A reason for cytosine deamination

A few people have notified me to let me know that front-loading is being discussed on UD by someone with the moniker ‘genomicus.’ In one place, genomicus states that cytosine deamination is a prediction of front-loading.  Someone else with the moniker “eigenstate” disagrees and writes:

The fail point here in this item is “so why would a front-loader choose cytosine as a base in DNA?”. It’s not sufficient to offer us *a* reason why you think cytosine would be chosen (and this is particularly devastating if you are offering this putative prediction in the context of an “intelligent design” explanation, an explanation with an unknown, inscrutable, mysterious designer). The choice must follow NECESSARILY from the hypothesis.

You are quite conspicuously working backwards from your conclusion. Coming up with a plausible choice — and given an unspecified, unknown, potentially omniscient and omnipotent designer, ALL choices are plausible — does not ground a prediction. First you lay out the hypothesis, the proposed mechanism, and then you deduce from that NECESSARY implications that proceed from that. If you can affirm what is entailed from your model, you got something! Sometimes those predictions are trivial or banal, and so don’t carry much weight. Other times they just don’t distinguish the hypothesis from other, competing hypotheses. But in this case, if you COULD establish that such a choice was ENTAILED from your proposed model, that would be quite substantial, indeed, I think.

I would not agree with genomicus that front-loading predicts the cytosine deamination story.  That whole story is more subtle and complex than that.  Let me explain.

In 2001, Poole, Penny, and Sjoberg published a paper in  Nat Rev Mol Cell Biol entitled, “Confounded cytosine! Tinkering and the evolution of DNA.”  In the abstract of this paper, they make the following assertion: “Early in the history of DNA, thymine replaced uracil, thus solving a short-term problem for storing genetic information-mutation of cytosine to uracil through deamination. Any engineer would have replaced cytosine, but evolution is a tinkerer not an engineer.

Is it really true that “any engineer would have replaced cytosine?   Poole, Penny, and Sjoberg are effectively arguing that because of its propensity to mutate through deamination, there is no rational reason for using cytosine as a base and it exists only as a “frozen accident.”  In other words, this aspect of cytosine is being used, at least in part, as an anti-design argument.

What I did is to draw from a teleological perspective to make a prediction.  The prediction was simply this:  Given its propensity to being damaged, there must be a reason cytosine was included as one of the four bases of DNA/RNA.  This prediction is entailed by the teleological hypothesis that life is ultimately rational; if life was designed, then there is a reason behind its architecture and composition.*

So it’s not that front-loading predicts cytosine would be used as a base.  It’s that a hypothesis of life’s design predicts there would be a reason cytosine was used as a base.

This prediction then provided the impetus to take a closer look at the relationship between the genetic code and cytosine deamination.  And as a result, I uncovered a pattern that no one else (AFAIK) has seen – a reason to include cytosine as a base.  A copy of my original description is posted here and I provide a more polished account in my book.

Let me summarize.  I don’t think front-loading predicts cytosine would be incorporated into the DNA.  I predicted that there would be a reason for including cytosine, and its propensity to deaminate, in response to Poole et al.’s assertion that “Any engineer would have replaced cytosine.”  That assertion has been refuted.  They asserted that no engineer would have used cytosine as part of the genetic material because of its predisposition for deamination. But it’s exactly this predisposition that might cause an engineer of evolution to include it.

 

*It is worth noting that non-teleologists, as a whole, agree with this logic.  For example, when they (and I) cite useless junk DNA as an argument against design, they (and I) are drawing from this logic.

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14 responses to “A reason for cytosine deamination

  1. Oh no- “they” were saying that you and ‘genomicus’ are one in the same.

    But anyway I agree that a designer using planning and fore-thought could intergrate a molecule that deanimates as part of an evolving design.

  2. LOL. No, I am not genomicus.

  3. Hi Michael,

    Interesting take on Genomicus’ conjecture. I appreciate that at least a distinction is made between a front-loading hypothesis (FLH) entailing cytosine as a base, and cytosine AS a choice having some telic driver behind.

    That is, even if cytosine is not entailed by the FLH directly, if it “happens to be chosen” so far as we can see in our observations, (and indeed that is what we observe), there should have (must have?) been a designer-based rationale for that choice.

    That said, though, I don’t see where that gets us, in terms of a prediction. For what it’s worth, Poole, et al, are making dubious assertions going the other way, in my view. That may not fit their current view of the engineering constraints, but as you point out (ostensibly, haven’t read your link yet, but will) other design considerations may obtain that Poole, et al, and others thinking about this have not yet taken account of.

