Humans descended from ape-like creatures? A skeptical look at the fossil record

_{Denyse O'Leary

September 28, 2013

Human evolution}

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From the new special edition of science and culture mag Salvo on science and faith:

Casey Luskin asks,”Has Science Shown That We Evolved from Ape-like Creatures?

It is not uncommon for evolutionary scientists like Wetherington (even those who teach at Christian universities) to be adamant about the evidence in favor of human evolution. Digging into the technical literature, however, we find a situation that’s starkly different from the one presented by Wetherington and many other evolutionary scientists who engage in public debates.

A closer look at the literature shows that hominin fossils generally fall into one of two categories—ape-like species or human-like species (of the genus Homo)—and that there is a large, unbridged gap between them. Despite the claims of many evolutionary paleoanthropologists, the fragmented hominin fossil record does not document the evolution of humans from ape-like precursors. In fact, scientists are quite sharply divided over who or what our human ancestors even were. Newly discovered fossils are often initially presented to the public with great enthusiasm and fanfare, but once cooler heads prevail, their status as human evolutionary ancestors is invariably called into question. More.

Comments

Vincent, thank you very much for the papers you cited in 31, 32, 33, and 34. A key part of my research these days focuses on the emergence of Geist ("spirit") from Natur ("nature"), as theorized by the German Idealists, and it will help me immensely to understand how contemporary scientists theorize that transition. Gratefully, KNKantian Naturalist_{September 29, 2013
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wd400:
With 20 year generations that’s 20 * 306,667 ~ 6 million years. You can quibble about mutation rate estimates and generation times, but they wont change the numbers such that this suddenly becomes impossible.
Who needs selection at all then? Perhaps I misunderstood the statement I was responding to;
Do these guys really think _all_ fixations between human and chimp have to be selective?
What do you mean by "fixations between humans and chimps"? Because now, in your response, you're talking about just humans. I interpreted you to be talking about similarities, but are you talking about differences?Mung_{September 29, 2013
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P.S. Although I think the anatomical changes leading from Homo habilis to Homo erectus to Heidelberg man may have been smooth, the changes in hominid brain structure were not. There were four major changes, which took place 3.5 million years ago, 1.8 million years ago, 700,000 years ago and 200,000 years ago. Another discontinuous change took place in our chromosomes, from 48 to 46 chromosomes, some time between 3,000,000 and 740,000 years ago . In short: there's plenty of room here for intelligent engineering of the human body.vjtorley_{September 29, 2013
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Finally, I'd like to point out that while the brain size of Heidelberg man (1100 to 1400 cubic centimeters) overlaps with that of modern human beings, the brain size of early Homo ergaster / erectus (around 700-850 cubic centimeters) does not. Normal human brains vary between 1050 to 1500 cubic centimeters for men and 976 to 1400 cubic centimeters for women (see here). The extreme range for human beings is 900 to 2,000 cubic centimeters (see here). I'm afraid that early Homo ergaster / erectus doesn't make the grade. It took nearly a million years for his brain to grow large enough to fall inside that range. Over that period, the increase was gradual, not sudden.vjtorley_{September 29, 2013
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I should say, however, that something very important in human evolution occurred 1.8 million years ago, in terms of brain evolution, and it's described in this article: How Our Ancestors Broke through the Gray Ceiling. The authors argue that by rights, hominid brains should have stopped growing at 700 cubic centimeters, but our ancestors somehow broke through that threshold. The authors argue that co-operative breeding was the behavioral change that made this possible. On that score, they're probably correct, but there's a lot of disagreement as to what kind of co-operative breeding it was. Was it grandmothers helping mothers to find food for their newborn babies, or was it dads helping mums, and making a commitment to stick together for the long term? For Homo erectus, it could have been the former. Only when we get to Heidelberg man, whose brain size falls within the modern human range, does the energetic cost of raising an infant become so great that monogamy would have been an absolute necessity for successful child-rearing. The authors of the paper also suggest that Homo erectus engaged in big-game hunting, but as Dubreuil argues in his paper, while there's good evidence that Homo erectus ate a lot of meat, there's no good evidence that he hunted large-scale game; probably he was an active scavenger, which means that he ate meat from carcasses that other animals had killed, and confronted any creature that tried to stop him eating. Hunting large-scale game was a risky enterprise which hominids who were unable to control their impulses would have chickened out of, as it required an ability to put the group's welfare ahead of your own, and maintain your resolve, even as a highly dangerous animal was charging right at you. Dubreuil argues that changes in the brain's prefrontal cortex made this impulse control possible - and even if you reject materialism (as I do), you can still acknowledge the fact that behaving morally requires having a brain that is wired up in the right way. Dubreuil is wary of claims that human culture emerged in a single step, but as he puts it:
Our conclusions must thus remain relatively modest. Consequently, I will not claim that there has been a single reorganization of the PFC [prefrontal cortex - VJT] in the human lineage and that it happened in Homo heidelbergensis [Heidelberg man - VJT]. I will rather contend that, if there is only one point in our lineage where such reorganization happened, it was in all likelihood there.
To be continued...vjtorley_{September 29, 2013
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Here's a quote that conveys the tenor of the new view among anthropologists:
Recent fossil and archaeological finds have complicated our interpretation of the origin and early evolution of genus Homo. It now appears overly simplistic to view the origin of Homo erectus as a punctuated event characterized by a radical shift in biology and behavior (Aiello and Anton 2012; Anton 2012; Holliday 2012; Pontzer 2012; Schwartz 2012; Ungar 2012). Several of the key morphological, behavioral, and life history characteristics thought to first emerge with H. erectus (e.g., narrow bi-iliac breadth, relatively long legs, and a more “modern” pattern of growth) seem instead to have arisen at different times and in different species. Further, accumulating data from Africa and beyond document regional morphological variation in early H. erectus and expand the range of variation in this species. These new finds also make the differences between H. erectus (s.l.) and Homo habilis (s.l.) less stark and suggest that regional variation in the former may reflect local adaptive pressures that result from inhabiting diverse environments in Africa and Eurasia. The mosaic nature of these acquisitions and the greater range of intraspecific variation, especially in H. erectus, call into question previous inferences regarding the selective factors behind the early evolution of our genus and its eventual dispersal from Africa. They also raise questions about when a modern pattern of life history might have emerged and what role, if any, it played in our early evolution.
