PZ Myers posted Entry 48 on March 26, 2004 01:45 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/47

One of the serious shortcomings of Intelligent Design is that it does nothing to provide any new or productive insights into the workings of biology. ID proponents seem to be at least vaguely aware of this failure, in that they do frequently claim to be thinking about working on a preliminary, tentative approach towards the beginnings of a potential research program (my paraphrase), but most of the effort has been directed towards political and legal enforcement of their ideas, rather than actually testing those ideas. One advantage of pursuing only legalisms is that they don't give scientists anything to grapple. Invariably, when ID proponents do dip their toes in the scientific waters, they end up getting eaten by the sharks that lurk there.

One example: Paul Nelson, of the Discovery Institute, has been peddling a peculiar idea he calls "ontogenetic depth" as a scientific concept that emerges from Intelligent Design. To his credit, he has been presenting this idea in legitimate science venues, at the Geological Society of America and Society for Developmental Biology meetings. Note that getting on the program at these meetings is not subject to peer-review, so it is not automatically a recognition of merit that this work has been presented publicly. It is a good sign that Nelson is willing to expose his work to criticism, though.

I'm going to give it some criticism here. "Ontogenetic depth" is a developmental idea, and I'm a developmental biologist. Today I also get to play shark.

What is "Ontogenetic depth"? Here is the definition, as written by Nelson himself and published online, at ISCID:

Ontogenetic depth is a measure of the distance (in terms of cell division and differentiation) between a single-celled state and an adult animal (metazoan) capable of reproduction. All animals begin their existence as a single cell, the fertilized egg. From that cell, many other cells arise, and become specialized for particular functional roles—for instance, as sensory organs, skeletal parts, or reproductive structures (such as ovaries). The ontogenetic depth of any species measures the developmental distance between the starting point, the egg, and the stage at which organisms in the species can successfully reproduce themselves.
Developmental biology has mapped the ontogenetic depth of a handful of species, in the so-called "model systems" of the discipline, such as the nematode Caenorhabditis elegans or the fruit fly Drosophila melanogaster. To explain the historical origin of any animal species (and arguably the same is true for plants), one must give an account of how that species' respective ontogenetic network—i.e., its process of differentiation—was constructed.

Unfortunately, I don't have a lot to go on here. "Ontogenetic depth" has not been published in any peer-reviewed journal, I have not attended any of Nelson's presentations on the subject, there are no methods described that would allow me to measure this value in any organisms, nobody other than Nelson and his collaborator, Marcus Ross, do anything with the idea, and all I've got are a transcript of an online chat and an accompanying pdf summary. It's enough, I suppose. It's clear that this is a poorly expressed and unusable idea based largely on misconceptions and faulty scholarship, with no actual research to back it up. I feel sympathy for Mr Ross, who has been suckered into an extraordinarily bad idea early in his academic career.

So what's wrong with "Ontogenetic depth"?

It's an unworkable idea. Nelson claims that ontogenetic depth is precisely measurable in extant species, and is therefore a good metric ("The ontogenetic depth of a handful of extant animals (from the model systems of developmental biology) is known with precision"). Unfortunately, this is simply not true. The sole example he gives is Caenorhabditis elegans, which has an exceptionally well understood pattern of stereotyped cell lineages that lead to the adult. This is not the case for other metazoans, and it's not simply because they have cells too numerous to count; it's also because most other animals don't have an invariant cell number. Even in C. elegans, Nelson has to say that the ontogenetic depth is somewhere between 7 and 9...so much for specificity (and so much for measuring developmental differentiation—the mysterious unitless number doesn't seem to describe the elegant precision of the nematode at all well).

It uses false assertions and confusing examples. The basis of Nelson's claims about the relevance of ontogenetic depth to evolution are simply wrong. He tries to argue that changes to the early lineage of organisms are "wreckers", that is that they are never viable, and therefore that patterns of early division can never change. He says,

When I was writing my dissertation, I asked one of my advisors if he knew of any cases of the heritable modication of early development . He couldn't think of a single example (other than a change from left-to-right shell coiling, or back again, in snails—the exception that proves the rule).

This is confusing in several ways. Nelson spends a fair amount of time discussing the highly ordered cleavages of C. elegans. Is he, and his advisor, really unaware of the many known mutations in that organism that change the lineages? It's a whole grand class of numerous mutations named lin; there are mutations that block subsets of divisions, add extra divisions, transform the pattern of one set of divisions to resemble another lineage, or change the timing of divisions.

And why is he even mentioning the direction of spiral cleavages in molluscs here? That's a change in the chirality of early divisions, not any change in the pattern of divisions themselves. I don't see that the orientation of divisions is even considered in his measurement of ontogenetic depth.

When he claims that changes in early divisions are invariably deleterious, I know that that is false from personal experience. The zebrafish embryos I work with have a canonical pattern of early divisions, but the animals can tolerate a significant amount of variation; heat shock or just spontaneous screw-ups can produce wacky cleavages, but the animals regulate and recover. Also look at what can be done with mammalian embryos: the inner cell mass can be dissociated, cells juggled around, and reassociated in part or in combination with other embryonic cells, about as thorough a scrambling of the pattern of early development as you can get, and the embryos can resume development normally.

It is also curious that Nelson discusses nematodes, cites Schnabel (1997), and manages to completely ignore that paper to claim that nematode lineages are absolutely fixed. Here is the abstract to that paper:

C. elegans is renowned for its invariant embryogenesis and functions as a major paradigm for a mode of development coupled to an invariant lineage. Recent work, however, suggests that the embryogenesis of the nematode is much more flexible than anticipated. The invariant premorphogenetic stage is formed from variable earlier stages through a sorting of cells. Cells do not act as individuals but already early in embryogenesis a regionalization of the embryo occurs. Cells are diversified by a binary specification of 'abstract' blastomere (regional) identities. The determination of tissues may thus be a very late event. It appears that C. elegans, although assigning cell fates in an invariant lineage pattern, uses the same strategies and mechanisms for embryogenesis as organisms with variable lineages.
Schnabel R (1997) Why does a nematode have an invariant cell lineage? Semin Cell Dev Biol 8:341-349.

