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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:
#47657: — 11/08  at  08:37 AM
As far as "gems in the rubbish" from crackpots:

I consider Sturgeon's Law (90% of everything is crap) to apply even to well-founded science. The business of science, and even of life in general, is to sift through our messy world, looking for whichever sort of "gems" we appreciate. On one level, that might be {CHON, water, minerals, free energy, etc}. On another, it might be {truth, beauty, utility, stability, ...}.

Either way, this search depends on all sorts of tradeoffs (resources, time, skill), and one of the basic issues is "alpha/beta pruning", that is, deciding where to focus your resources, and where to *withdraw* them. It comes down to choosing your own strategy....



#47669: — 11/08  at  09:10 AM
... it's an extremely high quality print; well bound, on heavy stock, and looking to last a thousand years.


Also known as "winning arguments through endurance, hardcopy version". :-~



#47684: — 11/08  at  09:42 AM
This refers to the “hydrino” free energy claims of the Blacklight Power company, which has been sending out press releases for five years now with nothing to show for it.

Did he ever have a scientific BS detector?

This is the same Dembski who posted some lame numerology about the "center" of the Bible recently.
http://pharyngula.org/index/weblog/comments/this_guy_is_supposed_to_be_a_mathematician/

The only question is whether he's that gullible or just assumes his readers are.



#47687: — 11/08  at  09:53 AM
Oops. That last one was meant for another thread on another site.



#47696: charlie wagner — 11/08  at  10:28 AM
Paul wrote:

"You don't come up with a theory first, and then invent the evidence to support it."

Neo-darwinists, take note....



#47697: — 11/08  at  10:29 AM
...The "geometric purity of his imagination!"

Damn, PZ, can you sculpt a phrase! Very, very nice!



#47738: — 11/08  at  01:48 PM
I will repeat an earlier request, PZ, which of these Susan Oyama's would one start with? The culture war one looks interesting, but presumbably that's not the one you had in mind here. And I'm leaning mildly toward the one she authored, rather than "just" edited, but some input when you have time would help!
Evolution's Eye: A Systems View of the Biology-Culture Divide (Science and Cultural Theory) by Susan Oyama;
The Ontogeny of Information: Developmental Systems and Evolution (Science and Cultural Theory) by Susan Oyama;
Cycles of Contingency : Developmental Systems and Evolution (Life and Mind: Philosophical Issues in Biology and Psychology) by Susan Oyama (Editor), et al.



's avatar #47739: PZ Myers — 11/08  at  02:04 PM
Start with The Ontogeny of Information. It gets the basic viewpoint across pretty effectively, I think.

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



#47749: coturnix — 11/08  at  02:59 PM
'Cycles' are so expensive!

BTW, I had no idea this guy was still around pushing his theory. I read his book a few years ago (never bothered to dissect it for Skeptic's Circle) and now I see he is posting comments on The Loom!



's avatar #47760: — 11/08  at  04:10 PM
"I think mathematicians are particularly prone to the idea that the most elegant theory is the one preferred by nature."

As someone said, theory is elegant but application is messy. Here it is a long way (a couple of billion years) between first evolution event and today. Plenty of mess.

Dreadful is on to something. What he mentions is not so specific to biology, but ID will give some of those. For example, invoking supernatural beings.

Flex is also on to something. I think it comes from that messy applications can always be improved. In theory. grin



#47774: — 11/08  at  05:17 PM
The comments about engineers reminded me of the old joke:

Engineers believe that equations approximate the world.
Physicists believe that the world approximates equations.
Mathematicians see no connection between the two.

djlactin is absolutely correct - it is potentially a good counterargument to "life is designed".



#47787: — 11/08  at  06:21 PM
Thanks for the reading tip, PZ. I'm off to Amazon and Ontogeny.

Well, if not immediately, then sometime this week...



#47872: — 11/09  at  03:08 AM
Quoth Charlie Wagner
"You don't come up with a theory first, and then invent the evidence to support it."


