Evolution and Functional Information

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Here, one of my brilliant MD PhD students and I study one of the “information” arguments against evolution. What do you think of our study?

I recently put this preprint in biorxiv. To be clear, this study is not yet peer-reviewed, and I do not want anyone to miss this point. This is an “experiment” too. I’m curious to see if these types of studies are publishable. If they are, you might see more from me. Currently it is under review at a very good journal. So it might actually turn the corner and get out there. An a parallel question: do you think this type of work should be published?

 

I’m curious what the community thinks. I hope it is clear enough for non-experts to follow too. We went to great lengths to make the source code for the simulations available in an easy to read and annotated format. My hope is that a college level student could follow the details. And even if you can’t, you can weigh in on if the scientific community should publish this type of work.

Functional Information and Evolution

http://www.biorxiv.org/content/early/2017/03/06/114132

“Functional Information”—estimated from the mutual information of protein sequence alignments—has been proposed as a reliable way of estimating the number of proteins with a specified function and the consequent difficulty of evolving a new function. The fantastic rarity of functional proteins computed by this approach emboldens some to argue that evolution is impossible. Random searches, it seems, would have no hope of finding new functions. Here, we use simulations to demonstrate that sequence alignments are a poor estimate of functional information. The mutual information of sequence alignments fantastically underestimates of the true number of functional proteins. In addition to functional constraints, mutual information is also strongly influenced by a family’s history, mutational bias, and selection. Regardless, even if functional information could be reliably calculated, it tells us nothing about the difficulty of evolving new functions, because it does not estimate the distance between a new function and existing functions. Moreover, the pervasive observation of multifunctional proteins suggests that functions are actually very close to one another and abundant. Multifunctional proteins would be impossible if the FI argument against evolution were true.

216 thoughts on “Evolution and Functional Information”

  1. Mung:

    I actually began with bias in favor of Swamidass. I’m amazed, in retrospect, at how little time it took for his left-handedness to show. I didn’t know exactly what was going on, but I saw clearly enough that he wasn’t giving me straight answers. When I got around to reading Durston’s response to Myers, which makes claims that Durston, Chiu, Abel, and Trevors did not get through peer review, everything fell in place. Matlock and Swamidass have responded to Durston only. They write:

    So it is important the faulty scientific claims in peer-reviewed publications are corrected, which is what we aim to do here.

    Bull… malarkey. Matlock and Swamidass are misrepresenting their response to the unreviewed polemic of Durston, which had gone unnoticed on the Web since 2009, as a response to the peer-reviewed publication of Durston et al. The “faulty scientific claims” turn out to be only one:

    swamidass: The specific claim in the literature is that the FSC of extant sequences is a good estimate of FI. The claim is that applying the MI formula to a sequence alignment of proteins with shared function can good estimate of the number of sequences with that function.

    Durston et al. do not make this claim, and that is why Matlock and Swamidass do not provide a quotation.

    In the end, there is self-interest in my response, because Swamidass would bring into the literature what Durston et al. failed to get into the literature. The Discovery Institute wants “scientific controversy,” and Swamidass would manufacture it for them.

  2. Wat? Seriously? Are they really this amazingly underhanded and deliberately dishonest?

  3. Rumraket: Wat? Seriously? Are they really this amazingly underhanded and deliberately dishonest?

    I genuinely wanted Swamidass to be one of the Good Guys. And perhaps he is, on the whole. But this certainly is a lapse.

    It boggles my mind, to see two scholars copy a 10-page document into their supplementary materials, without identifying the source (Power to Change Ministries — the copyright notice at the bottom of the page is actually not necessary). I’m having a very hard time dreaming up a reason for them to have done so, other than to conceal the fact that they’re responding to something a Christian apologist has disseminated through a website aimed at Christian students (primarily in Canada).

    The best I can imagine is that Matlock and Swamidass originally assumed that Durston was explaining what he and his colleagues (Chiu, Abel, and Trevors) had published. Scrutinizing the published article, I see shadows of the claims in Durston’s note, and I suppose that the reviewers/editors required Durston et al. to change quite a bit. The review process did not fail as Matlock and Swamidass indicate, and they are working to enter into the scientific literature what evidently was rejected.

  4. Tom English: I genuinely wanted Swamidass to be one of the Good Guys.

    While I consider myself to be a theistic evolutionist of sorts, it’s theistic evolutionists like Swamidass that lead me to resist classifying myself as one of “them.”

  5. I do my best to follow the arguments here, but without an acronym translator, I am lost.
    For example there are three acronyms in the sentence quoted below.

    The specific claim in the literature is that the FSC of extant sequences is a good estimate of FI. The claim is that applying the MI formula to a sequence alignment of proteins with shared function can good estimate of the number of sequences with that function.

    And just try googling MISA.
    I realize that commenters here generally know what they are talking about, but us lurkers can’t really learn too much when the conversation becomes obscure.

  11. The funny thing about Durston is how laughably wrong he is here:

    Elsewhere, I have proposed the following testable, falsifiable and verifiable hypothesis:

    Hypothesis: The ability to produce statistically significant levels of functional information is a unique attribute of intelligent minds.

    The key word here is “unique”; nothing else can do it.

    There’s absolutely no way he can derive that conclusion from looking at protein families in pfam. It’s made up bullshit through and through.

    Seriously, think about it for a minute. In pfam, for some protein family, there is listed all known variants of the protein used in known life. So there are all the amino acid sequences we know of, which correspond to that particular protein fold.

    How do you get from “I have that data” to “therefore only minds can make that kind of data”?

    The scientific evidence, therefore, from actual data available on Pfam, suggests that the information required to code for protein families is statistically very significant and, thus, tests positive for an intelligent source.

    No, it doesn’t. At all. This conclusion follows from nothing Durston says, or calculates, anywhere.

  13. Thank God I’m not holding my breath waiting for Swamidass or his “brilliant student” to reply to Durston’s critique.

  14. Rumraket,

    The information content of Pfam wrt intelligence seems remarkably sensitive to cladogenesis and extinction. Each mutation in a bifurcating tree reduces the ‘intelligence quotient’ of the dataset; each extinction increases it.

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