It's as if he read the title, copied one of the figures, and didn't pay any attention at all to the conclusions of the paper, which contradict what he claims.

The idea is based on bad metaphors. Oh, jeez, Nelson's "Marching Band" metaphor...where to start? He tries to explain development as something similar to what a marching band has to do to assemble formations on a playing field: individual bandmembers (cells) have to maneuver through a series of defined steps (development) to end up in a position that spells out something (the adult state).

This is not how development works.

Cells do not, in most cases, have a pre-programmed pattern of differentiation built into them, that they then follow rigidly to end up in a specific, fated state or position. Development is about flexibility, interaction, negotiation, and emergent properties. To state that a trumpet player who doesn't know his rules would lead to the college's name getting misspelled on the football field doesn't say a thing about whether changes in development are impossible. In many organisms, we can shoot the trumpet player, blindfold the clarinetists, tumble everyone around in a cement mixer, and add a gang of bagpipe-playing soccer hooligans, and the mess can still organize itself to spell out a message (probably not a polite message, but something coherent, at any rate). If Nelson wants to make a metaphor, it's going to have to be one that can account for the radical regulative reorganization that has been observed in real developmental biology.

The only way I can imagine Nelson would even propose such a bad model is that he is both unaware of the range of processes in development, and that he has been misled by exaggeration and mischaracterization of the processes in many of the most common model systems. One worrisome flaw in molecular developmental genetics research is that we rely on simple laboratory models—nematodes, fruit flies, zebrafish—that are not well representative. These animals all develop very rapidly and are relatively simple, which is convenient for research, but unfortunately means that they tend to be developmentally streamlined, with less redundancy and more inflexiblity than is good for us. Biologists also tend to look for changes with large-scale, robust effects, further biasing our knowledge of what kinds of changes are out there. Nelson has taken a sampling bias that we are aware of (and that he should be aware of, too; he cites Raff, who has discussed the problem in some detail in his book, The Shape of Life) and exaggerated it to a cartoonish degree. We know that our models bias our perception of development in a certain direction. Nelson has taken a bias and blown up the error into a natural law.

There is no research! Ontogenetic depth is a sloppily-defined concept with no theoretical support for its validity and no apparent operational utility. What can a scientist do with it? Nelson has a plan:

However, it should be possible, using modern analogues for fossil taxa—e.g., the extant monoplacophoran Neopilina for the extinct mollusc Scenella—to obtain good estimates on the ontogenetic depth requirements of many Cambrian forms. This is research we are now conducting. It is likely that reasonable estimates of the ontogenetic networks, and depth, required to specify such extinct organisms as Anomalocaris or Opabinia, will require no less complexity than that of modern animals.

To which I can only say, "what?"

He doesn't have a way to measure ontogenetic depth...at least, not any way that he has explained, and that can be justified.

There is no reason to think that this parameter even describes complexity better than, for instance, counting cell types at maturity, which is also a fuzzy and difficult job.

If you determine (in some way) that this modern mollusc is as complex as another modern mollusc, how can you then claim that that means that ancient molluscs were as complex as modern ones? Isn't that already your assumption when you claim that the modern form is an analogue of the extinct one?

We already know that the Cambrian fauna were complex. I don't quite see what we'd learn that would be new to have someone announce that they have invented a new metric (which doesn't seem very good) that shows that the Cambrian fauna were complex.

I don't think he is necessarily measuring complexity, so it's even worse. What do we learn from carrying out a convoluted process to determine that some animal in the Cambrian weighed 50 grams and had 1010 cells, and some other animal in the present day weighs 50 grams and has 1010 cells?

The actual goal of Nelson's 'research' is to conclude that developmental complexity is infrangible, and that if he shows Cambrian organisms to be complex, that it is therefore impossible for them to have evolved. One of his cheerleaders, Tristan Abbey, makes this explicit:

But that can't be true! The earliest stages of development are different among the various animal groups. They must have evolved somehow. But how? If development can't be touched, how did it change?
The simplest answer for IDists is that it didn't.

Nelson's research program seems to be counting cell divisions in extant organisms, and leaping to the unsupported conclusion that evolution is impossible if he gets similar numbers in two different groups. That conclusion is what is unsupported and untested by his methods. No one other than a few uninformed Intelligent Design creationists are claiming that "development can't be touched".

Those anecdotes... One last minor point. What is it with all these ID creationists and their little quotes from China? Wells does it, now Nelson does it:

I had with me (on top of my conference files) an overhead transparency, showing the complex regulatory sequence of an invertebrate developmental gene. And up walked the author of that very paper (a visiting American biologist), from which I had borrowed the figure.
Of course he spotted the diagram right away. "What do you plan to do with that?" he asked me.
"I thought I might use this in my talk," I said, "as a quick illustration of the complexity of embryonic regulation." The biologist smiled. Knowing that he was something of a critic of neo-Darwinism, I asked him what historical process he thought had assembled the complex regulatory sequence.
His answer really surprised me. "I don't know," he said, "but I do know that ordinary mutation and selection won't do it."
He went on to say that he thought our (that is, the biological community's) understanding of evolution lagged way behind its other knowledge.

An unattributed quote from a mysterious biologist attending a Discovery Institute sponsored meeting does not impress me in the slightest. I would like to know what a non-ordinary mutation might be, and why anyone should be surprised that a modern evolutionist would suggest that there is more to evolution than selection.

Reading Nelson's proposed research was rather like reading a very poor preliminary exam proposal from an unpromising graduate student. It would be grounds for flunking the poor sap out of the program on the spot. It's certainly not publishable, nor does it even hint at the potential for being publishable. And it's probably the best piece of work to emerge from the Intelligent Design crowd yet, which should give you an idea of the low quality material they've got.

