A Test of Common Descent vs. Common Function


(S. Joshua Swamidass) #1

This post is reposted from BioLogos, where I first wrote it Jan 2017. It is a direct test of common descent that appears in the literature. Here, we can test two alternate hypothesis:

  1. Similar proteins share a common history (common descent), and functions are gained and lost along this history.

  2. Proteins are similar due to common function, not because of any common history, and this creates the illusion of common history.


At a genetic level we see a great deal of similarity between organisms. This similarity is a fundamental feature of life, that has to be explained by any theory.

Evolution explains that this similarity as largely caused by shared history, by way of common descent. We see function often aligning in sensible ways on phylogenetic trees of sequences and organisms. Of course, this is not perfect, because we also know that life changes over time. As the YEC Walter ReMine accurately points out in The Biotic Message, function will not always follow a nested clade pattern in an evolutionary model. (He argued that YEC would always follow the nested clade pattern, but it turns out that biology does not always do so).

Anti-evolutionists in the ID and creationist camps explain this similarity as the caused by common function engineered by a common designer. The thought here is that any shared function we see aligning to phylogenetic trees is just an illusion. Trees are constructed by similarity measurements, and these measurements are shaped by shared function. Nothing is gained by constructing a false history through the phylogeny, and we would do better to just see similarity as caused by shared function, shared design.

So there is a field of bioinformatics that directly tests these two hypothesis for the immensely practical problem of determining the function of unknown sequences. The experiment is straight forward. We compare the accuracy of function prediction algorithms that use pairwise similarity (e.g. BLAST searches) to assign function with those that use phylogeny instead (e.g. SIFTER).

We find that phylogeny informed predictions are two times better than similarity informed predictions. This is a fairly direct test of the two hypothesis. If phylogenies are an illusion, that do not actually represent a true history, why do they predict function better than similarity? I would say this is evidence that phylogenies are more than just an illusion. They capture something about function that is more informative than just similarity, even though they are inferred from similarity.

So similarity is used to infer phylogenetic history, and this history is more correlated with function than similarity itself.

You can read some of the references. The figures are great too).

https://genome.cshlp.org/content/early/2011/09/22/gr.104687.109.html


(S. Joshua Swamidass) #2

@evograd, what do you think of this?


(S. Joshua Swamidass) #3

@John_Harshman, what are your thoughts on this. It is your area right?


(Blogging Graduate Student) #4

Looks interesting, I’ll have to check it out tomorrow.


(John Harshman) #5

It sounds reasonable to me. Clearly one would expect conflict between similarity and phylogeny if there were differences in evolutionary rate. Phylogenies are not formed by similarity, i.e. the most similar sequences are not necessarily the most closely related, absent a perfect molecular clock, and fortunately methods in current use do not assume a clock. And one would also expect function to track phylogeny better than it tracks similarity given a model in which function changes over the tree and tends not to reverse itself much.

Is it your intent to show this in the cartoon figure, in which D and B both have short intervening branches while B’s closer relatives A and C have long branches?

This is one test of the superiority of phylogenetic hypotheses to separate creation/function hypotheses. It’s far from the only one, but it’s novel, and consilience is always nice.


(S. Joshua Swamidass) #6

It does not appear to suffer from the same pitfalls as the tests that are actually billed as common descent tests. This one, for example, seems to fail (Beyond Reasonable Doubt? A Test for Common Ancestry).


(John Harshman) #7

I like Theobald’s paper better than some people do, but I wasn’t thinking about that, and I wasn’t thinking about universal common ancestry. The most obvious refutation of the notion that similarity is purely functional is to use junk sequences, e.g. introns, in phylogenetic analyses. And there’s also the agreement of different functional sequences among each other and with the introns; there is no particular reason, given separate creation, why they should agree, or why they ought to fit a nested hierarchy at all.


(S. Joshua Swamidass) #8

Yes, I agree. That is a great test. However, ID does not agree to the premise, and this leads to a large circular and repetitive argument about function. This avoids that ditch.

This test, however, ID has zero response to as of yet. We are coming up on two years, and I know @pnelson has seen it. This analysis does not make use of debated assumptions. That makes it harder to argue against.


(John Harshman) #9

That there are junk sequences? Not true; ID is not monolithic. Some IDers think there is no junk, some think ID predicts there will be no junk, some think both, one, or neither. More importantly, the data refute the claim that most of the human genome is functional, so this supposed ID position is untenable.


(S. Joshua Swamidass) #10

If you want to make that case, go for it. I think it is scientifically valid, even if it is rhetorically difficult. I just have firsthand experience of how that goes, and I want a way around it.


(Blogging Graduate Student) #11

Just to clarify, @swamidass linked to my thread about White et al. 2013, because he doesn’t agree that it’s a valid test. I mentioned Theobald 2010 in one of the first paragraphs, but the thread wasn’t about that article. From your reply I think you might have clicked on the link to the thread, skimmed the first part, seen the reference to Theobald 2010, and then assumed that Joshua was referring to that paper.


(Ashwin S) #12

Just for clarity, can you tell how function is defined in this test/field?


(S. Joshua Swamidass) #13

Read the papers. Look at the references. It should be clear.


(John Harshman) #14

Make a case for what, to whom? How what goes? Might I suggest that you limit your pronouns to those whose antecedents are completely clear from immediate context? Are you talking about convincing a creationist that there’s such a thing as junk DNA?


(S. Joshua Swamidass) #15

I do not like the term junk DNA, but yes. I am meaning that when faced with evidence for common descent that relies on an assumption of largely not functional DNA, it is difficult to convince them that DNA in question is largely non-functional.

The advantage here, with the SIFTER work, is that is also not polemic. It is just a pragmatic study that incidentally tests their hypothesis, in order to solve a real problem. That makes it hard to dismiss.


(John Harshman) #16

I’m curious. Why doesn’t he think it’s valid? It seems like nothing more than a consequence of the data fitting a tree better than they fit no tree. Unless there are branches of negative length, internal nodes must have a shorter patristic distance from each other than descendant nodes are from one another.


(S. Joshua Swamidass) #17

Extensive discussion on other thread. Read it and add your comments there. If I am wrong, once again, I want to know.


(John Harshman) #18

Why?

Seems to me that’s more their problem than anything else. I’m dubious about the possibility of convincing a committed creationist of anything unpleasant.

Has this worked on anyone so far? I’m dubious that a committed creationist can be convinced by any evidence of common descent. Anything can be denied.


(S. Joshua Swamidass) #19

Yup. I see people (including creationists) change their mind all the time. Many are very convincible. It helps to be a convincible person yourself, so you can understand firsthand how change happens. The key thing to remember is that it is never enough to be right. You also have to be trusted.


(John Harshman) #20

Do I understand you correctly that you have managed to convince committed creationists of the truth of common descent, and that you have done this frequently? Can you offer examples?