Pharyngula

Evo-devo is not the whole of biology

Sometimes a plan just comes together beautifully. I’m flying off to London tomorrow, and on the day I get back to Morris, I’m supposed to lead a class discussion on the final chapters of this book we’ve been reading, Endless Forms Most Beautiful. I will at that point have a skull full of jet-lagged, exhausted mush, and I just know it’s going to be a painful struggle. Now into my lap falls a wonderful gift.

There was a review in the NY Review of Books that said wonderful things about Carroll’s work, and in particular about the revolutionary nature of evo-devo. This prompted Jason Hodin, an evo-devo researcher himself (whose work I’ve mentioned before) to write a rebuttal and send it off to NYRB…which they chose not to publish. So he sent it to me, with permission to post it.

(If Pharyngula is going to be second choice to the NY Review of Books, I’m not going to complain.)

Anyway, I’m almost as guilty as Carroll of hawking the wares of the evo-devo bandwagon and traveling roadshow, so this is a welcome balancing corrective. The complete text is below the fold.

REVOLVING EVOLUTION

To the editors:

Ziff and Rosenfeld ("Evolving Evolution" May 11,
2006) set the bar pretty high for themselves. In the first line of their NYR
article they claim that the past 20 years have not only yielded "major
changes in our understanding of evolution," but indeed that these
purported changes have gone "virtually unnoticed." By the second
paragraph, we learn that the new field of study responsible for these major new
insights is Evo Devo, which is shorthand for the melding of the fields of
evolutionary and developmental biology.

The cover picture of the May 11 NYR issue is of a Drosophila
melanogaster
"fruit" fly embryo.
Since I spent nearly half of the past 20 years studying Evo Devo in this very
same critter, I wondered to myself: did I miss something? Was there some earth
shattering evolutionary insight that we have had concerning this noble insect
that managed to evade my notice? Was I too deep in the dense trees of my Ph.D.
research to see the forest of ground breaking discovery that surrounded me the
whole time?

Ziff and Rosenfeld (henceforth "Z&R") sprint
through the history of 20th century molecular genetics and reach the
following conclusion: all evidence pointed to the fact that organisms are
different due to each "having evolved its own unique set of genes over
millions of years." At first glance, this synopsis seems reasonable. There
must be a genetic basis for the differences between organisms. But it seems
that special emphasis is to be placed on the words "set of genes."
According to this supposedly dominant world-view, organisms are different
because they have different "sets of genes."

But wait a minute. Wasn’t it Gregor Mendel, the founder of
the field of genetics, who showed us that genes existed in different states?
There were round and wrinkled peas, and the differences between these two types
were not due to different "sets of genes," but instead to different versions (called alleles) of the very same genes! In fact,
the field of modern population genetics is much like the field of early 20th
century population genetics in supposing that differences among populations and
even species is due to unique combinations of alleles.

But perhaps what Z&R meant was that this basic
understanding of genetics was all forgotten until about 20 years ago. Was the
middle of the last century the Dark Age of biology, where we forgot our past,
and insisted that evolution must be the result of new "sets of genes"
appearing somehow in different organisms? And was it the sequencing of diverse
genomes in the past 20 years that has led to a biological Enlightenment?

Unfortunately, the historical record does not uphold this
just-so story of modern biology. For example, the evolutionary biologist Emil
Zuckerkandl used the relatively crude data available to him in 1975 to conclude
"that new structural genes must nearly consistently derive from
preexisting structural genes, and that new functions can be evolved only on the
basis of old proteins." Two years later, François Jacob wrote an influential
article in Science entitled "Evolution and Tinkering" in which he
stated:

"The appearance of new molecular
structures during much of biological evolution must…have rested on alteration
of preexisting ones. This is exemplified by the finding that large segments of
genetic information, that is of DNA, turn out to be homologous [evolutionarily
related], not only in the same organism, but also…among those that are
[evolutionarily] distant."

Z&R’s claims for the important discoveries attributable to
the past 20 years of research go further still: "surprising, too, is the
evidence that all animals, from worms to humans, probably descend from one or a
few primitive bacteria." Darwin would be shocked to hear that additional,
modern evidence supporting his fundamental principle of common descent would be
seen 150 years later as "surprising."

Straw men are around every corner in Z&R’s article. For
example, "the presence of a body plan in the genome, whether of a fly, a
whale, or a human, was unexpected by embryologists." One wonders where
these misinformed embryologists thought the body plan resided: in the cosmos
perhaps? If, instead, the authors are here referring to embryologists in a
pre-genetic age, their statement is true, but rather meaningless.

I don’t mean to denigrate my field of Evo Devo, nor do I
intend to suggest that no critical insights have come from it. Perhaps the most
important contribution of the field is methodological. For years, evolutionary
biologists have gone along their merry way, largely ignoring the rapidly
expanding fields of molecular biology, cell biology and development, with their
increasingly impenetrable jargon. For their part, researchers in the latter,
more "reductionist" fields planned and interpreted their experiments
in the absence of an explicit evolutionary perspective. As Z&R correctly
point out, the division between evolution and development traces back to the
NeoDarwinian synthesis in the early 20th century, where
developmental biologists were not at the table.

But this was an unnatural separation; Darwin himself stated
in Origin that developmental biology was
"one of the most important subjects in the whole round of history."
When Stephen Jay Gould published Ontogeny and Phylogeny in 1977, alongside other less visible but equally
insightful contributions by David Wake and Père Alberch, the two fields were
long overdue for reconciliation. Still, it took a few decades before the two
disciplines started to truly become reunited. That process came on the heels of
the Hox gene discoveries, so touted by Z&R and their modern Evo Devo hero,
Sean Carroll.

The finding of similarities in Hox gene display patterns in
fly and mouse embryos so impressed Carroll and other developmental biologists
that the "Hox code" seemed a possible Rosetta stone of evolution. It
was even claimed in the early 1990’s that this Hox pattern defined what it
meant to be animal! Putting aside the extreme provincialism inherent in this
focus on "animalness" (as Hox genes are absent from complex multicellular
creatures like fungi, algae and plants, without whom animals would not exist),
it turns out to be false that Hox genes are even necessary to produce an
animal. Sea urchin larvae, for example, which have bilateral symmetry, complex
organs, a full gut, a nervous system, muscles, and all other definitively
animal features, are formed in the absence of the canonical Hox gene
expression.

Still, the similarity in Hox gene displays in many animals
is notable. But here, again, Z&R follow Carroll’s lead in vastly
overemphasizing the importance and function of these genes in embryos. For
example, we are told by Z&R that "the production of Hox genes divides
the [fly] embryo into a series of segments," but this is not accurate. The
segmentation genes do this job, while Hox genes act later to confer identity on
the already defined segments. Interestingly, we are shown some of the data
supporting this idea in Figure 2 of Z&R’s article, but are not given the
full story.

Overstated claims for the importance of Hox genes do not
stop there. We are told that "the giraffe’s longer [neck] vertebrae may
have developed because of mutations in the Hox genes controlling the size of
our vertebrae." This intriguing hypothesis, unfortunately, is completely devoid
of any supporting evidence.

A nagging question remains: what have the similarity
in Hox gene displays shown us? Evolution is all about diversity, but the Hox
discovery points to sameness. Caroll’s 2005 book Endless Forms Most
Beautiful,
so lauded by Z&R, can be
described as one great genuflection over this very issue, and the conclusion is
that changes in gene regulation must underlie diversity. Nevertheless, as
Z&R note, this finding was not at all a novel discovery of the last 20
years. It has been the dominant paradigm of molecular genetics since François
Jacob and Jacques Monod’s pioneering work of the 1950’s and 60’s. Or, as Jacob
wrote in 1977: "What makes one vertebrate different from another is a
change in time of expression and in the relative amounts of gene
products." This sounds to me rather indistinguishable from what Z&R
call "Sean Carroll’s view [that] what creates diversity is the pattern in
which genes are turned ‘on’ and ‘off’."

Was this all a misreading of Carroll by Ziff & Rosenfeld
(neither of whom are biologists)? Is Carroll much more circumspect than his
reviewers? Was the nuance and subtlety of Carroll’s Endless Forms simply missed by Z&R? Not exactly. First of all,
as Carroll explains in the "Sources" section at the end of his book,
he "elected not to name every individual associated with every work
pertinent to the story" in the interest of his "broad audience."
In fact, he names almost no sources in the text, and it is reasonable for the
uninformed reader to assume that a lot of the ideas are Carroll originals. Here
for example, is the context in which Carroll describes his move to studying
‘fruit’ flies after completing his immunology Ph.D. in 1983:

The common perception [among
biologists]…was that the rules of development and physiology differed
enormously between mammals and bugs or worms.

This is simply not so. Examining any book on developmental
biology or animal physiology dating, say, from 1950-1985, will yield ample
evidence that biologists have long appreciated the fundamental developmental
and physiological commonalities among all animals. In fact, this understanding
even predated Darwin. Furthermore, insects in general, and Drosophila flies specifically, had been recognized as important
study organisms in both development biology and evolutionary biology for
decades preceding Carroll’s postdoctoral career choice. Despite the
implication, Carroll was walking a very well trodden path.

