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Original great ape? Probably not

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An 11.9 million-year-old ape fossil discovered in Catalonia, Spain, in 2002, and subsequently given the name Pierolapithecus catalaunicus, lived around the time when the great apes first appeared, according to Dr. Ashley Hammond, a University of Missouri anatomical expert who examined the creature’s pelvis and co-authored a recent study describing its morphology. Science Daily has a report on the study by Hammond et al., which is entitled, Middle Miocene Pierolapithecus provides a first glimpse into early hominid pelvic morphology, and which is due for publication in the Journal of Human Evolution later this year. Non-scientist readers who would like to know more about the fossil ape might like to read Victoria Woollaston’s report in The Daily Mail, here: it’s refreshingly jargon-free and has lots of great illustrations.

Hammond has carefully avoided making inflated claims for the fossil she examined: “Contrary to popular belief, we’re not looking for a missing link,” she says. Nevertheless, she feels confident that Pierolapithecus lived near the beginning of the time when the great apes first appeared, but before they had begun to diversify into humans, chimps, gorillas and orangutans. Additionally, she believes that the fossil ape dates from some time after the split between the great apes and the lesser apes (gibbons and siamangs), which are much smaller in size, and have relatively longer arms and smaller brains than the great apes. In plain English: if Pierolapithecus isn’t the original great ape, it’s a very near relative: close enough to a common ancestor of humans, chimps, gorillas and orangutans.

Hammond’s report goes on to add that Pierolapithecus had a wider pelvis than earlier fossil apes, which may be related to the ape’s need for greater lateral balance and stability while using its forelimbs. It seems to have engaged in a variety of upright activities, including vertical climbing. However, it lacked the long, curved finger bones that an ape would need for suspending itself from a tree branch. In an interview, Hammond stated:

“Today, great apes such as chimpanzees, orangutans, bonobos and gorillas use forelimb-dominated behaviors to swing below branches. But Pierolapithecus catalaunicus didn’t have the long, curved finger bones needed for suspension, so those behaviors evolved more recently.”

So, has the original great ape been found? Probably not. In fact, there are several good reasons to be skeptical of the proposal that Pierolapithecus may have been the ancestor of all great apes.

1. The date: is the fossil too young?

As the Science Daily report correctly noted, Pierolapithecus catalaunicus is only 11.9 million years old. But the fossils of the oldest known orangutan ancestor, Sivapithecus, date from 9 to 13.9 million years ago, which suggests that the new fossil may be ancestral to African apes but not the orangutan.

As if that were not bad enough, the molecular clock has recently been recalibrated by some scientists, who now date the human-chimp split to around 8 to 10 million years ago, instead of 4 to 7 million years ago, as was believed until recently. In a report published in Proceedings of the National Academy of Sciences last year, Langergraber et al. estimated the human-chimp split to have occurred somewhere between 6.8 and 11.6 million years ago, and the human-gorilla split between 10.9 and 17.2 million years ago (Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution, PNAS, 39, vol. 109, pp. 15716-15721, 25 September 2012). If that’s the case, then the supposed common ancestor of orangutans, humans, chimps and gorillas must have been considerably older. Around the same time last year, Aylwyn Scally and Richard Durbin published a review of molecular clock research conducted to date, (“Revising the human mutation rate: implications for the understanding human evolution” in Nature Reviews Genetics 13:745-753, October 2012, doi:10.1038/nrg3295) and suggested that the molecular clock used to date events in hominid prehistory may run more slowly than previously thought.

One startling implication of the new research, pointed out by science writer Ann Gibbons in a report in Science magazine (Vol. 338, 12 October 2012), entitled, Turning Back the Clock: Slowing the Pace of Prehistory, is that the date of the split between orangutans and other great apes would have to be revised upwards from 13-14 million years ago to anywhere from 34 to 46 million years ago – an impossible result that has researchers scratching their heads. “A human-orangutan split at 40 million years is absolutely crazy,” says paleoanthropologist David Begun of the University of Toronto, St. George, in Canada.