Cleary, Mr Wagner, you are totally unaware of the evidence that went into the formulation of the theory. Before you spout your ignorance (in the literal sense of the word: lack of knowledge), please read "On the origin of species"... here's a link: http://www.talkorigins.org/faqs/origin.html

You will see the Charles Darwin did not propose the theory from an armchair (unlike his grandfather Erasmus) but that he was was trying to explain what he had observed as a Naturalist on the Beagle, and what he had seen in his studies of barnacles. (Remember that he wrote this book in the 1860s: before the 'discovery' of genetics: one of his predictions was that the then-current view of nheritance as 'mixing of the bloods' must be wrong; and before biochemistry and the discovery that DNA is the genetc coding system). You will realize that an incredible genius he was.

Try to TRULY understand the evidence for evolution and the theory of how evolution occurred (different things!):
go to a reputable sectarian University and study biology for 4 years. Take courses in chemistry, physics, statistics, anatomy, biochemistry, physiology, genetics, systematics, biogeography, botany, zoology, statistics and, yes, even philosophy. And in the fourth year, take an Evolution course.

Then come back and tell me with a straight face that the theory came before the facts. And while you're at it, try to deny that the facts discovered since do not support the theory.

I guarantee you: once you KNOW the evidence, you will not question the theory. But until you do that, save yourself the embarassment and STFU.



#47887: charlie wagner — 11/09  at  08:00 AM
djlactin wrote:

"Cleary, Mr Wagner, you are totally unaware..."



Clearly, Monsieur djlactin, it is you who are unaware.
Before you criticize me, I suggest that you do your homework.
Start by reading the thousands of notes I've posted on talk.origins. Then read the hundreds of notes that I've posted on Panda's Thumb. Then read the dozens of notes I've posted here on Pharyngula.
If you're too busy for that, try just looking at my website at:
http://www.charliewagner.com
After you are sure that you know enough about me and what my positions are and what my credentials are, well maybe then you will have earned the right to say something like that.
For your information, Darwin's contribution was that he defeated the notion of special creation, that all living things were specially created by God. He also proposed a mechanism of natural selection, which acts on existing variation and allows the differential survival and reproduction of organisms with genetic characteristics that enable them to better utilize environmental resources.
However, Darwin attributed creative power to natural selection that it does not have. He was not able to, and to this day, no other scientists have been able to establish a link between these trivial effects and the emergence of highly organised structures, processes and biological systems. The failure of Darwinism is NOT that natural selection is wrong, it's that it doesn't have the ability to assemble, create or design new adaptations, it can only act on what already exists.



's avatar #47889: PZ Myers — 11/09  at  08:11 AM
That you have repeatedly posted nonsense does not constitute good credentials.

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



#47897: charlie wagner — 11/09  at  08:50 AM
Paul wrote:

" That you have repeatedly posted nonsense does not constitute good credentials."



`Twas brillig, and the slithy toves
Did gyre and gimble in the wabe:
All mimsy were the borogoves,
And the mome raths outgrabe.


"Beware the Jabberwock, my son!
The jaws that bite, the claws that catch!
Beware the Jubjub bird, and shun
The frumious Bandersnatch!"

He took his vorpal sword in hand:
Long time the manxome foe he sought --
So rested he by the Tumtum tree,
And stood awhile in thought.

And, as in uffish thought he stood,
The Jabberwock, with eyes of flame,
Came whiffling through the tulgey wood,
And burbled as it came!

One, two! One, two! And through and through
The vorpal blade went snicker-snack!
He left it dead, and with its head
He went galumphing back.

"And, has thou slain the Jabberwock?
Come to my arms, my beamish boy!
O frabjous day! Callooh! Callay!'
He chortled in his joy.


`Twas brillig, and the slithy toves
Did gyre and gimble in the wabe;
All mimsy were the borogoves,
And the mome raths outgrabe.


Now THAT is nonsense!



#47902: coturnix — 11/09  at  09:07 AM
Actually, Jabberwocky is NOT nonsense. Get Annotated Alice and learn. However, Charlie's assertions ARE nonsense.



#47928: charlie wagner — 11/09  at  10:11 AM
Coturnix wrote:

" Actually, Jabberwocky is NOT nonsense. "


“Few would dispute that Jabberwocky is the greatest of all nonsense poems in English.”

— Martin Gardner, The Annotated Alice



Thanks. I haven't dusted that one off in many years.