Carroll concludes Endless Forms thusly (my emphasis): "Virtually everything I
have described in chapters 3-10 has been discovered in the past 20 years…[and
has] forced biologists to rethink completely their picture of how
forms evolve." It is this kind of hyperbole that led Z&R to vastly
overstate the impact that Evo Devo in general, and Carroll in particular, has
had on evolutionary biology. Such hyperbole might increase book sales and keep
the grant money flowing in the short term, but it ultimately makes all of us
practitioners of Evo Devo look pretty silly.

In my opinion, one major contribution of the field of Evo
Devo has been in the synthesis itself, and this is still incomplete. If we are
to come to any subtle understanding of the diversity of life we must consider
all aspects of biology, from paleontology to genetics to development, cell and
molecular biology, field ecology and physiology, ALL in the context of
evolutionary biology. Perhaps the important insight of Evo Devo is merely a
reminder that this has been true all along. Some of us just forgot it for a
while.

Jason Hodin

Hopkins Marine Station

Pacific Grove, CA

To presage my classroom strategy on Wednesday the 18th of October: now discuss. Here, I’ll also mention that the ‘extreme provincialism inherent in this
focus on "animalness"’ is also discussed on Evolgen, and in this comment by Larry Moran. It’s not to suggest that evo-devo isn’t important, but that it isn’t the whole universe, and it did not come blasting out of nowhere.

Comments

  1. #1 Doug Blank
    October 9, 2006

    I think we all tend to enlarge our own importance in our fields, and overstate what we have done in the last twenty years. This tells a better story, and we feel better about all of that time we have spent in the lab. The truth is that science generally proceeds gradually, with punctuated events. Although we know *that* story very well, it just is no fun to be between the punctuations.

  2. #2 tristero
    October 9, 2006

    If I understand what he wrote (I’m not a scientist), Dr. Hodin’s main objection is that the accomplishments of evo-devo have been hyped by Carrol, especially the function of Hox genes in the expression of traits and the change thereby in understanding the mechanisms of evolution.

    If that is so, it is a pity that NYRB didn’t print the letter, because I read the original review and was fascinated. It would have been terrific to have had this very different perspective and to have read the reviewers’ respone to it. Nevertheless, I’m glad you “published” it, PZ.

  3. #3 Larry Moran
    October 9, 2006

    As Jacques Monod put it over 35 yearsago, “What’s true for E. coli is true for an elephant.

    Many of us switched from working with prokaryotes to working with eukaryotes because we believed that Monod was mostly correct, although we always hoped to find something new.

    There are some things about eukaryotes that are different, but not much. I’ve been following developmental biology for three decades and I’ve yet to see anything that has changed my basic understanding of evolution, or of gene regulation.

    Back in the late 1970’s we were teaching about the genetic switch in bacteriophage lambda and the well-understood pathways of development in phage infection. Modern students have no appreciation of these examples. It’s like there’s a whole generation who have forgotten about bacteria and bacteriophage. We also taught sporulation in B. subtilis–a wondeful example of how different cells communicate with each other during development. I doubt very much whether any modern student knows about this.

    As far as I can tell, evo-devo is mostly hot air.

    Here’s another book that could be required reading in a developmental biology course [Genes and Signals].

  4. #4 Scott Hatfield
    October 9, 2006

    PZ:

    Provincialism comes in different forms. Sure, to you guys who are actually doing developmental biology a lot of this is old-hat and Carroll’s book sounds a little overzealous. And, of course, the story of the lac operon and all that has been in the textbooks since the mid-1960’s.

    But I think it is also fair to say that the majority of workers in biology either now or in the 1990’s were/are not likely to be terribly familar with the details or implications of either gene regulation or gene expression.

    And the population of high school biology teachers? Please. Monod and Jacob’s pioneering work receives but two pages in the first text I used, and it wasn’t in the state standards, so guess what? It wasn’t taught. In fact, Ken Miller’s newest book (“the dragonfly book”) is, to the best of my knowledge, the only high school text that discusses Hox genes in any detail whatsoever, and even this book fails to make the point that the Evo Devo research programme fills in a missing piece of the puzzle, namely that which creationists mistakenly associate with the ‘absence of transitional forms’ and the ‘problem’ of the emergence of novelty.

    In fact, a full appreciation of the significance of this point only penetrated my mind this summer when I read Carroll’s book along with ‘The Plausibility of Life.’ I don’t think we should underestimate the impact that this understanding could have on the general public in terms of acceptance and support for teaching evolution. So, PZ, it wouldn’t worry too much about overselling Evo Devo. In fact, I say: preach it, brother!….SH

  5. #5 Kristine
    October 9, 2006

    I’ve read a lovely book, On Becoming a Biologist by John Janovy, in which he stated that, despite the wonderful new fields of knowledge opening up, studying the whole animal in its own habitat was the most important thing. I would extend that statement to any field, including the observation of human beings, whether from a scientific perspective or a socio-historical one or from the perspective of the literary writer and critic.

  6. #6 PZ Myers
    October 9, 2006

    Like Larry says, most of the basic principles were laid out by Jacob and Monod, and if we want to trace the real beginnings of the evo-devo revolution, it leads back to bacteria, and us galumphing animals aren’t in it at all.

    I won’t go as far as calling it all “hot air”, though. There is the idea of pattern formation and organization of tissues that you just aren’t going to find in single-celled organisms, except perhaps crudely in a biofilm. We are subject to that general rule of popularity in the public eye where charismatic megafauna trump the microscopic stuff—it’s just that in development, fruit flies are the charismatic megafauna.

    The Ptashne book is very good, and I think it also highlights a gap in our curriculum. Like many small schools, we have courses in cell biology and molecular biology where that subject would fit in well, but cell signaling is typically but one of many basic cellular processes that have to be covered. My course in development is descended from older courses in embryology, and what students expect is an overview of mammalian development—it’s shock enough that I push a strongly molecular perspective, and spend most of my time talking about invertebrates. A whole course in cell signaling and signal transduction would be wonderful to have here, but then we don’t have enough faculty and it would also skew the whole curriculum towards my biases, which I think would be great, but at a liberal arts college we have to balance differing perspectives with the constraints of a four year degree. It’s just not going to happen.

    I content myself with telling the students that there’s a whole bunch of interesting stuff going on here, that there are these cool molecular pathways that have been and are being worked out in various organisms other than our metazoan pals, and they ought to think about studying them in grad school.

  7. #7 PZ Myers
    October 9, 2006

    Although, I should mention that UMM biology has recently revised its curriculum, and one of our decisions was to shift more basic genetics to a freshman course, and turn our formerly required upper-level genetics class into an elective. That frees up some content in my genetics course (I won’t have to teach the cytology of mitosis/meiosis anymore! Yay!) and what I’m planning to do there is incorporate more material along the lines Larry mentions: signaling and transduction ala Ptashne.

    It’s a compromise. We try to wedge the important stuff in where we can. I wish we could just tell the university administration that, to do it justice, we need to expand the biology degree into a 6-year program. I don’t want to have to deal with the bodies of administrators dying of stroke, cardiac arrest, and apoplexy, though, and I fear a lot of parents would rather send their kids to schools with shorter times to graduation, too.

  8. #8 Caledonian
    October 9, 2006

    The students might also have some opinions about that.

  9. #9 Keith Douglas
    October 9, 2006

    PZ: Does your university distinguish between honours students and majors students? At McGill, where I did my undergraduate degree, some of the faculty of science honours programs do eat easily 5/6s or more of students’ total degree, compared with 2/3rds for some majors. I note also that both are much more than in arts, where I studied.

    I suppose you have insufficent teaching resources to offer some of the additional material you’d want to put in as a specialized minor, no?

  10. #10 PZ Myers
    October 9, 2006

    We have 7.5 faculty, and we have to teach everything from biochemistry to ecology, so yes, there are some major limits here. We give a very good broad overview of the field and we definitely emphasize scholarship and lab experience, so we give our students an excellent foundation, I think…but we don’t have time or the personnel to teach everything.

  11. #11 Stanton
    October 9, 2006

    Forgive me if I’m going off topic, but, has there been experiments done where they do things like graft portions of HOX genes from a stalk-eyed fly into the genome of a fruit fly, and see what develops, as a result?

  12. #12 lo
    October 9, 2006

    Great article, to bad it didn`t made it into the NYRB.

  13. #13 lo
    October 9, 2006

    @Larry Moran: Well what the past 50 years in particular gave us is an understanding of evolution on a broader scale – that is on a universal scale.

    And i think you got it all wrong about students these days – they are just as fascinated with the world as the older generations of scientists are, the difference is that thanks to the medial ways of learning and the expanded knowledge base we can get even a broader view and appreciation than the generations before us.

  14. #14 charlie wagner
    October 9, 2006

    Jason Hodin wrote:
    “Examining any book on developmental biology or animal physiology dating, say, from 1950-1985, will yield ample evidence that biologists have long appreciated the fundamental developmental and physiological commonalities among all animals. In fact, this understanding even predated Darwin.”

    Typical reaction of those who had to be carried, kicking and screaming, into a new paradigm: We knew it all along!

    Science, you gotta love it.

    BTW, I’ve decided to resume commenting here when I have something interesting to say. If you don’t want me to express my opinions here, now is the time to give the word.

  15. #15 Jonathan Lubin
    October 9, 2006

    I’m not surprised that the letter didn’t get published. My impression, after sending in a terse correction to a howler of a misderivation of an (important) word, is that the Editors of NYRB don’t print your letter unless you have a Name. There’s also the problem that the letter is considerably longer than most letters that NYRB publishes.