Scally and Durbin have attempted to explain away this problem by suggesting that the mutation rate was faster early on in primate evolution, and that it later slowed in the African apes. But the slowdown proposed would have to have been extraordinarily dramatic, argues Harvard University population geneticist David Reich, in a supplement to a paper he and his research team recently published (Nature Genetics, 44, 1161-1165 (2012), doi:10.1038/ng.2398). Reich estimates the split between orangutans and other great apes to have occurred 2.65 times earlier than the human-chimp split. So if 11.9 million-year-old Pierolapithecus catalaunicus is the original great ape, then humans and chimps split only 4.5 million years ago – which would mean that fossils of creatures such as Sahelanthropus, Orrorin and possibly also Ardipithecus, would no longer be on the line leading to human beings – a result that is not likely to make paleoanthropologists happy.

2. The location: shouldn’t it be in Africa or Asia, rather than Europe?

Since all the existing great ape species live in either Southeast Asia or Africa, the idea that Pierolapithecus, which lived in Spain, was an ancestor of all modern great apes doesn’t make a lot of sense. Also, most of the evolution of great apes and humans is supposed to have taken place in Africa.

It has been suggested that since the Mediterranean Sea expanded and contracted frequently in the past, Pierolapithecus could well have lived on two continents: Europe and Africa. But Professor David Pilbeam, who is currently Henry Ford II Professor of the Social Sciences at Harvard University and curator of paleoanthropology at the Peabody Museum of Archaeology and Ethnology in Cambridge, Massachusetts, USA, has pooh-poohed the idea that Pierolapithecus may be ancestral to modern great apes: “To me it’s a very long stretch to link this to any of the living apes,” he told BBC News in a 2004 interview, shortly after the original paper describing the ape was published in Science magazine (19 November 2004: Vol. 306 no. 5700, pp. 1339-1344). He added: “I think it’s unlikely that you would find relatives of the apes that live today in equatorial Africa and Asia up in Europe.

3. Anatomy: the fossil may not be ancestral to orangutans

David Begun, professor of paleoanthropology at the University of Toronto, Canada, told The New York Times in a 2004 interview that certain aspects of the fossil specimen’s face, palate and teeth made him inclined to believe that the species might be located farther down the evolutionary line of great apes than the common ancestor. In a BBC interview that same year, he explained his reasons for doubting that the creature was ancestral to orangutans: “I haven’t seen the original fossils. But there are four or five important features of the face, in particular, that seem to be closer to African apes. To me the possibility exists that it is already on the evolutionary line to African apes and humans.”

4. Rival contenders: a hodge-podge of hominids

It turns out that Pierolapithecus had lots of company. Not only did he have a contemporary, who lived in the same area – another mid-Miocene ape from Spain, named Anoiapithecus brevirostris, who also dates back to 11.9 million years ago – but there were ten other genera of apes from East Africa that may have been in the lineage leading up to the first appearance of the great apes, estimated by many scientists to have occurred around 13 million years ago: Proconsul, Rangwapithecus, Dendropithecus, Limnopithecus, Nacholapithecus, Equatorius, Nyanzapithecus, Afropithecus, Heliopithecus, and Kenyapithecus, an ape considered by some experts to have been the true ancestor of all great apes.

Other creatures from around that time include Otavipithecus, which is known from cave deposits in Namibia, and the monkey-like Dryopithecus, known from several sites in Eurasia and Africa.

To be fair, I would like to point out that Dr. Victoria Hammond, who examined the pelvis of Pierolapithecus recently, has downplayed the claim that this creature might have been the ancestor of all great apes. But the claim has a long history: it was made as far back as 2004 and is still made today. It’s about time that somebody punctured Pierolapithecus‘s balloon with a healthy dose of skepticism. Interesting ape fossil? Sure. But missing link it almost certainly ain’t.