    As soon as you arrive at “the designer would not do this…” or “would do that…”, I think the argument has become impotent, and that goes either way. It’s hard to resist saying “no the designer would NOT have done” when ID folks say “this is obviously the work of the designer”, but such denials are as baseless as the design conclusions that prompted them.

  4. Hi eigenstate0,

    You write

    That said, though, I don’t see where that gets us, in terms of a prediction. For what it’s worth, Poole, et al, are making dubious assertions going the other way, in my view.

    Yes, but a) Poole et al.’s assertion are in the peer reviewed literature and b) no one else from the scientific community has ever said the assertions were dubious.

    As for predictions, I can simply point to what I wrote above:
    This prediction then provided the impetus to take a closer look at the relationship between the genetic code and cytosine deamination. And as a result, I uncovered a pattern that no one else (AFAIK) has seen – a reason to include cytosine as a base.

    Whether or not this pattern has biological significance remains to be seen. Yet how is it that no biologist has noticed this pattern before? After all, it’s not as if the genetic code and cytosine deamination are esoteric topics in biological circles. All I can say I noticed it purely as a consequence of a teleological hypothesis.

    As soon as you arrive at “the designer would not do this…” or “would do that…”, I think the argument has become impotent, and that goes either way.

    Yes, this is quite similar to Duck/Rabbit.

    It’s hard to resist saying “no the designer would NOT have done” when ID folks say “this is obviously the work of the designer”, but such denials are as baseless as the design conclusions that prompted them.

    I do agree that lots of ID people have this bogus sense of certainty and knowledge about “the work of the designer” and are too quick to reach conclusions built on shifting sand. I come from the perspective that we live in an ambiguous world and even if design was true, it’s hard to see how it could be shown in any truly scientific sense. Since you are new here, I should make it clear that I do not think my design thinking is science. However, I don’t believe that an idea has to be scientific in order to have any value or merit. There is too much middle ground between scientific demonstration and baseless, impotent claims and, for me, it makes no sense to take such a binary approach to reality.

  5. Thanks for your input on this Michael.
    Let me ask you a quick question: if it is indeed discovered that cytosine deamination has played a major role in the origin of some key proteins, would that confirm any teleological hypotheses at all?

  6. Michael,

    Thanks for the reply. I just read through your 2009 post on cytosine deamination, being a “feature” rather than a “bug”. Perhaps that is a counter to Poole, et al, and one that would pass peer review muster.

    That’d be something, but in the context of a prediction on this issue, rooted in a designer, now you have a “design rationale” for cytosine deamination and an “anti-design rationale” for it. An FLH based would be ambivalent on cytosine, then, barring some new (to us) knowledge of the designer’s direct rationale for that choice.

    That is, you may have nullified the force of cytosine as an ‘anti-design’ indicator, but that doesn’t advance a cytosine-as-designer-choice prediction.

    In any case, I can salute the contribution that the pattern identification represents on this, no matter which way it augurs, ultimately.

    As for the “ambiguous world”, I’m not one with many complimentary things to say about ID, even when trying to be charitable, but having read most of your book (why no Kindle version, by the way? I’ve lost my copy, unfinished) I think your “consilience” approach is the most reasonable one I have come across that is still under the “tent of ID”.

    I’ve not commented here before today, or read much, but I’m familiar with that heuristic (a term I think I can use in lieu of ‘science’). I agree that the
    “binary” model is problematic, but I think it’s like the familiar American chestnuts about libertarian democracy: it sucks in lots of ways, but there’s nothing seemingly better. I agree there is much “middle ground” to consider, but lots of the science that we do have suggests we are inclined to promote baseless, impotent claims into that middle ground and erroneously call them…. “middling”.

  7. Hi Genomicus,

    Let me ask you a quick question: if it is indeed discovered that cytosine deamination has played a major role in the origin of some key proteins, would that confirm any teleological hypotheses at all?

    “Confirm” is too strong of a word here. To confirm a teleological hypothesis you would have to argue along the following lines: If life was designed, then cytosine deamination should play a major role in the origin of some key proteins, but if life was not designed, then cytosine deamination would not play a major role in the origin of some key proteins. And of course, you’d have to more than assert this. There should be some solid logic that would allow us to tie cytosine deamination to teleology while excluding any tie between cytosine deamination to non-teleology.

    If it was indeed discovered that cytosine deamination has played a major role in the origin of some key proteins, I would view that as support for the front-loading hypothesis. That is, it would be another clue that enhances the plausibility of front-loading, for we would find that this pattern that is buried in the genetic code has indeed facilitated the emergence of some key evolutionary transitions.

  8. eigenstate,

    I agree there is much “middle ground” to consider, but lots of the science that we do have suggests we are inclined to promote baseless, impotent claims into that middle ground and erroneously call them…. “middling”.

