of a complex network of veins and arteries, called the rete mirabile, which supported the creatures' retinas and allowed the fish to see better. The rete mirabile also appears to have evolved only once, about 250 million years ago. The capillaries that support the swim bladder and allow oxygen to be delivered to it appeared about 100 million years later. The swim bladder itself, however, arose independently in four different fish groups, Berenbrink and his collaborators report in the current issue of the journal Science. The team proposes that the evolution of the swim bladder accounts for part of the huge diversity of form and function in living fishes. For example, there are 198 species of Mormyroidea fish, all of which have swim bladders, yet there are only eight species of their close relatives, the Notopteridae, which lack the complex organ. == 1.5M yr old footprints of Homo ergaster have been found. Earliest Human Footprints Discovered Early humans had feet like ours and left lasting impressions in the form of 1.5 million-year-old footprints, some of which were made by feet that could wear a size 9 men's shoe.The findings at a Northern Kenya site represent the oldest evidence of modern-human foot anatomy. They also help tell an ancestral story of humans who had fully transitioned from tree-dwellers to land walkers. "In a sense, it's like putting flesh on the bones," said John Harris, an anthropologist with the Koobi Fora Field School of Rutgers University. "The prints are so well preserved ."Almost HumanHarris and other colleagues report in the Feb. 27 issue of the journal Science on finding several footprint trails within two sedimentary rock layers. An upper sedimentary layer included two trails of two prints each, one group of seven prints, and a variety of isolated prints. The lower layer had a trail of two prints and a single isolated print likely from a smaller, juvenile human.The researchers identified the footprints as probably belonging to a member of Homo ergaster, an early form of Homo erectus. Such prints include modern foot features such as a rounded heel, a human-like arch and a big toe that sits parallel to other toes.By contrast, apes have more curved fingers and toes made for grasping tree branches. The earliest human ancestors, such as Australopithecus afarensis, still possessed many ape-like features more than 2 million years ago the well-known "Lucy" specimen represents one such example.Make Me a Match These latest footprints at Ileret, Kenya, appear intriguingly close by to another early human site. Researchers in 1984 found a nearly complete Homo erectus skeleton, dubbed the "Turkana Boy" specimen, just across the waters of Lake Turkana.Turkana Boy's delicate foot bones were not well preserved. But the new footprints could represent the shoe that fits the wearer, so to speak."Many people have predicted this, but now we have the solid evidence for modern foot anatomy," Harris told LiveScience. "It's like a giant jigsaw puzzle, and those footprints complement the skeleton from the other end of the lake."Time May Change MeModern feet mark just one of several dramatic shifts in early humans, specifically regarding the appearance of Homo erectus around 2 million years ago. Homo erectus is the first hominid to have the same body proportions as modern Homo sapiens. We're seeing a very different hominid at this stage," Harris said, pointing to both an increase in size and change in stride during the relatively short time between Australopithecus (the first in this genus lived about 4 million years ago and the last died out between 3 million and 2 million years ago) and Homo erectus. The latter hominids would have been able to travel more quickly and efficiently over larger areas.This matches a pattern of more widely-distributed sites containing artifacts such as tools from 1.5 million to 1 million years ago, which may also point to wider-ranging early humans.Climate changing and shifting physical landscapes would have also forced the likes of Homo erectus to wander farther in search of food, Harris said. But increased walking and running abilities may have allowed them to start seriously hunting big game"You might even think in terms of dietary quality here, because maybe they're incorporating more meat into their diet," Harris said. "They would have competed with quite a large carnivore guild; lions, leopards, and all the cats that eat meat."The Tracks Lead OnThe Homo erectus footprints now lead further into the past of human evolution, as researchers may shift their focus to earlier examples of physical changes in human ancestor species."It's going to bring up controversy again about the Laetoli prints," Harris noted, referring to footprints preserved in volcanic ash roughly 3.6 million years ago in Tanzania. Anthropologists continue to debate whether these older footprints from an earlier "Lucy" type hominid show that Australopithecus walked about easily or awkwardly on two legs.Other findings may yet be revealed with the latest footprints at the Ileret site. The prehistoric landscape near various water sources was likely a muddy surface that preserved a whole range of animal tracks, Harris hinted perhaps fodder for additional studies in the future. Earliest 'human footprints' found Laser scanning was used to plot the exact dimensions of the prints The earliest footprints showing evidence of modern human foot anatomy and gait have been unearthed in Kenya. The 1.5-million-year-old footprints display signs of a pronounced arch and short, aligned toes, in contrast to older footprints. The size and spacing of the Kenyan markings - attributed to Homo erectus - reflect the height, weight, and walking style of modern humans. The findings have been published in the journal Science. The footprints are not the oldest belonging to a member of the human lineage. That title belongs to the 3.7 million-year-old Australopithecus afarensis prints found in Laetoli, Tanzania, in 1978. Those prints, however, showed comparatively flat feet and a significantly higher angle between the big toe and the other toes, representative of a foot still adapted to grasping. Exactly how that more ape-like foot developed into its modern version has remained unclear. The fossil record is distinctly lacking in foot and hand bones, according to lead author Matthew Bennett of Bournemouth University, UK. "The reason is that carnivores like to eat hands and feet," Professor Bennett told BBC News. "Once the flesh is gone there's a lot of little bones that don't get preserved, so we know very little about the evolution of hands and feet on our ancestors." The footprints were found near Ileret in northern Kenya. The site, on a small hill, is made up of metres of sediment which the researchers carefully cleared away. What they found was two sets of footprints, one five metres deeper than the other, separated by sand, silt, and volcanic ash. The team dated the surrounding sediment by comparing it with well-known radioisotope-dated samples from the region, finding that the two layers of prints were made at least 10,000 years apart. Another critical feature that the series of footprints makes clear is how Homo erectus walked. There is evidence of a heavy landing on the heel with weight transferred along the outer edge of the foot, progressing to the ball of the foot and lifting off with the toes. "That's very diagnostic of the modern style of walking, and the Laetoli prints don't give that same character," Professor Bennett said. The finding is a critical clue for mapping out the evolution of modern humans, both in terms of physiology and also how H. erectus fared in its environment. H. erectus was a great leap in evolution, showing increased variety of diet and of habitat, and was the first Homo species to make the journey out of Africa. "There's some suggestion out there that Homo erectus was able to scour the landscape for carcasses and meat...and was able to get there very quickly, had longer limbs and was much more efficient in terms of long distance travel," Professor Bennett added. "Now we're also saying it had an essentially modern foot anatomy and function, which also adds to that story." == Prehistoric fish pioneered sex Sex has been a fact of life for at least 380 million years, longer than previously thought. Internal fertilization was widespread among prehistoric fish living on ancient tropical coral reefs in the Devonian period, research published in the journal Nature on Wednesday showed. The discovery sheds new light on the reproductive history of all jawed vertebrates, including humans. "It shifts how we think about how reproduction evolved. You're a jawed vertebrate and I'm a jawed vertebrate, so this is our own history," said Zerina Johanson, a paleontologist at the Natural History Museum in London. Johanson and colleagues in Australia, where the fossils were unearthed, deduced that copulation was common among armored placoderms, extinct shark-like species, after finding embryos inside Materpiscis, Austroptyctodus and Incisoscutum placoderms. Finding fossil evidence of reproduction is rare and experts initially missed the signs in the case of one specimen, where a tiny embryo was at first thought to be a last meal. It was thought that such ancient fish would show a more primitive type of reproduction, with sperm and eggs combining externally in the water, as still happens with many modern fish. Adding to the evidence is the discovery of a modification in the pelvic fin on the belly of adult fish. The scientists believe this was used by the male to grip the female during mating, as happens with modern sharks. Placoderms, thought to be the oldest jawed vertebrates, were fearsome predators with bony armor covering their head and forming the biting surfaces of their jaws, which could act like self-sharpening scissors. Study of fossils shows sex is older than thought BANGKOK, Thailand The fossilized remains of two pregnant fish indicate that sex as we know it fertilization of eggs inside a female took place as much as 30 million years earlier than previously thought, researchers said on Thursday. Scientists from Australia and Britain studying 380 million-year-old fossils of the armored placoderm fish said they were initially confused when they realized that the two fish were carrying embryos. They originally thought the fish laid their eggs before fertilization. Once we found embryos in this group, we knew they had internal fertilization. But how the hell are they doing it? said John Long, the head of sciences at the Museum Victoria in Melbourne who wrote a paper on the discovery that appeared in Thursday's issue of the journal Nature. The answer came when the scientists re-examined the pelvis of the male placoderm. They realized the pelvis had a fin not seen on the female fish, and surmised it was likely used to grip its mate during fertilization, much as sharks do. In a nutshell, we have reinterpreted the structure of the pelvic bone in these placoderms to show they had a method for copulation, he said. Zerina Johanson, a paleontologist at the Natural History Museum who also took part in the study, said findings of internal fertilization showed that sex started a lot sooner than we thought. Scientists Find First Animal That Had Sex The armored fish, Materpiscis attenboroughi, may have given birth to its young tail-first, similar to some sharks and rays. Remains of embryos entombed in their fish mothers' wombs for 380 million years have been found in fossils from an ancient rock outcrop in Western Australia. The finding is a big deal because it suggests that sex goes way back. The prehistoric fish, called placoderms, are found at the base of the vertebrate evolutionary tree (in a large group we humans also belong to), so it now looks like sexual intercourse, and the mating behaviors that go along with it, were more widespread in these ancient animals than previously thought, said the scientists who made the discovery. The embryos were found in the body cavities of Incisoscutum ritchiei, an extinct jawed fish that lived from about 430 million years ago to 360 million years ago. Placoderms' heads and parts of their bodies were covered with bony armor. They were also some of the first jawed animals. The specimens were found in the Gogo Formation of Western Australia by John Long of the Museum Victoria in Melbourne, Australia. At first, he thought that animal remains found in the placoderm fossils were the animals' last meals, but after finding embryos in another group of placoderms, Long and his colleagues took a closer look and found that the new specimens were also the remains of unborn embryos. "We could see that the new specimens had the same bone structure as the previous embryos, were the same species as the adult, they did not have any broken or stomach-etched features (from digestive acids or from being chomped) and that they were at the same stage of growth as the previous embryos," Long wrote in an email. "All of these facts proved they were embryos, not prey items." The scientists' work was funded by the Australian Research Council. Sex evolution Because the embryos were found inside their mothers, these placoderms must have copulated to produce offspring instead of laying eggs and fertilizing them outside the mothers, as some species of fish and others animals do. And since these placoderms sit near the beginnings of the vertebrate tree of life, "it means that complex forms of mating evolved probably about the same time as jaws evolved," Long told LiveScience. To engage in sex, the fish would have needed the proper, er, equipment. The structure of the mating parts of Incisoscutum are related to the pelvic girdle and hind limb, or leg, as in humans. "These fish were using the hind limbs for the very first kind of vertebrate copulations," Long said. "We humans have an expression that 'we like to get a leg over,' but placoderms liked to get a leg in." Exactly where the placoderms fit in on the evolutionary tree is still a key question; fitting them into their proper place will help scientists better understand the evolution of the traits of internal fertilization of embryos and live birth. The findings of this study, detailed in the Feb. 26 issue of the journal Nature, "may prove to have far-reaching implications for our understanding of early vertebrate evolution," said Per Ahlberg of Uppsala University in Sweden in an accompanying editorial in the journal. Ahlberg was not involved in the study. Long and other scientists are continuing to turn up and examine placoderm fossils from sites in Australia and are learning more about the ancient creatures and their anatomy and other traits with improved technologies. "We are learning more about placoderms with each new discovery," Long said. == the whiptail lizards of the United States, several species of which are parthenogenic -- they are all females, and no males exist. The females all lay eggs that hatch without being fertilized, producing all female moffspring. The eggs don't develop until the female engages in sex -- with another female. One plays the role of "fem", the other plays the role of male. == Alien life 'may exist among us' Never mind Mars, alien life may be thriving right here on Earth, a major science conference has heard. Our planet may harbour forms of "weird life" unrelated to life as we know it, according to Professor Paul Davies, a physicist at Arizona State University. This "shadow life" may be hidden in toxic arsenic lakes or in boiling deep sea hydrothermal vents, he says. He has called on scientists to launch a "mission to Earth" by trawling hostile environments for signs of bio-activity. Weird life could even be living among us, in forms which we don't yet recognise, he told the American Association for the Advancement of Science (AAAS) meeting in Chicago. "We don't have to go to other planets to find weird life. "It could be right in front of our noses - or even in our noses," said the physicist. "It is entirely reasonable to expect we will find a shadow biosphere here on Earth. "But nobody has actually taken the trouble to look. "The question is why? The cost is not expensive - it would be a fraction of the money we spend searching for extraterrestrial life." 'Second genesis' Professor Davies was one of the speakers at a symposium exploring the possibility that life has evolved on Earth more than once. The descendants of this "second genesis" may have survived until today in a "shadow biosphere" which is beyond our radar because its inhabitants have biochemistry so different from our own. "All our microscopes are customised for life as we know it - so it's no surprise that we haven't found microbes with different biochemistry," said Professor Davies. "We don't quite know how weird life would look. It's as wide as the imagination and that's why it's really hard to look for." If it exists, weird life could be based on DNA and RNA - but with a slightly different genetic code or different amino acids. At the other end of the spectrum, we could find creatures which have more drastic differences. "Maybe one of the elements life uses - carbon, hydrogen, oxygen, nitrogen, phosphorus - could be replaced by something else," said Professor Davies. "When I say that, everyone immediately thinks of silicon life - because of Star Trek. But I'm not talking about anything that drastic. "For example, most of the jobs that can be done by phosphorus can be done by arsenic." Arsenic may be poisonous to humans, but it has chemical properties which might make it ideal in a microbe's machinery, he said. 'Mission to Earth' So how do we go about hunting for something we have never seen before? "There are two possibilities," said Prof Davies, Director of the BEYOND Center for Fundamental Concepts in Science. "One is that weird life is ecologically isolated, in niches beyond the reach of mankind." In this case, we must begin trawling the world's most inhospitable environments - deserts, salt lakes, and areas of high pressure, temperature or UV radiation. "We could have a 'mission to Earth'. There's a big long list of places we could be looking," observed Professor Davies. "For example, if we are looking for arsenic life, we could head for environments which are both arsenic rich and phosphorus poor - such as deep ocean vents. "There is also a heavily contaminated lake in California which is arsenic rich - Mono Lake - and we do find microbes in there which get their energy from arsenic. "But they don't actually incorporate the arsenic into themselves. They spit it back out again. They smoke but they don't inhale." On the other hand, it could be that "weird life" is actually all around us - intermingled with carbon based life. "In that case it's going to be really hard to detect - you have to find some way of filtering everything else out." This laborious process has been used to search for unknown organisms in seawater - by painstakingly filtering everything else away. If we did discover something unprecedented, "we'd all start arguing" said Professor Davies, a theoretical physicist. "The question would be whether this life was truly different, or whether there was a common precursor a deep branch on the main tree of life. "Also, how do we know we are dealing with separate Earth genesis and not a Mars genesis? "We know rocks do get traded between the two planets, and life could hitch a ride. "Personally, I'm only interested in establishing whether life happened more than once. If we find it has happened twice from scratch then its going to have happened all around the universe. "It's going to be teeming with life and there's a very good chance we are not alone." Life in the lab Another way to determine what alternative life might look like is to try to invent it ourselves. If we can create new molecules which can behave in life-like way, we may then go out and look for these in the environment, says Professor Steven Benner, of the University of Florida. His team have created perhaps the closest yet to a man-made alternative form of life. "We are announcing the first example of an artificial synthetic chemical system capable of Darwinian evolution," he told the conference. "Is it alive? Well, I can tell you that it is not self-sustaining. "You have to have a graduate student stand there and feed it from time to time, but it is evolving." The molecule is essentially a modified version of our own DNA double helix - but with six "letters" in its genetic alphabet, instead of four. These nucleotides pair up in strands, which can replicate, though only with the help of polymerase enzymes and heat. "Sometimes mistakes are made in pairing and these mistakes are maintained in the next generation - it is evolving," said Prof Brenner. "The next step is to apply natural selection to it, to see if it can evolve under selective pressure. "The accepted definition of life is a molecule capable of Darwinian evolution, so we are trying to put together molecules that are capable of doing it." But he questioned whether our definition of "living" is perhaps too "Earth-centric". "Remember - just because you are a chemical system which is self-sustaining and capable of Darwinian evolution, that doesn't mean that is the universal definition of life," he said. == Modern Homo sapiens originated in Africa 200,000 to 100,000 years ago, at which point a relatively small number of them, maybe 10,000 or so, began migrating into the Middle East, Europe, Asia and across the Bering land mass into the Americas. As they traveled, they seem to have completely or largely displaced archaic humans already living in the various continents, either through calculated acts of genocide, or simply outreproducing them into extinction. == Neanderthal mtDNA has ~200 differences from Human mtDNA, where Chimp mtDNA has ~1500 differences. == The first fossilized arthropods on land show up during the silurian era (giant scorpions appear during the silurian). Fossilized dragon flies don't show up until the carboniferous, at least 100 MY later. All winged insects living or extinct that we know about belong to a single branch of the Insecta that we've called Pterygota. == http://en.wikipedia.org/wiki/Chromosome_2#Evolution == The domestic dog would be classified as follows: Kingdom Animalia. Phylum Chordata. Class Mammalia. Order Carnivora. Family Canidae. Genus Canis. Species Canis lupus familiaris. The last is actually its subspecies category as the evidence supports the idea that the domestic dog evolved from the Grey wolf (Canis lupus). == Was The Humble Sponge Earth's First Animal? Fish swim. Birds fly. Humans walk, talk, and think. Animals exhibit such an array of diversity in shape and behavior that it's hard to imagine how a single organism could have given rise to them all. Yet Darwinian evolution requires that such an animal once lived. Mitch Sogin has been doing something humans do so well: He's been thinking. And he thinks he knows how the common ancestor of the animal kingdomthe animal "Eve"looked. It looked like a sponge, he says. For the past decade, Sogin, an evolutionary biologist at the Marine Biological Laboratory in Woods Hole, Massachusetts, has been sifting through clues in the genetic codes of simple marine organisms. The primeval whodunnit he aims to solve is this: Who, or more accurately, what life form, spawned the animal kingdom? Sponges, some 9,000 species in all, occupy virtually every aquatic habitat on Earth, from freshwater lakes to tropical seas and even Arctic waters. Although they seem motionless and lifeless to the untrained eye, these organisms are hard workers. A single sponge pumps many gallons of water through its body each day to strain out the tiny, one-celled organisms on which it feeds. Sponges have to filter about a ton of water for each ounce of food they ingest. For all that impressive activity, however, sponges are simple animals. They possess no nervous system or breathing apparatus, nor do they have limbs or the capacity to move. The Origin of Complexity Nevertheless, says Sogin, "the sponge has a lot of organization to it." In particular, it has two different types of cells, each of which plays an important role in the functioning of the whole. Sponge cells called choanocytes ("coe-ann-oh-sites") each project a minuscule filament. Choanocytes use these filaments, called flagella, to paddle water past themselves. Thousands of choanocytes beating their flagella in synchrony, like oarsmen on a Roman galley, propel a steady stream of water past the sponge's other cells, which are designed to capture and ingest the food particles the water contains. Sponges' ability to grow different cell types was an innovation that underlies In his laboratory at Woods Hole, Sogin and several colleagues compared genetic sequences from numerous marine organisms. In the analysis, they studied several species of sponges, sea anemones, and jellyfish, as well as an assortment of more complex animals such as mollusks and echinoderms. They also included examples of fungi and single-celled, choanocyte-like organisms called choanoflagellids, neither of which belong to the animal kingdom. Sogin extracted genetic material called RNA from the various organisms and compared two types of genetic data from each. The two types of RNA told slightly different versions of the family history of the animals, but both sets of evidence agreed on many accounts. Once deciphered, the genetic clues revealed that, of all animals, sponges are the most genetically distinct. Jellyfish and anemones share slightly more genetic similarities with each other and with other animals. This finding led Sogin to conclude that sponges occupy the oldest and lowest branch on the animal family tree. Because the higher branches have introduced additional innovations that account for animals' rich diversity, he says, the common ancestor of all animals probably resembled modern sponges much more closely than anything else alive today. Although sponges have changed little over the past 500 million or more years, Sogin is quick to note that no living sponge possesses the exact genes or form of the animal Eve. "Evolution is not a process that stops," he says. A Surprising Link That sponges are an essential part of our evolutionary heritage is a startling realization for many, but Sogin reached an even greater revelation when he looked slightly farther back on the animal lineage. "The special evolutionary relationship between animals and fungi was a big surprise," Sogin says. "In many regards, fungi are similar to primitive plants." Yet the fungus, he has concluded, shares "a unique, common evolutionary history with the animal." Some details of early animal evolution still remain to be worked out. In particular, Sogin would like to know whether certain types of fungi are more closely related to animals than other types. If they are, it would mean that the entire animal family is just a branch on the evolutionary tree of the fungi. In a sense, people and all animals would be highly evolved fungi. Another unanswered question is how some of the early branches of the animal family tree fit together. After sponges, Sogin thinks, jellyfish evolved, and then anemones, which gave rise to the first animal with bilateral symmetry. Once the step toward symmetry was made, animal evolution appears to have quickly gained momentum. But the precise order of those first awkward steps toward today's complex array of animal life, and what triggered evolution's accelerating pace, Sogin says, "is still a big mystery." -- Earliest Animals Were Sea Sponges, Fossils Hint Fossil steroids found underground in Oman show that early Earth was the scene of a sea sponge heyday more than 635 million years ago. The ancient chemicalssimilar to modern natural steroids such as estrogen and testosteroneare now the oldest known fossil evidence of animal life, says a new study led by Gordon Love of the University of California, Riverside. Based on chemical signatures inside sedimentary rocks, Love and colleagues think the sponges likely grew in colonies that blanketed areas of the ocean floor. Back then the supercontinent Rodinia, which had been Earth's dominant landmass for at least 350 million years, was in the process of breaking up, and the climate was extremely cold worldwide. Sponges evolved in shallow ocean basins, because the deeper seas did not yet contain oxygen, a necessity for almost all life. Although the environment was harsh at this timeabout a hundred million years before the evolutionary growth spurt known as the Cambrian explosiona lack of predators made life easier for the sponges. "There was no competition from more complicated animals, so sponges were probably thriving," Love said. "Compared with other times in our history, there were enormously high amounts of them." Spongy Roots Love and colleagues were able to date the sea sponges because the animals' chemical traces were found in rocks beneath glacial deposits from an ice age that ended about 635 million years ago. The scientists cut away the outer surfaces of the rock, cleaned the remaining core with solvents, and crushed what was left behind into a powder that could be chemically separated into its component parts. "It just so happens that these sponges produce very distinctive chemical structures," said Love, whose team describes their results in this week's issue of the journal Nature. Kevin Peterson of Dartmouth College and his colleagues had independently hypothesized that sponges lived about 650 million years ago based on biological clues in the genes of modern sponges. "To see to a robust, geochemical record of a tremendous amount of sponge mass at this time is very exciting," said Peterson, who was not involved in the new study. "At some point during this interval, sponges gave rise to more complex organisms, including eventually vertebrates," he said. "The origin of complex life is rooted in sponge biology, and that's what makes it so exciting for us." == How gorilla gestures point to evolution of human language (PhysOrg.com) -- Scientists at the University of St Andrews have discovered that gorillas have a more extensive repertoire of gestures than any other mammal. Researchers examined the communication signals of the gorilla, a great ape and one of our closest relatives. The study found that ape gestures are carried out with close attention to the potential audience: silent ones are only given when other apes can see them. The new study was conducted by Professor Richard Byrne, Dr Emilie Genty and Ms. Cat Hobaiter at the School of Psychology and Dr Thomas Breuer at the Max Planck Institute for Evolutionary Anthropology, Leipzig. Their study catalogued gestures - some given exotic sounding labels, like 'disco arms shake' - amongst several different gorilla groups. Professor Byrne explained, "There has always been speculation that the origins of human language might lie in gesture, an idea supported by the close proximity of the brain areas involved in language and gesture. Many researchers have therefore studied the gestural communication of the great apes for clues to the evolutionary origins of human gesture. "But there is a persisting puzzle: each population seems to use a somewhat different repertoire of gestures, suggesting that individuals learn their gestures; yet there is no sign of local `dialects of gesture, group-specific gesture traditions, as would be expected if they learnt the gestures from each other." The researchers were able to study gorillas at more sites than before, and were also able to draw upon previous work to investigate the gorilla repertoire, which eventually totalled 102 gesture types. Whilst some common gestures like 'arm swing with object' and 'tapping other' were shared by all groups they studied, others were found only at a few places; one, the 'disco arms shake', was unique to a single gorilla and performed only to a human, not to other gorillas. The investigators found that juvenile and adolescent animals, aged between three and ten years, were responsible for using the highest number of gesture types compared to a smaller variety used by infants under three, or by adults of either sex. Professor Byrne continued, "What we found was that, as we added more populations to the study, most gestures that had seemed specific to one individual or one site almost always turned up elsewhere. "Any two populations are likely to differ a lot in the repertoire of gestures shown, but all are drawn from a very large, species-wide 'pool' of possible gestural signals." Consequently, the team concluded that the gestures do not need to be learnt, because they are already part of the natural gorilla communicative repertoire. "What is particularly notable about great ape gesture repertoires, then, is not that they are acquired by learning (like human language), but that they are so much larger than repertoires of other mammals," said Professor Byrne. The new work throws light on another puzzle in the behaviour of great apes. Several studies have found that apes are capable of the "Do as I do" routine that children also enjoy, but their copies of human actions modelled for them are relatively inexact. Professor Byrne explained, "Dr Joanne Tanner and I studied a female gorilla that was able to do this, and we found that all her 'copies' of apparently novel human actions were really actions she'd done herself, sometimes years before: they matched the demonstrated actions pretty well, but not exactly. It was only because of Tanner's long-term data on the gorillas that we could find out what was going on. "So we think that, just as in the case of communicative gestures, the fact that apes have a huge repertoire of actions can explain how they imitate human demonstrations and why their copies are usually inexact: they are 're-using' actions from their own repertoire, not learning new ones." == One of the most widely debated and controversial topics of our time, Evolution is a biological term referring to the period of time in which Earth has evolved from initial creation into the lush populated planet we know today. The theory of evolution states that overtime, as new species began to evolve, the more dominant species were in greatest control of the Earths population. The more dominant a species, the more likely it would be able to reproduce and continue up the evolutionary ladder. Furthermore, characteristics from those dominant species would be the ones that would carry on to future generations. Otherwise known as natural selection or speciation, this gradual evolution accounts for the immensely diverse biological world we all live in today. In theory, evolution is believed to have taken billions and billions of years, which has frequently conflicted with the religious beliefs of many. The idea of evolution was first recorded on paper by Charles Darwin in his 1859 book The Origin of Species. Darwins book offered the world of science its first rational and well-argued theory for a manner by which evolutionary global change had occurred and would continue to occur over time. For more information on global and human evolution, Darwins theory of evolution and natural selection, the evolution of man, creation theories vs. evolution, and more, simply choose any evolution article or other interactive feature below. == * It is now clear that the evolutionary tree for early and modern humans looks more like a bush than the line represented in cartoons. All the hominid fossils found to date form a complex nexus of specimens, Prothero says, but Sahelanthropus tchadensis, found in 2001 and 2002, threw everyone for a loop because it walked upright 7 million years ago on two feet but is quite chimp-like in its skull size, teeth, brow ridges and face. It could be a common ancestor of humans and chimpanzees, but many paleoanthropologists will remain unsure until more fossils are found. Previously, the earliest ancestor of our Homo genus found in the fossil record dated back 6 million years. * -Most fossil giraffes have short necks and today's have long necks, but anatomist Nikos Solounias of the New York Institute of Technology's New York College of Osteopathic Medicine is preparing a description of a giraffe fossil, Bohlinia, with a neck that is intermediate in length. * Manatees, also called sea cows, are marine mammals that have flippers and a down-turned snout for grazing in warm shallow waters. In 2001, scientists discovered the fossil of a "walking manatee," Pezosiren portelli, which had feet rather than flippers and walked on land during the Eocene epoch (54.8 million years ago to 33.7 million years ago) in what is now Jamaica. Along with skull features like manatees (such as horizontal tooth replacement, like a conveyor belt), it also had heavy ribs for ballast, showing that it also had an aquatic lifestyle, like hippos. * Scientists know that mastodons, mammoths and elephants all share a common ancestor, but it gets hard to tell apart some of the earliest members of this group, called proboscideans, going back to fossils from the Oligocene epoch (33.7 million years ago to 23.8 million years ago). The primitive members of this group can be traced back to what Prothero calls "the ultimate transitional fossil," Moeritherium, from the late Eocene of Egypt. It looked more like a small hippo than an elephant and probably lacked a long trunk, but it had short upper and lower tusks, the teeth of a primitive mastodon and ear features found only in other proboscideans. * The Dimetrodon was a big predatory reptile with a tail and a large sail or fin-back. It is often mistaken for a dinosaur, but it's actually part of our mammalian lineage and more closely related to mammals than reptiles, which is seen in its specialized teeth for stabbing meat and skull features that only mammals and their ancestors had. It probably moved around like a lizard and had a jawbone made of multiple bones, like a reptile. Dinosaurs and birds * The classic fossil of Archaeopteryx, sometimes called the first bird, has a wishbone (fully fused clavicle) which is only found in modern birds and some dinosaurs. But it also shows impressions from feathers on its body, as seen on many of the theropod dinosaurs from which it evolved. Its body, capable of flight or gliding, also had many of dinosaur features teeth (no birds alive today have teeth), a long bony tail (tails on modern birds are entirely feathers, not bony), long hind legs and toes, and a specialized hand with long bony fingers (unlike modern bird wings in which the fingers are fused into a single element), Prothero said. * Sinornis was a bird that also has long bony fingers and teeth, like those seen in dinosaurs and not seen in modern birds. * Yinlong is a small bipedal dinosaur which shares features with two groups of dinosaurs known to many kids ceratopsians, the beaked dinosaurs like Triceratops, and pachycephalosaurs, known for having a thick dome of bone in their skulls protecting their brains. Yinlong has the thick rostral bone that is otherwise unique to ceratopsians dinosaurs, and the thick skull roof found in the pachycephalosaurs. * Anchisaurus is a primitive sauropod dinosaur that has a lot of lizard-like features. It was only 8 feet long (the classic sauropods later on could be more than 100-feet long), had a short neck (sauropods are known for their long necks, while lizards are not), and delicate limbs and feet, unlike dinosaurs. Its spine was like that of a sauropod. The early sauropods were bipedal, while the latter were stood on all fours. Anchisaurus was probably capable of both stances, Prothero wrote. Fish, frogs, turtles * Tiktaalik, aka the fishibian or the fishapod, is a large scaled fish that shows a perfect transition between fins and feet, aquatic and land animals. It had fish-like scales, as well as fish-like fin rays and jaw and mouth elements, but it had a shortened skull roof and mobile neck to catch prey, an ear that could hear in both land and water, and a wrist joint that is like those seen in land animals. * Last year, scientists announced the discovery of Gerobatrachus hottorni, aka the frogamander. Technically, it's a toothed amphibian, but it shows the common origins of frogs and salamanders, scientists say, with a wide skull and large ear drum (like frogs) and two fused ankle bones as seen in salamanders. * A creature on the way to becoming a turtle, Odontochelys semistestacea, swam around in China's coastal waters 200 million years ago. It had a belly shell but its back was basically bare of armor. Odontochelys had an elongated, pointed snout. Most modern turtles have short snouts. In addition, the roof of its mouth, along with the upper and lower jaws, was equipped with teeth, which the researchers said is a primitive feature for turtles whose mugs are now tipped with beaks but contain no teeth. == Occidental College geologist Donald Prothero in his book "Evolution: What the Fossils Say and Why It Matters" (Columbia University Press, 2007). == In early humans, jaws of steel Your mother told you not to use your teeth as tools to open something hard, and she was right. Human skulls have small faces and teeth and arent wellequipped to bite down forcefully on hard objects. Not so of our earliest ancestors, say scientists. Compressive stress in the cranium of Australopithecus africanus, an extinct early human, imposed by biting on the premolar teeth. Bright colors correspond to high stresses, and indicate that a bony pillar running alongside the opening of the nasal cavity acts as a strut that structurally reinforces the face against premolar loads. Research published in last weeks online issue of the research journal Proceedings of the National Academy of Sciences points to nutcracking abilities in our 2.5 million year old relatives that let them alter their diet to adapt to changing circumstances. Using computer modeling and simulation the same techniques engineers use to simulate how a car reacts to forces in a frontend collision evolutionary scientists built a virtual model of the skull of the human ancestor Australopithecus africanus. The plan was to see how the jaw operated and what forces it could produce. We started with a CT scan of a skull that is one of the most complete specimens of A. africanus that we have, said Mark Spencer, an Arizona State University assistant professor, who with doctoral student Caitlin Schrein at the university is part of an international research team behind the study. The skull under investigation is believed to come from a later ancestor of the populations that included Lucy, the most famous fossil skeleton in anthropology. Dated as about three million years old, Lucy is the most complete known fossil of a genus of prehistoric African human ancestors known as australopithecines. The Lucy ancestor investigated in the new work was a fossil dubbed STS5 and affectionately known as Mrs. Ples. The skull, discovered in 1947, has struts on the side of the nose, but no teeth. We meshed those data with another specimen with teeth to make the virtual model of the bone and tooth structure, Spencer said. Then we looked at chimpanzees, who share common features with Australopithecus, and took measurements of how their muscles work and added that to the model. We were able to validate this model by comparing it to a similar model built for a species of monkey called macaques. The result: a rainbowcolored virtual skull that illustrates forces absorbed by the cranial structure in simulated bites and how unusual facial features were suited to cracking hard nuts. It was like watching Mrs. Ples come to life, Spencer said. This reinforces the body of research indicating that facial specializations in species of early humans are adaptations due to a specialized diet, he went on. The enlargement of the premolars, the heavy tooth enamel and the evidence now that they were loading forcefully on the molars suggest the size of the objects were larger than the previously hypothesized small seeds and nuts. These fallback foods hard nuts and seeds were important survival strategies during a period of changing climates and food scarcity. == New Species Of Prehistoric Creatures Discovered In Isle Of Wight Mud Dr Steve Sweetmans discoveries, found hidden in mud on the Isle of Wight, are around 130 million years old and shed valuable light on the poorly understood world in which well known dinosaurs roamed. Steve, a research associate with the School of Earth and Environmental Sciences, has found in ancient river deposits, at least eight new dinosaurs, many different types of lizard, frogs, salamanders, and perhaps rarest of all from the time of the dinosaurs, six tiny mammals, some as small as a shrew. Palaeontologists have previously relied on conventional surface prospecting to collect fossils exposed naturally by weather and waves. Broken bits and pieces of bone stick out of the ground which often leads to a larger fossil being discovered. The techniques Steve adopted are far more thorough he carried some three and a half tonnes of mud along beaches and up cliffs in buckets and backpacks before driving samples back to his farm on the island where he has set up his own laboratory. He dried and sieved it until buckets of mud became bowls of sand and then examined every single grain under a microscope. It wasnt long before he was picking out tiny fossil bones and teeth. Steve said: It has taken me just four years of hard graft to make my discoveries. Living on the Isle of Wight made this research physically possible. You can get to most places within half an hour, so transporting tonnes of mud wasnt too much of an obstacle. It would have been near impossible if I had been based on the mainland. In the very first sample I found a tiny jaw of an extinct newt-sized, salamander-like amphibian and then new species just kept coming. Although we knew a lot about the larger species that existed on the island during the Early Cretaceous no-one had ever filled in the gaps. With these discoveries I can paint a really detailed picture of the creatures that scurried at the feet and in the shadows of the dinosaurs, he said. The research wouldnt have happened had it not been for a chance meeting with University of Portsmouth palaeontologist Dr Dave Martill on a beach on the south-west coast of the island. On this beach, while standing on ancient remains the famous Hypsilophodon Bed, Steve was persuaded to renew his interest in palaeontology and study for a PhD. Steve grew up on the Isle of Wight, sometimes referred to as Dinosaur Island as it is the richest source of dinosaur remains in Europe. He has always been interested in fossils and decided to return there after 25 years on the mainland. === Hairs that likely belonged to humans living 195,000 to 257,000 years ago in Africa have been identified in fossilized brown hyena dung, according to a new study that describes the first non-bony material in the early human fossil record. Until now, the oldest known human hairs were from a 9,000-year-old Chinchorro mummy from Arica, northern Chile. This latest discovery, made at Gladysvale cave, South Africa, exceeds the mummy's age by about 200,000 years. The findings, which have been accepted for publication in the Journal of Archaeological Science, further suggest that early humans faced tough competition from carnivores that either attacked the individuals outright, or scavenged on their dead. From an archaeological standpoint, however, the toothy animal's meal was a scientific windfall, since meat-eater dung can make an effective hair preservative. "The oldest known hairs (for all mammals) are found in carnivore feces, permafrost and amber," Lucinda Backwell, who led the study, told Discovery News. "It is the high calcium content in hyena coprolites (fossilized dung), together with the calcium-rich drip from the cave roof, which facilitated the fossilization process at Gladysvale," added Backwell, a University of Witwatersrand paleontologist. She and her team removed a 9.8-inch block of calcified hyena waste from a brown hyena latrine found in the cave. Such latrines are only used by one animal and are typically demarcated areas that measure about 6 feet round in size. The researchers then extracted 40 hairs from a single coprolite using fine tweezers. Although amino acid analysis detected no protein, and DNA sampling was not possible, very high magnification revealed that the size and shape of the hairs, along with their distinct cuticular scale patterns, best matched those of human hair. Scientists have pieced together a tale of human origins from the fossils of our ancestors. The tale is incomplete and its telling reshaped with fresh interpretation of the growing fossil record.Backwell said the date of the hyena waste "encompasses the known temporal range in Africa of archaic human species, such as Homo heidelbergensis and the emergence of the first anatomically modern humans." "The hairs could belong to either of them or, of course, to someone not yet recognized," she added. Since the hair's chemistry was transformed by the animal's digestive process, its natural pigmentation, and whether or not it was originally wavy or straight, cannot be determined at present. Nevertheless, Randy Susman, a professor in the Department of Anatomical Sciences at Stony Brook University, told Discovery News that the new study "is very interesting for a number of reasons." "First of all, the hair casts left in coprolites not only represent a very early occurrence of human hair, but they also document the fact that hominins were being consumed by hyenas," explained Susman. Bernard Wood, a George Washington University anthropologist, echoed Susman's view, adding that the discovery plays out like a great mystery with surprising clues. Wood said that, "in the spirit of Cluedo (a mystery crime fiction board game), the Backwell study shows that hyenas must be taken seriously as a possible perpetrator of this 'crime.'" He added, "But instead of 'blood on their hands, they have been found guilty of having 'hair in their poop!'" Backwell hopes future technological advances may shed greater light on what the person represented by the hair looked like, what the individual's overall state of health was before the hyena incident, and more. == The term "Darwinism" should not be used as a stand-in or synonym for evolution. While it's true that Darwin(and Alfred Russell Wallace) should get credit for articulating the theory of evollution in its earliest modern form, evolution is more than Darwin. It's more than Gregor Mendel, too. It's the sum of all these strands, and more that have been added since that time. If you're going to talk about it, a more neutral term would be "evolutionary biology" or just plain "evolution". Otherwise, I've found over time, that creationists and others who question that evolution has in the past, and continues to take place, all but accuse scientists of creating some Church of St. Darwin. Which is about as far from what is going on as you can get. == http://www.nybooks.com/articles/22356 new book by E. O. Wilson fascinating behavior has evolved among ants...one species actually farms fungus. the fungus is occasionally attacked by an invasive fungus that can destroy it...however some ants host a species of bacteria that lives ONLY in pits on the ants. these bacteria can attack the pest fungus, killing it. a great example of co-evolution... the ant society functions well without a head, or 'intelligent designer'. another remarkable feature in the evolution of fire ants was triggered by a change in the frequency of a single gene (evolution, by definition) that had a massive effect: In their native land fire ants form discrete colonies, with just one or a few queen ants at the center of each. This is how most ants live, but something very strange happened to the fire ants soon after they reached the United States. They gave up founding colonies by the traditional method of sending off flights of virgin queens, and instead began producing many small queens, which spread the colony rather in the way an amoeba spreads, by establishing extensions of the original body. Astonishingly, at the same time the ants ceased to defend colony boundaries against other fire ants. As Hlldobler and Wilson put it, "With territorial boundaries erased, local populations now coalesce into a single sheet of intercompatible ants spread across the inhabited landscape." This remarkable shift was caused by a change in the frequency of a single gene. == You can also take a look at http://en.wikipedia.org/wiki/Furcula for more relevant info. The furcula of Archaeopteryx lithographica is more acute and U-shaped than the furcula of dromaeosaurids, and appears intermediate between the furculae of nonavialan theropods and higher Avialae. - Norell, M. A., & P. J. Makovicky. 