#48111: — 11/09  at  08:07 PM
http://epc.buffalo.edu/authors/hennessey/data/essays/Jabber_epoetry.htm

In Martin Gardiner’s excellent annotated edition of Alice’s adventures, he claims “few would dispute the fact that ‘Jabberwocky’ is the greatest of all nonsense poems in English” (192). I must count myself among those few. If Carroll’s poem is so great a work of nonsense, why is there so little nonsense in it? In fact, if we compare the structure of Through the Looking Glass the book with that of ‘Jabberwocky’ the poem, we see that the looking glass poem is in fact the inverse image of the book. In Through the Looking Glass Alice begins in the sensible world, enters the nonsense world, and then returns to the sensible world. In ‘Jabberwocky’ we begin with nonsense, then enter into a world of sense where nonsense is killed, and then end with the castrated repetition of nonsense.



#48132: — 11/09  at  09:32 PM
Esteemed Mr Wagner...
I looked at your website and found nothing about your credentials... However, I did chuckle at your header:
"here begins Homo ignoramus"!!

If it please you noble sir: inform us ALL of your credentials: degrees, fields of specialization, institutions granting the degrees, and dates.

I have a B.Sc. in Biological Sciences (Simon Fraser University, 1980) and a Ph.D. in Ecological Entomology (The University of Manitoba, 1993).



#48138: — 11/09  at  09:58 PM
The failure of Darwinism is NOT that natural selection is wrong, it's that it doesn't have the ability to assemble, create or design new adaptations, it can only act on what already exists.


1) it can only act on what already exists. Correct! This explains the contingent, cobbled-together nature of organisms... A designer could have done much better.

2) 'ability'? 'design'? 'create'?? extremely poor choices of words.

3) no 'new adaptations': at what level are you speaking? rationalise, for example, how flight in birds/bats/pterodactyls/insects not a 'new adaptation'? also, i suggest that you examine the literature on the re-emergence of trichromatic vision in old-world primates (and new-world howler monkeys) among other things. i'd post a site for this but i'm sure you can find it easily if you choose.



#48227: — 11/10  at  11:59 AM
CHESS AND THE CREATIONIST STRATEGY.

I play competitive chess. I am not particularly good at it. I beat weaker players and lose to stronger players. BUT there are more weaker players than stronger (the distributon of strengths is a very broad-based pyramid).

How does this relate to Creationist strategy in the "debate" aganst evolution? Simple: in a chess game, I know that certain opening patterns have been refuted, AND that only strong players are aware of the refutations, AND that most of my opponents are weak, and are unaware of the refutation AND will not find it themselves.

Therefore, at my skill level, I can play these unsound openings and be pretty sure that my opponents do not know that they are unsound, and that they will fall into the traps I set. More often than not, I beat them.

Creationists can use unsound arguments (and convince many people that these are valid) because in most cases the person hearing the 'arguments' is unaware of the refutation. That the arguments are unsound is less important than the FACT that they win more often than not when they 'attack' opponents (citizens) who are not aware of the counterarguments.

Why is this observation important? Because the OVERALL strategy of creationists is to stop educators from informing the laity of the refutation!

The counter-strategy, as I see it: disseminate the refutation! Kansas has ordered that ID be taught to high school students. OK, let it be so (until the next schoolboard election!), but teach the teachers how to teach the students the refutation:

1) a 'designer' must be more complex than the object designed. Therefore postulating a designer to explain a bio-widget requires a more complex designer than the widget itself (especially if the 'Designer' is capable of monitoring the entire universe and punishing or rewardng all creatures in it) THEREFORE:
2) postulating a designer complicates the issue, rather than solving it.

SO: my proposition: EDUCATE THE EDUCATORS!



#48465: — 11/11  at  11:12 PM
djlactin, neat analogy. I find this sort of strategy is used in many more "debates" than just this one. However, we should always note that there are weak supportive players on all sides of an issue, and that both sides have clever players who know this. The temptation then arises to employ the rhetorical and "unsound" arguments and convince the weak and draw them to our side.

Oh, and If I recall correctly, Kansas has not "ordered that ID be taught to high school students"



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