My copy of A New Kind of Science, that is. As a person “who might perhaps rather not be named” — but as it happens is perfectly happy to be so — I point you with pride and great respect to Cosma Shalizi’s apropos and surprisingly timely review of Stephen Wolfram’s magnum whatsis.
Timely, because (perhaps by quantum cellular automata shit happening in the very fabric of the universe) the damned thing came up today in a conversation.
This is kinda nit-picky, I know, but one ‘graf in this review struck me as wrong:
“Another egregious weakness is biology. Wolfram displays absolutely no understanding of evolution, or what would be necessary to explain the adaptation of organisms to their environments. This is related to his peculiar views on methodology. If you want to get a rough grasp of how the leopard might get its spots, then building a CA model (or something similar) can be very illuminating. It will not tell you whether that’s actually how it works. This is an important example, because there is a classic theory of biological pattern formation, or morphogenesis, first formulated by Turing in the 1950s, which lends itself very easily to modeling in CAs, and with a little fine-tuning produces things which look like animal coats, butterfly wings, etc., etc. The problem is that there is absolutely no reason to think that’s how those patterns actually form; no one has identified even a single pair of Turing morphogens, despite decades of searching. Indeed, the more the biologists unraveling the actual mechanisms of morphogenesis, the more complicated and inelegant (but reliable) it looks. If, however, you think you have explained why leopards are spotted after coming up with a toy model that produces spots, it will not occur to you to ask why leopards have spots but polar bears do not, which is to say that you will simply be blind to the whole problem of biological adaptation.”
I’m not saying that Wolfram *does* have a good grasp on biology — I don’t want to defend on ANKoS at all. But my understanding is that lateral inhibition, originating with Turing, elaborated by Gierer and Meinhardt and continuing later with others, *is* a model which is used to describe (say) patterns which arise during development. I’m thinking here of spatial patterns in the embryo during drosophila development… but there are a ton of other examples. I got back from a retreat about two months ago where lateral inhibition models were even mentioned as a model for the way that yeast cells extend their “shmoos” during mating…
Maybe I should write about this at QoW sometime…
Maybe if we make noise enough, Shalizi will turn on comments….
Oh, and I know — Nijhout’s work (which as I recall made the cover of the big green Springer book) on butterfly wings is pretty clearly Turing patterns. And seashell patterns, ditto. And maybe something involved in apical meristem placement, but that escapes me at the moment. Too long not a botanist.
Yeah… I mean, like I said, I’m not a biologist. But I was listening to some biologists who (basically) were saying “the model of ‘lateral inhibition,’ inspired by Turing, is a good model for this phenomenon X with the following molecular components…”, so I feel comfortable in challenging at least *that* portion of his essay.
But overall, it was a fun read. I spent part of last night and this morning tracking down and reading the papers and reviews he links to. Reading Shalizi is always…. I feel like it boosts my creativity. His writing opens my mind — I usually come up with good ideas within 6 hours of reading something he’s written, even if it’s on a completely different subject
.
Turning on comments: never. If I did implement them, I’d feel obliged to keep up with them, and keep them spam-free, and this I really don’t have the time or the motivation to do.
Lateral inhibition: This might call for some clarification. Turing proposed a very specific, and very elegant, mechanism for lateral inhibition using only two chemicals, which mutually inhibited each other, one diffusing much more effectively than the other. The Turing mechanism has been demonstrated in artificial chemical systems. There are also biological systems which seem to use forms of lateral inhibition, but with a far more complicated chemical basis than paired Turing morphogens, which matters a lot for evolutionary issues (as Bill could explain better than I). In all honesty, however, it’s been a couple of years since I was reading up on this very actively. References would be appreciated.
Praise: Fortunately, you cannot see me blush.