Tag Archives: Evolution

Sex – a matter of perspective

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I am sure that many readers have already concluded that I do not understand the role of sex in either organic or biotic evolution. At least I can claim, on the basis of the conflicting views in the recent literature, the consolation of abundant company.

– George C. Williams, Sex and Evolution, 1975

 

What’s sex all about? This question has been exercising biologists since well before Williams’s time, but in the 1970’s, with the rise of ‘gene-centrism’ and the related controversy over group selection, a succession of prominent authors grappled with the problem, trying to fit it with current evolutionary theory to no-one’s particular satisfaction. Males were deemed an impediment to a female’s efforts to maximise her reproductive output, time wasted on these feckless types resulting in her only passing on 50% of her genes per offspring. From the perspective of a ‘selfish gene’, meanwhile, getting into every offspring seems a preferable fate to only getting into half of them. On the basis of these apparent large costs, a cryptic offsetting benefit of corresponding magnitude was assumed. Like Godot, it is yet to appear.

Yet sex is widespread. All eukaryotes either do it now, or possess tell-tale signs that their recent ancestors did. Given that it appears costly to individuals, and genes, how did it evolve and why does it persist?

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Pegging an IDist trope

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I‘ve always been a helix-turn-helix kinda guy. That’s the way I roll.

My thesis research involved a couple of repressors – homeodomain proteins—that bound to DNA via helix-turn-helix DNA-binding domains. They controlled cell-type fates. Combinatorially.

(I also worked on HDAC-mediated transcriptional silencing, although at the time I was totally unaware that that was what I was working on. Awwwkward. That’s a story for another time.) For my post-doc , I was surrounded by people studying the co-operative binding and sequence-specificity of various helix-turn-helix proteins, and how they achieve transcriptional activation. There was some pretty seminal work done, to which I contributed precisely nothing. Not a productive post-doc, you could say.

Anyhoo, I never really paid much attention to Zinc fingers. Which was rather remiss of me, since the sort of modular DNA-binding activity that they have is pretty much ideal for building networks that regulate gene expression. But hey, grad students can be rather parochial.

Then our dearest Sal posted an OP here on Zinc fingers, playfully entitled “Giving Evolutionary Biologists the Finger!”

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On variant genetic codes

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Craig Venter has achieved celebrity status in Creationist circles for little more than a slightly embarrassed smile. In a discussion involving, among others, Richard Dawkins, Lawrence Krauss and Paul Davies, Venter makes the eyebrow-raising statement that he does not regard Mycoplasma as the same ‘life-form’ as other prokaryotes, or eukaryotes. His reasoning was that they have ‘different genetic codes’. Dawkins reasonably points out that their codes are ‘all but identical’ (they differ in just one position, Trp for STOP). Creationist videos of the exchange tend to fade on the aforementioned smile given in response. The videos are presented, breathlessly, as “Venter denies Common Descent in front of Richard Dawkins!”. However … one difference? Is that really enough to justify a claim of separate origins? This would be like claiming that Norwegian and Swedish had separate origins on the strength of the difference between æ and ä or ø and ö. Continue reading →

Introduction to Evolutionary Informatics

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Introduction to Evolutionary Informatics, by Robert J. Marks II, the “Charles Darwin of Intelligent Design”; William A. Dembski, the “Isaac Newton of Information Theory”; and Winston Ewert, the “Charles Ingram of Active Information.” World Scientific, 332 pages.
Classification: Engineering mathematics. Engineering analysis. (TA347)
Subjects: Evolutionary computation. Information technology–Mathematics.1

Yes, Tom English was right to warn us not to buy the book until the authors establish that their mathematical analysis of search applies to models of evolution.

But some of us have bought (or borrowed) the book nevertheless. As Denyse O’Leary said: It is surprisingly easy to read. I suppose she is right, as long as you do not try to follow their conclusions, but accept it as Gospel truth.

In the thread Who thinks Introduction to Evolutionary Informatics should be on your summer reading list? at Uncommon Descent, there is a list of endorsements – and I have to wonder if everyone who endorsed the book actually read it. “Rigorous and humorous”? Really?

Dembski, Marks, and Ewert will never explain how their work applies to models of evolution. But why not create at list of things which are problematic (or at least strange) with the book itself? Here is a start (partly copied from UD):
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Genetic load and junk.

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Mung, to petrushka, elsewhere:

Everyone does not understand “genetic load” and those that do claim to understand are probably wrong. Why don’t you start an OP on genetic load and the genetic load argument? That would be interesting. Betting you won’t.

This is such an OP. I believe the genetic load argument*** was initially proposed by Susumu Ohno in 1972, whose paper also introduced the then-scare-quoted term “junk”. It’s brief, accessible, and worth a read for anyone who wishes to offer an opinion/understand (not necessarily in that order).

The short version: sequence-related function must be subject to deleterious mutations. Long genomes (such as those of most eukaryotes) contain too many bases for the entire genome to be considered functional in that way, given known mutation rates. The bulk of such genomes must either have functions that are not related to sequence, or no function at all.

Interestingly, the paper is hosted on the site of an anti-junk-er, Andras Pellionisz, a self-promoting double-PhD’d … er … maverick. Also of interest is that, contrary to some ID narratives, the idea was initially resisted by ‘Darwinists’, if that term is understood not as people who simply accept evolution, but as people who place most emphasis on Natural Selection. Perfectionism is not the sole preserve of Creationists.

More recent work has characterised the nonfunctional fraction, and this lends considerable empirical support to Ohno’s contentions.

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***[eta: in relation to genome size, not the first time anyone, ever, discussed genetic load!]