Pseudogene Discovery Pains Evolutionary Paradigm

The functional sequences with low or no homology found in Pauls paper.

This is a legitimate criticism. :slight_smile:

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Not only that, but pseudogenes only make up 5% of the human genome. Even if every pseudogene has function it does nothing to show that the majority of the human genome has function.

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Which of those functional sequences do not have homologs in the chimp and human genomes?

Wasn’t this discussed elsewhere on this site recently?

Are you thinking of this thread?

Recent de novo origin of human protein-coding genes

  1. David G. Knowles and
  2. Aoife McLysaght1

-Author Affiliations

  1. Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland

Abstract

The origin of new genes is extremely important to evolutionary innovation. Most new genes arise from existing genes through duplication or recombination. The origin of new genes from noncoding DNA is extremely rare, and very few eukaryotic examples are known. We present evidence for the de novo origin of at least three human protein-coding genes since the divergence with chimp. Each of these genes has no protein-coding homologs in any other genome, but is supported by evidence from expression and, importantly, proteomics data. The absence of these genes in chimp and macaque cannot be explained by sequencing gaps or annotation error. High-quality sequence data indicate that these loci are noncoding DNA in other primates. Furthermore, chimp, gorilla, gibbon, and macaque share the same disabling sequence difference, supporting the inference that the ancestral sequence was noncoding over the alternative possibility of parallel gene inactivation in multiple primate lineages. The genes are not well characterized, but interestingly, one of them was first identified as an up-regulated gene in chronic lymphocytic leukemia. This is the first evidence for entirely novel human-specific protein-coding genes originating from ancestrally noncoding sequences. We estimate that 0.075% of human genes may have originated through this mechanism leading to a total expectation of 18 such cases in a genome of 24,000 protein-coding genes.

From the abstract:

There are DNA homologs.

If you do find orphan genes with no DNA homologs, please present the sequence and show us why known processes of mutation would not be able to produce them.

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Depends on how we define homolog.

It’s your claim that they can. I know your working hard to improve Dawkins Model :slight_smile:

Yes that’s the one, tank you. Of the 56 human sequences that had below 50% similarity to the chimp genome, how much DNA are we talking about? How long are these sequences?

Beautiful figure, thanks for sharing this. It’s fascinating to see that (at least in this figure) the proportion of pseudogenes in the human genome is 5X larger than the proportion of exons!

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I prefer a rational definition. @T_aquaticus’s works in this case.

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How could we define homolog so that the genes in question have no chimp homologs? I’d have to reach way back to find a better example of your sheer bloodymindedness.

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The term “de novo” is really a misnomer in this context. There are indeed regions of the genome that develop the capability of being transcribed, and even fully expressed into polypeptides. However, these sequences did not simply appear out of the blue, but developed from sequences already present in the genome. If I understand how the BLAST tool works, it doesn’t do a great job of matching query sequence to un-annotated sequence (sequences not identified as translated or transcribed). So the lack of identified homologs for “de novo” genes does not tell the whole story. @T_aquaticus, please correct me if I’m wrong here.

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Those 56 sequences had an average length of 159bp, for a total of less than 9kb of sequence.

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@colewd

If you are going to be serious about this “no evolution above the level of Genus”, I suggest you buckle down and actually investigate that claim in the most narrow part of the evolutionary path that actually matters: the Order Primates.

You know as well as I do that even if we proved evolution above the Genus level in fish, or reptiles, that Creationists (maybe even you?) would simply double-down and say: yeah, but what about Primates?!

So… let’s just go right to that group!
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[ Click on the image to enlarge the fonts to maximum size! ]

There are 448 living species of Primates … and because they are living, they can have their genetic profiles compared. And we can drill down really deep, and really granular… to look at what the evidence actually shows.

So… Bill Cole… where in the Orders, Families and Genus’ of the Primates do you see a discontinuity worth discussing? Obviously, you can’t point to Homo sapiens as the discontinuity … because that’s the point that is trying to be proven ultimately. We need to examine some part of this group that doesn’t require references to humans.

It’s your circus… your monkeys (hey… did you see what I did there?)…

:smiley:

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what about the genes for a language?

What genetic evidence would convince you of a problem with the hypothesis that chimps and humans share a common ancestor solely from natural reproductive processes?

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Discontinuities in the nested hierarchy, obviously.