Here are some good things for you. Enjoy. Letter to Robb A Massey Look at the world of biology, you will find that new species do arise in vast numbers. Each geological period has thousands of species not found in any earlier periods. These species are obvioulsy derived from earlier species as animals and plants without ancestors is mythology. They appear in an evolutionry sequence world wide. Single cell sea life, multicell sea life, fish, amphibians, reptiles, mammals and birds. The earth is 4.55 billion years and most speciation took place in the last 570 million years since the beginning of the Precambrian. No modern species is found earlier than the beginning of the Tertiary. The comparison of DNA similarities shows the same degree of relationship as the fossils indicate. Humans and chimps have 98% identical DNA. Protein and amino acid sequences show the same degree of genetic relationship as the fossils. There are more mechanisms to speciation than just mutation. There is recombination during mating!, which is far more important than mutation alone. This process can produce a series of useful DNA associations without waiting for lucky point mutations of the proper kind. The oldest life on record is prokaryote bacteria, 3.85 billion years old, which had only a limited genetic code(assumed) so all later life is derived from these bacteria and all genetic changes since then are additions and modifications to this original genetic pattern. One thing which points to a clear genetic relationship of humans with the rest of the primates is the existence in the genetic code in all primates, including humans, is the psuedogene for producing vitamin C. A psuedogene is a once coding gene which no longer can code for a biological product. If you had two computer programs, which you wish to see if one is derived from the other, you can compare the details of the code. If the later one has blocks of code identical to the earlier one, and the later one has code block never accesses by the program, that is proof which would stand up in court that the later was copied from the earlier and modified. The big idea is this. Creationism is a totally religious model of the world, derived from a literal reading of Genesis. It was assumed to be true in the early days of science, in Christian Europe. As data about nature accumulated, largely collected by fundamentalist scientists, the fact became clear that Genesis does not describe this physical world but a mythical world from ancient Hebrew tribal traditions. There have been many attempts in this century to impose this model of the science material of the nation's school system, by force of law. Real science does not use police power to cause its ideas to be included in educational material. In the scientific community, ideas are tested many different ways and the results which pass these tests are included by text book writers, derived from primary scientific papers and journals. If new data requires a change, later textbooks replace obsolete mistaken data with new more accurate data. This is not a scandal or weakness, but healthy growth of knowledge. Fundamentalists delight in pointing out errors and even hoaxes in past science as evidence the whole system is wrong and corrupt. This is an error. Science is not immune to error but it has processes which expose and correct these errors. Theology has no such process as it is all based on faith, which is independent of external evidence completely. In the Federal Court trials resulting from the passage of anti-science laws by several southern states, the decisions was always that creationism is religion, based on Genesis and evolution is valid science, based on observation of the physical world. Creationists have NEVER produced the THEORY OF CREATIONISM which can be tested and examined for good predictive power. It assumes miraculous interventions by a deity, which can not be reproduced or used to make predictions. It assumes a young earth and a world flood. No physical evidence exists for either. The sum of all creationist attempts to validate its system is aimed at refuting modern science rather than establishing creationism with its own observations of nature and predictions derived from its assumptions. When creationism produces a set of explanations and predictions equal to or better than those of modern science, only then will it be considered a viable alternative. This is the process by which older scientific models were replaced by later scientific models. It was not done by passing laws threatening teachers with dismissal or prison. ======= "Fossils, genes and the evolution of animal limbs", N Shubbin, C Tabin and S Carrol, Nature, 388, 639-647, 1997. The authors show that segmentation genes (the Hox family) are critical for the development of limbs in both insect and vertebrates. Even though vertebrate and insect limbs evolved independentley, they rely