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Date: 2007/07/15 11:06:45, Link
Author: Paul Nelson
Hi all,

Thanks for setting up this area, Wes.  I'll be in Seattle this week, and hope to set up an open forum to discussion Explore Evolution (EE) at the EE webpage.  In the interim, I'll begin consolidating criticisms of EE, so that the other authors and I can draft omnibus replies.

Looking forward to a vigorous discussion,

Paul

Date: 2007/07/15 16:21:03, Link
Author: Paul Nelson
Steve & Wes,

If you can spell out the terms of the bet, I'll take it.

Any brand of single malt, under $100 (a bottle).   :)

Date: 2007/07/17 05:18:30, Link
Author: Paul Nelson
Steve,

I'll take your wager at 40 items, but specify the terms.

Date: 2007/07/17 05:23:11, Link
Author: Paul Nelson
Afarensis,

Do you have a copy of EE?  The passage in question refers not to any claim about linear increase in size, but to the practice of depicting fossil taxa on the same scale (in illustrations), without informing the reader that the actual specimens vary considerably in size.

Date: 2007/07/17 17:32:24, Link
Author: Paul Nelson
(from Seattle)

Albatrossity,

I missed that description of P.K. Chien when reviewing the galleys, but will check with the author who drafted the section (it wasn't me).  "Marine biologist" or "biologist" would be a better term.

Sorry you won't be wagering, Steve.

Date: 2007/07/18 07:07:06, Link
Author: Paul Nelson
Afarensis wrote:

Quote
Traits characterizing the reptile/mammal transition are not based on similarity in size.


Of course.  So why not depict the fossils at their actual size, then, rather than (without telling the reader) drawing some much larger, and others much smaller?

Date: 2007/07/18 07:37:53, Link
Author: Paul Nelson
Funny thing about the reptile-mammal illustration comparison, which Afarensis and other find puzzling and irrelevant.  Several people who did not know that the fossils were being scaled (without their knowledge), to make the morphological transition appear smoother, have told me they regard this practice as objectionable.

Why weren't we shown just how different in size these groups were? they ask.

Date: 2007/07/18 07:42:22, Link
Author: Paul Nelson
Oldman,

By "actual size," I mean on the same relative scale.

Date: 2007/07/20 09:54:07, Link
Author: Paul Nelson
Afarensis wrote:

 
Quote
The morphology that was transitioning was not based on size so "smoothing" the scaling to make them look similar is irrelevant.


Right.  But if size is irrelevant to the characters involved in the transitional series, and in any case is easily modified genetically, why not just depict the fossils using the same scale (so that the relative sizes of the actual specimens is clear to the reader)?  If size doesn't matter, showing the fossils as one might see them lined up in a museum drawer shouldn't be a problem.

The accurate representation of data is important, especially when most students will never see the actual fossils in question.

JAM, can you say which quotes from the box "Coming Out of Their Shell?" you find objectionable, and why?  Also, Burke's data were interpreted by Rieppel (2001) as disproving the "correlated progression" model for turtle evolution, advanced by Kemp and others.  Rieppel writes:

   
Quote
The turtle body plan is evidently highly derived, indeed unique among tetrapods.  The problem for an evolutionary biologist is to explain these transformations in the context of a gradualistic process.  Given the recently obtained developmental evidence [Rieppel cites Burke 1989 here], the theory of "correlated progression" presents an incomplete explanation of the turtle body plan....Ribs can only be located either deep to, or superficial to, the scapula.  There are no intermediates, and there is only one way to get from one condition to the other, which is the redirection of the migration, through the embryonic body, of the precursor cells that will form the ribs.


O. Rieppel, "Turtles as hopeful monsters," BioEssays 23 (2001):987-991; pp. 990-991.

For his part, Kemp responds:

   
Quote
[Correlated progression] stands in contrast to an alternative view of the origin of turtles, expressed most recently by Rieppel (2001 [citing Burke]), that the rib-vertebrae-carapace-limb complex is too radically different from the ancestral amniote condition to have evolved gradually, but must have resulted from a macromutational event caused by a radical change in early development.  The difficulty with Rieppel's hypothesis is that it must account for how this sudden developmental change also caused what must have been simultaneous, but functionally integrated shifts in many other traits, notably the musculature, limb function, central neural control of locomotion, ventilation mechanism, dietary shift away from faunivory and so on: it is unrealistic in the extreme that any single macromutation could have such a comprehensive effect.


