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Tuesday, May 17, 2005

Endless Forms Most Beautiful

I just finished Sean B. Carroll's Endless Forms Most Beautiful: The New Science of Evo-Devo the other day, and I must confess: I was initially a bit disappointed. It has a few weaknesses. For one, I didn't learn anything new from it; I had already read just about everything mentioned in the book in the original papers. It also takes a very conservative view of evolutionary theory, and doesn't mention any of the more radical ideas that you find bubbling up on just about every page of Mary Jane West-Eberhard's big book. One chapter, the tenth, really didn't fit in well with the rest—the whole book is about pattern, and that chapter is suddenly talking about a few details in the evolution and development of the human brain.

So I read the whole thing with a bit of exasperation, waiting for him to get to the good stuff, and he never did. But then after thinking about it for a while, I realized what the real problem was: he didn't write book for me, the inconsiderate bastard, he wrote it for all those people who maybe haven't taken a single course or read any other books in the subject of developmental biology. I skimmed through it again without my prior biases, and realized that it's actually a darned good survey of basic concepts, and that I'm going to find it very useful.

Take, for instance, chapter 5, titled, "Dark Matter of the Genome: Operating Instructions for the Toolkit". It's a simple overview of regulatory logic, explaining what regulatory regions are, describing the kinds of logical operators to which they correspond, and bringing in the idea of genetic switches and modules. This is difficult stuff to teach; I generally charge in with specific examples and try to draw out some general understanding by showing the details. But on reading this, I see a better way. I'm going to have to model a lecture on this chapter and ease students in with an overview of the big picture (in other words, I am so stealing Carroll's work).

He also does an excellent job of tying together paleontology and development, explaining how the concepts of modularity and genetic switches that he'd just covered are not just useful for understanding how butterflies get spots on their wings, but also makes the transformations we observe in the fossil record more comprehensible. Why are developmental biologists suddenly getting so interested in evolutionary biology? Because for the past 100+ years, we've been building a conceptual toolkit for analyzing embryos, and we've just recently noticed that applying those tools to evolutionary questions gives us a powerful perspective.

The final chapter is simply excellent, and carries a message I try in my own clumsy way to communicate, too. It has two themes: "Evo Devo as a Cornerstone of a More Modern Synthesis", in which he explains how developmental biology is inspiring a revolution in evolutionary thinking, and "Evo Devo and Teaching Evolution", where he discusses how this interdisciplinary mode of thinking helps us understand biology better. He also addresses the battle with creationists, and is appropriately dismissive of their pseudoscientific claims while warning us all to wake up to their political shenanigans.

Here's an excerpt from the section on teaching evo devo. It might irritate some of the evolutionary traditionalists, but I think he has many good points here.

The evolution of form is the main drama of life's story, both as found in the fossil record and in the diversity of living species. So, let's teach that story. Instead of "change in gene frequencies," let's try "evolution of form is change in development." This is, of course, a throwback to the Darwin-Huxley era, when embryology played a central role in the development of all evolutionary thought. There are several advantages of an embryological approach to teaching evolution.

First, it is a small leap to go from the building of complexity in on generation from an egg to an adult, to appreciating how increments of change in the process, assimilated over greater time periods, produce increasingly diverse forms.

Second, we now have a very firm grasp of how development is controlled. We can explain how tool kit proteins shape form, that tool kit genes are shared by all animals, and that differences in form arise from changing the way they are used. The principle of descent by modification (of development) is clear.

Third, an enormous practical advantage is the visual nature of the Evo Devo perspective. The Chinese proverb I cited in chapter 4, "Hearing about something a hundred times is not as good as seeing it once," is sound educational doctrine. We learn more by combining visuals with text. Let's show the students embryos, Hox clusters, stripes, spots, and the glory of making animal form. The evolutionary concepts follow naturally.

A fourth benefit of this approach is that it brings genetics much closer to the powerful evidence of paleontology. Dinosaurs and trilobites are the poster children of evolution, and they inspire the vast majority of those who touch them. By placing these wonders of the ancient past in a continuum from the Cambrian to the present, life's history is made much more tangible. It would indeed be a wonderful world if every student had guided, repeated classroom contact with some fossils.

If you're a developmental biologist, this book may make you snooze. But if you're anyone else, I recommend Endless Forms Most Beautiful highly—this is the primer that will bring you up to speed on the basics of evo devo in a pleasant way. It's full of butterfly wings and zebra stripes and exotic arthropods and molecules in stripes, and along the way you learn a fair bit of developmental biology.