  16. #16 Martin Brazeau
    October 9, 2006

    Amen!

    I was sort of perplexed by a lot of Carroll’s statements about the might of the evo-devo “revolution”. I am, however, in complete agreement with Jason Hodin about what the value of evo-devo has been: a synthesis, an attempt to express each others discoveries in the same language so that we might learn to explain these observations in terms of the knowledge of disparate but related fields.

    Granted, however, Carroll does a fine job of driving home the point about the modular nature of animal development and the importance of regulatory evolution in governing this. Modularity is potenitally a powerful concept for explaining morphological transformations. In the same way that new genes must be derived from pre-existing ones, a lot of morphological novelty can perhaps be explained in terms of the re-use of pre-existing developmental mechanisms. While variations of the idea certain go back before the 80s, we now have a plethora of data from disparate animal systems that suggest that this is true.

    That’s the way I see it… but what the hell do I know? I’m a paleontologist!

  17. #17 Clastito
    October 9, 2006

    C’mon. I mean, of course we all hate S. Carroll a little…but give modern, molecular Evo-Devo its due. Who was taking dorso-ventral inversion seriously before Dpp? Who was expecting anything like conservation of orthologous genes after 600 million year old splits? Of course highly conserved embryological, non-molecular aspects were known, but embryological variation had been higlighted in the process of rejecting hackel too.
    There certainly WAS a revolution after the molecularization of development, and the limitations of the neodarwinian synthesis DID stand out. The idea of a multidisciplinary synthesis is still good, but we don’t need it to be neodarwinian any more, that is, with a hegemonical role for population genetics and adapatationism (this hierarchy, with every other discipline present yet subdued, actually impedes it form being a true “synthesis”) That SHOULD be over…but science has its own “conservatives” (Even S Carrol wants to miss this point… praising darwin all the time pays off pretty good in angloamerican culture).

  18. #18 Ichthyic
    October 9, 2006

    BTW, I’ve decided to resume commenting here when I have something interesting to say. If you don’t want me to express my opinions here, now is the time to give the word.

    based on seeing your past posts on PT, I say:

    word.

  19. #19 charlie wagner
    October 9, 2006

    Icthyic wrote:
    “based on seeing your past posts on PT, I say: word.”

    Lucky for me, you are not the owner of this blog.

  20. #20 Mong H Tan, PhD
    October 9, 2006

    Hello, Pharyngula Readers, Everybody, Mind, and Spirit! 🙂

    Tristero said: If I understand what he wrote (I’m not a scientist), Dr. Hodin’s main objection is that the accomplishments of evo-devo have been hyped by Carrol, especially the function of Hox genes in the expression of traits and the change thereby in understanding the mechanisms of evolution.

    If that is so, it is a pity that NYRB didn’t print the letter, because I read the original review and was fascinated. It would have been terrific to have had this very different perspective and to have read the reviewers’ respone to it. Nevertheless, I’m glad you “published” it, PZ.

    Kristine said: I’ve read a lovely book, On Becoming a Biologist by John Janovy, in which he stated that, despite the wonderful new fields of knowledge opening up, studying the whole animal in its own habitat was the most important thing.

    I would extend that statement to any field, including the observation of human beings, whether from a scientific perspective or a socio-historical one or from the perspective of the literary writer and critic. And,

    Martin Brazeau said: I was sort of perplexed by a lot of Carroll’s statements about the might of the evo-devo “revolution”. I am, however, in complete agreement with Jason Hodin about what the value of evo-devo has been: a synthesis, an attempt to express each others discoveries in the same language so that we might learn to explain these observations in terms of the knowledge of disparate but related fields.

    Granted, however, Carroll does a fine job of driving home the point about the modular nature of animal development and the importance of regulatory evolution in governing this.

    Modularity is potentially a powerful concept for explaining morphological transformations. In the same way that new genes must be derived from pre-existing ones, a lot of morphological novelty can perhaps be explained in terms of the re-use of pre-existing developmental mechanisms.

    Wow, everyone just took the good comments out of my mouth–considering that they are not even biologists! However, I do sense that a response to the lengthy Hodin rebuttal above, would certainly open up a new can of worms–ie, in the frontiers of Evo-Devo research–that the NYRB editors (including Carroll and the book reviewers) probably might not have had anticipated before!

    While talking about worms, is there a Homeobox equivalent in the nematodes, such as C. elegans, whose genome has had all been well mapped out?

    Thank you all for your kind attention and cooperation in this matter–just a food for thought, from a self-introspective Darwinist evolutionist perspective. Happy reading, thinking, scrutinizing, and enlightening! 🙂

    Best wishes, Mong 10/9/6usct1:12p; author Gods, Genes, Conscience and Gods, Genes, Conscience: Global Dialogues Now; a cyberspace hermit-philosopher of Modern Mind, whose works are based on the current advances in interdisciplinary science and integrative psychology of Science and Religion worldwide; ethically, morally; metacognitively, and objectively.

  21. #21 Steve LaBonne
    October 9, 2006

    As a long-time NYRB subscriber, I’m always torn between being glad that they make the attempt to bring some news of science to the literati, and sad that they generally don’t do it very well. I think Carroll can readily be excused for being pardonably excited about his field and wanting to share that excitement with a general audience; but I’m less indulgent toward that review, which was indeed painfully sophomoric.

  22. #22 Ricardo Azevedo
    October 9, 2006

    Mong H Tan asked: “While talking about worms, is there a Homeobox equivalent in the nematodes, such as C. elegans, whose genome has had all been well mapped out?”

    C. elegans do have Hox genes but the cluster has desintegrated. They also appear to have lost several Hox genes: they have no homologues of pb/Hox2, Hox3, Dfd/Hox4, Antp, Ubx or abd-A. For more info see this paper< \a>.

  23. #23 amphioxus
    October 9, 2006

    ” There certainly WAS a revolution after the molecularization of development”.
    I am with Clastito. Twenty-four years ago, most biologists were dumbfounded when the Hox genes of Drosophila were found in mice; and only when a few years later Duboule and Krumlauf etc. started to demonstrate that the Hoxes actually had analogous functions, they really believed that these were the same genes. And when it was found that a gene linked to mammary cancer in mice was an orthologue of a gene (Wingless) linked to fly wing morphogenesis, the initial reaction again was disbelief. Clearly this type of findings was not what most biologists had foreseen. Of course they all knew that François Jacob had written that evolution makes ‘a roulette out of an old bicycle’s wheel’. But was he referring to anatomical structures or to genes? Evolution is much easier to understand once you realize that genes are re-used and recycled for different uses. I feel that in those days “Darwinism” was proven true more powerfully than evolutionists had even dared to predict.

  24. #24 Larry Moran
    October 9, 2006

    amphioxus says,

    I am with Clastito. Twenty-four years ago, most biologists were dumbfounded when the Hox genes of Drosophila were found in mice; …

    When the first homeotic genes were sequenced (Ubx and Antp) it was quickly recognized that they had a helix-turn-helix DNA binding motif similar to that found in many bacterial proteins such as lac repressor and cro. None of us were very surprised. It fit very well with what we were expecting. Fruit flies were just fancy bacteria.

    When proteins with the same DNA binding motif were found in mice it was just more confirmation that the same principles of transcription regulation worked in eukaryotes and bacteria.

    I doubt very much that most biologists were dumbfounded. We weren’t surprised to find similar genes in bacteria and fruit flies so why should anyone have been surprised that other animals had them? After all, mice and fruit flies diverged less than a billion years ago.

    Remember that by the mid-1980’s we already had plenty of examples of genes that were similar in bacteria and eukaryotes. This was just one more.

  25. #25 Clastito
    October 9, 2006

    Nonsense. Helix turn helix DNA binding is so general a thing. You would truly expect thta its presence in bacteria would imply it was present in any organism.
    To jump from there to quite specific morphological similarities (eye of the fly, dorso ventral polarization etc)… these are not as general as DNA binding, if you get what I mean.
    In fact these similarities were officially upheld to be convergences (lest face ridicule), so when they were found to express similar genes it was a biiiiig surprise. Period. To deny it is cynical.

  26. #26 windy
    October 9, 2006

    In fact these similarities were officially upheld to be convergences (lest face ridicule), so when they were found to express similar genes it was a biiiiig surprise.

    Got any references for that?

  27. #27 Clastito
    October 9, 2006

    Check the whole dorso-ventral inversion story between the protostomes and deuterostomes, Gould has written a lot about it.

  28. #28 Scott Hatfield
    October 9, 2006

    I think a lot of you folk are missing the point. The degree to which developmental biologists or even biologists in general might have anticipated or have been intellectually prepared for the discovery of Hox genes etc. is not the issue. The ‘revolution’ is not this or that fact, but the growing synthesis between developmental biology and evolution, and (especially) what the former can do to help bolster the teaching of the latter.

    Is Carroll overstating his case? Let me put it to you this way: when every high school biology text in the country explicitly shows how Hox genes and genetic switches etc. can generate the diversity of life, when every high school biology teacher can counter the misleading ‘micro/macro’ distinction so enamored of creationists by pointing to Evo Devo, *then* we might want to gently encourage Carroll to ratchet it down a bit.

    But since we haven’t hit the millenium yet in that department…..well, you get the idea….SH

  29. #29 Larry Moran
    October 9, 2006

    Perhaps we could focus this discussion if every fan of evo-devo were to identify the most important conceptual advance in evolutionary theory that has come out of evo-devo in the past twenty years.

