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Monday, November 07, 2005

Lifecode

Echoed on the Panda's Thumb

I've been reading a strange book by Stuart Pivar, LifeCode: The Theory of Biological Self Organization (amzn/b&n/abe/pwll), which purports to advance a new idea in structuralism and self-organization, in competition with Darwinian principles. I am thoroughly unconvinced, and am unimpressed with the unscientific and fabulously concocted imagery of the book.

There exists a real difference of opinion between two approaches to biology, the functionalist and structuralist views, and it influences how we look at evolution. The functionalist position is the one most people are familiar with: populations contain organisms with differing fitnesses, selection promotes the individuals with the better functional adaptations, and the properties of populations change over time to improve their functional status.

Structuralism is harder to get across. A key figure in historical structuralism is D'Arcy Wentworth Thompson and his book, On Growth and Form (amzn/b&n/abe/pwll); Thompson summarized it most tersely in this aphorism:

Everything is the way it is because it got that way.

The emphasis in structuralism is on process and history and interactions with the environment; what Thompson means is that form is a consequence of developmental and evolutionary processes (although no Darwinist, Thompson was entirely on board with evolution), and that the understanding of why organisms look as they do lies in understanding how they are assembled. Stephen J. Gould, in his forward to On Growth and Form, explained Thompson's guiding principles this way:

This hybrid theory of Pythagoras and Newton argues that physical forces shape organisms directly (with "internal" and genetic forces responsible only for producing raw material, admittedly in gradients and programmed timings, for construction under principles of physics)—and that the ideal geometries beloved by classical Athens pervade organic form because natural law favors such simplicity as an optimal representation of forces.

As you might guess, Thompson is very popular with developmental biologists. It's not just that he privileged our discipline with importance, but that he was a fascinating writer, extremely erudite, and his book is rich with observations and insight. He didn't just claim that physics and geometry dictated aspects of form, but he carefully documented it with examples. Cells tend to be round, for instance, not because they need explicit genetic instructions to assume that shape, but because extant physical forces configure it that way in the absence of other specific internal efforts to change it.

I mention Gould and Thompson intentionally, because as it turns out, Pivar claims the mantle of both Gould and structuralism. In LifeCode, he lays out his theory of morphogenesis based on topological distortions of cells. He was a personal friend of SJ Gould's, and has recently made friends among the anti-evolutionists and Intelligent Design creationists by claiming that Gould did not believe that natural selection played a major role in evolution, that he was suppressed by "anti-antidarwinist forces", and that heterochrony was "Stephen Jay Gould's theory of evolution." It's all very peculiar. I'm not going to bother with these claims—they've been dealt with elsewhere—except to say that I think they are ludicrous.

Instead, Pivar sent me a copy of his book to review, so I'll focus on that. I am a fan of Gould's and I rather intensely despise creationists, so taking that tack would not predispose me to evaluate it charitably. However, I also appreciate the ideas of structuralism (especially as expressed in that quote by Gould above), think Thompson was a demi-god in the pantheon of developmental biology, and favor the hybrid perspective of West-Eberhard, so instead I sat down with it as I would to a new book by that better known structuralist, Brian Goodwin(amzn/b&n/abe/pwll)—critically, but with an inclination to enjoy some new ideas.

I was disappointed.

I will say this: it is very pretty. Pivar has a website for the book, with some of the artwork on display. It's visually striking stuff.

Unfortunately, it has almost nothing to do with reality. His theory (which is also explained on a website) is all about topological manipulations of embryonic forms, and he uses the artwork to show his models for how the embryo is distorted by physical forces to generate various structures…and they simply do not bear any relationship to cell and tissue movements in any embryo I've ever seen. Here, for instance, is his explanation for the development of the skull.

skull?
Cheetah Skull and Brain. The brain is an enclosed membrane within the brain case. With expansion, it bulges and extrudes through six fenestrae, extruding to form nasal, optic, and auditory sacs.

The head forms from the polar cap, which consists of three flat, broad segments of the polar sphere appearing as three concentric, ringed zones. The segments are divided into four quadrants. Each of the resulting twelve parts develops a circular hole at the center. The six fenestrae of the future dorsal side will form the nasal, optic, and auditory capsules. The ventral half produces the jaw. The architectural scheme of the skull results as concurrent, deep, invaginating infolds along the dorsal and ventral midlines fuse, sealing off enclosing cavities in each hemisphere. These meet internally and form the floor of the brain case and the roof of the mouth. These cavities are analogous to the structure in plants that produce the anthers.