1999. Important Features of the Dromaeosaur Skeleton II: Information from Newly Collected Specimens of _Velociraptor mongoliensis_. American Museum Novitates 3282:1-45. A number of articulated theropod specimens, including _Segisaurus_, oviraptorids, _Sinornithoides_, and an allosaurid, show that the furcula or clavicles of nonavian theropods articulated with the anterior edge of the acromion process of the scapula, without contacting the coracoid. - Makovicky, P. J., & P. J. Currie. 1998. The Presence of a Furcula in Tyrannosaurid Theropods, and its Phylogenetic and Functional Implications. Journal of Vertebrate Paleontology 18(1):143-149. The presence of a furcula in this articulated specimen [of _Scipionyx_] eliminates every doubt about the interpretation of similar structures in other theropods. - Dal Sasso, C. & M. Signore. 1998. Exceptional soft-tissue preservation in a theropod dinosaur from Italy. Nature 392:383-387. Over the course of the twentieth century it became clear that clavicles are widespread throughout Dinosauria and that furculae were present in most non-avian theropods. - Yates, A. M., & C. C. Vasconcelos. 2005. Furcula-Like Clavicles In The Prosauropod Dinosaur _Massospondylus_. Journal of Vertebrate Paleontology 25(2):466468. The discovery of the furcula for _Tyrannosaurus rex_ verifies the prediction of one by Carpenter and Smith and increases the number of taxa with this structure. - Larson, P., & J. K. Rigby Jr. 2005. Furcula of _Tyrannosaurus rex_. In "The Carnivorous Dinosaurs" edited by Kenneth Carpenter, pp. 247-255. Bloomington: Indiana University Press. The _Allosaurus_ furculae from Cleveland-Lloyd Dinosaur Quarry show the following variations... - Chure, D. J., & J. H. Madsen. 1996. On the Presence of Furculae in some Non-Maniraptoran Theropods. Journal of Vertebrate Paleontology 16(3):573-577. The furcula appears as a single, robust boomerang-shaped form in Late Jurassic and Cretaceous tetanuran theropods, identical to the structure seen in _Archaeopteryx_, _Confuciusornis_, and other basal birds. - Padian, K. 2004. Basal Avialae. In "The Dinosauria, Second Edition", edited by David Weishampel, Peter Dodson, and Halszka Osmlska, pp. 210-231. Berkeley: University of California Press. We report the occurrence of a furcula (fused clavicles) in both species of the Early Jurassic coelophysid theropod dinosaur _Syntarsus_... - Tykoski, R. S., C. A. Forster, T. Rowe, S. D. Sampson, & D. Munyikwa. 2002. A Furcula in the Coelophysid Theropod _Syntarsus_. Journal of Vertebrate Paleontology 22(3):728733. There are even suggestions that furculae were present in forms earlier than the coelophysids: Here we report on a well-preserved and articulated specimen of the prosauropod _Massospondylus carinatus_ with a clavicle pair in life position. The clavicles are joined in a furcula-like arrangement... [Yates & Vasconcelos 2005] More correctly, a wishbone is formed from the fusion of *two* collar bones, one from either side of the body. == http://listverse.com/science/top-10-signs-of-evolution-in-modern-man/ == http://www.pbs.org/wgbh/nova/id/tran-nf.html http://www.pbs.org/wgbh/nova/id/tran-nf.html Fossil Evidence In 2004, a field crew digging in the Canadian Arctic unearthed the fossil remains of a half-fish, half-amphibian that would all but confirm paleontologists' theories about how land-dwelling tetrapods (four-limbed animals, including us) evolved from their fish ancestors. The animal was a so-called lobe-finned fish that lived about 375 million years ago. Named Tiktaalik rosae by its discoverers, it is a classic example of a transitional form, one that bridges the evolutionary gap between two quite different types of animal. Below, see this and four other well-known fossil transitions, which clearly indicate Darwinian evolution inaction.Rima Chaddha Notes Dates, in millions of years ago, give the estimated age of known fossils. Fish to amphibians Eusthenopteron looked and behaved a lot like modern fish, but hidden within its fins were the precursors of the arm and leg bones of four-limbed land animals. The later Tiktaalik took a further step toward terrestrial life with early wrist and finger bones that allowed the animal to prop itself up and poke its head from the water of the shallow swamps it favored. Tiktaalik's skeleton indicates that it probably breathed both through gills, like Eusthenopteron, and through a lung-like structure, like the later Ichthyostega and modern amphibians. Ichthyostega's even stronger limbs probably developed so that it could maneuver around thick vegetation in its marshy habitat and even haul itself along muddy banks when necessary. Reptiles to mammals Despite its distinctly lizard-like appearance, Dimetrodon possessed a suite of traits more common to later mammals than to its close relatives, the true reptiles. Most notably, the sail protruding from Dimetrodon's back allowed the animal to partially regulate its body temperature, marking what could have been a major point in the transition to warm-bloodedness. The later Thrinaxodon didn't have a sail but was probably covered in fur and might have been warm-blooded like the early mammal Morganucodon. Another documented shift toward mammals took place in the mouth: Dimetrodon had differentiated teeth and a strong bite, although it gulped its prey whole like true reptiles do even today. Thrinaxodon developed a stronger lower jaw and could chew, but it was Morganucodon that sported both sharp teeth and grinding molars like we have today. Reptiles to birds Few topics spark as much controversy among paleontologists as the transition from reptiles to birds. Experts don't know what Archaeopteryx's closest dinosaur ancestor looked likefossils haven't yet been foundbut they think it might have looked somewhat like Velociraptor (hence our showing it here, despite its much later age). Archaeopteryx, the first known bird, did share a common ancestor with Velociraptor as well as traits this ancestor would have had: sharp claws for grasping prey and long hind legs and a stabilizing tail for running, for example. Yet Archaeopteryx also had feathers indicative of early flight, although the orientation of its shoulder joint and its lack of a bony breastbone imply the animal was more of a glider than many modern birdsit couldn't lift its wings above its back or flap them for extended flight. Archaeopteryx's later bird relative, Yanornis, had a bone structure more conducive to bird flight as we know it today. It could flap its wings and, like many modern birds, it had a short, aerodynamic tail. Like Archaeopteryx, however, Yanornis did retain some dinosaurian features, including teeth. Land mammals to aquatic mammals Pakicetus may have looked somewhat like a dog with hoofs, but it was actually an early cetaceana group that comprises the dolphins, porpoises, and whales. The proof, scientists say, lies in Pakicetus's ears, which were intermediate between those of terrestrial and fully aquatic mammals, and in its triangular, whale-like teeth. Pakicetus and its relatives were possibly fish-eating scavengers that ventured into the water to find live prey. Although the later Ambulocetus had tiny hoofs on its hind legs and could probably walk, its toes were webbed like those of modern mammals adapted for swimming. Its fossilized bones suggest that Ambulocetus undulated its spine vertically in the water like the still later Basilosaurus (as well as modern otters and whales) and not side-to-side like fish. Although Basilosaurus had tiny, weak hind "legs" left over from its evolutionary past, the animal was probably fully aquatic. Its sturdy front flippers were particularly adapted for the water, though they still had an arm-like bone structure as in those of modern cetaceans. Quadrupedal primates to bipedal primates The early ape Dryopithecus was probably a common ancestor to humans and the other great apes. Although Dryopithecus lived mainly in trees, fossil evidence shows that the animal walked on all fours whenever it descended to the forest floor. In fact, humans' more recent ancestor, Australopithecus afarensis, retained some remnants from its quadrupedal past, such as hind toes suited for climbing and a wrist joint indicating it sometimes knuckle-walked. But Australopithecus probably stood upright most of the time: Its femur was shaped similarly to that of the later Homo erectus and could bear the stress of habitual upright movement. Both protohumans' femurs were also angled inward to an almost knock-kneed position. This helped Australopithecus and H. erectus maintain their balance on two legs, just like we do today. == Darwin's Predictions Ahead of his time is putting it moderately for Charles Darwin. The father of evolution had conjectures that were only proved, or greatly substantiated, decades after his death in 1882, in some cases not until recently. Today, evidence that unequivocally supports his theory of evolution by natural selection, as well as other surmises he had, comes from an array of scientific disciplines, including paleontology, geology, biochemistry, genetics, molecular biology, and, most recently, evolutionary developmental biology, or "evo devo." "The notion that all these lines of evidence could converge and give a common answer to the question of where we came from is truly powerful," says Brown University biologist Kenneth Miller. "This is the reason why scientific support for the theory of evolution is so overwhelming." Here, bone up on Darwin's most prophetic ideas. == Digital scans of "Lucy" take pre-humans inside out HOUSTON (Reuters) Digital X-rays have turned Lucy, perhaps the world's best-known pre-human, inside out, and may answer questions about how our ancestors came down from the trees and walked, scientists said on Friday. The team at the University of Texas in Austin, in collaboration with the Ethiopian government, completed the first high-resolution computed tomography or CT scan of the human ancestor, who lived 3.2 million years ago. "These scans we've completed at the University of Texas permit us to look at the internal architecture -- how her bones are built," anthropology professor John Kappelman, who helped lead the work scanning all 80 pieces of the skeleton, told Reuters in an interview. Scientists hope studying a "virtual" Lucy will offer further clues about the human ancestor's lifestyle. Lucy, found in Ethiopia in 1974, is the best-preserved example of Australopithecus, a species of pre-human. "It opens it up to people who, instead of having to travel to some distant museum to see the original, can actually call it up on the desktop," Kappelman said. Kappelman said the scans could tell more about how Lucy's bones fit together -- and thus whether she and her kind climbed trees as well as walked. "We're quite certain this set of studies we're going to be conducting here with the CT data are going to go some distance to resolving this long-standing question," Kappelman said. Lucy's fossil is visiting the United States as part of a world premiere exhibit organized by the Houston Museum of Natural Science. The 3-foot- (1-meter) tall skeleton is about 40 percent complete. "It's going to help us fill us in what was one of the earlier stages ... of our evolution to really better understand the behaviors of an extinct cousin. In some ways it's like ... being able to tune the time machine back to 3 million years ago, jump in and pop back and be able to reconstruct what this fossil was doing on a day-to-day basis," Kappelman said. "She's arguably now and I think will be for a long time, the most famous fossil on planet Earth," he added. -- Afarensis is a 3.5-2.8 million year old hominin from the Kada Hadar member of the Hadar formation in the Middle Awash, Ethiopia. He is approximately 41 inches tall, weighs approximately 60 pounds and has a cranial capacity of a whopping 410 cc (approximately). Afarensis is currently considered to be transitional between apes and humans and displays some traits of both. Since he spends a lot of time on the couch watching monster movies, some observers question whether he is an obligate biped. == New Protocetid Whale from the Middle Eocene of Pakistan: Birth on Land, Precocial Development, and Sexual Dimorphism Philip D. Gingerich1*, Munir ul-Haq2, Wighart von Koenigswald3, William J. Sanders4, B. Holly Smith5, Iyad S. Zalmout1 1 Museum of Paleontology and Department of Geological Sciences, University of Michigan, Ann Arbor, Michigan, United States of America, 2 Geological Survey of Pakistan, Quetta, Pakistan, 3 Steinmann-Institut fur Geologie, Mineralogie und Palaontologie, Universitat Bonn, Bonn, Germany, 4 Museum of Paleontology, University of Michigan, Ann Arbor, Michigan, United States of America, 5 Museum of Anthropology, University of Michigan, Ann Arbor, Michigan, United States of America Abstract Background Protocetidae are middle Eocene (4937 Ma) archaeocete predators ancestral to later whales. They are found in marine sedimentary rocks, but retain four legs and were not yet fully aquatic. Protocetids have been interpreted as amphibious, feeding in the sea but returning to land to rest. Methodology/Principal Findings Two adult skeletons of a new 2.6 meter long protocetid, Maiacetus inuus, are described from the early middle Eocene Habib Rahi Formation of Pakistan. M. inuus differs from contemporary archaic whales in having a fused mandibular symphysis, distinctive astragalus bones in the ankle, and a less hind-limb dominated postcranial skeleton. One adult skeleton is female and bears the skull and partial skeleton of a single large near-term fetus. The fetal skeleton is positioned for head-first delivery, which typifies land mammals but not extant whales, evidence that birth took place on land. The fetal skeleton has permanent first molars well mineralized, which indicates precocial development at birth. Precocial development, with attendant size and mobility, were as critical for survival of a neonate at the land-sea interface in the Eocene as they are today. The second adult skeleton is the most complete known for a protocetid. The vertebral column, preserved in articulation, has 7 cervicals, 13 thoracics, 6 lumbars, 4 sacrals, and 21 caudals. All four limbs are preserved with hands and feet. This adult is 12% larger in linear dimensions than the female skeleton, on average, has canine teeth that are 20% larger, and is interpreted as male. Moderate sexual dimorphism indicates limited male-male competition during breeding, which in turn suggests little aggregation of food or shelter in the environment inhabited by protocetids. Conclusions/Significance Discovery of a near-term fetus positioned for head-first delivery provides important evidence that early protocetid whales gave birth on land. This is consistent with skeletal morphology enabling Maiacetus to support its weight on land and corroborates previous ideas that protocetids were amphibious. Specimens this complete are virtual Rosetta stones providing insight into functional capabilities and life history of extinct animals that cannot be gained any other way. Citation: Gingerich PD, ul-Haq M, von Koenigswald W, Sanders WJ, Smith BH, et al. (2009) New Protocetid Whale from the Middle Eocene of Pakistan: Birth on Land, Precocial Development, and Sexual Dimorphism. PLoS ONE 4(2): e4366. doi:10.1371/journal.pone.0004366 Editor: Paul Sereno, University of Chicago, United States of America Received: November 11, 2008; Accepted: December 23, 2008; Published: February 4, 2009 Copyright: 2009 Gingerich et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: Research was supported by the Geological Survey of Pakistan, National Geographic Society (5537-95), U. S. National Science Foundation (9714923, 0517773), German Alexander von Humboldt Stiftung, and University of Michigan. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. Introduction Archaeoceti are basal cetaceans that document the evolutionary transition of whales from land to sea during the Eocene before the appearance of modern Mysticeti and Odontoceti [1]. Archaeocetes are primitive compared to later cetaceans in retaining cheek teeth with shearing crests, flexible elbow joints, and well-formed hind limbs with feet and toes (Figure 1). Skulls with long jaws, pointed incisors, and cuspate cheek teeth indicate that archaeocetes were specialized piscivores. Figure 1. Skeletons of the Eocene archaeocete whales Dorudon atrox and Maiacetus inuus in swimming pose. (A, B) Dorudon atrox (5.0 m; 36.5 Ma) based on UM 101222 and 101215 [11] in lateral and dorsal views, respectively. (C, D) Maiacetus inuus (2.6 m; 47.5 Ma) based on male specimen GSP-UM 3551 in lateral and dorsal views, respectively. doi:10.1371/journal.pone.0004366.g001 Two stages of archaeocete evolution, Protocetidae and Basilosauridae, are known from articulated skeletons. Protocetidae are middle Eocene in age (Lutetian-Bartonian, 4937 Ma), and comprise fifteen genera and 16 species that range from South Asia and Africa to North America [2]. All are found in marine sedimentary rocks. The best known protocetids are 2 to 3-meter long primitive forms such as Artiocetus and Rodhocetus represented by skulls and partial skeletons with artiodactyl-like ankle bones [3]. These were amphibious foot-powered swimmers [4] that retained fully developed hind limbs connected to the vertebral column, enabling limb-supported locomotion on land. Maiacetus, described below, was part of this early diversification (Figure 1C, D). Basal archaeocetes have long been interpreted as amphibious, feeding in the sea but returning to land to rest, mate, and give birth [5], [6]. Late early Eocene and early middle Eocene pakicetid and ambulocetid archaeocetes, known from less complete remains, were almost certainly semiaquatic like protocetids [7], [8], [9]. Basilosauridae are late middle Eocene and late Eocene in age (Bartonian-Priabonian, 4034 Ma) and were widely distributed in the world's oceans. The best known is the 5-meter long Dorudon (Figure 1A, B). Basilosauridae retained protocetid-like skulls, but their hind limbs were greatly reduced, making them fully aquatic. Basilosaurids had a powerful tail with a terminal fluke and were clearly tail-powered swimmers like modern whales [10], [11]. Generalized Eocene protocetid and basilosaurid Archaeoceti such as Maiacetus and Dorudon were on or near the main line of early whale evolution leading to later Mysticeti and Odontoceti, which appeared at the end of the Eocene or beginning of the Oligocene. Two specimens of a new early middle Eocene (ca. 47.5 Ma) protocetid whale are described below, providing the first nearly complete skeleton of a protocetid whale, the first remains of a fetal skeleton of an archaeocete, and the first direct evidence for birth, life history, and sexual dimorphism in early archaeocetes at a time when whales were still amphibious mammals spending some time on land and some time in the sea. Methods Field Methods Fossil specimens described here were located during surface surveys in Pakistan in 2000 and 2004. These were found as articulated skeletons, and each specimen was separated into blocks of manageable size along cracks during excavation. The blocks were encased in plaster jackets and transported to the laboratory for preparation. Preparation The two specimens described here were prepared differently. The three plaster jackets of the adult female (GSP-UM 3475) were opened and cleaned to expose the articulated bones (Figure 2). The ventral surface of the cranium of the female whale was stabilized, supported by a fitted fiberglass cradle, and then turned and cleaned to expose the dorsal side of the cranium. Bones of the left forelimb were removed from the second jacket individually. The thorax and lumbus of the mother whale and the fetal skull and skeleton were stabilized in situ in the third jacket with only the side shown here being cleaned (Figure 2). Figure 2. Adult female and fetal skeletons (type) of the protocetid Maiacetus inuus. Skull of the adult female (GSP-UM 3475a) is colored beige with brown teeth; her postcranial skeleton is colored red; the fetal skeleton (GSP-UM 3475b) is colored blue with red teeth. Blue dashed lines indicate the contours of the three field jackets and the red dashed line marks the edge of erosion. doi:10.1371/journal.pone.0004366.g002 The nine plaster jackets of the adult male (GSP-UM 3551) were prepared manually with a micro-airscribe. Each block containing bones was molded and cast to create an archive of the position of the bones as found in the field. Each block was then fully prepared to free individual skeletal elements. These associated elements were then assembled into a full skeletal mount for exhibition in the University of Michigan Exhibit Museum (see Figure 1A, B). Imaging The fetal dentition described here was imaged with computed tomography using a Philips Tomoscan AVE1 scanner at the Radiologische Klinik, Universitat Bonn (Germany). Terminology Ma, geological age in millions of years before present. Anatomical Abbreviations in Text. C, cervical vertebra; Ca, caudal vertebra; L, lumbar vertebra; Mc, metacarpal; Mt, metatarsal; R, rib; S, sacral vertebra; and T, thoracic vertebra. Teeth are numbered sequentially from front to back (mesial to distal), with upper and lower incisors (I), canines (C), premolars (P), and molars (M) distinguished by superscripts and subscripts, respectively. Institutional Abbreviations. GSP-UM, Geological Survey of Pakistan-University of Michigan collection, housed in Quetta, provincial capital of Balochistan; UM, University of Michigan Museum of Paleontology, Ann Arbor, Michigan, United States of America. Results Systematic Paleontology Mammalia Linnaeus, 1758 Cetacea Brisson, 1762 Archaeoceti Flower, 1883 Protocetidae Stromer, 1908 Protocetinae Stromer, 1908 Maiacetus gen. nov. Etymology. Maia, mother, and ketos, whale (Greek): named for the sex and gravid state of the holotype. Type Species. Maiacetus inuus sp. nov. Diagnosis. Medium-sized protocetid archaeocete with a skeleton 2.6 m in length and an estimated weight of 280390 kg. Skull has the medium-length rostrum, anteriorly-positioned nares, large mandibular canals, narrow frontal shield, broad cranial base, and large tympanic bullae typical of early protocetids. Differs from contemporary Artiocetus clavis and Rodhocetus balochistanensis in having solidly co-ossified left and right dentaries. In the ankle, the astragalus has deep proximal and distal trochleae as in Rodhocetus, but differs in having an indented dorsolateral border; cuboid is less deeply notched for the calcaneum than in Artiocetus and more deeply notched than in Rodhocetus. Metacarpals, carpal phalanges, and all hind limb elements are shorter relative anterior thoracic centrum length than comparable ratios in Rodhocetus. Maiacetus inuus sp. nov. Figures 1CD, 59, 10C, 11B Etymology. Inuus, god of fecundity (Latin): named to acknowledge both the exceptional recovery of a gravid female in the cetacean fossil record, and the importance of life history in mammalian evolution. Holotype. GSP-UM 3475a, articulated skull, thorax, and left forelimb of an adult female. Holotype contains the skull and partially ossified skeleton of a near-term fetus, GSP-UM 3475b (Figure 2). The mother is a young adult as shown by the complete eruption of the permanent dentition, limited tooth wear, fusion of most epiphyses, and presence of a fetus. Type Locality. Kunvit, Kohlu District, eastern Balochistan Province, Pakistan (Figure 3). GPS coordinates are 30.0963N and 69.7908E (WGS84 datum). Figure 3. Map showing localities of some Eocene whales in eastern Balochistan (Pakistan). Map showing the Kunvit area in the southwestern part of Lakha Kach syncline, northwest of the town of Rakhni. Red diamonds mark type localities for Artiocetus clavis (GSP-UM 3458), Rodhocetus balochistanensis (GSP-UM 3485) [3], Protosiren eothene (GSP-UM 3487) [49], Makaracetus bidens (GSP-UM 3570; from younger beds of the overlying Domanda Formation) [2], and Maiacetus inuus (GSP-UM 3475a, b, female, fetal skeleton). Localities are in the upper part of the Habib Rahi Formation of early Lutetian age [12]. The red circle marks the locality of the referred specimen of Maiacetus inuus (GSP 3551, male), yellow circles show localities of other archaeocete specimens, and white circles show localities of other vertebrate specimens. doi:10.1371/journal.pone.0004366.g003 Referred Specimen. GSP-UM 3551, virtually complete skeleton interpreted as male (see below; Figures 1C, D, 9). Found in Kunvit, Kohlu District, eastern Balochistan Province, Pakistan in the same strata and about 1 km from the holotype (Figure 3). GPS coordinates are 30.1051N and 69.7926E (WGS84 datum). Age. All specimens are from upper beds of the Habib Rahi Formation, a succession of interbedded marine marls and shales. The marls are approximately 1020 cm thick, and the shales are approximately 1 meter thick. The marls thin and the shales thicken toward the top of the section [12]. The age of the Habib Rahi Formation has been established on the east side of the Sulaiman Range at Rakhi Nala 35 km southeast of Kunvit [13], [14]. The specimens described here were found near the top of the major flooding sequence in the early Lutetian stage of the middle Eocene, calibrated to approximately 47.5 Ma (Figure 4). Figure 4. Temporal constraints on the age of Maiacetus inuus. Red rectangle highlights the platy limestones and marls of the upper part of the marine Habib Rahi Formation. Nannoplankton Sphenolithus spininger and Helicosphaera bramlettei indicative of NP zones 1415 have been reported from the Habib Rahi Formation [13]. The age of Maiacetus inuus is about 47.5 Ma. Figure from [14]. doi:10.1371/journal.pone.0004366.g004 Diagnosis. As for the genus. Description of Maiacetus inuus Adult Female Skeleton (GSP-UM 3475a). The adult female skeleton (GSP-UM 3475a) and its associated fetal skeleton (GSP-UM 3475b) were collected in three blocks: (1) a cranial block with the female skull, cervical vertebrae, some anterior thoracic vertebrae, and partial scapulae; (2) a block containing the left forelimb of the adult female; and (3) a block containing the thorax of the adult mother whale, and the skull and remaining skeleton of the fetus (Figure 2). Blocks 2 and 3 were slightly displaced (35 cm) relative to block 1 along a small fault or joint surface after the specimen was buried and fossilized. This movement deformed immediately adjacent bones and may have destroyed parts of bones near the fault. Some bone pieces removed from the fault zone during collection fit onto bones of one block or the other. The adult female skull and skeleton came to rest on their dorsal surfaces before burial, as is typical for archaeocetes. This stomach-up orientation may be caused by a buildup of gases in the abdomen during decomposition. Skulls are seemingly more stable lying on their dorsal surface than in any other position. The nearly complete skull of the adult female has been exposed in ventral and dorsal views (Figures 5, 6). It measures 56 cm in length (Table 1). Salient features of the skull include a relatively narrow and anteroposteriorly-elongated rostrum, with premaxillae expanded anteriorly in front of the canine teeth. The rostrum widens posteriorly and is relatively broad at the position of the left and right upper molars. Figure 5. Skull of Maiacetus inuus (GSP-UM 3475a; female). Skull in ventral view (A) with interpretive shading and labels (B). Shaded components include skull bones (grey), teeth (brown), hyoids (orange), and postcranial bones (red). Osteological abbreviations: Ba., basihyal; Basicr., basicranium; C, cervical vertebra; Dent., dentary; Exoc., exoccipital; Jug., jugal; L, left; Max., maxilla; R, right, rib; Scap., scapula; Squ., squamosal; St., stylohyal; Stern., sternebrum; T, thoracic vertebra; Th., thyrohyal; Tym., tympanic. doi:10.1371/journal.pone.0004366.g005 Figure 6. Skull of Maiacetus inuus (GSP-UM 3475a; female). Skull in dorsal view (A) with interpretive shading and labels (B). Shaded components include skull bones (grey), teeth (brown), and postcranial bones (red). Osteological abbreviations: Dent., dentary; Front., frontal; Jug., jugal; L, left; Lac., lacrimal; Max., maxilla; Nas., nasal; Par., parietal; Pmax., premaxilla; R, right, rib; Scap., scapula; Squ., squamosal. doi:10.1371/journal.pone.0004366.g006 Table 1. Skeletal measurements (cm) of Maiacetus inuus compared to those of the previously known protocetids Artiocetus clavis and Rodhocetus balochistanensis, which are also from the early middle Eocene of Pakistan [3]. doi:10.1371/journal.pone.0004366.t001 On the dorsal surface of the cranium, the external nares open above the upper canine teeth (Figure 6). The nasals are narrow and extend posteriorly to overlap the frontals. Expanded frontals form a frontal shield with prominent supraorbital processes. The frontal shield is not as broad relative to the rest of the skull as it is in later protocetids. The jugals are relatively thin and flare posteriorly. The skull is broadest across the left and right squamosals. There is a low sagittal crest and a moderately developed nuchal crest. On the ventral surface of the cranium the glenoid fossa for articulation of the dentary is open and relatively flat as in other early protocetids. Remnants of the basihyal, tympanohyals, and stylohyal bones can be identified on the ventral surface of the basicranium (Figure 5). The tympanic bullae are large with a sigmoid process well developed laterally and involucrum well developed medially. The mandibular symphysis is solidly fused from the anterior end of the dentaries to a position beneath P2 (Figure 5). The ventral portions of the dentaries are hollow posteriorly, and the mandibular canal is well developed. The canal cannot be measured, however, due to dorsoventral compression of the dentaries. Dorsoventral compression of the adult female skull has pushed some of the crowns of lower teeth into the bones of the cranium and some crowns of upper teeth into the left dentary (Figures 5, 6). The upper dental formula is 3.1.4.3 (incisors, canines, premolars, molars). Partial or complete crowns of all upper teeth are exposed in the right premaxilla and maxilla (Figure 5), except for M3, which is known in the adult male (GSP-UM 3551; see below). All incisors are caniniform with simple conical crowns on a single root. I12 are large and I3 is relatively small (Table 2). The canine is moderate in size and simple in form, with a conical crown on a single root. P1 has a simple crown and is single-rooted, while P24 have more elongated crowns and double roots. Upper molars have a simple large external paracone, with little development of a metacone. Protocones on upper molars are not exposed in the adult female skull but are well developed in the adult male (GSP-UM 3551; see below). P3 has the anteroposteriorly longest crown in the upper dentition (Figure 5). Table 2. Measurements (mm) of teeth in female and male specimens of Maiacetus inuus. doi:10.1371/journal.pone.0004366.t002 The lower dental formula, like the upper, is 3.1.4.3. I13, C1, and P13 are present in the left dentary (Figure 6), and the remaining premolar and lower molars are known in the adult male (GSP-UM 3551; see below). Again, all incisors are caniniform with simple conical crowns on a single root. I1 is relatively small (judging from the root), I2 is large, and I3 is small (Figure 6, Table 2). Lower canine C1 is moderate in size and simple in form, with a conical crown on a single root. Lower P1 is small, and P23 have anteroposteriorly longer crowns. The longest tooth in the lower dentition was probably P3, but this cannot be determined with confidence from the specimens at hand. The cervical vertebrae (C1C7) of the adult female (GSP-UM 3475a) are preserved in articulation in the cranial block, but these are difficult to study or measure individually (Figures 2, 5). The first three thoracic vertebrae and a remnant of the fourth (T1T4) are preserved in articulation posterior to the cervicals. Nothing has been recovered of T5, which was evidently lost during displacement of cranial and thoracic blocks along the intervening fault or joint surface. The vertebral column continues in the thoracic block. T6 is represented by a piece of the centrum, while the remaining thoracic vertebrae (T713) and lumbar vertebrae (L1L4 and part of L5) are preserved in articulation (Figure 2). A sternebrum and some ribs are present in the cranial block (Figures 5, 6). The ribs continue into the thoracic block, where they are preserved for the most part in order. The distal ends of the right ribs lie on top of the vertebral centra, whereas distal ends of the left ribs are displaced more laterally. Ribs in the thoracic block can only be identified by counting backward from the most distal rib (R13). The left forelimb was preserved in articulation on the left side of the thorax (Figures 2, 7). A fragment of the left scapula lies under the left squamosal, and a fragment of the right scapula lies under the anterior ribs on the right side of the cranium. Much of the left scapula and the proximal end of the left humerus were damaged at the juncture of the cranial and forelimb blocks. The distal end of the humerus is relatively narrow with a shallow trochlea and deep olecranon fossa for articulation with the ulna. The radius and ulna are well preserved although somewhat flattened (Figure 7). Figure 7. Left radius, ulna, carpus and manus of Maiacetus inuus (GSP-UM 3475a, female). Open areas are reconstructed. Abbreviations: C, cuneiform; L, lunar; M, magnum; P, pisiform; S, scaphoid; Tr, trapezium; Trd, trapezoid; U, unciform. doi:10.1371/journal.pone.0004366.g007 The distal row of carpal bones is alternating rather than serial relative to the proximal row. Metacarpal I is the smallest, metacarpals III and IV are the largest, and metacarpal III is distinctly longer than metacarpal IV. With the exception of the pollex (digit I), all of the proximal phalanges are about the same length (the proximal phalanx of digit I is not known). Similarly, middle phalanges of digits II through V are similar in length, although phalanx III-2 is distinctly more robust. Terminal phalanges of digits I and V are simple and pointed and probably did not bear a hoof, whereas the blunt end of terminal phalanx II-3 indicates that it was hoof bearing. Terminal phalanges II-3, III-3, and IV-3 in the adult male (GSP-UM 3551) all bore hooves. Preservation of the vertebral column ends at L5. Nothing remains of L6, the sacrum, or the tail. Very little of a hind limb is preserved in the adult female (Figure 2). The left ilium is represented only by the crescent-shaped anterior margin. The distal left femur, patella, and proximal end of the left tibia are preserved in articulation, but the rest of the left hind limb and all of the right hind limb are missing. Fetal Skeleton within Adult Female (GSP-UM 3475b). The fetal skeleton (GSP-UM 3475b) is preserved within the ribcage of the type specimen (GSP-UM 3475a) (Figure 2, colored blue). This immature individual is interpreted as a fetal skeleton, rather than an ingested meal, because of the absence of any damage to the skull. Protocetids had shearing molars used to slice and chew their prey. The skull of the fetal skeleton could not have survived such mastication and be as well preserved as it is. The fetal skeleton preserves the skull, some cervical and thoracic vertebrae, ribs, and portions of the fore- and hind limbs. The skull includes the cranium and left and right lower jaws, with crowns and roots of many deciduous teeth in place in the upper and lower jaws. The surfaces of the fetal bones are porous in contrast to the smoother surfaces of adult bones. The fetal skeleton has a preserved length of about 33 cm, and probably had a total length approximately twice the preserved length. The length of the fetal skull, as preserved, is 15 cm, and this probably measured 17 cm when the missing anterior end of the rostrum is added (Figure 8). Identifiable bones include the left frontal, the left jugal, the occipital with left and right condyles flanking the foramen magnum, and the left and right dentaries. Figure 8. Fetal skull of Maiacetus inuus (GSP-UM 3475b). (A)Photograph showing bones (shaded white) and teeth (shaded brown) in lateral view. (B)CT image overlain on tooth-bearing part of fetal skull in lateral veiw. Abbreviations: left frontal (L. Front.), left jugal (L Jug.), occipital (Occip.) with left and right condyles flanking the foramen magnum, and left and right dentaries (L dent., R dent.). Teeth are shaded brown, with darker brown representing enamel, and lighter brown representing roots and exposed dentine. White and black labels identify teeth of the left and right sides, respectively. Dotted lines trace outlines of fully formed crowns of left dP3 and dP4. These crowns are visible on the surface (A) where thin bone of the maxilla is pressed over more rigid underlying crowns, and as denser masses in the CT scan (B). Remaining teeth are identified by size and position relative to dP3 and dP4. Note presence of the developing crown of permanent left M1 posterodorsal to the crown of left dP4 (dorsal to the left jugal and posterior to the left frontal). Partial crown of right M1 (unlabeled) is visible just below and posterior to left M1. doi:10.1371/journal.pone.0004366.g008 The fetal dentition is largely intact but interpretation is complicated by bilateral compression of the skull (Figure 8A, B). Left upper teeth are displaced dorsally relative to right upper teeth, and the left dentary is displaced slightly anteriorly relative to the right dentary. Teeth from both left and right sides, being denser and harder than surrounding fetal bone, all show on the exposed left side of the skull. The largest tooth in each quadrant is the distinctive fourth deciduous premolar. These four premolars (left and right dP4 and dP4), serve as landmarks for identification of more anterior and posterior teeth. Anterior to dP4 and dP4, there are partial crowns of all of the third deciduous premolars (left and right dP3 and dP3), as well as upper and lower deciduous canines. Teeth anterior to dP3 and dP3 were identified by their morphology and by their stage of development, using an undescribed protocetid skull with a good deciduous dentition for comparison. Posterior to dP4, there are partial crowns of the left and right first permanent upper molars visible below the left frontal and above the left jugal (Figure 8,). Left M1 is the most clearly exposed and it appears to have the main paracone cusp almost fully formed, with the crown as a whole about one-half mineralized. Crowns of left and right lower permanent molars are not visible but were presumably also partially mineralized. Cervical and anterior thoracic vertebrae are compressed in articulation, and the ribs are preserved as narrow ribbons of porous bone pressed onto the ventral surfaces of the mother's thoracic vertebrae. Parts of seven long bones are evident. The largest of these are presumably humeri, and there may be remnants of ulnae and radii as well. Seven long bones would exceed the number expected in a pair of protocetid forelimbs, and so some may pertain to the hind limbs. More precise identification is hindered by the absence of ossified epiphyses. Adult Male Skeleton (GSP-UM 3551). The most complete skeleton of Maiacetus inuus is that of a second adult (Figure 1C, D) found in articulation in the field (Figure 9). The skull lacks the anterior portion of the rostrum, while the vertebral column and fore- and hind limbs are virtually complete. The specimen is interpreted as male because it is larger than the female skeleton described above, the canine teeth are larger relative to the size of other teeth, and the pelvic morphology is male (see below). Comparative measurements are provided in Tables 13. Figure 9. Skeleton of Maiacetus inuus (GSP-UM 3551, male). Skeleton as preserved in left lateral view. Gray shading is marl matrix (see Figure 1C, D for skeletal restoration). doi:10.1371/journal.pone.0004366.g009 Table 3. Vertebral centrum measurements (mm) for adult male Maiacetus inuus (GSP-UM 3551; Figure 9). doi:10.1371/journal.pone.0004366.t003 The male skull is similar to that of the female described above. Here again the anterior rostrum is narrow but it expands rapidly at mid length toward the posterior end of the skull. The palate is much broader posteriorly than it is anteriorly. The frontal shield is expanded with broad supraorbital processes, but it is again narrower than that of later protocetids. Lacrimal bones are exposed on the face anterior to the orbits. The high, narrow, and deep nuchal area is bordered ventrolaterally by robust, broadly-spaced parocciptal processes, suggesting the presence of powerful neck muscles. Tympanic bullae are large, robust, and firmly attached to the underside of the endocranium. The convex occipital condyles are oriented posteriorly. The mandibular symphysis is fused as far posteriorly as the distal margin of P2. The large mandibular foramen leading to the mandibular canal is mediolaterally narrow and dorsoventrally deep (depth estimated as 7 cm). It opens internally at the posterior end of the dentary. The mandibular condyles are positioned well below the apex of the coronoid process, and the gonial angle of the mandible is compressed and square in outline (viewed laterally; Figure 1A). Upper and lower incisors are missing in the adult male (GSP-UM 3551), but the upper canine (C1) is large and anteroposteriorly expanded. The upper first premolar (P1) is small, while P2 is closer in size to P3 and P4. P3 has the largest crown of the upper cheek teeth. P3-M3 are closely spaced with no diastemata. A protocone is well developed on P4 and on M1. This primitive cusp decreases in size on M2 and nearly disappears on M3. In the lower dentition, C1 and P1 are represented only by impressions of the crowns and roots. The crown of the lower canine crown is longer anteroposteriorly and the root thicker than in the female (GSP-UM 3475a), while P1 is small. Lower P2, P3, and P4 are all relatively large, with P3 or P4 the largest of the lower cheek teeth. The lower molars are closely spaced, with a high anterior cusp (protoconid) and lower posterior cusp (hypoconid). The vertebral formula (cervicals, thoracics, lumbars, sacrals, caudals) is 7C-13T-6L-4S-21Ca for a total of 51 vertebrae, which differs by only two caudal vertebrae from the formula found in some primitive artiodactyls [15]. Precaudal vertebrae increase in size along the series as in other protocetids (Table 3). The atlas (C1) has broad transverse processes, moderately deep and curved prezygapophyses, and a complex foraminal pathway for the vertebral arteries to accommodate motion of the skull. In C3C7 the orientation of zygapophyses, the saddle-shape of vertebral body surfaces, and the imbrication of transverse processes suggest that the neck was more capable of dorsiflexion than lateral rotation. Anterior thoracic vertebrae have long spinous processes for muscles and ligaments inserting on the exoccipital region and nuchal area of the skull to stabilize the head. Thoracic T11, the diaphragmatic vertebra, has thoracic-like prezygapophyses and lumbar-like postzygapophyses. T12 is the anticlinal vertebra with a vertical neural spine (Figure 1A). In the lumbus, anterodorsally inclined spinous processes, non-revolute zygapophyses, and the anteroventral orientation of transverse processes indicate the potential for dorsoventral flexion of the trunk and vertebral column in general. Flexion, however, was limited by the anteroposterior width and length of the spinous processes of the lumbar vertebrae. The sacrum is composed of four vertebrae, the first three fully co-ossified and the fourth with fused pleurapophyses. Robust auricular processes are present on S1 for articulation with ilia of the pelvis. The spinous processes of all sacral vertebrae have massive bases. Presence of a solidly fused sacrum precluded smooth undulatory motion of the body during swimming. The caudal series is composed of 21 vertebrae (Figures 1C, D, 9). The first 14 caudals have associated hemal arches or chevron bones. Anterior caudals are robust, with substantial spinous processes, metapophyses, and transverse processes. The latter are divided in Ca 46. Mid-caudal vertebrae are also large but have more diminutive processes. The size and complexity of vertebrae in the posteriormost part of the tail decrease rapidly following the last chevron-bearing caudal (Figures 1C, D, 9). The ribs are elongate and moderately curved, with no sign of pachyostosis or osteosclerosis. All but the last few are double-headed. The sternum includes eight elements with a T-shaped manubrium, six sternebrae, and an elongate xiphisternum. The delicate scapula is longer than wide, with a projecting acromion and shallow glenoid; the coracoid process forms a large tubercle above the glenoid. The scapular spine divides the scapular blade unequally into smaller anterior and larger posterior portions. The humerus is relatively long, flattened, and anteriorly curved. Proximally, the head is ovoid with a narrow bicipital groove. Distally, the humerus is narrow with a deep trochlea for the ulna. Posteriorly, there is a deep olecranon fossa. The convex articulation for the radial head is located lateral to the ulnar trochlea. The medial epicondyle is robust and projecting. Ulna and radius are shorter than the humerus (Figure 7). The ulna is flattened and has a large, blade-shaped olecranon process. The trochlear notch of the ulna projects farther anteriorly, locking into the humeral olecranon fossa during extension. The notch is bifid with a broad articulation distally for the radius. Although the radius and ulna are not coossified, they were fixed in a pronated position. The head of the radius, the shortest forelimb element, has a square contour and saddle-shaped surface. The radial shaft, unlike that of the humerus and ulna, has a subtriangular cross-section. The robust distal end of the radius has a distinct oval, flat articular surface for the carpus. The carpus is composed of a series of proximal and distal carpals that vary in shape from ovoid to polygonal (Figure 7). Proximal and distal carpal rows are staggered with interlocking articulations. The pisiform projects strongly ventrally, more than required to maintain the aponeurosis of the carpal tunnel, providing a powerful mechanical advantage for the flexor carpi ulnaris. The prominent medial malleolus on the humerus provides the origin for this muscle. The pisiform resembles the fifth metacarpal (Mc-V) in size and morphology. The carpals are transversely arched providing a deep ventral tunnel for flexor tendons. Digits three and four are dominant and metacarpal length decreases in the order of Mc-III, Mc-IV, Mc-II, Mc-V, and Mc-I (Table 1). Large, paired sesamoids are located on the ventral surfaces of the head of each metacarpal. Proximal phalanges are long and relatively thin, as are middle phalanges. Distal phalanges are much shorter and somewhat more robust. The manus is shorter than the pes and has more delicate terminal phalanges. The innominate is anchored to the sacrum. The ilium is short anterposteriorly relative to the length of the pelvis. The round, well buttressed acetabulum is notched with a pit for the ligamentum teres. The obturator foramen is large. The ischium is large, flattened, and extends farther from the acetabulum than does the ilium (Figure 1A). The pubic notch formed by inferior rami of left and right pubic bones is V shaped (Figure 10), as expected in a male. The robust femora are short relative to the length of the distal segments of the hind limb. The femoral head is rounded with a deep fovea capitis femora. Robust muscle attachment sites on the femur include prominent greater and lesser trochanters, a deep intertrochanteric fossa, and a distally extended lateral crest for insertion of vastus lateralis. The distal condyles of the femur are offset from one another, which served to rotate the tibia medially during flexion. The relatively long tibia has a robust proximal end and deeply trochleated distal end shaped to receive the astragalus. The