    Clastito, would you like to start?

  30. #30 Clastito
    October 9, 2006

    When convergence happened to be homology, the issue of developmental constraints was back. The study of Development can no longer be swept aside as the study of merely “proximal”, non-evolutionary mechanisms. Understanding development allows you to understand evolutionary possibilities.

  31. #31 charlie wagner
    October 9, 2006

    Larry Moran wrote:

    “Perhaps we could focus this discussion if every fan of evo-devo were to identify the most important conceptual advance in evolutionary theory that has come out of evo-devo in the past twenty years.

    Clastito, would you like to start?”

    How about if I start Larry 🙂

    The most important conceptual advance to come out of biology in the last 20 years is the understanding that the same genes, the same parts turn up again and again from one species to another. We’re all made of the same fabric, we’re part of the same web, and there’s some humility in the idea that’s appropriate.
    Not to mention the fact that almost everything Ernst Mayr said and believed about evolution was wrong.

  32. #32 Kaleberg
    October 9, 2006

    I’m inclined to go with Z&R’s sense of wonder. Sure, no one expected the moon to be anything but a world made out of rock, but when people actually went to the moon, walked around on it, and brought some of the rocks back to Earth it was an amazing confirmation.

    When Hox and related developmental genes were discovered it was another amazing confirmation. Everyone realized that there were similarities in segmentation processes in animals, and everyone expected that genes somehow coded for this, but actually finding the genetic sequences involved, and that they did their jobs so directly, was an amazing confirmation.

    I remember trying to explain email, security certificates and computer viruses to my parents back in the mid-1970s. Though I probably convinced them that their tuition money had been well spent, it is unlikely that they had the slightest clue as to what I was talking about. Twenty years later, all I had considered old had become new and amazing. Getting evo-devo, and its myriad successes, out in the public eye is important. The fact that so much of evo-devo was anticipated speaks to the success and validity of Darwin’s theory. We need more books like this.

    One of the big problems one has popularizing science is that the greater world is 20, 30 or even 50 years behind the cutting edge. People STILL talk about high tension wires, and the ether and the ether tension theory of light was debunked over a century ago. This difference in point of view requires a different use of rhetoric than would be used on the cutting edge. An X-ray astronomer friend of mine used to joke about the tedium of having to give his talks on quotidien 25 million degree plasma streams and boring black hole singularities. Even before Chaucer cranked out his The Astrolabe for Dummies, science popularizers had to compromise their message to reach the general public. Unlike religious authors, obfuscation worked against them, and they had to speak the language of their audience.

    Carroll’s review sounds appropriate enough for a popular publication. Hodin’s more careful analysis would be more suitable for a review in Science or Nature.

  33. #33 Mong H Tan, PhD
    October 10, 2006

    Ricardo Azevedo: Thanks for the C. elegans info; which means the Hox genes may be probably present (in one way or another) in all organisms that would have had a body plan–contrary to what Hodin has had proclaimed above: “Sea urchin larvae, for example, which have bilateral symmetry, complex organs, a full gut, a nervous system, muscles, and all other definitively animal features, are formed in the absence of the canonical Hox gene expression.”

    Is he or am I missing something here, by an evolutionary induction? Or, he just won’t venture that the Hox genes might have had not been incorporated (or fossilized) in the more primitive multi-cellular organisms?

    Clastito: I was wondering if we would cross path again. Anyway, nice knowing you past 2 weekends ago at the PT website. In the heat of our discussions, the PT dodos filtered out my subsequent entries in support of your critical arguments therein.

    In case you and Anton Mates haven’t noticed, I post my responses here, Flock of Dodos (courtesy of ScienceBlogsUSA; October 3); here, Let’s begin the Dialogue and Reconciliation of Science and Religion Now! (PhysOrgEU; October 3); and mentioned again here, Half right: A smart battle against Intelligent Design (ScienceBlogsUSA; October 4), for the record! 🙂

    Thank you all for your kind attention and cooperation in this matter–just a food for thought, from a self-introspective Darwinist evolutionist perspective. Happy reading, thinking, scrutinizing, and enlightening! 🙂

    Best wishes, Mong 10/9/6usct11:25p; author Gods, Genes, Conscience and Gods, Genes, Conscience: Global Dialogues Now; a cyberspace hermit-philosopher of Modern Mind, whose works are based on the current advances in interdisciplinary science and integrative psychology of Science and Religion worldwide; ethically, morally; metacognitively, and objectively.

  34. #34 amphioxus
    October 10, 2006

    Larry Moran: “When Hox and related developmental genes were discovered it was another amazing confirmation.”

    Amazing confirmation? Normally, one is amazed by something that does not confirm expectations. Still, it is a good description of the way these findings were received. It was as if some scientists began to realize for the first time that there was no alternative for the theory they already believed to be correct.
    Is there is a paper before 1983 that speculates that regulatory genes of flies, worms and mammals are more or less the same? References please.
    Proteins and DNA were known to be universal; therefore it was only logical that biochemical interactions between them would involve the same tricks. While the helix-turn-helix motif is common to all species, the lambda repressor is not a homeodomain protein. People really were amazed that different bauplans are encoded by similar sets of genes… Of course, structural genes is a different story.

    Only very recently there was still a lot of excitement that mammals have essentially the same number of genes as flies and worms, the difference being in some gene duplications. Of course, why would you need more genes for a mouse than for a worm? To write their books and papers Jacob and Monod did not need an alphabet with more letters than I do to write a simple note. But again, it had not been predicted. Well, perhaps in the pub.

  35. #35 windy
    October 10, 2006

    …which means the Hox genes may be probably present (in one way or another) in all organisms that would have had a body plan–contrary to what Hodin has had proclaimed above: “Sea urchin larvae, for example, which have bilateral symmetry, complex organs, a full gut, a nervous system, muscles, and all other definitively animal features, are formed in the absence of the canonical Hox gene expression.”
    Is he or am I missing something here, by an evolutionary induction? Or, he just won’t venture that the Hox genes might have had not been incorporated (or fossilized) in the more primitive multi-cellular organisms?

    I assume he means that the Hox genes are present but are mostly not active during larval development, only during adult development.

    I don’t quite get your last sentence, though echinoderms are hardly one of the “more primitive” multicellular groups.

  36. #36 miko
    October 10, 2006

    I think the important contributions of evo-devo are just starting to come out, and they are mechanistic, not big principles. Kirschner and Gerhart (Plausability of Life) also overstate the novelty of their thesis, but at least they name names and cite the literature, and rarely gloss over complexity in the service of reinforcing their point. They also have a section they that explicitly state their ideas, in point form.

    Besides Carroll’s clunky writing (I don’t know what writer could make troubleshooting in situs exciting, but it’s not Carroll), I was endlessly frustrated by his breezy picking out (and not citing) self-serving tidbits from the literature.

    Anyway K&G focus on the actual ways in which (rather than simply the fact that) developmental processes both constrain and facilitate evolutionary change, and how similar sets of genes can be deployed differently within and between organisms.

    I think that it has been known for a long time that evolutionary changes can only make sense as changes in embryonic development. Biologists generally ignored this fact for much of the 20th century for experimental and technical (and partly cultural) reasons, not because they didn’t think it was true. Molecular genetic studies of development and a better understanding of cell biology are revealing boht HOW development constrains and HOW it facilitates evolutionary change, not merely that it does. For example, how the development of the muscles, nerves, and blood vessels can accomodate a morphological change in the skeletal elements to still give rise to a functional limb. Or how a vertebrate invention, neural crest cells (like axons and muscle precursors) embody properties that allow for highly plastic and exploratory developmental mechanisms that can give rise to rich and diverse morphological types.

    Anyway, to me, that’s what Evo-Devo is. Not a “what?” but a “how?”. The thing is, the “How?” questions are very technical and neither the questions or the answers would probably be interesting to a general audience. Reintroducing great old ideas as new ones, dressed up with new buzzwords from mol-cell-bio, is splashier and makes it easier to generate breathless, gee-whiz science articles.

  37. #37 JJP
    October 10, 2006

    The whole evo-devo thing is over-hyped. How could developmental processes be anything other than the product of natural selection? As for developmental constraints – enough off the Gouldian crap please. Constraints in organisms arise because of limits in resources, hence trade-offs, in behavior or life history traits. Alternatively constraints arise due to stabilizing selection; certain traits under strong stabilizing selection will form part of the selective regime for other phenotypic traits, as phenotypic evolution is best understood as a process of combinatorial optimization (including developmental phenotypes). Optimization is a meaningless concept without the notion of limiting boundary conditions/an optimization criterion (constraints if you must). Gould didn’t seemingly know the first thing about the significance of optimization theory within evolutionary biology. Then again he did write a 1400 plus page book on evolutionary biology without any substantial discussion of the work of Hamilton, Maynard Smith, or Price to name three of the most important and original evolutionary biologists of the post-war period.

  38. #38 Clastito
    October 10, 2006

    Oh yeah… another “natural economist”, its all optimization of the benefits, no need to know anything about development.
    Slapping mathematics onto crappy thinking does not make it as good as newtonian mechanics, you know… you are still as soft as climatology or economy. I would never waste my time on that crap, honestly. Not with the progress of evo-devo going on.