This is a remarkable story, especially since, try as you might, you will see absolutely none of the described features present in the developing embryo. The jaw arises as a caudal condensation, for instance, and extends forward during development. There aren't any of these regular fenestrae, there isn't a ventral invagination, and most importantly, the vertebrate head never looks like any of his intermediate stages. These are pure confabulations.

He attempts to explain many phenomena in development, all with the same stunning failure to attempt to look at real organisms, favoring instead the geometric purity of his imagination. His explanations of gastrulation, while more abstract, are notably lacking in any association with actual data. I've watched gastrulation occur; I have friends who study cell and tissue movements in zebrafish gastrulation; I've written software that is used to analyze changes in embryo shape and cell migration. Let me tell you, nothing in this book is even an approximation of what we actually see.

I'm afraid all of these artistic inventions are in the service of a theory that is unappealing, uninteresting, and without the slightest bit of predictive power. Here is his idea, briefly: all cells and embryos are donuts, and how they turn themselves inside out determines their future morphology. To be fair, I'll transcribe it as he has written it:

The shape assumed by the surface enveloping the primordial germ plasm is a geometric or topological form called the sickle torus, a kind of torus that can be described as one spheroidal surface inside another, interconnected at the poles by a narrow funnel vortex. Its cross section is sickle shaped as opposed to the circular cross section of simpler doughnut-shaped torus.

The toroidal egg cell surface is fluid. It is in constant axial flow like smoke rings or magnetic fields but substantially slower.

Toroidal streaming imposes on the membrane sheet the relentless cycle of alternate compression and expansion suffered as the sheet passes through the narrow vortices. The membrane becomes empatterned by radial and circumferential subdivisions. This pattern guides the expansion of the membrane to the mature egg-cell plasma membrane and later, as separate cells, guides the formation of the standard adult phyletic body.

Doesn't help much, does it?

Again, none of this—sickle torus, rings of axial flow, toroidal streaming, radial and circumferential subdivisions—is in evidence. How it generates the complex form of an organism is not obvious. How his theory can be reconciled with a large body of embryological evidence that directly contradicts virtually all of it is not clear, and Pivar has chosen not to address any of it. And a book full of geometrically interesting sketches neither explains nor supports Pivar's theory.

I have to add another compliment for the book, though. In addition to the lovely artwork, it's an extremely high quality print; well bound, on heavy stock, and looking to last a thousand years. It seems no expense was spared getting it published, which is in contrast to the content, and is unusual for such flagrant crackpottery. It may well be popular among creationists, who can always be trusted to favor glossy superficialities over substance.

To Mr Pivar, I would suggest a simple rule. Theories are supposed to explain observation and experiment. You don't come up with a theory first, and then invent the evidence to support it.


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Comments:
#47560: coturnix — 11/07  at  08:04 PM
Why do so many otherwise brilliant philosophers of biology absolutely DESPISE Brian Goodwin? I have only read the Leopard. Has he written something more technical or philosophical that set the whole field off against him?



#47561: Ron Zeno — 11/07  at  08:16 PM
When you don't have anything of substance to say, put your time and money into saying it well and you will be rewarded. ;)



#47568: Tom Ames — 11/07  at  08:54 PM

Theories are supposed to explain observation and experiment. You don't come up with a theory first, and then invent the evidence to support it.


PZ, that's such a quaint twentieth century notion.



's avatar #47569: Raven — 11/07  at  08:57 PM
From his website:

In the bold, innovative, and lavishly illustrated “Life Code,” chemist and mechanical engineer Stuart Pivar spells out a challenge to entrenched dogma that may ultimately persuade biologists to shift their focus from genes to algorithms and physio-chemical process in order to understand how nature produces the forms of living things.


Uh-huh--yet another engineer telling biologists how wrong they are about biology.

How many times have we seen this particular movie again?



's avatar #47570: — 11/07  at  08:59 PM
The website was dense (or perhaps it was me), but to me it seems to say that selforganisation control organisms instead of that organisms may use selforganisation (cell membranes, et cetera). 'Explains all' is typical for crackpot theories.

BTW, the imagery reminds me of the diagrams of galaxy evolution from elliptical to spiral galaxies (or vice versa) that was popular once. They have been retired as graphical fantasies as far as I know; the human mind invents patterns from little or no information.



#47571: Bill Tozier — 11/07  at  09:02 PM
On Brian Goodwin, despising: Partly, I think, because of an affiliation & association with Mae-Wan Ho.



's avatar #47572: — 11/07  at  09:07 PM
Engineers, especially retired ones, are known to boldly go there no engineer has gone before, or should go. They can drive physicists nuts at times.