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Comments:
#25175: coturnix — 05/17  at  10:42 AM
Thank you. I was waiting for this review. As it appears to be good for teaching, I may buy it one day when I have more money. In the meantime, I'll splurge on West-Eberhard.



#25179: — 05/17  at  11:41 AM
OK, looks like more books to add to the library. Have you done a recommended reading list for non-biology trained people?



#25184: Jason Rosenhouse — 05/17  at  12:09 PM
Speaking as someone who is not a developmental biologist, I found almost every age of Carroll's book to be a revelation. I've been seriously interested in evolutionary biology for several years now, but somehow had not managed to learn about most of the things Caroll was discussing. It seemed to me that one of the messages of the book was that some substantial morphological changes between different branches of life's tree are actually rather simple to explain at the genetic level.



#25185: charlie wagner — 05/17  at  12:13 PM
I'm proud of Sean.
It sounds like he's finally starting to get it.

"Researchers now know that life's building metterials are few, and they were "invented" near the dawn of animals."

Yes, the same genes, the same processes are used again and again across a diverse range of forms and species. And that fact is of profound significance.

The book just came via Fedex this morning. I just turned the first page...more later.

http://www.charliewagner.com
http://enigma.charliewagner.com



's avatar #25195: PZ Myers — 05/17  at  03:57 PM
Take page 299 to heart, Charlie.
Developmental genetics has been shedding new light on the making of complexity and the evolution of diversity for twenty years. Creationists just plain refuse to see it. How is such overt evidence ignored or dismissed? I can't pretend to understand the psychological mechanisms that allow humans to deny reality. But I do understand the desperate political and rhetorical tactics of those who, holding a losing hand, refuse to accept it.
He's talking about you. And I think pretending that Sean Carroll supports your goofy views of evolution counts as one of those desperate rhetorical tactics.

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



#25196: — 05/17  at  04:09 PM
It looks very much like s good read for use curious amateurs. Thanks for the pointer.



#25197: charlie wagner — 05/17  at  04:41 PM
Paul wrote:

"He's talking about you."

That's a misrepresentation and you know it. There's nothing at all "goofy" about my views on evolution. I've never denied that evolution occurred or that all living organisms are closely related and probably had a common origin. And I have never supported creationists and their religious agenda and you damn well know that.
You just refuse to give me the satisfaction of admitting that most everything I've said in talk.origins and other venues has been shown to be correct, from "junk DNA" to modularity. Go back and read the thousands of notes I've posted on these matters over the past 5 years.
I think that when it comes to "denying reality" it applies more to you than me.
The evidence is there for all to see. Just read Sean's book and then Google on my name in talk.origins and see for yourself who said these things first.



#25198: pough — 05/17  at  04:50 PM
Yes, the same genes, the same processes are used again and again across a diverse range of forms and species. And that fact is of profound significance.


I like it! It reminds me of two things. One is a fantastic quote by Charles Darwin that Dembski quotes lately on his blog, about his dog growling at movement caused by wind. The other is pretty much the entire works of Douglas Hofstadter, especially those parts about the brain and pattern-recognition.



's avatar #25199: PZ Myers — 05/17  at  05:06 PM
I have read your views on evolution, Charlie, and they're goofy. You believe in mysterious bounds on novelty that can only be overcome with the aid of some kind of undefined cosmic intelligence. You do not believe that evolution by natural mechanisms is supported by any of the evidence. You do not believe that there is any junk DNA -- you think it contains the encrypted code for all past and future organisms. None of these crazy ideas has been shown to be correct.

You're a crackpot. Your loony beliefs are entirely opposed by the material in Carroll's book. Yet now you want to claim that he is validating you? What a kook.

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



#25201: — 05/17  at  05:53 PM
A great post on how/why one changes one's mind. I have Carroll's book but haven't read it yet although I'm looking forward to it, now, even more so for I've not read the original papers. I like how you link this book to one of your responsibilities at UM-Morris, teaching. In the words of the trade, a reflective practitioner at work! There is a review in the current issue of Science of Carroll's book that provides some useful perspectives, at least they did for me. I recall the first review I read of West-Eberhard and muttered something to myself along the lines of "Even though you are without any expertise here, this is MUST reading." It seems to fit in the "tour-de-force" category. Your continued praise of this clearly magnificent book tells/reminds/gnaws at me that I MUST do this. In the meantime please keep extolling its virtues. Thanks again.



#25202: — 05/17  at  06:12 PM
Ken Ham claims each new discovery validates YEC. Kooks aren't lying. They just don't know any better.