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Comment #248

Posted by RBH on March 26, 2004 2:18 PM (e)

Maybe someone should be collecting these anecdotes about authority figures. They’re closely related to quote mining operations, though often with the cloak of anonymity drawn ‘round the protagonist. There are two from Nelson (the unidentified adviser and the unidentified biologist) and one from Dembski (his Koza question) so far just here on TPT.

RBH

Comment #250

Posted by Matt on March 26, 2004 2:48 PM (e)

PZ wrote:

“…they do frequently claim to be thinking about working on a preliminary, tentative approach towards the beginnings of a potential research program…”

Calvin (of “Calvin & Hobbes”) called this “visualizing the actualization process.” Only this is clearly a few more steps removed from actuality.

Regarding Nelson’s value for the “Ontogenetic Depth” of C. elegans: I’m guessing he looked at a figure similar to one from Gilbert’s Developmental Biology (p. 510 in the 4th edition, and taken after Pines 1992(1)). This is a cell lineage chart showing all the divisions and fates for all of the cells in the hermaphroditic adult. The figure shows eight ultimate cell types (cuticle-making cells, nervous system, pharynx, intestine, vulva, gonad, egg, sperm). One major cell lineage is not grouped into any category, and of course the male would have one less cell type.

Hence an ontogenetic depth of 7-9.

If this is how ontogenetic depth is calculated, may I just say “huh?

And who was on Nelson’s committee? Who was the mystery advisor? Was he a biologist?

(1) Pines, M. (ed.). 1992. From Egg to Adult. Howard Hughes Med. Inst., Bethesda, pp.30-38.

Comment #251

Posted by ArtK on March 26, 2004 2:50 PM (e)

As a former collegiate band-geek, I had a great time reading the rebuttal to Nelson’s analogy. It’s clear that Mr. Nelson has never seen the Stanford band (or other “scramble” bands) whose marching style looks much like they shot the trumpet and blindfolded the clarinets.

On a different note (argh!), bravo to this site, and the many others (including Pharyngula) addressing ID head on. I’m only on the periphery of biology (integrating life-sciences databases such as PubMed, GenBank, search tools like Blast and HMMER) and this has been a great education.

I’ve also been passing these sites on to my friend, who teaches science pedagogy to elementary and middle school teachers. She hasn’t run into an IDist yet, but it’s bound to happen some day soon.

Keep up the good work!

Comment #253

Posted by Andy Groves on March 26, 2004 3:33 PM (e)

I sent Paul Nelson these thoughts on his “marching band” idea last year:

I have never played in a marching band - but the principle of band choreography as I understand it relies on follow-the-leader most of the time. Certain key marchers guide a series of smooth lines and curves, which shift position and shape over time.

The moves are planned out in advance - but when you write that “it is intuitively obvious that the members must have their instructions in place before they venture out onto the field”, you are both right and wrong. Yes, of course the band members have rehearsed their moves before, and know broadly speaking what moves they should execute. However, on the day, with the crowds cheering, the cheerleaders flaunting and the adrenalin pumping, you follow your leader.

A cell destined to be a C. elegans muscle cell does not “know” what fate is in store until it receives the instructions to tell it what to do. Cells have neither the choreography worked out first - even for animals with invariant lineages like C. elegans - nor do they have master control cells that choreograph their movements throughout their developemnt.

At any point, the cell’s “knowledge” is the proteins it is making, and the bits of DNA that are transcriptionally active or quiet. Embryonic development is much more like a Mexican wave - you pay attention to the people sitting on your left and right at any given time….

Andy

Comment #254

Posted by PZ Myers on March 26, 2004 3:40 PM (e)

nd who was on Nelson’s committee? Who was the mystery advisor? Was he a biologist?

His advisor was William Wimsatt, a philosopher. He says “one of his advisors” made that claim, so it’s not clear that Wimsatt is responsible for that particularly glaring bit of ignorance.

Comment #255

Posted by Mark Perakh on March 26, 2004 3:50 PM (e)

Regardless of whether Nelson’s concept is any good or crock (which it perhaps is, judging from what PZ as a bilogist thinks of it) to me, a non-biologist, it looks like something having no relevance to the consistent lack or research program proposals from the ID camp. Even if Nelson’s concept were reasonable, in what way would it be based on Intelligent Design conceptul set? I see no connection.

Comment #258

Posted by Andrea Bottaro on March 26, 2004 4:25 PM (e)

Mark:
I think Paul’s goal is to develop a quantifiable “metric” for developmental complexity. Ultimately, I imagine, he would hope to show that there are “gaps” in this metric’s values that are unbridgeable by known evolutionary mechanisms. Another form of negative argumentation, I guess, but regardless, I think the approach is both so hopelessly simplistic (why would counting cell divisions from fertilized egg to new gamete tell us anything significant about complexity?) and so hopelessly complex (how is one going to be able to count cell divisions from fertilized egg to new gamete in more than a few experimental organisms?), to be ultimately useless.

Comment #259

Posted by Wesley R. Elsberry on March 26, 2004 4:26 PM (e)

Mark, it’s something that would be “evidence against evolution”, therefore it’s ID. Unless, of course, you’re pushing a lesson plan with “evidence against evolution”, in which case it’s not. Is that clear?

Comment #261

Posted by Andy Groves on March 26, 2004 4:49 PM (e)

I think the essence of Paul’s approach is to provide a metric for an organism, ideally an organism that appeared in teh Cambrian. If the number is greater than x, the organism is too complex to have evolved. If less, it’s a possibility. Quite how you find out what ‘x’ is, or whether it applies to all organisms under all circumstances is not clear….….

Andy

Comment #262

Posted by kumar on March 26, 2004 5:04 PM (e)

Given the comments cited by Dr. Myers, I suspect that Nelson et al, wish to aruge that the earliest
Cambrian fauna were as complex (using their metric) as extant fauna. Ergo, a gap too large to bridge from unicellular organisms.

Cell types though are only one measure of organismal complexity. It’s not clear why it should be the only/principal one.