  39. #39 miko
    October 10, 2006

    JJP wrote: “How could developmental processes be anything other than the product of natural selection?”

    Ummm, who said they weren’t?

    “As for developmental constraints – enough off the Gouldian crap please.”

    That concept far predates Gould and is not remotely controversial. The way organisms evolve is through changes in embryology to generate new morphologies. This is a complicated process, and it is far from clear what aspects of development can be altered in the service of this process and to what degree.

    Your general use of the word “constraint”–limited resources–has nothing to do with the idea of developmental contraints. Your talking about the “bean bag” genetics of the most simplistic kind. Like what modellers use.

    It’s almost like you don’t any idea what you’re talking about.

  40. #40 miko
    October 10, 2006

    yikes, sorry for the typos and grammar… coffee machine broken.

  41. #41 JJP
    October 11, 2006

    miko

    your comment about ‘bean bag’ genetics betrays your limited understanding of evolutionary biology. Was Hamilton’s work simply bullshit in your view?

    Moreover developmental constraints isn’t a useful concept when postualted as some alternative to natural selection (the Gouldian position), after all those developmental systems and the constraints (or rather boundary conditions) they impose on subsquent phenotypic evolution, are maintained by stabilizing selection!

  42. #42 Clastito
    October 11, 2006

    I think Hamilton is speculation: No actual altruistic genes, or in fact, the “supergenes” required for his scenarios, have been found, much less shown that selection for such genes produces inclusive fitness… reality is much more epigenetic.
    Alotta theory, not enough potatoes.

    I think JPP that you are quite evidently rocking your wooden horse with phrases like:

    “How could developmental processes be anything other than the product of natural selection? ”

    Let me rephrase that: How can selection favor anything that cannot be produced by development?

    “after all those developmental systems and the constraints (or rather boundary conditions) they impose on subsquent phenotypic evolution, are maintained by stabilizing selection!”

    Wrong. If development does not offer stabilizing mechanisms (in your terms, genetic variation for stabilization of a trait) ,selection will be incapable of “summoning” a developmental mechanism to stabilize the phenotype.

  43. #43 Clastito
    October 11, 2006

    Similarly, no matter how much selection could favor a phenotypic change, if development is “rigid”, selection will remain powerless.

  44. #44 windy
    October 11, 2006

    I think Hamilton is speculation: No actual altruistic genes, or in fact, the “supergenes” required for his scenarios, have been found, much less shown that selection for such genes produces inclusive fitness… reality is much more epigenetic.
    Alotta theory, not enough potatoes.

    http://mbe.oxfordjournals.org/cgi/content/full/23/8/1460

    The Evolutionary Origin of an Altruistic Gene

    “…Here, we show that reproductive altruism (i.e., a sterile soma) in the multicellular green alga, Volvox carteri, evolved via the co-option of a life-history gene whose expression in the unicellular ancestor was conditioned on an environmental cue (as an adaptive strategy to enhance survival at an immediate cost to reproduction) through shifting its expression from a temporal (environmentally induced) into a spatial (developmental) context.”

  45. #45 Clastito
    October 11, 2006

    Some people mean by an altruistic gene any gene necessary for altruistic behavior, which normally includes genes that are also necessary for other things (such as survivial enhancement in the example above) . But a true scenario “a la hamilton” calls for something much more specific. A gene or supergene BY ITSELF (a replicator) is selectable and increases its frequency in the population, by producing an atruistic behavior and inclusive fitness…such that the “selfishnes” of that gene will explain the altruism at the organismal level.
    Any evidence for the fulfillmenet of a such a scenario, with actual genes, would be very interesting. I would be very thankful to anyone showing me such a case.

  46. #46 windy
    October 11, 2006

    No, they are saying that the “altruistic” gene evolved by modification from a “gene necessary for other things”, here delay of cell division. Obviously, the modified form of the gene is not necessary for survival, since the unicellular relatives survive just fine.

    And look, it talks about development too! What’s not to like? 🙂

    Consistent with being an altruistic gene (Queller 2000), regA is expressed conditionally, in a developmental context.

    I’m not sure what you want here – a gene that does not descend by modification from some other, necessary gene? Why would we expect that?

  47. #47 Clastito
    October 11, 2006

    I think that study looks fine. It’s neat how it shows that inhibition of reproduction as a survival mechanism in unicellular ancestral forms uses a different version of the same gene used inhibition of reproduction in the somatic cells of their multicellular descendants.

    All I am saying is that it does not provide evidence of gene-level selection for the evolution of altruism, as in “proof endorsing hamilton’s logic for exaplaining altruism”.

    You said

    “Obviously, the modified form of the gene is not necessary for survival, since the unicellular relatives survive just fine”

    Certainly, but that does not prove that altruism evolved by selection for that gene.

    Note, by the way, the role of exaptation (another piece of “crappy gouldian thinking” I guess, according to some rusty conservatives). If this is a survival gene in the ancestor, then at least one paralog redundant copy must have been available before it could become a gene involved in “somatization”

  48. #48 Clastito
    October 11, 2006

    In fact, Windy, Hamilton is not even cited in that paper.

  49. #49 windy
    October 11, 2006

    If this is a survival gene in the ancestor, then at least one paralog redundant copy must have been available before it could become a gene involved in “somatization”

    Not if the conditions of survival changed. You might describe what kind of “proof” you would accept for the evolution of gene-based altruism.

  50. #50 Clastito
    October 11, 2006

    I doubt that onditions changed, I think inhibition of reproduction was present throughout the process of acquiring multicellularity. Anywa, the paper states that there are multiple copies, a family of genes, so I consider the evidence is on my side.

    So, this is the evidence hamilton requires:

    A hamilton scenario is one of selection at the gene level: therefore, you need a replicator (gene or supergene) that is able by its own self to produce an effect of altruistic behavior in the organism that contains it. The mere discovery of a gene like this would be interesting.

    But equally necessary to prove Hamilton, would be to point out a case in which there is a population where there is variation for such a gene; those who have the gene, presenting more altruistic behavior that those who do not have it; a case that shows how despite the altrusitic sacrifices by individuals bearing this gene, the effect of inclusive fitness has positively selected this gene, increasing its frequency in a population.
    That is, a nice field or laboratory example of the process of selection for an actual altruistic gene.

  51. #51 JJP
    October 11, 2006

    Clastito – So ‘development’ is prior to natural selection that does or does not allow for selection. Are you sure about that? All developmental systems arise from variation and natural selection. It’s rather elementary. As for a very well documented example of the dynamics of inclusive fitness may I suggest you read up about polyembryonic wasps?

    As for Gould read this – http://www.slate.com/id/2016/
    or even better this – http://chronicle.com/free/v48/i27/27a01401.htm
    or this – http://bostonreview.net/BR25.2/alcock.html
    or this – http://www.umsl.edu/~engjcarr/web_documents/0415970148.16.rev.pdf#search=%22stephen%20jay%20gould%20wrong%20pdf%22

  52. #52 miko
    October 12, 2006

    JJP,

    I still can’t understand where you’ve gotten the impression that anyone thinks developmental mechanisms aren’t under selection or didn’t evolve, and it makes me suspect either a straw man or that you still don’t understand the concept of developmental constraints.

    Development is the process of developing phenotypes, and developmental mechanisms themselves are also phenotypes, though incredibly invariant ones compared to more obvious morphological traits. Obviously, the developmental mechanisms in existence today are a vanishingly small subset of possible embryologies that have been fixed by historical contingency and their critical roles in generating viable offspring. The adult phenotypes these processes can generate is huge, but is not infinite… some potentially viable and successful phenotypes are inaccessible to, say, mammalian embryology. Not because they are physiologically, physically, or logically impossible, just because development is the way it is.

    What phenotypes and morphologies are plastic and which are rigid? Which are possible but selected against and which are impossible?

    What embryological innovations had to occur to allow, say the stiff, relatively immobile fin of a basal shark-like fish, evolve into the free-wheeling diversity of limbs we see today? (A: probably, a novel epithelial to mesenchymal transition of muscle precursors- Neyt et al, Nature, 2000). What embryological changes allowed Darwin’s finches to rapidly exploit such a variety food resources? (A: in part, regulation of BMP expression in the upper beak during development- Abzhanov et al, Science 2004).

    These are the types questions Evo/Devo asks and how they try to answer them. It is understanding the mechanistic links between genotype and phenotype, and how these links are altered during evolution.

  53. #53 JJP
    October 12, 2006

    miko – I got the impression from posts that come out with gems like “Let me rephrase that: How can selection favor anything that cannot be produced by development? So in this person’s so-called mind ‘development’ is implied to be prior to selection or arises via some non-selectionist mechanism!

    miko I’m happy with your description of combinatorial phenotypic optimization. But unfortunately the people attacking straw men are the self-styled ‘radicals’ of evolution biology. Developmental processes are, in no way whatsoever, a ‘problem’ or ‘challenge’ for the adaptationist view. Unfortunately people like Gould have gotten away with complete bullshit on this topic for years.