And here's another:
The origin of Homo holds particular sway for us and has often been seen as the point in our evolution when the balance tips from a more ape-like to a more human-like ancestor. By the turn of this century, a conventional wisdom had grown up around the origin of Homo and particularly Homo erectus that cast this species as the first hominin to take important biological and behavioral steps in the direction of modern humans (Anton 2003; Shipman and Walker 1989). Homo erectus was envisioned as a large-brained, small-toothed, long-legged, narrow-hipped, and large-bodied hominin with relatively low sexual dimorphism. By virtue of a higher-quality, perhaps animal-based diet, H. erectus is said to have ranged farther, cooperated more, and quickly dispersed from Africa (Aiello and Key 2002; Anton, Leonard, and Robertson 2002; McHenry and Coffing 2000; Walker and Leakey 1993). The paucity of early Homo fossils of Homo habilis sensu lato (including Homo rudolfensis) meant that comparisons of Australopithecus (?Paranthropus) were made to H. erectus (including Homo ergaster) rather than to other early Homo. And the distinctions between Australopithecus and Homo were perhaps overemphasized by the diminutive size of the most complete Australopithecus skeleton (A.L. 288-1; Lucy), on the one hand, and the surprisingly large size of the most complete H. erectus skeleton (KNM-WT 15000; Nariokotome boy), on the other (e.g., Ruff 1993). The comparisons between H. erectus and Homo sapiens were so strongly drawn that the inclusion in the genus of some of the earliest species, such as H. habilis and H. rudolfensis, was seriously questioned on the basis of their more australopith-like postcranial skeleton, among other things (Wood and Baker 2011; Wood and Collard 1999, 2007). The fossil record never ceases to upset conventional wisdom, and over the past 2 decades, new discoveries from East and South Africa, Georgia, and even Indonesia have challenged these stark distinctions between Australopithecus and H. erectus and within non-erectus early Homo. In particular, new small-bodied and small-brained finds from the Republic of Georgia and Kenya call to question claims for universally large size in H. erectus (e.g., Gabunia et al. 2000; Potts et al. 2004; Simpson et al. 2008; Spoor et al. 2007) and focus our attention instead on the range of variation within that taxon. This variation in H. erectus has most often been referred to as sexual dimorphism and/or regional/climatic adaptations (Anton 2008; Spoor et al. 2007), although short-term accommodations and phenotypic plasticity are likely to have played an important role (see Anton 2013). And larger-sized, longer-legged Australopithecus have been found (Haile-Selassie et al. 2010), as have members of that genus who may share some postcranial characteristics with Homo (Asfaw et al. 1999; Berger et al. 2010; Kibii et al. 2011; Kivell et al. 2011; Zipfel et al. 2011). Additionally, new fossil remains of non-erectus Homo and new work on previously known remains emphasize the diversity of the early members of the genus and the ways in which they differ from Australopithecus (Blumenschine et al. 2003; Spoor et al. 2007).
To be continued...vjtorley_{September 29, 2013
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I'd also like to point out that until a few years ago, many anthropologists believed there was a huge gap between Australopithecus and Homo erectus, and some of them also believed that Homo habilis was really on the Australopithecus side of the fence. Collard and Wood argued as much in 1999, and again in their 2007 paper, Defining the genus Homo. That picture is now out of date. Recent papers published in 2012 - see here, here and here show that the transition from Australopithecus to Homo habilis was about the same size as that from Homo habilis to early Homo erectus. As for the transition from Homo erectus to Heidelberg man, it's been known for a long time that this was a fairly smooth one, anatomically speaking - so much so that some anthropologists, such as John Hawks, don't even recognize Heidelberg man as a separate species. To be continued...vjtorley_{September 29, 2013
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I'm afraid I would have to (very respectfully) disagree with Casey's claim that "the fragmented hominin fossil record does not document the evolution of humans from ape-like precursors." He does make some very good points in his article in Salvo magazine, but I think the fossil evidence for the fact of human evolution is strong, despite the presence of several gaps. Here's why. There are indeed gaps in the human fossil record, but there are no gaps between the first true human beings and their immediate (non-human) precursors. The real gaps in the record are between those precursors and the common ancestor of humans and apes. We still don't know what the common ancestor of humans and apes was, and we don't know where Australopithecus came from. There is a gap between Australopithecus and early Homo, who appeared about 2.3 or 2.4 million years ago, but it's not a huge one. There's also a gap between early Homo and Homo ergaster (or erectus if you prefer), but once again, it's smaller than we thought it was ten years ago. From an anatomical standpoint, there isn't a real gap between Homo ergaster (or erectus) and Heidelberg man. (From a neurological and chromosomal standpoint, the situation may well be very different.) But Heidelberg man (and not Homo erectus) was the first true human being, in terms of possessing reason. Benoit Dubreuil argues in a 2010 paper that Heidelberg man was the first hominid capable of what he calls co-operative feeding and co-operative breeding - that is, altruistically taking part in group hunting expedition for large animals such as mammoths and saber-tooth tigers, even at considerable risk to one's own life, and making a commitment to enter into a monogamous relationship with a woman and help raise her child over a prolonged and extended period. Those are quintessentially human commitments, requiring a great deal of self-sacrifice, coupled with a rational capacity to envisage the long-term future. You can see the difference between Homo ergaster / erectus (who appeared 1.8 million years ago) and Heidelberg man (who appeared at least 750,000 years ago) in their tools, too. A tool like this: http://www.cope.co.za/archaeo/images/master%20axe%20fullsize%20side%20b.jpg (made in Kathu Pan, South Africa, 750,000 years ago, by an unknown hominid) or like this: http://upload.wikimedia.org/wikipedia/commons/thumb/e/ee/Boxgrove_handaxe.jpg/450px-Boxgrove_handaxe.jpg (made by Heidelberg man in Boxgrove, at least 500,000 years ago) possesses an artistic symmetry and beauty that is altogether lacking in a tool like this: http://static.guim.co.uk/sys-images/Guardian/Pix/pictures/2011/8/31/1314790652152/Early-human-hand-axe-008.jpg (made by early Homo erectus, 1.76 million years ago). I might add that the very earliest forms of Homo erectus (found in Dmanisi, Georgia) didn't even make hand-axes. To be continued...vjtorley_{September 29, 2013
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For a prime example of evolution's failed predictions of vestigial organs, in October 2007, the appendix was found to have essential purpose in the human body:
Appendix has purpose: Excerpt: "The appendix acts as a good safe house for bacteria," said Duke surgery professor Bill Parker. http://en.wikinews.org/wiki/Scientists:_appendix_has_purpose Over sixty years ago we find these words from the prestigious Quarterly Review of Biology, “There is no longer any justification for regarding the vermiform appendix as a vestigial structure” (Straus, 1947). https://uncommondescent.com/human-evolution/they-knew-the-human-appendix-did-a-job-sixty-years-ago-actually/ Surgical removal of the tonsils and appendix associated with risk of early heart attack - June 2011 Excerpt: The surgical removal of the appendix and tonsils before the age of 20 was associated with an increased risk of premature heart attack in a large population study performed in Sweden. Tonsillectomy increased the risk by 44% (hazard ratio 1.44) and appendectomy by 33% (HR 1.33). The risk increases were just statistically significant, and were even higher when the tonsils and appendix were both removed. http://medicalxpress.com/news/2011-06-surgical-tonsils-appendix-early-heart.html#share
as to biogeography. Here are a few sites that show how Darwinists avoid falsification from the biogeographical data of finding numerous and highly similar species in widely separated locations:
More Biogeographical Conundrums for Neo-Darwinism – March 2010 http://www.evolutionnews.org/2010/03/sea_monkeys_are_the_tip_of_the032471.html The Case of the Mysterious Hoatzin: Biogeography Fails Neo-Darwinism Again – Casey Luskin – November 5, 2011 Excerpt: If two similar species separated by thousands of kilometers across oceans cannot challenge common descent, what biogeographical data can? The way evolutionists treat it, there is virtually no biogeographical data that can challenge common descent even in principle. If that’s the case, then how can biogeography be said to support common descent in the first place? http://www.evolutionnews.org/2011/11/the_case_of_the_mysterious_hoa052571.html As Evidence of Darwinian Evolution, Biogeography Falls Well Short of Satisfying - Jonathan M. - December 6, 2012 http://www.evolutionnews.org/2012/12/as_evidence_of5067151.html
See also Simon Conway Morris on widespread convergent evolution i.e. Darwinian rescue device saves the day again!, but most people would consider a sign of weakness in your theory! But who's quibbling about such a minor detail as an unfalsifiable scientific theory? That's all secondary to the fact that atheists get to promulgate their unfalsifiable theory unchallenged in public school right?bornagain77_{September 29, 2013
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Along that line, Dawkins' claimed 'strongest, most irrefutable, piece of evidence' for common descent between apes and man fell completely apart when scrutinized for integrity:
Dawkins Best Evidence Refuted - video http://www.youtube.com/watch?v=IfFZ8lCn5uU
As to Atavisms, the examples cited by wiki are
Hind legs on whales[2] or snakes Hind fins on dolphins[2] Extra toes on horses, as in archaic horses[7] Re-emergence of sexual reproduction in the flowering plant Hieracium pilosella and the Crotoniidae family of mites.[8] Teeth in chickens [9]
As to hind legs on whales you may be surprised to learn:
An Email Exchange Regarding "Vestigial Legs" Pelvic Bones in Whales by Jim Pamplin Excerpt: The pelvic bones (supposed Vestigial Legs) of whales serve as attachments for the musculature associated with the penis in males and its homologue, the clitoris, in females. The muscle involved is known as the ischiocavernosus and is quite a powerful muscle in males. It serves as a retractor muscle for the penis in copulation and probably provides the base for lateral movements of the penis. The mechanisms of penile motion are not well understood in whales. The penis seems to be capable of a lot of independent motion, much like the trunk of an elephant. How much of this is mediated by the ischiocavernosus is not known. In females the anatomical parts are smaller and more diffuse. I would imagine that there is something homologous to the perineal muscles in man and tetrapods, which affect the entire pelvic area - the clitoris, vagina and anus. The pelvic rudiments also serve as origins for the ischiocaudalis muscle, which is a ventral muscle that inserts on the tips of the chevron bones of the spinal column and acts to flex the tail in normal locomotion. James G. Mead, Ph.D. - Curator of Marine Mammals - National Museum of Natural History - Smithsonian Institution https://uncommondescent.com/intelligent-design/is-darwinism-a-better-explanation-of-life/#comment-454624
Well that certainly doesn't fit the Darwinian narrative! Moreover the horse fossil sequence is far more questionable than you seem to believe:
"The construction of the whole Cenozoic family tree of the horse is therefore a very artificial one, since it is put together from non-equivalent parts, and cannot therefore be a continuous transformation series". Dr. Heribert Nilsson - Evolutionist - Former Director of the Swedish Botanical Institute. For the last century or so, this fine animal has been put to a more unfortunate use. Its alleged ancestry has been used as one of the key ‘proofs’ of evolution. It started in 1879 with the American paleontologist O.C. Marsh and the famous evolutionist T.H. Huxley, known as ‘Darwin’s bulldog.’ Since then, many museums and popular books have presented a neat series starting from the dog-sized, four-toed ‘dawn horse’ or ‘Eohippus,’ which supposedly lived 50 million years ago. The next creature is usually a larger creature like Mesohippus, which had three toes. The next one was larger still, for example Merychippus, which had two of the toes smaller than the third. Finally, there is the large modern horse, Equus, with only one toe, while all that is left of the other two are ‘vestigial’ splint bones.3 Some of the diagrams also show trends in tooth changes, with increasing hypsodonty (high-crowned teeth). This is supposed to demonstrate a change from browsing on bushes to grazing on grass. How clear-cut is it, really? Two horses galloping through a field of yellow flowersAs the biologist Heribert-Nilsson said, ‘The family tree of the horse is beautiful and continuous only in the textbooks,’4 and the famous paleontologist Niles Eldredge called the textbook picture ‘lamentable’5 and ‘a classical case of paleontologic museology.’6 As shown in a detailed thesis by Walter Barnhart,7 the horse ‘series’ is an interpretation of the data. He documents how different pictures of horse evolution were drawn by different evolutionists from the same data, as the concept of evolution itself ‘evolved.’ The non-evolution of the horse http://creation.com/the-non-evolution-of-the-horse
You other examples of Atavisms all have gaping holes in them as well as to proving the point that you think (wish?) it does, which it doesn't, as this following video highlights in regards to latent 'cyclical' variations:
Phenotypic Plasticity - Lizard cecal valve (cyclical variation)- video http://www.youtube.com/watch?v=zEtgOApmnTA
so lets go on to you claim for Vestigial structures and biogeography.