T.S. Kemp, "The concept of correlated progression as the basis for a model for the evolutionary origin of major new taxa," Proc. R. Soc. B. 274 (2007):16671673; pp. 1669-1670.

Date: 2007/07/20 15:57:50, Link
Author: Paul Nelson
There's no problem with scaling up or down in illustrations so that anatomical features can be seen.

Not telling the reader that one is making some skulls very much bigger, and others much smaller, however, or failing to provide the dimensions of the actual fossils -- that's problematic.  This is especially the case with extinct groups (e.g., therapsids), where the reader will have no frame of reference.

Date: 2007/07/23 14:57:58, Link
Author: Paul Nelson
Sorry to have been away from the discussion: my travel schedule has kicked in again.  I'll have only infrequent net access for the next two weeks.

I talked with Discovery and a moderation-light Explore Evolution (EE) critique board there is a live possibility.  I say "moderation-light," because the critical posts will need to address the content of EE, not my failure to publish my monograph, DI funding sources, etc.  Except for that content requirement, however, and the usual no-vulgarity stuff, the board should be totally open.

Given my travel, the board won't be operational until mid-August.  Until then, keep posting here, and I'll continue compiling criticisms.

One quick reply, about the use of quotations in scientific writing.  I agree that quoted material occurs very rarely in primary research publications.  Quotes occur frequently in science books, however: take a look, for instance, at Gould's The Structure of Evolutionary Theory, or Dawkins's The Ancestor's Tale.

I'll check back in from my hotel in Rome.

P.S. to Lenny and JAM: if you can specify terms, with a dollar cap of $1,000 and some practical way to set up an escrow account where both parties' money will be on deposit, your bet sounds very attractive.  But let's see precise terms.

Date: 2008/02/01 08:12:54, Link
Author: Paul Nelson
I sent the design detection experiment proposal to Jeff Shallit, and he said it wasn't worth doing.  I think I also sent the proposal to Wesley.  The idea was to have a large archive of bitstrings, of varying lengths, identified only by curation tags, and to ask people to pick out which strings were intelligently caused, and how they discovered that.  (I'd be happy to send the original proposal, as a pdf, to anyone who's interested: contact me at [EMAIL=nelsonpa@alumni.uchicago.edu.]nelsonpa@alumni.uchicago.edu.[/EMAIL])  Jeff's reasons for debunking the idea struck me as pretty good, although right now I can't remember which was the most compelling.

Since then, some friends have come up with a much better design detection experiment idea -- one that might actually teach us something.  One of Jeff's objections to the bitstring proposal was that the experiment would do little to move the ID debate along.  We're refining the new proposal, and then I'll send it along to Jeff for critique.

Since this is the Explore Evolution (EE) thread, here's an update.  I got no nibbles at Discovery for my suggestion, late last summer, of a moderation-free, or moderation-light, forum to discuss EE.  I've been stopping in here periodically to see if new critiques of EE have been posted, but mostly, the thread is comments about me stopping by, which -- although providing entertainment for ATBC readers -- doesn't help me much as an EE author.  But, after a very busy fall 2007 travel & lecture schedule, I've got some time in my Chicago office, so [ta da] am starting my own webpage and blog.

Yes, I know -- just what the world needs, another blog.  I'll have a sub-page there for EE discussion.  The second edition of EE should be out fairly soon, with corrections, revisions, etc.

Date: 2008/02/04 08:43:30, Link
Author: Paul Nelson
Hi Alb, and others,

Chien's description has been changed to "biologist."

The second edition corrects errors in the first, updates the bibliography, etc.  Every book contains mistakes, and EE is no exception (I hear you tittering back there).

Date: 2008/02/29 10:44:16, Link
Author: Paul Nelson
Another periodic update.  Has any participant in this thread compiled a list of specific errors (in EE) he or she wishes to discuss?  Let me know, either here or via email (nelsonpa@alumni.uchicago.edu).