In any case, ‘metrics’ for measuring the complexity of organisms is certainly not a topic that only ID’ists find unembarrassing. Consider, for example, the work of Daniel McShea–an unembarrassed evolutionist–on the (various) measures of organismal complexity.

Complexity is more complex than Nelson et al think. Again, McShea: Evolution, 56(3), 2002, pp. 441?452
A COMPLEXITY DRAIN ON CELLS IN THE EVOLUTION OF MULTICELLULARITY
DANIEL W. MCSHEA
Department of Biology, Duke University, Durham, North Carolina 27708-0338

Abstract. A hypothesis has been advanced recently predicting that, in evolution, as higher-level entities arise from associations of lower-level organisms, and as these entities acquire the ability to feed, reproduce, defend themselves,
and so on, the lower-level organisms will tend to lose much of their internal complexity (McShea 2001a). In other words, in hierarchical transitions, there is a drain on numbers of part types at the lower level. One possible rationale
is that the transfer of functional demands to the higher level renders many part types at the lower level useless, and thus their loss in evolution is favored by selection for economy. Here, a test is conducted at the cell level, comparing
numbers of part types in free-living eukaryotic cells (protists) and the cells of metazoans and land plants. Differences are significant and consistent with the hypothesis, suggesting that tests at other hierarchical levels may be worthwhile.

Comment #264

Posted by PZ Myers on March 26, 2004 5:19 PM (e)

I see no connection.

I don’t either, except for the fundamental one that unites all creationists: anti-evolutionism. He’s striving for that creationist holy grail, evidence that there really is a magical barrier that prevents the transmutation of species.

Comment #271

Posted by Loren Petrich on March 26, 2004 7:20 PM (e)

Here is a simple approximate formula for ontogenetic depth:

log(2,Ncells)

the logarithm of the number of cells to base 2 - that’s the minimum average number of divisions needed to produce each cell in an organism.

This is ~ log(2,(organism mass)/(cell mass)) ~ 3*log(2,(organism size)/(cell size))

so ontogenetic depth is hardly anything special.

Comment #272

Posted by Matt Brauer on March 26, 2004 8:04 PM (e)

Loren wrote:

Here is a simple approximate formula for ontogenetic depth:
log(2,Ncells)

Is this how Nelson represents it? It it simply a function of cell number?

If so, it implies that the larger coral reefs are more “developmentally complex” than we are, doesn’t it?

I can’t believe that that’s all there is to this.

Comment #273

Posted by PZ Myers on March 26, 2004 8:11 PM (e)

No, he implies that it incorporates number of cell types, organs, tissues, the complexity of the ontogenetic network, etc. I don’t see how, and he doesn’t explain in enough detail to understand what he’s up to. When I see C. elegans reduced to the number range 7-9, though, I immediately suspect something extremely simplistic.

Comment #276

Posted by Loren Petrich on March 26, 2004 9:09 PM (e)

An adult C. elegans nematode has 959 cells, making its cell-division number a little less than 10. Which is close to Paul Nelson’s estimate of 7-9.

Comment #281

Posted by Matt on March 27, 2004 12:57 AM (e)

Reading the ISCID transcript, it appears that Nelson says that C. elegans has 7-9 cell divisions (which is correct). I do not se where he says that this is equal to the “ontogenetic depth” of the animal, however.

(Of course, he does still claim that that value is known “with precision.)

Comment #288

Posted by PZ Myers on March 27, 2004 6:55 AM (e)

I don’t see where he states the ontogenetic depth of anything, anywhere in that paper; “7-9” was one of the few specific values he said, while making all those claims of precision and simultaneously claiming that it incorporates “ontogenetic networks” (how do you get a number for that?) and all these other aspects of the organism.

It’s very confusing.

Here is this parameter that Nelson claims is central to his ‘research program’, that is in the title of his posters and the online paper, that he makes grand claims for while telling us that it can be determined with precision, and nowhere does he explain how it is calculated. Nor does he give us even tabular examples of values. And the vague definitions he give us seem to be instances of kitchen-sinkism.

I can sympathize with the problem of quantifying complex problems in biology. I’ve got a student working on characterizing behavior in multiple strains of zebrafish; it’s not easy! But what we’ve ended up doing is using multiple tests and getting multiple values, and defining everything operationally. That’s what you have to do when working with messy complexity like that: tell people exactly how you measured it in multiple examples, so they can possibly replicate what you’ve done (and also see things you’ve missed or misinterpreted). Nelson hasn’t done any of that.

Comment #290

Posted by Paul A. Nelson on March 27, 2004 7:20 AM (e)

It’s helpful to have critical attention directed to ontogenetic depth (hereafter, OD), the “ten guinea” term (as Andy Groves dubbed it last year) for the developmental metric Marcus Ross and I are trying to articulate.

Answers to a few questions, and some clarifications:

1. The biologist in the China story is Eric Davidson of Caltech. The figure on the overhead was a diagram showing the regulatory region of the Endo16 gene in sea urchins. I was sitting on a low wall in front of the central dining hall, waiting for lunch to be served, when Davidson and his girlfriend walked up.

Davidson and I had several remarkable discussions (during and after meals, and after conference sessions), which I would like to describe – only I think the gentlemanly thing to do would be to send my write-up to Davidson first for his approval. These were, after all, largely private conversations (Davidson’s girlfriend and occasionally other meeting participants were privy to some of them). That’s why I didn’t name him when I first mentioned the incident.

By “ordinary mutation,” Davidson meant single nucleotide base-pair changes, and more generally the sort of allelic variation studied in microevolutionary analyses.

2. The dissertation advisor would didn’t know of any examples of the heritable modification of early cleavage patterns was Leigh Van Valen.

Please note the adjective: heritable – meaning stably transmissible past the F1 generation. Embryos have amazing capacities to endure pertubations, some of which PZ mentioned. But I know of no cases of the observed modification of earliest cleavage patterns in metazoans, where the change is stably transmitted to the offspring past F1. Without heritability, no evolution. PZ, if you do know of any, I’d very much appreciate learning about that.