on these segmentation genes. ======= The 'problem' of 'fine tuning' is discussed by Andrei Linde in his excellent article in the November 1994 Scientific American, or Alan Guth in his book 'The Inflationary Universe', 1997. ----- Life in Darwin's Universe G. Bylinsky, Omni Sept 79 The Evolution of Ecological Systems May, Scientific American, Sept 1978 Chemical Evolution and the Origin of Life Dickerson, Scientific American, Sept 1978 The Evolution of the Earliest Cells Schopf, Scientific American, Sept 1978 The Evolution of Multicellular Plants and Animals Valentine, Scientific American, Sept 1978 Miller SL. (1997). Peptide nucleic acids and prebiotic chemistry Nat Struct Biol , 4, 167-9. Bohler C, Nielsen PE, and Orgel LE. (1995). Template switching between PNA and RNA oligonucleotides Nature , 376, 578-81. Nielsen PE. (1993). Peptide nucleic acid (PNA): a model structure for the primordial genetic material? Orig Life Evol Biosph , 23, 323-7. Deamer DW. (1997). The first living systems: a bioenergetic perspective. Microbiol Mol Biol Rev , 61, 239-61. Schuster P. (1993). RNA based evolutionary optimization. Orig Life Evol Biosph , 23, 373-91. Connell GJ, and Christian EL. (1993). Utilization of cofactors expands metabolism in a new RNA world. Orig Life Evol Biosph , 23, 291-7. Schwartz AW. (1997). Speculation on the RNA Precursor Problem J Theor Biol , 187, 523-7. ------- The best estimate of mutation *frequency* that I know of in higher metazoans comes from plants (corn, to be precise) because they have an extended haploid stage where some loss-of-function mutations can be directly observed. The underlying *rate* of mutational events at the molecular level in corn is probably not significantly different than that in mammals because most point mutational events are due to the basic chemistry of DNA and errors in replication in all organisms. Plant polymerases are not significantly more or less accurate than mammalian ones. And deletions and insertions occur in all metazoans. All the mutations I am mentioning are forward mutation rates, and, AFAIK, any loss-of-function mutation will produce the phenotype. > Gene # gametes examined # of mutations mutation freq > R->r 554,786 273 4.92 X 10^-4 I->i 265,391 28 1.06 X 10^-4 Pr->pr 647,102 7 1.10 X 10^-5 Su->su 1,678,736 4 2.4 X 10^-6 Y->y 1,745,280 4 2.2 X 10^-6 Sh->sh 2,469,285 3 1.2 X 10^-6 Wx->wx 1,503,744 0 <0.7 X 10^-6 > Notice that there is a 500-fold (at minimum) range in values for this small sample of genes, depending upon the particular gene being examined. Thus looking at mutation frequencies *only* for those genes that produce the most commonly observed mutant phenotypes can be wildly misleading wrt to the rate in an average gene (a point I think I have made several times). [I suspect that the high values represent genes with considerable internal sequence duplication, which can greatly increase the frequency of deletions in particular, rather than some sort of difference in the rate of point mutation in these genes. --- How to evolve irreducible complexity: Method 1: Duplication and variation. Some kinds of mutations can duplicate segments of the genome, leading to redundant copies of parts or even of entire systems. More nearly neutral mutations, such as point mutations, can then cause the redundant parts to specialize. Also, the orginal duplication need not be exact, leading directly to the formation of a protein with different functionality. Two formerly identical parts can specialize divergently so that their new functions no longer overlap, and both would then be necessary. Other redundant parts will eventually be removed by random mutations. Method 2: Exadaption or Emergent Properties A system can gradually evolve to fulfill one function but gradually acquire a second function in the process. It can then specialize on the second function until the first function is no longer obvious. Parts can also serve more than one function and switch from one system to another. Method 3: Coevolution Parts need not be integral. They can grow gradually from smaller parts, and two or more parts can grow more-or-less in unison. For example, a strong muscle needs a strong base to support it, but starting from a puny muscle and a really flimsy base, both can grow stronger together. Method 4: Random assemblage. Duplication and variation will create several unused parts that hang around just because they're not hurting anything and because no deletion mutations have yet removed them. Also, some enzymes produce secondary metabolites that stay as long as it's not harmful and the primary metabolite is still needed. If enough such random parts exist, it's entirely possible that some of them may come together to do something useful. ==== "Mutations . . . are the basis of evolution," states The World Book Encyclopedia. 1 Similarly, paleontologist Steven Stanley called mutations "the raw materials" for evolution. 