Tomkins on the human vitellogenin pseudogene

Does anyone else want to chime in with their thoughts on the technical aspects of Tomkins’ paper? I made a start over at biologos:

Tomkins’s article: Challenging the BioLogos Claim that a Vitellogenin (Egg-Laying) P | Answers in Genesis

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even if its indeed a remnant of a vit gene we can explain it by convergent loss. so we dont need common descent to explain it.

Convergent loss is less parsimonious. You are invoking literally hundreds of independent losses to explain what a single loss in an ancestor explains. And that’s before we consider whether the locus shows nesting hiearchical structure in similarity(wanna take bets?).

Also, why would the creator create organisms that don’t and never did develop egg-yolk with an egg-yolk gene just to have it become a pseudogene later? Did Adam and Eve lay eggs?

There’s absolutely nothing about this pseudogene’s existence that is consistent with independent creation, much less young Earth creationism.

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where did you got this number from?

maybe because this gene is a multifunctional gene and thus may never used for egg-yolk in these creatures?:

Think about it. You think every species that has this pseudogene has independently lost it, right? No common descent.

Perhaps you think common descent works at some arbitrary taxonomic level(families? orders?), and that would then bring the number of independent losses down. But what level is that? You’d have to concede an awful lot of common descent to get below a hundred independent losses, and it would be funny to see just how different all those organisms are, genetically and morphologically, just so you can try to make your absurdly unparsimonious rationalization slightly more paletable.

Then why lose it? You started by inventing the excuse that the pseudogene is shared because everyone who has it has independently lost it to inactivating mutations.
You’re making no sense, and seem to just make up rationalizations on the spot. You have no idea what your position even is here about why this gene exists and has the particular sequence it does, you’re just mindlessly making up excuses to deny common descent even if you have to contradict earlier rationalizations you’ve made.

i think that the family level should be the correct one (in general but not always). since we are basically talking about the same creature.

2 options:

  1. it was neutral to the creature. so a simple mutation can make it loss.
  2. it was beneficial to the creature to loss it.

again: an explanation without a common descent.

So it was intelligently designed with a specific function that was neutral to the creature or beneficial to lose what the intelligent designer put in?

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I think there’s enough wrong with the paper to warrant me writing an extended blog post on the subject over on evograd.wordpress.com. I’m really busy at the moment, but maybe in a few weeks I’ll find time.

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Yes I noticed one issue is the fact that the locus recruits histones and transcription factors is claimed to be an indication that it’s functional. But all DNA is wrapped up in nucleosomes, and transcribed at some low level whether functional or not. The fact that there is some “biochemical activity” to use the ENCODE parlance, is not good evidence for function at all.

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And his transcription factor binding evidence consists of a single binding site. He mentions 6 transcription factors that bind there, but 5 are FOX-family transcription factors with essentially the same consensus binding motif, and the last one is SRY, again with a very similar binding motif. This all makes sense given that even his figure 3 shows that the motifs are all overlapping on a single spot! Finding a single conserved motif that matches essentially a single TF in the middle of nowhere isn’t good evidence of function!

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under some circumstance its possible why not? even according to evolution many genes have been lost after that they were beneficial. the OR family is a good case of that. bottom line: there is no evidence for evolution here.

You can always come up with convoluted alternative explanations - for literally every piece of scientific data. They don’t trump the parsimonious explanations that fit neatly into an already-substantiated theory.

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There is no evidence the universe wasn’t created last Thursday, despite what the Last-Tuesdayists believe.

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Possible function in the vitellogenin pseudogene is a red herring. The evidence for common descent is the difference in sequence conservation between the exons and introns. If there has been relaxed selection in the functional vtg exons the evidence for common ancestry still stands.

In fact, the difference in sequence conservation between exons and introns in functional genes is absolutely wonderful evidence for evolution and common descent, so this may be a case of ID/creationists being hoisted by their own petard. They may be drawing attention to even more problematic evidence for their position.

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You’re right, and this is the point that Venema focuses on in his article, but I feel that we should also be addressing Tomkins claims about functionality, given that they’e massively overstated.

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Hoo boy, the more I investigate the claims Tomkins makes from his figures, and how he constructed those figures in the first place, the worse it gets. I think it’s frankly impossible that he was writing that article in good faith. The flaws go beyond errors that could be chalked up to ignorance, and definitively into deliberate deceptions.

The challenge will be breaking down all the technicalities of all the relevant UCSC tracks into an accessible blog post…

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As I read around, I realise I’m nearly 3 years behind on this subject! I see that a substantial discussion including members of this forum (e.g. @swamidass and @roohif) was had on this subject in 2016. This thread by VJ Torley seems like a good summary:

I’ll try not to spend too much time rehashing the same points - I think I have plenty of new content to bring to the table.

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Yup, that was a key exchange with @agauger where she eventually acknowledged that this was evidence for common descent.

I’m glad I’m not the only one who thought to do the alignment myself to see the extent of the human vitellogenin pseudogene. Using mVISTA rather than BLAST to do the multispecies alignment, I could easily identify about 3,100bp of human VTG, or about 7% of the gene. Total is probably slightly higher, if I included all the very small regions of similarity. A far cry from Tomkins’ claim the the entire pseudogene is represented by just 150bp. And that’s just the gene sequence itself, ignoring the non-gene matches that establish synteny.

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I’m making satisfying but slow progress. Only 4 paragraphs into Tomkins’ results and I’ve already had to write 2000 words in response (to his 500) and construct 3 quite detailed figures. Another fulfilment of Brandolini’s BS asymmetry principle.
On the plus side, I think this will be one of my best debunking blog posts.

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