Alb, I'm not quite sure what your additional questions about Paul Chien concern.  We've changed his description to "biologist," which is accurate (he's the former chairman of the Dept. of Biology at University of San Francisco, etc.).  Do you disagree with Chien's argument that, if the conditions were right for fossilizing metazoan embryos, macroscopic body fossils could also have been preserved?  I'd welcome details, or literature citations, challenging that point.

My survey of the other questions above shows mostly "when did you stop beating your wife"-type questions -- e.g., Steve Story's [Steve, have you actually read EE?] or Lenny's -- or topics where I've already given my last word (e.g., the mammal-like reptiles illustration discussion, with Afarensis).   

I'm still interested, however, in learning about specific errors in EE.  In fact, I'll provide a free review copy of the book to anyone who promises actually to read it, and to notify me of any mistakes they may find.  Please email me with your name and regular mailing address if you'd like a copy of the book.

I'll continue to stop by here daily to see what mistakes readers have found in the first edition of EE.  

Thanks.

Date: 2008/02/29 11:45:54, Link
Author: Paul Nelson
Hi Alb (David),

I've seen personally Paul Chien's SEMs of fossil embryos from Chengjiang, where for several years he did fieldwork under the supervision of paleontologist J.Y. Chen.  The degree of preservation of these embryos is astonishing (for instance, cellular structures and yolk granules are unmistakable).  Chien is qualified to express an opinion in this area.

But I agree with you that additional documentation is needed for the general point on p. 31; here's a recent paper:

Quote
We conclude that a careful interpretation of all available evidence, particularly paleontological data, presents strong evidence that most major animal lineages originated in a relatively short period of time and therefore that the Cambrian radiation represents a real and significant event in the history of life, and not some artifact of taphonomy or of a poor fossil record.


Paulyn Cartwright and Allen Collins, "Fossils and phylogenies: integrating multiple lines of evidence to investigate the origin of early major metazoan lineages," Integrative and Comparative Biology 47 (2007):744-751; p. 749, emphasis added.

We'll provide additional support from the literature for Chien's position.

Date: 2008/02/29 11:48:46, Link
Author: Paul Nelson
I just noticed that Paulyn Cartwright is in the EEB program at the U of Kansas, Lawrence.  Your neighborhood.

Date: 2008/03/01 10:10:10, Link
Author: Paul Nelson
Replies to various:

Fusilier, you requested Edge of Evolution in your PM.  I assume you want Explore Evolution?  Let me know.

Alb, I think I will contact Cartwright and Collins.  The phosphorite beds at Chengjiang that yield fossil embryos lie directly beneath the "Cambrian Explosion" (macroscopic body fossil) strata.  When I was there in 1999, I heard debate about whether those lower strata were early Cambrian or preCambrian.

Doc Bill -- I'm sorry, I missed your question about an error in EE.  Do you mind posting it again?  Thanks.

Date: 2008/03/05 10:48:11, Link
Author: Paul Nelson
Hi Alb,

I've stated my interest (above): I'm looking for evidence of specific errors in Explore Evolution.  But this thread has a tendency to wind along in tendentious directions, subject to the vagaries of those posting here. For instance:

You originally raised a concern about the description of Paul Chien, which I answered: in the second edition of EE, he will be described as a "biologist."  You then said that the real issue, actually, was relying on Chien as an authority about fossilization potential, whatever his description, and that independent support for his point about pre-Cambrian and Cambrian fossils was lacking.

However, many paleontologists reject the view (which you apparently support) that the lack of fossil evidence for the common ancestors of the "Cambrian Explosion" phyla is due to poor or incomplete sampling.  Chien argues that if fossil embryos could be preserved, in phosphorite beds lying directly below the Cambrian Explosion strata at Chengjiang -- I've seen these formations first-hand, along with Chien -- then body fossils should also be found, if they indeed existed.  This is in support of EE's general point that the missing fossils are not missing for lack of sampling.  (I'm going to contact Cartwright and Collins about this, too.)

