How common is common descent?

_{Denyse O'Leary

June 7, 2011

Human evolution}

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How common is common descent?A question worth asking, in light of a new paper: Casey Luskin advises (Evolution News & Views, June 3, 2011) that “Study Reports a Whopping “23% of Our Genome” Contradicts Standard Human-Ape Evolutionary Phylogeny”:

We’ve recently discussed different genetic studies on primate relationships were finding contradictory evolutionary trees. As discussed, one recent study found data that conflicted with the standard primate phylogenetic tree, reporting that “for ~0.8% of our genome, humans are more closely related to orangutans than to chimpanzees.” We then commented:

0.8% of our genome might not sound like a lot, but that equates to over 20 million base pairs. That’s means that over 500 times more raw genetic information than was used in the PLoS Genetics paper (to purportedly create a “robust new phylogenetic tree”) is supposedly pointing in the wrong phylogenetic direction. Since that time, another paper has been pointed out to me that shows that even far more genetic data is contradicting the standard evolutionary phylogeny of humans and apes. A 2007 article in the journal Molecular Biology and Evolution states:

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.

(Ingo Ebersberger, Petra Galgoczy, Stefan Taudien, Simone Taenzer, Matthias Platzer, and Arndt von Haeseler, “Mapping Human Genetic Ancestry,” Molecular Biology and Evolution, Vol. 24(10):2266-2276 (2007).)

The article goes on to state that “[t]he human genome is a mosaic with respect to its evolutionary history.” In other words, some parts of the genome tell one evolutionary story while others tell a different, contradictory story. Our genome is not painting a consistent picture of common descent. The paper continues …