relatively long, thin fibula has articular surfaces proximally for the tibia and distally for the calcaneum. Figure 10. Pelvic morphology in the extant sexually-dimorphic fallow deer Dama dama compared to that of male Maiacetus inuus. Pelves are viewed ventrally. Sexes differ in the shape of the notch separating inferior rami of left and right pubes. (A) Female Dama dama has the more U-shaped pubic notch labeled in red. (B) Male Dama dama has the more V-shaped pubic notch labeled in red. (C) Male Maiacetus inuus, GSP-UM 3551, has the V-shaped pubic notch labeled in red. Drawings of Dama dama are from [29]. Part of the right pubic ramus of GSP-UM 3551 is restored from the left side. doi:10.1371/journal.pone.0004366.g010 The ankle, preserved in articulation on both sides in GSP-UM 3551, resembles that of larger-bodied Rodhocetus balochistanensis more than that of similar-sized Artiocetus clavis (Figure 11). The astragalus is double-pulleyed with a trough-shaped trochlea for the tibia and an opposing trochlea for the navicular. Other astragalar facets include a narrow convex articular surface for the cuboid adjacent to the deeply notched surface for the navicular, a small curved surface laterally for articulation with the ectal facet of the calcaneum, a proximodistally elongated convex facet ventrally for long excursion on the calcaneal sustentacular surface, and a small facet adjacent to the cuboid facet for articulation with the calcaneum. On the calcaneum, the tuber is long and robust; the sustentaculum is oval, small, and shelf-like; the ectal facet is convex and confluent with the curved facet for the fibula; and the distal cuboid facet is slightly concave and obliquely oriented. The deeply concave navicular has a proximal keel for articulation with the astragalus, and distal facets for articulation with the ento-, meso-, and ectocuneiform (Figure 11). The cuneiforms are small and subrectangular with simple articular surfaces for the second and third metatarsals (Mt-II and Mt-III). It is possible that a tiny distal extension of the entocuneiform accommodated a very diminutive (but unrecovered) Mt-I. A pair of proximal articular surfaces on the cuboid include a concave medial portion for the astragalus and an obliquely notched, flatter surface for articulation with the distal surface of the calcaneum. Distally, the cuboid has a larger, flat articular surface for Mt-IV and a smaller articular surface for Mt-V. Figure 11. Comparison of right ankle bones of Artiocetus, Maiacetus, and Rodhocetus. (A)Astragalus and cuboid of Artiocetus clavis (GSP-UM 3458, type, reversed). (B)Ankle of Maiacetus inuus (GSP-UM 3551). (C)Ankle of Rodhocetus balochistanensis (GSP-UM 3485, type). Specimens are drawn to approximately the same astragalus+cuboid length, and viewed dorsally. Blue arrow points to distinctive indentation in lateral margin of astragalus of M. inuus; red arrows point to the broad and deep, narrow and intermediate, and narrow and shallow indentations in the calcaneum and lateral margins of cuboids. Abbreviations: Ast., astragalus; Cal., calcaneum; Cub., cuboid; Ecc., ectocuneiform; Enc., entocuneiform; Mec., mesocuneiform; Nav., navicular. doi:10.1371/journal.pone.0004366.g011 Pedal digits III and IV are largest. Lengths decrease in the sequence Mt-IV, Mt-III, Mt-V, and Mt-II. Each metatarsal head has paired facets ventrally for articulating sesamoid bones. Proximal and middle phalanges are long and relatively thin. Ungual phalanges are much shorter, ventrally flattened, and ornamented with dorsal tubercles and sulci to accommodate extensor tendons. Discussion Extraordinary Fossils The fossils described here include the first association of adult female and fetal whale skeletons, the latter apparently near term and in birth position (GSP-UM 3475a, b) (Figure 2). The adult male skeleton (GSP-UM 3551) found nearby is exceptionally complete (Figure 9). Together these specimens document a new protocetid whale preserving a complete vertebral column and complete fore- and hind limbs. The vertebral formula of Maiacetus is similar to that preserved in the other protocetids Rodhocetus and Qaisracetus (7C-13T-6L-4S) [14], [16], and in addition indicates the presence of 21 caudal vertebrae. As in all living semiaquatic mammals, the limbs are relatively short and pelvic girdles provide a direct connection to the vertebral column for weight-bearing. The ankles are artiodactyl-like, with a double-pulley astragalus, notched cuboid, and curved fibular facet characteristic of artiodactyls [3]. Metapodials are elongated, and the manual and pedal digits were almost certainly webbed. Maiacetus has a piscivorous dentition and, like other early protocetids, is interpreted as an amphibious, semiaquatic, foot-powered swimmer that fed in the sea and came ashore to rest, mate, and give birth, as anticipated by Fordyce [5]. While the hind limbs were capable of bearing the weight of the body on land, the proportions of the limbs and the long phalanges of both hands and feet would have limited terrestrial locomotion and prevented Maiacetus from traveling any substantial distance from water. Maiacetus differs from other early protocetids in having dentaries fused at the mandibular symphysis (Figure 5), ankles of distinct proportions (Figure 11), and limbs slightly different in proportion from those of other early protocetids (Figures 12, 13). These differences suggest that there are feeding and swimming specializations among protocetids that remain to be clarified. Figure 12. Proportion-adjusted skeletal profiles of middle and late Eocene archaeocete whales Maiacetus inuus and Dorudon atrox, respectively. (A)Maiacetus inuus, a semiaquatic foot-powered swimmer from the Middle Eocene. (B)Dorudon atrox, a fully-aquatic tail-powered swimmer from the Late Eocene. Baseline is mean length of anterior thoracic vertebrae (stippled box). Sacral vertebrae are enclosed in a second stippled box where sacrals can be identified (e.g., by co-ossification). Maiacetus has a profile more like that of mammals capable of supporting their weight on land, whereas Dorudon has the profile of a modern whale. Interpretation of profiles and the method of median serial-multiple-regression estimation of body weights is explained in [50]. Abbreviations: TCNDSFB, longest tooth length, condylobasal cranium length, narial position, dentary length, symphysis position, mandibular foramen height; and bulla length, respectively; SHRC, scapula, humerus, radius, and Mc-III lengths, respectively; IFTT, innominate, femur, tibia, and Mt-III lengths, respectively. doi:10.1371/journal.pone.0004366.g012 Figure 13. Principal components plot of trunk and limb skeletal proportions for Maiacetus inuus and a representative sample of 50 extant semiaquatic mammals. Maiacetus inuus is similar to Rodhocetus species, but lacks elongation of the manus, hind limb, and pes characteristic of the latter. Maiacetus is about equally aquatic (PC-II) to Rodhocetus but less specialized as a hind-limb swimmer (PC-III). It falls closest to the giant otter (Pteronura brasiliensis) among extant mammals. Background and comparative data for this analysis are documented and explained in [4]. doi:10.1371/journal.pone.0004366.g013 Birth on Land Presence of an intact fetal skeleton (GSP-UM 3475b) enables the first unequivocal determination of sex for an archaeocete: GSP-UM 3475a is female. The presence of one fetal skeleton and no trace of a second indicates that birth in Maiacetus involved a single calf. Early archaeocetes thus resemble all extant large semiaquatic mammals, which invest their energy in gestation and parenting of a single infant per breeding event [17]. The rostrum of the fetal skeleton is pointing opposite that of the mother (Figure 2). Posterior orientation of the fetal head occurs in the initial stage of birth in artiodactyls (Figure 14C). However, given the shorter neck in Maiacetus, this may have been the fetal position during all of late gestation. Because the head of the fetal skeleton of Maiacetus is not in the mother's pelvic canal, the fetus may have been near term but not full term. Partially formed M1 crowns in the fetal cranium suggest that the fetus was at least near term. Figure 14. Head versus tail presentation of near- and full-term calves in a domestic cow and harbor porpoise. Domestic cow (Bos taurus) calf (blue) in (A) ninth and final month of gestation before turning (axially rotating), (B) turned as the birth process begins, and (C) with forelimbs and head partially extruded in the initial stage of birth (from [51], [52]). Harbor porpoise (Phocaena phocaena) (D) with full-term calf (blue) with tail partially extruded in the initial stage of birth (from [18]). doi:10.1371/journal.pone.0004366.g014 The fetal skeleton is positioned for head-first birth, a universal birthing posture in large-bodied land mammals, but one that is anomalous in fully-aquatic marine mammals [18], [19], [20]. A near-term fetus in an ungulate or whale may rotate about its long axis as it passes through the birth canal, but it cannot turn head-to-tail (Figure 14AC). Discovery that early whales delivered calves like land mammals indicates that birth in semiaquatic protocetids still took place on land. Cephalic presentation at birth is generally held to be advantageous on land as it enables a newborn to breath during labor. Caudal presentation at birth, in contrast, is generally held to be advantageous at sea as it may reduce the risk of drowning [18]. Caudal presentation may also hold an advantage in water, because it orients the newborn calf to swim parallel to the mother rather than away from her. This might be important for communication, initiation of nursing, and protection from predators. Cephalic presentation does not incur the same risks on a solid substrate. Birth at sea was a prerequisite for the first fully-aquatic whales, the Basilosauridae (including Dorudon; Figure 1C, D), which evolved from Protocetidae later in the Eocene. Basilosauridae have reduced hind limbs that no longer contact the vertebral column and could not support the weight of the body on land. Hence they could no longer come out of the sea onto land to give birth. With their innominate decoupled from the vertebral column, the birth canal in basilosaurids may have been considerably larger than that in protocetids. This would have permitted birth of larger, more precocial infants, and we would predict that a near-term basilosaurid fetal skeleton, if found intact, would be positioned to be born tail-first as is seen in living whales. Precocial Development The dentition of the fetal skeleton (GSP-UM 3475b) can be mapped in detail (Figure 8). Here partial crowns of the first permanent upper molars (left and right M1) are visible posterior to dP4 (best exposed on the left side). The main paracone cusp appears almost fully formed, with the crown as a whole being about one-half mineralized. Formation of the crowns of many deciduous teeth, and particularly formation of M1, indicates that the fetal skeleton of Maiacetus was advanced in development and near full term. Altricial-to-precocial birth status in mammals is generally represented on a behavioral spectrum scored from I to IV. Altricial I lies at one extreme (birth with eyes closed, naked, and nidicolousor nest-dwelling), and precocial IV at the other (birth with eyes open, haired, and nidifugous or nest-fleeing) [21]. Dental development provides a parallel indication of birth status (Table 4). The state of the dentition at birth is a direct indicator of the ability of a newborn to supplement mother's milk with other foods. Natural selection can separately adjust a newborn's ability to feed itself, sense its environment, regulate its temperature, and move [24], yet there is also an overall association of these aspects of newborn maturity. Table 4 shows that mineralization of the dentition at birth corresponds to the classic categories of neonate maturity. In generalized mammals, crowns of the deciduous dentition appear to be largely mineralized in utero. The permanent dentition, however, shows an enormous range, with some mammals showing no mineralization of permanent teeth at all (e.g., a newborn bear cub [22]), and others having all adult crowns fully formed (e.g., newborn guinea pig [23]). While eruption of teeth through the gums in living mammals is informative, the clearest association with precocial categories IIIV is some degree of mineralization of the permanent dentition, beginning with the first molar and in some cases extending to mineralization of later developing teeth. Table 4. Developmental maturity categories of Langer [21] and mineralization of first molar M1 and other permanent teeth in newborn terrestrial mammals compared to the early whale Maiacetus inuus. doi:10.1371/journal.pone.0004366.t004 The fetal skeleton of Maiacetus described here shows development of the deciduous dentition to have been well underway, with partial mineralization of upper first permanent molars in utero. The fetal dentition of Maiacetus is as developed as that of a newborn fallow deer (Table 4). Thus Maiacetus was clearly a precocial mammal. Precociality involves a high degree of maternal investment starting from conception and extending through relatively long periods of gestation and lactation to nutritional independence of the calf. Marine mammals living today are all precocial, and energy is channeled to early growth [25]. Semiaquatic young must be able to move soon after birth to avoid predators on land and in the sea, and fully aquatic young must be able to swim to keep pace with their mothers [17]. Larger newborn body size is also an important component of precociality because it reduces the newborn's surface-to-volume ratio and enhances its ability to maintain its body temperature on exposed shorelines and in the water. Artiodactyls, the group ancestral to whales [3], give birth to young that range from slightly precocial (pigs) to highly precocial (sheep, deer, giraffe). Whales probably evolved from anthracobunid artiodactyls, a stem group that may be closely related to Hippopotamidae [26]. Hippopotamid young lie at the precocial end of the birth spectrum [27], [28], and it is reasonable to infer that precociality was primitive for whales and their closest artiodactyl ancestors. Precociality may be a key life history trait that enabled the earliest whales to navigate the land-sea transition. Sexual Dimorphism The type specimen of Maiacetus inuus, GSP-UM 3475a, has a fetus in utero and is clearly female. We interpret the referred adult skeleton of Maiacetus (GSP-UM 3551) as male because it contains no fetus, averages 12% larger in linear measurements than the known female, and has canine teeth that are 20% larger (Tables 1, 2). A 12% difference in linear measurements of male and female Maiacetus yields an expected weight difference of about 39% (Table 1). Relatively large canines are commonly found in male mammals that use these teeth in threat displays and fighting. In addition, the pelvis of GSP-UM 3551 is well preserved and has a V-shaped pubic notch, formed by the inferior rami of the left and right pubes, which is characteristic of males (Figure 10). The notch is broader and U-shaped in females that give birth to a single large fetus, such as the fallow deer Dama dama [29]. Dimorphism of body size in marine mammals ranges from females that are larger than males (Hawaiian monk seal and Gervais' beaked whale at the extreme) to males that are much larger than females (sperm whale, southern elephant seal, and Hooker's sea lion at the extreme) [17], [30]. Here we quantify the difference in terms of body length (Figure 15). The mating system is not known for all marine mammals, but when known, a male-female length difference greater than about 16% (0.15 on a natural log scale) indicates a territorial or harem mating system [31]. Intense male-male competition is associated with marked sexual dimorphism and often spatial aggregation of females related to the accessibility of food and shelter. A male-female length difference less than 16% corresponds to a more generalized aquatic, or dispersed, mating system, in which males have less opportunity to guard and monopolize females. Figure 15. Mating systems and sexual dimorphism in marine mammals. Sexual dimorphism of males and females is quantified for 105 species of cetaceans, pinnipeds, sirenians, and the sea otter, expressed as male-minus-female length in natural log units [17], [30]. Territorial and harem systems that involve intense male-male competition and spatial aggregation of females have male-female dimorphism greater than about 0.15 (dashed line) [31]. Maiacetus inuus falls in the group of dispersed mating systems with limited aggregation and limited male control of mating. Both cetaceans and pinnipeds span the entire range shown here, although mating systems are known for relatively few species [32]. doi:10.1371/journal.pone.0004366.g015 The male-female length difference of 12% (0.11 on a natural log scale) in Maiacetus indicates moderate sexual dimorphism and probably limited male-male competition for mates. Limited opportunity to monopolize mates suggests in turn that food and shelter were dispersed in protocetid habitats. This is corroborated by the geographically extensive but environmentally uniform shallow marine deposits of the Habib Rahi Formation, which were deposited on a broad, shallow marine shelf that would have provided little spatial aggregation of food or shelter. Much remains to be learned about mating systems in cetaceans because their behavior is so difficult to study [32]. At present, body size dimorphism is itself sometimes used as a measure of contest competition between males [17]. Maiacetus suggests that sexual dimorphism appeared early in cetacean evolution. Males were larger than females, but the difference was modest on the scale of dimorphism observed in marine mammals today. Conclusions We describe exceptional specimens of a new early middle Eocene (47.5 Ma) protocetid whale, Maiacetus inuus, that include an adult female skeleton, a near term fetal skeleton, and an adult male skeleton. Maiacetus differs in size and proportions from younger, more derived basilosaurids such as Dorudon atrox (Figures 1, 12, 13), but it is close in size and similar in proportions to a composite skeleton of Rodhocetus balochistanensis/kasranii (Figure 13). Maiacetus retains many characteristics of its terrestrial forebears, including shearing cheek teeth with protocones on upper molars, a vertebral formula very close to that of primitive artiodactyls, a forelimb retaining mobile digits, a pelvis and hindlimb anchored on the vertebral column; and a double-pulley astragalus within the ankle. The feet of Maiacetus are not as elongated as those of Rodhocetus, indicating that Maiacetus may have been a slightly less specialized foot-powered swimmer (Figure 13). Preservation of an intact near-term fetal skull and partial skeleton indicates that birth in early archaeocetes involved a single calf that was born head-first as in land mammals, not tail-first as in living whales. This, in turn, indicates that birth almost certainly took place on land during this phase of early whale evolution. The presence of partially mineralized permanent first molars in the fetal skull indicates precocial development, which may have been a key life history trait in early whales facilitating the transition from land to sea. Sexual dimorphism in body and canine size are moderate, suggesting limited competition among males for mates. Acknowledgments We thank Imran A. Khan, M. Talib Hasan, S. Ghazanfar Abbas, A. Latif Khan, H. Ghaur, Intizar H. Khan, and M. Sadiq Malkani, Geological Survey of Pakistan, for sustained collaboration; William J. Sanders, John Graf, and Amber Heard for specimen preparation and casting in the University of Michigan Museum of Paleontology; Daniel Erickson and Michael Cherney for mounting the male skeleton in the University of Michigan Exhibit Museum; Philip Myers for access to comparative collections in the University of Michigan Museum of Zoology; Heinrich Schuller (Bonn) for CT scans of the fetal skull; Patrick Guerin (Brussels) and Jorg Habersetzer (Frankfurt) for help with CT interpretation. For photography, we thank Georg Oleschinski (Bonn), and for drawings we thank Bonnie Miljour (Michigan; Figures 1C, D, 9, 11), Doug Boyer (Michigan; Figure 1A, B), and Dorothea Kranz (Bonn; Figure 7). Derek Briggs (Yale), Jes Rust (Bonn), Ryan Bebej (Michigan), and Paul Sereno (Chicago) read and improved the manuscript. Author Contributions Performed the experiments: ISZ. Analyzed the data: PDG MuH WvK WJS BHS. Wrote the paper: PDG MuH WvK WJS BHS ISZ. Participated in field work: PDG MuH ISZ. Contributed geological interpretations: PDG ISZ MuH. Developed chronological framework: PDG MuH ISZ. Carried out functional analysis of skeletons: PDG WJS ISZ. Interpreted life history: PDG BHS. References 1. Kellogg R (1936) A review of the Archaeoceti. Carnegie Institution of Washington Publications 482: 1366. Find this article online 2. Gingerich PD, Zalmout IS, Haq M-u, Bhatti MA (2005) Makaracetus bidens, a new protocetid archaeocete (Mammalia, Cetacea) from the early middle Eocene of Balochistan (Pakistan). Contributions from the Museum of Paleontology, University of Michigan 31: 197210. Find this article online 3. Gingerich PD, Haq M-u, Zalmout IS, Khan IH, Malkani MS (2001) Origin of whales from early artiodactyls: hands and feet of Eocene Protocetidae from Pakistan. Science 293: 22392242. Find this article online 4. Gingerich PD (2003) Land-to-sea transition of early whales: evolution of Eocene Archaeoceti (Cetacea) in relation to skeletal proportions and locomotion of living semiaquatic mammals. Paleobiology 29: 429454. Find this article online 5. Fordyce RE (1980) Whale evolution and Oligocene southern ocean environments. Palaeogeography, Palaeoclimatology, Palaeoecology 31: 319336. Find this article online 6. Gingerich PD, Wells NA, Russell DE, Shah SMI (1983) Origin of whales in epicontinental remnant seas: new evidence from the early Eocene of Pakistan. Science 220: 403406. Find this article online 7. Bajpai S, Gingerich PD (1998) A new Eocene archaeocete (Mammalia, Cetacea) from India and the time of origin of whales. Proceedings of the National Academy of Sciences USA 95: 1546415468. Find this article online 8. Madar SI, Thewissen JGM, Hussain ST (2002) Additional holotype remains of Ambulocetus natans (Cetacea, Ambulocetidae), and their implications for locomotion in early whales. Journal of Vertebrate Paleontology 22: 405422. Find this article online 9. Madar SI (2007) The postcranial skeleton of early Eocene pakicetid cetaceans. Journal of Paleontology 81: 176200. Find this article online 10. Gingerich PD, Smith BH, Simons EL (1990) Hind limbs of Eocene Basilosaurus isis: evidence of feet in whales. Science 249: 154157. Find this article online 11. Uhen MD (2004) Form, function, and anatomy of Dorudon atrox (Mammalia, Cetacea): an archaeocete from the middle to late Eocene of Egypt. University of Michigan Papers on Paleontology 34: 1222. Find this article online 12. Haq M-u, Malkani MS (1999) Geology of Rakhni Quadrangle (39 F/16), Barkhan and D. G. Khan Districts, Balochistan and Punjab Provinces, Pakistan. Geological Survey of Pakistan, Information Release 705: 134. Find this article online 13. Kothe A, Khan AM, Ashraf M (1988) Biostratigraphy of the Surghar Range, Salt Range, Sulaiman Range and the Kohat area, Pakistan, according to Jurassic through Paleogene calcareous nannofossils and Paleogene dinoflagellates. Geologisches Jahrbuch, Hannover, Reihe B 71: 187. Find this article online 14. Gingerich PD, Haq M-u, Khan IH, Zalmout IS (2001) Eocene stratigraphy and archaeocete whales (Mammalia, Cetacea) of Drug Lahar in the eastern Sulaiman Range, Balochistan (Pakistan). Contributions from the Museum of Paleontology, University of Michigan 30: 269319. Find this article online 15. Franzen JL (1981) Das erste Skelett eines Dichobuniden (Mammalia, Artiodactyla), geborgen aus mitteleozanen Olshiefern der Grube Messel bei Darmstadt (Deutschland, S-Hessen). Senckenbergiana Lethaea, Frankfurt 61: 299353. Find this article online 16. Gingerich PD, Raza SM, Arif M, Anwar M, Zhou X (1994) New whale from the Eocene of Pakistan and the origin of cetacean swimming. Nature 368: 844847. Find this article online 17. Boness DJ, Clapham PJ, Mesnick SL (2002) Life history and reproductive strategies. In: Hoelzel AR, editor. Marine mammal biology: an evolutionary approach. Oxford: Blackwell Science. pp. 278324. 18. Slijper EJ (1956) Some remarks on gestation and birth in Cetacea and other aquatic mammals. Hvalradets Skrifter Scientific Results of Marine Biological Research, Oslo 41: 162. Find this article online 19. Marsh H, Heinsohn GE, Marsh LM (1984) Breeding cycle, life history and population dynamics of the dugong, Dugong dugon (Sirenia: Dugongidae). Australian Journal of Zoology 32: 767788. Find this article online 20. Caldwell DK, Caldwell MC (1985) Manatees: Trichechus manatus, Trichechus senegalensis, and Trichechus inunguis. In: Ridgway SH, Harrison R, editors. Handbook of Marine Mammals, Volume 3. New York: Academic Press. pp. 3366. 21. Langer P (2008) The phases of maternal investment in eutherian mammals. Zoology 111: 148162. Find this article online 22. Dittrich L (1960) Milchgebissentwicklung und Zahnwechsel beim Braunbaren (Ursus arctos L) und anderen Ursiden. Gegenbaurs Morphologisches Jahrbuch 101: 1141. Find this article online 23. Harman MT, Smith A (1936) Some observations of the development of the teeth in Cavia cobaya. Anatomical Record 66: 97111. Find this article online 24. Derrickson EM (1992) Comparative reproductive strategies of altricial and precocial eutherian mammals. Functional Ecology 6: 5765. Find this article online 25. Gaillard J-M, Pontier D, Allaine D, Loison A, Herve J-C, et al. (1997) Variation in growth form and precocity at birth in eutherian mammals. Proceedings of the Royal Society of London, Series B 264: 859868. Find this article online 26. Boisserie J-R, Lihoreau F, Brunet M (2005) The position of Hippopotamidae within Cetartiodactyla. Proceedings of the National Academy of Sciences USA 102: 15371541. Find this article online 27. Lang EM (1975) Das Zwergflusspferd Choeropsis liberiensis. Wittenberg: A. Ziemsen Verlag. 28. Eltringham SK (1999) The hippos: natural history and conservation. London: Poyser/Academic Press. 29. Lemppenau U (1964) Geschlechts- und Gattungsunterschiede am Becken mitteleuropaischer Wiederkauer. Munchen: Ludwig-Maximilians-Universitat, Ph.D. dissertation. 30. Trites AW, Pauly D (1998) Estimating mean body masses of marine mammals from maximum body lengths. Canadian Journal of Zoology 76: 886896. Find this article online 31. Weckerly FW (1998) Sexual size dimorphism: influence of mass and mating systems in the most dimorphic mammals. Journal of Mammalogy 79: 3352. Find this article online 32. Connor RC, Mann J, Tyack PL, Whitehead H (1998) Social evolution in toothed whales. Trends in Ecology and Evolution 13: 228232. Find this article online 33. Nievelt AFHv, Smith KK (2005) To replace or not to replace: the significance of reduced functional tooth replacement in marsupial and placental mammals. Paleobiology 31: 324346. Find this article online 34. Tomich PQ, Devick WS (1970) Age criteria for the prenatal and immature mongoose in Hawaii. Anatomical Record 167: 107113. Find this article online 35. Berkovitz BKB (1973) Tooth development in the albino ferret (Mustela putorius) with special reference to the permanent carnassial. Archives of Oral Biology 18: 465471. Find this article online 36. Mellanby M (1929) Diet and the teeth: an experimental study. Part I. Dental structure in dogs. His Majesty's Stationery Office, Medical Research Council, London, Special Report Series 140: 1526. Find this article online 37. Tonge CH, McCance RA (1973) Normal development of the jaws and teeth in pigs, and the delay and malocclusion produced by calorie deficiencies. Journal of Anatomy 115: 122. Find this article online 38. McKean CF, Jump EB, Weaver ME (1971) The calcification pattern of deciduous teeth in miniature swine. Archives of Oral Biology 16: 639648. Find this article online 39. Hellgren EC, Lochmiller RL, Thomas MW, Grant WE (1984) Cyclopia, congenital limb deformity, and osteomyelitis in the collared peccary, Tayassu tajacu (L). Journal of Wildlife Diseases 20: 354357. Find this article online 40. Oka SW, Kraus BS (1969) The circumnatal status of molar crown maturation among the Hominoidea. Archives of Oral Biology 14: 639659. Find this article online 41. Kraus BS, Myers RE, Clark GR (1969) Teratogenic effects of carotid ligation on the developing dentition of the Rhesus monkey. Teratology 2: 163172. Find this article online 42. Schwartz GT, Samonds KE, Godfrey LR, Jungers WL, Simons EL (2002) Dental microstructure and life history in subfossil Malagasy lemurs. Proceedings of the National Academy of Sciences USA 99: 61246129. Find this article online 43. Luckett WP, Maier W (1982) Development of deciduous and permanent dentition in Tarsius and its phylogenetic significance. Folia Primatologica 37: 136. Find this article online 44. Shinz HR (1937) Ossifikationsstudien beim neugebornenen Schwein und beim neugeborenen Tapir. Vierteljahrsschrift der Naturforschenden Gesellschaft, Zurich 82: 2144. Find this article online 45. Weinreb MM, Sharav Y (1964) Tooth development in sheep. American Journal of Veterinary Research 25: 891908. Find this article online 46. Brown WAB, Chapman NG (1991) Age assessment of fallow deer (Dama dama): from a scoring scheme based on radiographs of developing permanent molariform teeth. Journal of Zoology, London 224: 367379. Find this article online 47. Hall-Martin AJ (1976) Dentition and age determination of the giraffe Giraffa camelopardalis. Journal of Zoology, London 180: 263289. Find this article online 48. Kubota K, Komuro H, Nagasaki F, Tsuboi M, Matsumoto K (1961) The calcification of teeth of the fur seals. Okajimas, Folia Anatomica Japonica 37: 389419. Find this article online 49. Zalmout IS, Haq M-u, Gingerich PD (2003) New species of Protosiren (Mammalia, Sirenia) from the early middle Eocene of Balochistan (Pakistan). Contributions from the Museum of Paleontology, University of Michigan 31 (3): 7987. Find this article online 50. Gingerich PD (1998) Paleobiological perspectives on Mesonychia, Archaeoceti, and the origin of whales. In: Thewissen JGM, editor. Emergence of Whales: Evolutionary Patterns in the Origin of Cetacea. New York: Plenum Publishing Corporation. pp. 423449. 51. Stoss AO (1944) Tierarztliche Geburtskunde und Gynakologie: einschliesslich der Krankheiten der Neugebornenen, Zweite Auflage. Stuttgart: Ferdinand Enke. 52. Baier W, Schaetz F (1958) Tierarztliche Geburtskunde, Begrundet von A. O. Stoss. Dritte, vollig neu gestaltete Auflage. Stuttgart: Ferdinand Enke. == Ants tricked into raising butterflies Flitting across your yard, butterflies seem friendly and harmless. But at least one type has learned to raise its young as parasites, tricking ants into feeding it and giving special treatment. The pupae of the European butterfly Maculina rebeli exude a scent that mimics the ants and make themselves at home inside the ant nest. Once they become a caterpillar they even beg for food like ant larvae, researchers report in Fridays edition of the journal Science. But, not content just to be fed, the butterflies even manage to demand special treatment, Jeremy A. Thomas of Britains University of Oxford and colleagues report. It turns out that ant queens make subtle sounds that signal their special status to worker ants. The caterpillars have learned to mimic those sounds, the researchers say, earning high enough status to be rescued before others if the nest is disturbed. In times of food shortage, nurse ants have been known to kill their own larvae and feed them to the caterpillars pretending to be queen ants, they added. In nature, the real ant queen and the caterpillar keep to different parts of the ant colony and would not encounter one another, the report said. But in an experiment, a butterfly pupa pretending to be an ant queen was placed in a chamber with worker ants and four real ant queens. The ant queens began to attack and bite the caterpillar, but the workers intervened, biting and stinging their own queens, which they then pulled to a far corner of the chamber while other workers attended the pupa. == Fossil snake said to break length record Scientists have recovered fossils from a 60millionyearold South American snake whose length and weight might make todays anacondas and reticulate pythons seem a bit cuter and more cuddly. Named Titanoboa cerrejonensis by its discoverers, the size of the snakes vertebrae suggest it weighed 1,140 kilograms (2,500 pounds) and spanned 13 meters (42.7 feet)at least, U.S. researchers say. The longest snake species today is the reticulated python of Southeast Asia, which grows to 10 meters. A report on the new find appears in this weeks issue of the research journal Nature. At its greatest width, the snake would have come up to about your hips, said Indiana University Bloomington geologist David Polly, who identified the position of the fossil vertebrae that made a size estimate possible. The size is pretty amazing. But our team went a step further and asked, how warm would the Earth have to be to support a body of this size? Crews led by Smithsonian Tropical Research Institute geologist Carlos Jaramillo and University of Florida, Florida Museum of Natural History vertebrate paleontologist Jonathan Bloch discovered the fossils in the Cerrejon Coal Mine in northern Colombia and investigated what the snakes environment might have been like. Paleontologist Jason Head of the University of TorontoMississauga, the reports lead author, used information gleaned by his collaborators to make an estimate of Earths temperature 58 to 60 million years ago in an area encompassed by modernday Colombia. Paleontologists have long known of a rough correlation between a time periods temperature and the size of its coldblooded creatures. As the Earths temperature increases, so does the upper size limit on poikilotherms. There are many ways the anatomy of a species is correlated with its environment on broad scales, Polly said. If we understand these correlations better, we will know more about how climate and climate change affect species, as well as how we can infer things about past climates from the morphology of the species that lived back then. Assuming the Earth today is not particularly unusual, Head estimated a snake of Titanoboas size would have required an average annual temperature of 30 to 34 degrees C (86 to 93 F) to survive. By comparison, the average yearly temperature of todays Cartagena, a Colombian coastal city, is about 83 F. Tropical ecosystems of South America were surprisingly different 60 million years ago, said Bloch. It was a rainforest, like today, but it was even hotter and the coldblooded reptiles were all substantially larger. The result was, among other things, the largest snakes the world has ever seen... and hopefully ever will. The tropical rainforest at Cerrejon appears to have thrived at a temperature of 32 C (90 F), five degrees warmer than the upper temperature limit for tropical rainforests in modern times, researchers said. These data challenge the view that tropical vegetation lives near its climatic optimum, and it has profound implications in understanding the effect of current global warming on tropical plants, said Carols Jaramillo, a palaeobotanist at the Smithsonian Topical Research Institute. Evolution has produced a wide variety of gigantic animals over the last several hundred million yearsdinosaurs, ancient dragonflies and todays blue whale, to name a few. Why some species lineages produce monsters remains a matter of debate among evolutionary biologists and ecologists. The scientists classify Titanoboa as a boine snake, a type of nonvenomous constrictor that includes anacondas and boas. Polly extrapolated the placement of Titanoboa fossil vertebrae by comparing the fossils structure to the vertebrae of todays boine snakes. Snake vertebrae get bigger near a snakes midsection, but they are also structured differently than vertebrae closer to a snakes head or tail. Using a computer model he wrote, Polly estimated the fossil vertebrae originate near Titanoboas middle. That means that if Pollys model is incorrect about the bones placement, the snake could have been even bigger. == Fetal remains suggest these creatures gave birth on land Fossils from two early whales a male and a rare pregnant female shed light on how these ancestors to modern whales made the leap from walking on land to ruling the sea. The fetal remains, found with the 47.5 million-year-old pregnant female, were positioned head down, suggesting these creatures gave birth on land, while spending much of the rest of their time in the water. Initially, the tiny fetal teeth stumped University of Michigan paleontologist Philip Gingerich, whose team discovered the fossils in Pakistan in 2000 and 2004. "When I first saw the small teeth in the field, I thought we were dealing with a small adult whale, but then we continued to expose the specimen and found ribs that seemed too large to go with those teeth," Gingerich, whose study appears in the Public Library of Science journal PLoS ONE. The fetal skeleton is the first specimen of the extinct whale group known as Archaeoceti, and the find represents a new species named Maiacetus inuus, a hybrid of the words for "mother whale" and Inuus, the name of a Roman fertility god. The fetus was positioned head down like other land animals, allowing it to begin breathing right away. This suggests the group had not yet made the leap to giving birth in the water like modern whales, which are born tail first to allow them to start swimming right after birth. The 8.5-foot (2.59-meter) male, which was collected in the same fossil beds as the female, is about 12 percent bigger and had fangs that were 20 percent larger than those of the female. Gingerich said these well developed choppers suggest the creatures spent a large portion of their time catching and eating fish. Both fossils had four flipper-like legs that could have supported their weight on land, but only for short distances, suggesting these whales likely came on shore to mate, rest and give birth, Gingerich said. "Reference: PLoS ONE Gingerich PD, ul-Haq M, von Koenigswald W, Sanders WJ, Smith BH, et al. (2009) New Protocetid Whale from the Middle Eocene of Pakistan: Birth on Land, Precocial Development, and Sexual Dimorphism. PLoS ONE 4(2): e4366. doi:10.1371/journal.pone. 0004366 == Deborah Heiligman is the author, most recently, of "Charles and Emma: The Darwins' Leap of Faith." == For example, Darwin described evolution as the growth of a tree, the ``Tree of Life. '' The tree began with a single, original organism at the root, with myriad species branching off from the trunk. Biologists increasingly say that evolution resembles a web or a bush rather than a tree. Microbes constantly swap DNA. Hybrid plants and animals cross species lines, blurring sharp lines between species. ``We understand evolution pretty well,'' said W. Ford Doolittle , a Darwin supporter and biologist at Dalhousie University in Halifax, Nova Scotia . ``It's just that it's more complex than Darwin imagined.'' == A hominoid or ape is a member of the superfamily Hominoidea: extant members are the lesser apes (gibbons) and great apes. * A hominid is a member of the family Hominidae: all of the great apes. * A hominine is a member of the subfamily Homininae: gorillas, chimpanzees, humans (excludes orangutans). * A hominin is a member of the tribe Hominini: chimpanzees and humans. * A hominan is a member of the sub-tribe Hominina: modern humans and their extinct relatives. == This now over 12 years old study of subterranean life on earth suggests that, given conditions on Mars as then known, rock-eating microbes there could be found between 10 & 20 meters below the surface. A more recent estimate suggests 7.5 m (~25 feet). Life may indeed be quite common in the universe. So far we've surveyed only a single world, however, this one, a not statistically significant sample. We're lucky to have liquid surface water, a large moon & magnetic field, making the evolution of multicellular life possible in exposed areas, but microbes could possibly self-assemble on other planets & moons even in our own solar system. Polycyclic aromatic hydrocarbon (PAH) compounds, the templates for assembling RNA in one abiogenetic hypothesis, are common in the universe. Tiny vesicles in rocks act as the first cell "membranes" in another hypothesis, containing the organic chemical reactions of metabolism & replication before the formation of lipid membranes. Like PAHs, lipids self-assemble in aqueous solution. == Researchers believe they have found a potential way to regenerate nerves by stimulating a gene and said on Thursday they hope their work in worms may some day help people with spinal cord injuries. The gene is part of a network, or pathway, of four genes that appear to be essential for nerve repair, they reported in the journal Science. "We found a pathway that not only regenerates nerves in the worm, but also exists in humans, and we think it serves the same purpose," Michael Bastiani of the University of Utah in Salt Lake City, who led the study, said in a statement. Bastiani said the gene could serve as a target for a future drug that could "vastly improve the ability of a neuron to regenerate after injury." In humans, nerve fibers in the arms and legs can regenerate, but in the brain and spinal cord, they do not. Many teams are working to understand why. Bastiani's team looked to nematode worms for clues. Using an advanced research technique called RNA interference, the team systematically blocked the action of 5,000 worm genes to isolate those important for nerve repair. They found a gene called dlk-1 was essential to the process at every stage of the worm's life. When they used genetic engineering to block this gene network, the worms were unable to repair nerve damage. But when they stimulated the gene -- making it more active than normal -- worms with damaged nerves recovered much more quickly. Curiously, this network of genes is not used by the nervous system during normal development in the embryo, but it is essential for nerve repair after birth. "Most of us believed that virtually everything we found in regeneration also would be involved in development," Bastiani said. Bastiani and colleagues noted that to be effective, the dlk-1 gene must be stimulated soon after injury to make a protein that stimulates repair, suggesting there might be "a time window in which you have to activate this pathway." Many teams have been working on finding ways to block proteins that inhibit nerve repair in adults. Last year, a team at Children's Hospital Boston reported in the journal Science they were able to stimulate nerve regeneration in mice with damaged optic nerves by turning off proteins that keep adult nerve cells from growing. A separate team from the biotechnology firm Genentech Inc was able to stimulate nerve regeneration by blocking chemical signals that create a hostile environment for nerve repair. == Rethinking the Genetic Theory of Inheritance January 18th, 2009 in Medicine & Health / Genetics Scientists at the Centre for Addiction and Mental Health (CAMH) have detected evidence that DNA may not be the only carrier of heritable information; a secondary molecular mechanism called epigenetics may also account for some inherited traits and diseases. These findings challenge the fundamental principles of genetics and inheritance, and potentially provide a new insight into the primary causes of human diseases. Your mother's eyes, your father's height, your predisposition to disease-- these are traits inherited from your parents. Traditionally, 'heritability' is estimated by comparing monozygotic (genetically identical) twins to dizygotic (genetically different) twins. A trait or disease is called heritable if monozygotic twins are more similar to each other than dizygotic twins. In molecular terms, heritability has traditionally been attributed to variations in the DNA sequence. [Video presentation available at the website http://www.physorg.com/news151507849.html ] Dr. Art Petronis, head of the Krembil Family Epigenetics Laboratory at the Center for Addiction and Mental Health, discusses new evidence that DNA may not be the only carrier of heritable information; a secondary molecular mechanism called epigenetics may also account for some inherited traits and diseases. These findings challenge the fundamental principles of genetics and inheritance, and potentially provide a new insight into the primary causes of human diseases. Video: Center for Addiction and Mental Health CAMH's Dr. Art Petronis, head of the Krembil Family Epigenetics Laboratory, and his team conducted a comprehensive epigenetic analysis of 100 sets of monozygotic and dizygotic twins in the first study of its kind. Said Dr. Petronis, "We investigated molecules that attach to DNA and regulate various gene activities. These DNA modifications are called epigenetic factors." The CAMH study showed that epigenetic factors - acting independently from DNA - were more similar in monozygotic twins than dizygotic twins. This finding suggests that there is a secondary molecular mechanism of heredity. The epigenetic heritability may help explain currently unclear issues in human disease, such as the presence of a disease in only one monozygotic twin, the different susceptibility of males (e.g. to autism) and females (e.g. to lupus), significant fluctuations in the course of a disease (e.g. bipolar disorder, inflammatory bowel disease, multiple sclerosis), among numerous others. "Traditionally, it has been assumed that only the DNA sequence can account for the capability of normal traits and diseases to be inherited," says Dr. Petronis. "Over the last several decades, there has been an enormouseffort to identify specific DNA sequence changes predisposing people to psychiatric, neurodegenerative, malignant, metabolic, and autoimmune diseases, but with only moderate success. Our findings represent a new way to look for the molecular cause of disease, and eventually may lead to improved diagnostics and treatment." An advance online publication of this study will be available on the Nature Genetics website on January 18, 2009. == RNA RNA, a chemical related to DNA, can be used as the basis of a system in which pairs of molecules endlessly reproduce each other. The system allows molecules to evolve in ways that could throw light on the origins of life. The work furthers the fortunes of the 'RNA world' hypothesis1 . This body of thought suggests that early in the evolution of life RNA was used both to store genetic information (a role now taken by DNA) and catalyse chemical reactions (something now mostly left to proteins). Andy Ellington of the University of Texas at Austin predicts that the paper will be seen as "a watershed event" for people thinking about early life: "This is going to have a huge impact with respect to the RNA world." But the authors of the paper caution that their work does not prove that life on earth evolved this way. "This is a system that embodies self-replication, mutability and heritability we're not trying to put too fine a historical point on it," says Gerald Joyce at the Scripps Research Institute in La Jolla, California, a champion of the RNA world hypothesis and one of the researchers who carried out the work, published online in Science2 . Immortal activity Joyce and his colleague Tracey Lincoln made paired RNA catalysts, each of which could assemble the other when supplied with the right building blocks. Then the scientists mixed the paired molecules with RNA building blocks in test tubes. Because the RNA 'enzymes' were not perfect, and made different forms of each other, the original pairs mutated into new, 'recombinant' forms that out-competed the originals. The 'winning' enzymes changed depending on the conditions in the reaction mixture, such as the concentration of various RNA building blocks. Joyce's group had already made enzymes capable of catalyzing their own replication, but they could only reproduce themselves a limited number of times. The new enzymes can reproduce themselves indefinitely. "This is the first time outside of biology where you have immortalized molecular information, " says Joyce. David Penny, a theoretical biologist at Massey University in Palmerston North, New Zealand, says the work fulfils a prediction made decades ago by Nobel laureate Manfred Eigen and biophysicist Peter Schuster. In the 1970s, the pair proposed that 'hypercycles' networks of enzymes that replicate each other could give rise to self-sustaining populations of early life forms3 . "This is proof of principle that an RNA self-replicating system is possible," says Penny. Evolving solutions Ellington says that the observation that different winning enzymes emerge in different conditions is crucial because it further undermines the intelligent- design idea that life is too complex to have arisen without the intervention of a supernatural being. "This paper shows that Darwinian evolution wins out," he said. "Joyce is emphatically knocking down a straw horse of the intelligent- design community." But the system is a long way from being the origin of life recapitulated in a test tube. Eric Smith, a researcher in the field at the Santa Fe Institute in New Mexico, agrees that the work is elegant and important. But he points out that Joyce's enzymes have benefited from years of study and tinkering in the lab, and are being asked to perform relatively simple operations. "What we can do in the lab is such a tiny fraction of what we would need to do to make strong arguments about the origin of life that there is huge room for imagination and presumptions to influence research directions, right or wrong," he says. Other prominent scientists, such as Craig Venter of the J. Craig Venter Research Institute in Rockville, Maryland, and Jack Szostak, of the Howard Hughes Medical Institute in Chevy Chase, Maryland, are also trying to create life in the lab. But while Venter is using a topdown approach trying to 'boot up' a cell with an entirely synthesized genome Joyce and Szostak take a bottomup strategy by attempting to recreate the events that could have led to the existence of genes, cells and life as it is now. Joyce says the next major step would be to create a system that doesn't just do the same thing over and over, but can evolve the ability to perform new tasks. "The goal here is to make life in the lab, and we have not achieved that, because the system does not within itself have the ability to present novel functions. But ultimately, that's where we want to go," he says. References 1. Gilbert, W. Nature 319, 618 (1986). | Article 2. Lincoln, T. A. & Joyce, G. F. Science 10.1126/science. 