Many leading paleontologists, with no ID position to speak of, agree:

 
Quote
Rates of evolution have varied significantly among and within branches throughout life's history, and many of the branches, large as well as small, are cryptogenetic (cannot be traced into ancestors).  Some of these gaps are surely caused by the incompleteness of the fossil record (chap. 5), but that cannot be the sole explanation for the cryptogenetic nature of some families, many invertebrate orders, all invertebrate classes, and all metazoan phyla.


James Valentine, On the Origin of Phyla (Univ. of Chicago Press, 2004), p. 35.

Does Valentine think the animal phyla share common ancestry?  Yes.  Does he think that their common ancestry is documented by fossils?  No.

Which is what Chien is saying.

I've already agreed to strengthen the literature support for this point in the second edition of EE.

One person, fusilier, took me up on my offer of a free review copy of EE.  Anyone else?

Now, if you want to argue about what you perceive as the real motivations for writing EE (Alb), or about unspecified ID fiction-writing (Doc Bill), or other such "when did you stop beating your wife" topics, sorry -- not interested.

Anyone who points out specific factual errors in EE, however, will have my full attention.

Date: 2008/03/06 09:21:04, Link
Author: Paul Nelson
Hi Alb and others,

There's not much more to say on the Chien business.  You think he's not qualified; we do.  In any case, many paleontologists agree that the absence of fossil ancestors for the Cambrian phyla is not due to poor sampling, or to the wrong conditions for fossilization, and we'll be adding significant literature support from them to the next edition.

Doc Bill -- you'll notice that I said Valentine thinks the Cambrian phyla share a common ancestor. Thus, by implication, he thinks the transitional taxa existed.  The transitions are not documented, however, in the fossil record.  "Remains unknown" -- the language you cite from chapter 5 -- is entirely consistent with the discussion in EE.

Valentine does argue, however, that the missing fossils say something about the mode of evolution at the origin of bodyplans.  That is, he regards their absence not as strictly negative evidence, but as carrying an historical signal:

 
Quote
The paucity of ancestors may well be an important bit of evidence as to the mode of evolution of body plans (Valentine and Erwin 1987).  What sort of evolutionary conditions would be least likely to produce a recognizable fossil record during the origin of a major morphological innovation?


J. Valentine, On the Origin of Phyla (Chicago, 2004), p. 188.

His answer? Soft-bodied ancestors, which entails that "each phylum that is durably skeletonized evolved its hard parts independently," although "it is not possible to dismiss the sudden appearance of novel bodyplans as resulting entirely from soft-bodied ancestral histories" (p. 188).  Bottom line: "If the Cambrian explosion is not a taphonomic artifact [our point in EE; note the noun], it must reflect some very special circumstances in life's history" (p. 189).

BTW, Doc Bill, have you read, or seen, EE?

Back to Alb.  The list of reviewers will be added to the second edition.  I'll post the names here later today (don't have the file handy at the moment).

I can't make out what you see as an error in EE's discussion of embryology.  Before we get started on that, however, may I know if you consider yourself competent to wade into the details?  I wouldn't want to begin, only to find you bailing out at some point, as you just did with paleontology, because it's not your area of interest or knowledge.

About re-packaged creationism.  Sorry, that line of argument is premised on a wholly illiberal (unsound) assumption that I don't accept (no one should accept it), namely, that teachers and students are not entitled to talk about scientific matters which may overlap with historically creationist arguments.  I encourage anyone reading this thread to follow out the implications of that position.

Here's an example to help you get started.  My grandfather, Byron Nelson (1893-1972), included illustrations and discussion in his creationist book After Its Kind, first published in 1927 -- reissued in 1995 by Ron Numbers of the Univ. of Wisconsin, in a Garland Press series -- showing fossil stasis.  Almost fifty years later -- roughly, in the mid-70s -- Gould, Eldredge, Stanley, and other evolutionary theorists began to argue that "[fossil] stasis is data," meaning that the stability through time of fossil forms is evidentially significant.

So, can teachers and students talk about fossil stasis?

Date: 2008/03/06 20:44:44, Link
Author: Paul Nelson
Here's the list of reviewers for EE (this file was on an old computer; apologies for the delay in posting).  This information will be included in the second edition; it was omitted from the first because of a production error.