2 And geneticist Peo Koller declared that mutations "are necessary for evolutionary progress." One single cell of bacteria was used to produce a culture. The culture was then split in half, and one half was intruduced to low levels of an antibiotic. After a certain length of time, both groups were subjected to high levels of the same antibiotic. The half that were already exposed usually had mutated and had become resistant. The other half was not, and died. No new genetic material was added. The only way those bacteria became resistant was through mutation. Mutation provides the raw materials, Natural selection turns them into new species. ============ Transitional forms are generally lacking at the species level, but they are abundant between larger groups." Gould, S.J. (1983) "Evolution as Fact and Theory," reprinted in _Hen's Teeth and Horse's Toes_, pp. 253-262. This was originally published in _Discover_ magazine, May 1981. -------- [Q.] I thought evolution was just a theory. Why do you call it a fact? [A.] 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 all 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. [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.] 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 [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 [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.] 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.ediacara.org/hope.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 ------ Science is a methodology for studying the repeatable qualities of public observations. This methodology includes the building of productive models, the rigourous slicing of those models with the razor, and the subjegation of those models to public scrutiny. ---- Scientists commonly use the word "fact" to mean anything in which they have so much collective confidence, that there is no longer any consideration of falsity (the phraseology that it would be "perverse" to deny the truth of the "fact" comes, I believe, from S.J. Gould). A fact is a direct statement about an observation. A theory is a productive model that explains multiple facts. ----- The primitive chordates are believed to have used gill slits for filter feeding. Actual gills, which do absorb oxygen, are a later development and it's even questionable whether our more recent crossopterygian ancestors had them. _The Developing Human_ Some of those branchial grooves develop into little pockets in the pharyngeal/laryngeal/auditory area, including the depression into which tonsils fit, develops into the Eustachian tube. The source is _Development of Vertebrate Anatomy_, by Joy B. Phillips. The first branchial pouch develops into the middle ear. Also the second, third, and fourth pair of branchial pouches develop into the tonsils, thyroid, parathyroid and thymus glands and ultimobranchial bodies. And one branchial arch contributes to the jaws. We never had gills. We had these general branchial structures that went on to make the structures listed above. Fish adapt the same primitive structures to form gills (and various glands, and other facial structures, etc.) Chordates have six branchial arches. "...all chordates, including vertebrates, pass through a pharyngula stage in which a dorsal nerve cord, notochord, and somites are integral components. Ascidians share this developmental body plan, but develop into very nonchordate adults. The developmental body plan reflects the processes of ontogeny that produce the 'phylotypic' stage that foreshadows the features elaborated in the adult. The phylotypic stage occurs after organogenesis has begun, and is shared by all members of a phylum before the divergence of their later stages. Adult structures derived from further development of the phylotypic stage are indeed homologues in having historical continuity in evolution." R. Raff, _The Shape of Life_, chapter 6. As we've learned more about genetic mechanisms, we have discovered a number of possible ways of changing the array of information on a chromosome. Some of these are: single base pair change deletion of gene segment reduplication of gene segment (see my chapter on the evolution of the parathyroid hormone gene in "Principles of Bone Biolgy", JP Bilezikian, LG Raisz and GA Rodan, eds, Academic Press, San Diego, 1996, pp 405-417.) repositioning of control elements (e.g. adjacent to a new gene) chromosomal rearrangements (18 such arrangements that have occurred to separate chimps from humans as they diverged from their common ancestor) chromosomal reduplications chromosomal deletions ====== Defeating Darwinism" by Phillip E. Johnson fundie ===== http://207.102.62.65:80/~randallg/capella/evoldiag.jpg fossil skulls ===== The largest mammals in the Late Cretaceous were more the size of a large house cat or a fox. ==== 15. Zel'dovich, Yakob B. and Grishchuk, L. P. "Structure and Future of the 'New' Universe," in Monthly Notices of the Royal Astronomical Society, 207 (1984), pp. 23P-28P 16. Vilenkin, Alexander. Birth of Inflationary Universes," in Physical Review D, 27(1983). pp. 2848-2855. 