    Gould presented correlated growth as an instance of “the limits placed upon selection by structure and development”, along with the “production of nonadaptive structures by developmental correlation” as part of his catalogue of phenomena that supposedly stand outside the scope of “the adaptationist programme” . Gould’s implied contrast between the various ideas he describes and the adaptationism and selectionism of the Modern Synthesis is transparently but breathtakingly bogus. In the case of variations in the pace of evolutionary change, the evolution of adaptively neutral nucleotides, and correlated growth, the contrast is bogus because none of these processes has any bearing on the evolution of complex functional structure, and that is the one central feature of evolution that adaptation by means of natural selection is ‘designed’ to explain. Only natural selection produces complex functional structure, and in this sense it is the only answer to “how” evolution occurred. In the case of inherited constraints on functional structure, the supposed contrast is bogus because inherited constraint is an integral and indispensable component of natural selection.

    Anyone under the impression that developmental ‘constraints’ are not the product of selection (and are maintained by stabilizing selection) are out to lunch or simply intellectually dishonest as in the case of Gould.

  54. #54 Clastito
    October 12, 2006

    What about polyembryonic wasps is so much more hamiltonian than other situations of altruism between highy related individuals? No evidence of selection for an actual altruist gene, there or anywhere.

    “All developmental systems arise from variation and natural selection. It’s rather elementary”

    Yeah, yeah yeah, you already told us, “How could developmental processes be anything other than the product of natural selection?”

    Please do not repeat it again. We get the idea. “Natural selection is everything”. You are un ultra-ultra darwinian.

    “So in this person’s so-called mind ‘development’ is implied to be prior to selection or arises via some non-selectionist mechanism!”

    Yeah yeah yeah. Because “natural selection MUST be everything” I guess suggesting it is not is good reason for a heart attack.

    Actually, you are playing a pretty cheap game, JPP. You are conflating “Evolution” and “natural selection”. Not very academia of you (Though it can work among lay people, amateurs and creationists, I grant you)

    You are making a quite typical autobrainwash that ultradarwinians impose on themselves. You admit that there are constraints that can affect evolutionary possibilities beyond the powers of natural selection, but you comfort yourself saying “these constarints are but the result of previous natural selection”. But think again, JPP. If NOW evolutionary possibilities are subjected to something other than selection, what on earth tells you that the previous direction taken by evolution was only the result of natural selection? pretty obviously, constraints have affecting the direction of evolution the whole time. Constraints are immediate, always present, moment by monet part of evolution that escapes your optimization models (other than in the shape of a black box) and requires you to STUDY biology and natural history, JPP. To study systematics, to study development, to study paleontology, if you are to tackle any REAL evolution of a lineage and not just play in your head with perfect little models that are perfectly useless.

    About natural selection being the only thing that explains complex adpataions, I think I’ve never heard such brazen ideological prejudice. Actually, bring me ANY case, the eye, the mammalian middle ear, the bacterial flagellum.. and INVARIABLY we will find the role of exaptaion: allowed by the funtional ambivalence of a structure, plus more than on structure performing the sam function. There is practically NO understanding of the evolution of complex adaptations, without this “dishonest” Gouldian thinking.

    Of course I skipped the antigouldian rantings you sent. Don’t be frivolous. Let’s keep it at the journal level, shall we.

  55. #55 dawkins_fan_boy
    October 12, 2006

    In making spandrels into a biological metaphor, Gould blends two legitimate Darwinian concepts, but he spuriously represents this blended concept as an alternative or supplement to the idea of adaptation through natural selection. One of these legitimate Darwinian concepts is pleiotropy or multiple genic effects: what Darwin calls correlated growth. The other legitimate Darwinian concept is
    the idea that previously existing structures can be altered through natural selection to fulfill adaptive functions. Darwin offers as an example the swim bladder that in the course of evolution is transformed into a lung (2003, chap. 6, p. 214). The tetrapod body plan also caught Darwin’s attention (pp. 219-220) and has remained a favorite example among evolutionists. The forelimbs evolve from fins to legs, and from legs sometimes to wings and sometimes to flippers.Another favorite example, discovered after Darwin’s time, is that of the reptilian jaw bones that have been transformed into the mammalian ossicles–the bones of the inner ear. (See Young, 1992, pp. 185-186; Moore, 1993, pp. 176-177, 412-414.) For adaptations that use either previous adaptive structures or previous structures of no adaptive value, Gould and Vrba (1982) have invented the term “exaptation.” This term is a variant of a term that was previously current–“preadaptation”– and the concept is itself a commonplace in standard Darwinian theory.

  56. #56 Clastito
    October 12, 2006

    It’s kind of sad that Dawkisn seems to have trouble distinguishing exaptation from homology. It takes a Gould to underline the importance of the role of redundancy.
    Nods of acknowledgement from ultradarwinians are usually followed by total dismissal of the issue. Darwin himself is not that much about “the origin of species by means of preadapataion”, isn’t he. The ultimate hegemony of natural selection was as precious to him as to the conservatives of nowadays.

  57. #57 windy
    October 12, 2006

    It’s kind of sad that Dawkisn seems to have trouble distinguishing exaptation from homology.

    Why not, nature doesn’t seem to make a clear distinction either.

    Darwin himself is not that much about “the origin of species by means of preadapataion”, isn’t he. The ultimate hegemony of natural selection was as precious to him as to the conservatives of nowadays.

    Preadaptation isn’t a “means”. I think it was good to replace the loaded term “preadaptation”, but you seem to have trouble distinguishing your political views from the scientific ones.

    In the second place, we may sometimes attribute importance to characters which are really of very little importance, and which have originated from quite secondary causes, independently of natural selection. We should remember that climate, food, &c., probably have some little direct influence on the organisation; that characters reappear from the law of reversion; that correlation of growth will have had a most important influence in modifying various structures; and finally, that sexual selection will often have largely modified the external characters of animals having a will, to give one male an advantage in fighting with another or in charming the females. Moreover when a modification of structure has primarily arisen from the above or other unknown causes, it may at first have been of no advantage to the species, but may subsequently have been taken advantage of by the descendants of the species under new conditions of life and with newly acquired habits. To give a few instances to illustrate these latter remarks. If green woodpeckers alone had existed, and we did not know that there were many black and pied kinds, I dare say that we should have thought that the green colour was a beautiful adaptation to hide this tree-frequenting bird from its enemies; and consequently that it was a character of importance and might have been acquired through natural selection; as it is, I have no doubt that the colour is due to some quite distinct cause, probably to sexual selection. A trailing bamboo in the Malay Archipelago climbs the loftiest trees by the aid of exquisitely constructed hooks clustered around the ends of the branches, and this contrivance, no doubt, is of the highest service to the plant; but as we see nearly similar hooks on many trees which are not climbers, the hooks on the bamboo may have arisen from unknown laws of growth, and have been subsequently taken advantage of by the plant undergoing further modification and becoming a climber. The naked skin on the head of a vulture is generally looked at as a direct adaptation for wallowing in putridity; and so it may be, or it may possibly be due to the direct action of putrid matter; but we should be very cautious in drawing any such inference, when we see that the skin on the head of the clean-feeding male turkey is likewise naked. The sutures in the skulls of young mammals have been advanced as a beautiful adaptation for aiding parturition, and no doubt they facilitate, or may be indispensable for this act; but as sutures occur in the skulls of young birds and reptiles, which have only to escape from a broken egg, we may infer that this structure has arisen from the laws of growth, and has been taken advantage of in the parturition of the higher animals.

    Yeah, that Darwin, what an adaptation nazi.

  58. #58 Clastito
    October 12, 2006

    “you seem to have trouble distinguishing your political views from the scientific ones”

    That’s a pretty gratuitous statement. Have I introduced any political notionsat all? The way you act it would seem you feel there is something potentially wrong about darwinism, that you so hurry to place the bandage before the wound is made.

    The point is, I don’t care for the fact that Darwin drew inspiration from the economists that fathered right wing economical theory. The inspiration source for ideas does not allow to judge their scientific value. If they are truly scientific they can be judged according to their corresondence with nature. Right?

    That paragraph of Darwin is certainly very interesting. Note precisely how he uses facts of natural history to test and discard selectionist explanations.
    It reminds me of the sore complaints Darwin made against those who would see everything to be natural selection (JJP: You are on notice).
    Darwin is certainly an interesting character, a sophisticated mind and a great naturalist and biologist in general. I think he lived troubled by some logical deadends in his thinking (such as how to handle the concept of the principle of divergence or the inheritance of acquired traits) and it is true, I think, that some of his most “progressist” and “competitive” notions of natural selection and adaptation had an ideological gleam to them, both unto himself and to others, that stole much of the thunder from other important topics and ended in an overmephasis of selection.

    And, in fact, discussion of laws of growth and of non-adapative traits (specially on the continent), had preceded the well informed and scholarly Darwin. Is this what “Darwinism”, therefore, is about? Once again, I insist: darwin did not fater in arguing the hegemony of natural selection as the “main” evolutionary mechanism. What else, if not, is proper “darwinism”?? Natural selection was truly HIS idea… and overmephasizing its importance was his comprehensible mistake too.

  59. #59 Clastito
    October 12, 2006

    BTW, I have no indication that anyone here really understands what I mean, when I talk about redundancy in exaptation… do your homework. Gould says exaptation usually requires 1) funtional ambivalence of a structure 2) more than 1 structure that performes the same function.

  60. #60 windy
    October 12, 2006

    So? You were not so keen to accept something on the basis of “Hamilton says”, why is “Gould says” any better? Is the concept of exaptation requiring redundancy and functional ambivalence demonstrably better for understanding evolution than any old preadaptation concept? I’m not saying it isn’t, but how do we test it?