1167856 2009 (2008). 3. Eigen, M. & Schuster, P. The Hypercycle: A Principle of Natural Self-Organization (Springer, 1979). == Origin Of Life On Earth: Simple Fusion To Jump-start Evolution With the aid of a straightforward experiment, researchers have provided some clues to one of biology's most complex questions: how ancient organic molecules came together to form the basis of life. Specifically, this study demonstrated how ancient RNA joined together to reach a biologically relevant length. RNA, the single-stranded precursor to DNA, normally expands one nucleic base at a time, growing sequentially like a linked chain. The problem is that in the primordial world RNA molecules didn't have enzymes to catalyze this reaction, and while RNA growth can proceed naturally, the rate would be so slow the RNA could never get more than a few pieces long (for as nucleic bases attach to one end, they can also drop off the other). Ernesto Di Mauro and colleagues examined if there was some mechanism to overcome this thermodynamic barrier, by incubating short RNA fragments in water of different temperatures and pH. They found that under favorable conditions (acidic environment and temperature lower than 70 degrees Celsius), pieces ranging from 10-24 in length could naturally fuse into larger fragments, generally within 14 hours. The RNA fragments came together as double-stranded structures then joined at the ends. The fragments did not have to be the same size, but the efficiency of the reactions was dependent on fragment size (larger is better, though efficiency drops again after reaching around 100) and the similarity of the fragment sequences. The researchers note that this spontaneous fusing, or ligation, would be a simple way for RNA to overcome initial barriers to growth and reach a biologically important size; at around 100 bases long, RNA molecules can begin to fold into functional, 3D shapes. Journal reference: 1. Samanta Pino, Fabiana Ciciriello, Giovanna Costanzo and Ernesto Di Mauro. Nonenzymatic RNA ligation in water. J. Biol. Chem, == Artificial molecule evolves in the lab A new molecule that performs the essential function of life - self-replication - could shed light on the origin of all living things. If that wasn't enough, the laboratory-born ribonucleic acid (RNA) strand evolves in a test tube to double itself ever more swiftly. "Obviously what we're trying to do is make a biology," says Gerald Joyce, a biochemist at the Scripps Research Institute in La Jolla, California. He hopes to imbue his team's molecule with all the fundamental properties of life: self-replication, evolution, and function. Joyce and colleague Tracey Lincoln made their chemical out of RNA because most researchers think early life stored information in this sister molecule to DNA. And unlike the stuff of our genomes, RNA molecules can catalyse chemical reactions. "We're trying to jump in at the last signpost we have back there in the early history of life," Joyce says. Molecular brew Rather than start with RNA enzymes - ribozymes - present in other organisms, Joyce's team created its own molecule from scratch, called R3C. It performed a single function: stitching two shorter RNA molecules together to create a clone of itself. Further lab tinkering made this molecule better at copying itself, but this is not the same as bringing it to life. It self-replicated to a point, but eventually clogged up in shapes that could no longer sew RNA pieces together. "It was a real dog," Joyce says. To improve R3C, Lincoln redesigned the molecule to forge a sister RNA that could itself join two other pieces of RNA into a functioning ribozyme. That way, each molecule makes a copy of its sister, a process called cross replication. The population of two doubles and doubles until there are no more starting bits of RNA left. "We just let them cook, let them amplify themselves silly," he says Lab evolution Not content with achieving one hallmark of life in the lab, Joyce and Lincoln sought to evolve their molecule by natural selection. They did this by mutating sequences of the RNA building blocks, so that 288 possible ribozymes could be built by mixing and matching different pairs of shorter RNAs. What came out bore an eerie resemblance to Darwin's theory of natural selection: a few sequences proved winners, most losers. The victors emerged because they could replicate fastest while surrounded by competition, Joyce says. "I wouldn't call these molecules alive," he cautions. For one, the molecules can evolve only to replicate better. Reproduction may be the strongest - perhaps only - biological urge, yet even simple organisms go about this by more complex means than breakneck division. Bacteria and humans have both evolved the ability to digest lactose, or milk sugar, to ensure their survival, for instance. Joyce says his team has endowed its molecule with another function, although he will not say what that might be before his findings are published. More fundamentally, to mimic biology, a molecule must gain new functions on the fly, without laboratory tinkering. Joyce says he has no idea how to clear this hurdle with his team's RNA molecule. "It doesn't have open-ended capacity for Darwinian evolution." Missing witness A life-mimicking molecule will also need to assemble itself from simpler components than two halves, says Michael Robertson, a biochemist at the University of California, Santa Cruz. Both DNA and RNA currently replicate with the help of a protein enzyme that joins individual nucleotide "letters". Early life may have done the same, or it could have joined short stretches of RNA, Robertson says. Moreover, efforts to create more life in the labs will eventually hit a philosophical wall, not a technical one. "If somebody makes something great in the lab, it's fantastic. But really the origin of life on Earth is an historical problem that we're never going to be able to witness and verify," he says. === Akin to "Play it again, Sam" Darwin never mentioned survival of the fittest. It was in fact Herbert Spencer (27 April 1820 Aa?a?? 8 December 1903) an English philosopher, prominent classical liberal political theorist, and sociological theorist of the Victorian era. Spencer developed an all-embracing conception of evolution as the progressive development of the physical world, biological organisms, the human mind, and human culture and societies. As a polymath, he contributed to a wide range of subjects, including ethics, religion, economics, politics, philosophy, biology, sociology, and psychology. He is best known for coining the phrase "survival of the fittest," which he did in Principles of Biology (1864), after reading Charles Darwin's On the Origin of Species.This term strongly suggests natural selection, yet as Spencer extended evolution into realms of sociology and ethics, he made use of Lamarckism rather than natural selection. == Entropy refers to the number of available energy microstates in a thermodynamic system; it has very little to do with the spatial order of matter. An energy microstate is simply any mechanism that can carry energy (e.g., each way a molecule can vibrate or rotate). Thermodynamics is about the bookkeeping of energy; not spatial order. The distinction is crucial. For example, atoms can condense into spatially ordered crystals. But they can do this only if excess energy is carried away into the surrounding environment via additional energy states, such as photons, phonons, or other atoms. Thus the atoms forming a crystal condense into fewer energy states (a local entropy decrease) as a result of even more energy states becoming available globally (global increase in entropy). The crystalline spatial order arises from electromagnetic interactions and the rules of quantum mechanics, along with any emergent properties of matter as it condenses into more complex systems; never by "overcoming entropy". When atoms and molecules are forming crystals or living systems, matter and energy are always being exchanged with a larger environment. The field of condensed matter physics reveals that order, complexity, and emergent phenomena are ubiquitous in the universe, from the formation of protons and neutrons out of quarks and gluons, to atoms and molecules, to solids and liquids and organic compounds, all the way to the formation of living systems. The variety and complexity are enormous and depend on the energy ranges and materials available. Yet no laws of thermodynamics are being violated anywhere. There are no ID/creationist "entropy barriers" prohibiting order and complexity from arising, and no ID/creationist has ever demonstrated such a barrier (it could be worth a Nobel Prize if one did). The "paradox" arises only because of misconceptions promulgated by the ID/creationists. == Life got bigger in two, millionfold leaps, researchers say Earth's creatures come in all sizes, yet scientists believe they all descend from the same singlecelled organisms that first populated the planet. So how did life go from bacteria to the blue whale? It happened primarily in two great leaps, and each time, the maximum size of life jumped up by a factor of about a million, said Jonathan Payne, a geologist and environmental scientist at Stanford University in California. Both leaps coincided with periods when there was a great increase in the amount of oxygen in the atmosphere, Payne said. A paper detailing the research appeared in the Dec. 22 online early edition of the research journal Proceedings of the National Academy of Sciences. The first fossilized bacteria date to about 3.4 billion years ago, although life likely arose several hundred million years before, Payne said. Between 2.7 and 2.4 billion years ago, cyanobacteria, formerly known as bluegreen algae, originated and were of particular importance because they give off oxygen in the process of drawing energy from light. Plants, which do the same thing, descend from cyanobacteria. The singlecelled bacteria remained Earth's largest life form, cranking out the oxygen, until about 1.6 billion years ago, Payne added. Then a new life form shows up in the fossil record whose maximum size is about 'a million times bigger than anything that had come before. Those organisms are called eukaryotes. Eukaryotes have cells of more complex structure than bacteria. Their cells contain a nucleus and other compartments dedicated to specific functions. This shows 'organization matters for size, Payne said. For bacteria, the relative lack of it 'continues to be a limitation on size. About 600 million years ago, at the same time as another major boost in the amount of oxygen in the atmosphere, life grew again, Payne went on. This time, it was a millionfold size leap of multicellular ity. Payne said there are multicellular eukaryotes in the fossil record for several million years before this size leap, but the real explosion didn't happen until the oxygen level bumped up. So why do the size leaps seem to hinge on the amount of oxygen in the air? 'There are a few things that could be going on, Payne said. The most important is that eukaryotes need oxygen for metabolism. If they want to eatin other words, 'take organic matter and burn it up to have energy... they need oxygen. Payne said the first boost in atmospheric oxygen might have come because of the proliferation of oxygen generating cyanobacteria. The causes of the second boost are less certain, Payne added, but the timing and magnitude of the jumps up in maximum size are clear, and affected vast numbers of species. 'Whatever is controlling this second size increase appears to operate across many different groups, he said. 'There also appears to be an increase even in the maximum size of groups of organisms like multicellular algae, so the size increase doesn't appear to be limited just to animals. == Ancient "Chewing" Reptile Linked With Leap in Animal Diversity Researchers have discovered the first known example of a land-based vertebrate that had the ability to fully chew and digest plants for food. This trait is important because it enables animals to break down and efficiently process many different kinds of vegetation. The development of a sophisticated chewing ability paved the way to the emergence of a wide variety of plant-eating animals, say the researchers, who reported their findings in the June 7 issue of the journal Nature. The evidence came from the fossilized skull of what the scientists said was a gangly, big-eyed, large-toothed land-dwelling reptile, called Suminia getmanovi. It lived 260 million years agoabout 50 million years before dinosaurs. "The real boost in the success of vertebrates on land started with the ability to process plant material efficiently," said Robert Reisz, a professor at the University of Toronto in Mississauga. His collaborator and co-author of the paper in Nature was Natalia Rybczynski, who is now at Duke University. The research was funded by the National Geographic Society and the Natural Sciences and Engineering Research Council of Canada. Changing Ecosystem The advent of chewing as seen in Suminia paved the way to the first great burst of diversity among terrestrial herbivores, according to the researchers. This diversity is mirrored today in the ecosystem of land-based animals that evolved over time. The modern-day animal kingdom has many herbivores, which serve as food for a much smaller number of carnivores. Plant-eating species such as gazelles and antelope are abundant, for example, while carnivores such as lions and leopards are relatively much more scarce. "There is a link between the time when land-dwelling herbivores started processing food in the mouth and a great increase in animal diversity," said Reisz. "So you can say that the evolution of the modern terrestrial ecosystem, with lots of herbivores supporting a few top predators, is based on animals efficiently eating the greenery on land." Before this evolution of diversity, the scientists explained, the ecosystem was very different. According to Reisz, the first terrestrial herbivore appeared on land about 290 million years ago. But herbivores at that time had a more rudimentary style of eating. They tore the leaves off the plant and swallowed them whole, and the leaves were then processed in the animals' guts. == Suminia, however, developed a much more advanced way of eating. Microscopic analysis of the reptile's teeth revealed marks indicating that Suminia used its back teeth to chew with a shearing motion that enabled it to shred plant material more effectively. The researchers said the skull, which was discovered in 1990 in central Russia, looks like that of a monkey or a rodent, with huge eyes and large, distinctive teeth. Dating techniques indicate the animal lived in the Paleozoic era, about 260 million years ago. "Suminia is the best example we have from such an early era of an animal that is adapted to high-fiber herbivory," said Rybczynski. "It was clearly more specialized to eat coarse, fibrous food than anything else of the time." Common Trait of Mammals Developing a more advanced system of chewing enabled ancient herbivores and their descendants to increase their intake of food and process it more efficiently. By shredding leaves into small bits before swallowing, they can absorb the maximum amount of energy and nutrients in the plants they eat. A class of reptiles related to Suminia, called dicynodonts, were the first successful land-dwelling and plant-eating vertebrates, which means they were probably also efficient in processing their food, the researchers said. But dicynodonts had beaks rather than teeth, so they technically were not able to chew. In contrast, Suminia's teeth were highly pronounced and similar to the teeth of some plant-eating reptiles and dinosaurs. "What is immediately striking about this animal is that it has really large teeth and they occlude, or meet," Rybczynski said. "This is unlike iguanas, crocodiles, and most other non-mammalian vertebrates, whose teeth don't even touch. Since the teeth occluded, we knew that Suminia had some sort of specialized chewing mechanism." Today, mammals are the animals that chew their food, particularly plants, most intensively. Suminia was distantly related to a class of reptiles that eventually evolved into mammals. The researchers speculate that an advanced chewing ability is tied to the "warm-blooded" nature of mammals (and perhaps dinosaurs). To maintain a high body temperature and high metabolism, mammals need an efficient way to digest and absorb nutrients from food. In contrast, "cold-blooded" animals, such as modern-day lizards and many of their ancient reptile ancestors, do not have the same energy requirements. Herbivores that lack a well-developed chewing ability tend to eat the more tender leaves, flowers, and buds of plants, Rybczynski said. Minimal oral processing of vegetation is associated with a slower rate of digestion. The iguana, for example, swallows vegetation and allows it to digest for a long time. == A recent paper has announced the discovery of Anchiornis huxleyi (pronounced "an-key-ornis"), a theropod dinosaur from western Liaoning, China. The age of the deposits it was entombed in are uncertain (they're of "Jurassic-Cretaceous age"), but in a phylogenetic analysis Anchiornis comes out as a bit more primitive than Archaeopteryx. Anchiornis is the smallest known non-avian dinosaur, and probably weighted no more than 110 grams when alive. It was slightly longer than one foot in length, but unfortunately, the head, part of the neck, and the end of the tail are missing, so an accurate measurement of its length isn't possible. Like Archaeopteryx, no sternum is preserved, and a wishbone is present. The ulna (a bone in the forelimb) is slightly bowed, and only slightly thicker than the radius (another forelimb bone), which may argue against Anchiornis being able to fly, but the first phalanx of manual digit II is almost as thick as the ulna, which (to me) may be a point in favor of flight, since flight feathers attach to that bone in Archaeopteryx and living birds. But although patches of feathers were found, no flight feathers were discovered with the fossil. In addition, I've read that additional specimens have been found that are more complete, and in better condition, than the example described in the current paper, so expect to hear more about this animal in 2009. Xu X., Zhao Q., M. Norell, C. Sullivan, D. Hone, G. Erickson, Wang X.-L., Han F.-L., & Guo Y. 2009. A new feathered maniraptoran dinosaur fossil that fills a morphological gap in avian origin. Chinese Science Bulletin. Available on-line athttp://www.springerlink.com/content/p5k5310462451jq3/fulltext.pdf == FOSSIL Lagerstatten comparable to that of the Burgess Shale potentially provide the detail necessary to resolve and assess the so-called Cambrian Explosion of multicellular life1,2; distributional and taphonomic biases, however, often limit the generalizations that can be drawn. Here I report widespread occurrences of Burgess Shale-type fossils in shallow-shelf sediments of the Lower Cambrian Mount Cap Formation, District of Mackenzie, Northwest Territories, Canada. These borehole assemblages significantly expand the known geographical and ecological range of such fossil biotas and document the early appearance of both wiwaxiid polychaetes and filter-feeding crustaceans. The ability of this latter group to exploit microplanktic primary productivity marks a fundamental shift in trophic structuring and may distinguish Phanerozoic from pre-Phanerozoic ecosystems. == Darwin's Sacred Cause, by Adrian Desmond and James Moore == Feathered dinoasurs from Cretaceous Sapornis, Jixiangornis, Jeholornis, Shenzhouraptor, Boluochia, Concornis, Enantiornis, Yixianornis, Eoalulavis, Liaoningornis, Eoenantiornis, Sinornis, Gansus, Hongshanornis. == Panderichtys - Sauripterus - Elginerpeton - Obruchevichtys - Hynerpeton - Ichtyostega - Acanthostega - Pederpes finneyae - Tiktaalik - Tulerpeton - Ventastega -- all are transitionals somewhere between a fish and an amphibian. == Mary Jane West-Eberhard. 2005. Developmental plasticity and the origin of species differences. Proceedings National Academy of Sciences USA 102, Suppl. 1:6543-6549 Mary Jane West-Eberhard: Phenotypic accommodation: Adaptive innovation due to developmental plasticity. Journal of Experimental Zoology Part B ( Molecular and Developmental Evolution) 304B:610-618 (2005) Behavior and evolution. In MOLDS, MOLECULES, AND METAZOA: Growing Points in Evolutionary Biology. Grant, P. R. and Horn, H. (eds.), Princeton University Press, pp. 57-75. (1992) == Archaeopteryx holds a unique place in history. When the first specimen was discovered about a century and a half ago, just a year after Charles Darwin published "On the Origin of Species," its shared reptile-avian features provided the strongest evidence yet for the theory of evolution. The Jurassic-era fossil has a beaklike mouth, winglike forelimbs, long feathers and feet for perching. But it also has reptilelike teeth in its jaws, claws on its fingers and a long tail. A little over a foot long, it could probably fly but without the grace of modern birds. "If you want to find a single fossil which is a missing link in the evolution of dinosaurs into birds, this is it," said University of Manchester paleontologist Phil Manning. "It's a bird with sharp teeth, claws and a long bony tail. If you were to freeze-frame evolution, you would end up with archaeopteryx.'''' == Pakicetids - clearly not whales http://en.wikipedia.org/wiki/Pakicetid : Whales - clearly not pakicetids http://en.wikipedia.org/wiki/Whale : Evolution from pakicetids to whales http://en.wikipedia.org/wiki/Whale_evolution == The Latest Face of Creationism in the Classroom Creationists who want religious ideas taught as scientific fact in public schools continue to adapt to courtroom defeats by hiding their true aims under ever changing guises Key Concepts Creationists continue to agitate against the teaching of evolution in public schools, adapting their tactics to match the roadblocks they encounter. Past strategies have included portraying creationism as a credible alternative to evolution and disguising it under the name intelligent design. Other tactics misrepresent evolution as scientifically controversial and pretend that advocates for teaching creationism are defending academic freedom. Professors routinely give advice to students but usually while their charges are still in school. Arthur Landy, a distinguished professor of molecular and cell biology and biochemistry at Brown University, recently decided, however, that he had to remind a former premed student of his that without evolution, modern biology, including medicine and biotechnology, wouldnt make sense. The sentiment was not original with Landy, of course. Thirty-six years ago geneticist Theodosius Dobzhansky, a major contributor to the foundations of modern evolutionary theory, famously told the readers of The American Biology Teacher that nothing in biology makes sense, except in the light of evolution. Back then, Dobzhansky was encouraging biology teachers to present evolution to their pupils in spite of religiously motivated opposition. Now, however, Landy was addressing Bobby Jindalthe governor of the state of Louisianaon whose desk the latest antievolution bill, the so-called Louisiana Science Education Act, was sitting, awaiting his signature. Remembering Jindal as a good student in his genetics class, Landy hoped that the governor would recall the scientific importance of evolution to biology and medicine. Joining Landy in his opposition to the bill were the American Institute of Biological Sciences, which warned that Louisiana will undoubtedly be thrust into the national spotlight as a state that pursues politics over science and education, and the American Association for the Advancement of Science, which told Jindal that the law would unleash an assault against scientific integrity. Earlier, the National Association of Biology Teachers had urged the legislature to defeat the bill, pleading that the state of Louisiana not allow its science curriculum to be weakened by encouraging the utilization of supplemental materials produced for the sole purpose of confusing students about the nature of science. But all these protests were of no avail. On June 26, 2008, the governors office announced that Jindal had signed the Louisiana Science Education Act into law. Why all the fuss? On its face, the law looks innocuous: it directs the state board of education to allow and assist teachers, principals, and other school administrators to create and foster an environment within public elementary and secondary schools that promotes critical thinking skills, logical analysis, and open and objective discussion of scientific theories being studied, which includes providing support and guidance for teachers regarding effective ways to help students understand, analyze, critique, and objectively review scientific theories being studied. Whats not to like? Arent critical thinking, logical analysis, and open and objective discussion exactly what science education aims to promote? As always in the contentious history of evolution education in the U.S., the devil is in the details. The law explicitly targets evolution, which is unsurprisingfor lurking in the background of the law is creationism, the rejection of a scientific explanation of the history of life in favor of a supernatural account involving a personal creator. Indeed, to mutate Dobzhanskys dictum, nothing about the Louisiana law makes sense except in the light of creationism. Creationisms Evolution Creationists have long battled against the teaching of evolution in U.S. public schools, and their strategies have evolved in reaction to legal setbacks. In the 1920s they attempted to ban the teaching of evolution outright, with laws such as Tennessees Butler Act, under which teacher John T. Scopes was prosecuted in 1925. It was not until 1968 that such laws were ruled to be unconstitutional, in the Supreme Court case Epperson v. Arkansas. No longer able to keep evolution out of the science classrooms of the public schools, creationists began to portray creationism as a scientifically credible alternative, dubbing it creation science or scientific creationism. By the early 1980s legislation calling for equal time for creation science had been introduced in no fewer than 27 states, including Louisiana. There, in 1981, the legislature passed the Balanced Treatment for Creation-Science and Evolution-Science in Public School Instruction Act, which required teachers to teach creation science if they taught evolution. PAGE 1 === Creationists who want religious ideas taught as scientific fact in public schools continue to adapt to courtroom defeats by hiding their true aims under ever changing guises The Louisiana Balanced Treatment Act was based on a model bill circulated across the country by creationists working at the grassroots level. Obviously inspired by a particular literal interpretation of the book of Genesis, the model bill defined creation science as including creation ex nihilo (from nothing), a worldwide flood, a relatively recent inception of the earth, and a rejection of the common ancestry of humans and apes. In Arkansas, such a bill was enacted earlier in 1981 and promptly challenged in court as unconstitutional. So when the Louisiana Balanced Treatment Act was still under consideration by the state legislature, supporters, anticipating a similar challenge, immediately purged the bills definition of creation science of specifics, leaving only the scientific evidences for creation and inferences from those scientific evidences. But this tactical vagueness failed to render the law constitutional, and in 1987 the Supreme Court ruled in Edwards v. Aguillard that the Balanced Treatment Act violated the Establishment Clause of the First Amendment to the Constitution, because the act impermissibly endorses religion by advancing the religious belief that a supernatural being created humankind. Creationism adapts quickly. Just two years later a new label for creationismintelligent designwas introduced in the supplementary textbook Of Pandas and People, produced by the Foundation for Thought and Ethics, which styles itself a Christian think tank. Continuing the Louisiana Balanced Treatment Acts strategy of reducing overt religious content, intelligent design is advertised as not based on any sacred texts and as not requiring any appeal to the supernatural. The designer, the proponents say, might be God, but it might be space aliens or time-traveling cell biologists from the future. Mindful that teaching creationism in the public schools is unconstitutional, they vociferously reject any characterization of intelligent design as a form of creationism. Yet on careful inspection, intelligent design proves to be a rebranding of creationismsilent on a number of creation sciences distinctive claims (such as the young age of the earth and the historicity of Noahs flood) but otherwise riddled with the same scientific errors and entangled with the same religious doctrines. Such a careful inspection occurred in a federal courtroom in 2005, in the trial of Kitzmiller v. Dover Area School District. At issue was a policy in a local school district in Pennsylvania requiring a disclaimer to be read aloud in the classroom alleging that evolution is a Theory...not a fact, that gaps in the Theory exist for which there is no evidence, and that intelligent design as presented in Of Pandas and People is a credible scientific alternative to evolution. Eleven local parents filed suit in federal district court, arguing that the policy was unconstitutional. After a trial that spanned a biblical 40 days, the judge agreed, ruling that the policy violated the Establishment Clause and writing, In making this determination, we have addressed the seminal question of whether [intelligent design] is science. We have concluded that it is not, and moreover that [intelligent design] cannot uncouple itself from its creationist, and thus religious, antecedents. The expert witness testimony presented in the Kitzmiller trial was devastating for intelligent designs scientific pretensions. Intelligent design was established to be creationism lite: at the trial philosopher Barbara Forrest, co-author of Creationisms Trojan Horse: The Wedge of Intelligent Design, revealed that references to creationism in Of Pandas and People drafts were replaced with references to design shortly after the 1987 Edwards decision striking down Louisianas Balanced Treatment Act was issued. She even found a transitional form, where the replacement of creationists by design proponents was incompletecdesign proponentsists was the awkward result. More important, intelligent design was also established to be scientifically bankrupt: one of the expert witnesses in the trial, biochemist Michael Behe, testified that no articles have been published in the scientific research literature that provide detailed rigorous accounts of how intelligent design of any biological system occurredand he was testifying in defense of the school boards policy. Creationists who want religious ideas taught as scientific fact in public schools continue to adapt to courtroom defeats by hiding their true aims under ever changing guises Donning a Fake Mustache Failing to demonstrate the scientific credibility of their views, creationists are increasingly retreating to their standard fallback strategy for undermining the teaching of evolution: misrepresenting evolution as scientifically controversial while remaining silent about what they regard as the alternative. This move represents only a slight rhetorical shift. From the Scopes era onward, creationists have simultaneously employed three central rhetorical themes, sometimes called the three pillars of creationism, to attack evolution: that evolution is unsupported by or actually in conflict with the facts of science; that teaching evolution threatens religion, morality and society; and that fairness dictates the necessity of teaching creationism alongside evolution. The fallback strategy amounts to substituting for creationism the scientifically unwarranted claim that evolution is a theory in crisis. Creationists are fond of asserting that evolution is a theory in crisis because they assume that there are only two alternatives: creationism (whether creation science or intelligent design) and evolution. Evidence against evolution is thus evidence for creationism; disproving evolution thus proves creationism. The judge in McLean v. Arkansas, the 1981 case in which Arkansass Balanced Treatment Act was ruled to be unconstitutional, succinctly described the assumption as a contrived dualism. Yet by criticizing evolution without mentioning creationism, proponents of the fallback strategy hope to encourage students to acquire or retain a belief in creationism without running afoul of the Establishment Clause. Creationisms latest face is just like its earlier face, only now thinly disguised with a fake mustache. Underscoring the conscious decision to emphasize the supposed evidence against evolution, the Institute for Creation Research, which promotes creation science, candidly recommended immediately after the Edwards decision that school boards and teachers should be strongly encouraged at least to stress the scientific evidences and arguments against evolution in their classes ... even if they dont wish to recognize these as evidences and arguments for creation. Similarly, the Discovery Institute, the de facto institutional headquarters of intelligent design, saw the writing on the wall even before the decision in the Kitzmiller ruling that teaching intelligent design in the public schools is unconstitutional. Although a widely discussed internal memorandumThe Wedge Documenthad numbered among its goals the inclusion of intelligent design in the science curricula of 10 states, the Discovery Institute subsequently retreated to a strategy to undermine the teaching of evolution, introducing a flurry of labels and slogansteach the controversy, critical analysis and academic freedomto promote its version of the fallback strategy. Academic freedom was the creationist catchphrase of choice in 2008: the Louisiana Science Education Act was in fact born as the Louisiana Academic Freedom Act, and bills invoking the idea were introduced in Alabama, Florida, Michigan, Missouri and South Carolina, although, as of November, all were dead or stalled. And academic freedom was a central theme of the first creationist movie to tarnish the silver screen: Expelled: No Intelligence Allowed. (Science columnist Michael Shermer eviscerated Expelled in his review in the June 2008 issue of Scientific American, and the magazines staff added commentary on www.SciAm.com.) Portraying the scientific community as conspiring to persecute scientists for their views on creationism, Expelled was ostensibly concerned with academic freedom mainly at the college level, but it was used to lobby for the academic freedom legislation in Missouri and Florida aimed at the public schools. (The movie, by the way, was a critical failure and jam-packed with errors.) Creationists who want religious ideas taught as scientific fact in public schools continue to adapt to courtroom defeats by hiding their true aims under ever changing guises The appeal of academic freedom as a slogan for the creationist fallback strategy is obvious: everybody approves of freedom, and plenty of people have a sense that academic freedom is desirable, even if they do not necessarily have a good understanding of what it is. The concept of academic freedom is primarily relevant to college teaching, and the main organization defending it, the American Association of University Professors, recently reaffirmed its opposition to antievolution laws such as Louisianas, writing, Such efforts run counter to the overwhelming scientific consensus regarding evolution and are inconsistent with a proper understanding of the meaning of academic freedom. In the public schools, even if there is no legal right to academic freedom, it is sound educational policy to allow teachers a degree of latitude to teach their subjects as they see fitbut there are limits. Allowing teachers to instill scientifically unwarranted doubts about evolution is clearly beyond the pale. Yet that is what the Louisiana Science Education Act was evidently created, or designed, to do. The Worm in the Apple The real purpose of the lawas opposed to its ostensible support for academic freedombecomes evident on analysis. First, consider what the law seeks to accomplish. Arent teachers in the public schools already exhorted to promote critical thinking, logical analysis and objective discussion of the scientific theories that they discuss? Yes, indeed: in Louisiana, policies established by the state board of education already encourage teachers to do so, as critics of the bill protested during a legislative hearing. So what is the laws true intent? That only a handful of scientific topicsbiological evolution, the chemical origins of life, global warming, and human cloningare explicitly mentioned is a hint. So is the fact that the bill was introduced at the behest of the Louisiana Family Forum, which seeks to persuasively present biblical principles in the centers of influence on issues affecting the family through research, communication and networking. And so is the fact that the groups executive director was vocally dismayed when those topics were temporarily deleted from the bill. Second, was there in fact a special need for the Louisiana legislature to encourage teachers to promote critical thinking with respect to evolution in particular? No evidence seems to have been forthcoming. Patsye Peebles, a veteran science teacher in Baton Rouge, commented, I was a biology teacher for 22 years, and I never needed the legislature to tell me how to present anything. This bill doesnt solve any of the problems classroom teachers face, and it will make it harder for us to keep the focus on accurate science in science classrooms. And of course, the National Association of Biology Teachers, representing more than 9,000 biology educators across the country, took a firm stand against the bill. In neighboring Florida, the sponsors of similar bills alleged that there were teachers who were prevented from or penalized for teaching the holes in evolution. But no such teachers were ever produced, and the state department of education and local newspapers were unable to confirm that the claimed incidents of persecution ever occurred. And, third, what are these holes in evolution, anyhow? The savvier supporters of bills such as Floridas and Louisianas realize that it is crucial to disclaim any intention to promote creationism. But because there is no scientifically credible challenge to evolution, only long-ago-debunked creationist claptrap [see 15 Answers to Creationist Nonsense, by John Rennie; Scientific American, June 2002], the supporters of such bills are forced to be evasive when asked about what material would be covered. Creationists who want religious ideas taught as scientific fact in public schools continue to adapt to courtroom defeats by hiding their true aims under ever changing guises In Florida, for example, a representative of the Discovery Institute dithered when asked whether intelligent design constituted scientific information in the sense of the bill, saying, In my personal opinion, I think it does. But the intent of this bill is not to settle that question, and adding, unhelpfully, The intent of this bill is ... it protects the teaching of scientific information. Similarly, during debate on the Senate floor, the bills sponsor was noticeably reluctant to address the question of whether it would license the teaching of creationism, preferring instead to simply recite its text. Thus, despite the lofty language, the ulterior intent and likely effect of these bills are evident: undermining the teaching of evolution in public schoolsa consequence only creationists regard as a blessing. Unfortunately, among their numbers are teachers. A recent national survey conducted by researchers at Pennsylvania State University reveals that one in eight U.S. high school biology teachers already presents creationism as a valid scientific alternative to Darwinian explanations for the origin of species, with about the same percentage emphasizing that many reputable scientists view creationism as a scientifically valid alternative to evolution. Not all creationist teachers are as extreme as John Freshwater, a Mount Vernon, Ohio, middle school teacher who became immersed in legal troubles over his religious advocacy in the classroom, which included not only teaching creationism but also, allegedly, using a high-voltage electrical apparatus to brand his students with a cross. But even the less zealous will probably take laws such as Louisianas as a license to miseducate. Such laws are also likely to be used to bully teachers who are not creationists: nationally, three in 10 already report pressure to present creationism or downplay evolution. These bills will also further encourage school districts where creationists are politically powerful to adopt antievolution policies. A statement by a member of the Livingston Parish School Board who supported the Louisiana bill is instructive. After saying both sidesthe creationism side and the evolution sideshould be presented, he explained that the bill was needed because teachers are scared to talk about creation. How plausible is it, then, that the laws provision that it is not to be construed to promote any religious doctrine will be honored in practice? As conservative columnist John Derbyshire commented, the Act will encourage Louisiana local school boards to unconstitutional behavior. Thats what its meant to do. The Future of Steady Misrepresentation What are the legal prospects of the creationist fallback strategy? A case in Georgia, Selman v. Cobb County School District, is suggestive, if not decisive. In 2002 the Cobb County board of education, bowing to the demands of local creationists, decided to require warning labels for biology textbooks. Using a phrase employed by creationists even before the Scopes trial in 1925, the labels described evolution as a theory, not a fact, while remaining silent about creationism. Five parents in the county filed suit in federal district court, arguing that the policy requiring the labels was unconstitutional, and the trial judge agreed, citing the abundant history linking the warning labels with creationist activity in Cobb County in particular and linking the fallback strategy with creationism in general. The case was vacated on appeal because of concerns about the evidence submitted at trial, remanded to the trial court and settled on terms favorable to the parents. It remains to be seen whether the fallback strategy will survive constitutional scrutiny elsewherebut it is likely that it will be challenged, whether in Louisiana or elsewhere. Creationists who want religious ideas taught as scientific fact in public schools continue to adapt to courtroom defeats by hiding their true aims under ever changing guises In the meantime, it is clear why the Louisiana Science Education Act is pernicious: it tacitly encourages teachers and local school districts to miseducate students about evolution, whether by teaching creationism as a scientifically credible alternative or merely by misrepresenting evolution as scientifically controversial. Vast areas of evolutionary science are for all intents and purposes scientifically settled; textbooks and curricula used in the public schools present precisely such basic, uncomplicated, uncontroversial material. Telling students that evolution is a theory in crisis isto be blunta lie. Moreover, it is a dangerous lie, because Dobzhansky was right to say that nothing in biology makes sense except in the light of evolution: without evolution, it would be impossible to explain why the living world is the way it is rather than otherwise. Students who are not given the chance to acquire a proper understanding of evolution will not achieve a basic level of scientific literacy. And scientific literacy will be indispensable for workers, consumers and policymakers in a future dominated by medical, biotechnological and environmental concerns. In the sesquicentennial year of On the Origin of Species, it seems fitting to end with a reference to Charles Darwins seminal 1859 book. In the first edition of Origin of Species, Darwin was careful to acknowledge the limits to his project, writing, I am convinced that natural selection has been the main but not the exclusive means of modification. Nevertheless, he was misinterpreted as claiming that natural selection was entirely responsible for evolution, provoking him to add a rueful comment to the sixth edition: Great is the power of steady misrepresentation; but the history of science shows that fortunately this power does not long endure. The enactment of the Louisiana Science Education Act, and the prospect of similar legislation in the future, confirms Darwins assessment of the power of steady misrepresentation. But because the passage of such antievolution bills ultimately results from politics rather than science, it will not be the progress of science that ensures their failure to endure. Rather it will take the efforts of citizens who are willing to take a stand and defend the uncompromised teaching of evolution. == Scientist Finds 140 Million-Year-Old Web Martin Brasier, a paleobiologist from Oxford University, found a spider web believed to date back to the Mesozoic era, 140 million years ago. The web was found in a prehistoric piece of amber. An amateur fossil hunter found the piece of amber two years ago on an English beach. The threads of the web are about 1 millimeter long. The web is proof that webs have been weaved by spiders in a circular fashion way back in prehistoric times, claims Simon Braddy, a paleobiologist from the University of Bristol. == A new study mapping the evolutionary history of animals indicates that Earth's first animal--a mysterious creature whose characteristics can only be inferred from fossils and studies of living animals--was probably significantly more complex than previously believed. The study, which was funded by the National Science Foundation (NSF), is the cover story of the April 10, 2008 issue of Nature. Using new high-powered technologies for analyzing massive volumes of genetic data, the study defined the earliest splits at the base of the animal tree of life. The tree of life is a hierarchical representation of the evolutionary relationships between species that was introduced by Charles Darwin. Shaking Up the Tree of Life Among the study's surprising findings is that the comb jelly split off from other animals and diverged onto its own evolutionary path before the sponge. This finding challenges the traditional view of the base of the tree of life, which honored the lowly sponge as the earliest diverging animal. "This was a complete shocker," says Dunn. "So shocking that we initially thought something had gone very wrong." But even after Dunn's team checked and rechecked their results and added more data to their study, their results still suggested that the comb jelly, which has tissues and a nervous system, split off from other animals before the tissue-less, nerve-less sponge. The presence of the relatively complex comb jelly at the base of the tree of life suggests that the first animal was probably more complex than previously believed, says Dunn. While cautioning that additional studies should be conducted to corroborate his team's findings, Dunn says that the comb jelly could only have achieved its apparent seniority over the simpler sponge via one of two new evolutionary scenarios: 1) the comb jelly evolved its complexity independently of other animals, after it branched off onto its own evolutionary path; or 2) the sponge evolved its simple form from more complex creatures--a possibility that underscores the fact that "evolution is not necessarily just a march towards increased complexity," says Dunn. "This scenario would provide a particularly dramatic example of that principle." How Old is Old? How long ago did the earliest comb jelly diverge" "Unfortunately, we don't have fossils of the oldest comb jelly," laments Dunn. "Therefore, there is no way to date the earliest jelly and determine when it diverged." After diverging from other species, the comb jelly probably continued to evolve, says Herendeen. Therefore, today's comb jelly--a common creature--probably looks very different that did the earliest comb jelly. Moreover, the tentacled, squishy but bell-less comb jelly developed along a different evolutionary path than did the classically bell- shaped jellyfish, says Patrick Herendeen, an NSF program director. Such divergences mean that "the jellyfish type of body form has independently evolved several times," says Herendeen. Remaining Gaps in the Tree of Life While reversing the evolutionary order of the sponge and comb jelly, Dunn's study also resolved some long-standing questions about other species. Among these was whether millipedes and centipedes are more closely related to spiders than to insects. The answer: spiders. But despite these and other important evolutionary insights provided by Dunn's team, the tree of life remains a work in progress. "Scientists currently estimate that there are a total of about 10 million species of organisms on earth," says Dunn. "But so far, only about 1.8 million species--most of which are animals--have been described by science. Very few of these species have, so far, been positioned in the tree of life." A Methodological Breakthrough But at least some of