#25206: — 05/17  at  08:35 PM
As I read the first paragraph of your post and then the first sentence of the second paragraph, I was thinking to myself "But you're not the main audience for it, knucklehead!" Then I got further into the second paragraph. Sorry for the thought. smile

RBH



#25229: — 05/18  at  01:34 AM
At a slight tangent:

PZ, or indeed any informed individual (Wagners, JADs, Heddles and their ilk need not apply),

I've been looking to improve my formal understanding of evolutionary biology for a while. I am familiar with the popular works (e.g. all of Dawkins and all of Gould, plus a couple of notable worthies) having read many of them backwards and forwards. I have also recently finished the main works of Darwin (Origin, Descent, and Expressions).

What I am currently reading is Mayr's "Toward a new philosophy of biology", I have his "Evolution and the diversity of life" and Gould's brick to go until I have exhausted my personal library.

I was wondering 1) where do I go next, and 2) if you had any recommendations for other books, or even a few selected review articles that would kick me off in the rightish direction. I have pulled a few much cited reviews out of SciFinder, but without a better appreciation of the field (which is LARGE!) I am unsure where best to start.

If it helps, I am relatively biologically literate (I work at the chemistry/biology interface much of the time, at least intellectually if not practically), so I'm not scared of the real literature!

Any info appreciated, thanks very much in advance.



#25239: John Wendt — 05/18  at  06:53 AM
PZ, have you read Carroll's other book, From DNA to Diversity? It seems more technical, but it also looks kind of short.

I enjoyed Endless Forms a lot. What we need now is something that ties in natural selection. (Carroll gives it a nod in passing.) This would give us both arrival and survival of "the fittest".



's avatar #25240: PZ Myers — 05/18  at  07:55 AM
Yes, I've read it -- it's more of a textbook than something to read for fun.

About natural selection: heh. I thought it was conservatively selectionist, and Nature's review chews him out for putting too much emphasis on selection. The guy can't win.

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



's avatar #25241: PZ Myers — 05/18  at  07:56 AM
Louis -- check out the link to Mary Jane West-Eberhard's book.

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



#25257: charlie wagner — 05/18  at  01:15 PM
Paul wrote:

You're a crackpot. Your loony beliefs are entirely opposed by the material in Carroll's book. Yet now you want to claim that he is validating you? What a kook.


Just as the soft rains fill the streams, pour into the rivers and join together in the oceans, so may the power of every moment of your goodness flow forth to awaken and heal all beings, those here now, those gone before, those yet to come.
By the power of every moment of your goodness may your heart's wishes be soon fulfilled as completely shining as the bright full moon, as magically as by a wish-fulfilling gem.
By the power of every moment of your goodness may all dangers be averted and all disease be gone. May no obstacle come across your way. May you enjoy fulfillment and long life.
For all in whose heart dwells respect, who follow the wisdom and compassion, of the Way, may your life prosper in the four blessings of old age, beauty, happiness and strength.

Regards, Charlie Wagner



#25344: — 05/19  at  10:41 PM
Books

heavy side
'There is another Carroll' who wrote _Patterns and Processes of Vertebrate Evolution_ - very good
Coyne & Orr's _Speciation_ voted best of breed even by reviewers who carp about it.
Valentine's _The Origin of Phyla_ all the rage at the moment - I'm on it
Benton's _Vertebrate Paleontology_ a major new text in a field that doesn't get major new texts very often. Haven't read it - look for the web site too

summery side
Tijs Goldschmidt's _Darwin's Dreampond: Drama in Lake Victoria_
Lewontin's _The Triple Helix_
Roughgarden's _Evolution's Rainbow_ how summery can you get? There's even sex in it, sort of
Schilthuizen's _Frogs Flies & Dandelions: The making of species_
Margolis' _It started With Copernicus_
and if you still haven't read _Darwin's Black Box_ all I can say is Golly gee whiz you probably haven't even read _Good Omens_



#25366: Sean Carroll — 05/20  at  08:56 AM
Carroll here. Thanks to all for their comments on my book.
I thought I should confirm that it was written for a broad audience, but I think the pros can mine some stuff from it as well.
Just to let you know that I have a second book coming out (also with Norton) in 2006 that will deal with selection in depth, again for a broad audience.
Please don't let me appearance here stifle your comments, it is more helpful to me if people are candid.



's avatar #25370: PZ Myers — 05/20  at  09:28 AM
Don't hesitate, we're an irreverent bunch. The mere presence of a highly qualified author won't stifle anyone.