  61. #61 windy
    October 12, 2006

    Once again, I insist: darwin did not fater in arguing the hegemony of natural selection as the “main” evolutionary mechanism. What else, if not, is proper “darwinism”?? Natural selection was truly HIS idea… and overmephasizing its importance was his comprehensible mistake too.

    And I guess overemphasizing the laws of gravity was Newton’s ‘mistake’…

    I have a different impression. Darwin “faltered” a lot in presenting his idea, if you can call so his poring over uncertainties and getting sidetracked to all kinds of things. IIRC sexual selection was then seen as rather separate from natural selection, rather than simply a part of it, so one cannot say he pooh-poohed the possibility of more than one “main force” contributing to divergence. And what about common descent? Is that not an important contribution of “proper darwinism” distinct from NS?

    And another point but not about Darwin… if natural selection has been so completely overemphasized and overused as an explanation, why did people act so surprised when widespread signs of recent positive selection were discovered in the genomes of modern humans?

  62. #62 Clastito
    October 12, 2006

    Windy, allow me to suggest, that you need to think more about exaptation. In any case, think about the case of the bladders of teleosts. Darwin thought a bladder evolved into a lung… functional ambivalence is there, but what about redundancy? Now, do you think any evidence can be retrieved to test if there was any redundancy in this particular story of lungs and bladders?

    “I guess overemphasizing the laws of gravity was Newton’s ‘mistake’…”

    I don’t know about that… I don’t think he downplayed his achievements, no? What is veeeery probable is that OTHERS did overemphasize newton’s work. I know for a fact that others have overemphasized selection to ridiculous extremes. Far beyond what was allowed by the good caution of Darwin.

    Even so, I think Darwin quite naturally decided to make his bet for his own idea pretty clear… knowing at the same time that several of his colleagues at the time sincerely thought he could be wrong. He DID insist several times, quite convinced, that he believed that natural selection was the main mechanism of evolution.

    About Newton…didn’t quite some time pass until the next great leaps in physics? And I would not be surprised at all if there had been in between many a professor that insisted on not straying too far from newton.
    Clear, groundbreaking advances are difficult in science.. so when they are achieved they can be so treasured by scientists that a major shakeup may be necessary to realize there can be anything else!!!

    Common descent was weel discussed in academia before darwin: lamarck had popularized it already. That’s Lamarck’s, if anyone’s, though of course darwin deserves honorable mention for paying greater attention to proving it carefully and thus satisfy the demands of the doubting thomases. Darwin stated he wanted two things: FIRST, to convince his colleagues of common descent, and second, that natural selection was the main evolutionary mechanism. He certainly succeeded in the first. In the second, he succeeded too much with some, and very little with others….

    About those widespread signs of positive selection….Caution!!! Are you clear what they actually provide evidence for? What scenarios do you think we are allowed to imagine form this evidence? I think there is a greta dela confusion about what ithis kind of data actually mean.
    I predict that people making too much of a scenario for each of these genes, will land flat on their faces at the end of the day ….

  63. #63 Steviepinhead
    October 12, 2006

    Clastito, really, what the heck are you actually on about?

    If you think there are other primary mechanisms driving evolution, beyond natural selection, spit them out. Lay out your case. If natural selection doesn’t adequately, to your mind, explain altruism, or bladder ==> lungs, or whatever, and you don’t see exaptation as getting there in the bladder – lungs case, then what? Exactly? Do you see as the mechanism?

    Surely not something supernatural? So, spill, what?

    So far, your writing is long on critique and snarking about what other folks have overemphasized or overlooked or …something, but also long on misspelled words, odd turns of syntax, and general fogginess.

    Get down to it, dude. I’m with Windy, to this point.

  64. #64 Clastito
    October 12, 2006

    Stevie,
    Mutation and selection occurs and is an important and unavoidable part of understanding evolution. But equally real and important are developmental constraints and the occurrence of exaptation. To think that evolution is about any one of these things on its own, will inevitably leads to a bad, insufficient understanding of evolution.

    Do you think there is room for silly supernatural crap in this discussion? Do not give that crap such credit, or you will let your fear of it force you into believing everything HAS to be natural selection and “that’s it”. That would be pretty dumb, would’nt it.

    This is a scientific discussion here stevie, you’re at a mere anti-creationist level, sorry. Come back when you are ready.

  65. #65 miko
    October 13, 2006

    JJP,

    Concepts can and should be discussed on their merits, not who has favored them, mirepresented them, or accused them of being part of this or that academic fad or clique. Gould was a propagandist for his own interpretations of evolutionary theory, and a stubborn and bullying one. But I don’t give a shit what he said, thought about, or how he interpreted the term “developmental contraints.” He doesn’t (didn’t) own the idea… it both precedes him and has been much more carefully defined and deployed as a set of testable hypotheses by working scientists.

    Your only problem with it seems to be the misguided import Gould gave it as somehow being something separate from the rest of evolutionary theory as others conceived it. Which, I’ll say it again, no one seriously thinks. It does involve thinking about some new concepts to incorporate development into modern evolutionary theory. This process of incorporation seems actually to be remarkably smooth, and has not forced any crises in darwinian theory, despite the usual hysterical tone of the evolution discourse. Get over Gould, man, he’s dead and smart people have been actually working on these subjects rather than engaging in the usual mud-slinging grandstanding of evolutionary biology.

    Evo-devo is primarily about how variation is generated, not about how selection occurs.

    The current issue of Current Biology has good, short primers on a lot of these concepts, including constraints, from level-headed, working biologists. Check it out.

  66. #66 Mong H Tan, PhD
    October 13, 2006

    Windy: “I assume [Hodin] means that the Hox genes are present but are mostly not active during larval development, only during adult development. I don’t quite get your last sentence, though echinoderms are hardly one of the ‘more primitive’ multicellular groups.”

    I think Hodin was attacking “the canonical Hox gene expression” out of his own ignorance; and I believe the “more primitive” term was meant to compare the multicellular organisms anatomically?!

    Clastito: “But a true scenario ‘a la Hamilton’ calls for something much more specific. A gene or supergene BY ITSELF (a replicator) is selectable and increases its frequency in the population, by producing an altruistic behavior and inclusive fitness…such that the ‘selfishness’ of that gene will explain the altruism at the organismal level. Any evidence for the fulfillment of such a scenario, with the actual genes, would be very interesting. I would be very thankful to anyone showing me such a case.”

    I think we should not fall for the spell of Dawkinsian Evolutionism in The Selfish Gene (1976); however, in this book Gene in Conflict (2006) the authors (Austin Burt and Robert Trivers) believe that they have had found the Biology of selfish genetic elements?! Then again, I would be very nervous to see that ethologists (like Dawkins) and anthropologists (like Trivers) who would be able to explain their animal behaviorism at the genetic molecular level, especially by their misinterpretations of Darwinism–the Natural Selection of species at the organismal level!

    Windy: “…you seem to have trouble distinguishing your political views from the scientific ones.”

    This statement should define Dawkinsian Evolutionism, precisely! Not Clastito, Windy! 🙂

    Clastito: “Once again, I insist: Darwin did not falter in arguing the hegemony of natural selection as the ‘main’ evolutionary mechanism.”

    I think Natural Selection (NS) was the best terminology that Darwin and contemporaries could use to describe their then Observations of species at the organismal level, in the 19th century. However, to still use the NS to describe genes at the molecular level, that is the diehard Dawkinsian Evolutionism since 1976–a Scientism at its best; that’s why Evolutionism has had established Dawkins the Oxford’s Emperor in Darwinism who has no clothes, ever since! And, unwittingly, Dawkinsian Evolutionism has had become the target of the ID neocreationist anti-Darwinism campaign since the 1990s, that Dawkins and his groupies didn’t even realize it–even today!

    Clastito: “Darwin stated he wanted two things: FIRST, to convince his colleagues of common descent, and second, that natural selection was the main evolutionary mechanism. He certainly succeeded in the first. In the second, he succeeded too much with some, and very little with others….”

    I would agree to that!

    Steviepinhead: “Clastito, really, what the heck are you actually [talking] about? If you think there are other primary mechanisms driving evolution, beyond natural selection, spit them out. Lay out your case.”

    Clastito: “Mutation and selection occurs and is an important and unavoidable part of understanding evolution. But equally real and important are developmental constraints and the occurrence of exaptation. To think that evolution is about any one of these things on its own, will inevitably lead [one] to a bad, insufficient understanding of evolution.”

    I would agree to that; and Dawkinsian Evolutionism has had indeed implanted “a bad, insufficient understanding of Evolution” into the public psyche worldwide, as explained above and elsewhere, Natural selection is recursive (PhysOrgEU; September 10).

    Thank you all for your kind attention and cooperation in this matter–just a food for thought, from a self-introspective Darwinist evolutionist perspective. Happy reading, thinking, scrutinizing, and enlightening! 🙂

    Best wishes, Mong 10/13/6usct2:32a; author Gods, Genes, Conscience and Gods, Genes, Conscience: Global Dialogues Now; a cyberspace hermit-philosopher of Modern Mind, whose works are based on the current advances in interdisciplinary science and integrative psychology of Science and Religion worldwide; ethically, morally; metacognitively, and objectively.

  67. #67 Steviepinhead
    October 13, 2006

    We’ll just note that, Clastito, despite the height advantage afforded by his high horse, failed to answer specific questions about the mechanism whereby evolution turned bladders into lungs, or how–if not by natural selection–altruistic behaviors evolve.