the tree of life's remaining gaps will likely be filled through the use of high-powered analytic approaches pioneered in Dunn's study--which involved using more than 100 computers to analyze more data than incorporated into any previous comparable evolutionary study. "Dunn's high-powered approach is just what we need to continue assembling the tree of life," says Herendeen. "We are going to see a lot of this approach in the future." Dunn explains one of the advantages of his team's approach: "Even though we looked at fewer than 100 species, they were sampled in such a way that they inform the relationships of major groups of animals relative to each other. Therefore, this study, and others like it, will have implications for the placement of far more species than just those that are sampled." Remaining Challenges But no matter how many high-tech analytic tools scientists use to analyze the genetics of organisms, they must still conquer "the exact same challenges that naturalists faced 200 years ago," says Dunn. "We still don't even know enough about many species to have a good idea where to look for them." "And even as it is getting easier and cheaper to analyze the DNA of organisms with increasingly powerful computers, it is getting more expensive and difficult to find, collect, and identify organisms." For example, Dunn's team had to use remotely operated underwater vehicles to collect one of the comb jellies included in this study. Dunn concludes: "It may come as a surprise to some that the many that huge advances in technology actually bring us right back to the same challenges that naturalists faced 200 years ago: the day-to-day practical challenges of just figuring out what lives on our planet, where to find it and how to collect it." == Amish gene 'limits heart disease' A gene mutation which protects the heart against a high-fat diet has been found in the Amish population. Researchers found 5% of the US Amish population in Lancaster, Pennsylvania have a mutation in a protein which breaks down fatty particles. Those with the mutation had higher levels of "good" HDL-cholesterol and lower levels of "bad" LDL-cholesterol, the journal Science reported. It is hoped the finding will lead to new therapies to reduce cholesterol. The researchers used blood samples from 800 volunteers in the Old Order Amish community to look for DNA markers that might be associated with levels of fat particles called triglycerides in the blood stream. High blood levels of triglycerides, one of the most common types of fat in food, have been linked to heart disease. They found a mutation in the APOC3 gene, which encodes a protein - apoC-III - that inhibits the breakdown of triglycerides. As part of the study, participants drank a high-fat milkshake and were monitored for the next six hours. Individuals with the mutation produced half the normal amount of apoC-III and had the lowest blood triglyceride levels - seemingly because they could break down more fat. They also had relatively low levels of artery-hardening - a sign of cardiovascular disease. Protection Study leader Dr Toni Pollin, assistant professor of medicine at the University of Maryland School of Medicine, said: "Our findings suggest that having a lifelong deficiency of apoC-III helps to protect people from developing cardiovascular disease. "The discovery of this mutation may eventually help us to develop new therapies to lower triglycerides and prevent cardiovascular disease," she added. The researchers believe the mutation was first introduced into the Amish community in Lancaster County by a person who was born in the mid-1700s. It appears to be rare or absent in the general population. == Ancient armored amphibian had world's oddest bite A peculiar amphibian that was clad in bony armor prowled warm lakes 210 million years ago, catching fish and other tasty snacks with one of the most unusual bites in the history of life on Earth. The creature called Gerrothorax pulcherrimus, which lived alongside some of the early dinosaurs, opened its mouth not by dropping its lower jaw, as other vertebrate animals do. Instead, it lifted back the top of its head in a way that looked a lot like lifting the lid of a toilet seat. "It's weird. It's the ugliest animal in the world," Harvard University's Farish Jenkins, one of the scientists who describe the mechanics of its bite in the Journal of Vertebrate Paleontology, said in a telephone interview on Friday. "You almost can't imagine holding your jaws still and lifting your head back to take a bite," Jenkins said. "There are some vertebrates that will lift their heads slightly or the upper jaws (when they bite). Some salamanders do it slightly. Some fish do it slightly. But no animal is known to have done it this extensively," Jenkins added. The scientists think Gerrothorax lurked at the bottom of a lake, then with a sudden movement of the skull created a mouth gape that entrapped any fish unfortunate enough to swim by. Gerrothorax measured about 3 feet (1 meter) long and was stoutly protected by bony body armor reminiscent of chain mail. It had a very flat body and very flat head, short, stubby limbs and well-developed gills, Jenkins added. Its jaws were lined with sharp teeth. And the roof of its mouth was studded with large fangs to keep any slippery fish from escaping its chomp. With a special adaptation of the joint between its skull and first neck vertebra, Gerrothorax could raise its head relative to its lower jaw by as much as 50 degrees, giving it the wide gape necessary to swallow its prey. Gerrothorax is one of a group of odd amphibians called plagiosaurs with no modern descendants that vanished along with numerous other species 200 million years ago in a mass extinction at the end of the Triassic Period. Its fossils were found in the Fleming Fjord Formation of east Greenland. "That the same species is found in Greenland as well as Western Europe and Scandinavia suggests that their unique structure was hugely successful," Anne Warren of La Trobe University in Melbourne, Australia, another of the scientists, said in a statement. It was armored for good reason. It lived alongside massive, crocodile-like reptiles called phytosaurs and larger, predatory amphibians. Other fossils show dinosaurs, flying reptiles called pterosaurs and early mammals lived alongside it. == Teams of scientists at the universities of Oregon and North Carolina explained it. They "determined for the first time the atomic structure of an ancient protein, revealing in unprecedented detail how genes evolved their functions." "This is the ultimate level of detail," said the evolutionary biologist Joe Thornton. "We were able to see exactly how evolution tinkered with the ancient structure to produce a new function that is crucial to our own bodies today. Nobody's ever done that before." Unfortunately, this momentous discovery was announced almost too late to be mentioned in Ben Stein's film. It wasn't totally too late, but it would have been a great inconvenience for the editor. What tools did the scientists use? Supercomputer programs and, I quote, "ultra-high energy X-rays from a stadium-sized Advanced Photon Source at Argonne National Laboratory near Chicago to chart the precise position of each of the 2,000 atoms in the ancient proteins." == Evolution involves holding onto your winnings and investing them wisely. You don't even have to know to how to hold onto your winnings. Evolution does it for you; it is the bank in which useful genetic mutations deposit themselves. There is a very slow rate of return, but it's compounded. At the end of one eon, you get your bank statement and find your pittance has grown into an orang utan. At the end of the next eon, it has grown into Charles Darwin. Scientists, at least 99.875 percent of them, believe that in the long run only useful mutations deposit in this bank. Those mutations with no use, or a negative effect, squander their savings in a long-running bunko game, and die forgotten in the gutter. == Various forms of eyes have evolved 26 different times that scientists know about, == The lungfish is also a lobe finned fish. At least three genera of lungfish are known == New flying reptile species found A new fossil species of flying reptile with a wingspan the size of a family car has been uncovered by scientists. A researcher at the University of Portsmouth has identified the new type of pterosaur, the largest of its kind ever to have been discovered. It would have flown in the skies above Brazil 115 million years ago. Mark Witton estimated that the pterosaur had a wingspan of 16.4ft (5m) and would have been more than 39in (1m) tall at the shoulder. The partial skull fossil, found in Brazil, is the first example of a chaoyangopteridae, a group of toothless pterosaurs, to be found outside China. Mr Witton said: "Some of the previous examples we have from this family in China are just 60cm (2ft) long - as big as the skull of the new species. "Put simply, it dwarfs any chaoyangopterid we've seen before by miles." Mr Witton has named the new species Lacusovagus, meaning lake wanderer, after the large body of water in which the remains were buried. It had lain in a German museum for several years after its discovery in the Crato formation of the Araripe Basin in north east Brazil, which is well known for its fossils. Liked large prey "Usually fossils like this are found lying on their sides but this one was lying on the roof of its mouth and had been rather squashed, which made even figuring out whether it had teeth difficult. "Still, it's clear to see that Lacusovagus had an unusually wide skull, which has implications for its feeding habits - maybe it liked particularly large prey. "The remains are very fragmentary, however, so we need more specimens before we can draw any conclusions. "The discovery of something like this in Brazil - so far away from its closest relatives in China - demonstrates how little we actually know about the distribution and evolutionary history of this fascinating group of creatures." == http://www.smithsonianmag.com/science-nature/neanderthals.html?c=y&page=1 Neanderthals == The Great Paleozoic Crisis: Life and Death in the Permian_ == "Domestic" or "bread wheat" can be crossed with wild emmer wheat and the F1 hybrid is viable and can be fertile - - 1-2% of the time. Modern bread wheat varieties have 42 chromosomes and evolved from crosses between wild emmer, (T. dicoccoides: 28 chromosomes; 4N) and goat grass (14 chromosomes; 2N). All varieties of wheat grown today was originally derived from wild 14 chromosome wheat (einkorn). So, 14 is the diploid number (2N) of chromosomes for wheat. Einkorn and other 14-chromosome (2N) wild grass crosses produced the tetraploid 28 (4N) chromosome wheat. http://www.answers.com/topic/the-natural-history-of-wheat "Wild emmer wheat (Triticum dicoccoides Korn, 2n = 4x = 28, genome AABB) were earlier crossed to two Indian bread wheat (T. aestivum L., 2n = 6x = 42, genome AABBDD) . . . The germination of F1 seeds and seedling growth up to the 3-4 tiller stage was normal. . . Crosses were repeated and the partially fertile pentaploid F1 hybrid, Sonalika x T. dicoccoides was selfed. Two out of eleven F2 segregants were observed to have spikes similar to that of the F1 hybrid." http://www.shigen.nig.ac.jp/wheat/wis/No71/p29/1.html "In direct crosses between the T. dicoccoides selection and the susceptible T. aestivum cultivars, the pentaploid interspecific hybrids were highly sterile (fertility of 12% by self-pollination); the F2 population segregated in a 3 resistant:1 susceptible ratio. In bridge-crosses between the fertile tetraploid progeny of a previous T. dicoccoides-T. durum cross and susceptible T. aestivum cultivars, the fertility was markedly improved (approximately 50% when T. aestivum served as pollinator); the F1 pentaploid hybrids of these three-way crosses segregated in a pattern fitting a 1 resistant:1 susceptible ratio." http://www.springerlink.com/content/v48256521351144m/ Of course, because of differences in genome ploidy, as well as differences in accumulated recessive alleles in the various "breeds" of wheat and grass, some of these hybrids will often suffer "hybrid necrosis, hybrid chlorosis and hybrid dwarfness." Consider that producing a viable offspring requires that enough information be present while producing virile offspring requires that both the genetic information be present as well as the proper chromosomal structure (see link below). Again, the fact that humans and apes do not produce viable much less fertile hybrids while jaguars and cheetahs produce both viable and fertile offspring is a good clue to the idea that humans and apes are not as functionally close, genetically speaking, as are jaguars and cheetahs - or emmer and bread wheat for that matter. The grey tree frog Hyla chrysoscelis is so identical to the grey tree frog Hyla versicolor that they can't be identified in the field, yet they too are utterly incapable of producing fertile offspring. This is another case of ploidy differences. H. versicolor is tetraploid (4N = 48) while H. chrysoscelis is diploid (2N = 24). Female H. versicolor frogs that mate with male H. chrysoscelis frogs produce viable, but sterile offspring - like mules (as a cross between the horses and donkeys). Sterility is often a problem of chromosomal arrangement rather than a problem of chromosomal information. http://www.detectingdesign.com/donkeyshorsesmules.html Again, compare this with the fact that humans and apes do not produce viable much less fertile offspring. So why is it possible for emmer and wheat, or for H chrysoscelis and H versicolor, to cross those "signfiicant functional gene pool differences", but not for humans and chimps to do the same? Your wheat and tree frog examples both produce viable offspring and your wheat example can even produce fertile offspring. The reason why the tree frogs in your example produce viable, but sterile, offspring is likely due to chromosomal structural differences rather than informational differences. The lack of ability to produce viable offspring (not just sterile offspring), given the same chromosomal ploidy number, indicates a significant informational difference between the two genomes. Why is it, in your view, that emmer grass can cross the "sequence space" to a different species that can't interbreed with it, but chimps could not cross the (much closer) "sequence space" to humans? Emmer grass is not informationally different, qualitatively, from other forms of wheat or ancestral wheat-like grasses. That is why crosses between these types of plants can produce viable and even fertile offspring. This is not the case for human-ape crosses. No viable offspring much less fertile offspring can be produced. That has nothing to do with it. As noted before for you, these differences are likely the result of functional non-coding sequences within the genomes that is often quite different and unique between humans and apes. It seems that functional complexity at such very high levels is based more on non- coding DNA than coding DNA - much much more. Genomic sizes of various creatures reflect this hypothesis with many simpler forms having similar numbers of genes, but far less non-coding DNA (formerly known as 'junk-DNA'). Emergent functional "complexity" therefore seems to be much more closely related to the amount of non-coding DNA vs. coding DNA. That's nice. How is that different in any other species? Why is nit that OTHER species can cross "sequence space" to new species, but only HUMANS can't have crossed the (much smaller) "sequence space" between them and apes? Based on lower-level sub-cellular systems that we know much more about. Target ratios are based on specific emergent systems of function that are known if at least a fair degree of detail. The functional differences between humans and chimps is not known is sufficient detail as of yet. == Sex Life Of Killer Fungus Finally Revealed Biologists at The University of Nottingham and University College Dublin have announced a major breakthrough in our understanding of the sex life of a microscopic fungus which is a major cause of death in immune deficient patients and also a cause of severe asthma. The discovery of a sexual cycle in the fungal pathogen Aspergillus fumigatus is highly significant in understanding the biology and evolution of the species and will shed new light on its ability to adapt to new environments and its resistance to antifungal drugs. It is hoped the results of this research will lead to new ways of controlling this deadly disease and improved treatments for patients infected with it. First described 145 years ago this killer fungus, until now, had no known sexual cycle and was only thought to reproduce by production of asexual spores. But researchers from the School of Biology at The University of Nottingham and from University College Dublin, have finally been able to induce sexual reproduction in this potentially lethal pathogen showing, for the first time, that A. fumigatus possesses a fully functional sexual reproductive cycle. Dr Paul Dyer is an expert in the sexual development and population variation of fungi and co-author of a new article in Nature on the topic. Dr Dyer said: This discovery is significant for providing both good and bad news. The bad news is that we now know that Aspergillus fumigatus can reproduce sexually, meaning that it is more likely to become resistant to antifungal drugs in a shorter period, and the sexual spores are better at surviving harsh environmental conditions. The good news is that we can use the newly discovered sexual cycle as a valuable tool in laboratory experiments to try to work out how the fungus causes disease and triggers asthmatic reactions. Once we understand the genetic basis of disease we can then look forward to devising methods to control and overcome the fungus. The spores of A. fumigatus, which feeds on dead or decaying organic matter, are widespread in the atmosphere. It has been estimated that everybody inhales around 200 spores each day. These spores are normally eliminated by the innate immune response. However, this fungus has become the most prevalent airborne fungal pathogen due to its ability to cause infections in hosts with a weakened immune system, with at least a 50 per cent mortality rate in humans. Four per cent of patients in modern European teaching hospitals have invasive aspergillosis; it is the leading infectious cause of death in leukaemia and bone marrow transplant patients. The fungus is also associated with severe asthma and sinusitis. Almost one-fifth of all fungi have no known sexual stage these include many Aspergillus, Penicillium, Coccidioides and Malassezia species which are of major economic and medical importance. However, some of these species have apparently functional sex related genes and this research could lead to a sexual revolution for many other of these supposed asexuals. The research was carried out in collaboration with Dr Hubert Fuller and his final year PhD student Celine OGorman from the UCD School of Biology and Environmental Science at University College Dublin. The study was funded by an IRCSET Postgraduate Research Scholarship, an EC Marie Curie Training Fellowship and a grant from the British Mycological Society, which facilitated research visits by Celine OGorman to The University of Nottingham. Many fungi reproduce by sexual means. The molecular-genetic and physiological mechanisms controlling sex in fungi are being investigated at The University of Nottingham with the aim of devising new methods for the control of fungal diseases and promoting sex in beneficial species. The consequences of sex for genetic variation and evolution are being studied in model species of fungi including plant pathogens and Antarctic lichen-forming fungi. == Christian de Duve. "A Guided Tour of the Living Cell" (Nobel laureate and organic chemist) == http://www.actionbioscience.org/evolution/pigliucci.html == Why did Darwin call "Natural Selection" by that term. He was contrasting it to "Artificial Selection", the specific breeding of plants and animals for preferred attributes. He also stressed that it's not just medicine, but the understanding and development of disease that demands understanding evolution. Some of the advances in evolution were made while studying disease and disease vectors, not just potential treatments. But then he goes into other areas, including Conservation and Ecology, Biotechnology, and even understanding ourselves. == Richard Fortey "Trilobite! Eyewitness To Evolution". ISBN 0-00-257012-2 == Single-celled giant upends early evolution G. sphaerica's traces are spitting image of the old, Precambrian fossils Matz/ NOAA/HBOI A collected specimen of Gromia sphaerica cleaned of sediment. The one-celled creature was found making tracks on the ocean floor off of the Bahamas. Slowly rolling across the ocean floor, a humble single-celled creature is poised to revolutionize our understanding of how complex life evolved on Earth. A distant relative of microscopic amoebas, the grape-sized Gromia sphaerica was discovered once before, lying motionless at the bottom of the Arabian Sea. But when Mikhail Matz of the University of Texas at Austin and a group of researchers stumbled across a group of G. sphaerica off the coast of the Bahamas, the creatures were leaving trails behind them up to 20 inches long in the mud. The trouble is, single-celled critters aren't supposed to be able to leave trails. The oldest fossils of animal trails, called 'trace fossils', date to around 580 million years ago, and paleontologists always figured they must have been made by multicellular animals with complex, symmetrical bodies. But G. sphaerica's traces are the spitting image of the old, Precambrian fossils; two small ridges line the outside of the trail, and one thin bump runs down the middle. At up to 1.2 inches in diameter, they're also enormous compared to most of their microscopic cousins. "If these guys were alive 600 million years ago, and their traces got fossilized, a paleontologist who had never seen this thing would not have a shade of doubt attributing this kind of trace to the activity of a big, multicellular, bilaterally symmetrical animal," Matz said. "This is a very important discovery," Shuhai Xiao of Virginia Polytechnic Institute said. "The fact that protists can make traces has important implications for how we interpret many trace fossils." The finding could overturn conventional thinking on a mysterious time in the evolution of early life known as the Cambrian Explosion. Until about 550 million years ago, there were very few animals leaving trails behind. Then, within 10 million years an unprecedented blossoming of life swarmed across the planet, filling every niche with hard-bodied, complex creatures. "It wasn't a gradual development of complexity," Matz said. "Instead these things suddenly seemed to burst out of a magic box." Charles Darwin first noticed the Cambrian Explosion and thought it was an artifact of a poorly preserved fossil record. The precambrian trace fossils were left by multicellular animals, he reasoned, so there must be some gap in fossils between the nearly empty Precambrian and the teeming world that quickly followed. But if the first traces were instead made by G. sphaerica, it would mean the Explosion was real; it must have been a diversification of life on a scale never before seen. Genetic analysis of the water-filled G. sphaerica cells also reveals tantalizing clues that it could be the oldest living fossil on the planet. "There's a 1.8 billion-year-old fossil in the Stirling formation in Australia that looks just like one of their traces, and with a discoidal body impression similar to these guys." Matz said. "We haven't proved anything, but we might be looking at the ultimate living macroscopic fossil." == Milky Way's sweetness throughout The sweet discovery was made at the Plateau de Bure observatory in France A simple sugar that is an ingredient of life has been found for the first time in a relatively hospitable part of the galaxy. As molecules go, glycolaldehyde is not an impressive one, but its link to the origins of life make it significant. It can react to form ribose, a key constituent of the nucleic acid RNA. The study, in Astrophysical Journal Letters, is important as it shows organic molecules in a region of space where planets could form. Glycolaldehyde was first discovered toward the galactic centre in 2000. But the extreme conditions there made it unclear if the molecule could form in the rest of the galaxy. To find out, Maria Teresa Beltran of the University of Barcelona and colleagues trained the Plateau de Bure array of radio telescopes on a large star-forming region called G31.41+031, about 26,000 light years away. Known as a hot molecular core, the region is dense with newly formed stars. In the radio emission from the core, the team found several radio and microwave signatures of the presence of glycolaldehyde. I believe that many more of these molecules will show up in the near future Roberto Neri, Institute for Millimetre Radio Astronomy Comparison of those spectral signatures with a computer model of how the molecules form on tiny grains of interstellar dust suggest the glycolaldehyde is a few hundred thousand years old. "The importance of this discovery lies in the fact that the glycolaldehyde has been detected towards a region where planets orbiting newly formed stars are expected to exist - and planets could be the cradle of life," says co-author of the study Claudio Codella of the Institute of Radio Astronomy in Florence, Italy. The results will spur further research to look for complex molecules that up to now have only been seen in the galactic centre. "The search for prebiotic molecules in star-forming regions is still in the fledgling stages but the door is open now," says co-author Roberto Neri, an astronomer at the Institute for Millimetre Radio Astronomy, home to the Plateau de Bure facility. "I believe that many more of these molecules will show up in the near future," he adds. == How the turtle's shell evolved The turtle only had a shell covering its underside A newly discovered fossil from China has shed light on how the turtle's shell evolved. The 220 million-year-old find, described in Nature journal, shows that the turtle's breast plate developed earlier than the rest of its shell. The breast plate of this fossil was an extension of its ribs, but only hardened skin covered its back. Researchers say the breast plate may have protected it while swimming. The turtle fossil, found near Guangling in south-west China, is thought to be the ancestor of all modern turtles, although it differs markedly; it has teeth rather than a bony plate, the shell only covers its underside and it has a long tail. The fossil find helps to answer key questions about the evolution of turtles, Dr Xiao-Chun Wu from the Canadian Museum of Nature was one of the first to examine the fossil. Aquatic life "Since the 1800s, there have been many hypotheses about the origin of the turtle shell," explained Dr. Wu. "Now we have these fossils of the earliest known turtle. They support the theory that the shell would have formed from below as extensions of the backbone and ribs, rather than as bony plates from the skin as others have theorised," Dr Wu explained. The researchers say this idea is supported by evidence from the way modern turtle embryos develop. The breast plate grows before the shell covering their backs. O. semitestacea probably lived in shallow waters The fossilised turtle ancestor, which has been named Odontochelys semitestacea, meaning half-shelled turtle with teeth, probably inhabited the river deltas or coastal shallows of China's Nanpanjiang trough basin - the area where the fossil was unearthed. Researchers say the development of the shell to first protect the underside points to a mainly aquatic lifestyle. Dr Olivier Rieppel from Chicago's Field Museum also examined the fossil. "This strongly suggests Odontochelys was a water dweller whose swimming exposed its underside to predators. Reptiles living on the land have their bellies close to the ground with little exposure to danger," he said. The researchers say further evidence to support the idea that this species lived mainly in water comes from the structure and proportions of the fossil's forelimbs, which closely resemble those of modern turtles that live in similar conditions. Turtle phylogeny remains controversial, although a consensus seems to be building, based upon latest genetic & fossil evidence & cladistic analyses, that they are diapsids ("reptiles" with two holes in their heads behind their eyes) instead of the last surviving members of the more basal group Anapsida (lacking such openings), ie that while "anapsid", they have secondarily lost the two diagnostic "post-orbital fenestrae". Interestingly, their possible close relatives, the extinct sauropterygia (plesiosaurs & their marine reptile relatives), lost one of the two holes. == Our Ancestors Had Floppy, Flexible Feet A juvenile white-handed gibbon walks along a pole in the Wild Animal Park Planckendael, Belgium. Credit: Evie Vereecke/University of Liverpool. An older brother named Yang of one of the other white-handed gibbons in the Wild Animal Park Planckendael, Belgium, shows off his bipedal strut. Credit: Evie Vereecke/University of Liverpool. Our ape-like ancestors might have walked like todays gibbons, whose super bendy feet give them a floppy strut. The modern human foot first evolved in our ancestors around 1.8 million years ago, said Evie Vereecke of the University of Liverpool in England. But studies suggest that even before our advanced feet emerged, our mostly tree-climbing ancestors were walking upright for short stints. Vereecke wanted to find out how they would have done that without specialized walking feet. She turned to gibbons. This family of primates shares a common ancestor with the great apes (chimps, gorillas, orangutans and humans). Gibbons walk upright up to 12 percent of the time, Vereecke said. Like other modern apes, gibbons sport a flexible joint midway along the foot. While we still have the joint, we don't have the flexibility that gibbons and other apes have. That flexibility is essential for climbing trees and grasping onto branches, but perhaps not for ambling around on flat surfaces. Vereecke videotaped gibbons walking about at Belgium's Wild Animal Park of Planckendael. She then digitized the animals' foot movements and developed a computer model, which showed the animals moved sort of like ballerinas, landing on their toes before the heel touched the ground. This allowed the animals to stretch the toes' tendons and store energy in them. Once their toes touched down, gibbons then lifted the heel first, effectively bending the foot to form an upward-turned arch. That bending maneuver stretched the toes' tendons even more, storing more elastic energy for use as the foot eventually pushed off the ground. Unlike gibbons' flat feet, we have arched feet with an elastic band along the sole. When we put weight on our feet, the arch stretches that band, storing elastic energy. At push off, the elastic band recoils, releasing energy for propulsion at the end of the stride. In essence, our feet go from an arched or upside-down "U" shape to flat when walking, while gibbons' feet change from flat to "U" shaped. "This gibbon research shows us that even if you have these flat, flexible feet, you can walk upright quite efficiently," Vereecke told LiveScience, "and that it doesn't restrict or limit your abilities even though you don't have this specialized foot structure as modern humans." She said gibbons aren't a perfect model for how human ancestors, such as the early human ancestor dubbed Lucy, walked about. At 3.2 million years old, Lucy is one of the most famous early human ancestors and the first Australopithecus afarensis skeleton ever found. But gibbons could still shed light on how early humans walked. "We have some fossil remains of hominin feet, and those indicate that our early ancestors had floppy, flexible feet," Vereecke said. "Although they didn't look like a gibbon, they likely had flexible feet and walked upright." The research is detailed in the Nov. 14 issue of the Journal of Experimental Biology. == Bacterial decay was once viewed as the mortal enemy of fossilization. But new research suggests resilient colonies of bacteria, called biofilms, may have actually helped preserve the fossil records most vulnerable stuff: animal embryos and soft tissues.Scientists have found that bacteria can invade dying embryo cells and form densely packed biofilms in those those cells. These completely replace the cell structure and generate a replica of the embryo, say the researchers, who call this formation of bacteria filling out the shape of an embryo a pseudomorph. The investigators, led by Indiana University Bloomington biologists Rudolf and Elizabeth Raff, report their findings in this weeks early online issue of the research journal Proceedings of the National Academy of Sciences.The bacteria consume and replace all the cytoplasm in the cells, generating a little sculpture of the embryo, said Elizabeth Raff, the reports lead author. But certain conditions must be met if the bacteria are going to aid the preservation process. For one, she explained, the embryo must have died in a low-oxygen environment, such as the bottom of a deep ocean or buried in lakeside mud. Oxygen would make embryos self-destruct as digestive enzymes break free and wreak havoc.Then, bacteria able to survive in low-oxygen conditions must then infest the cells of the dying embryo, Raff said. The bacteria form biofilms, crowded assemblies of bacterial cells held together by sticky fibers made of proteins and sugars. As the biofilms fill the embryo cells, the tiny bacteria insinuate themselves between and among the structures within the cells, forming a faithful representation of the cells innards.Last, the bacteria must leave a permanent record. In the case of finely preserved fossil embryos, the bacteria likely excrete tiny crystals of calcium phosphate which eventually replace the bacterial sculptures. These crystals, Raff said, provide the support for embryo and soft tissue fossilization.High resolution imaging of a trove of half-a-billion-year-old animal embryo fossils from Doushantuo, China, offered scientists tantalizing evidence that bacteria may have been involved in the preservation of the delicate cells, Raff said.The Raffs studied early-stage embryos of two Australian sea urchin species, Heliocidaris erythrogramma and Heliocidaris tuberculata. The experimental results with modern embryos were compared to the high resolution images of fossil embryos prepared by colleagues from China, England, Sweden, and Switzerland.Although it is impossible to know whether bacteria aided the preservation of 550-million-year-old embryo fossils from Doushantuo and elsewhere, the Raffs argue the evidence they gathered strongly favors the view that bacteria are a fundamental force in fossil formation, as rapid biological processes must be available to convert highly delicate cells into a stable form and trigger mineralization.This work is important because it helps us understand fossilization as a biological as well as geological process, Elizabeth Raff said. It gives us a window onto the evolution of the embryos of the earths first animals. == When in need, some amoebae seek the support of kin, researchers say.The starving microbes seek each other out and form groups in which some sacrifice themselves. As a result of their deeds, others are able to travel some distance away, where they may find more food.Although this phenomenon has been long documented, it wasnt clear the extent to which these associations are based on relatedness, according to the scientists, from Baylor College of Medicine and Rice University in HoustonThese single cells aggregate based on genetic similarity, though not true kinship, said research team member Gad Shaulsky, a geneticist at Baylor. The process nonetheless demonstrates a discrimination between self and non-self similar to that seen in immune system cells of higher organisms, he added. The study appears online Nov. 24 in the online research journal PloS Biology.The amoeba Dictyostelium discoideum starts life as a single-celled organism. As long as it has ample food and a pleasant environment, its happy to stay that way. But when food is scarce, the creatures band together and form whats effectively a multi-cellular organism. The cells then sort themselves into two roles. Some cells become spores, which can survive and reproduce. Others perish, and in the process form an inanimate stalk that holds the live spores aloft. This helps the spores to disperse far awayfar enough to reach new surroundings with, possibly, new food opportunities.Research into these microbial groupings, called aggregates, helps scientists understand biofilmstenacious colonies of bacteria or fungi that can harm humans and other mammals, said Joan Strassmann of Rice University, another of the researchers. For example, people with cystic fibrosis are vulnerable to the formation of biofilms that can damage the lungs.In previous work, Strassman and collaborators found that some Dictyostelium cells cheat the system. They consistently avoid the biochemical chain of events that leads to death, and instead become spores. In the new study, the researchers found that by banding together based on genetic similarity, amoebae reduce the benefit of cheating. Thats because even though some cells will die, they get to propagate some of their genes anyway, because the the cells that do live are relatives.The preference for related companions isnt exclusive, said Shaulsky, but its a preference. That way, they minimize the risk that cells of their genetic similarity will die. In the laboratory, the scientists mixed cells from genetically distinct strains and found that they segregate into clusters of genetically similar individuals after theyve joined into aggregates.Strassman said the cells use molecular mechanisms to distinguish more and less related peers. Similar mechanisms seem to operate in multicellular organisms like humans, allowing cells to recognize each other as being part of the body or alien. Dictyostelium is thus a model for understanding other multi-cellular organisms, said Elizabeth Ostrowski, a post-doctoral researcher at Rice.Cooperation is one of the success stories of the evolution of life, said Strassmann. Part of that success involves allowing cooperation in a way that controls conflict. One of the best ways to control conflict is cooperating with genetically similar individuals. == Computational Biochemist Uncovers A Molecular Clue To Evolution. Computational Biochemist Uncovers A Molecular Clue To Evolution http://www.sciencedaily.com/releases/2008/09/080910120953.htm ScienceDaily (Sep. 10, 2008) A Florida State University researcher who uses high-powered computers to map the workings of proteins has uncovered a mechanism that gives scientists a better understanding of how evolution occurs at the molecular level. Such an understanding eventually could lead to the development of new and more effective antiparasitic drugs. Wei Yang is an assistant professor in FSU's Department of Chemistry and Biochemistry and a faculty member in the university's Institute of molecular biophysics. Working with colleagues from FSU, Duke University and Brandeis University, he recently produced remarkable computer models of an enzyme that carries the unwieldy name of inosine monophosphate dehrydrogenase, or IMPDH for short. IMPDH is responsible for initiating certain metabolic processes in DNA and RNA, enabling the biological system to reproduce quickly. In creating these simulations of IMPDH, we observed something that hadn't been seen before, Yang said. Previously, enzymes were believed to have a single 'pathway' through which they deliver catalytic agents to biological cells in order to bring about metabolic changes. But with IMPDH, we determined that there was a second pathway that also was used to cause these chemical transformations. The second pathway didn't operate as efficiently as the first one, but it was active nevertheless. Why would an enzyme have two pathways dedicated to the same task? Yang and his colleagues believe that the slower pathway is an evolutionary vestige left over from an ancient enzyme that evolved over eons into modern-day IMPDH. The finding is significant for several reasons, Yang said. First of all, this offers a rare glimpse of evolutionary processes at work on the molecular level, Yang said. Typically when we talk about evolution, we're referring to a process of adaptation that occurs in a population of organisms over an extended period of time. Our research examines such adaptations at the most basic level, which helps scientists to develop a fuller picture of how evolution actually occurs. This also represents a big step forward in our efforts to create computational simulations of biological processes, Yang said. In this case, we first made a prediction of the enzyme structure via computer and later verified it through direct observation in a laboratory, rather than the other way around. This is a most unusual accomplishment, and one that indicates we are becoming more advanced in our ability to answer questions relating to biological functions at the molecular level. Because of the key role that IMPDH plays, scientists have focused on developing new antiparasitic drugs that target it, Yang said. Our research will certainly contribute to this process. Joseph Schlenoff, the chairman of FSU's Department of Chemistry and Biochemistry, praised Yang's computational methods as extremely powerful because they are rigorous, make few assumptions and approximate the complexity of the real world. The accurate predictions that result represent success that has been promised to us for so long by scientists using computers. Collaborating with Yang on the project were Gavin J.P. Naylor, an associate professor in FSU's Department of Scientific Computing; Donghong Min, a postdoctoral associate in the Institute of Molecular Physics; Hongzhi Li, a former postdoc in the Institute of Molecular Physics; Clemens Lakner, a graduate assistant in the Department of Biological Science; David Swofford, a research scientist at Duke University and former FSU faculty member; Lizbeth Hedstrom, a professor of biochemistry at Brandeis University; and postdocs Helen R. Josephine and Iaian S. MacPherson, both of Brandeis. Enzymatic Atavist Revealed in Dual Pathways for Water Activation, that was published this summer in PLoS Biology, a peer-reviewed, open-access journal published by the Public Library of Science. Dan Herschlag, a professor of biochemistry at Stanford University, edited the paper for PLoS Biology. He praised it for its innovative approach. This work reveals basic aspects of how enzymes work and how they have evolved, Herschlag said. The study melds experiment and computation in a powerful fashion and represents a model for how to use interdisciplinary research to answer important questions. Journal reference: 1. Min et al. An Enzymatic Atavist Revealed in Dual Pathways for Water Activation. PLoS Biology, 2008; 6 (8): e206 DOI: 10.1371/journal.pbio.0060206 == Here's a list of traits that are common to some (or all) theropod dinosaurs and Archaeopteryx: Absence of a prefrontal bone in the skull. Absence of a postfrontal bone in the skull. Antorbital fenestra. All teeth are anterior to the eye. Nasal openings at end of snout. Hollow long bones. Furcula (AKA wishbone). Acrocoracohumeral ligament situated as in crocodiles. Deltopectoral crest distally projected. Bowed ulna. Semilunate carpal. Manual phalangeal formula of 23400. Absence of interclavicle bone. Pneumatic vertebrae. Gastralia. Perforate acetabulum. Ascending process on the astragalus. Ankle hinged between astragalus + calcaneum and the distal tarsals. Digitigrade foot. First metatarsal does not originate from the ankle. Vestigial fifth metatarsal. Pedal phalangeal formula of 23450. Hyperextendible second toe. Obligate bipedalism. And the clincher: feathers. == Darwinism is powerful enough to explain life because of its ability to deal, in simple terms, with the improbability and complexity of living things. It uses a simple rule: Random mutation and cumulative natural selection leads to gradual, incremental changes which, over long periods of time, leads to the complexity and diversity seen in living thing == In the past five years or so, phylogeny of the squamates, ie lizards, snakes & kin, has been shaken up by genomic analysis, much as with birds & mammals. http://en.wikipedia .org/wiki/ Toxicofera The newly discovered diversity of squamate species producing venoms is a treasure trove for those seeking to develop new pharmaceutical drugs; many of these venoms lower blood pressure, for example. Previously known venomous squamates have already provided the basis for medications such as Ancrod, Captopril, Eptifibatide, Exenatide and Tirofiban. If this new clade should prove valid, higher level squamate phylogeny would be revamped to unite Suborder Amphisbaenia (small, worm-like, largely legless lizards) with the gekko & skink infraorders in one group versus iguanas, snakes & Infraorder Anguimorpha (monitors, Gila monster, alligator lizards, galliwasps, slow-worms, etc, previously lumped with gekkos & skinks among the hard tongues in Suborder Scleroglossa) in the venomous sister taxon. Controversy continues, fueled by recent fossil discoveries, over snake evolution, arraying taxonomists arguing for a marine origin, related to the mosasaurs, Cretaceous marine predators, against those supporting terrestrial, burrowing ancestors. http://www.newscien tist.com/ article/dn9020- oldest-snake- fossil-shows- a-bit-of- leg.html Squamates, with the New Zealand tuatara, form clade Lepidomorpha, sister taxon to Archosauromorpha, containing crocs, birds & their extinct relatives, such as the flying reptile pterosaurs. The position of turtles also remains controversial. Among extinct marine reptiles, ichthyosaurs were diapsid reptiles related to both lepidosaurs & archosaurs, while plesiosaurs were lepidosaurs. As noted, mosasaurs were not only lepidosaurs but certainly squamates & possibly next of kin to snakes. == -Class (or Superclass) Chondrichthyes, the cartilaginous fish, like sharks, skates & rays -Class (or Superclass) Osteichthyes, the bony fish --Subclass (or Class) Actinopterygii, containing the tens of thousands of ray-finned fish species, whose fins attach directly to the shoulder & pelvic girdles --Subclass (or Class) Sarcopterygii, the lobe-finned fish & their descendants, we tetrapods, with arm & leg bones attached to the shoulder & pelvis ---Order Actinistia (or Coelacanthinamorpha ), the living members of which taxon are the two coelacanth species ---Order Rhipidistia (or Choanata), living members of which are tetrapods & lungfish ----Suborder Dipnomorpha, living members of which are the six lungfish species from South America, Africa & Australia ----Suborder Tetrapodomorpha -----Superfamily Rhizodontida, extinct, often giant Paleozoic freshwater lobe-fins, who featured hands & feet often more derived than those of their osteolepid kin -----Superfamily Osteolepidida ------Family Tristichopteridae, which includes the famous lobe-fin Eusthenopteron ------Family Elpistostegalia, including Panderichthyes, with both small digits & fin rays, and highly derived "fishapod" Tiktaalik, which also had a neck & rudimentary wrist-like bones. Sarcopterygians are generally accepted to belong to Class (or Superclass) Osteichthyes, characterized by their skeletons of bone instead of cartilage. However, due to the vast differences between Sarcopterygii & Osteichthyes in fin, respiratory & circulatory structures, some taxonomists are now beginning to consider Sarcopterygii a sister class (or superclass) to Osteichthyes, instead of a taxon below them. (Assignment of ranks, such as Superclass, Class, Subclass, Superorder, Order, Suborder, etc, in Linnaean nomenclature to clades of related organisms isn't hard & fast.) Our tetrapod ancestors, the first land vertebrates, evolved from highly derived elpistostegalian lobe-finned fish in the Late Devonian period. The first tetrapods had seven or eight digits at the ends of their hands & feet rather than the now standard five, which developed in the following Early Carboniferous Period. Tetrapods developed adaptations helpful in their shallow water environments, which enabled their descendants to live on land. == Elpistostegalia, the family of Late Devonian lobe-finned fish, including genera Panderichthyes & highly derived "fishapod" Tiktaalik, from which evolved tetrapods, the first land vertebrates, has recently been found already to sport digits before their fin rods were entirely replaced by fingers & toes. http://www.scienced aily.com/ releases/ 2008/09/08092209 0843.htm Elpistostegalia is sister taxon to the Tristichopteridae, which family includes the famous lobe-fin Eusthenopteron. Both groups belong to superfamily Osteolepidida, which shares Suborder Tetrapodomorpha with superfamily Rhizodontida (giant Paleozoic freshwater lobe-fins). Within Order Choanata or Rhipidistia, Tetrapodomorpha is sister taxon to the Dipnomorpha, living members of which are the lungfish species. Sister taxon to Rhipidistia is Actinistia (or Coelacanthinamorpha ), the clade whose living members are the two coelacanth species. We tetrapods, plus our distant lungfish & coelacanth cousins, are all members of Sub-Class Sarcopterygii, the lobe-finned fish & their descendants. Our sister taxon within Class Osteichthyes, the bony fish, is Actinopterygii, containing the tens of thousands of ray-finned fish species, whose fins attach directly to the shoulder & pelvic girdles, without the intervening arm & leg bones of the lobe-finned fish & their tetrapod kin. == If evolutionary biology is *not* science, how on earth do you think that all those universities, research institutes and all the other places in which it is studied, researched and taught could have been deceived? == http://www.plesiosaur.com/creationism/index.php anti-creation == Proteins strangle cell during division New type of cell division discovered http://www.eurekalert.org/pub releases/2008-11/nofs-psc112508.php A Swedish