OD is an attempt to define one dimension of a problem unsolved by neo-Darwinism, namely, how body plans arise and are modified. This problem, as PZ knows, has a distinguished lineage in evolutionary theory, although it is little understood by those who assume that macroevolution is just a whole lot of microevolution over long enough spans of time – what we might call the “village smart ass” view, as (for instance) usually presented on talk.origins, and – shamefully – rarely contradicted there by t.o. readers who perfectly well know better.

I’ll have more to say later: weekends around this house are for the kididdles, errands, and housework.

But keep the criticism coming!

Comment #291

Posted by Paul A. Nelson on March 27, 2004 7:44 AM (e)

One additional comment, about the absence of examples of heritable change in early development.

Last October, Marcus Ross and I presented a poster at the U of Chicago evo-devo meeting [“Problems with Characterizing the Protostome-Deuterostome Ancestor”]. Jason Hodin, a developmental biologist at Friday Harbor, tucked a handwritten note beneath the poster panel, objecting to our statement that body-plan disrupting mutations are not tolerated by metazoans (with the possible exception of losses of structures). He tucked a note because we missed each other at the poster session. The note said, with triple underlining, that developmental biology knows many dozens of examples of related taxa with very different ontogenetic patterns – e.g., direct and indirect developers in frogs, sea urchins, etc.

That’s true, but that wasn’t our point. There are few if any observed (rather than inferred) examples of the heritable modification of early development. If there were, Shubin and Marshall could not claim that “many of the characters that evolved during the origin of phyla are no longer able to change” (N. Shubin and C. Marshall, “Fossils, genes, and the origin of novelty,” in Deep Time [The Paleontological Society, 2000], pp. 324-340; p. 335).

The support for Shubin and Marshall’s claim is what happens to organisms when their body-plan characters are disrupted during ontogeny – as learned from Drosophila, C. elegans, etc.

I emailed Jason to see if he knew of any cases of the heritable modification of cleavage patterns, to pick a particular developmental character. Never heard back.

Comment #295

Posted by PZ Myers on March 27, 2004 8:25 AM (e)

Your request for early heritable cleavage mutants isn’t even well formed.

What do you mean by early? If you mean the first sets of blastomere cleavages, it doesn’t make sense to ask for them: in most organisms, those cleavages aren’t very specifically regulated. The reason you don’t see changes there is that in many animals it isn’t controlled in any relevant genetic sense: cells carry out orderly, frequent divisions, but their configuration is a consequence of interactions with each other, yolk cells, and membranes, not some modifiable genetic specification. There are mitotic mutations, but they mess up far more than just the early divisions.

Also, please note that any genes affecting early cleavages in most organisms are going to be maternal. Think about it.

You are basically asking for a discrete genetic mutant in an epigenetic process. It’s just weird. It doesn’t make sense.

If you want genes that kick in and act specifically on cell fates at a time when cells actually have genetically specified cell fates, yeah, we got those.

I’ve already mentioned the nematode mutants. Changes in pedigree are well known. Why did you fail to notice them?

For flies, try browsing the Interactive Fly. They’ve got lists of genes grouped by stage of activity. You can trace those back to find mutants.

In my particular field of zebrafish development, I can think of several mutants that disrupt early events in epiboly and gastrulation. Some are viable, some are maintained in the heterozygotes; all are definitely heritable. See:

Kane et al., (1996) The zebrafish epiboly mutants. Development 123:47-55.

Solnica-Krezel et al. (1996) Mutations affecting cell fates and celluar rearrangements during gastrulation in zebrafish. Development 123:67-80.

Now about that ontogenetic depth thing: how the heck do you calculate it?

Comment #298

Posted by Matt on March 27, 2004 9:10 AM (e)

I hate to make Paul feel like he’s being piled on here, but he’s failed to answer the salient question about OD: what is it?

This conversation is beginning to remind me of the scene from Seinfeld in which Elaine tries to get an editor from the New Yorker to explain why a particular cartoon is supposed to be funny.

Mr. Elinoff: Oh! yeah… That’s a rather clever jab at inter-office politics, don’t you think?
Elaine: Yeah… but why is it that the animals enjoy reading the email?
Mr. Elinoff: Well Miss Benes, cartoons are like gossamer, and one doesn’t dissect gossamer.
Elaine: Well, you don’t have to dissect if you can just tell me. Why this is suppose to be funny?
Mr. Elinoff: Ha! It’s merely a commentary on contemporary mores. (slides the magazine to her)
Elaine: But what is the comment? (she slides the magazine back to him).
Mr. Elinoff: It’s a slice of life.
Elaine: No it isn’t.
Mr. Elinoff: Pun?
Elaine: I don’t think so.
Mr Elinoff: Vorshtein?
Elaine: That’s not a word…..You have no idea what this means do you?
Mr Elinoff: No.
Elaine: Then why did you print it?
Mr. Elinoff: I liked the kitty.

Paul has claimed that he has a metric (the “OD”) that is a function of many complex variables, and that apparently quantifies the kind of cell lineage fate map that has been published for C. elegans. He further claims that this value is know “with precision” for a number of model organisms.

What he fails to reveal is how this value is calculated or whether the function is unique for a given developmental lineage. Is the function weighted more towards some variables over others? Does it truly apply to organisms whose development is not as sterotyped as elegans?

It’s really easy for a philosopher to postulate a hypothetical function of many unspecified variables. But in the real world (in the mathematics world even) the properties of this function need to be evaluated, or it might as well be a verbal model.

Let me repeat this point: unless the function has actually been defined and at least some of its properties rigorously explored, Paul would be a lot more honest to simply concede that all he has is a verbal model. The precision he claims for the OD of some organisms is not possible unless he’s done this work.

You can’t claim that your concept is “like gossamer, and one doesn’t dissect gossamer.” Nor can you simply describe it by the properties you hope it will eventually have: “it’s a function that objectively integrates all of the features of the developmental trajectory of any given organism.”