The only thing we know is that we don’t know

Some of us are old enough to remember the times when the term “hominid” referred to a family believed to contain humans and their prehistoric ancestors but not the great apes (gorillas, chimps and orangutans), who were classed in a separate family: Pongidae. Back in those days, Ramapithecus was widely touted as the ancestor of the hominids. Now Ramapithecus has been wiped off the map, as a taxon: it’s been reclassified as Sivapithecus, and far from being a human ancestor, it’s now regarded as being on the line leading to orangutans. Humans are now placed in the same family as chimps, gorillas and orangutans. At the present time, just about the only thing one can confidently say about any hominid fossil is that any claims that are currently made about its place in our family tree are almost certainly wrong. There’s still a lot we don’t know yet.

What’s really puzzling, though, is that more scientists aren’t sitting up and taking notice of a very impressively researched paper by Dr. Branko Kozulic, entitled, Proteins and Genes, Singletons and Species, showing that that the sequenced genome of each species contains hundreds, or even thousands, of unique genes – the genes that are not shared with any other species. Kozulic argues that these unique genes and proteins, singletons, define the character of each and every species, and calculates that the odds of these proteins appearing as a result of undirected processes are astronomically low. Now that’s a finding that should give every Darwinist a massive headache. Stay tuned!

Another piece of evidence that has cut very hard against neo-Darwinian expectations has been the finding of 'species specific' alternative splicing:
Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F
As to genetic similarity, Evolutionists were completely surprised by this genetic study of kangaroos:
Kangaroo genes close to humans Excerpt: Australia's kangaroos are genetically similar to humans,,, "There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order," ,,,"We thought they'd be completely scrambled, but they're not. There is great chunks of the human genome which is sitting right there in the kangaroo genome," http://www.reuters.com/article/science%20News/idUSTRE4AH1P020081118 First Decoded Marsupial Genome Reveals "Junk DNA" Surprise - 2007 Excerpt: In particular, the study highlights the genetic differences between marsupials such as opossums and kangaroos and placental mammals like humans, mice, and dogs. ,,, The researchers were surprised to find that placental and marsupial mammals have largely the same set of genes for making proteins. Instead, much of the difference lies in the controls that turn genes on and off. http://news.nationalgeographic.com/news/2007/05/070510-opossum-dna.html
I'm just left wondering exactly where evolutionists should place the kangaroos on their cartoon drawings that show man evolving from apes. Perhaps they can place them next to Zebrafish which show a 'surprising' similarity to humans here:
Family Ties: Completion of Zebrafish Reference Genome Yields Strong Comparisons With Human Genome - Apr. 17, 2013 Excerpt: Researchers demonstrate today that 70 per cent of protein-coding human genes are related to genes found in the zebrafish,,, http://www.sciencedaily.com/releases/2013/04/130417131725.htm
Yet, as has been highlighted in this post, there are a growing number of completely unique, 'species specific', ORFan genes that are now being found,,,
"More than 6 percent of genes found in humans simply aren't found in any form in chimpanzees. There are over fourteen hundred novel genes expressed in humans but not in chimps." Jerry Coyne - ardent and 'angry' neo-Darwinist - professor at the University of Chicago in the department of ecology and evolution for twenty years. He specializes in evolutionary genetics. Genes from nowhere: Orphans with a surprising story - 16 January 2013 - Helen Pilcher Excerpt: Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing. http://ccsb.dfci.harvard.edu/web/export/sites/default/ccsb/publications/papers/2013/All_alone_-_Helen_Pilcher_New_Scientist_Jan_2013.pdf An integrated encyclopedia of DNA elements in the human genome - Sept. 6, 2012 Excerpt: Analysis,,, yielded 57 confidently identified unique peptide sequences in intergenic regions relative to GENCODE annotation. Taken together with evidence of pervasive genome transcription, these data indicate that additional protein-coding genes remain to be found. http://www.nature.com/nature/journal/v489/n7414/full/nature11247.html
Where will the ORFan gene percentage finally end up? Nobody really knows, but whatever the final percentage turns out to be its not going to be pleasant for neo-Darwinists:
Common Ancestry: Wikipedia vs. the Data - Casey Luskin - October 5, 2012 Excerpt: In fact, the largest category of genes here is eukaryotic (cells with a nucleus) genes that have no homolog among prokaryotes (cells without a nucleus) -- they don't even have any possible candidate ancestors to explain where these genes came from, much less a consistent pattern of similarity pointing to one particular ancestor. http://www.evolutionnews.org/2012/10/common_ancestry_1065001.html
But as mentioned previously, the alternative code makes this much worse. The reason why is that now not only do neo-Darwinists have to try to explain how genes can pop out of nowhere by Darwinian mechanisms, (and believe me they will try), but now neo-Darwinists must try to explain how entire 'species specific' alternative splicing codes can pop out of nowhere. The reason why finding 'species specific' alternative splicing codes is so devastating to neo-Darwinian (bottom up) evolution is best understood by taking a look at what Richard Dawkins said about what would happen if one were to 'randomly' change the regulatory genetic code once it is in place:
Venter vs. Dawkins on the Tree of Life - and Another Dawkins Whopper - March 2011 Excerpt:,,, But first, let's look at the reason Dawkins gives for why the code must be universal: "The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation...this would spell disaster." (2009, p. 409-10) OK. Keep Dawkins' claim of universality in mind, along with his argument for why the code must be universal, and then go here (linked site listing 23 variants of the genetic code). Simple counting question: does "one or two" equal 23? That's the number of known variant genetic codes compiled by the National Center for Biotechnology Information. By any measure, Dawkins is off by an order of magnitude, times a factor of two. http://www.evolutionnews.org/2011/03/venter_vs_dawkins_on_the_tree_044681.html
Bottom line is that if any regulatory code, such as the genetic code or the alternative splicing code, is 'randomly changed' in part, it throws the entire code out of whack and will be 'instantly catastrophic', to use Richard Dawkins' most appropriate term! Installing a regulatory code is a all or nothing, 'top down', take it or leave it deal. And that is what makes this particular piece of evidence so devastating for neo-Darwinists! It is good to remember just how hard it was to crack the alternative splicing code:
Breakthrough: Second Genetic Code Revealed - May 2010 Excerpt: The paper is a triumph of information science that sounds reminiscent of the days of the World War II codebreakers. Their methods included algebra, geometry, probability theory, vector calculus, information theory, code optimization, and other advanced methods. One thing they had no need of was evolutionary theory,,, http://crev.info/content/breakthrough_second_genetic_code_revealed
supplemental note:
"In the last ten years, at least 20 different natural information codes were discovered in life, each operating to arbitrary conventions (not determined by law or physicality). Examples include protein address codes [Ber08B], acetylation codes [Kni06], RNA codes [Fai07], metabolic codes [Bru07], cytoskeleton codes [Gim08], histone codes [Jen01], and alternative splicing codes [Bar10]. Donald E. Johnson – Programming of Life – pg.51 - 2010
I think that Phillip Johnson did an excellent job of summarizing the inordinate bias that is given to the hypothetical transitional fossils between man and apes:
Phillip Johnson - ,,,"Likewise with the ape-men. That is another area where fossilization is very rare. And where the bones of humans and apes are rather similar anyway. So (someone) can find a variant ape bone, its pretty easy to give it a story about how it is turning into a human being. If you tell the story well enough, and successfully, you get your picture on the cover of National Geographic and you become rich and famous. This could effect your judgement. One of the things that amused me is that there are so many fossil candidates for human ancestry, and so very, very, few that are candidates for ancestors of the great apes. There should be just as many (if not more) but why not? Well any economist can give you the answer to that. Human ancestors have a great American value so they are produced at a much greater rate. Now these were also grounds to be suspicious with what was going on. That there was obviously so much subjectivity. ,, The Standard explanation for why the fossil record is not more supportive of Darwinian expectations than it is, if you find that out at all (that the fossil record does not fit Darwinian expectation), is that there are so few fossils, (thus) most things aren't fossilized. That is why (we are told by Darwinists) that the fossil record has so many gaps. Not that the theory has many gaps but that the fossil record has so many gaps. Yet that is odd if the problem is the greatest where the fossil record is most complete and if the confirming examples are found where fossils are rarest. that doesn't sound like it could be the explanation." - Phillip Johnson - April 2012 - audio/video http://www.youtube.com/watch?v=FJDlBvbPSMA&feature=player_detailpage#t=903s