17. Vilenkin, Alexander. Quantum Creation of Universes," in Physical Review D, 30 (1984). pp.509-511. 18. Hartle, James B. and Hawking, Steven W. "Wave Function of the Universe," in Physical Review D, 28(1983), pp.2960-2975. ======= http://www.chemistry.ucsc.edu/Projects/origins1.html origin of life. [1] Larralde R, Robertson MP, and Miller SL. (1995). Rates of decomposition of ribose and other sugars: implications for chemical evolution. Proc Natl Acad Sci U S A , 92, 8158-60. [2] Schwartz AW. (1997). Speculation on the RNA Precursor Problem J Theor Biol , 187, 523-7. [3]Schwartz AW. (1997). Prebiotic evolution: selecting for homochirality before RNA. Curr Biol , 7, R477-9. Babinec P, and Krempasky J. (1994 Aug). Synergetic mechanisms of chiral symmetry breaking in prebiotic evolution. Gen Physiol Biophys, 13, 267-73. [4] Ertem G, and Ferris JP. (1996). Synthesis of RNA oligomers on heterogeneous templates. Nature , 379, 238-40. Bohler C, Nielsen PE, and Orgel LE. (1995). Template switching between PNA and RNA oligonucleotides. Nature , 376, 578-81. [5]Ding PZ, Kawamura K, and Ferris JP. (1996). Oligomerization of uridine phosphorimidazolides on montmorillonite: a model for the prebiotic synthesis of RNA on minerals. Orig Life Evol Biosph , 26, 151-71. [6]Baumann U, and Oro J. (1993). Three stages in the evolution of the genetic code. Biosystems , 29, 133-41. ==== The sample which tested old was submarine pillow basalt from the 1801 eruption and was being used as a control to determine the reliability of K-Ar dating with regards to this particular kind of formation. Kolb and Turner, "The Early Universe", (Frontiers in Physics Lecture Note Series, Addison Wesley, 1990). A nontechnical one is: "Particle Physics in the Cosmos", R. Carrigan and W. Trower (Eds), (Readings from Scientific American Magazine, 1989). If the universe were easy to understand, it would work differently and we would not be here. "The Self-Aware Universe -- How Consciousness Creates the Material World", by Amit Goswami, Ph.D., with Richard E. Reed and Maggie Goswami. This one is pretty far out and attempts to "shatter the widely popular belief held by Western science that matter is the primary 'stuff' of creation, and proposes instead that consciousness is the true foundation of all we know and perceive." After reading some of this, James, I'm even *more* "wooly about what consciousness is". http://www.wolfram.com/~terryr/apps/Asteroid3753.html ======= 1. Jacob Bronowski, "The Ascent of Man," Little, Brown & Co., Boston, 1973, p. 13. 2. Perscott Lecky, "Self Consistency, A Theory of Personality," Island Press, New York, 1937. 3. Philip Handler, ed., "Biology and the Future of Man," Oxford University Press, New York, 1970, p. 492. 4. Norbert Wiener, "Cybernetics: Control and Communication in the Animal and the Machine," John Wiley & Sons, New York, 1948. 5. Norbert Wiener, "The Human Use of Human Beings: Cybernetics and Society," Houghton Mifflin Co., New York, 1950. 6. Maxwell Maltz, "Psycho-Cybernetics," Prentice-Hall, New Jersey, 1960. 7. F. M. Esfandiary, "Up-Wingers: A Futurist Manifesto," Popular Library, New York, 1973, p. 137. 8. Barbara Hubbard, "The Futurist," February 1974, Volume VIII, No. 1, p. 28-30. 9. Edmund W. Sinnot, "Mind, Matter, and Man," Harper & Rowe, New York, 1957. ===== In the case of evolution, we have fossils going back about 40-65 million years ago (all the way back to the Eocene), and from there up. Granted, there are gaps, but considering that we've been looking for only about a hundred years, what can you expect. It took longer than that for us to learn how to make tools, and then it took about 100,00 years before we got much past that. So, you've got small insectivores in the Eocene. In the Oligocene, you have larger mammals, including some early primates (demonstrate characteristics: have post-orbital bar, have grasping hands, etc). By the Miocene, we have fully functional primates, including the dryopiths, ramapiths, and pliopiths. It's generally assumed (I think) that australopiths came out of ramapiths (they show the next step, and ramapith were the largest of the Miocene hominoids). So, now you've got about 7 species of australopiths, including the robust australopithecines, which were most likely an evolutionary dead-end. Next, we've got the homo line, starting with homo habilis, at about 2.5 million years ago. The first tool-makers/users, we think, since they've been found with stone tools intermixed. Then, you've got your homo erectus, the species that scientists are convinced, now, that we came from. These fellows were almost exactly like us post-cranially, and only had slightly more massive bones. Their skulls show a large cranial volume, around 900-1100 