“The thyroid gland, pituitary gland, thymus, pineal gland, and coccyx, … once considered useless by evolutionists, are now known to have important functions. The list of 180 “vestigial” structures is practically down to zero. Unfortunately, earlier Darwinists assumed that if they were ignorant of an organ’s function, then it had no function.” "Tornado in a Junkyard" - book - by former atheist James Perloff Vestigial Organs: Comparing ID and Darwinian Approaches - July 20, 2012 Excerpt: A favorite criticisms of ID is that it is a science stopper. The opposite is true. The Live Science article shows that the "vestigial organs" argument has not changed for over a century, since Wiedersheim coined the term and listed over a hundred examples (in 1893). Evolutionary theory, in fact, has been worse than a science stopper: its predictions have been flat out wrong. Only a handful of alleged vestigial organs remains from Wiedersheim's original list, and each of those is questionable. http://www.evolutionnews.org/2012/07/vestigial_organ062281.html
Evolutionists try to have their cake and eat it too with their definition of the word vestigial:
From Jerry Coyne, "Evolution-of-the-Gaps" and Other Fallacies - Jonathan M. - December 5, 2012 Excerpt: Coyne anticipates the typical response to the argument from vestigiality: "Opponents of evolution always raise the same argument when vestigial traits are cited as evidence for evolution. "The features are not useless," they say. "They are either useful for something, or we haven't yet discovered what they're for." They claim, in other words, that a trait can't be vestigial if it still has a function, or a function yet to be found. But this rejoinder misses the point. Evolutionary theory doesn't say that vestigial characters have no function. A trait can be vestigial and functional at the same time. It is vestigial not because it's functionless, but because it no longer performs the function for which it evolved. (p. 58)" But surely, by Coyne's reckoning, this loose definition of "vestigiality" would entail that every organ and structure is vestigial, since, in Coyne's view, all traits have evolved from something else. As Jonathan Wells explains in his own review of the book, "If the human arm evolved from the leg of a four-footed mammal (as Darwinists claim), then the human arm is vestigial. And if (as Coyne argues) the wings of flying birds evolved from feathered forelimbs of dinosaurs that used them for other purposes, then the wings of flying birds are vestigial. This is the opposite of what most people mean by "vestigial." http://www.evolutionnews.org/2012/12/from_jerry_coyn_15067091.html
bornagain77_{September 29, 2013
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Some more (inconsistencies) ERVs that don't fit into the naturalistic evolutionary assumption of common descent:
PTERV1 in chimpanzee, African great apes and old World monkeys but not in humans and asian apes (orangutan, siamang, and gibbon). http://www.sciencedaily.com/releases/2005/03/050328174826.htm Conservation and loss of the ERV3 open reading frame in primates. http://www.ncbi.nlm.nih.gov/pubmed/15081124 ERV3 sequences were amplified by PCR from genomic DNA of great ape and Old World primates but not from New World primates or gorilla, suggesting an integration event more than 30 million years ago with a subsequent loss in one species. From ancestral infectious retroviruses to bona fide cellular genes: role of the captured syncytins in placentation. http://www.ncbi.nlm.nih.gov/pubmed/22695103 We focus on the recent discovery of genes derived from the envelope glycoprotein-encoding (env) genes of endogenous retroviruses that have been domesticated by mammals to carry out an essential function in placental development… Remarkably, the capture of syncytin or syncytin-like genes, sometimes as pairs, was found to have occurred independently from different endogenous retroviruses in diverse mammalian lineages such as primates–including humans–, muroids, leporids, carnivores, caviids, and ovis, between around 10 and 85 million years ago. Retroviruses push the envelope for mammalian placentation http://www.pnas.org/content/109/7/2184.short Domestication of the syncytin genes represents a dramatic example of convergent evolution via the cooption of a retroviral gene for a key biological function in reproductive biology. In fact, syncytin domestication from a retroviral envelope gene has been previously shown to have independently occurred at least seven times during mammalian evolution…
Based on this data, certain cases of widespread and similar retroviral genes are attributed to the Darwinian 'rescue device' of convergent evolution.
Many more cases of anomalous ERVs https://uncommondescent.com/intelligent-design/life-project-architecture/#comment-449621
Further notes
The Human Lineage Was Somehow “Purged” - Cornelius Hunter - April 2012 Excerpt: Another such feature is the lack of endemic infectious retroviruses in humans. The problem is that these viruses are present in the other primates, and so according to evolutionists these viruses must be present in their common ancestor which, again according to evolution, would be an ancestor of humans as well.,, In other words, when evolution spontaneously created humans our DNA must have been “purged.” We got a do-over! Hilarious. http://darwins-god.blogspot.com/2012/04/unbelievableevolution-in-complete-free.html More Counterpoints on ERVs - JonathanM - May 2011 Excerpt: 'In the absence of a feasible naturalistic mechanism to account for how evolution from a common ancestor could have occurred, how can we be so sure that it did occur? In such a case, one ought to reasonably expect there to be some quite spectacular evidence for common ancestry. Unfortunately for Darwinists, however, the evidence for common ancestry is paper thin on the ground.' http://www.evolutionnews.org/2011/05/more_points_on_ervs046761.html
there are many more studies suggesting non-random and preferential positioning of retrovirus sequences. This kind of data is very antagonistic to the notion of re-used ERV sites having to be an ‘amazing coincidences’.
Perpetually mobile footprints of ancient infections in human genome http://www.sciencedirect.com/science/article/pii/S0014579398004785 Although not available for HERVs at this point, the results for other retroelements demonstrate that transcriptionally active genome regions might be preferred targets for retrovirus integration and that the site selection during retroposition can be influenced by many factors A good example of retroelement–host interaction gives the study of de novo insertions of Ty1 and Ty3 yeast retrotransposons that are analogues of endogenous retroviruses. Most of the integration sites were found clustered upstream of the genes transcribed by RNA polymerase III. There were identified `hot spots’ containing integration sites used up to 280 times more frequently than predicted mathematically. A recent study of the de novo retroviral integration demonstrated also preference for scaffold- or matrix-attachment regions (S/MARs) flanked by DNA with high bending potential.
etc.. etc.. etc.., But you get the idea!bornagain77_{September 29, 2013
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Theistic Evolutionist claims:
There is overwhelming evidence for common descent. What is the creationist explanation for chromosome 2 in humans? Humans and chimp sharing endogenous retroviruses? Atavisms? Vestigial structures? It’s evidence for evolution, as is biogeography.
Save for the fact that all the evidence you listed is highly questionable evidence of common descent, (of man from apes), you might have had a point:
It's cherry picking season! Excerpt: the ch2 fusion is cherry picking among many genetic signatures that show no common ancestry. Evolutionary biologist Richard Sternberg remarked: “Of all the known ITSs [interstitial telomeric sequences], and there are many in the genomes of chimps and humans, as well as mice and rats and cows…, the 2q13 ITS is the only one that can be associated with an evolutionary breakpoint or fusion. The other ITSs, I hasten to add, do not square up with chromosomal breakpoints in primates. In brief, to hone in on the 2q13 ITS as being typical of what we see in the human and chimp genomes seems almost like cherry-picking data. Most are not DNA scars in the way they have been portrayed.”, Richard Sternberg, Evolution News And Views, 2009. Sternberg cites Interstitial telomeric sequences (ITSs) are not located at the exact evolutionary breakpoints in primates. Likewise, creation geneticist Jeffrey Tomkins has written: “I developed software that enables the scanning of whole chromosomes for internal telomere content. … Surprisingly, I discovered that the entire human genome contains many completely intact internal telomere sequences. My preliminary data suggests that the internal regions of human chromosomes are composed of 0.19 to 0.25 percent 100% sequence identity intact telomere sequences. While this may seem to be a very small amount, consider that chromosome 2 (the supposed fusion product) contains over 91,000 (0.23 percent) intact internal telomere sequences. Fewer than 300 of these can be attributed to the so-called fusion site. Chromosome Y was the most internally dense telomere containing chromosome (0.25 percent).”, Designed DNA Blog, 2012 https://uncommondescent.com/intelligent-design/spring-it-on-em-and-watch-the-fur-fly/#comment-431951
Many more notes are here:
Refutation Of Chromosome 2 argument https://docs.google.com/document/d/1enllGchcY4Thz0xWFG8Rj8Y0bddOcBdIzKeoY1XxSqs/edit
As to endogenous retroviruses:
The definitive response on ERV’s and Creation, with Dr. Jean Lightner http://www.youtube.com/watch?v=feHYEgzaGkY Refutation Of Endogenous Retrovirus - ERVs - Richard Sternberg, PhD Evolutionary Biology - video http://www.metacafe.com/watch/4094119 Sternberg, R. v. & J. A. Shapiro (2005). How repeated retroelements format genome function. Cytogenet. Genome Res. 110: 108-116. Retrovirus in the Human Genome Is Active in Pluripotent Stem Cells - Jan. 23, 2013 Excerpt: "What we've observed is that a group of endogenous retroviruses called HERV-H is extremely busy in human embryonic stem cells," said Jeremy Luban, MD, the David L. Freelander Memorial Professor in HIV/AIDS Research, professor of molecular medicine and lead author of the study. "In fact, HERV-H is one of the most abundantly expressed genes in pluripotent stem cells and it isn't found in any other cell types. http://www.sciencedaily.com/releases/2013/01/130123133930.htm Transposable Elements Reveal a Stem Cell Specific Class of Long Noncoding RNAs - (Nov. 26, 2012) Excerpt: The study published by Rinn and Kelley finds a striking affinity for a class of hopping genes known as endogenous retroviruses, or ERVs, to land in lincRNAs. The study finds that ERVs are not only enriched in lincRNAs, but also often sit at the start of the gene in an orientation to promote transcription. Perhaps more intriguingly, lincRNAs containing an ERV family known as HERVH correlated with expression in stem cells relative to dozens of other tested tissues and cells. According to Rinn, "This strongly suggests that ERV transposition in the genome may have given rise to stem cell-specific lincRNAs. The observation that HERVHs landed at the start of dozens of lincRNAs was almost chilling; that this appears to impart a stem cell-specific expression pattern was simply stunning!" http://www.sciencedaily.com/releases/2012/11/121125192838.htm Retroviruses and Common Descent: And Why I Don’t Buy It - September 2011 Excerpt: If it is the case, as has been suggested by some, that these HERVs are an integral part of the functional genome, then one might expect to discover species-specific commonality and discontinuity. And this is indeed the case. https://uncommondescent.com/evolution/retroviruses-and-common-descent-and-why-i-dont-buy-it/
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TE, I want to jump in real quick and tell you 'thank you' for the substantial response you gave to me on that old 2006 thread last week. You sent me on a field trip where I will have to do some study, reading, and thought. Thank You.Upright BiPed_{September 29, 2013
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There is overwhelming evidence for common descent. What is the creationist explanation for chromosome 2 in humans? Humans and chimp sharing endogenous retroviruses? Atavisms? Vestigial structures? It's evidence for evolution, as is biogeography. I have never understood why design and evolution have to be at odds.TheisticEvolutionist_{September 28, 2013
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#19 Sixthbook
So if there is disagreement amongst evolutionists it’s just healthy debate and a sign of good science
In this case, the reason why there's so much disagreement and debate, is because we have so many intermediate fossils in a gradual series from ape-like creatures to humans, that it is subjective as to where to draw lines between the various species. There are also many closely related species (or sub-species, again, up for debate) living side by side with subtle differences which makes it difficult to discern who are ancestors and who are side branches. But, aren't these the kind of classification controversies you'd expect to find if evolution occurred? If only there were gaps it would all be so much simpler.
but if there’s disagreement among creationists it’s evidence against creationism?
When those that say that it is "obvious" as to which fossils are human and which are ape, argue endlessly amongst themselves as to which are obviously ape and which are obviously human - is that evidence against the claim that it is, indeed, "obvious"? I would say so. Reading Creationist literature is like watching a bunch of people arguing that there's only black and white - and meanwhile they are all looking at shades of gray and arguing amongst themselves as to which are black and which are white.goodusername_{September 28, 2013
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I always amazed that "A simple statistical test for the alleged “99% genetic identity” between humans and chimps posts hasn't been removed. Read it, you'll find the autors shows on average ~62% of 30bp long sequences from human and chimp show exact identity. ie, 0.62 = 30^p where "p" is the percent of human and chimp bases that are exactly the same. It's simple to see from there that p = 0.62^(1/30) ~ 98.4%. That's a familiar number...wd400_{September 28, 2013
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Oh, and damming is what beavers do. :-)Querius_{September 28, 2013
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The sad thing about evolutionists who are clinging to their desperate hope that mutations can account for variation, new genes, and new body plans is that they're missing out on other naturalistic causes. Before hyperventilating about the 98% genetic similarity between chimps and humans, or whatever it is this week, check out a baseline comparison of other species with humans: Cat: 90% Cow: 80% Mouse: 75% Fruit Fly: 60% Banana: 50% Not quite so impressive now . . .Querius_{September 28, 2013
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Regarding creationist classification of apes and humans: So if there is disagreement amongst evolutionists it’s just healthy debate and a sign of good science, but if there’s disagreement among creationists it’s evidence against creationism? I think I’m finally understanding how the world works! You might try reading what I've written. Creationists say there is a very clear distinction between humans and (other) apes.The fact they can't agree on where this distinction falls is pretty damming, isn't it?wd400_{September 28, 2013
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Regarding creationist classification of apes and humans: So if there is disagreement amongst evolutionists it's just healthy debate and a sign of good science, but if there's disagreement among creationists it's evidence against creationism? I think I'm finally understanding how the world works! Anyways, this disagreement would jsut further prove the creationist point that origins science is speculative, meaning that people can look at the same evidence and arrive at different conclusions because they are relying on untestable assumptions.sixthbook_{September 28, 2013