If you continue to do that, I think we’re all more that justified in asking, again: “But what is the concept?

“I liked the kitty” is not a good enough answer.

Comment #308

Posted by Frank Schmidt on March 27, 2004 12:25 PM (e)

It’s been a long time (20+ yrs) since I read Davidson’s book, but was he referring to positional information, e.g., polar substances in the egg? This was a pretty well-known phenomenon back then and in no way incompatible with the Darwinian paradigm.

Comment #333

Posted by PZ Myers on March 28, 2004 6:53 AM (e)

Note that Cosma Shalizi has posted a most excellent rebuttal to Nelson’s ideas from the perspective of evolutionary computation. He’s hampered by the same lack of specificity in Nelson’s descriptions that made it difficult for me to wrestle with it, but it’s clear that Nelson is unaware of a large and relevant literature on the topic.

Comment #368

Posted by RBH on March 28, 2004 8:27 PM (e)

I really like Shalizi’s analysis. It’s reminiscent of backpropagation in multi-layer neural nets, which was invented a few decades ago. Error evaluation is on the output of the net, and that error is propagated back through the network to alter synaptic weights that are far removed from the output. While one can explicitly evolve the weights between hidden layers with a GA, it’s not necessary in a backprop context.

RBH

Comment #398

Posted by Paul A. Nelson on March 29, 2004 6:08 AM (e)

Quick note – I’m drafting an omnibus reply (to points raised here and in Shalizi’s commentary), with title and epigraph from a Rolling Stones song. I’ll post it tomorrow.

Comment #400

Posted by Ed Brayton on March 29, 2004 6:39 AM (e)

Paul-

Thanks for the note, I look forward to reading your reply. I think it says a lot about you that you are willing to engage criticisms and take your arguments into the Lion’s den, so to speak. It’s far too easy (and far too common) for those on our side of the fence to derisively dismiss anyone on the other side of the fence as ignorant know-nothings (just as it is easy and common for those on your side of the fence to dismiss theistic evolutionists as unwitting dupes of the materialist conspiracy, or cowards, as Bill Dembski calls them, etc), but I don’t think those arguments serve anyone’s cause. We had someone leave a comment the other day that said only an idiot would support ID, and I corrected them immediately. There are certainly circumstances in which one is justified in calling another person ignorant or dishonest, and I have no trouble doing so in those situations. But to make that into a blanket statement is to argue with one’s ego instead of one’s brain.

Comment #403

Posted by Andy Groves on March 29, 2004 8:15 AM (e)

Just to add a word of support for Ed’s position.
I have exchanged e-mails on and off with Paul Nelson for over a year, read his contributions in the ISCID forums and managed to have a short chat with him at the SDB conference in Boston last year. He has always been consistently pleasant and willing to discuss his ideas in a reasonable way.

Several years ago, before I started corresponding with Paul, I accused him and Jonathan Wells of “chickening out” of an earlier SDB meeting in the talk.origins group. The very polite note I received back (explaining his absence), and his subsequent willingness to talk with me have made me rather ashamed of being so intemperate in my dismissal of his motives at that time.

I hope Paul continues to contribute here and allows us to put his ideas under the microscope.

Andy

Comment #404

Posted by PZ Myers on March 29, 2004 8:16 AM (e)

I hope the centerpiece of your reply will be a careful and thorough description of the methodology of determining ontogenetic depth.

Comment #689

Posted by PZ Myers on April 6, 2004 9:19 AM (e)

By the way, where the heck is that reply from Nelson?

Comment #716

Posted by RBH on April 6, 2004 6:50 PM (e)

Stuart Kauffman, in Origins of Order, has a discussion of cell differentiation through phylogenetic history. As I recall, he argues that the number of cell types increases as a fractional power of the number of genes. Of course, he was writing in the early ’90s; I don’t know how that estimate is affected by the recent reduction in the estimate of the number of human genes due to the Human Genome Project data and other more recent estimates of the numbers of genes in other organisms. I read Kauffman’s book quite a while ago, and won’t have time to revisit it for a while (surgery beckons), but I’ll summarize it when I can if it seems relevant here.

RBH

Comment #731

Posted by Paul A. Nelson on April 7, 2004 4:45 AM (e)

I’m lecturing at the University of Maine (Orono) today, but will try to post the reply when I return to Chicago tomorrow. It’s pretty long: I think I’ll put it up at ISCID and link from here.

Comment #732

Posted by PZ Myers on April 7, 2004 5:52 AM (e)

That section of Kauffman’s book was the weakest, as far as I’m concerned. The estimates of the numbers of cell types in different organisms are horribly, horribly poor – everyone is echoing the same ancient, flawed estimates from a few old papers. I simply don’t believe the numbers, and I don’t think rough guesses by histologists accurately reflect the number of stable cell states at all.

Comment #1306

Posted by Andy Groves on April 19, 2004 11:12 AM (e)

We’re on the edge of our barstools for that article, Paul….….

Andy
(the smooth-talking barsteward)

Comment #1318

Posted by PZ Myers on April 19, 2004 1:07 PM (e)

I think he’sh hoping we’ll get properly shtewed at the bar, and won’t notishe that he’sh shnuck out.

Ishn’t it your turn to pay for a round?

Comment #1328

Posted by Andy Groves on April 19, 2004 1:47 PM (e)

Listen, I bought my last round in the Cretaceous, and I know for a fact that some of the regulars haven’t bought a round since Devonian times…….

And in any case, I thought you were on the wagon? Or does that not include cleaning products?

Comment #1333

Posted by PZ Myers on April 19, 2004 2:14 PM (e)

Age of Fishes, that’s me. It’ll be my turn to buy again when the next metazoan phylum branches off the chordate clade.

Cleaning products? No wonder I’m blowing bubbles every time I say something.

Comment #1334

Posted by Andy Groves on April 19, 2004 2:23 PM (e)

“But it’s still a metazoan!!!”

