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Saturday, January 01, 2011

Y chromosome further evidence that human-chimp DNA similarity is in 70% range

Not 98% or 99%, as every motor mouth on Hoax TV can tell you, between 9-11 hair fixes.

A friend writes to say:
In 2008 I made the prediction (based on data available from the draft chimpanzee genome) that the human and chimpanzee genomes were about 70% the same overall. This has now been confirmed for the Y chromosome in a detailed study.
The study found
As expected, we found that the degree of similarity between orthologous chimpanzee and human MSY sequences (98.3% nucleotide identity) differs only modestly from that reported when comparing the rest of the chimpanzee and human genomes (98.8%)15. Surprisingly, however, >30% of chimpanzee MSY sequence has no homologous, alignable counterpart in the human MSY, and vice versa (Supplementary Fig. 8 and Supplementary Note 3).

In aggregate, the consequence of gene loss and gain in the chimpanzee and human lineages, respectively, is that the chimpanzee MSY contains only two-thirds as many distinct genes or gene families as the human MSY, and only half as many protein-coding transcription units (Table 1).
He cautions that the authors of the Nature paper do not think that their findings for the Y chromosome are true for the whole genome.

Perhaps not, but it is nice to see sane people working on genetic similarity issues for once.

The paper is: Chimpanzee and human Y chromosomes are remarkably divergent in structure
and gene content, Nature 463, 536-539 (28 January 2010) | doi:10.1038/nature08700

The human Y chromosome began to evolve from an autosome hundreds of millions of years ago, acquiring a sex-determining function and undergoing a series of inversions that suppressed crossing over with the X chromosome1, 2. Little is known about the recent evolution of the Y chromosome because only the human Y chromosome has been fully sequenced. Prevailing theories hold that Y chromosomes evolve by gene loss, the pace of which slows over time, eventually leading to a paucity of genes, and stasis3, 4. These theories have been buttressed by partial sequence data from newly emergent plant and animal Y chromosomes5, 6, 7, 8, but they have not been tested in older, highly evolved Y chromosomes such as that of humans. Here we finished sequencing of the male-specific region of the Y chromosome (MSY) in our closest living relative, the chimpanzee, chieving levels of accuracy and completion previously reached for the human MSY. By comparing the MSYs of the two species we show that they differ radically in sequence structure and gene content, indicating rapid evolution during the past 6 million years. The chimpanzee MSYcontains twice as many massive palindromes as the human MSY, yet it has lost large fractions of the MSY protein-coding genes and gene families present in the last common ancestor. We suggest that the extraordinary divergence of the chimpanzee and human MSYs was driven by four synergistic factors: the prominent role of the MSY in sperm production, ‘genetichitchhiking’ effects in the absence of meiotic crossing over, frequent ectopic recombination within the MSY, and species differences in mating behaviour. Although genetic decay may be the principal dynamic in the evolution of newly emergent Y chromosomes, wholesale renovation is the paramount theme in the continuing evolution of chimpanzee, human and perhaps other older MSYs.

Did you get that? “Wholesale renovation.” No doubt there’ll be more real news to come.

But don't expect to hear it from Hoax TV. 70%? Doesn't quite have the same ring as 99%, does it.


He said it: As a butcher eyes a sheep, so the Darwinists eyed paleontologist Steve Gould (1941-2002)?

David Berlinski recalls Gould’s tetchy relationship with the iron rice bowls of the Darwin establishment:

Of course, if the fossil record does not fit the theory, it is always possible to adjust the theory to fit the record. In science, an enterprising theoretician has several degrees of freedom within which to maneuver before the referee reaches ten and the final bell comes to clang. Steven Jay Gould, who was trained as a paleontologist, surveyed the fossil evidence early in the 1970s and came to the obvious conclusion that either the theory or the evidence must go.
What went, on his scheme of things, was the neo Darwinian orthodoxy by which species change into different species by means of an endless series of infinitesimal changes, continuously, like the flow of syrup. Instead, Gould argued, biological change must have been discontinuous, with vast changes taking place at once. Such was his model of punctuated equilibria.
It fits the fossil record far better (if it makes sense, even, to talk of scientific fit here), but the model achieves faithfulness to the facts only by chucking out the chief concepts of the Darwinian theory itself, and while paleontologists have been glad to have had Gould's company, evolutionary theorists have looked over what he has written with the cool, slitted, appraising glance of a butcher eyeing a sheep.
- David Berlinski, "The Evidence for Evolution," in Black Mischief: Language, Life, Logic, Luck," Harcourt Brace Jovanovich: Boston MA, Second Edition, 1988, pp. 300-302.
My impression is that Gould thought at first that revealing the facts of Darwinism’s failures (the trade secret of paleontology) would just be a lark. He soon learned otherwise, and ended up capitulating to the Darwinists in public while doubting in private. A friend told me he would not likely have signed the Steves list (Darwin lobby’s list of loyalist guys named Steve).

Well, he’s dead now, and we’ll never know, but I sense a story, and it would be interesting to hear more.

(Note: Here is an instance of Wiki Answers forced to admit, however evasively, that there was a serious issue there.)


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