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



#30308: — 06/29  at  12:13 PM
Let me say first that I enjoyed reading this book. It provides a very informative and accessible summary of advances in developmental genetics and how these may be used to understand both minor and major differences in form among taxa. In its enthusiasm and cogency, it is a model for the distillation of a complicated field into a form suitable for the educated general reader.

However, where it falls short of the best pop science literature is in selling its readers short, not trusting them enough to understand the nuances, by tying its "story" up in a nice neat bow. (Rant alert: when will science writers stop using the "our story begins" cliche? If you want your readers to take you seriously, don't make your exposition sound like a fairy tale.) There are many serious unanswered questions in the intersection of evol and development, as there are in any area of active scientific inquiry. But one wouldn't know it from reading this book.

In my view, this glossing over is most obvious in the context of the book's major themes. Disappointingly, and somewhat contradictorily, Carroll's book seems to overstate the current consensus and state of knowledge in developmental genetics, while at the same time maintaining an extremely conservative position in its interpretation of the implications of these advances to evolutionary explanations of form and their relationship to darwinism.

To the first point, there are a couple of obvious examples, and many smaller ones. In particular, Carroll ends his discussion on how regulatory networks control pattern with statements that left me shaking my head in wonder at the logical leaps of faith he requires of the reader. Two examples were most striking.

In sweeping aside the mildly skeptical reader's concerns that he'd only shown very simple examples of regulatory networks, he writes that:
"...I would need at least one thousand pages to write out the logic of making a fly, and several thousand pages to write out the making of a human."
As if the state of understanding in the field is so advanced, that the only thing holding it back is a lack of paper. Would that this were true, but I don't think we're there yet. (Or at least I didn't turn up any hits with my Highwire search for "The complete regulatory network for human development.") Of course, Carroll knows this, but he does his readers (most of whom presumably are not biologists) a disservice by leaving the wrong impression.

Similarly in the same chapter (c5, p116), Carroll acknowledges the 800 pound gorilla breathing heavily next to the anxious reader for the last 30 pages or so: if the expression patterns of regulatory proteins are dependent on previously laid down patterns, then where do THOSE previous patterns come from? He answers that they are controlled by still earlier patterns of regulatory proteins. Which, of course, are controlled by still earlier patterns, etc, in a near infinite regress that terminates in asymmetries in the oocyte. Logical enough, and it may even be true, but has anyone plausibly demonstrated, either experimentally or with data-driven simulations, that this entire chain of regulatory pattern formation cascades from gradients in the oocyte? Are no other mechanisms of pattern formation (e.g. Turing-esque reaction diffusion mechanisms, of which Carroll seems dismissive) necessary to modulate these dynamics? I'm just asking. Because it really isn't obvious to me that the current evidence warrants the leap that the combination of oocyte asymmetry + combinatoric regulatory networks is both necessary and sufficient for the patterns discussed. I suppose others may be less skeptical. But it rings of the central dogma, and we all know what happened to that.

Moving on, his conservative interpretation of how all this fits with darwinism, all I can say is where are all the old structuralists? I came to this book with enthusiasm, having some familiarity with Carroll's work (I've been out of the field for quite a while, though I'm still an interested observer). I was kind of hoping that it might pick up where the structuralists left off 10-20 years ago. Not that I thought Carroll was a structuralist (and certainly not a marxist, as many of them were/are!). It just seems that now that developmental genetics has matured to the point of (nearly) understanding the basis of biological pattern, the (still valid and compelling) critiques of darwinism advanced by the structuralists and others are ripe for resurrection. Instead, the book claims that evo-devo (a terrible moniker) is the third and final step in completing the evolutionary synthesis. hmmmm. There are very good logical and philosophical reasons to disagree with this assessment. It is a shame that at least some of the book was not dedicated to a more sensitive discussion of the impact of "generative rules and mechanisms" in evolutionary explanations of form vis a vis darwinism. An opportunity lost.

On this last point, I want to raise a general question about the state of evol biology. From my perspective, it seems that criticisms of the synthesis have become muted over the last 10-15 years and this raises concerns about the vitality of the field. Have critics (like the structuralists) been muzzled for fear that ANY criticism of darwinism fuels the arguments of creationists? Not that the muzzling is overt or conspiratorial. I just wonder if, in general, evolutionists of all stripes (mild pun, read the book) are more circumspect in their criticisms, knowing how their words might be used to undermine evolutionary science.

If so, this is unfortunate. An argument can be made that darwinian "function talk" (and not just popularized versions of it) left the barn door of science education wide open for the anti-science intelligent design crowd. I would suggest that a fully developed version of the comparative development approach to studying evolution, including a considered analysis of its explanatory content vis a vis darwinism, could slam the door shut.



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