Board of Reviewers, Explore Evolution

E.C. Ashby, Ph.D.
Regents’ Professor and
Distinguished Professor Emeritus
School of Chemistry & Biochemistry
Georgia Institute of Technology
Atlanta, Georgia

Daniel Ely, Ph.D.
Professor of Biology
University of Akron
Akron, Ohio

Bruce Evans, Ph.D.
Professor of Biology
Huntington University
Huntington, Indiana

W. Michael Gray
Professor and Chair
Department of Biology
Bob Jones University

David Jones, Ph.D.
Professor of Biochemistry
Grove City College
Grove City, Pennsylvania

Dean Kenyon, Ph.D.
Emeritus Professor of Biology
San Francisco State University
San Francisco, California

Scott Kinnes, Ph.D.
Professor
Departments of Biology & Chemistry
Azusa Pacific University
Azusa, California

Alan H. Linton   M.Sc., PhD.,
D.Sc., F.R.C.Path., Hon. Assoc.
R.C.V.S.
Emeritus Professor of Bacteriology
University of Bristol
United Kingdom

Pattle Pun, Ph.D.
Professor of Biology
Wheaton College
Wheaton, Illinois

John Silvius, Ph.D.
Professor of Biology
Cedarville University
Cedarville, Ohio

Robert Waltzer, Ph.D.
Associate Professor of Biology
Belhaven College
Jackson, Mississippi

William Wise, MSEd
Science Department Head & Biology Instructor
Broken Arrow South Intermediate High School
Broken Arrow, Oklahoma

Date: 2008/03/06 20:50:04, Link
Author: Paul Nelson
Steve and Jim -- same question I asked Doc Bill:

Have you actually seen, or read, Explore Evolution?

If not, I'll be happy to send you review copies, gratis.

Date: 2008/03/06 21:09:29, Link
Author: Paul Nelson
Actually, Jim -- I could deliver your copy of EE personally.  I'll be lecturing (with Angus Menuge) at the University of Wisconsin-Milwaukee, on April 1, 2008.  Kenosha isn't that far away...

Alb, if you have a copy of Donald Prothero's new textbook from Columbia Univ. Press, Evolution: What the Fossils Say and Why It Matters (2007), take a look at p. 110.  I'll post more about the use of Haeckel's embryos in biology textbooks tomorrow.

Date: 2008/03/06 21:13:02, Link
Author: Paul Nelson
Steve,

Have you personally read the book?

Date: 2008/03/06 21:37:50, Link
Author: Paul Nelson
Steve,

I scrolled through the thread, and I can't find any discussion of the actual contents of EE from you.  Lots of stuff from Lenny, Alb, and others.

But nothing from you.  Can you point me to the questions you raised, based on your own reading of EE?

Date: 2008/03/06 21:58:15, Link
Author: Paul Nelson
So you'd stand by Lenny's specific critiques -- i.e., endorse them as representing your own position, since you've read the book and agree with Lenny's assessment of the contents?

I ask because I'll be referring to particular discussions in EE over the next few days, and am interested in your view, given that Lenny is no longer participating in the thread.

Date: 2008/03/07 12:23:06, Link
Author: Paul Nelson
As most of the participants in this thread want to talk about EE as “repackaged creationism,” “warmed-over creationism,” "creationism redux" -- let’s call this “refried creationism,” or RC for short -- I’ve tried to draft a concise argument expressing the RC criticism as identifying a serious error in EE.  How about this:

1.  Topic A has been discussed in creationist writings, either historically or currently.

2.  Thus, topic A is not material fit for a public school science textbook.

That can’t be what RC entails, however.  A creationist textbook may give a perfectly accurate description of (say) the mechanisms of photosynthesis, yet one wouldn’t want to exclude photosynthesis from teaching materials or classroom discussion on those grounds.

So, on the assumption that there’s more to RC than (1) & (2), can someone here express the “refried creationism” criticism succinctly, in a short propositional form (i.e., as an argument) explaining why scientific topics that may have been discussed in creationist writings are nevertheless illegitimate material for science instruction?

Thanks.  I'd also value the comments of anyone on whatever formulations of RC are posted.