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Though outliers, I’ve even found studies for percent similarity figures as low as 62%,, A simple statistical test for the alleged “99% genetic identity” between humans and chimps – September 2010 Excerpt: The results obtained are statistically valid. The same test was previously run on a sampling of 1,000 random 30-base patterns and the percentages obtained were almost identical with those obtained in the final test, with 10,000 random 30-base patterns. When human and chimp genomes are compared, the X chromosome is the one showing the highest degree of 30BPM similarity (72.37%), while the Y chromosome shows the lowest degree of 30BPM similarity (30.29%). On average the overall 30BPM similarity, when all chromosomes are taken into consideration, is approximately 62%. https://uncommondescent.com/intelligent-design/a-simple-statistical-test-for-the-alleged-99-genetic-identity-between-humans-and-chimps/ and even as low as 49% Do Human and Chimpanzee DNA Indicate an Evolutionary Relationship? Excerpt: the authors found that only 48.6% of the whole human genome matched chimpanzee nucleotide sequences. [Only 4.8% of the human Y chromosome could be matched to chimpanzee sequences.] http://www.apologeticspress.org/articles/2070 as if that was not devastating enough to the 99% similarity myth, orphan genes are now being found in each new genome that is sequenced: Genes from nowhere: Orphans with a surprising story – 16 January 2013 – Helen Pilcher Excerpt: When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these “orphan genes” are high achievers (are just as essential as ‘old’ genes),,, But where do they come from? With no obvious ancestry, it was as if these genes appeared out of nowhere, but that couldn’t be true. Everyone assumed that as we learned more, we would discover what had happened to their families. But we haven’t-quite the opposite, in fact.,,, The upshot is that the chances of random mutations turning a bit of junk DNA into a new gene seem infinitesmally small. As the French biologist Francois Jacob wrote 35 years ago, “the probability that a functional protein would appear de novo by random association of amino acids is practically zero”.,,, 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 Even Jerry Coyne states: "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. Thus, take from it what you will, but I'm not nearly as impressed with the 98.5% similarity number as wd400 seems to be!bornagain77_{September 28, 2013
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as to wd400's stated 98.5 percent similarity: Guy Walks Into a Bar and Thinks He’s a Chimpanzee: The Unbearable Lightness of Chimp-Human Genome Similarity – 2009 Excerpt: One can seriously call into question the statement that human and chimp genomes are 99% identical. For one thing, it has been noted in the literature that the exact degree of identity between the two genomes is as yet unknown (Cohen, J., 2007. Relative differences: The myth of 1% Science 316: 1836.). ,,, In short, the figure of identity that one wants to use is dependent on various methodological factors. http://www.evolutionnews.org/2009/05/guy_walks_into_a_bar_and_think.html Even ignoring the subjective bias of ‘various methodological factors’ that Darwinists introduce into these similarity studies, the first inkling, at least for me, that something was terribly amiss with the oft quoted 99% similarity figure was this,,, Humans and chimps have 95 percent DNA compatibility, not 98.5 percent, research shows – 2002 Excerpt: Genetic studies for decades have estimated that humans and chimpanzees possess genomes that are about 98.5 percent similar. In other words, of the three billion base pairs along the DNA helix, nearly 99 of every 100 would be exactly identical. However, new work by one of the co-developers of the method used to analyze genetic similarities between species says the figure should be revised downward to 95 percent. http://www.caltech.edu/content/humans-and-chimps-have-95-percent-dna-compatibility-not-985-percent-research-shows and then this,,, Chimps are not like humans – May 2004 Excerpt: the International Chimpanzee Chromosome 22 Consortium reports that 83% of chimpanzee chromosome 22 proteins are different from their human counterparts,,, The results reported this week showed that “83% of the genes have changed between the human and the chimpanzee—only 17% are identical—so that means that the impression that comes from the 1.2% [sequence] difference is [misleading]. In the case of protein structures, it has a big effect,” Sakaki said. http://cmbi.bjmu.edu.cn/news/0405/119.htm this had caught my eye in 2008,,, Chimpanzee? 10-10-2008 – Dr Richard Buggs – research geneticist at the University of Florida …Therefore the total similarity of the genomes could be below 70%. http://www.idnet.com.au/files/pdf/Chimpanzee.pdf And then this caught my eye in 2011: Study Reports a Whopping “23% of Our Genome” Contradicts Standard Human-Ape Evolutionary Phylogeny – Casey Luskin – June 2011 Excerpt: For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place. (of note; 1/3 of our genes is equal to about 7000 genes that we do not share with chimpanzees) http://www.evolutionnews.org/2011/06/study_reports_a_whopping_23_of047041.html In late 2011 Jeffrey P. Tomkins, using an extremely conservative approach, reached the figure of 87% similarity: Genome-Wide DNA Alignment Similarity (Identity) for 40,000 Chimpanzee DNA Sequences Queried against the Human Genome is 86–89% – Jeffrey P. Tomkins – December 28, 2011 Excerpt: A common claim that is propagated through obfuscated research publications and popular evolutionary science authors is that the DNA of chimpanzees or chimps (Pan troglodytes) and humans (Homo sapiens) is about 98–99% similar. A major problem with nearly all past human-chimp comparative DNA studies is that data often goes through several levels of pre-screening, filtering and selection before being aligned, summarized, and discussed. Non-alignable regions are typically omitted and gaps in alignments are often discarded or obfuscated. In an upcoming paper, Tomkins and Bergman (2012) discuss most of the key human-chimp DNA similarity research papers on a case-by-case basis and show that the inclusion of discarded data (when provided) actually suggests a DNA similarity for humans and chimps not greater than 80–87% and quite possibly even less. http://www.answersingenesis.org/articles/arj/v4/n1/blastin Genomic monkey business – similarity re-evaluated using omitted data – by Jeffrey Tomkins and Jerry Bergman Excerpt: A review of the common claim that the human and chimpanzee (chimp) genomes are nearly identical was found to be highly questionable solely by an analysis of the methodology and data outlined in an assortment of key research publications.,,, Based on the analysis of data provided in various publications, including the often cited 2005 chimpanzee genome report, it is safe to conclude that human–chimp genome similarity is not more than ~87% identical, and possibly not higher than 81%. These revised estimates are based on relevant data omitted from the final similarity estimates typically presented.,,, Finally, a very recent large-scale human–chimp genome comparison research report spectacularly confirms the data presented in this report. The human–chimp common ancestor paradigm is clearly based more on myth and propaganda than fact. http://creation.com/human-chimp-dna-similarity-re-evaluated Then earlier this year, 2013, with better resolution of data, and still using an extremely conservative approach, Tomkins reached the figure of 70% genetic similarity between chimps and humans: Comprehensive Analysis of Chimpanzee and Human Chromosomes Reveals Average DNA Similarity of 70% – by Jeffrey P. Tomkins – February 20, 2013 Excerpt: For the chimp autosomes, the amount of optimally aligned DNA sequence provided similarities between 66 and 76%, depending on the chromosome. In general, the smaller and more gene-dense the chromosomes, the higher the DNA similarity—although there were several notable exceptions defying this trend. Only 69% of the chimpanzee X chromosome was similar to human and only 43% of the Y chromosome. Genome-wide, only 70% of the chimpanzee DNA was similar to human under the most optimal sequence-slice conditions. While, chimpanzees and humans share many localized protein-coding regions of high similarity, the overall extreme discontinuity between the two genomes defies evolutionary timescales and dogmatic presuppositions about a common ancestor. http://www.answersingenesis.org/articles/arj/v6/n1/human-chimp-chromosomebornagain77_{September 28, 2013