#47574: — 11/07  at  09:53 PM
To be fair, sometimes you can start with a pure theory, such as group theory (*), and reality will oblige you with examples of it. This is a lot more likely to happen in physics than biology, though.

This sounds like a case of getting fascinated by cool topological transformations and inferring that nature must therefore be equally fascinated by them.

I think mathematicians are particularly prone to the idea that the most elegant theory is the one preferred by nature. I remember reading that in the 50s (when coding theory was hot) it was hypothesized that amino acid triplets were overlapping, neatly finessing the probably of where to start the frame and a clever code was worked out for them that does this. Unfortunately that isn't really what happens.

(*) Somebody could reasonably claim that group theory is motivated in part by geometric transformations already observed experimentally, but it has had many less anticipated applications.



#47575: — 11/07  at  09:58 PM
"It's all very peculiar. I'm not going to bother with these claims—they've been dealt with elsewhere—except to say that I think they are ludicrous."

"These are pure confabulations."

One of these is about Pivar's claims about Gould and the other is about his claims about embryonic development, but either could be about either.



#47576: — 11/07  at  10:02 PM
"To be fair, sometimes you can start with a pure theory, such as group theory (*), and reality will oblige you with examples of it."

The point was about empirical theories. Examples of group theory aren't evidence *of* group theory -- that's a category mistake.



#47578: — 11/07  at  10:23 PM
Honestly, I don't know thing zero about developmental biology. Heck, until my girlfriend (who is a biologist) corrected me, I was still calling it embryology. From what very little I do know about the stuff, even I can say those diagrams are hogwash. I've seen enough to know, with a pretty good degree of certainty, that skulls do not develop from anything like that.

Hah! I can't wait until Dembski gets his hands on this... I just know some kind of butchered, qualitative and wrong account of differentiable manifolds and Lie groups is going to be used to justify this. I'm putting money on it. Seriously, I'm getting the betting pool going now.

Engineers, especially retired ones, are known to boldly go there no engineer has gone before, or should go. They can drive physicists nuts at times.

Hah! They drive mathematicians up the wall at times, too. I can personally vouch for that.



's avatar #47584: Zeno — 11/07  at  11:27 PM
I think mathematicians are particularly prone to the idea that the most elegant theory is the one preferred by nature. I remember reading that in the 50s (when coding theory was hot) it was hypothesized that amino acid triplets were overlapping, neatly finessing the probably of where to start the frame and a clever code was worked out for them that does this. Unfortunately that isn't really what happens.
Yeah, I think PaulC is referring to DeBruijn sequences, which are cool and helped me get a master's degree. Too bad they didn't work out as a model for amino acid coding.

For some reason, Pivan is reminding me of Stephen Wolfram and his "new kind" of science. Except that Pivan is a crank and Wolfram, well, kind of isn't, though he seems to be toying with the fringe a bit. Just a thought.



#47585: — 11/07  at  11:29 PM
Looks like crazy stuff! But still,.. I am intrigued.

Before I go to checking this stuff out on my own, which books do you fellas recommend I read in order to better aquaint myself with developmental biology, Evo-Devo, and biological self-organization. I am but a novice when it comes to these things but I am wanting to expand my knowledge.

Perhaps unfortunately, I tend to have been "designed" with much more of a philosophical rather than scientific mind and therefore I am searching for books geared towards the lay reader. Any suggestions that you have, I would be much abliged.

MS

BTW, Crackpot teleology may have a very little something to offer real science. You never know what the crazies might stumble on to.



's avatar #47588: PZ Myers — 11/07  at  11:43 PM
For those with a philosophical bent, I recommend Oyama. Serious and thoughtful stuff that deals with the same issues Pivar brings up, but from a reality based perspective.

PZ Myers
Division of Science and Math
University of Minnesota, Morris



#47589: — 11/07  at  11:44 PM
Mark Studdock wrote
BTW, Crackpot teleology may have a very little something to offer real science. You never know what the crazies might stumble on to.
Maybe. But the signal to noise ratio is lousy, making it an inefficient waste of time to slog through the dreck trying to find a nugget that more than likely is not there.

RBH



#47590: coturnix — 11/07  at  11:44 PM
Well, on evo-devo, I have not read Sean Carroll's book yet, but PZ recommends it often. "Biased Embryos and evolution" by Wallace Arthur is excellent and very readable for lay audience.

On self-organization, perhaps "At home in the Universe" by Stuart Kauffman is OK.



#47591: coturnix — 11/07  at  11:45 PM
I second Susan Oyama.