Date: 2008/03/07 12:52:02, Link
Author: Paul Nelson
Alb,

Let's take a specific example to focus the discussion.  Suppose Topic A is stasis of form (either in fossil lineages, or from fossil-to-extant taxa), which I mentioned above.

Page 25 of EE illustrates this phenomenon or pattern with nautiloids, comb jellies, and ginkgo leaves.  My grandfather's creationist book After Its Kind featured many similar illustrations.

But here in my office I also have Eldredge and Stanley's classic monograph Living Fossils (Springer, 1984), and papers are published all the time in the primary literature on stasis and living fossils.

So, is the topic "What is stasis of form, and what might it mean for understanding of the history of life?" a fit topic for a public school biology textbook?

I hope, since you're thinking about this, that you could express your view of "refried creationism" (RC) in succinct propositional form, with the premises numbered or clearly distinguished -- helps in the discussion.

Date: 2008/03/07 12:57:24, Link
Author: Paul Nelson
Leftfield wrote:

Quote
I think step 1A in the RC argument is that the creationist perspective on topic A is not supported by any peer-reviewed scientific publications.


Well, that's where RC becomes problematic, as I think Alb and the other professional biologists reading this thread know.

I appreciate the amplification.  We'll come to to the peer-reviewed business further on, I expect.

Date: 2008/03/07 13:33:45, Link
Author: Paul Nelson
Venus,

Is it morally wrong to evaluate current theories of evolution, in the light of the available evidence?

Before you answer, try this experiment, without using Google or other search engines to identify the source and author. Read the following passage, and ask yourself whether you'd allow this material in a public school science classroom, strictly in terms of its content.  Lay aside for the moment the identity of the author, his/her theoretical commitments, and the publication venue:

 
Quote
The popular theory of evolution is the modern synthesis (neo-Darwinism), based on changes in populations underpinned by the mathematics of allelic variation and driven by natural selection.  It accounts more for adaptive changes in the colouration of moths, than in explaining why there are moths at all.  This theory does not predict why there were only 50 or so modal body plans, nor does it provide a basis for rapid, large scale innovations.  It lacks significant connection with embryogenesis and hence there is no nexus to the evolution of form.  It fails to address the question of why the anatomical gaps between phyla are no wider today than they were at their Cambrian appearance.

Date: 2008/03/07 14:45:48, Link
Author: Paul Nelson
Alb asked,

 
Quote
What about the problem with the statement in EE about Haeckel's embryos, for example?


We’re juggling relative terms -– “many” versus “some” versus “a few” textbooks have used Haeckel's drawings, or derivatives of them.  I don’t know what textbooks you have in your office.  Are any of them in this brief survey?

http://www.discovery.org/a/3935

Donald Prothero just re-published the Romanes 1910 figure, based on Haeckel, although he attributes the material to von Baer; he also supports the validity of ontogeny recapitulating phylogeny.  So use of the drawings persists.

What needs to be done -– and we’ve haven’t done it -– is a thorough (exhaustive) survey of high school and college textbooks, so that actual frequency of usage of Haeckel-derived drawings, and their context, can be determined.  The document I linked to provides a start, but it’s not exhaustive.

I could see changing “many” (on p. 69) to “some,” but I’d have to persuade my co-authors.

Date: 2008/03/07 14:56:59, Link
Author: Paul Nelson
Alb,

Thanks for this formulation:

 
Quote
1.  Topic A has been discussed in creationist writings, either historically or currently.

2. Topic A has been shown to be a quote-mine, a strawman, easily accommodated by modern evolutionary theory, or otherwise non-controversial in the minds of modern evolutionary biologists.

3. No new data relevant to Topic A, either casting new doubt on modern evolutionary theory or that is unable to be accommodated by modern evolutionary theory, has been provided by competent scientists and published in the peer-reviewed mainstream scientific literature.

4.  Thus, topic A is not material fit for a public school science textbook.


"Quote-mine," "strawman," and "easily accomodated" leave considerable room for debate, of course (but that's OK -- debate makes life interesting); in any case, I accept this as grounds for ongoing discussion.

Venus, the author of that passage was evolutionary geneticist George Miklos, from his long paper "Emergence of organizational complexities during metazoan evolution: perspectives from molecular biology, palaeontology and neo-Darwinism," Memoirs of the Association of Australasian Palaeontologists 15 (1993):7-41.  The cited material comprises the first five sentences of the paper's abstract.