Comment #1364

Posted by RBH on April 19, 2004 11:25 PM (e)

A couple of weeks ago Paul Nelson wrote

I’m lecturing at the University of Maine (Orono) today, but will try to post the reply when I return to Chicago tomorrow. It’s pretty long: I think I’ll put it up at ISCID and link from here.

Bump.

RBH

Comment #1526

Posted by RBH on April 26, 2004 10:46 AM (e)

On March 29 Paul Nelson wrote

Quick note – I’m drafting an omnibus reply (to points raised here and in Shalizi’s commentary), with title and epigraph from a Rolling Stones song. I’ll post it tomorrow.

Bump.

Comment #1534

Posted by Matt Brauer on April 26, 2004 2:12 PM (e)

Give the guy a break, RBH. He’s got to get his book out first.

Comment #1538

Posted by PZ Myers on April 26, 2004 2:18 PM (e)

I wonder if this is like the day-age explanation of Genesis – when Nelson says a “day”, he really means a few million years.

However long it’s going to take, I guess I won’t wait up for him.

Comment #1546

Posted by Andy Groves on April 26, 2004 3:16 PM (e)

Apparently Paul Nelson is a Young Earth Creationist (something that I have not discussed with him, but would very much like to), so when he says a day, I think we can assume he means a day….….…..

Paul? PAUL? Where aaaaaaare yoooooo….……????

Comment #1547

Posted by PZ Myers on April 26, 2004 3:21 PM (e)

Maybe he’s been raptured…? Aren’t those obdurate creationists supposedly prone to that sort of thing?

Comment #1551

Posted by Andy Groves on April 26, 2004 3:44 PM (e)

I see…… Paul Nelson goes to heaven and Bill Dembski opens a barbecue. What is this telling us?

Comment #1555

Posted by Paul A. Nelson on April 26, 2004 5:04 PM (e)

No, I’m still here. Maybe if you guys can give my out-of-state lectures for me [you know the design shtick, shouldn’t be too hard], I can finish this overly-long response.

Comment #1558

Posted by Andy Groves on April 26, 2004 5:20 PM (e)

How many lectures do you give a month? If it’s more than Paul Meyerz, we cut you a break. If it’s less, you have to clean out the monster pit at Brazos Barbecue….…. with your tongue.

Comment #1562

Posted by PZ Myers on April 26, 2004 5:31 PM (e)

Hold it, Andy – this could be fun. Can you imagine the look on their faces when people show up at the local community church for the advertised lecture on Intelligent Design by Paul Nelson, and you and/or me stroll out to the lectern and start our line of patter?

So, yeah, Paul, I’d be happy to fill in for you. My time is fairly flexible after 5 May, so just ask everyone to contact me and I’ll come out to give a talk. I bet we could even arrange for both me and Andy to give an exciting and laugh-filled tag-team roasting of Intelligent Design creationism.

Comment #1566

Posted by Andy Groves on April 26, 2004 5:40 PM (e)

OK, you’re on. I’m sure I could get my hands on some special…..erm……costumes for us, if the Sisters of Perpetual Indulgence can oblige. What’s your inside leg measurement?

Comment #1568

Posted by PZ Myers on April 26, 2004 6:04 PM (e)

10”.

Comment #1622

Posted by Andy Groves on April 27, 2004 2:32 PM (e)

I’ll put that down as “medium”, I think.

Comment #1637

Posted by Gary Hurd on April 27, 2004 9:33 PM (e)

No, I’m still here. Maybe if you guys can give my out-of-state lectures for me [you know the design shtick, shouldn’t be too hard], I can finish this overly-long response.

I have covered worse assignments. All it would take is a good anti-emetic, and a rubber chicken. I actually have both near to hand. The rubber chicken is to show the difference between something natural and something designed. For a college class, maybe I would order out, and use a rubber dick. That would add the political part of intelligent design creationism to the talk.

Comment #1672

Posted by Loren Petrich on April 29, 2004 11:05 AM (e)

Paul Nelson reminds me of something very odd. When doing an interview with an Egyptian journalist in the late 1960’s, author Gore Vidal took the time to visit the construction site of the Aswan Dam. He wanted to know how many Russians were working there, and his guide would say “We’re completely open. We’ll tell you everything you want to know.” Etc. A performance that that guide would repeat several times, while never revealing how many Russians were working on the Aswan Dam.

Source: Reflections upon a Sinking Ship

Comment #1685

Posted by Andy Groves on April 29, 2004 3:58 PM (e)

To be fair, when a manuscript is returned from a peer-reviewed journal for revision, it is common practice (in my field at least) for the journal to allow up to three months for a revised version….……

Comment #1948

Posted by RBH on May 8, 2004 2:17 PM (e)

Syntax Error: mismatched tag 'li'

Comment #1949

Posted by RBH on May 8, 2004 2:21 PM (e)

Oops. Add “cell type” to the list of “parameters” in the last paragraph.

RBH

Comment #1953

Posted by PZ Myers on May 8, 2004 6:31 PM (e)

That IDURC article is from last September, and I did cite it – it’s one of the few references to “ontogenetic depth” that you can find anywhere, and it’s damningly shallow. It starts, “One of the most powerful tools against common descent is virtually unknown: ontogenetic depth. This isn’t surprising, of course, as it is a relatively new concept.” Wrong on all counts. It is not a powerful tool of any kind, since it’s never been explained how to use it. And the reason it is unknown isn’t surprising, but Abbey’s wrong about the reason why: it’s because it is vague and useless.

Comment #2597

Posted by RBH on May 22, 2004 9:21 PM (e)

Paul wrote some time ago

Quick note – I’m drafting an omnibus reply (to points raised here and in Shalizi’s commentary), with title and epigraph from a Rolling Stones song. I’ll post it tomorrow.

Posted by: Paul A. Nelson at March 29, 2004 06:08 AM

Bump.

