# Pseudogene Discovery Pains Evolutionary Paradigm

**URL:** <https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128>\
**Category:** Side Conversation\
**Created:** [May 9, 2019, 3:48am UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128 "2019-05-09T03:48:24Z")\
**Posts on this page:** 20\
**Page:** 3

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [May 9, 2019, 10:32pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/41 "2019-05-09T22:32:35Z")

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> [@colewd](#):
>
> Depends on how we define homolog.

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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**Author:** ![cwhenderson](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/cwhenderson/32/72_2.png) [@cwhenderson](https://discourse.peacefulscience.org/u/cwhenderson)\
**Post date:** [May 9, 2019, 10:42pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/42 "2019-05-09T22:42:05Z")

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> [@colewd](#):
>
> Recent de novo origin of human protein-coding genes

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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**Author:** ![evograd](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/evograd/32/1233_2.png) [@evograd](https://discourse.peacefulscience.org/u/evograd)\
**Post date:** [May 10, 2019, 5:38am UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/43 "2019-05-10T05:38:52Z")

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> [@Rumraket](#):
>
> 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?

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

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**Author:** ![gbrooks9](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/gbrooks9/32/7979_2.png) [@gbrooks9](https://discourse.peacefulscience.org/u/gbrooks9)\
**Post date:** [May 10, 2019, 6:41am UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/44 "2019-05-10T06:41:50Z")

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> [@colewd](#):
>
> It’s your claim that they can. I know your working hard to improve Dawkins Model 🙂

@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!  
.  
.

**[Click on the image to enlarge the fonts to maximum size!]**

 ![image](https://us1.discourse-cdn.com/flex016/uploads/peacefulscience/original/2X/0/0b2e168bb8592aa36406355bf8e75880a27a142c.png)

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?)…

😃

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**Author:** ![scd](https://avatars.discourse-cdn.com/v4/letter/s/6f9a4e/32.png) [@scd](https://discourse.peacefulscience.org/u/scd)\
**Post date:** [May 10, 2019, 10:23am UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/45 "2019-05-10T10:23:14Z")

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> [@T\_aquaticus](#):
>
> Can you point to a single difference between the chimp and human genomes that is a problem?

what about the genes for a language?

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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [May 10, 2019, 1:56pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/46 "2019-05-10T13:56:35Z")

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> [@gbrooks9](#):
>
> 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.

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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**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [May 10, 2019, 2:21pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/47 "2019-05-10T14:21:47Z")

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> [@colewd](#):
>
> 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?

Discontinuities in the nested hierarchy, obviously.

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**Author:** ![T\_aquaticus](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t_aquaticus/32/1249_2.png) [@T\_aquaticus](https://discourse.peacefulscience.org/u/T_aquaticus)\
**Post date:** [May 10, 2019, 2:42pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/48 "2019-05-10T14:42:46Z")

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> [@cwhenderson](#):
>
> 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.

I’m only a novice when it comes to the ins and outs of BLAST, so don’t take my comments as gospel.

BLAST doesn’t use annotation, so that isn’t a problem. It simply searches for matches between sequence using user defined settings. You can change the specificity for a match, including penalties for gaps and the like.

I wouldn’t be surprised at all if there are short segments (~1000 base pairs) in any genome that has no detectable homology to other genomes since there are all sorts of mechanisms that can produce them. Funky recombination events and DNA breaks can produce all sorts of sequences. What is really strange is that ID/creationists think the emergence of new functional sequence is a problem for evolution when this is something the theory says should happen.

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**Author:** ![T\_aquaticus](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t_aquaticus/32/1249_2.png) [@T\_aquaticus](https://discourse.peacefulscience.org/u/T_aquaticus)\
**Post date:** [May 10, 2019, 2:44pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/49 "2019-05-10T14:44:04Z")

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> [@colewd](#):
>
> 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?

Finding exact copies of genes from very distant species that are not found in other ape genomes or in the rest of the mammal tree. For example, there are mice that carry an exact copy of a jellyfish gene for green fluorescent protein, and that was produced by design.

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**Author:** ![T\_aquaticus](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t_aquaticus/32/1249_2.png) [@T\_aquaticus](https://discourse.peacefulscience.org/u/T_aquaticus)\
**Post date:** [May 10, 2019, 2:44pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/50 "2019-05-10T14:44:42Z")

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> [@scd](#):
>
> what about the genes for a language?

Why don’t you find those human genes and compare them to the chimp genome?

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**Author:** ![scd](https://avatars.discourse-cdn.com/v4/letter/s/6f9a4e/32.png) [@scd](https://discourse.peacefulscience.org/u/scd)\
**Post date:** [May 10, 2019, 2:56pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/51 "2019-05-10T14:56:45Z")

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> [@Mercer](#):
>
> Discontinuities in the nested hierarchy, obviously.

about 1\3 of gorila genes contradict the primate phylogeny. evolution is now wrong? im sure not.

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**Author:** ![T\_aquaticus](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t_aquaticus/32/1249_2.png) [@T\_aquaticus](https://discourse.peacefulscience.org/u/T_aquaticus)\
**Post date:** [May 10, 2019, 2:59pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/52 "2019-05-10T14:59:04Z")

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> [@scd](#):
>
> about 1\3 of gorila genes contradict the primate phylogeny. evolution is now wrong? im sure not.

Evolution predicts the relative amount of incomplete lineage sorting that we should see, so no, it isn’t wrong. As we move to more distant branches the amount of ILS goes down, as we would expect with evolution.