    Peroration is not adequate argumentation.

  68. #68 Clastito
    October 14, 2006

    This is very, very sad….can it be that no one here knows the evidence on the actual story of lungs and bladders????

  69. #69 M.C.Arunan
    October 15, 2006

    Dear all,
    If we knew it all the time, why, till recently, even biologists of no mean scientific repute, went on plumbing for more than 80,000 genes for homosapiens? Biology teachers(following textbook versions) still go to town in a similar mindless fashion; not to talk about the media go on ‘manufacturing consent’ for the existence of genes for memory,schizoprenia, criminality, and even for Nobel Prizes!

    Masters students of mine assume that the E.coli has a ‘mind’ to ‘know’ when lactose is present in the medium!They are perturbed beyond words, when shown the elegant mechanistic explanation of Jacob& Monod for this ‘cosciousness’ of E.coli! With the dominant Hindu theology of “all pervading consciousness” in which they and their elders are soaked with no easy escape, it is no surprise at all. The western creationist lobby did not make science teachers’life in third world countries any better.
    M.C.Arunan,
    Brain Research & Cognitive Sciences Laboratory,
    Department of Life sciences,
    Sophia College for women, Mumbai-400 026, India.

  70. #70 thwaite
    October 16, 2006

    For Clastito’s question of fact on lung evolution from bladders in teleosts:
    I got curious and spent a few minutes in google and scholar.google – quickly apparent the story is more complex than Darwin could have known, and is still unresolved.

    Couple of links, will take a bit to digest:
    classroom lecture summarizing a cladogram for teleost swim bladders and implying they actually emerged from lungs, in two steps (no sources cited).

    technical review article, 2001.

    “Twenty Ways to Lose Your Bladder”: common natural mutants in zebrafish and widespread convergence of swim bladder loss among teleost fishes
    — pertinent to the evoDevo issues of lability and ‘constraints’

  71. #71 Mong H Tan, PhD
    October 16, 2006

    M.C.Arunan: “Masters students of mine assume that the E. coli has a ‘mind’ to ‘know’ when lactose is present in the medium! They are perturbed beyond words, when shown the elegant mechanistic explanation of Jacob& Monod for this ‘consciousness’ of E. coli! With the dominant Hindu theology of ‘all pervading consciousness’ in which they and their elders are soaked with no easy escape, it is no surprise at all. The western creationist lobby did not make science teachers’ life in third world countries any better.”

    This is very interesting, since you’re getting into a whole new field of the Evolution and Consciousness issues, that my own research (since 1990) has had guided me to the cortical neuronal membrane, as a magical place of Consciousness as directed by the particle-wave functions of membrane “memophors,” the imagery membrane components that may be likened to the particle-wave functions of phosphors being coated on a TV tube–a new theory that I’ve had presented in my 2006 book Gods, Genes, Conscience (please see Chapter 15 The Universal Theory of Mind); and also discussed briefly elsewhere, Macro Wave-particle (PhysOrgEU; October 2).

    For your convenience, and neuro-electrochemically–if you would make a quick review of the Frontispiece of Gods, Genes, Conscience listed below–the main medium that projects imageries in and of our Mind, as a reflection of Consciousness into our brain, is Light (the optical quanta of photons, as shown in the Square inset) through and by our visual circuitry, as follows:

    Perceptivity through the retina –> imagery-memory modulation –> particle-wave functions of imagery-memory on the cortical neuronal membrane (please see the Circular inset) –> “memophorescence”–like phosphorescence of TV phosphors –> “memophorescenicity” –> infinite creativity or fluidity of imagery-memory,

    thereby making us, the scientist-Observer-philosopher as well as the “memory manipulator” or “thinker” in this stream of visual Consciousness, being modulated on the cortical membrane, as exemplified by a projection or imagination of the Creation of Adam, in a modern wannabe Michelangelo’s spherical mind! 🙂

    Likewise unique, at the single-cell, organismal level, such as E. coli, its “consciousness” is also conducted by the “sensing” of the electrochemical gradients by and across its vital cellular membrane. As such, by shear coincidence, the Metaphysics of Consciousness in all living things as pervaded in Hinduism and/or others, was not that far off after all, from our modern empirical Science of Consciousness, as Jacob& Monod attempted to explain above, albeit molecularly!

    Thank you all for your kind attention and cooperation in this matter–just a food for thought, from a self-introspective Darwinist evolutionist perspective. Happy reading, thinking, scrutinizing, and enlightening! 🙂

    Best wishes, Mong 10/16/6usct1:26p; author Gods, Genes, Conscience and Gods, Genes, Conscience: Global Dialogues Now; a cyberspace hermit-philosopher of Modern Mind, whose works are based on the current advances in interdisciplinary science and integrative psychology of Science and Religion worldwide; ethically, morally; metacognitively, and objectively.

  72. #72 Steviepinhead
    October 16, 2006

    Thanks, thwaite.

    (But a hearty heigh-ho and “No thanks!” to Clastito for his usual hand-waving.)

  73. #73 thwaite
    October 16, 2006

    Right-o, Steviepinhead. I thought that discussion ended tellingly.

    The most lucid discussion of the loss of lungs in teleost fishes is by Carl Zimmer in his AT THE WATER’S EDGE …how Life Came Ashore and Then Went Back to the Sea, 1998, about page 100. This unfortunately isn’t part of the excerpts at his website or elsewhere, but it’s a popular and widely available book for both its topic and writing. I mean, where else would you learn that “A clue to the true evolution of lungs may lie in the fact that you can kill a trout by making it swim hard. … After a few minutes of racing, most fish without lungs die.”
    He prominently highlights research by Colleen Farmer of Brown on the question of why teleosts (late and sans lungs) are so much more prevalent now than the earlier/older lunged fishes. The speculation is about aerial predators’ emergence at 220MYA and their effect on near-surface lunged fishes, which deep-diving teleosts avoided. No discussion of developmental constraints, FWIW.

  74. #74 Steviepinhead
    October 16, 2006

    Thanks again, thwaite, I’ve got “Water’s Edge,” but it’s been a few years–and a few neurons. I’ll take another look.

    Googling indicates that TalkOrigins has a one-liner (in its transitional fossils FAQ) supportive of lung => bladder evolution. And, just to come full circle back to Evo-Devo, I saw an article, “Deconvoluting Lung Evolution…”–not absorbed in full on a busy day–investigating a developmental regulatory gene, PTHrP, that is expressed in swim bladders and lungs:
    http://ajrcmb.atsjournals.org/cgi/content/full/31/1/8.

  75. #75 Torbjörn Larsson
    October 16, 2006

    Clastito:
    “About Newton…didn’t quite some time pass until the next great leaps in physics? And I would not be surprised at all if there had been in between many a professor that insisted on not straying too far from newton.”

    I’m not a historian, but I think you may have a simplified view of the history of science. Newton was concurrent with “the next great leap”. Leibniz devised a dynamics with kinetic and potential energy and relative space. Lagrange was later the synthetisator of these two theories.

  76. #76 Clastito
    October 17, 2006

    OK, so do we have any clarity now, that this was not the perfecting of respiratory functions of a bladder into a lung? And, I’m still disappointed. No one is talking about redundancy and its evolutionary implications, and so I remain unconvinced that anyone has given exaptation proper thought. Adaptationist explanations, a dime a dozen, can be made for everything, yet unless we do like Darwin and contrast them with actual data from natural history, you will simply never will discover that most of those imagined are simply false!
    Please try to articulate how the logic of redundancy fits into all of this, beyond adaptationism. It might help if you look at the more basal splits among the living actinopterygians
    By the way Stevie… I cant help making you notice, that you are SOOOO sensitive. Are you ever so kind with creationsist? I am under the impression that for people like you, the best thing about knowing something of science, is that you feel it gives you some kind of free pass to insult and bash other fellows “cause you are right”. But just watch you twitch now, I feel I have been pretty nice and sugar coated in comparison with the way amateur ultradarwinians deal with anyone who is different.

  77. #77 Jason Hodin
    January 3, 2007

    wow…I just came across this thread for the first time almost 3 months after the fact! Sorry I wasn’t around to contribute to the discussion. Nevertheless, I am quite confident that my unpublished letter has now generated a heck of a lot more interesting and useful discussion than had it been chopped to bits by the editors and then spit out onto the back pages of the NYRB. 🙂

    One point to mention, in case anyone ever sees this very late post: I have recently been involved in a multi-authored publication called “What Is Metamorphosis?”, which is the opening piece in a symposium issue of the the journal Integrative and Comparative Biology. That is a for-profit, restricted access journal, so we posted an open access version of all of the symposium papers here.

    The relevance of this symposium to the discussion above relates to the observation made by many of those posting here that “evo-devo” all too often means just animals (with the occasional plant thrown in almost as an afterthought). Our symposium – “Metamorphosis: A multi-kingdom approach” – was a conscious effort to provide a counter-example.

    Enjoy!

    Thanks PZ

  78. #78 Ichthyic
    January 3, 2007

    Jason –

    the link to the symposium papers does not work for me; could you just post the whole link please?

    thanks

  79. #79 Jason Hodin
    January 9, 2007

    Ichthyic

    sorry about that. not sure what happened there.

    http://www.metamorphnet.org/SICB2006/2006Symp.html

    peace
    jason

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