research group, partly financed by NWO, has discovered a new mechanism for cell division in a microorganism found in extremely hot and acidic conditions. The results of the research offer insights into evolution, but also into the functioning of the human body. The research has been recently published in PNAS, the magazine of the American National Academy of Sciences. Thijs Ettema, member of the research group, received a Rubicon grant from NWO in 2006 to gain experience abroad. The new mechanism for cell division was discovered in Sulfolobus acidocaldarius, a microorganism found in hot springs in Yellowstone National Park. The organism is a member of the third main group of life on earth, the Archaea. Archaea, like bacteria, are unicellular organisms but in terms of evolution they are more closely related to another main group of living things, the eukaryotes (humans, animals, plants, fungi, etc). Strangler proteins Until now little was known about the proteins that control cell division in the Archaea. With the use of immunofluorescence the researchers determined the location of these proteins in the cell and in doing so discovered that three proteins play a crucial role in the cell division of Sulfolobus acidocaldarius. Once the whole chromosome has been replicated, these three proteins form a band-like structure over the cell equator. One chromosome is then found on each side of this band. The band then squeezes the cell into two so that two new daughter cells are formed. At first it looks like mitosis, as discussed in many a biology lesson. However, mitosis is the process whereby the chromosomes are distributed between the two daughter cells. Cell division is the process whereby the two daughter cells are separated. It is striking that these cell division proteins are not related to other proteins known to be involved in cell division. Some of the proteins in the new type of cell division are similar to proteins in other eukaryotes that have a completely different function. The study shows that the proteins involved in cell division in Sulfolobus acidocaldarius are related to the so-called ESCRT proteins. In eukaryotes, and therefore also in humans, these proteins are involved in protein transport within the cell. It has recently been shown that the HIV virus makes use of the ESCRT transport system to escape from the host cell. Studying the process of cell division in Sulfolobus acidocaldarius could therefore lead to new insights into the processes involving ESCRT proteins, such as HIV particle release. Evolution Some theories suggest that in evolutionary terms the Archaea are the predecessors of eukaryotes. This is confirmed by the fact that genes involved in cell division in Sulfolobus acidocaldarius are related to eukaryotic genes. In one way or another, these organisms are related to us humans. The study shows that this resemblance is possibly somewhat closer than at first thought. Among other things, microbiologist Thijs Ettema has taken a closer look at the resemblance between the cell division proteins and the ESCRT proteins. Ettema carried out his research in Sweden at the University of Uppsala. Ettema obtained his doctorate from Wageningen University and Research Centre in 2005. He was awarded a Rubicon grant from NWO in 2006. Rubicon offers post-docs who have recently gained their doctorate the possibility of gaining experience at a centre of excellence abroad. Publication details: Ann-Christin Lindas, Erik A. Karlsson, Maria T. Lindgren, Thijs J. G. Ettema, and Rolf Bernander A unique cell division machinery in the Archaea, PNAS, November 5, 2008 == Skulls Add to "Out of Africa" Theory of Human Origins Pattern of skull variation bolsters the case that humans took over from earlier species The shapes of skulls from around the world may have opened a new window onto the exodus of the first humans from Africa. According to a new report, groups of skulls from local populations are less diverse the farther those populations settled from the ancestral continent. The result supports the popular scientific theory that modern humans swept "out of Africa" some 50,000 years ago and supplanted earlier species such as Neandertals. It may also help researchers better pinpoint where in Africa modern humans came from and how messy the exodus could have been, says evolutionary geneticist William Amos of the University of Cambridge in England. Amos, Cambridge evolutionary biologist Andrea Manica and their colleagues analyzed shape data from 4,666 male skulls, all less than 2,000 years old, collected from 105 places around the world. For each location, they compared the variation in 37 different measurements with the distance the population's ancestors would have had to travel to get there from Africa. (Cairo and New York City appear relatively close on a map, but early humans would have had to hoof it across Asia and the Bering Strait to reach North America from Africa.) As smaller bands broke off from larger settlements, they would have carried with them a less diverse subset of the bigger group's genes, which partly translate into anatomical features such as skull shape. So the farther early Homo sapiens trod from their homeland, the less variable their skulls should become. Unless, that is, they bred with previously established populations of Neandertal or other early humans, which would have injected new genes and boosted variability. The researchers found no signs of interbreeding, they report online today in Nature. "What you find is a very nice linear decline of variability as you move farther away from Africa," Amos says. Prior studies had identified an identical trend in the diversity of simple genetic sequences or markers. "The beauty of the skulls," Amos says, "is there are so many of them and they come from populations that are not very well represented genetically," such as aboriginal Americans and Australians. He notes that additional skulls from African populations could help map early human migrations from or to Ethiopia, where the oldest known human remains originate. Physical anthropologist Erik Trinkaus of Washington University in St. Louis says few experts doubt the out-of-Africa scenario in broad terms. "The issue is how much modern humans spreading out of Africa after 50,000 years ago interbred with regional groups of archaic humans, where and when"something we may never know, he says. The new study, he contends, only "reinforce[s] the idea of a special isolation of modern humanity from anything less 'pure.'" Amos says that even very limited interbreeding would have disrupted the skull trend if the offspring had survived and propagatedalthough the extent of that limit has yet to be worked out. The big unknown, he says, is the messiness of the African exodus, including its timing among different groups. Mathematical models of migration could shed light on that problem, he says, adding that the skull data "open up lots of nice testable hypotheses." == Primates and birds separated about 280 million years ago. == Modern species of Latimeria are distinguishable from their extinct relatives, such that the closest affinities are no closer than the genus level. == Stuart Kauffman, a truly brilliant and dogged scientist, has a theory of "autocatalysis" that explains away the creationists' position that the emergence of life is too complicated to ever happen by random chance. John Holland provides a mathematical basis and creates computer models for self-emergent and self-organizing systems (including DNA). Christopher Langton is the founder of the "artificial life" branch of science, and Murray Gell-Mann is the Pulitzer-Prize-winning scientist who discovered quarks and now studies the complexities of fragile ecosystems such as the Brazilian rain forest. == Gould The modern theory of evolution does not require gradual change. It in fact, the operation of Darwinian processes should yield exactly what we see in the fossil record. It is gradualism that we must reject, not Darwinism. [] Eldredge and I believe that speciation is responsible for almost all evolutionary change. Moreover, the way in which it occurs virtually guarantees that sudden appearance and stasis shall dominate the fossil record. All major theories of speciation maintain that splitting takes place rapidly in very small populations. The theory of geographic, or allopatric, speciation is preferred by most evolutionists for most situations (allopatric means in another place). A new species can arise when a small segment of the ancestral population is isolated at the periphery of the ancestral range. Large, stable central populations exert a strong homogenizing influence. New and favorable mutations are diluted by the sheer bulk of the population through which they must spread. They may build slowly in frequency, but changing environments usually cancel their selective value long before they reach fixation. Thus, phyletic transformation in large populations should be very rare as the fossil record proclaims. But small, peripherally isolated groups are cut off from their parental stock. They live as tiny populations in geographic corners of the ancestral range. Selective pressures are usually intense because peripheries mark the edge of ecological tolerance for ancestral forms. Favorable variations spread quickly. Small peripheral isolates are a laboratory of evolutionary change. What should the fossil record include if most evolution occurs by speciation in peripheral isolates? Species should be static through their range because our fossils are the remains of large central populations. In any local area inhabited by ancestors, a descendant species should appear suddenly by migration from the peripheral region in which it evolved. In the peripheral region itself, we might find direct evidence of speciation, but such good fortune would be rare indeed because the event occurs so rapidly in such a small population. Thus, the fossil record is a faithful rendering of what evolutionary theory predicts, not a pitiful vestige of a once bountiful tale. "The Episodic Nature of Evolutionary Change," The Panda's Thumb, New York: W. W. Norton, 1980, pp. 182-184. == Simple Eyes Of Only Two Cells Guide Marine Zooplankton To The Light Larvae of marine invertebrates worms, sponges, jellyfish - have the simplest eyes that exist. They consist of no more than two cells: a photoreceptor cell and a pigment cell. These minimal eyes, called eyespots, resemble the 'proto-eyes' suggested by Charles Darwin as the first eyes to appear in animal evolution. They cannot form images but allow the animal to sense the direction of light. This ability is crucial for phototaxis the swimming towards light exhibited by many zooplankton larvae. Myriads of planktonic animals travel guided by light every day. Their movements drive the biggest transport of biomass on earth. "For a long time nobody knew how the animals do phototaxis with their simple eyes and nervous system," explains Detlev Arendt, whose team carried out the research at EMBL. "We assume that the first eyes in the animal kingdom evolved for exactly this purpose. Understanding phototaxis thus unravels the first steps of eye evolution." Studying the larvae of the marine ragworm Platynereis dumerilii, the scientists found that a nerve connects the photoreceptor cell of the eyespot and the cells that bring about the swimming motion of the larvae. The photoreceptor detects light and converts it into an electrical signal that travels down its neural projection, which makes a connection with a band of cells endowed with cilia. These cilia - thin, hair-like projections - beat to displace water and bring about movement. Shining light selectively on one eyespot changes the beating of the adjacent cilia. The resulting local changes in water flow are sufficient to alter the direction of swimming, computer simulations of larval swimming show. The second eyespot cell, the pigment cell, confers the directional sensitivity to light. It absorbs light and casts a shadow over the photoreceptor. The shape of this shadow varies according to the position of the light source and is communicated to the cilia through the signal of the photoreceptor. "Platynereis can be considered a living fossil," says Gaspar Jekely, former member of Arendt's lab who now heads a group at the MPI for Developmental Biology, "it still lives in the same environment as its ancestors millions of years ago and has preserved many ancestral features. Studying the eyespots of its larva is probably the closest we can get to figuring out what eyes looked like when they first evolved." It is likely that the close coupling of light sensor to cilia marks an important, early landmark in the evolution of animal eyes. Many contemporary marine invertebrates still employ the strategy for phototaxis. ------------------------------------------------------------------------ Journal reference: 1. Jekely et al. Mechanism of phototaxis in marine zooplankton. Nature, 2008; 456 (7220): 395 DOI: 10.1038/nature07590 == Pakicetids - clearly not whales http://en.wikipedia.org/wiki/Pakicetid Whales - clearly not pakicetids http://en.wikipedia.org/wiki/Whale Evolution from pakicetids to whales http://en.wikipedia.org/wiki/Whale_evolution == Woolly Mammoth Genome Sequence May Bring Beast Alive (Update1) The DNA of the extinct woolly mammoth, a relative of the elephant that roamed northern climes thousands of years ago, has been mostly deciphered in a scientific effort that could lead one day to recreating a live copy of the beast. About four-fifths of the extinct mammoth's DNA will be published tomorrow in the journal Nature, said Stephan Schuster, a professor of microbial ecology at Pennsylvania State University in University Park, who leads the project. The rest hasn't been analyzed because the creature's genome is longer than scientists had anticipated, he said. DNA is the chemical code for making organisms, and having the mammoth's genome might some day allow scientists to recreate it with sophisticated genetic techniques, Schuster said. The project has halted, however, because $1 million in funding has already been exhausted and animal's genome is at least one-third bigger than scientists thought it would be, he said. ``We hope that this study generates enough excitement to show that the project ought to be brought to a proper end,'' he said yesterday in a telephone interview. ``It's only a matter of money and time.'' The market for genetic analysis may grow as prices for equipment and supplies drop, and applications in research and medicine increase, analysts have said. Roche Holding AG, Illumina Inc., Helicos BioSciences Corp., and Danaher Corp. make systems to sequence DNA. Invitrogen Corp. is scheduled to complete its $6.7 billion purchase of sequencer maker Applied Biosystems Inc. Nov. 21. Invitrogen executives said in June that they made the offer because of the potential market for cheap genomic analysis. Resurrecting the Mammoth A full mammoth genome would raise the possibility of resurrecting the species through genetic experimentation, he said. That would involve making about 400,000 changes in 20,000 genes in a modern elephant's DNA, and implanting an altered embryo in an elephant to develop, he said. ``A lot of what would be needed is already on hand,'' Schuster said. ``There's only this gap in the knowledge of the mammoth genome that's missing.'' The human genome, which was fully decoded in 2003 in a $2.3 billion project, is made up 3 billion pairs of chemicals, called bases, that carry the instructions cells use to make proteins, tissues and organs. Scientists thought the elephant genome would be roughly the same size, Schuster said; they were wrong. Hair Better for DNA Analysis The woolly mammoth genome and that of the elephant are each about 4 billion base pairs long. The length of the genome has further complicated the project, which used DNA from mammoth hair rather than cells. The nuclei of the mammoth cells, which contain DNA, have been too badly degraded to use in the project, Schuster said. The findings, while partial, allow researchers to ```see' evolution of genes under selection in real time by accessing genetic information from historical and ancient samples,'' said Jeremy Austin, deputy director of the Australian Centre for Ancient DNA at the University of Adelaide, in a statement. A comparison with the modern elephants shows that the species evolved just half as quickly as large primates, which include gorillas, chimpanzees, and humans, Schuster said. ``Humans probably evolved faster because until about 100,000 years ago, they were prime prey for leopards, lions and tigers,'' he said. ``Elephants and mammoths didn't have to worry about getting chewed up by a big cat, and didn't have to change as quickly. == A brief encounter and life erupts Scientists have pinpointed the single event that led to our world of plants and animals Scientists have identified the single chance encounter about 1.9 billion years ago to which almost all life on Earth owes its existence. It saw an amoeba-like organism engulf a bacterium that had developed the power to use sunlight to break down water and liberate oxygen. The bacterium was probably intended as prey but instead it became incorporated into its attackers body turning it into the ancestor of every tree, flowering plant and seaweed on Earth. The encounter meant life on the planet could evolve from bacterial slime into the more complex forms we see today. That single event transformed the evolution of life on Earth, said Paul Falkowski, professor of biogeochemistry and bio-physics at Rutgers University in New Jersey. The descendants of that tiny organism transformed our atmosphere, filling it with the oxygen needed for animals and, eventually, humans to evolve. It had been thought such organisms emerged many times over on the early Earth, but the unique nature of the event has become clear from studies of chloroplasts, the bodies in plant cells that absorb sunlight and use its energy to generate nutrients and oxygen. They show that the genes within chloroplasts, and the proteins they produce, are so similar in all plants, ranging from tiny algae to oak trees, that they must all be the direct descendants of a single cell. It is an astonishing thought that a single random encounter between two tiny cells so long ago could have had such huge consequences, said Falkowski, who will describe the latest research to next months meeting of the American Geophysical Union. Falkowskis group at Rutgers is one of several around the world using powerful scientific tools such as DNA analysis to work out how life evolved after Earth was formed about 4.5 billion years ago. They have also refined methods for dating ancient rocks using radioactive isotopes. This method can show as well how much oxygen was in the atmosphere when the rocks were formed. Such evidence suggests primitive life emerged up to 3.5 billion years ago but only as bacterial-type organisms. Then, more than 2.2 billion years ago, one group, the cyanobacteria, evolved the ability to use sunlight to break down water, making nutrients and liberating oxygen. This event was a breakthrough, but cyanobacteria were inefficient, so oxygen levels in the air remained minimal. It took several hundred million more years before the chance encounter that would lead to flowering plants took place a hiatus showing how unlikely it was to happen at all. Nick Lane, a researcher at University College London and author of Oxygen: The Molecule that Made the World, said a picture of life evolving through a series of unique chance events was emerging. Oxygen energises all life, and makes it big, he said. Nothing else can provide the energy needed to fuel the demands of multicellular organisms. True photosynthesis evolved only once, and the chance encounter that gave rise to plants also happened just once. These were two freak accidents in the 3.5 billion-year history of life on Earth. As oxygen accumulated, he added, plants could grow ever larger. Animals evolved as these new food sources became available. One puzzle has been why oxygen accumulated in the air at all because plants are consumed by organisms that use oxygen to break them down. This should mean oxygen is used up as fast as it is generated. Falkowski suggests that, in reality, many plants never are consumed by other organisms and are instead permanently incorporated into rocks through geological processes. In the sea, dead marine phytoplankton sink to the bottom and become incorporated into sediments that turn into rocks such as chalk. The white cliffs of Dover are made of the compressed remains of trillions of such organisms. Falkowski calculates that in the past 2 billion years, about 15 billion billion tons of carbon has been removed from the atmosphere and locked into the Earths crust by such means. He said: The burial of large amounts of organic carbon by plants, especially over the past 750m years, caused a sharp rise in atmospheric oxygen, which almost certainly triggered the explosion of animal life seen since then. == A new Homo erectus fossil suggests that females had large, wide pelvises in order to deliver large-brained babies. Being born with a larger brain meant our ancestor became independent far more quickly than modern human infants. The new finding, published in Science magazine, conflicts with earlier ideas that suggest they had a tall, thin body shape adapted for running. Homo erectus is thought to be the first human-like creature to move out of Africa to colonise the world. The now extinct hominid species may also have been the first to control fire. Wide hips The near-complete 1.4 million-year-old female pelvis was found near Gona in northern Ethiopia. As it was pieced together, the archaeologists were struck by the unusual width of the pelvis. Scott Simpson, a palaeontologist from Case Western Reserve University in Cleveland, Ohio, US, was one of those who made the discovery. "Proportionally her hips are wider than those of modern humans," he says. The limiting factor on how large a brain a newborn may posess is how wide its mothers hips can be. Seems that nature couldn't figure out how to put poon ABOVE the pubic bone instead of between the legs in an upright-walking animal ... so I guess we've reached a sort of evolutionary impasse. The only way to birth bigger-brained babies is if women become nine feet tall ... or waddle slowly around on massive hips, looking like over-ripe pears with arms and legs. Yea, you could get away with it in 'civilized' conditions ... but 'civilization' comes and goes. Kinda hard to chase down a rabbit for dinner if you've got a 3-foot-wide pelvis ..... I guess we'll have to find ways to get more horsepower out of our existing brains if we're to solve our bigger problems. 'Nature' can't help us - so it's up to the neurochemists and genetic engineers from now on. The issue is that while an IQ equal to todays 300 might solve all kinds of current problems - would the extra smarts also be used to CAUSE even more problems ? Homo erectus didn't have to worry about global warming, balancing economies, nuclear proliferation, jammed freeways or video recorders that always blink "12:00" :-) == The kind of keratin-making genes that lead tomammalian hair are in common with birds and reptiles, implying that parts of hair-making capability occurred in an earlier common ancestor than previously thought. == The Wolf and Jackal can interbreed and produce fertile hybrid offspring, which are sometimes known as huskals and the resulting hybrid offspring is fertile - and can reproduce. == Evolution's new wrinkle Proteins with cruise control provide new perspective A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution. The research, which appears to offer evidence of a hidden mechanism guiding the way biological organisms respond to the forces of natural selection, provides a new perspective on evolution, the scientists said. The researchers -- Raj Chakrabarti, Herschel Rabitz, Stacey Springs and George McLendon -- made the discovery while carrying out experiments on proteins constituting the electron transport chain (ETC), a biochemical network essential for metabolism. A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order. "The discovery answers an age-old question that has puzzled biologists since the time of Darwin: How can organisms be so exquisitely complex, if evolution is completely random, operating like a 'blind watchmaker'?" said Chakrabarti, an associate research scholar in the Department of Chemistry at Princeton. "Our new theory extends Darwin's model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness." The work also confirms an idea first floated in an 1858 essay by Alfred Wallace, who along with Charles Darwin co-discovered the theory of evolution. Wallace had suspected that certain systems undergoing natural selection can adjust their evolutionary course in a manner "exactly like that of the centrifugal governor of the steam engine, which checks and corrects any irregularities almost before they become evident." In Wallace's time, the steam engine operating with a centrifugal governor was one of the only examples of what is now referred to as feedback control. Examples abound, however, in modern technology, including cruise control in autos and thermostats in homes and offices. The research, published in a recent edition of Physical Review Letters, provides corroborating data, Rabitz said, for Wallace's idea. "What we have found is that certain kinds of biological structures exist that are able to steer the process of evolution toward improved fitness," said Rabitz, the Charles Phelps Smyth '16 Professor of Chemistry. "The data just jumps off the page and implies we all have this wonderful piece of machinery inside that's responding optimally to evolutionary pressure." The authors sought to identify the underlying cause for this self-correcting behavior in the observed protein chains. Standard evolutionary theory offered no clues. Applying the concepts of control theory, a body of knowledge that deals with the behavior of dynamical systems, the researchers concluded that this self-correcting behavior could only be possible if, during the early stages of evolution, the proteins had developed a self-regulating mechanism, analogous to a car's cruise control or a home's thermostat, allowing them to fine-tune and control their subsequent evolution. The scientists are working on formulating a new general theory based on this finding they are calling "evolutionary control." The work is likely to provoke a considerable amount of thinking, according to Charles Smith, a historian of science at Western Kentucky University. "Systems thinking in evolutionary studies perhaps began with Alfred Wallace's likening of the action of natural selection to the governor on a steam engine --- that is, as a mechanism for removing the unfit and thereby keeping populations 'up to snuff' as environmental actors," Smith said. "Wallace never really came to grips with the positive feedback part of the cycle, however, and it is instructive that through optimal control theory Chakrabarti et al. can now suggest a coupling of causalities at the molecular level that extends Wallace's systems-oriented approach to this arena." Evolution, the central theory of modern biology, is regarded as a gradual change in the genetic makeup of a population over time. It is a continuing process of change, forced by what Wallace and Darwin, his more famous colleague, called "natural selection." In this process, species evolve because of random mutations and selection by environmental stresses. Unlike Darwin, Wallace conjectured that species themselves may develop the capacity to respond optimally to evolutionary stresses. Until this work, evidence for the conjecture was lacking. The experiments, conducted in Princeton's Frick Laboratory, focused on a complex of proteins located in the mitochondria, the powerhouses of the cell. A chain of proteins, forming a type of bucket brigade, ferries high-energy electrons across the mitrochondrial membrane. This metabolic process creates ATP, the energy currency of life. Various researchers working over the past decade, including some at Princeton like George McClendon, now at Duke University, and Stacey Springs, now at the Massachusetts Institute of Technology, fleshed out the workings of these proteins, finding that they were often turned on to the "maximum" position, operating at full tilt, or at the lowest possible energy level. Chakrabarti and Rabitz analyzed these observations of the proteins' behavior from a mathematical standpoint, concluding that it would be statistically impossible for this self-correcting behavior to be random, and demonstrating that the observed result is precisely that predicted by the equations of control theory. By operating only at extremes, referred to in control theory as "bang-bang extremization," the proteins were exhibiting behavior consistent with a system managing itself optimally under evolution. "In this paper, we present what is ostensibly the first quantitative experimental evidence, since Wallace's original proposal, that nature employs evolutionary control strategies to maximize the fitness of biological networks," Chakrabarti said. "Control theory offers a direct explanation for an otherwise perplexing observation and indicates that evolution is operating according to principles that every engineer knows." The scientists do not know how the cellular machinery guiding this process may have originated, but they emphatically said it does not buttress the case for intelligent design, a controversial notion that posits the existence of a creator responsible for complexity in nature. Chakrabarti said that one of the aims of modern evolutionary theory is to identify principles of self-organization that can accelerate the generation of complex biological structures. "Such principles are fully consistent with the principles of natural selection. Biological change is always driven by random mutation and selection, but at certain pivotal junctures in evolutionary history, such random processes can create structures capable of steering subsequent evolution toward greater sophistication and complexity." The researchers are continuing their analysis, looking for parallel situations in other biological systems. == "No mutation that increases genetic information has ever been discovered." It is hard to define what one should understand by "increase" of genetic information in this case but we know that many new Hox genes evolved via gene duplication and this clearly represents "increase" of genetic information. Neutral mutation may change the genetic information without increasing it (when a neutral base substitution occurs). Mutations have occurred, e.g. in the HoxC-8 gene enhancers of mice when compared with those of whales and chicks but no one has shown that these mutations may be responsible for the drastic changes in their body plans. Amoeba dubia has genes and the volume of information in its DNA is more than 200 times larger than our human genome (it contains 670,000,000,000 base pairs). A sponge, the simplest of all living animals, has more than twice the number of genes humans have. Our human genome, from the view of the genetic information content is comparable to one of the simplest known worms, Cenorhabditis elegans. One should know that while variation in the shape and size of beaks in Darwin's finches is not related to changes in genetic information, it DEMONSTRABLY, and hence CERTAINLY, depends on inherited changes in the epigenetic information determining changes in the expression patterns of genes, especially of BMP (BMP4 and to a lesser extent genes BMP2 and BMP7) and calmodulin genes. By changing the patern of expression of these genes, Abzhanov et al. (2006) have succeeded in manipulating the shape and size of the beak in Darwin's finches so that produce beaks resembling those of other species in nature. Extensive experimental evidence on the evolution of animals based on changes in epigenetic information, without changes in genes, is provided in chapters 14 through 20 of the Epigenetic Principles of Evolution (2008) but most of that evidence can be read in my website epigeneticscomesofage.com The creationist speculations that mutational evidence of the above type "refutes evolutionary theory" have been favored by the fact that many biologists still are reluctant to recognize the role of the epigenetic information, in determining the evolution of the living world without changes in gens (mutations). == Evolution has been a part of official Catholic theological teaching since 1950 (Pius XII "Humani Generis") == Certainly viruses can insert there own DNA into the host. And I assume that occasionally a phagocyte incorporates its victim's DNA (or part of that) into its own. Prokaryotes can share DNA. Bacteria can take DNA up from the environment and stuff it into their genomes. Look up antibiotic resistance to get a bunch of papers about horizontal transfer of resistance genes. Eukaryotes sometimes take up symbiotes. Mitochondria and chloroplasts are ancient examples of this and a lot of their DNA got transferred to the eukaryote's genome. More recently some eukaryotic algae have become chloroplast like oganelles. I wouldn't doubt that some of their DNA got transferred to their host. There are fragments of mitochondrial genomes in your genomic DNA. They are called pseudogenes, but they are bits of mitochondrial DNA that was transferred into the nucleus recently enough to tell that it is mitochondrial sequence. Eukaryotic cells can still take up DNA and get it into the nucleus (very low frequency event). We also find foreign DNA circulating in our blood. It probably enters through wounds or breaks in your intestines. This DNA probably has a small chance of incorporating into one of your body cells, but unless it turned cancerous and we got a population of cells to study or somehow got into a germ cell we would probably not detect it. And, because speciation is often a process rather than an event, there can be degrees of separation and gene flow between populations that meet some or all of the species definitions. For example, in wild sunflowers, there are two species that form a hybrid which is optimal in the environment between the two environments that are optimal for the two species. Although the interspecies hybrid is *largely* sterile (like a mule) there is *some* gene flow between the species.- I keep waiting for someone to do the analysis of the horse and donkey mitochondrial DNA and genomic DNA. Years ago there was evidence that the two didn't seem to tell the same story. The nuclear genes and pseudogenes that were sequenced between the two indicated just as great or greater difference between horse and donkey than between humans and chimps, but the mitochondrial sequence indicated a much more recent separation between the horse and donkey than between humans and chimps. This seems to be a case of horizontal transmission of the mitochondrial genome without significant transfer of nuclear encoded genes. We can see how this could happen by looking at the rare offspring of mules. They would have their mule mothers mitochondrial sequence, but if the cross was back to a donkey the viable offspring have the full donkey chromosome set. Hinnies bred back to a horse could have the full horse chromosome set with a donkey mitochondrial genome. The chromosomes are so mixed up with multiple translocations and other chromosomal mutations not just the difference in chromosome number that the chromosomes do not pair properly and the most likely viable embryo would have a full set of one species or the other. == Octopuses share 'living ancestor' Many of the world's deep-sea octopuses evolved from a common ancestor that still exists in the icy waters of the Southern Ocean, a study has shown. "Megaleledone setebos, a shallow-water circum-Antarctic species endemic to the Southern Ocean. It is the closest living relative to the clade of deep-sea octopuses. The specimen shown is a juvenile; adults reach a total length of nearly 1 metre. " == Scientists estimate there are at least 1 million species of marine organisms on Earth. But as of now, only about 230,000 are known. == Geneticists Lynn Jorde and Henry Harpending of the University of Utah propose that the variation in human DNA is minute compared to that of other species. They also propose that during the Late Pleistocene, the human population was reduced to a small number of breeding pairs a no more than 10,000, and possibly as few as 1,000 a resulting in a very small residual gene pool. Various reasons for this hypothetical bottleneck have been postulated, one being the Toba catastrophe theory. == There are 5000 lizard species. There are 1000 rat species. == DNA Chunks, Chimps And Humans: Marks Of Differences Between Human And Chimp Genomes Researchers have carried out the largest study of differences between human and chimpanzee genomes, identifying regions that have been duplicated or lost during evolution of the two lineages. The study, published in Genome Research, is the first to compare many human and chimpanzee genomes in the same fashion. The team show that particular types of genes - such as those involved in the inflammatory response and in control of cell proliferation - are more commonly involved in gain or loss. They also provide new evidence for a gene that has been associated with susceptibility to infection by HIV. "This is the first study of this scale, comparing directly the genomes of many humans and chimpanzees," says Dr Richard Redon, from the Wellcome Trust Sanger Institute, a leading author of the study. "By looking at only one 'reference' sequence for human or chimpanzee, as has been done previously, it is not possible to tell which differences occur only among individual chimpanzees or humans and which are differences between the two species. "This is our first view of those two important legacies of evolution." Rather than examining single-letter differences in the genomes (so-called SNPs), the researchers looked at copy number variation (CNV) - the gain or loss of regions of DNA. CNVs can affect many genes at once and their significance has only been fully appreciated within the last two years. The team looked at genomes of 30 chimpanzees and 30 humans: a direct comparison of this scale or type has not been carried out before. The comparison uncovered CNVs that are present in both species as well as copy number differences (CNDs) between the two species. CNDs are likely to include genes that have influenced evolution of each species since humans and chimpanzees diverged some six million years ago. "Broadly, the two genomes have similar patterns and levels of CNVs - around 70-80 in each individual - of which nearly half occur in the same regions of the two species' genomes," continues Dr Redon. "But beyond that similarity we were able to find intriguing evidence for key sets of genes that differ between us and our nearest relative." One of the genes affected by CNVs is CCL3L1, for which lower copy numbers in humans have been associated with increased susceptibility to HIV infection. Remarkably, the study of 60 human and chimpanzee genomes found no evidence for fixed CNDs between human and chimp and no within-chimp CNV. Rather, they found that a nearby gene called TBC1D3 was reduced in number in chimpanzee compared to human: typically, there were eight copies in human, but apparently only one in all chimpanzees. The authors suggest that it might be evolutionary selection of CNDs in TBC1D3 that have driven the population differences. Consistent with this novel observation, TBC1D3 is involved in cell proliferation (favoured category) and is on a core region for duplication - a focal point for large regions of duplication in human genome. "It is evident that there has been striking turnover in gene content between humans and chimpanzees, and some of these changes may have resulted from exceptional selection pressures," explains Dr George Perry from Arizona State University and Brigham and Women's Hospital, another leading author of the study. "For example, a surprisingly high number of genes involved in the inflammatory response - APOL1, APOL4, CARD18, IL1F7, IL1F8 - are completely deleted from chimp genome. In humans, APOL1 is involved in resistance to the parasite that causes sleeping sickness, while IL1F7 and CARD18 play a role in regulating inflammation: therefore, there must be different regulations of these processes in chimpanzees. "We already know that inactivation of an immune system gene from the human genome is being positively selected: now we have an example of similar consequences in the chimpanzee." CNVs in humans and chimpanzees often occur in equivalent genomic locations: most lie in regions of the genomes, called segmental duplications, that are particularly 'fragile'. However, one in four of the 355 CNDs that the team found do not overlap with CNVs within either species - suggesting that they are variants that are 'fixed' in each species and might mark significant differences between human and chimpanzee genomes. DNA Samples and analysis The project used DNA samples from 30 chimpanzees (29 from W Africa, one from E Africa): the chimpanzee reference was produced using DNA from Clint, the chimpanzee whose DNA was used for the genome sequence. Human DNA samples were obtained from following participants: ten Yoruba (Ibadan, Nigeria), ten Biaka rainforest hunter-gatherers (Central African Republic) and ten Mbuti rainforest hunter-gatherers (Democratic Republic of Congo). The human reference is a European-American male from the HapMap Project (NA10852). CNVs and CNDs were detected using a whole-genome tilepath of DNA clones spanning the human genome used previously to map human CNVs: this platform can reveal structural variants greater than around 10,000 base-pairs in size. This work was funded by the Wellcome Trust, the LSB Leakey Foundation, the Wenner-Gren Foundation for Anthropological Research, the National Institutes of Health, The University of Louisiana at Lafayette-New Iberia Research Center and the Howard Hughes Medical Institute. The authors thank the Human Genome Diversity Project, the Coriell Institute for Medical Research, the Integrated Primate Biomaterials and Information Resource, New Iberia Research Center, and the Primate Foundation of Arizona for samples. ------------------------------------------------------------------------ Journal references: 1. The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 2005; 437 (7055): 69 DOI: 10.1038/nature04072 2. Perry et al. Copy number variation and evolution in humans and chimpanzees. Genome Research, 2008; 18 (11): 1698 DOI: 10.1101/gr.082016.108 == Junk' DNA proves functional Singapore - In a paper published in Genome Research on Tuesday, scientists at the Genome Institute of Singapore (GIS) report that what was previously believed to be "junk" DNA is one of the important ingredients distinguishing humans from other species. More than 50% of human DNA has been referred to as "junk" because it consists of copies of nearly identical sequences. A major source of these repeats is internal viruses that have inserted themselves throughout the genome at various times during mammalian evolution. Using the latest sequencing technologies, GIS researchers showed that many transcription factors, the master proteins that control the expression of other genes, bind specific repeat elements. The researchers showed that from 18 to 33% of the binding sites of five key transcription factors with important roles in cancer and stem cell biology are embedded in distinctive repeat families. Major driver for evolution Over evolutionary time, these repeats were dispersed within different species, creating new regulatory sites throughout these genomes. Thus, the set of genes controlled by these transcription factors is likely to significantly differ from species to species and may be a major driver for evolution. This research also shows that these repeats are anything but "junk DNA", since they provide a great source of evolutionary variability and might hold the key to some of the important physical differences that distinguish humans from all other species. The GIS study also highlighted the functional importance of portions of the genome that are rich in repetitive sequences. "Because a lot of the biomedical research use model organisms such as mice and primates, it is important to have a detailed understanding of the differences between these model organisms and humans in order to explain our findings," said Guillaume Bourque, PhD, GIS Senior Group Leader and lead author of the Genome Research paper. Understanding of diseases "Our research findings imply that these surveys must also include repeats, as they are likely to be the source of important differences between model organisms and humans," added Dr Bourque. "The better our understanding of the particularities of the human genome, the better our understanding will be of diseases and their treatments." "The findings by Dr Bourque and his colleagues at the GIS are very exciting and represent what may be one of the major discoveries in the biology of evolution and gene regulation of the decade," said Raymond White, PhD, Rudi Schmid Distinguished Professor at the Department of Neurology at the University of California, San Francisco, and chair of the GIS Scientific Advisory Board. "We have suspected for some time that one of the major ways species differ from one another - for instance, why rats differ from monkeys - is in the regulation of the expression of their genes: where are the genes expressed in the body, when during development, and how much do they respond to environmental stimuli," he added. "What the researchers have demonstrated is that DNA segments carrying binding sites for regulatory proteins can, at times, be explosively distributed to new sites around the genome, possibly altering the activities of genes near where they locate. Gene regulatory DNA sequences "The means of distribution seem to be a class of genetic components called 'transposable elements' that are able to jump from one site to another at certain times in the history of the organism. "The families of these transposable elements vary from species to species, as do the distributed DNA segments which bind the regulatory proteins." White also added, "This hypothesis for formation of new species through episodic distributions of families of gene regulatory DNA sequences is a powerful one that will now guide a wealth of experiments to determine the functional relationships of these regulatory DNA sequences to the genes that are near their landing sites. "I anticipate that as our knowledge of these events grows, we will begin to understand much more how and why the rat differs so dramatically from the monkey, even though they share essentially the same complement of genes and proteins." == Dawkins says Darwin was actually experimenting with sweet peas, and came within a hairs bredth of independently discovering Mendelian genetics. == WELLINGTON, New Zealand A rare reptile with lineage dating back to the dinosaur age has been found nesting on the New Zealand mainland for the first time in about 200 years, officials said Friday. Four leathery, white eggs from an indigenous tuatara were found by staff at the Karori Wildlife Sanctuary in the capital, Wellington, during routine maintenance work Friday, conservation manager Rouen Epson said. "The nest was uncovered by accident and is the first concrete proof we have that our tuatara are breeding," Epson said. "It suggests that there may be other nests in the sanctuary we don't know of." Tuatara, dragon-like reptiles that grow to up to 32 inches, are the last descendants of a species that walked the earth with the dinosaurs 225 million years ago, zoologists say. They have unique characteristics, such as two rows of top teeth closing over one row at the bottom. They also have a pronounced parietal eye, a light-sensitive pineal gland on the top of the skull. This white patch of skin called its "third eye" slowly disappears as they mature. A native species to New Zealand, tuatara were nearly extinct on the country's three main islands by the late 1700s due to the introduction of predators such as rats. They still live in the wild on 32 small offshore islands cleared of predators. A population of 70 tuatara was established at the Karori Sanctuary in 2005. Another 130 were released in the sanctuary in 2007. The sanctuary, a 620-acre wilderness minutes from downtown Wellington, was established to breed native birds, insects and other creatures securely behind a predator-proof fence. Empson said that the four eggs the size of pingpong balls were unearthed Friday but that there were likely more because the average nest contains around ten eggs. The eggs were immediately covered up again to avoid disturbing incubation. If all goes well, juvenile tuatara could hatch any time between now and March, she said. == There are 15,000 known species of trilobites. == http://www.gate.net/~rwms/hum_ape_chrom.html ape human chromosomes == Part of the problem seems to be that you imagine that species are hard & fast, discrete categories. They're not. Related sexual organisms do eventually reach a point at which they can no longer produce fertile offspring upon breeding, but there are often many intermediate subspecies. Many instances of ring species have been posted here. My example was zebras. The most northerly subspecies can interbreed freely with the next most northerly, & so on until you reach the most southerly subspecies, but the most northern & most southern subspecies do not reliably produce fertile offspring. In effect, all species are ring species, but usually with the intermediates extinct, as is the case with humans & chimps, for instance. == As far as biologists are concerned, there is no difference btw micro- & macro-evolution except time. To them the terms aren't very useful or meaningful. They're both the same process. You can see species & genera evolve all the time, but it's rarer in a human lifetime to witness evolution of new orders & classes of living organisms. To creationists, though, the terms mean something entirely different. And wrong. They deny that "macroevolution" exists, although of course they can't tell you what a "kind" is or what genetic barriers could possibly keep one "kind" from evolving into another, as is plainly visible in the fossil record, from comparative anatomy, in the genomes of all living things & from all the other evidence in the world. == When elpistostegalian fish developed digits, they didn't immediately become a new class of animal. Although existing sarcopterygian fish & tetrapods are considered separate classes now, thanks to accumulated differences & 400 million years of reproductive separation, they share common ancestors back in the Early Devonian. == Evolution proceeds by different processes at different rates, but there are limits to the changes these processes can achieve in a single generation or short period of time. Over longer periods, much greater degrees of change can occur, as genetic difference between reproductively isolated populations, species, genera, families, orders & classes accumulate. == Fungi. The world depends on fungi, because they are major players in the cycling of materials and energy around the world. They're necessary for the health of other organisms. Some 60,000 species are known, and it's been estimated by experts that more than 1.5 million exist. == http://en.wikipedia.org/wiki/Haploid#Haploid_%20and_monoploid http://www.polyploidy.org/index.php/Parade_of_Polyploids A frog species in the genus Xenopus arose from polyploidy, rare in animals. == The genomes humans and chimps are only 1.4% different. == The major functional difference between the large amphibians (tetrapods) of the Early Carboniferous Period (Mississippian Epoch, c. 359 to 318 mya) & the first little reptiles in the Late Carboniferous (Pennsylvannian Epoch, c. 318 to 299 mya) is the amniotic egg, which freed reptiles from reliance on water for reproduction. Additional differences include further adaptations to life on land such as stronger legs & girdles (shoulder & pelvis), different vertebrae & more powerful jaw muscles. Following are some stages in the evolution of big amphibians into the first reptiles. Labyrinthodont means "maze-tooth" & refers to the tetrapods showing this feature. The astragalus is a bone in the ankle joint. Ancestral tetrapods had rachitomous vertebrae, which are complex & composed of a number of elements. More derived tetrapods & reptiles evolved "gastrocentrous" vertebrae. Sarcopterygian refers to the class of fish from which tetrapods evolved, the lobe-fins. http://www.palaeos. com/Vertebrates/ Units/190Reptilo morpha/190. 