Vitellogenin and Common Ancestry: Tomkins’ false dichotomy

Genes have many ways of giving evidence about their evolutionary past.
This is a companion discussion topic for the original entry at

from the article:

" evidence of function does not erase the evidence for prior history "-

why not? if we showed that its have a function then its not the remain of pseudogene but a functional one.

about changing one function to another: i dont think its possible. if for example we need to evolve a protein that bind 2 substrates we need at least 2 binding sites. even one binding site need about dozens amino acids. so its a huge jump in the s equence space.

Hi dcs,

New protein-protein binding sites do not need dozens of amino acid changes. Scientists have watched new binding sites form with far more modest changes (for example, 5 amino acid changes in this example.)

Changing five amino acids in one protein is going to leave a large number of amino acids unchanged - as well as the DNA that codes for them. Those sequences are the evidence of prior history.

In this example, even if the one VIT1 fragment Tomkins acknowledges is a functional regulatory sequence, it doesn’t erase the evidence that this fragment was once part of a functional VIT gene.

And it happens in every one of us every day, in real time!

hi dennis. interesting paper. but first- i think that a protein-protein interaction it’s different from protein-non protein interaction. because they made from another components. secondly- not all binding sites will need dozens amino acid. some of them will need more and some of them will need less. one interesting experiment that was done by jack szostak showed that about 45 amino acid need to make an atp binding site:

so its depends in the complexity of the function that we are talking about.

Hi dcs - discussing how evolution can explore sequence space is an interesting question, but it’s hardly the topic of this post. Perhaps start a new topic if you’d like to discuss that. Here’s what I’ve written on the issue in the past:

This post is about how the VIT1 region in humans shows clear signs of a prior function, despite degradation and (possible) neofunctionalization of one small portion of it. Let’s try keep the discussion on that. Thanks.

Hi @DennisVenema Dr Venema,
I’d like to comment on your statement “The major problem with this argument is that it subscribes to a false dichotomy: that this sequence is either a VIT1 pseudogene fragment or a functional part of another gene. From an evolutionary perspective, there is no issue with it being both. Part of evolutionary theory is the expectation that occasionally some sequences, after losing their original function, may come under natural selection to be repurposed to another function.”

It seems to me that this is a shift in stance. In the 13th chapter of the Origin, Darwin contrasts functional and historical explanations for the homology of the vertebrate pentadactyl limb and concludes that, if it were designed, we would expect to see a functional reason for the similarity of this structure in different taxa. He argues that, for this and other cases, there is no functional reason for their similarity (“Nothing can be more hopeless than to attempt to explain this similarity of pattern in members of the same class, by utility or by the doctrine of final causes."), therefore this structure is better explained in terms of descent by modification. And, of course, this mode of argumentation continues to this day among evolutionary biologists.

But what about when we discover that the characteristic in question is functional after all? I think you and others are correct that that this is compatible with descent by modification, by proposing, for example, that this is a pseudogene which has undergone exaptation, but I think the putative reason for preferring descent by modification over and against design as an explanation is removed if the characteristic is revealed to be functional.

Do you agree?

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