#47593: — 11/08  at  12:02 AM
Uh-huh--yet another engineer telling biologists how wrong they are about biology.


Hey this is book is a GREAT tool for evolutionists, actually!

It shows how an engineer (Intelligent? Designer) would have set up developmental processes to exploit avantages presented by physics and geometry. And it has no correspondence with what these processes actually look like.

It merely illustrates how illogical and contingent biological structures are. Strike four against the ID guerillas.


"...theology and geometry..." Ignatius J. Reilly.



#47597: — 11/08  at  12:22 AM
Thank you for the recommendations. I will be sure to check out Susan Oyama. And Carrol's book is already on it's way to my house.

RBH, Your comment might be true. It would certainly not be wise to devout too much of ones time to slogging through the dreck of crackpot theorizing. However, in the case of Pivar, if the pictures really are as cool as PZ Meyer's says, it might be at least aesthetically worthwhile. Like taking a stroll through a gallery of postmodern paintings. No bearing on reality yet somehow occasionally pleasing.



#47599: — 11/08  at  12:29 AM
Pivar manages to hit plenty of the points on the Crackpot Index.

That brings up the question of whether biology shouldn't have its own crackpot index instead of having to borrow from the physicists. If biology wants to be Top Science, it needs its own crackpot index, and it needs 38 items on it so it tops the physics index.

I had a look at Pivar's site and I think we could come up with plenty of items for an idex there.

Here's a start in no particular order, from Pivar's first page:

- Casting your theory as the culmination of the work of a series of others who are way more famous and who nobody else puts in the same sentence as your name until you did. (Para 2)

- Claiming there is no published precedent for your work. (Para 4)

- Claiming you're up against dogma. (Para 5)

- Claiming your theory presents a new paradigm. (Para 1)

- Claiming your theory is complete (i.e. not like evolution that had to have bits like genetics tacked onto it) and explains all observations in a broad field of science (Para 3)

- Claiming the unusual nature of your theory requires an unusual way of explaining it (Para 1)

Not sure how many points to assign any of these but its a start.



#47617: — 11/08  at  02:42 AM
Well, I've done some developmental biology in my 2nd student year, and I can tell you that the picture of the skull is crap. It rather works with buds of little developed stem cells and I believe hormones already play a role here in controling how far a but grows, that is how your limbs and fingers/toes grow if I'm correct. And about the brain in the skull, it is rather the other way around that the eyes and nasals find connections with the brain.



#47624: — 11/08  at  03:48 AM
PZ, again more book requests - when are you going to get that reading list onto your sidebar?



#47625: — 11/08  at  03:58 AM
Which Oyama do you suggest, given that I am a developmental biologist and am relatively familiar with the debate?



#47641: — 11/08  at  07:38 AM
Several years ago I came up with a definition for the peculiar psychological state that engineer's inhabit.

An engineer is someone who will examine any object or idea and immediately knows how to improve it. Nine times out of ten they are wrong.

As an engineer, I’m regularly guilty of that behavior myself. I wouldn’t call it hubris, it’s a creative outlet. But the engineering mindset leads to problems on occasion. The American automotive engineering world is an amazing example of this behavior. Every few years we get a new program and design new products from scratch. This is inefficient, expensive, and often leads to new problems, but ultimately it’s far more fun.

It can also, especially when dealing with things outside our field, lead to stupidity. I’ve seen schemes for playing the stock market tracking over two hundred variables. Some co-workers go to Las Vegas a couple times a year with a blackjack or roulette scheme designed to break the bank. Sometimes they learn, sometimes they just get mad that the universe didn’t follow their model.

It doesn’t surprise me in the least that an occasional engineer will think that they know more than an expert through a cursory examination of a field of knowledge. There is the possibility that they do have an insight which was overlooked. However, the probability is much greater than the experts have already considered, examined, and rejected that particular insight.

An engineer is someone who believes they can improve anything, and is usually wrong.

Cheers,

-Flex



#47646: Ricardo Azevedo — 11/08  at  07:56 AM
Great article, PZ -- although reading that book does sound exceedingly masochistic. I believe this passage is very telling on the source of Pivar's insights, though:
It is in constant axial flow like smoke rings or magnetic fields but substantially slower.

As a relative newcomer to developmental systems theory, I found Cycles of Contingency, edited by Oyama and others, a good introduction to the field.

As for Brian Goodwin, I think it's his deep hostility to natural selection that turns so many people off -- myself included. Having said that, John Maynard Smith wrote a great essay defending Goodwin's structuralist approach to developmental biology (I actually heard him deliver it a few years ago at the London School of Economics).



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