100.html 1. Anthracosaur ("Coal Lizard") stage: Proterogyrinus or another early anthracosaur (late Mississippian) -- Classic labyrinthodont- amphibian skull & teeth, but with reptilian vertebrae, pelvis, humerus & digits. Still has fish skull hinge. Amphibian ankle. Five-toed hand & a 2-3-4-5-3 (almost reptilian) phalangeal count. http://en.wikipedia .org/wiki/ Anthracosaur 2. Derived Anthracosaur stage: Limnoscelis, Tseajaia (late Carboniferous) -- Amphibians apparently derived from the early anthracosaurs, but with additional reptilian features: structure of braincase, reptilian jaw muscle, expanded neural arches. 3. Proto-cotylosaur stage: Solenodonsaurus (mid-Pennsylvanian) -- An incomplete fossil, apparently between the anthracosaurs & the cotylosaurs. Loss of palatal fangs, loss of lateral line on head, etc. Still just a single sacral vertebra, though. 4. Protorothyrid stage: Hylonomus, Paleothyris (early Pennsylvanian) -- These are protorothyrids, very early cotylosaurs (primitive reptiles). They were quite little, lizard-sized animals with amphibian-like skulls (amphibian pineal opening, dermal bone, etc.), shoulder, pelvis, & limbs, & intermediate teeth & vertebrae. Rest of skeleton reptilian, with reptilian jaw muscle, no palatal fangs & spool-shaped vertebral centra. Probably no eardrum yet. Many of these new "reptilian" features are also seen in little amphibians living today (which also sometimes have direct-developing eggs laid on land), so perhaps these traits just came along with the small body size of the first reptiles. Note that the environment of Pennsylvannian proto-reptiles, the swamps that became coal fields, was similar to the moist tropical forests in which some small amphibians today lay their eggs on land, sometimes encased in foam, much as reptilian eggs are encased in a shell. whether rubbery, leathery or hard (calcareous) . Monotreme mammal eggs are also soft, like most reptiles' (although not archosaurs, ie crocs & birds). The small (~20 cm with tail), lizard-like reptile Hylonomus lived 315 mya. Though discovered in Canada in 1852 by pioneering geologists Lyell & Dawson, it remains the earliest confirmed reptile (Westlothiana from Scotland is older but may be an amphibian). It had small sharp teeth & probably ate little invertebrates, such as millipedes or early insects, many of which were then larger than now. Fossils of Hylonomus occur in the remains of fossilized tree stumps in Joggins, Nova Scotia. It's thought that after harsh weather, the tree tops would crash down & the stumps became hollowed out due to rot. Hylonomus individuals seeking shelter would enter but get trapped, starving to death. http://en.wikipedia .org/wiki/ Hylonomus Early amniotes promptly diverged into synapsids, the line leading to mammals, & diapsids, the line leading to lizards, snakes, crocs & birds. Already alongside Hylonomus, a precursor of later reptiles, have been found fossils of the basal pelycosaur Archaeothyris (a synapsid) & the basal diapsid Petrolacosaurus. As noted, the most important change from amphibian to reptile is the development of the amniotic egg. It is not hard to see how this developed, since there is a smooth gradient in nature between being completely submersed in water & being bone-dry --- for example, the eggs of turtles, which are leathery rather than hard-shelled, are laid in damp sand at the shoreline. It is trivial to observe that if eggs are at risk of drying out, characteristics which make them less likely to do so will, other things equal, be selected for. The changes in the bony anatomy during the same period reflect the necessities of a life spent more on land (hence the fusion of bones to produce the astragalus, for example) & less time in the water (hence the loss of the lateral line). Some of these changes are tabulated below (hope the table comes through; if not, see link): http://skepticwiki. org/index. php/Intermediate _Forms_Between_ Classes Evolutionary Stage | Early Amphibians | Anthracosaurs | Palaeothyris | Modern Reptiles---- --------- --------- --------- --------- --------- -------(eg Proterogyrinus) Vertebrae Rachitomous Gastrocentrous Gastrocentrous Gastrocentrous Contact between dental and parietal No Yes Yes Yes Intertemporal Yes Yes No No Otic notch Yes Yes No No Mesotarsal No No Yes Yes Astralagus No No Yes Yes Lateral line Yes Yes No No Sarcopterygian skull hinge Yes Yes No No Sphenethmoid Yes Yes No No Sacral vertebrae 1 1 2 2-3 Stapes Massive Massive Slender Slender Teeth Labyrinthodont Labyrinthodont Intermediate Reptilian Pineal opening Yes Yes Yes No Eardrum No No No Yes == The First Living Systems: a Bioenergetic Perspective, MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, June 1997, p. 239-261) (The enigma of the origin of life and its timing, Microbiology (2002), 148, 21-27), Getting All Turned Around Over The Origins of LIfe on Earth, Science Vol 267, p. 1265) == Triticale is the cross of wheat (genus Triticum) with rye (genus Secale). New species & genera can appear in a single generation or two as a result of polyploidy. This is more common in plants, but also happens in fungi & animals. http://www.polyploi dy.org/index. php/Parade_ of_Polyploids == The chimp 2p and 2q chromosomes are found welded end-to-end in the human genome, with telomeres (normally found only at chromosome ends) right at the join. Such fusions are rare but have been observed in nature. == Whiptail lizards can't produce any fertile eggs unless they engage in sexual intercours ince there are only females in the species and no males. == The key development in reptile evolution was the amniotic egg, which freed land vertebrates from reliance on water for reproduction. Our skeletons, skin & other features also became better adapted to life on land. Even today there are small amphibians who are able to lay their eggs not in water but in moist tropical rain forests (jungles), & there are reptiles, like sea turtles, who lay leathery eggs in wet sand, so that a continuum exists between shell-less eggs in water & dry shelled eggs on land. The fossil record, biochemistry, embryology, genetics & every other area of study plainly show that fish evolved into tetrapods (land vertebrates) , that tetrapods evolved into amniotes (reptiles), that amniotes evolved into diapsids & synapsids, that diapsids evolved into lepidosaurs (including lizards & snakes) & archosaurs, that archosaurs evolved into crocodilians & birds & that synapsids evolved into mammals. == Nearly half of human DNA consists of repetitive DNA, including transposons, which can "transpose" or move around to different positions within the genome. A type of transposon called retrotransposons are transcribed into RNA and then reintegrated into the genomic DNA. The most common form of retrotransposons in the human genome are Alu elements, which have more than one million copies and occupy approximately 10 percent of the human genome. "Alu elements are a major source of new exons. Because Alu is a primate-specific retrotransposon, creation of new exons from Alu may contribute to unique traits of primates, so we want to better understand this process," said the study's senior author Yi Xing, Ph.D., assistant professor of internal medicine and biomedical engineering, who holds a joint appointment in the University of Iowa Carver College of Medicine and the UI College of Engineering. To study the impact of Alu-derived exons on human gene expression, the researchers used a high-density exon microarray. The technology has nearly six million probes for monitoring the expression patterns of all human exons. Using data generated by these microarrays, the scientists analyzed 330 Alu-derived exons in 11 human tissues. The team then identified a number of exons with interesting expression and functional characteristics. "Hundreds of exons in the human genome were created from Alu elements. The whole-genome exon microarray allowed us to quickly identify exons that most likely contribute to the regulation of gene expression and function," said Lan Lin, Ph.D., University of Iowa postdoctoral fellow in internal medicine and the lead author of this study. Analysis of one human gene, SEPN1, which is known to be involved in a type of muscular dystrophy, along with comparative data from chimpanzee and macaque tissues, suggested that the presence of a muscle-specific Alu-derived exon resulted from a human-specific change that occurred after humans and chimpanzees diverged evolutionarily. "In this case, this exon is only expressed at a high level in the human muscle but not in any other human or non-human primate tissue, so this implies that the exon plays a functional role in muscle, and this role is human-specific, " said Xing, who is also affiliated with University of Iowa Center for Bioinformatics and Computational Biology. == http://www.newscientist.com/channel/life/dn13620?DCMP=NLC-nletter&nsref=dn13620 evolution misconceptions == Rats have evolved into over 50 species and have been around for about 1.8 million years, == http://evolution.berkeley.edu/evolibrary/misconceptions faq.php#b6 http://www.pbs.org/wgbh/evolution/sex/guppy/low bandwidth.html http://evolution.berkeley.edu/evolibrary/article/lines 01 http://talkorigins.org/faqs/comdesc/ http://www.ecologyconnections.ca/evoresearch.php Eusthenopteron. Panderichtys. Tiktalik. Elginerpeton. Acanthostega. Ventastega. Icthyostega. Hynerpeton. Tulerpeton. == Ancient Fish Heads for Land Scientists are learning more about how some fish became landlubbers. According to a new study of a "missing link" fossil presented here yesterday at the annual meeting of the Society of Vertebrate Paleontology, these adventurous swimmers were already losing their ability to feed by suction before their fins evolved into limbs. By giving up the skill, which involves deforming the skull to create a vacuum that draws in prey, the fish were more able to raise their heads out of the water--and breathe air. The missing link, a meter-long predator known as Tiktaalik roseae, was discovered in sandstone in northern Canada in 2004. Like all fishes, it had fins and scales. But in other aspects of its anatomy, it resembled four-limbed animals called tetrapods (Science, 7 April 2006, p. 33). Tiktaalik had a neck, for example, and a relatively flat, elongated skull. It also lacked another classic fish feature, the gill-covering bone called the operculum. Details of the braincase, which in fish consists of a set of bones nestled inside the skull, remained hidden inside the rock, however, and preparators spent years carefully exposing the bones. Now an analysis by paleontologist Jason Downs of the Academy of Natural Sciences in Philadelphia, Pennsylvania, and colleagues shows how the braincase was becoming more like that of tetrapods. Overall, the braincase was more rigid, Downs says. Fish have very flexible skulls, a loose collection of bones that move around easily and allow them to suction-feed. In Tiktaalik, the joints between various bones in the braincase are more complex, suggesting that they did not allow as much motion. Another important transition is evident in Tiktaalik's hyomandibular bone, which is essential for gill breathing. In fish, this bone coordinates the motions of the braincase, the palate, and the gill skeleton. But in tetrapods, the bone has lost these connections and shrunk, becoming part of the middle ear. Primitive fish have a boomerang-shaped hyomandibular bone, but Tiktaalik's is shorter and straight--tending toward the tiny dimensions of primitive tetrapods. It is connected to the braincase but not to the gill skeleton, which would have allowed the head more flexibility to move up and down. The braincase is also described by the same authors today in Nature. The change in the hyomandibular bone suggests that gill respiration was becoming less important for Tiktaalik, says paleontologist Jennifer Clack of the University of Cambridge in the United Kingdom. She notes that all the modifications point in one direction: an animal that it getting better and better at raising its head out of shallow water to breathe air. Rather than a big transition in the braincase, as it had seemed before from other species, Tiktaalik shows how the evolution of the tetrapod braincase is "actually achievable by small, gradual steps," Clack says. == Humble beginnings. An experiment in the 1950s with primordial gases and sparks produced some of life's building blocks. Did Volcanoes Spark Life on Earth? A once-discarded idea about how life started on our planet has been given a new life of its own, thanks to a serendipitous find. The story traces back to the early 1950s, when chemists Stanley Miller and Harold Urey of the University of Chicago in Illinois tried to recreate the building blocks of life under conditions they thought resembled those on the young Earth. The duo filled a closed loop of glass chambers and tubes with water and different mixes of hydrogen, ammonia, and methane--gases presumed at the time to be the main constituents of the atmosphere billions of years ago. Then, in an attempt to confirm a hypothesis that lightning may have triggered the origin of life, they zapped the mixture with an electrical current. The researchers then analyzed the gunk that began to collect after a few hours. The residue contained traces of some of the amino acids that make up proteins. Their presence suggested that the molecular precursors of life could form through a simple electrochemical process. The problem was that theoretical models and analyses of ancient rocks eventually convinced scientists that Earth's earliest atmosphere was not rich in hydrogen. Last year, after Miller's death, two of his former graduate students--geochemists Jim Cleaves of the Carnegie Institution of Washington (CIW) in Washington, D.C., and Jeffrey Bada of Indiana University, Bloomington--were examining samples left in their mentor's lab. They discovered the vials of products from the original experiment and decided to take a second look with updated technology. Using extremely sensitive mass spectrometers at NASA's Goddard Space Flight Center in Greenbelt, Maryland, Cleaves, Bada, and colleagues found traces of 22 amino acids in the experimental residues. That is about double the number originally reported by Miller and Urey and includes all of the 20 amino acids found in living things, the scientists report tomorrow in Science. So could lightning have helped jump-start life on Earth? Possibly, Cleaves says. Although Earth's primordial atmosphere was not hydrogen-rich, as were the chambers in the Miller-Urey experiment, gas clouds from volcanic eruptions did contain the right combination of molecules. It is possible that volcanoes, which were much more active early in Earth's history, seeded our planet with life's ingredients. The big question is what happened next--how did those molecules turn into self-replicating organic compounds? "That's the frontier," Cleaves says, "and we're sort of stuck there." The new study "highlights how easy it is to make the building blocks of life in plausible prebiotic conditions," says geochemist Robert Hazen of CIW, who was not involved in the research. At the same time, he says, the findings reinforce "the pioneering insight and experiments of Stanley Miller and Harold Urey." == Some flirtatious yeast cells have confirmed a part of Charles Darwins theory of evolution that was never tested as successfully as the rest of the theory, biologists say.This somewhat special part of the theory is the concept of evolution through sexual selection.In general, evolutionary theory holds that species gradually change because of certain mutations that spread through their populations. These mutations spread if, and only if, theyre beneficialso that individuals possessing them survive longer, reproduce more or both. Thus the mutated trait appears increasingly often in succeeding generations.Evolution has been observed in action numerous times, because in short-lived species, many forms of evolution occur fast enough for humans to watch the changes occur.But one form of evolution has not been directly seen: evolution through sexual selection, notes a paper in the Oct. 7 online issue of the research journal Proceedings of the Royal Society B. This variety of evolution is what biologists believe accounts for the appearance of sexual-advertising traits such as a peacocks bright tail, or perhaps musical ability.Such traits are believed to evolve for much the same reason as others: those who have a certain characteristic mate more, and thus spread the genes for that feature. The chief difference between this form of evolution and others is that with sexual selection, the driving factor in the process is sexual competition, rather than other exigencies of survival more generally.Sexual selection is an intriguing aspect of evolution because it drives the evolution of traits that on their face, would seem less than beneficial, said Duncan Greig of University College in London, one of the papers authors.For example a peacocks tail might be conspicuous to predators, he noted in an email. Or for a human equivalent: Ferrari drivers might be more likely to end up splatted against a tree than Buick drivers. For both examples, the simple explanation is that the cost is more than balanced by the benefit of extra mating.In the new paper, Greig, along with David W. Rogers of Imperial College in London, claim to have observed evolution through sexual selection for the first time. Our yeast system is a powerful tool for investigating the genetics of sexual selection, they wrote.Yeast cells occur in two different mating types, somewhat akin to male and female. Each type signals to potential partners of the other type by producing an attractive chemical, called a pheromone. But cells vary widely in how strongly they can signal; the differences are genetic.Rogers and Greig engineered one of the sexes of yeast cells, called MAT-alpha, to have either very high or very low signaling strength. They then mixed both types of cells with those of the opposite sex group, called MATa. This mixing was done in two different ways: in one, the MAT-alpha cells were few, and so faced little competition among each other; in the other, they were many, so that they faced tough competition for mating opportunities.Only under the high-competition situation, the strong-signalling gene variant spread quickly through the population at the expense of the weak-signalling variant, Rogers and Greig found. This matched the predictions of sexual selection theory, they added. We have tested the simplest possible sexual selection scenario, they wrote. Observing the real time evolution of novel sexually selected traits, and preferences for them, is the ultimate test for sexual selection theory. == Using Math to Explain How Life on Earth Began How did self-replicating molecules come to dominate the early Earth? Using the mathematics of evolutionary dynamics, Martin A. Nowak can explain the change from no life to life Back in March the press went crazy for Martin A. Nowaks study on the value of punishment. A Harvard University mathematician and biologist, Nowak had signed up some 100 students to play a computer game in which they used dimes to punish and reward one another. The popular belief was that costly punishment would promote cooperation between two equals, but Nowak and his colleagues proved the theory wrong. Instead they found that punishment often triggers a spiral of retaliation, making it detrimental and destructive rather than beneficial. Far from gaining, people who punish tend to escalate conflict, worsen their fortunes and eventually lose out. Nice guys finish first, headlines cheered. It wasnt the first time Nowaks computer simulations and mathematics forced a rethinking of a complex phenomenon. In 2002 he worked out equations that can predict the way cancer evolves and spreads, such as when mutations emerge in a metastasis and chromosomes become unstable. And in the early 1990s his model of disease progression demonstrated that HIV develops into AIDS only when the virus replicates fast enough so that the diversity of strains reaches a critical level, one that overwhelms the immune system. Immunologists later found out he had the mechanism right [see How HIV Defeats the Immune System, by Martin A. Nowak and Andrew J. McMichael; Scientific American, August 1995]. Now Nowak is out to do it again, this time by modeling the origin of life. Specifically, he is trying to capture the transition from no life to life, he says. Trained as a biochemist, the 43-year-old Nowak believes that mathematics is the true language of science and the key to unlocking the secrets of the past. He began exploring the mathematics of evolution as a graduate student at the University of Vienna, working with fellow Austrian Karl Sigmund, a leader in evolutionary game theory. Evolutionary dynamics, as Nowak named the field, involves creating formulas that describe the building blocks of the evolutionary process, such as selection, mutation, random genetic drift and population structure. These formulas track, for example, what happens when individuals with different characteristics reproduce at different rates and how a mutant can produce a lineage that takes over a population. At the home of the Program for Evolutionary Dy--namics at Harvard, the blackboard is chalked with equations. Nowak has been busy working on how to whittle down the emergence of life into the simplest possible chemical system that he can describe mathematically. He uses zeroes and ones to represent the very first chemical building blocks of life (most likely compounds based on adenine, thymine, guanine, cytosine or uracil). Nowak refers to them as monomers, which, in his system, randomly and spontaneously assemble into binary strings of information. Nowak is now studying the chemical kinetics of this system, which means describing how strings with different sequences will grow. The fundamental principles of this idealized scheme, he says, will hold true for any laboratory-based chemical system in which monomers self-assemble, in the same way as Newtons equations describe how any planet goes around the sun, and it doesnt matter what that planet is made of, Nowak explains. Math helps us to see what the most crucial and interesting experiment is. It describes a chemical system that can be built, and once its built, you can watch the origin of evolution. Could it really be that simple? Right now the system exists only on paper and in the computer. Although it is easy to model mathematically, making the system in the lab is tricky because it starts without any enzymes or templates to help the monomers assemble. Its hard to imagine an easy way to make nucleic acids, says David W. Deamer, a biomolecular engineer at the University of California, Santa Cruz. There had to be a starting material, but were very much into a murky area, and we dont have good ideas about how to re-create it in the laboratory or how to get it to work using just chemistry and physics without the help of enzymes. In the 1980s biochemist Leslie E. Orgel and his group at the Salk Institute for Biological Studies in San Diego showed that a strand of RNA can act as a template for making another strand of complementary RNAa phenomenon called nonenzymatic template-directed polymerization. Figuring out how nucleotides might self-assemble without templates, however, has proved harder. I want a process that can comprise polymers, Nowak says. Irene Chen, a cellular origins researcher at Harvard, says one way that monomers of RNA or DNA might form polymers in the absence of enzymes is by adding a compound called imidazole to one end of the monomers, making them more reactive and their polymerization quicker and easier. Lipids or clay might also be essentialother researchers have shown that they can help speed up the reaction. At Rensselaer Polytechnic Institute, for instance, chemist James P. Ferris induced adenine nucleotides to assemble into short polymers of RNAstrands 40 to 50 nucleotides long on a kind of mineral clay that may have been common in the prebiotic world. Using his mathematical model, Nowak looks at chemical reactions that lead to these kinds of strands and assigns rate constants to the reactions. That is, he imagines that strings with different binary information grow at different rates, with some taking in monomers faster than others. Then he calculates their distributions. Small differences in growth rates, he has noticed, result in small differences in abundance; sequences that grow slower are less common in the population, getting outcompeted by faster ones. This I find great, Nowak exclaims, because now you have selection prior to replication in a completely natural way. Some strands mutate, and sometimes one sequence accelerates the reaction rates of other sequences, demonstrating the kind of cooperation that Nowak has long argued is a fundamental principle of evolution. Taken together, he says, the result is a lifelike chemical system ripe with evolutionary dynamics. He calls this system prelife because it has the qualities of lifegenetic diversity, selection and mutationbut not replication. Typically mutation and selection are seen as consequences of replication. If suddenly, for example, only large, hard seeds were available to the finches of the Galapagos Islands, those with bigger, stronger beaks would be more likely to survive and, generation after generation, would become more common in the population. Selection for a trait, be it beak size or something else, depends on passing down the genes for that trait to offspring. But Nowak says his model shows there can be selection prior to replicationwhich means that maybe there is selection for replication. If this kind of selection is possible, he notes, maybe it can help explain the origin of life. All that is necessary is for a few strings to suddenly develop the ability to make copies of themselvesthe way some researchers believe certain strands of RNA first became dominant on the primitive earth. Enough free monomers would have to be around to make replication advantageous, Nowak points out, and the replicating strings must be able to use up the monomers faster than the nonreplicating strings. According to his calculations, only when the rate of replication went beyond a certain threshold would the equilibrium of the system change, allowing life to emerge. Life destroys prelife, he states. All of this happened at some stage. Nowak hopes that his model will guide experiments. When it comes to understanding the beginning of evolution, building the chemical system he describes mathematicallya system in which only two types of monomers self-assemble and then self-replicateis the simplest thing you can do, he says. Mathematics is the proper language of evolution. I dont know what the ultimate understanding of biology will look like, but one thing is clear: its all about getting the equations right. == Among the 5,433 genes in the P. vivax genome, the researchers found 346 that help the parasites trick the immune system. == Goldmine bug DNA may be key to alien life A bug discovered deep in a goldmine and nicknamed "the bold traveller" has got astrobiologists buzzing with excitement. Its unique ability to live in complete isolation of any other living species suggests it could be the key to life on other planets. A community of the bacteria Candidatus Desulforudis audaxviator has been discovered 2.8 kilometres beneath the surface of the Earth in fluid-filled cracks of the Mponeng goldmine in South Africa. Its 60C home is completely isolated from the rest of the world, and devoid of light and oxygen. Dylan Chivian of the Lawrence Berkeley National Laboratory, California, studied the genes found in samples of the fluid to identify the organisms living within it, expecting to find a mix of species. Instead, he found that 99.9% of the DNA belonged to one bacterium, a new species. The remaining DNA was contamination from the mine and the laboratory. "The fact that the community contains only one species stands one of the basic tenets of microbial ecology on its head," says Carl Pilcher, director of the NASA Astrobiology Institute, who was not involved in Chivian's DNA analysis but whose colleagues made the initial discovery that there were microbes living in this particular fissure two years ago. Evolutionary biologist E. O. Wilson says the discovery is so important he will at once begin to mention it in his lectures on biodiversity. Lonely bug A community of a single species is almost unheard of in the microbial world. It means the ecosystem's only species must extract everything it needs from an otherwise dead environment. "Virtually all other known ecosystems on Earth that don't use sunlight directly do use some product of photosynthesis," says Pilcher. Deep-sea vent communities, for instance, are too far down to directly use sunlight but they do use oxygen dissolved in seawater, and that oxygen is produced by photosynthesising plankton at the surface. Chivian's analysis shows that D. audaxviator gets its energy from the radioactive decay of uranium in the surrounding rocks. It has genes to extract carbon from dissolved carbon dioxide and other genes to fix nitrogen, which comes from the surrounding rocks. Both carbon and nitrogen are essential building blocks for life as we know it, and are used in the building blocks of proteins, amino acids. D. audaxviator has genes to produce all the amino acids it needs. D. audaxviator can also protect itself from environmental hazards by forming endospores tough shells that protect its DNA and RNA from drying out, toxic chemicals and from starvation. It has a flagellum to help it navigate. Ancient origins? "One question that has arisen when considering the capacity of other planets to support life is whether organisms can exist independently, without access even to the Sun," says Chivian. "The answer is yes and here's the proof. It's philosophically exciting to know that everything necessary for life can be packed into a single genome." Chris McKay, of NASA's Ames Research Center says that D. audaxviator is an amazing discovery, and represents the kind or organism that could survive below the surface of Mars or Saturn's sixth largest moon Enceladus. Some of the bacterium's genes appear to be inherited from a related species. Others have been found in archaea, a group of organisms evolutionarily distinct from bacteria. Chivian says D. audaxviator may have evolved as it travelled down through the cracks in the rock, and acquired archaea genes through horizontal gene transfer from populations it crossed on its way down. "It can't handle oxygen," he says. This suggests it has not been exposed to pure oxygen for a long time. The water in which D. audaxviator lives has not seen the light of day in over 3 million years, and this could be an indication of how old the species is. In fact, the species got its name from its long journey towards the centre of the Earth. In Jules Verne's novel by that name, the fictional Professor Lindenbrock's journey is triggered by the following message in Latin: "descende, Audax viator, et terrestre centrum attinges" meaning "descend, bold traveller, and attain the center of the Earth". == Rock Offers Mirror-Image Clues to Life's Origins For more than 150 years, scientists have known that the most basic building blocks of life -- chains of amino acid molecules and the proteins they form -- almost always have the unusual characteristic of being overwhelmingly "left-handed." The molecules, of course, have no hands, but they are almost all asymmetrical in a way that parallels left-handedness. This observation, first made in the 1800s by French chemist Louis Pasteur, is taught to introductory organic chemistry students -- until recently with the caveat that nobody knew how this came to be. But research into the question has picked up in recent years, focusing on a 200-pound chunk of rock found 40 years ago in Murchison, Australia. A meteorite that broke off an asteroid long ago, it brought to Earth a rich collection of carbon-based material from far away in the solar system. While the Murchison meteorite does not have any once-living material, it is telling researchers new things about how life may have started on Earth, and how that almost universal protein left-handedness came to be. The answer they believe they have found is that 3 billion to 4 billion years ago, before life on Earth began, similar meteorites crashed regularly into the planet -- delivering the amino acids that would later be incorporated into all living things. The meteorites did this by providing building blocks with a slight preponderance of that handedness (known scientifically as chirality) that makes life possible. "We know that all amino acids start mirror-image the same, but in living things they have this handedness," said Ronald Breslow, a Columbia University researcher who published recently on the topic. "This change doesn't happen spontaneously, and we've never been able to reproduce it in the laboratory" under conditions similar to early Earth. "The answer to where it comes from looks increasingly like meteorites," he added, "from extraterrestrial bodies falling to Earth. It's a complex story, but we're beginning to understand it better." Breslow and his colleagues made significant progress recently when they proved that the Murchison amino acids could transfer their left-handedness to otherwise symmetrical amino acids. They then found that small degrees of chirality could be dramatically amplified in a water solution under conditions similar to the early Earth. Their conclusion: Even the relatively limited number of additional left-handed amino acids in the meteorites could, under the right conditions, lead to a world where almost all amino acids and proteins end up left-handed. Their papers appeared in the journal Organic Letters and in the Proceedings of the National Academy of Sciences. This transformation is essential to life because if all the amino acids and proteins -- which in time became the basic substance of the RNA and DNA that organize life through genes -- were equally left- and right-handed, they could never have bonded into the stable compounds needed for the infrastructure of living things. The story is made even more complex by the likelihood that most or all of the amino acids in asteroids, meteors and comets traversing the solar system -- molecules that can be part of a living entity or not -- were initially evenly right- or left-handed. So how did meteorites bring in slightly more left-handed amino acids? The most common theory is that some were transformed by radiation from a certain kind of faraway neutron star, the dense and very highly charged remnant of a massive star that had collapsed. The ultraviolet, circular-polarized light from these stars hit the asteroids as they sped through space and caused a disproportionately large number of left-handed amino acids to form before they hit Earth as meteorites. (In other solar systems bathed by different neutron stars, the effect of the polarized light would be to turn more amino acids right-handed, potentially leading to right-handed molecular worlds.) Daniel Glavin, an astrobiologist at the Goddard Space Flight Center in Greenbelt, said he and his colleagues recently discovered that a particular amino acid in the Murchison meteorite, isovaline, was disproportionately left-handed at a level of almost 18 percent. Other left-over-right imbalances had mostly been in the single digits. The logical conclusion, Glavin said, is that the imbalance arose on a water-containing asteroid or comet well before it broke up. "There are signs that this compound existed in a watery environment and that the change in handedness happened because of that," he said. Chirality is a simple concept that is hard to fully grasp. A "chiral" molecule is one that cannot be superimposed on its mirror image. Like left and right hands that have a thumb and fingers in the same order but are mirror images, chiral molecules have the same things attached in the same order but are mirror images and not the same. To make things a bit more complex, while almost all proteins are left-handed, almost all sugars are right-handed. When researchers initially reported the higher proportion of left-handed amino acids in the Murchison meteorite -- which now resides at the Smithsonian's National Museum of Natural History -- the news was met with skepticism. The main criticism was that the meteorite was no doubt contaminated by earthly chirality when it struck, accounting for the overabundance of left-handedness. Further study, however, has shown that some of the disproportionately left-handed Murchison amino acids are rare on Earth and contain much more of the heavy isotope of carbon (with an extra neutron) than is found in organic carbon on Earth. Some researchers conclude that chirality and its complex origins make it less likely that life exists on other planets. But Breslow and Glavin hold the opposite view. "I think this kind of chemistry could exist on many other planets and asteroids," Breslow said. "Meteorites crash into celestial bodies all the time. Given at all similar conditions that early Earth had, I don't see why some of those meteorites couldn't have the same effect when they hit other planets, too." == A flighted ancestor of ostriches is called Struthio coppensi and lived in the Early Miocene - about 23 milion years ago. === Lake Victoria in Africa has 850 different species of Chiclid fish, from a single ancestor. http://en.wikipedia.org/wiki/Cichlid === Lake Valley, New Mexico. This is sometimes called the crinoid capital of the world. There are 400 species of Mississipian fossils that have been found in Lake Valley. Yes, they are all Mississipian. They are all extinct. == The species of the genus Latimeria are known only from modern specimens, and no fossilized remains of these species have been found. Modern species of Latimeria are distinguishable from their extinct relatives, such that the closest affinities are no closer than the genus level. The lobed-finned fish that are alive today are different than the lobed-finned fish of 325 million years ago. == Out of Greece came evolution. Anaximander, Aristotle believed in evolution. == James Moore , Evolution and Wonder : Understanding Charles Darwin (July 20,2006) on Charles Darwins view of religion, adaptation, and creation. Audio interview Denis O. Lamoureux, , Theological Insights from Charles Darwin PSCF 56.1:2-12 (3/2004). Jerry Bergman, "A Brief History of the Modern American Creation Movement," Contra Mundum No 7 Spring 1993. Harry Cook, "Wonderful Life: Burgess Shale and the History of Biology," PSCF 47 (September 1995): 159. Harry Cook, & Hank D. Bestman, A Persistent View: Lamarckian Thought in EarlyEvolutionary Theories and in Modern Biology PSCF 52.2: 86-97 (6/2000). Edward O. Dodson , Toldot Adam: A Little-Known Chapter in the History of Darwinism PSCF 52.1: 47-54 (3/2000). Garry V. Ferngren, and Ronald L. Numbers, C. S. Lewis on Creation and Evolution:The Acworth Letters,1944-1960 PSCF 48.1 28-33 (3/1996). J. W. Haas, Jr., The Rev. Dr. William H. Dallinger F.R.S.: Early Advocate of Theistic Evolution and FoeofSpontaneous Generation PSCF 52.2: 107-117 (6/2000). Christopher B. Kaiser, "The Creationist Tradition in the History of Science" PSCF 45 (June 1993): 80. Mark A. Kalthoff, A Different Voice from the Eve of The Origin: Reconsidering John Henry Newman onChristianity, Science, and Intelligent Design PSCF 53.1: 14-23 (3/2001). Sara Joan Miles, "From Being to Becoming: Science and Theology in the Eighteenth Century," PSCF 43 (December 1991): 215. Sara Joan Miles, Charles Darwin and Asa Gray Discuss Teleology and Design PSCF 53.3:196-201.(9/2001). Ronald L. Numbers, "Creating Creationism: Meanings and Usage Since the Age of Agassiz - Part 3." (web link). Michael Roberts, Was Darwin a Christian? PSCF 52.2:84-85 (6/2000). Frank J. Smith, "Presbyterians & Evolution in the 19th Century: The Case of James Woodrow, "Contra Mundum No. 6 Winter 1993. == Mysterious DNA Found to Survive Eons of Evolution Scientists have discovered mystery snippets of mammal DNA that have survived eons of evolution and yet have no apparent purpose. The finding reveals just how much we don't know about the secrets hidden in our genome and that of other animals. Most genes change throughout evolution via mutations; useless ones eventually get weeded out of the population while the helpful modifications take hold. However, about 500 regions of our DNA - the body's instruction code made up of base pairs of molecules - have apparently remained intact throughout the history of mammalian evolution, or the past 80 million to 100 million years, basically free of mutations. "Mutations are introduced into these regions just as they are everywhere else, but they're swept out of the genome much more quickly," said researcher Gill Bejerano, professor of developmental biology and computer science at Stanford University. "These regions seem to be under intense purifying selection - no mutations take hold permanently. " And what's more, many of those sequences do not appear to code for any obvious function, or phenotype, in the body. Researchers suspect they do serve an important purpose, but have yet to figure out exactly what that purpose is. (These sequences are not the same as non-coding or "junk" DNA, for which no function has been identified. Also, most junk DNA has not been conserved for eons like these segments.) Ultraconserved regions The researchers call these mystery snippets "ultraconserved regions," and found that they are about 300 times less likely than other regions of the genome to be lost during the course of mammalian evolution. Bejerano and his graduate student Cory McLean detailed the finding in the Oct. 2 issue of the journal Genome Research. The fact that these segments haven't been weeded out by natural selection implies that they serve an important function in mammals. Yet mice in the lab bred to lack these DNA strands appear healthy and don't seem to be missing any vital genes. Wondering if the odd results were simply some fault of the lab experiment, and perhaps the mice really weren't as well off as they seemed, the researchers investigated whether any other mammals were also blithely living without these regions. Amazingly, they found that was not the case. The researchers compared ultraconserved sequences of at least 100 base pairs shared by humans, macaques and dogs with the DNA of rats and mice. They found that less than one-tenth of 1 percent of the segments shared among the primates and dogs were missing in the rodents. In contrast, about 25 percent of regular, not ultraconserved, regions in the first group were absent in the mice and rats. "What's striking about this research is that [the regions] really are almost never lost," Bejerano told LiveScience. "You're asking if a species can live without these regions, and the resounding answer from our paper is that they seem to have an effect that is strong enough that evolution would weed [individuals without the regions] out of an evolving population." Potential purposes Scientists have some guesses about what these strange segments might be used for. Perhaps these DNA strands actually code for multiple layers of information, Bejerano suggested. In that case, each layer could be redundant, with other segments serving the same purpose in other contexts, but together they provide a vital backup system. Or, they could be crucially important, but only at specific times in a species' history. "Imagine that these regions somehow protect you from a disease that only strikes the population every once in a while," Bejerano said. "Once every 10,000 years you have this cleansing event, and only those with the region would actually stick around. That's one guess." == Sexual reproduction has a significant adaptation advantage over asexual reproduction because it allows for more genetic variety. More genetic variety means that the population of organisms can adapt more quickly to environmental change. Yeast can reproduce either sexually or asexually. Therefore, they demonstrate that such an evolutionary path is possible. Second, yeast will naturally choose to reproduce asexually in a stable environment and sexually in a stressful (i.e.changing) environment. == The striking Vendian fossil Spriggina and its close relative Marywadea make up the Sprigginida, a clade of soft-bodied organisms that are restricted to the Precambrian. Spriggina is known largely from the Ediacara Hills of south Australia, near Adelaide. The organism had a crescent-shaped head and numerous segments tapering to the posterior end; it is only about three centimeters long. == Mice only have slightly more conventional genes (around 22,000) than a simple worm, the results clearly indicate that while proteins comprise the essential components of our cells, the development of multicellular organisms like mammals is controlled by vast amounts of regulatory noncoding RNAs that until recently were not suspected to exist or be relevant to our biology. Moreover, since most proteins are similar among mammals it also suggests that many of the differences between species may be embedded in the differences in the RNA regulatory control systems, which are evolving much faster than the protein components. == Around a million years ago, an ape so large that it's now known as Gigantopithecus roamed the bamboo forests of South Asia. Standing nine feet tall, weighing from 600 to 1,000 pounds, and with a bamboo-crushing jaw the size of a mailbox, this was a truly strong creature. But today, all that remains of Gigantopithecus are a few fossil teeth and jawbones in museum vaults. == Many people confuse evolutionary theory with Lamarckism, named for the French naturalist Jean-Baptiste Lamarck (1744-1829). In one sense Lamarck was an evolutionist in that he favored the view that new species had evolved from ancestral species, but he was mistaken about the mechanism by which species change, and about the time required for these changes. Lamarck thought that the mechanism for biological change was the transmission to the next generation of characteristics acquired during the life span of an individual. His most famous example is that of the giraffe. According to Lamarck, the giraffe's ancestors had shorter necks, and they would stretch their necks to reach higher foliage in trees. Their descendants then inherited longer necks because the characteristics of these newly stretched necks of the parents were passed down to their offspring. Moreover, Lamarck thought that the evolution of a new species could occur within a few generations or even one. His position was reasonable for its time, yet it happens to be incorrect. == Over the past 40 million years, more than 600 species of elephants have roamed the earth. Today only three species remainthe savanna elephant and the forest elephant of Africa, and the Asian elephant. There are two genera of extant elephants: Elaphus and Loxodonta. list of the extinct genera: http://www.elephant.se/proboscidea.php == The 100% match of DNA sequences in the pseudogene region of beta-globin was proof that humans and gorillas shared a recent common ancestor. == Mitochondria are the main sites of biological energy generation in eukaryotes. These organelles are remnants of a bacterial endosymbiont that took up residence inside a host cell over 1,500 million years ago. Comparative genomics studies suggest that the mitochondrion is monophyletic in origin. Thus, the original mitochondrial endosymbiont has evolved independently in anaerobic and aerobic environments that are inhabited by diverse eukaryotic lineages. This process has resulted in a collection of morphologically, genetically and functionally heterogeneous organelle variants that include anaerobic and aerobic mitochondria, hydrogenosomes and mitosomes. Current studies aim to determine whether a central common function drives the retention of mitochondrial organelles in different eukaryotic organisms. == 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 is 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 is 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/ == 1. Did we evolve from monkeys? Humans did not evolve from monkeys. Humans are more closely related to modern apes than to monkeys, but we didn't evolve from apes, either. Humans share a common ancestor with modern African apes, like gorillas and chimpanzees. Scientists believe this common ancestor existed 5 to 8 million years ago. Shortly thereafter, the species diverged into two separate lineages. One of these lineages ultimately evolved into gorillas and chimps, and the other evolved into early human ancestors called hominids. http://www.primates.com/pierolapithecus/ Scientists in Spain have discovered fossils of an ape species from about 13 million years ago that they think may have been the last common ancestor of all living great apes, including humans. The new ape species and its possible place in prehuman evolution are described in today's issue of the journal Science by a research team led by Dr. Salvador Moya-Sola of the Miquel Crusafont Institute of Paleontology in Barcelona. The fossil remains were found near Barcelona and named Pierolapithecus catalaunicus. About 25 million years ago, Old World monkeys diverged from the primate line that led eventually to apes and humans. About 11 million to 16 million years ago, another branching occurred, when primates known as the great apes - which now include orangutans, chimpanzees, gorillas and humans - split from the lesser apes, represented by today's gibbons and siamangs. The lineage leading to humans branched off from the chimpanzee line an estimated seven million years ago. == Stress and Mutations A few years ago, when he was first starting to think about this, Romesberg encountered a paper in a scientific journal that discussed certain genes that "make mutations," as he put it. When these genes are deleted from cells, the cells lose their ability to mutate, even when subjected to massive amounts of ultraviolet light. This brought Romesberg to the conclusion that mutation is a programmed stress response a survival mechanism. If the cell senses damage, and if the damage persists beyond its ability to repair it, the cell will turn on its mutation machinery and open the floodgates for evolution" 2. Rate new allele reaches fixation (or at least becomes established in the population). Other mechanisms affecting the fixation of new mutations include drift, nonrandom mating, and migration (gene flow). If they controlled for nonrandom mating and eliminated migration, then drift has a larger role. There is a nice population genetics package - Populus http://www.cbs.umn.edu/populus/ down load and play with the mendelian genetics programs. They're easy to run and you can test the drift hypothesis your self. == Although many have heard that being heterozygous for sickle cell anemia (having one copy each of the good and bad alleles) is beneficial in some areas of Africa due to the protective benefit it provides against malaria, many do not know that this relationship also seems to be prevalent in the US concerning cystic fibrosis (CF) and secretory diarrheas. In CF, a chloride channel in the lungs does not function properly and so less chloride is allowed to flow into the airways of the lung. With less chloride there is less water that follows, and with less water you get more mucous which leads to a variety of problems for the lungs. This is not generally a problem for those who are only carriers (i.e. heterozygous) of CF, however, and in fact in some circumstances it may provide a direct benefit in other parts of the body. Aside from the lungs, other organs use the same chloride channel are still moderately impeded even if the person is only a carrier for a defective channel. Interestingly, this is exactly the case with intestine which, like the lungs, uses the channel to help secrete water into the intestinal lumen. Normally this is not significant enough of a problem to affect the individual much, but it does become relevant with secretory diarrheas. In cholera, one form of secretory diarrhea, a toxin produced by the bacterium leads to the constant efflux of chloride through the channel no matter what the body wants it to do, and so along with the chloride goes a large volume of water. This loss of fluid is so severe that it is actually the greatest cause of death from cholera. People with one copy of a defective chloride channel, however, are unable to lose as much chloride as a result of the toxin and so experience much water loss and much less mortality as a result of the disease. This has perhaps, it is theorized, led to CF being the most prevalent autosomal recessive disorder in the United States with 1 in 20 adults being carriers. == vestigial organs The eyes of cave fish? The eyes of cave salamanders? The pelvises inside the skin of pythons? The legs inside some other lizards that never get outside of the skin? The perfectly formed wings housed underneath fused wing covers within flightless beetles (such as the weevils of the genus Lucanidae)? The third molars (otherwise known as wisdom teeth) which develop in over 90% of all adult humans yet never erupt from the gums, and in one third of all individuals they are malformed and impacted? == "Sex" [a life cycle with syngamy & meiosis] first arose in unicellular organisms, since many unicellular eukaryotes still show it today. The first multicellular organisms thus would already have been sexually reproductive at the outset; there would have been some sort of gamete-forming areas in even the earliest animals with differentiated tissues. Some living types of algae and fungi do illustrate intermediate stages in the evolution of differentiated sperms and eggs [oogamy] from undifferentiated gametes [isogamy] == The theory of evolution describes the mechanisms that cause evolution. So evolution is both a fact and a theory. See the Evolution is a Fact and a Theory FAQ, the http://www.talkorigins.org/faqs/evolution-fact.html Introduction to Evolutionary Biology FAQ and the Five Major http://www.talkorigins.org/faqs/faq-intro-to-biology.html Misconceptions about Evolution FAQ. http://www.talkorigins.org/faqs/faq-misconceptions.html#proof COMPARATIVE GENETICS: Which of Our Genes Make Us Human? Ann Gibbons Science 1998 September 4; 281: 1432-1434. (in News Focus) HUMAN EVOLUTION: Y Chromosome Shows That Adam Was an African Ann Gibbons Science 1997 October 31; 278: 804-805. (in Research News) Miocene Primates Go Ape Ann Gibbons and Elizabeth Culotta Science 1997 April 18; 276: 355b-356b. (in Research News) A Hominoid Genus from the Early Miocene of Uganda Daniel L. Gebo, Laura MacLatchy, Robert Kityo, Alan Deino, John Kingston, and David Pilbeam Science 1997 April 18; 276: 401-404. (in Reports) Human or Chimp? 