RBH

Comment #3427

Posted by RBH on June 5, 2004 12:08 PM (e)

Paul Nelson wrote

Quick note – I’m drafting an omnibus reply (to points raised here and in Shalizi’s commentary), with title and epigraph from a Rolling Stones song. I’ll post it tomorrow.

Posted by: Paul A. Nelson at March 29, 2004 06:08 AM

Two months plus and counting. The Rolling Stones song that seems most apropos is “(I can’t get no) Satisfaction.”

RBH

Comment #3909

Posted by RBH on June 16, 2004 1:27 PM (e)

Ontogenetic depth is beginning to spawn a literature

Concerning Richard B. Hoppe and his requests for Paul Nelson to provide support for his Intelligent Design claims about Ontogenetic Depth:

Paul Nelson’s “depth” tales sounded tall.
Richard Hoppe thought, “it’s past time to call
Nelson’s ontogenetic-
clad apologetic.”
Quoth Richard, “So where’s the beef, Paul?”

I doubt that he’ll find satisfaction,
nor even a lucid reaction.
Behind the smoke screen
there’s an ID machine
building weapons of media distraction.

A meal of Intelligent Design
when served with the fruit of divine
is lacking in beef,
which supports my belief
that it’s tripe marinating in whine.

RBH

Comment #3963

Posted by Andy Groves on June 17, 2004 8:15 PM (e)

Paul Nelson is scheduled to present a poster entitled:

Problems with characterizing the protostome-deuterostome ancestor.

at the Society for Developmental Biology meeting in Calgary this summer. I won’t be going this year, but if any Thumb readers are there, perhaps they could remind Paul he owes us a response?

Comment #3965

Posted by PZ Myers on June 17, 2004 8:25 PM (e)

Hee hee. Guess who’s going? First name starts with a “P”, middle initial “Z”, last name has some indeterminate chaotic spelling, but at least usually it starts with an “M”.

Comment #4047

Posted by Andy Groves on June 21, 2004 9:28 PM (e)

I know your little game, Penelope Zanzibar Mudd-Resstler….…..

But sheriously, say hi to Paul from me if you see him. He’s really quite amiable in person. Remind him we were having a perfectly lovely e-mail exchange until you dumped on him. Where did the love go…….?

Comment #4605

Posted by Andy Groves on July 6, 2004 3:47 PM (e)

Two months plus and counting.  The Rolling Stones song that seems most apropos is “(I can’t get no) Satisfaction.”

Make that three months…….

Paul???….……. Paul…….???? Where aaaaaare yooooooo……?

Comment #4607

Posted by Keith on July 6, 2004 3:57 PM (e)

Perhaps Paul is “in [his] basement room, with [his] needle and [his] spoon,” working on an answer …

Comment #4615

Posted by PZ Myers on July 6, 2004 5:38 PM (e)

Paul is right here. What are you talking about?

Oh. You mean that other Paul. The one who left us all hanging.

Comment #4938

Posted by RBH on July 12, 2004 12:27 PM (e)

Andy Groves wrote

Paul Nelson is scheduled to present a poster entitled:

Problems with characterizing the protostome-deuterostome ancestor.

at the Society for Developmental Biology meeting in Calgary this summer. I won’t be going this year, but if any Thumb readers are there, perhaps they could remind Paul he owes us a response?

So PZ won’t have to hunt it up:

Poster Session II MacEwan Ballroom
Tuesday, July 27, 1-3 PM

254 B29 Problems with characterizing the protostome-deuterostome ancestor. P.A. Nelson, M.R. Ross. Discovery Institute, Seattle , WA ; Univ. of Rhode Island , Kingston , RI.

RBH

Comment #13535

Posted by Paul Nelson on January 13, 2005 11:05 AM (e)

Don’t miss this paper by Azevedo et. al in the latest (13 Jan 2005) Nature. A workable (i.e., usable) measure of ontogenetic depth, maybe.

Comment #13542

Posted by PZ Myers on January 13, 2005 11:49 AM (e)

I’m working on it now.

Funny how it draws the exact opposite conclusion you did, if it is a workable measure of ontogenetic depth.

Comment #13547

Posted by Andrea Bottaro on January 13, 2005 12:07 PM (e)

Paul, dang, you’ve been scooped! ;-)

That’s actually a good paper. I don’t think it necessarily reaches the opposite conclusions as Paul, nor the same. It just shows how a serious quantitative analysis of organismal complexity, from a developmental standpoint, may look like. Nothing like ontogenetic depth (which, give Paul’s reluctance to expound on it, I now believe doesn’t even exist, beyond its catchy name).

It’s an interesting approach, but at this point I think it has limited applicability (complete genealogies of cell lineages have to be identified, which we can get for a handful of simple organisms and a few organ/systems in more complex ones). The conclusion is that developmental pathways are less complex than they seem, but more than they could be, “squeezed” between the selective pressure to simplify development and the constraints that prevent simplification.

The wider implications still escape me, though. I gotta have some grappa with this.

Comment #13561

Posted by Paul Nelson on January 13, 2005 1:05 PM (e)

Andrea, I want some grappa, too. A large goblet full, please. ;-)

Of course ontogenetic depth exists. It’s simply the distance from fertilization to reproductive capability in any metazoan. Eggs are fertilized; eventually, they develop into organisms that produce more eggs or sperm or both. The trick – the challenge – is how to measure this distance, objectively, meaning that others can do so and come up with the same number. We see the Sun in the sky. It’s out there. Now, how far away is the Sun, in terms of some objective unit? One can perceive a distance, or depth ;-) and yet not be able to measure it. Astronomers have been refining their methods since Aristarchus: “…finding the sun’s geocentric parallax is extremely difficult, and involves measurements of the most delicate and accurate kind” (Motz, Essentials of Astronomy, p. 241).

PZ, the Kusserow et al. paper in that same issue of Nature, on the Wnt gene family in anemones, looks very interesting as well.

Comment #20712

Posted by watch moi on March 17, 2005 4:49 AM (e)

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