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**Author:** ![scd](https://avatars.discourse-cdn.com/v4/letter/s/6f9a4e/32.png) [@scd](https://discourse.peacefulscience.org/u/scd)\
**Post date:** [May 10, 2019, 3:00pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/53 "2019-05-10T15:00:13Z")

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> [@T\_aquaticus](#):
>
> For example, there are mice that carry an exact copy of a jellyfish gene for green fluorescent protein, and that was produced by design.

but we do find such cases in nature. and scientists solving it by convergent loss or convergent evolution or LGT.

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**Author:** ![pnelson](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/pnelson/32/876_2.png) [@pnelson](https://discourse.peacefulscience.org/u/pnelson)\
**Post date:** [May 10, 2019, 3:01pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/54 "2019-05-10T15:01:03Z")

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> [@T\_aquaticus](#):
>
> Why don’t you find those human genes and compare them to the chimp genome?

What distinguishes a chimp from a human?

Not DNA, really. Not proteins – many proteins in you, and in a chimp, are amino-acid-by-amino-acid identical.

Jonathan Marks (2009, p. 246; emphasis added) understands:

> It is not that difficult to tell a human from an ape, after all. The human is the one walking, talking, sweating, praying, building, reading, trading, crying, dancing, writing, cooking, joking, working, decorating, shaving, driving a car, or playing football. Quite literally, from the top of our head (where the hair is continually growing, unlike gorillas) to the tips of our toes (the stoutest of which is non-opposable), one can tell the human part from the ape part quite readily if one knows what to look for. Our eye-whites, small canine teeth, evaporative heat loss, short arms and long legs, breasts, knees, and of course, our cognitive communication abilities and the productive anatomies of our tongue and throat are all dead giveaways. **However, they are not readily apparent in a genetic comparison**.

Until evolutionary biology can connect these anatomical, physiological, and behavioral differences – no chimps are reading this right now – to their causative DNA differences in the chimp and human genomes, respectively, all the DNA comparisons in the world won’t really bear on the unsolved evolutionary puzzle.

_Pace_ Jared Diamond, we are _not_ the “third chimpanzee.”

You can access the Marks 2009 paper here:

[[PDF] What is the viewpoint of hemoglobin, and does it matter? | Semantic Scholar](https://pdfs.semanticscholar.org/eb69/37bff4e7ac87db4405a21162eabacd462950.pdf)

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**Author:** ![T\_aquaticus](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t_aquaticus/32/1249_2.png) [@T\_aquaticus](https://discourse.peacefulscience.org/u/T_aquaticus)\
**Post date:** [May 10, 2019, 3:02pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/55 "2019-05-10T15:02:45Z")

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> [@scd](#):
>
> but we do find such cases in nature. and scientists solving it by convergent loss or convergent design or LGT.

Name one gene shared by just humans and jellyfish that is not shared by any other species group.

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**Author:** ![T\_aquaticus](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t_aquaticus/32/1249_2.png) [@T\_aquaticus](https://discourse.peacefulscience.org/u/T_aquaticus)\
**Post date:** [May 10, 2019, 3:03pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/56 "2019-05-10T15:03:55Z")

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> [@pnelson](#):
>
> What distinguishes a chimp from a human?
> 
> Not DNA, really.

Then how do you explain the phenotypic differences between chimps and humans? What is causing it?

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**Author:** ![pnelson](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/pnelson/32/876_2.png) [@pnelson](https://discourse.peacefulscience.org/u/pnelson)\
**Post date:** [May 10, 2019, 3:04pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/57 "2019-05-10T15:04:44Z")

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> [@T\_aquaticus](#):
>
> Then how do you explain the phenotypic differences between chimps and humans? What is causing it?

A Nobel Prize awaits the biologist who answers that question.

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**Author:** ![T\_aquaticus](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t_aquaticus/32/1249_2.png) [@T\_aquaticus](https://discourse.peacefulscience.org/u/T_aquaticus)\
**Post date:** [May 10, 2019, 3:06pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/58 "2019-05-10T15:06:57Z")

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> [@pnelson](#):
>
> A Nobel Prize awaits the biologist who answers that question.

Then it seems that you only have an argument from ignorance. You are only citing our ignorance of which specific DNA differences are causing specific phenotypic differences.

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**Author:** ![scd](https://avatars.discourse-cdn.com/v4/letter/s/6f9a4e/32.png) [@scd](https://discourse.peacefulscience.org/u/scd)\
**Post date:** [May 10, 2019, 3:09pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/59 "2019-05-10T15:09:41Z")

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> [@T\_aquaticus](#):
>
> Name one gene shared by just humans and jellyfish that is not shared by any other species group.

i can show you something similar like this one:

> **[Bacteria and Humans Have Been Swapping DNA for Millennia](https://www.the-scientist.com/features/bacteria-and-humans-have-been-swapping-dna-for-millennia-32779)**
>
> Bacteria inhabit most tissues in the human body, and genes from some of these microbes have made their way to the human genome. Could this genetic transfer contribute to diseases such as cancer?

the magic word is LGT. evolution is false now?

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**Author:** ![pnelson](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/pnelson/32/876_2.png) [@pnelson](https://discourse.peacefulscience.org/u/pnelson)\
**Post date:** [May 10, 2019, 3:10pm UTC](https://discourse.peacefulscience.org/t/pseudogene-discovery-pains-evolutionary-paradigm/6128/60 "2019-05-10T15:10:04Z")

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> [@T\_aquaticus](#):
>
> You are only citing our ignorance of which specific DNA differences are causing specific phenotypic differences.

Look in a mirror. You are the one who claims that DNA similarities and differences are the locus of explanatory significance.

Very early in our friendship, I asked Josh Swamidass to show me where, in the chimp and human genomes (respectively), the loci were that explained why humans have white sclera, and chimp, colored sclera. A very minor phenotypic difference; we’re not talking about the origins of language.

Josh didn’t know then (a few years ago), and no one knows today.

So color me underwhelmed about DNA comparisons.

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