I'll be out for the remainder of the day, but will try to return to the discussion tomorrow morning.  Thanks to all involved for the exchange.

Date: 2008/03/10 10:50:29, Link
Author: Paul Nelson
Alb,

Thanks for posting the link to my UD article.

Do you think Prothero should have reprinted the Romanes / Haeckel drawings?

Date: 2008/03/10 11:15:54, Link
Author: Paul Nelson
I'll be responding to JAM's objection about the genetics of body size next.

Jim Wynne and Alb asked about why the Debate page at the Explore Evolution website was inactive.  Short version: I wanted a discussion board there, like this one, with no (or only light -- e.g., no vulgarity) moderation.  Others disagreed, and there the issue has stalled.  Given however that the work of responding to critics would probably fall largely (or entirely) to me, as it has in this thread, I decided to continue participating here until my own webpage, www.bioadagio.com, is active.

Once www.bioadagio is up, there will be a separate page there for open, unmoderated discussion of Explore Evolution.

Date: 2008/03/10 20:06:07, Link
Author: Paul Nelson
Alb,

If the evidence shows that only a small percentage of textbooks use Haeckel-derived figures, I'll urge that we change "many" to "a few."

Tracy, Prothero's term "well-developed gills" is a character found in adult fish (and some amphibians).  The term "fish-like," which Prothero repeatedly uses, refers to fish -- again, the morphological standard of comparison is an adult organism, not an embryo.  This is classical Haeckelian recapitulation, and not von Baer's view at all.

Prothero's caption reads:

 
Quote
As embryologist Karl Ernst von Baer pointed out in the 1830s, long before Darwin published his ideas about evolution, all vertebrates start out with a very fish-like body plan in embryology, including the predecessors of gills and a long tail.  As they develop, many lose their fish-like features on their way to becoming reptiles, birds, and mammals.


This is wrong on multiple counts.  Von Baer did not think that embryos passed through stages that resembled (as "fish-like" implies) the adults of other species.  In fact, the fourth of his laws explicitly denies this; von Baer rejected the common ancestry of the animals.  And "starts out" is false: the stage (mis)represented in the Prothero figure is actually well into vertebrate development.  Egg sizes, cleavage patterns, and modes of gastrulation are profoundly different within the vertebrates.

The new edition of Explore Evolution will include significantly expanded bibliographic resources on the relationship of embryological evidence to theories of common ancestry.

More tomorrow, on JAM's genetics of body size question.

Date: 2008/03/10 20:09:12, Link
Author: Paul Nelson
Afarensis,

I'll send you a pdf of that paper by Richardson, along with his more recent work, if you can give me an email address to use.

Date: 2008/03/13 08:59:09, Link
Author: Paul Nelson
Replies to various,

Gary,

I apologize: I thought you were joking, given the "No, I don't wanna read yer stinkin' book!" reactions of some others here. Please send me a PM with your mailing address.

Seussical reaction to the offer of a free copy of EE:

"I will not read it in a bar,
I will not read it in a car,
I will not read it here or there,
I will not read it anywhere,
I do not want yer stinkin' book,
and as far as I'm concerned,
you're a complete idiot."

Sorry, couldn't rhyme that last bit. ;-)

The offer of a free copy of EE continues for anyone else, of course, including those who previously responded seussically.

JAM -- still collecting data on body size.  The issue has turned out to be far more interesting than I could have guessed.

Doc Bill -- why turtles?  Why not?  Turtles are cool.  Here's the bigger point (sorry, JAM, can't help myself), from a recent survey by Massimo Pigliucci:

   
Quote
Is There Something Missing from the Modern Synthesis?

...