50 Genes Are the Key http://www.nytimes.com/library/national/science/102098sci-chimps.html http://www.bbc.co.uk/horizon/hopefulmonsters.shtml http://inia.cls.org/~welsberr/evobio/evc/argresp/sequence.html http://lummi.stanford.edu/class/anthro276/WWW/EvAnth.html Talk Origins Archive FAQ http://www.talkorigins.org/origins/faqs-qa.html Suspicious Creationist Credentials FAQ http://www.talkorigins.org/faqs/credentials.html Talk.Origins Archive's Creationism FAQs http://www.talkorigins.org/origins/faqs-creationists.html Many people of Christian and other faiths accept evolution as the scientific explanation for biodiversity. See the God and http://www.talkorigins.org/faqs/faq-god.html Evolution FAQ and the Interpretations of Genesis FAQ. http://www.talkorigins.org/faqs/interpretations.html == 1] the support for the concept of evolutionary common descent isn't so much from paleontology as from all of comparative biology. 2] It isn't just that the transitionals \look similar to [whatever] but have some differences\, but instead it requires more careful comparisons and analyses of the detailed patterns of similarities and differences among the fossils and their putative relatives. Shared similarities among species that are due to common descent will show a hierarchically nested pattern of groups within groups within groups. [You might look up phylogenetic systematics or cladistics for more info on the types of analytical methods used: http://www.ucmp.berkeley.edu/clad/clad4.html The finders of fossils of an new type of early australopithecine might say something more like here is a very early hominid fossil that is in-betweenhumans and apes in these specific ways. This pattern of shared features is very consistent with it being an early species of the human group, at some point after the origin of the group from the last common ancestor of modern chimps and modern humans.\ fossil...or, Enough to document lots of interesting evolutionary transitions: The nested hierarchical pattern was recognized long before the concept of evolution provided the explanation for its existence. The fact that independent data sets like DNA and morphology tend to give highly compatible results [the twin nested hierarchies] is even more compelling evidence. http://www.talkorigins.org/origins/faqs-evolution.html http://www.talkorigins.org/faqs/faq-transitional.html http://www.talkorigins.org/faqs/fossil-hominids.html http://www.talkorigins.org/faqs/archaeopteryx.html http://www.dinosauria.com/jdp/jdp.htm http://www.talkorigins.org/faqs/horses.html http://www.neoucom.edu/Depts/Anat/Whale.html Zimmer, Carl. 1998. At the water's edge: macroevolution and the transformation of life. New York : Free Press. Padian, K. & L. M. Chiappe. 1998. The origin of birds and their flight. Scientific American 278[2]: 38-47 [Feb. 1998]. Padian, K. & L. M. Chiappe. 1998. The origin and early evolution of birds. Biological Reviews 73: 1-42. == Most paleontologists have agreed based on a variety of empirical evidence that birds are the direct descendants of a particular group of dinosaurs, but a consistent minority of scientists has disagreed (which, contrary to claims by supporters of pseudo-science, isn't a sign of crisis at all, but rather of a healthy critical debate among scientists). One of the "bones" of contention, so to speak, was represented by the development of fingers in birds and dinosaurs: both kinds of animals have three fingers as adults, as opposed to the five that are normal for vertebrates in general. Until now, however, scientists thought that while dinosaurs retained digits n. 1, 2 and 3, birds had lost n. 1 and retained the three middle digits. This would count as evidence against a close phylogenetic connection between the two groups. But new molecular developmental work has actually shown that what looks superficially like digit n. 2 in birds is really the standard first digit of vertebrates in general. Molecular biologists have been able to determine this by examining which genes are involved in the formation of the various digits in the developing bird embryo. Therefore, what seemed until recently an out of place piece of the puzzle turns out to fit perfectly with the prevailing hypothesis. This is the way science works: if new evidence supports the accepted hypothesis, the latter receives further confirmation and grows in strength and acceptance; if enough new pieces of evidence don't fit, eventually the hypothesis is discarded in favor of an alternative that explains things better. == A.G. Cairns-Smith, 1986 Andrew Scott, 1999 Freeman Dyson Timeline of Materialism, Spontaneous Generation, and Blindwatchmaking Views == here on Earth. 90 percent of terrestrial soil bacteria cannot be grown in culture. == "The analysis revealed clear evidence that photosynthesis did not evolve through a linear path of steady change and growing complexity but through a merging of evolutionary lines that brought together independently evolving chemical systems -- the swapping of blocks of genetic material among bacterial species known as horizontal gene transfer." == POITIERS, FRANCE-Michel Brunet removes the cracked, brown skull from its padlocked, foam-lined metal carrying case and carefully places it on the desk in front of me. It is about the size of a coconut, with a slight snout and a thick brow visoring its stony sockets. To my inexpert eye, the face is at once foreign and inscrutably familiar. To Brunet, a paleontologist at the University of Poitiers, it is the visage of the lost relative he has sought for 26 years. "He is the oldest one," the veteran fossil hunter murmurs, "the oldest hominid." Brunet and his team set the field of paleoanthropology abuzz when they unveiled their find last July. Unearthed from sandstorm-scoured deposits in northern Chad's Djurab Desert, the astonishingly complete cranium-dubbed Sahelanthropus tchadensis (and nicknamed Toumai, which means "hope of life" in the local Goran language)-dates to nearly seven million years ago. It may thus represent the earliest human forebear on record, one who Brunet says "could touch with his finger" the point at which our lineage and the one leading to our closest living relative, the chimpanzee, diverged. == Pachycynodon -- A bearlike terrestrial carnivore with several sea-lion traits. == Piltdown was an indisputable fraud. No one knows for sure who perpetrated it. It was fairly sophisticated so it is likely that someone with a scientific background was involved. The most interesting name among the suspects is Sir Arthur Conan Doyle. Piltdown fooled scientists for about 40 years (though beginning in 1925, some scientists found discrepancies that they couldn't explain and after 1930 or so most discussions of hominid evolution didn't mention Piltdown). In 1953 it was formally denounced as a fraud by evolutionary scientists. The primary evidence was the inconsistent way that the teeth were worn down. The reasons that the fraud took so long to expose were the relatively weak tools available to the people who found Piltdown: chemical tests and dating techniques taken for granted today were not available; the analysis of the details of tooth wear was less worked out; the simple knowledge of geology was much less detailed. Of course the people who found Piltdown may have been the perpetrators of the fraud as well. == Residual amino acids have been found in fossil shells of mollusks up to 80 million years old. == Patterson, In several animal and plant groups, enough fossils are known to bridge the wide gaps between existing types. In mammals, for example, the gap between horses, asses and zebras (genus Equus) and their closest living relatives, the rhinoceroses and tapirs, is filled by an extensive series of fossils extending back sixty-million years to a small animal, Hyracotherium, which can only be distinguished from the rhinoceros-tapir group by one or two horse-like details of the skull. There are many other examples of fossil 'missing links', such as Archaeopteryx, the Jurassic bird which links birds with dinosaurs (Fig. 45), and Ichthyostega, the late Devonian amphibian which links land vertebrates and the extinct choanate (having internal nostrils) fishes. . . [from Lionel Theunissen's page at http://www.talkorigins.org/faqs/patterson.html] "When quoting scientists like Patterson or Gould as saying 'there are no transitional forms' they neglect to mention that they are only referring to transitional forms at the species level. They know full well that Gould has stated that transitional forms between orders and families are in fact abundant, and even a cursory read of Dr. Patterson's book will yield numerous examples of transitional forms." The overall point is that, even if we cannot prove that any *individual* fossil or species is a transitional, we *can* prove that *most* of the ones we suppose to be transitionals really are transitionals or very closely related to organisms that *were* transitionals. We can do this because the pattern is one that forces the conclusion that transitionals existed and that the species were *not* all separately created (but merely on common patterns in many cases). Evolution says that species arise over time and gradually (i.e., not in single huge leaps from one species to another overnight), even in punctuated equilibrium theories. Evolution says because the mechanism that it uses for explaining things is an *incremental* mechanism, involving single steps that are always relatively small, because new traits must start out in such a way as not to disrupt the entire organism (one reason the Cambrian explosion was possible was that, at that time, the existing species were simple enough that fairly major changes could occur relatively rapidly, with a short reproductive cycle and with major changes in body form not requiring major *physiological* changes as well -- increasing complexity of integration of many distinct parts in a rigid format has caused a great slowdown because of the necessity that all new parts be added in such a way as to integrate with *many* existing parts, not just a few). In the case of evolution, we have a *process* that either leads to adaptation or extinction, and which explains adaptation in terms of the three factors of replication, modifications that may themselves be passed on, and natural selection to determine *which* modifications *do* get passed on. For any sufficiently slowly-changing environment, this process will produce progressive adaptations in at least *some* species so as to "track" the changes in the environment (actually, this tracking is not perfect, and may often lag somewhat behind) There are many cases where a morphologically intermediate form is also *well* established as a *transitional* form as well. These would be cases where the fossil record is fairly complete, showing a good grouping of species over levels such that we can be pretty sure that no *other* species could be the transitional than the one candidate for a particular "slot" in the sequence. == Evolutionary change is observed in the field occuring at rates far too fast to allow for a complete fossil record. The fossil record is spotty for well known reasons. The pattern in the fossil record is entirely consistent with Darwinian evolution (and Punctuation is simply a call for plurality: *some* evolution happens in small populations in geographically restricted ranges and at relatively high rates, none of which is a violation of Darwinism). Evolution by natural selection is, therefore, the *best available* explanation. It should be abandoned or reconsidered if contradicted by the evidence or when a competing theory of comparible explanitory power is introduced. It should not be abandoned based on an inability to find evidence in quantities or qualities which would be nice to have, but we have no reason to expect exist. Life can be arranged, with some effort, into a clearly nested heirarchy. This pattern is predicted by common descent with modification, and not predicted by design or design economy arguments for similarity. Similarities as a result of heredity are a well-observed phenomena and it can quite reasonably be argued that morphological similarity, of a certain kind and quality, is evidence of a hereditary connection. Similarity implies common descent is not a 'bare' assumption, it is based on fundamental observations. === [Q.] I thought evolution was just a theory. Why do you call it a fact? [A.] The phenomena of biological evolution are changes in the heritable characteristics of populations over time. That these occur is a fact. Biological evolution refers to the common descent of all living organisms from shared ancestors. The evidence for this historical evolution -- genetic, fossil, anatomical, etc. -- is so overwhelming that it is also considered a fact. The theory of evolution describes the mechanisms that cause evolution. So evolution refers to both fact and theory. [U.] http://www.talkorigins.org/faqs/evolution-fact.html http://www.talkorigins.org/faqs/faq-intro-to-biology.html http://www.talkorigins.org/faqs/faq-misconceptions.html#proof [Q.] Don't you have to be an atheist to accept evolution? [A.] No. Many people of Christian and other faiths accept evolution as the scientific explanation for biodiversity. [U.] http://www.talkorigins.org/faqs/faq-god.html http://www.talkorigins.org/faqs/interpretations.html [Q.] Isn't evolution just an unfalsifiable tautology? [A.] No. Evolutionary theory is in exactly the same condition as any other valid scientific theory, and many criticisms of it that rely on philosophy are misguided. [U.] http://www.talkorigins.org/faqs/evolphil.html [Q.] If evolution is true, then why are there so many gaps in the fossil record? Shouldn't there be more transitional fossils? [A.] Due to the rarity of preservation and the likelihood that speciation occurs in small populations during geologically short periods of time, transitions between species are uncommon in the fossil record. Transitions at higher taxonomic levels, however, are abundant. [U.] http://www.talkorigins.org/faqs/faq-transitional.html http://www.talkorigins.org/faqs/fossil-hominids.html http://www.talkorigins.org/faqs/punc-eq.html http://www.talkorigins.org/origins/postmonth/feb98.html [Q.] No one has ever directly observed evolution happening, so how do you know it's true? [A.] Evolution has been observed, both directly and indirectly. It is true. [U.] http://www.talkorigins.org/faqs/faq-misconceptions.html#observe http://www.talkorigins.org/faqs/comdesc/ [Q.] Then why has no one ever seen a new species appear? [A.] Speciation has been observed both in the laboratory and in nature. [U.] http://www.talkorigins.org/faqs/faq-speciation.html http://www.talkorigins.org/faqs/speciation.html [Q.] Doesn't the perfection of the human body prove Creation? [A.] No. In fact, humans (and other animals) have many suboptimal characteristics. [U.] http://www.talkorigins.org/faqs/jury-rigged.html [Q.] According to evolution, the diversity of life is a result of chance occurrence. Doesn't that make evolution wildly improbable? [A.] Evolution is not simply a result of random chance. It is also a result of non-random selection. [U.] http://www.talkorigins.org/faqs/chance.html http://www.talkorigins.org/faqs/faq-misconceptions.html#chance [Q.] Doesn't evolution violate the second law of thermodynamics? After all, order cannot come from disorder. [A.] Evolution does not violate the second law of thermodynamics. Order emerges from disorder all the time. Snowflakes form, trees grow, and embryos develop, etc. [U.] http://www.talkorigins.org/faqs/thermo.html http://www.talkorigins.org/faqs/faq-misconceptions.html#thermo [Q.] Didn't Darwin renounce evolution on his deathbed? [A.] The Darwin deathbed story is false. And in any case, it is irrelevant. A scientific theory stands or falls according to how well it is supported by the facts, not according to who believes it. [U.] http://www.talkorigins.org/faqs/hope.html [Q.] Where can I learn more about evolution? [A.] You might start with the talk.origins FAQs. If, however, you want a deeper understanding of evolution, a library would be a more appropriate place to look. The FAQs listed below provide some good references. [U.] http://www.talkorigins.org/faqs/reading-list.html http://www.talkorigins.org/faqs/faq-intro-to-biology.html http://www.talkorigins.org/faqs/evolution-definition.html [Q.] How do you know the earth is really old? Lots of evidence says it's young. [A.] According to numerous, independent dating methods, the earth is known to be approximately 4.5 billion years old. Most young-earth arguments rely on inappropriate extrapolations from a few carefully selected and often erroneous data points. [U.] http://www.talkorigins.org/faqs/faq-age-of-earth.html http://www.talkorigins.org/origins/faqs-youngearth.html [Q.] But radiometric dating methods rely on the assumptions of non- contamination and constant rates of decay. What if these assumptions are wrong? [A.] Isochron dating techniques reveal whether contamination has occurred, while numerous theoretical calculations, experiments, and astronomical observations support the notion that decay rates are constant. [U.] http://www.talkorigins.org/faqs/isochron-dating.html http://www.talkorigins.org/faqs/faq-age-of-earth.html [Q.] I heard that the speed of light has changed a lot. This means that light from galaxies billions of light years away might not be billions of years old. Is this true? [A.] Barry Setterfield's hypothesis of a decaying speed of light was based on flawed extrapolations from inaccurate measurements, many of which were taken hundreds of years ago. [U.] http://www.talkorigins.org/faqs/c-decay.html [Q.] If the Earth is so old, doesn't that mean the Earth's decaying magnetic field would have been unacceptably high at one time? [A.] No. The Earth's magnetic field is known to have varied in intensity and reversed in polarity numerous times throughout the planet's history. [U.] http://www.talkorigins.org/faqs/magfields.html [Q.] Isn't the fossil record a result of the global flood described in the Book of Genesis? [A.] No. A global flood cannot explain the sorting of fossils observed in the geological record. This was recognized even prior to the proposal of evolutionary theory. [U.] http://www.talkorigins.org/faqs/faq-noahs-ark.html http://www.talkorigins.org/origins/postmonth/apr02.html [Q.] What about those fossils that cut through multiple layers? [A.] They have natural explanations: tree-roots that grew into soft, underlying layers of clay, and fossils found in inclined strata. They can also be observed forming in modern environments. [U.] http://www.talkorigins.org/faqs/polystrate.html [Q.] What about those human footprints that appear next to dinosaur footprints? [A.] The "man-tracks" of the Paluxy Riverbed in Glen Rose, Texas were not man tracks at all. Some were eroded dinosaur tracks, and others were human carvings. [U.] http://www.talkorigins.org/faqs/paluxy.html [Q.] Didn't they find Noah's Ark? I saw something on TV about this. [A.] The producers of America's 1993 CBS television show, "The Incredible Discovery of Noah's Ark," were hoaxed. Other ark discovery claims have not been substantiated. [U.] http://www.talkorigins.org/faqs/ark-hoax.html [Q.] The odds against a simple cell coming into being without divine intervention are staggering. [A.] And irrelevant. Scientists don't claim that modern cells came into being through random processes. They are thought to have evolved from more primitive precursors. [U.] http://www.talkorigins.org/faqs/abioprob/ [Q.] Creationists are qualified and honest scientists. How can they be wrong? [A.] The quality of an argument is not determined by the credentials of its author. Even if it was, a number of well-known creationists have questionable credentials. Furthermore, many creationists have engaged in dishonest tactics like quoting out of context or making up references. [U.] http://www.talkorigins.org/faqs/credentials.html http://www.talkorigins.org/origins/faqs-creationists.html http://www.talkorigins.org/faqs/quotes/ http://www.talkorigins.org/faqs/homs/misquotes.html [Q.] What about Immanuel Velikovsky? Didn't he show that the Earth has experienced a lot of major catastrophes? [A.] No, he simply claimed that certain written legends must have described real events. [U.] http://www.talkorigins.org/origins/faqs-catastrophism.html http://www.talkorigins.org/faqs/faq-velikovsky.html [Q.] Where can I find more material on the Creation/Evolution debate? [A.] Contact the National Center for Science Education, or see the TalkOrigins Archive and its \Other links\ page. [U.] http://www.NatCenSciEd.org/ http://www.talkorigins.org/faqs/reading-list.html http://www.talkorigins.org/faqs/organizations.html http://www.talkorigins.org/origins/other-links.html [Q.] What about \intelligent design\? [A.] \Intelligent design\ advocates often use the very same arguments that the young-earth creationists have used in the past. The Archive does have some FAQs on Behe's \irreducible complexity\, Jonathan Wells's \icons of evolution\, and Dembski's \specified complexity\ (see questions below). Further essays on \intelligent design\ can be found on our sister site, TalkDesign, and also at the TalkReason site. [U.] http://www.talkdesign.org http://www.talkreason.org http://www.talkdesign.org/faqs/hunch/hunch.html [Q.] Doesn't irreducible complexity (as described in Behe's _Darwin's Black Box_) shown that some biomechanical systems could not evolve gradually, but must have all their parts created at once? [A.] Behe's \irreducible complexity\ considers only an unrealistically simplistic model of evolution. Evolutionary mechanisms that Behe doesn't consider, such as functional change and coevolution, make irreducible complexity not only possible, but expected. [U.] http://www.talkorigins.org/faqs/behe.html http://www.talkdesign.org/faqs/icdmyst/ICDmyst.html [Q.] Hasn't Jonathan Wells shown that Darwinist claims about such "icons of evolution" as the peppered moth, Haeckel's embryos, and Darwin's finches have been disproven? If so, why are these claims still found in biology textbooks? [A.] Scientists _have_ been complaining for decades about the poor quality of science instruction in school and about the content of science textbooks. However, Dr. Wells's arguments include many false statements, many misunderstandings of the science involved, and many misunderstandings of the significance of the subjects that he pontificates on. [U.] http://www.talkorigins.org/faqs/wells/ http://www.ncseweb.org/pdf/QRBreview.pdf [Q.] Doesn't William Dembski's \specified complexity\ mean that an intelligent designer had to be responsible for the observed complexity and diversity of living things? [A.] The sophistication of Dembski's arguments is superficial. One of the most thorough examinations of Dembski's ideas is available on the Archive. [U.] http://www.talkorigins.org/design/faqs/nfl/ http://www.talkdesign.org/faqs/present_arguments.html http://www.talkdesign.org/faqs/demskiscompass.html http://www.antievolution.org/people/dembski_wa/ [Q.] Isn't it true that scientists are abandoning evolution? [A.] That is not even remotely true. [U.] http://home.entouch.net/dmd/moreandmore.htm [offsite] http://www.talkorigins.org/faqs/steve/ http://www.talkorigins.org/faqs/edwards-v-aguillard/amicus1.html [Q.] If evolution is true, why don't you take Dr. Kent Hovind's $250,000 challenge and make yourself rich? [A.] Kent Hovind's $250,000 challenge is a propaganda ploy and nothing more, rather like the \doctorate\ Hovind claims from Patriot University. [U.] http://www.talkorigins.org/faqs/hovind/ [Q.] Don't you know that the earth is round? [A.] Yes, we do. We keep a copy of the "International Flat Earth Society" flyer here to document that real people in modern times do assert that the earth is flat, not because *we* think the earth is flat. [U.] http://www.talkorigins.org/faqs/flatearth.html == Sex [a life cycle with syngamy & meiosis] first arose in unicellular organisms, since many unicellular eukaryotes still show it today. The first multicellular organisms thus would already have been sexually reproductive at the outset; there would have been some sort of gamete-forming areas in even the earliest animals with differentiated tissues. Some living types of algae and fungi do illustrate intermediate stages in the evolution of differentiated sperms and eggs [oogamy] from undifferentiated gametes [isogamy] == The only organism which uses RNA exclusively are retroviruses. The only difference between ribose and deoxyribose is the reduction of a hydroxyl group on the ribose #2 carbon. Biochemically, this reduction is catalyzed by a single enzyme. In addition, ribonucleic acids use the base uracil, in place of the base thymidine which is found in deoxyribonucleic acids. The difference here is a single methyl group, which isn't even involved in hydrogen bonding with opposite bases in the spiral.. == 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." 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 Douglas J. Futuyma, Evolutionary Biology, 2nd ed., 1986, Sinauer Associates == Before 2.4 billion to 2.2 billion years ago, the Earth's atmosphere contained almost no oxygen and could support only single-celled forms of life. The first complicated cells, like the ones that make up today's plants and animals, appear in 2.1 billion-year-old fossils just after the rise of oxygen. theory of high levels of hydrogen-containing methane gas, which acquired its hydrogen indirectly from water, also would account for why early Earth didn't freeze. "Three billion years ago, the sun was only 4/5ths as bright as it is now. The Earth should have frozen over," he said. But methane, a powerful greenhouse gas, would have kept the Earth warm. == In human DNA, the 21-hydroxylase gene sequence, as well as an adjacent gene encoding complement C4, has been duplicated; i.e., nearly identical copies of DNA segments lie adjacent to each other, each copy containing a complement C4 gene and a steroid 21-hydroxylase sequence. However, only the B copy of the 21-hydroxylase gene is functional; the A copy in all humans is a pseudogene, i.e., it contains multiple mutations including an 8 bp deletion that would prevent its function. The corresponding A copy sequence of chimpanzee has been examined; it contains the same crippling 8 bp deletion seen in the human pseudogene (Kawaguchi, Am J Hum Genet 50:766-80, 1992). If the LCA is very far back up the tree, I suspect that mutations will make very old retroposons unrecognizable. == Artiodactyla (the group cattle belong to) and Cetacea (whales) have been evolving separately for quite a long time. The Last Common Ancestor of whales and cows probably lived sometime in the early Eocene, nearly 60 million years ago. == Crick _Life Itself, Its Origin and Nature_ == We have plenty of intermediates in the dino to bird transition. See: http://www.talkorigins.org/faqs/archaeopteryx/info.html http://www.accessexcellence.org/WN/SUA10/earlybird697.html http://www.cnn.com/TECH/9705/20/bird.dinosaur/ http://cas.bellarmine.edu/tietjen/images/missing_link_ties_birds.htm http://www.actionbioscience.org/evolution/benton2.html http://www.bulletin.ac.cn/ACTION/2002040302.htm How about Horses: http://www.talkorigins.org/faqs/horses/ http://www.flmnh.ufl.edu/natsci/vertpaleo/fhc/firstCM.htm http://chem.tufts.edu/science/evolution/HorseEvolution.htm http://www.talkorigins.org/faqs/horses/eohippus_hyrax.html How about whales: http://www.talkorigins.org/faqs/evolution-research.html#whale-legs http://www.neoucom.edu/Depts/Anat/whaleorigins.htm http://www.angelfire.com/fl/direpuppy/mindblocks.html http://www.indiana.edu/~ensiweb/lessons/wh.n.mkg.html http://www.cosmiverse.com/news/science/science05090201.html http://www.enchantedlearning.com/subjects/whales/allabout/Evol.shtml == Sarich, V. M., and A. C. Wilson. 1967. Rates of albumin evolution in primates. Proc. Natl. Acad. Sci. USA 58:142-148. Felsenstein, J. 1987. Estimation of hominoid phylogeny from a DNA hybridization data set. J. Mol. Evol. 26:123-131. Hayasaka, K., T. Gojobori, and S. Horai. 1988. Molecular phylogeny and evolution of primate mitochondrial DNA. Mol. Biol. Evol. 5:626-644. == The overwhelming evidence puts ducks and chickens together (Galloanserae), and penguins and pigeons together (Neoaves). == Robert Richards' _The Meaning of Evolution_ (Chicago 1992) == Organisms can and do adapt to their environment. A tree in the forest is tall and has most of its leaves at the top, whereas the same tree growing in an open field would be more rounded, probably shorter, and with more leaves on the lower branches. That is a form of adaption to the environment. What it cannot do, is pass its adaptions on to it progeny. == Correlation of growth. Darwin used this phrase to describe the observed phenomenon that a change in one part of an organism was often accompanied by change in another apparently unrelated part. Darwin correctly attributed this to unknown aspects of the the laws of variation on which his theory could say little. Law of reversion. Darwin used this term to describe the then-mysterious phenomenon of the reappearance of ancestral characteristics after many generations. == Retroviruses (and retrotranspon events more generally) do represent the conversion of genetic information in RNA into genetic information in DNA. However, this can be thought of as exchanging one type of genetic media for another slightly different one, rather than an altering genetic material on the basis of environmental cues. Even more interesting is the scrapie protein (similar to mad cow disease) which looked superficially like an infectious genetic protein. Upon closer inspection, however, it seems that it acts more like an aberrant self-assembling enzyme (causing normal protein to switch conformation to the scrapie conformation) than it does as genetic material. The scrapie protein has no effect on the DNA coding for the scrapie protein and is not transmitted to offspring (although there are DNA variants that code for proteins that have increased susceptibility to form the aberrant conformation). These DNA variants *are* transmitted to offspring. The only way the environment seems to influence the genetic construction of future generations is via selection. == Journal of Human Evolution == The probability of any single nucleotide mutating (point mutation) is about 10^-9/generation (with a rather wide range of variance). == Recessive traits like cystic fibrosis can be due to several hundred different individual variants or there can be 200 different forms of beta thalasemia (due to different deletions) in localized areas of the mediteranean == The English sparrows we have in the US today are desceded from a few introduced in New York in the late 1800's. They quickly spread over the continent. There are variations among populations in the US today. The ones in the north are bulkier, with more average as per unit of surface area, for instance. == Single stranded RNA is much more unstable than DNA, but double-stranded RNA is quite respectably stable. == In the molecular fate of the pseudogenes or the non-functional motifs; it illustrates what generally happens to the sequence whose function is no longer impacts positively on the fitness and thus falls out of favor with natural selection. What happens exactly depends on the particular sequence, but on average one finds a lot of mutations there, including the ones that are not tolerated in the functional sequences - stops, frame-shifts, mutations of the \conserved\ residues that play role in catalysis etc. After some (long) time we might no longer recognize the sequence original shape, as it deviates further and further from the functional ancestor, but it will linger around long enough for us to see a plethora of these sequences whose former function can be easily inferred. In other words, cellular genomes carry around not only the finished products, but also works in progress as well as the remains of already dead projects. == The better adapted an organism is to its environment the better the chance that such a large change would be harmful. No one in science believes that evolution took place in this fashion, and the genetic record bears this out. In fact, the extremely low probability of such mutations being successful is why creationists attempt to claim that evolution depends upon them. Punctuated equilibrium requires no such large mutations within a single generation. It simply says that over the time that a species exists (eons), changes within that species tend to occur over relatively short periods of time compared to longer times of relative stasis. A relatively short period to a paleontologist is a very long time == Biological evolution is a change in the genetic characteristics of a population over time. That this happens is a fact. Biological evolution also refers to the common descent of living organisms from shared ancestors. The evidence for historical evolution -- genetic, fossil, anatomical, etc. -- is so overwhelming that it is also considered a fact. The theory of evolution describes the mechanisms that cause evolution. So evolution is both a fact and a theory. See the Evolution is a Fact and a Theory FAQ, the http://www.talkorigins.org/faqs/evolution-fact.html Introduction to Evolutionary Biology FAQ and the Five Major http://www.talkorigins.org/faqs/faq-intro-to-biology.html Misconceptions about Evolution FAQ. http://www.talkorigins.org/faqs/faq-misconceptions.html#proof Evolution has been observed, both directly and indirectly. It is true. See the Five Major Misconceptions about Evolution FAQ. http://www.talkorigins.org/faqs/faq-misconceptions.html#observe Speciation has been observed, both in the laboratory and in nature. See the Observed Instances of Speciation FAQ and another FAQ http://www.talkorigins.org/faqs/faq-speciation.html listing some more observed speciation events. http://www.talkorigins.org/faqs/speciation.html == Evolution is defined as "the genetic transformation of populations through time, created by alterations in the genetic makeup of populations from generation to generation. The consequences of this process are changes in the adaptations and diversity of populations. This mechanism of descent with modification is responsible for the pattern and variety of life on earth: a tall order for so simple a concept. The theory part of the "theory of evolution" is concerned with how these changes in genetic makeup occur and what effect they have on populations. == Aiello & Dean "Evolutionary anatomy" == There are 37 genera of monkeys in the Old World. http://en.wikipedia.org/wiki/Genus one genus turning into another, in the dog-like animals turning into horses Hyracotherium is not the same genus of animal as Equis. http://www.talkorigins.org/faqs/horses/horse_evol.html Evolution is better described as descent with modifications. All smaller taxinomic groups fit neatly inside other, larger groups, and there is no insurmoutable division between any of these groups. == Finch Evolution Grant PR, Grant BR. Unpredictable evolution in a 30-year study of Darwin's finches. Science. 2002 Apr 26;296(5568):707-11. Grant PR, Grant BR, Petren K. A population founded by a single pair of individuals: establishment, expansion, and evolution. Genetica. 2001;112-113:359-82. Grant PR, Grant BR. Non-random fitness variation in two populations of Darwin's finches. Proc R Soc Lond B Biol Sci. 2000 Jan 22;267(1439):131-8. == The coelosaurs fit the description of an ancestor of birds.. == A genome is the collective word for the set of genes carried in the cells of an organism. As organisms move into new niches, old structures will either be pressed into new uses, or become unused. In the former case, natural selection will favor changes that adapt the old structures to new uses (that is, they become nascent structures). Examples are the wing of _Archaeopteryx_, with its avian plumage over a lengthened but otherwise typical theropod arm, or the flattened but not finned tail of the marine iguanas of the Galapagoes. In the latter case, either natural selection will let any changes have the same chances as any other, or favor changes that reduce the energy and resource costs of the disused part (by shrinking and simplifying it). Since most mutations will tend to degrade a complex structure, the lack of selection, all by itself, will tend to wear down unused structures (e.g. a random change to an eye is more likely to blind it than make it see better; only the early death of most such mutants in populations that need vision prevent all species from going blind.). Information theory is not an application of the second law of thermodynamics; entropy in Shannon information theory is a different concept from entropy in thermodynamics. Nor does the creation model incorporate information theory, so much as allude to it, and plaster its terms over arguments having nothing to do with information theory _strictu sensu_. If you can suspect that vampire cheek teeth (which some vampire bats have none of, and others have several of) might have some function, what *couldn't* you suspect of having a function? If a structure truly had no function at all, how would one ever be sure of it (since simply noting that it has no discernable function, and clearly lacks the functions of its homologs, is evidently insufficient). You cannot find any function for vampire molars, or cave fish eyes Eyes (in cave fish) that don't sense light at all certainly have reduced functionality. Wings of flightless birds surely have less functionality than the wings of flying birds. And the cheek teeth of vampire bats seem to have extremely reduced functionality, given that such bats don't chew. The teeth of fetal baleen whales don't develop into functional teeth (or any other kind of teeth) in baleen whales that have been born, and the same goes for their hind limb buds. All these structures seem to have severely reduced functionality. It is not neccesary to establish that the explanation is neoDarwinian. The claim of vestigiality is a claim about modification of functional ancestral structures; it says nothing about the mechanism of such modification except that it must work by incremental modification of existing structures. It happens that mutation, natural selection, and genetic drift are the only demonstrated mechanisms for doing this, but vestigial organs would still stand as evidence of common descent if some other mechanism could be demonstrated. The apparent vestiges are corroborations of common descent, regardless of mechanism. What distinguishes the nonfunctional or reduced-functional structures expected on evolutionary grounds is the existence of homologous structures with obvious functions in otherwise similar species. And, again, this is part of the general pattern of dissimilar structures serving similar purposes, and similar structures serving dissimilar purposes that evolution predicts, given a pattern of opportunistic and _ad hoc_ modifications of existing species for new functions in new environments. Vestigial organs exist, and imply common descent. The vestiges are offered as evidence of common descent; they are explicable in terms of mutation and natural selection, and other mechanisms are not known which might explain them. Disuse in the Darwinian sense is not a Lamarckian mechanism. == http://www.talkorigins.org/faqs/abioprob/ http://www.talkorigins.org/faqs/abioprob/abioprob.html http://www.resa.net/nasa/origins_life.htm http://www.infidels.org/library/modern/richard_carrier/addendaB.html http://www.talkorigins.org/origins/postmonth/apr98.html http://www.talkorigins.org/origins/postmonth/jan02.html http://hem.hj.se/~josv/artsubj.htm#bioabiochem === In his book 'Chance and Necessity', Monod (1971) discussed the role of mutation in evolution. Recognizing that the occurrence of mutation has nothing to do with the teleonomy (purpose) of an organism, he concluded 'chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free, but blind, at the very root of the stupendous ediface of evolution.' Chance plays an important role not only in the occurrence of mutation but also in the fixation of mutant genes, whether or not these genes are advantageous. Survival of a species also depends on various chance factors. == "Darwin's Cathedral: Evolution, Religion and the Nature of Society" by David Sloan Wilson. (2002) == PCNA is a member of the "sliding clamp" family of proteins, which are so-named because of their unique shape and function. Sliding clamps are ring-shaped proteins that slide along strands of DNA. DNA is fed through the hole in the center, and the PCNA acts as a docking mechanism for other proteins that need to interact with the DNA to make repairs or copies or to take part in other genetically regulated tasks. Genes that code for sliding clamp proteins are present in all forms of life except for some viruses. In humans, at least a dozen proteins are known to dock with PCNA. Each of them docks with PCNA by inserting a kind of key known as a PCNA-interacting protein, or "PIP-box," which binds chemically to the PCNA and holds the docked protein on the DNA strand. == Different alleles or forms of a gene (meaning different DNA sequences) need not produce different phenotypes. For example, a significant number of sequence changes in the third nucleotide of a codon produces a protein with the same amino acid sequence. So you can have two different alleles (DNA sequences) with these different third nucleotide codons even though there is no difference in the protein they make or in the phenotype that that protein produces. However, the important feature of a 'selectively neutral allele' is not whether or not it produces a different protein or phenotype, but whether the difference, if any, in the phenotype that is produced has an effect on reproductive success. While it is certainly true that silent allele differences (such as those third nucleotide changes) are often selectively neutral, so are many changes that produce an amino acid difference. There can be proteins with different aa sequence that have no significant functional difference wrt what those proteins do. And there can even be changes in DNA and their proteins that have an observable phenotypic effect (such as coat color) without that phenotypic difference having a significant effect on reproductive success (at least in some environments), which is the metric by which one determines selective neutrality. Allele difference is determined at the DNA level. Selective neutrality is determined at the phenotypic level. == Evolution http://www.talkorigins.org/faqs/faq-transitional/part2a.html#primate http://www.talkorigins.org/faqs/homs/ http://www.handprint.com/LS/ANC/evol.html http://www.asu.edu/clas/iho/science.htm http://www.anthro.ucdavis.edu/faculty/mchenry/miocene.htm http://www.lions.odu.edu/~kkilburn/203_lectures/evo16.pdf http://wwww.dur.ac.uk/t.c.rae/CT/folia_rae.pdf http://arjournals.annualreviews.org/doi/full/10.1146/annurev.anthro.29.1.147 ?cookieSet=1 http://faculty.uca.edu/~benw/biol4415/lecture10c/ http://www.anthro.ucdavis.edu/courses/su02/ant1/Reader.pdf http://www.d.umn.edu/cla/faculty/troufs/anth1602/pcprimpr.html http://biology.fullerton.edu/biol409/ch/ch17.html www.lions.odu.edu/~kkilburn/203_lectures/evo16.pdf http://assets.cambridge.org/0521571243/sample/0521571243WSC00.PDF http://www.cmnh.org/kadabba/temporarybackgrounder.htm http://members.aol.com/darwinpage/hominid.htm http://www.origins.tv/darwin/hominid.htm http://www.asa3.org/archive/evolution/199901/0038.html