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!”
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
: Engineering mathematics. Engineering analysis. (TA347
: 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):
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.
[eta: link to comment]
***[eta: in relation to genome size, not the first time anyone, ever, discussed genetic load!]