    Understood. But the problem is that even if life and evolution were designed, science would not be able to detect this.

  9. Michael,
    Understood. But the problem is that even if life and evolution were designed, science would not be able to detect this.

    I don’t disagree.

  10. Yea I know, after posting my comment I wished I hadn’t used the word “confirm.”

    So, to summarize your position, front-loading doesn’t predict that cytosine deamination has played a major role in the origin of key proteins, but if that was indeed the case, it’d be another clue in favor of front-loading? Makes sense to me.

  11. Eigenstate,

    I don’t disagree.

    I’m impressed. Most ID people disagree because they want ID to be science(for various reasons). Most critics (in my experience) disagree because they want to the claim – “There is no scientific evidence for ID” – to have meaning.

  12. @Michael,

    I’m impressed. Most ID people disagree because they want ID to be science(for various reasons). Most critics (in my experience) disagree because they want to the claim – “There is no scientific evidence for ID” – to have meaning.

    I may hedge on your claim but only slightly; if lfe and evolution were designed, science would not necessarily be able to detect this. I’d even go so far as to say it probably wouldn’t be able, which was close enough for a litote in my answer: I don’t disagree.

    Again, I’m a pretty staunch critic of ID, but that really amounts to valuing the integrity of the tools and epistemology of science, which the ID movement (I’m being trained currently to take pains to distinguish the movement from the conceptual framework) is wont to mangle and abuse.

    But if life were designed, Dembski’s CSI would be hopeless as ever, for example. But your idea of a “consilience” — and that was a key insight on your part, using that word — is one that I would say would be the… means of discovery for me to some kind of non-scientific but rational, or at least carefully thoughtful conclusions about life-as-designed.

    I don’t see the consilience you do for design, so I’m a critic in that sense. But the heuristic, the “consilience heuristic” is one that if any WERE to be successful, I should think it should be something like that.

  13. But if life were designed, Dembski’s CSI would be hopeless as ever, for example. But your idea of a “consilience” — and that was a key insight on your part, using that word — is one that I would say would be the… means of discovery for me to some kind of non-scientific but rational, or at least carefully thoughtful conclusions about life-as-designed.

    I agree (LOL!). But seriously, CSI in life won’t go anywhere in science because the S cannot be objectively determined. But let’s overlook that, as perhaps a deeper problem is that the ID community has always had it backwards. They argue like this: “If CSI exists in life, then life was designed.” If they wanted ID to be like science, they should have argued, “If life was designed, then life should be full of CSI.”

    But the problem, as I see it, is that the design of life does not really predict ubiquitous, high levels of CSI. Such life forms would be incredibly fragile, not robust. Designing life so that it is fragile does not sound like an intelligent design to me.

    But then again, I think ID has been misnamed, as there is no focus on whether or not a design is intelligent (I touched on this back in 2010):

    http://designmatrix.wordpress.com/2010/02/19/where-is-the-i/

    Interestingly enough, Dembski recently acknowledged in an interview that the I in ID does not really mean I:

    The reason we put the adjective “intelligent” in front of the noun “design” is not to stress that the design we find in nature is optimal or good or morally acceptable. Rather, it is to underscore that the design we find in biology and in the universe more generally is actual. Richard Dawkins opens his book The Blind Watchmaker by stating “Biology is the study of complicated things that give the appearance of having been designed for a purpose.”

    For Darwinian biologists, all such design is merely an appearance. The “intelligent” in “intelligent design” underscores that we’re not just dealing with an appearance of design, but rather with actual design.

    So while the question of suboptimal or bad design may be interesting, it is not central to intelligent design as a scientific program, which in the first instance is interested in looking for evidence of design überhaupt.

    So I’m not sure why they didn’t call “Intelligent Design” “Actual Design.” It’s not a trivial point. Anyway, if your interest in whether or not a design is an intelligent design is secondary and tangential, I suppose it makes sense that no one in the ID movement would question the assumption that CSI in life should exist and be detectable.

  14. Mike Gene:
    What do you think of this paper:
    “Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape,” Biology Direct.

    They seem to argue that the genetic code isn’t the most optimal genetic code:
    “Thus, the standard genetic code appears to be a point on an evolutionary trajectory from a random point (code) about half the way to the summit of the local peak. The fitness landscape of code evolution appears to be extremely rugged, containing numerous peaks with a broad distribution of heights, and the standard code is relatively unremarkable, being located on the slope of a moderate-height peak.”

    What kind of implications does this have for your views? (It’s a paper back from 2007, so you might have already discussed this somewhere.)

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