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75 mutations per generation??? Interestingly, even mutation rate of 75 per generation is far greater than what even evolutionists agree is an acceptable mutation rate since detrimental mutations will accumulate far faster than ‘selection’ can eliminate them in any given genome: Human evolution or extinction - discussion on acceptable mutation rate per generation (with clips from Dr. John Sanford) - video http://www.youtube.com/watch?v=aC_NyFZG7pM "it would in the end be far easier and more sensible to manufacture a complete man de novo, out of appropriately chosen raw materials, than to try to fashion into human form those pitiful relics which remained… it is evident that the natural rate of mutation of man is so high, and his natural rate of reproduction so low, that not a great deal of margin is left for selection… it becomes perfectly evident that the present number of children per couple cannot be great enough to allow selection to keep pace with a mutation rate of 0.1..if, to make matters worse, u should be anything like as high as 0.5…, our present reproductive practices would be utterly out of line with human requirements." Hermann Muller quoted by John Sanford; Appendix 1, Genetic Entropy moreover The Frailty of the Darwinian Hypothesis "The net effect of genetic drift in such (vertebrate) populations is “to encourage the fixation of mildly deleterious mutations and discourage the promotion of beneficial mutations,” http://www.evolutionnews.org/2009/07/the_frailty_of_the_darwinian_h.html But neutrality is a dubious proposition: Sanford’s pro-ID thesis supported by PNAS paper, read it and weep, literally - September 2010 Excerpt: Unfortunately, it has become increasingly clear that most of the mutation load is associated with mutations with very small effects distributed at unpredictable locations over the entire genome, rendering the prospects for long-term management of the human gene pool by genetic counseling highly unlikely for all but perhaps a few hundred key loci underlying debilitating monogenic genetic disorders (such as those focused on in the present study). https://uncommondescent.com/darwinism/sanfords-pro-id-thesis-supported-by-pnas-paper-read-it-and-weep-literally/ Inside the Human Genome: A Case for Non-Intelligent Design - Pg. 57 By John C. Avise Excerpt: "Another compilation of gene lesions responsible for inherited diseases is the web-based Human Gene Mutation Database (HGMD). Recent versions of HGMD describe more than 75,000 different disease causing mutations identified to date in Homo-sapiens." I went to the mutation database website cited by John Avise and found: HGMD®: Now celebrating our 100,000 mutation milestone! Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over? Kondrashov A.S. http://www.ingentaconnect.com/content/ap/jt/1995/00000175/00000004/art00167 Rate, molecular spectrum, and consequences of human mutation - Michael Lynch - 2009 Excerpt: it is difficult to escape the conclusion that the per-generation reduction in fitness due to recurrent mutation is at least 1% in humans and quite possibly as high as 5%. http://www.pnas.org/content/107/3/961.full Dr. John Sanford "Genetic Entropy and the Mystery of the Genome" 1/2 - video http://www.youtube.com/watch?v=pJ-4umGkgos Genetic Entropy in Human Genome is found to be 'recent': Human Genetic Variation Recent, Varies Among Populations - (Nov. 28, 2012) Excerpt: Nearly three-quarters of mutations in genes that code for proteins -- the workhorses of the cell -- occurred within the past 5,000 to 10,000 years,,, "One of the most interesting points is that Europeans have more new deleterious (potentially disease-causing) mutations than Africans,",,, "Having so many of these new variants can be partially explained by the population explosion in the European population. However, variation that occur in genes that are involved in Mendelian traits and in those that affect genes essential to the proper functioning of the cell tend to be much older." (A Mendelian trait is controlled by a single gene. Mutations in that gene can have devastating effects.) The amount variation or mutation identified in protein-coding genes (the exome) in this study is very different from what would have been seen 5,000 years ago,,, The report shows that "recent" events have a potent effect on the human genome. Eighty-six percent of the genetic variation or mutations that are expected to be harmful arose in European-Americans in the last five thousand years, said the researchers. The researchers used established bioinformatics techniques to calculate the age of more than a million changes in single base pairs (the A-T, C-G of the genetic code) that are part of the exome or protein-coding portion of the genomes (human genetic blueprint) of 6,515 people of both European-American and African-American decent.,,, http://www.sciencedaily.com/releases/2012/11/121128132259.htm And wd400 your presupposition that mutations must be neutral derives from where exactly? theoretical considerations not empirical evidence right?? Kimura's Quandary Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in responce to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most 'evolution' must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom's (neo-Darwinism's) very validity. John Sanford PhD. - "Genetic Entropy and The Mystery of the Genome" - pg. 161 - 162 A graph featuring 'Kimura's Distribution' is shown in the following video: Evolution Vs Genetic Entropy - Andy McIntosh - video http://www.metacafe.com/watch/4028086 Majestic Ascent: Berlinski on Darwin on Trial - David Berlinski - November 2011 Excerpt: The publication in 1983 of Motoo Kimura's The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura's theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. "A critique of neo-Darwinism," the Dutch biologist Gert Korthof boasted, "can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science." By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian. http://www.evolutionnews.org/2011/11/berlinski_on_darwin_on_trial053171.html Ann Gauger on genetic drift - August 2012 Excerpt: The idea that evolution is driven by drift has led to a way of retrospectively estimating past genetic lineages. Called coalescent theory, it is based on one very simple assumption — that the vast majority of mutations are neutral and have no effect on an organism’s survival. (For a review go here.) According to this theory, actual genetic history is presumed not to matter. Our genomes are full of randomly accumulating neutral changes. When generating a genealogy for those changes, their order of appearance doesn’t matter. Trees can be drawn and mutations assigned to them without regard to an evolutionary sequence of genotypes, since genotypes don’t matter. Truly pathetic wd400! And we haven't even gotten to the fact that you are lying about the percentage of sequence dissimilarity.bornagain77_{September 28, 2013
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Oh, and how can it be that Sanford et al don't think all human fixations are the result of selection? There are ~20 million on them, and they reckon human evolutoin requires "tens of millions" of selective transformations? Why should we take these people seriously?wd400_{September 28, 2013
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No, but based upon the fossil record, you don’t have all the time in the world to fix all these similarities under a model of random drift. You guys are too much. Under neutrality the fixation rate is equal to the per-individual mutation rate. Estimates of the human mutation rate are around 2.5E^-8, or ~ 75 mutations per generation using the same approximations as above. So we'd need 23 million mutations *75 mutations per gen ~ 306,667 generations With 20 year generations that's 20 * 306,667 ~ 6 million years. You can quibble about mutation rate estimates and generation times, but they wont change the numbers such that this suddenly becomes impossible.wd400_{September 28, 2013
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wd400, before we get into sequence dissimilarity, let's reiterate the main point I was making to you, YOU HAVE NO DEMONSTRATED MECHANISM FOR NEO-DARWINISM!. Comprehend? Everything you claim for a purely materialistic transition between apes and man is nothing more than fantasy!
Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) - October 2010 Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator. http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies Response to John Wise - October 2010 Excerpt: A technique called "saturation mutagenesis"1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans--because none of the observed developmental mutations benefit the organism. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/ A review of The Edge of Evolution: The Search for the Limits of Darwinism The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155). http://creation.com/review-michael-behe-edge-of-evolution "The immediate, most important implication is that complexes with more than two different binding sites-ones that require three or more proteins-are beyond the edge of evolution, past what is biologically reasonable to expect Darwinian evolution to have accomplished in all of life in all of the billion-year history of the world. The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the world in the last 4 billion years, so the odds are against a single event of this variety in the history of life. It is biologically unreasonable." - Michael Behe - The Edge of Evolution - page 146
Moreover, all the foundational presuppositions under-girding neo-Darwinism have now been shown to be compromised as to being true,
Modern Synthesis Of Neo-Darwinism Is False – Denis Nobel – video http://www.metacafe.com/w/10395212 ,, In the preceding video, Dr Nobel states that around 1900 there was the integration of Mendelian (discrete) inheritance with evolutionary theory, and about the same time Weismann established what was called the Weismann barrier, which is the idea that germ cells and their genetic materials are not in anyway influenced by the organism itself or by the environment. And then about 40 years later, circa 1940, a variety of people, Julian Huxley, R.A. Fisher, J.B.S. Haldane, and Sewell Wright, put things together to call it ‘The Modern Synthesis’. So what exactly is the ‘The Modern Synthesis’? It is sometimes called neo-Darwinism, and it was popularized in the book by Richard Dawkins, ‘The Selfish Gene’ in 1976. It’s main assumptions are, first of all, is that it is a gene centered view of natural selection. The process of evolution can therefore be characterized entirely by what is happening to the genome. It would be a process in which there would be accumulation of random mutations, followed by selection. (Now an important point to make here is that if that process is genuinely random, then there is nothing that physiology, or physiologists, can say about that process. That is a very important point.) The second aspect of neo-Darwinism was the impossibility of acquired characteristics (mis-called “Larmarckism”). And there is a very important distinction in Dawkins’ book ‘The Selfish Gene’ between the replicator, that is the genes, and the vehicle that carries the replicator, that is the organism or phenotype. And of course that idea was not only buttressed and supported by the Weissman barrier idea, but later on by the ‘Central Dogma’ of molecular biology. Then Dr. Nobel pauses to emphasize his point and states “All these rules have been broken!”. Professor Denis Noble is President of the International Union of Physiological Sciences.
Moreover, the sheer disconnect between phenotype and genotype is a universe wide chasm that neo-Darwinism can never hoped to bridged in bottom up materialistic fashion,,
Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information - Jonathan Wells - published online May 2013 Excerpt Conclusion:,, Many scientists have pointed out that the relationship between the genome and the organism - the genotype-phenotype mapping = cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” [150]. According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms [151], and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping [152]. So non-protein-coding regions of DNA that some previously regarded as “junk” turn out to encode biological information that greatly increases the known information-carrying capacity of DNA. At the same time, DNA as a whole turns out to encode only part of the biological information needed for life. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0009 https://uncommondescent.com/intelligent-design/darwins-dilemma-remains-unresolved-what-lees-paper-didnt-discuss/#comment-472108
Moreover, the polyfunctional complexity to be explained, even if you did have an example of even a single molecular machine and/or protein being generated by Darwinian processes, which you don't, is unfathomably complex! Complex in an extremely integrated fashion that far beyond what our best computer programmers could ever hope to generate by concerted effort.
Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - published online May 2013 Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43]. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 also see modular complexity
Without a demonstrated mechanism for neo-Darwinism (in fact the only demonstrations we have evidence of compromise neo-Darwinian mechanisms), we are left with nothing but the imagination of Darwinists that such unfathomable complexity can be had by blind material processes!bornagain77_{September 28, 2013
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wd400: Do these guys really think _all_ fixations between human and chimp have to be selective? No, but based upon the fossil record, you don't have all the time in the world to fix all these similarities under a model of random drift. Heck, you don't even have the time needed to fix them all under selection!Mung_{September 28, 2013
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(and do they actually think the whole genome is functional? Every base of every intron is there for a reason?)wd400_{September 28, 2013
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This is significant because the ape-to-man scenario requires tens of millions of selective nucleotide substitutions in the human lineage. Lol. Humans and chimps have ~98.5% identity over 3 billion bp. So, there are 0.015 * 3 billion = 45 million differences between humans and chimps. Only half of those were fixed in the human lineage so there are only ~23 million fixations in our linages. Do these guys really think _all_ fixations between human and chimp have to be selective?wd400_{September 28, 2013
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wd400, but why do we have quotes like these from leading evolutionists? "A number of hominid crania are known from sites in eastern and southern Africa in the 400- to 200-thousand-year range, but none of them looks like a close antecedent of the anatomically distinctive Homo sapiens…Even allowing for the poor record we have of our close extinct kin, Homo sapiens appears as distinctive and unprecedented…there is certainly no evidence to support the notion that we gradually became who we inherently are over an extended period, in either the physical or the intellectual sense." Dr. Ian Tattersall: - paleoanthropologist - emeritus curator of the American Museum of Natural History - (Masters of the Planet, 2012) 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) http://www.y-origins.com/index.php?p=home_more4 “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. (emeritus curator at the American Museum of Natural History) 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 Objective evaluation of the evidence or promissory Darwinism for Mr wd400? My bet is that he 'wants' Darwinism to be true so badly that he cannot fathom how pathetic his evidence actually is to the point he wants to be true beforehand! And even if wd400 could provide a gradual sequence of fossils that everyone, even Darwinists, could agree on, he still, as an atheistic neo-Darwinist, has no demonstrated mechanism to appeal to to explain how such changes could take place: Thou Shalt Not Put Evolutionary Theory to a Test - Douglas Axe - July 18, 2012 Excerpt: "For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be 'neutral'). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (>100 million years). My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they're in the position of insisting that something is a scientific fact without having the faintest idea how it even could be." Doug Axe PhD. http://www.evolutionnews.org/2012/07/thou_shalt_not062351.html Douglas Axe co-author of Science & Human Origins - video http://www.youtube.com/watch?v=XxMmLakH2LQ Thus neo-Darwinian conjectures are based on fantasy not empirical evidence!,, Moreover,, Using Numerical Simulation to Better Understand Fixation Rates, and Establishment of a New Principle - "Haldane's Ratchet" - Christopher L. Rupe and John C. Sanford - 2013 Excerpt: We then perform large-scale experiments to examine the feasibility of the ape-to-man scenario over a six million year period. We analyze neutral and beneficial fixations separately (realistic rates of deleterious mutations could not be studied in deep time due to extinction). Using realistic parameter settings we only observe a few hundred selection-induced beneficial fixations after 300,000 generations (6 million years). Even when using highly optimal parameter settings (i.e., favorable for fixation of beneficials), we only see a few thousand selection-induced fixations. This is significant because the ape-to-man scenario requires tens of millions of selective nucleotide substitutions in the human lineage. Our empirically-determined rates of beneficial fixation are in general agreement with the fixation rate estimates derived by Haldane and ReMine using their mathematical analyses. We have therefore independently demonstrated that the findings of Haldane and ReMine are for the most part correct, and that the fundamental evolutionary problem historically known as "Haldane's Dilemma" is very real. Previous analyses have focused exclusively on beneficial mutations. When deleterious mutations were included in our simulations, using a realistic ratio of beneficial to deleterious mutation rate, deleterious fixations vastly outnumbered beneficial fixations. Because of this, the net effect of mutation fixation should clearly create a ratchet-type mechanism which should cause continuous loss of information and decline in the size of the functional genome. We name this phenomenon "Haldane's Ratchet". http://creationicc.org/more.php?pk=46bornagain77_{September 28, 2013
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