ccs. That's pretty large, for a non-human. Anyway, on a side track, then, there's neanderthalensis, which was just recently determined through DNA testing to not be our ancestor. Finally, there're the specimens of early homo sapiens, archaic homo sapiens, which still show brow ridges and exhibit a skull volume almost equal to ours (it should be noted that Neanderthals had an average skull volume GREATER than ours, but they were bigger all around, too, so this may not have made much difference). And, last but not least, you have anatomically modern homo sapiens, like Cro-Magnon man, from about 40,000 years ago to the present. Now, I'll grant that there are gaps: most notably in the areas between the ape-human split (although it's been postulated that australopithecus ramidus might be that ancestor), and in the area between erectus and homo sapiens (I'm not sure about that one, but I'm pretty sure there's a gap there. A rather big jump from erectus to sapiens, if there isn't). So, we've got a wonderful track from the mid-Miocene hominoids all the way to us, with gaps in a few places, but rest assured that these will eventually be filled with the proper species, since we've really had only enough time to scratch the surface of hominid evolution. ---- "The area from east to south Africa where most fossil hominids have been found is small, and founder populations of additional hominid speces might have occurred in the vast areas of western, central and north Africa that have not yet been explored. (Indeed, australopithecine fossils 3.5-3.0 million years old have very recently been discovered in Chad, in central Africa.) Literally dozens of allospecies of _ramidus_, _afarensis_, _robustus_, _habilis_, and _erectus_ could have lived in unexplored parts of Africa. The suddeness of some of the transition in the fossil record could be explained by 'budding'. This means that the new descendant type originated somewhere in a peripherally isolated population and established contact with the parental species only after it had completed its genetic restructuring. The chance that we will ever discover the location of such an isolate is rather slight." _This is Biology_; Mayr, p. 234 "When only a few hominid fossils were known, it was easy to classify them into species: _afarensis_, _africanus_, _habilis_, _erectus_, and _sapiens_. Each of these names represented between 0.25 and 1.5 million years. In recent years numerous finds are either intermediate in time between typical specimens or from different geographical regions, ========== Another letter ------ Here are some ideas which will help you to understand evolution. In a small population there are only so many traits to accentuate or eliminate by selection. In a larger population, there are more varieties of genes to be selected for. Over time, mutations can add new genes, not previously available, to modify the group. Speciation is primarily a result of recombination of existing genes, not recent mutations. New species usually occur in a small population in a distinctly different enviroment than the population as a whole. If there is a shift in the environment where the whole population lives, one of the local varieties may now become the most fit type to multiply and spread, possibly replacing the parent population. The exact details of speciation are VERY complex, due to the many environmental and genetic mechanisms which interact. The experts are still debating the details. A new species does not have to be initial ideal, but merely good enough to survive and multiply. As new mutation of genetic variations are produced, then the new population becomes more fit for the new environment, eventually becoming a large widespread population. Only then will some of them have a chance for fossilization. This will make a distinct break in the fossil record. A lack of fossils does not mean a lack of living animals at one time. Natural selection produces stability in a stable environment. It als produces rapid change in a changed enviroment. This is seen in the work of Gould in the lake Turkana snail studies. I am a physicist by profession but I read much on these subjects. Read some works by Gould to better understand evolution. There are several good ones to choose from. Dawkins wrote two works of value, "Climbing Mount Improbable" and "The Blind Watchmaker". Avoid relying on any creationist literature as it has a goal of selling a particular religion, not scientific validity. The talk.origins home page at http://www.talkorigins.org is a useful source of data and other areas have good URL sources for evolution data. Another very useful book is "Science and Earth History" by A. N. Strahler (Prometheus). This one explains the larger view of astronomy, geology and evolution. It also refutes the claims of creationists in great detail. END***************************************************************************