I thought Casey Luskin did a fine job going through the literature and finding the true state for this line of evidence:
Read Your References Carefully: Paul McBride's Prized Citation on Skull-Sizes Supports My Thesis, Not His - Casey Luskin - August 31, 2012 Excerpt of Conclusion: This has been a long article, but I hope it is instructive in showing how evolutionists deal with the fossil hominin evidence. As we've seen, multiple authorities recognize that our genus Homo appears in the fossil record abruptly with a complex suite of characteristics never-before-seen in any hominin. And that suite of characteristics has remained remarkably constant from the time Homo appears until the present day with you, me, and the rest of modern humanity. The one possible exception to this is brain size, where there are some skulls of intermediate cranial capacity, and there is some increase over time. But even there, when Homo appears, it does so with an abrupt increase in skull-size. ,,, The complex suite of traits associated with our genus Homo appears abruptly, and is distinctly different from the australopithecines which were supposedly our ancestors. There are no transitional fossils linking us to that group.,,, http://www.evolutionnews.org/2012/08/read_your_refer_1063841.html McBride Misstates My Arguments in Science and Human Origins - Casey Luskin September 5, 2012 Excerpt: At the end of the day, I leave this exchange more confident than before that the evidence supports the abrupt appearance of our genus Homo. http://www.evolutionnews.org/2012/09/mcbride_misstat063931.html
Just how prone this line of evidence is to fraudulent misrepresentation by Darwinists is highlighted in the following articles:
Paleoanthropology Excerpt: In regards to the pictures of the supposed ancestors of man featured in science journals and the news media Boyce Rensberger wrote in the journal Science the following regarding their highly speculative nature: "Unfortunately, the vast majority of artist's conceptions are based more on imagination than on evidence. But a handful of expert natural-history artists begin with the fossil bones of a hominid and work from there…. Much of the reconstruction, however, is guesswork. Bones say nothing about the fleshy parts of the nose, lips, or ears (or eyes). Artists must create something between an ape and a human being; the older the specimen is said to be, the more apelike they make it.... Hairiness is a matter of pure conjecture." http://conservapedia.com/Evolution#Paleoanthropology "National Geographic magazine commissioned four artists to reconstruct a female figure from casts of seven fossil bones thought to be from the same species as skull 1470. One artist drew a creature whose forehead is missing and whose jaws look vaguely like those of a beaked dinosaur. Another artist drew a rather good-looking modern African-American woman with unusually long arms. A third drew a somewhat scrawny female with arms like a gorilla and a face like a Hollywood werewolf. And a fourth drew a figure covered with body hair and climbing a tree, with beady eyes that glare out from under a heavy, gorilla-like brow." “Behind the Scenes,” National Geographic 197 (March, 2000): 140 https://uncommondesc.wpengine.com/intelligent-design/human-evolution-skull-1470-it-turns-out-has-a-multiple-personality-disorder/
One can see that 'artistic license' for human evolution being played out on the following site.
10 Transitional Ancestors of Human Evolution by Tyler G., March 18, 2013 http://listverse.com/2013/03/18/10-transitional-ancestors-of-human-evolution/
Please carefully note, on the preceding site, how the sclera (white of the eye), a uniquely human characteristic, was brought in very early on, in the artists' reconstructions, to make these cartoon ape-men fossils appear much more human than they actually were, even though the artists making the reconstructions have no clue whatsoever as to what the colors of the eyes, of these supposed transitional fossils, actually were.
Evolution of human eye as a device for communication - Hiromi Kobayashi - Kyoto University, Japan Excerpt: The uniqueness of human eye morphology among primates illustrates the remarkable difference between human and other primates in the ability to communicate using gaze signals. http://www.saga-jp.org/coe_abst/kobayashi.htm
supplemental note:
"alleged restoration of ancient types of man have very little, if any, scientific value and are likely only to mislead the public" Earnest A. Hooton - physical anthropologist - Harvard University “We have all seen the canonical parade of apes, each one becoming more human. We know that, as a depiction of evolution, this line-up is tosh (i.e. nonsense). Yet we cling to it. Ideas of what human evolution ought to have been like still colour our debates.” Henry Gee, editor of Nature (478, 6 October 2011, page 34, doi:10.1038/478034a), Icon Of Evolution - Ape To Man - The Ultimate Deception - Jonathan Wells - video http://vimeo.com/19080087 When we consider the remote past, before the origin of the actual species Homo sapiens, we are faced with a fragmentary and disconnected fossil record. Despite the excited and optimistic claims that have been made by some paleontologists, no fossil hominid species can be established as our direct ancestor. Richard Lewontin - "Human Diversity", pg.163 (Scientific American Library, 1995) - Harvard Zoologist Evolution of the Genus Homo - Annual Review of Earth and Planetary Sciences - Tattersall, Schwartz, May 2009 Excerpt: "Definition of the genus Homo is almost as fraught as the definition of Homo sapiens. We look at the evidence for “early Homo,” finding little morphological basis for extending our genus to any of the 2.5–1.6-myr-old fossil forms assigned to “early Homo” or Homo habilis/rudolfensis." http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.earth.031208.100202 Man is indeed as unique, as different from all other animals, as had been traditionally claimed by theologians and philosophers. Evolutionist Ernst Mayr (What Evolution Is. 2001) “Something extraordinary, if totally fortuitous, happened with the birth of our species….Homo sapiens is as distinctive an entity as exists on the face of the Earth, and should be dignified as such instead of being adulterated with every reasonably large-brained hominid fossil that happened to come along.” Anthropologist Ian Tattersall, The Fossil Trail: How We Know What We Think We Know about Human Evolution (Oxford: Oxford University Press, 1996), 246. (curator at the American Museum of Natural History)
I think this is the best case of investigative journalism I've seen yet on this site, and I work for some. englishmaninistanbul
Ba77 @3, good stuff; I wouldn't have guessed about the abundance of unique domains. As a side note, Branko Kozulic is on the bio-complexity editorial team. Chance Ratcliff
Is there any evidence for human/primate biological relationship besides looking the same?? No! If a creator wanted to put a special being into the best type of body within the limited equation of biological forms then it would also be a option that man was just given a like looking body as a primate but unrelated by descent etc. One would never know this if the only option for looking like apes is because look alikes are evidence done of descent. Evolutionists push god into a corner. Anyways its still just lines of reasoning and not about biological scientific evidence that persuades people we are apes aplenty. Robert Byers
This as well Chance:
Proteins and Genes, Singletons and Species - Branko Kozuli? Excerpt: Horizontal gene transfer is common in prokaryotes but rare in eukaryotes [89-94], so HGT cannot account for singletons in eukaryotic genomes, including the human genome and the genomes of other mammals.,,, A recent study, based on 573 sequenced bacterial genomes, has concluded that the entire pool of bacterial genes -the bacterial pan-genome-looks as though of infinite size, because every additional bacterial genome sequenced has added over 200 new singletons [111]. In agreement with this conclusion are the results of the Global Ocean Sampling project reported by Yooseph et al., who found a linear increase in the number of singletons with the number of new protein sequences, even when the number of the new sequences ran into millions [112]. The trend towards higher numbers of singletons per genome seems to coincide with a higher proportion of the eukaryotic genomes sequenced. In other words, eukaryotes generally contain a larger number of singletons than eubacteria and archaea.,,, Today, almost ten years since the announcement of the first draft of the human genome sequence, no structural assignment is available for about 38% of human proteins [64]: at present we thus lack basic information about a large fraction of the proteins of human proteome[115].,,, That hypothesis - that evolution strives to preserve a protein domain once it stumbles upon it contradicts the power law distribution of domains. The distribution graphs clearly show that unique domains are the most abundant of all domain groups [21, 66, 67, 70, 72, 79, 82, 86, 94, 95], contrary to their expected rarity.,,, http://vixra.org/pdf/1105.0025v1.pdf
From the OP: Proteins and Genes, Singletons and Species