Comments

How common is common descent? Pretty common. And the Bible teaches it too.Mung_{June 9, 2011
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anaruiz you state: 'What I meant was that when they came down from the trees they probably walked on two feet because it’s easier to carry more food with your hands.' Then why don't moms have four arms since having four arms would be easier to raise children with??? :)bornagain77_{June 8, 2011
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I place my faith soley in Jesus Christ. What I said is based on the Ardi fossil. What I meant was that when they came down from the trees they probably walked on two feet because it's easier to carry more food with your hands.anaruiz_{June 8, 2011
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anaruiz you state: 'Our ancestors used to traversed trees, and when they came down from them, they walked on two feet immediately, they were never knuckle walkers.' WOW, just WOW, so one day a monkey, tired of all the monkey business of swinging around in trees, decides he's through with all that BS, and 'immediately' stands upright and walks away. Man that would be some kind of miracle!!!,,, So anaruiz, what you are really saying is that neo-Darwinists have their own miracle stories, just so long as they don't include the miracle maker Himself; Shoot anaruiz, I think your blind faith in neo-Darwinian miracles deserves its very own hallelujah chorus; Händel Messiah - Hallelujah Chorus http://www.youtube.com/watch?v=usfiAsWR4qUbornagain77_{June 8, 2011
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This is an off the cuff remark, but the sentence you quote, junkdnaforlife, appears to be a reflection of the fact that chimps and gorillas appear to be more derived and humans appear to reflect a more ancestral state. Our ancestors used to traversed trees, and when they came down from them, they walked on two feet immediately, they were never knuckle walkers.anaruiz_{June 7, 2011
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Observable evidence has been percolating for a few years now concerning this type of thing... “People often think we evolved from ancestors that look like apes, but no, apes in some ways evolved from ancestors that look like us..." “It has been a popular idea to think humans are modified chimpanzees. From studying Ardipithecus ramidus, or Ardi, we learn that we cannot understand or model human evolution from chimps and gorillas.” http://www.kent.edu:8014/research/owen_lovejoy.cfm It becomes harder to reconcile the 23% incongruity in the human/chimp genome when the closest fossil to the common ancestor seems to lead to the conclusion... "we cannot understand or model human evolution from chimps and gorillas." It seems incongruity may mean incongruity.junkdnaforlife_{June 7, 2011
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I would like to reiterate that evolutionists cannot account for the origination of even one unique gene or protein, much less the over one thousand completely unique ORFan genes found distinctly imbedded within the 20,000 genes of the human genome: Could Chance Arrange the Code for (Just) One Gene? "our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236)." http://www.creationsafaris.com/epoi_c10.htm "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” 2004: - Doug Axe ,,,this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences." http://www.mendeley.com/research/estimating-the-prevalence-of-protein-sequences-adopting-functional-enzyme-folds/ Evolutionists were recently completely surprised by this genetic study of kangaroos since it does not fit their imaginary tree they are continually try to draw from 'cherry picked' data sets: 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/idUSTRE4AH1P020081118bornagain77_{June 7, 2011
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as to anaruiz quote here: 'These polymorphisms remained until the individual alleles eventually got fixed in the lineages of contemporary humans, chimps, and gorillas, respectively. ' ,,,save for the fact that using neo-Darwinists very own mathematical equations for calculating fixation of individual alleles, the numbers simply don't crunch: Waiting Longer for Two Mutations - Michael J. Behe Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that 'for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years' (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless "using their model" gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model. http://www.discovery.org/a/9461 Dr. Sanford calculates it would take 12 million years to “fix” a single base pair mutation into a population. He further calculates that to create a gene with 1000 base pairs, it would take 12 million x 1000 or 12 billion years. This is obviously too slow to support the creation of the human genome containing 3 billion base pairs. http://www.detectingtruth.com/?p=66 further notes: The genetic evidence is certainly not as neat and tidy as neo-Darwinists would have us believe. For prime example at how biased neo-Darwinists are with genetic evidence, I refer to this study: Human Gene Count Tumbles Again – 2008 Excerpt: Scientists on the hunt for typical genes — that is, the ones that encode proteins — have traditionally set their sights on so-called open reading frames, which are long stretches of 300 or more nucleotides, or “letters” of DNA, bookended by genetic start and stop signals.,,,, The researchers considered genes to be valid if and only if similar sequences could be found in other mammals – namely, mouse and dog. Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences. These orphans looked like proteins because of their open reading frames, but were not found in either the mouse or dog genomes.,,, Alternatively, the genes could have been more ancient creations — present in a common mammalian ancestor — that were lost in mouse and dog lineages yet retained in humans. If either of these possibilities were true, then the orphan genes should appear in other primate genomes, in addition to our own. To explore this, the researchers compared the orphan sequences to the DNA of two primate cousins, chimpanzees and macaques. After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes. (The 1,177 ORFan genes in humans are completely unique to our lineage) http://www.sciencedaily.com/releases/2008/01/080113161406.htm In fact it turns out that the authors of the preceding ‘kick the ORFans out in the street’ paper actually did know that there was clear and unbiased evidence strongly indicating the ORFan genes encoded proteins but chose to ignore that strong evidence in favor of their preconceived evolutionary bias of forcing the genetic sequences of chimps and humans to be as similar as possible. That is EXACTLY how you ARE NOT suppose to practice science!!!: https://uncommondescent.com/intelligent-design/proteins-fold-as-darwin-crumbles/#comment-358547 A survey of orphan enzyme activities Abstract: We demonstrate that for ~80% of sampled orphans, the absence of sequence data is bona fide. Our analyses further substantiate the notion that many of these (orfan) enzyme activities play biologically important roles. http://www.biomedcentral.com/1471-2105/8/244 Dr. Howard Ochman - Dept. of Biochemistry at the University of Arizona Excerpt of Proposal: Although it has been hypothesized that ORFans might represent non-coding regions rather than actual genes, we have recently established that the vast majority that ORFans present in the E. coli genome are under selective constraints and encode functional proteins. https://uncommondescent.com/intelligent-design/proteins-fold-as-darwin-crumbles/#comment-358868 Moreover a significant portion of completely unique ORFan genes are found in each new genome sequenced: ORFan Genes Challenge Common Descent - Paul Nelson - video with references in description http://www.vimeo.com/17135166 Moreover new ORFan genes are found to be just as essential as older genes: Age doesn’t matter: New genes are as essential as ancient ones – December 2010 Excerpt: “A new gene is as essential as any other gene; the importance of a gene is independent of its age,” said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. “New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked.” http://www.sciencedaily.com/releases/2010/12/101216142523.htm New genes in Drosophila quickly become essential. - December 2010 Excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal (later) stage and (but was) also found in the larval (early) stages. http://www.sciencemag.org/content/330/6011/1682.abstractbornagain77_{June 7, 2011
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The allele in question didn't become fixed into the population of our ancestors at the same time as most of the rest of the genome.
The analyses in the paper deals with genomic DNA and the assumption is that all differences between humans, chimps, and gorillas are fixed. So the term allele doesn't seem to fit in this context. What is observed is that some fixed differences observed today between species are descendants of polymorphisms in the ancient population common to humans, chimps and gorillas. These polymorphisms remained until the individual alleles eventually got fixed in the lineages of contemporary humans, chimps, and gorillas, respectively.
So now, when a gene points in the wrong evolutionary direction, evolutionists just assume (quite conveniently) that the allele in question didn't become fixed into the population of our ancestors at the same time as most of the rest of the genome.
The sequences would only contradict the tree if there wouldn't be an explanation for the observation. But there is a that can reconcile the incongruent evolutionary relationships of 23% of the human genome compared to the accepted species tree.anaruiz_{June 7, 2011
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