Abstract Recent experimental data from proteomics and genomics are interpreted here in ways that challenge the predominant viewpoint in biology according to which the four evolutionary processes, including mutation, recombination, natural selection and genetic drift, are sufficient to explain the origination of species. The predominant viewpoint appears incompatible with the finding that the sequenced genome of each species contains hundreds, or even thousands, of unique genes - the genes that are not shared with any other species. These unique genes and proteins, singletons, define the very character of every species. Moreover, the distribution of protein families from the sequenced genomes indicates that the complexity of genomes grows in a manner different from that of self-organizing networks: the dominance of singletons leads to the conclusion that in living organisms a most unlikely phenomenon can be the most common one. In order to provide proper rationale for these conclusions related to the singletons, the paper first treats the frequency of functional proteins among random sequences, followed by a discussion on the protein structure space, and it ends by questioning the idea that protein domains represent conserved units of evolution.
Conclusion The huge amount of DNA sequence data accumulated over the past decade has provided key insights about uniqueness of living organisms. The most important insight is that the genome of each species contains hundreds, or even thousands, of unique genes - the genes that are not shared with any other species. The origin of species is thus intrinsically related to these unique genes. Each unique gene, and accordingly each novel functional protein encoded by that gene, however, represents a major problem for evolutionary theory because unique proteins are as unrelated as the proteins of random sequences - and among random sequences functional proteins are exceedingly rare. Experimental data reviewed here suggest that at most one functional protein can be found among [[10^20]] proteins of random sequences. Hence every discovery of a novel functional protein (singleton) represents a testimony for successful overcoming of the probability barrier of one against at least [[10^20]], the probability defined here as a “macromolecular miracle”. More than one million of such “macromolecular miracles” are present in the genomes of about two thousand species sequenced thus far. Assuming that this correlation will hold with the rest of about 10 million different species that live on Earth [157], the total number of “macromolecular miracles” in all genomes could reach 10 billion. These [[10^10]] unique proteins would still represent a tiny fraction of the [[10^470]] possible proteins of the median eukaryotic size. If just 200 unique proteins are present in each species, the probability of their simultaneous appearance is one against at least [[10^4,000]]. Probabilistic resources of our universe are much, much smaller; they allow for a maximum of [[10^149]] events [158] and thus could account for a one-time simultaneous appearance of at most 7 unique proteins. The alternative, a sequential appearance of singletons, would require that the descendants of one family live through hundreds of “macromolecular miracles” to become a new species - again a scenario of exceedingly low probability. Therefore, now one can say that each species is a result of a Biological Big Bang; to reserve that term just for the first living organism [21] is not justified anymore. This view about species differs sharply from the predominant one according to which speciation is caused by reproductive isolation of two populations [159, 160] mediated by difficult to find speciation genes [161-163]. Evolutionary biologists of earlier generations have not anticipated [164, 165] the challenge that singletons pose to contemporary biologists. By discovering millions of unique genes biologists have run into brick walls similar to those hit by physicists with the discovery of quantum phenomena. The predominant viewpoint in biology has become untenable: we are witnessing a scientific revolution of unprecedented proportions.
Chance Ratcliff
Great OP, thanks.
"What’s really puzzling, though, is that more scientists aren’t sitting up and taking notice of a very impressively researched paper by Dr. Branko Kozulic, entitled, Proteins and Genes, Singletons and Species, showing that that the sequenced genome of each species contains hundreds, or even thousands, of unique genes – the genes that are not shared with any other species. Kozulic argues that these unique genes and proteins, singletons, define the character of each and every species, and calculates that the odds of these proteins appearing as a result of undirected processes are astronomically low. Now that’s a finding that should give every Darwinist a massive headache. Stay tuned!"
Heh. Considering the Convergent Evolution label for homoplasy, and the Rapid Evolution label given to instances of phenotypic plasticity, I'm predicting another label will arise, intended to imply that such ORFans are consistent with evolutionary theory. Perhaps Spontaneous Evolution will do. ;) Chance Ratcliff

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