What, then, is the problem?  Without trivializing the great successes of evo-devo, it is hard to escape the feeling that we are making significant progress in understanding relatively circumscribed problems in the origin of form [he mentions butterfly eye-spots], and that advances are being made more at the interface between population genetics and developmental biology than in the broader field of evo-devo.  For instance, baffling evolutionary novelties like the turtle carapace remain almost unscathed mysteries, with some speculation concerning their origin, but little in the way of detailed scenarios and solid empirical evidence (Rieppel 2001; Cebra-Thomas et al. 2005).  In some sense, this is precisely the same sort of problem that bothered Goldschmidt so much during the shaping of the MS [Modern Synthesis], and although his proposed solutions (genomic mutations and hopeful monsters) are not tenable, the uneasy feeling that we are not yet tackling the big questions remains.


Massimo Pigliucci, "Do we need an extended evolutionary synthesis?" Evolution 61 (2007):2743-2749; p. 2745, emphasis added.

If it is possible that (a) turtles share common ancestry with other reptiles, then it is also possible that (b) they do not.  If one denies the possibility of (b), however, (a) becomes a necessary truth, and impossible to test (because it will be the case, come what may).  The proposition of evolutionary theory, "turtles evolved from unknown reptilian ancestors" would then no longer be empirical, i.e., subject to the testimony of evidence, because no data could count against it.

Erasmus, moths exist to provide employment for entomologists, naturally.  Also to flutter around candles and camping lanterns during the summer. :)

Date: 2008/03/20 09:23:02, Link
Author: Paul Nelson
Another update --

I have three weeks of travel coming up, starting tomorrow (South Carolina & then Brazil), but I'll try to check in here periodically. I'm continuing to work on JAM's question about body size, which has resolved itself into two sub-questions (a) how does one infer the genetic basis of traits for extinct taxa? and (b) what is the relevance of variation under domestication to possible ranges of variation for extinct or natural (i.e., not domesticated) groups?

Question for Wesley: what do you see as the canonical formulation (by Eldredge and Gould) of punctuated equilibria?  Do you see any contradictions, or simply changes of emphasis, between their 1972, 1977, and subsequent (e.g., 1993) papers?

Alb, a semi-biggish favor: would you mind sending me the complete list of textbooks you've examined, in re Haeckel's embryos? Please indicate title, authors, date of publication, level [e.g., high school, college introductory, college advanced], brief description of content on embryology as evidence for common descent, and anything else you think bears on the matter.  Thanks.  As described, that's actually a BIG favor, but I'd greatly appreciate the information.  Email: nelsonpa@alumni.uchicago.edu

Date: 2008/04/16 08:25:42, Link
Author: Paul Nelson
Hello all,

I'm back from Brazil, and catching up with stuff.  Thanks to Alb for his hard work on the textbooks and Haeckel business -- much appreciated.  I'm doing my own additional survey using the textbook collection at the Univ. of Chicago science library.  Gary, please let me know when your copy of EE arrives (it's being sent from Seattle), and I apologize for any delays in the shipping.

I have some media appearances to do here in Chicago for Expelled, but after the film opens on Friday, life should quiet down a bit and I can rejoin the EE festival here.

Date: 2008/04/22 11:25:28, Link
Author: Paul Nelson
Hi, Alb.

Question for JAM, if he's still reading this thread -- does he have (know) any data on size variation in wild canid populations?

Date: 2008/04/23 10:40:20, Link
Author: Paul Nelson
Alb said,

Quote
Don't you think you could answer some of them, rather than just ask questions of your own and pretend that ours don't exist?


Here's a quick recap.  JAM cited a paper from Science in support of his question to me about the genetic basis of size differences.  The paper concerned variation in dogs.  I read it, thought about it, and wondered about a couple of things:

1.  How do we determine the genetics of size differences for extinct taxa?  The original context of JAM's question involved scaling illustrations of the mammal-like reptile transition.

2.  The variation in canids was in domesticated, not wild, populations.  Hence I wondered if JAM had additional data about size variation in natural populations, because I think there are important (evidentially relevant) differences between domesticated and wild populations, with respect to evolution.

So my question to JAM stems from trying to follow up his question to me.

Date: 2008/04/25 08:53:14, Link
Author: Paul Nelson
JAM wrote:

Quote
The answer is that since we know that the underlying molecular mechanisms are incredibly conserved, it's not a problem.


This assumes the point at issue.  To wit: We already know the mammal-like reptiles are related by descent with modification, via the natural selection of randomly-arising variation (or an array of unknown evolutionary mechanisms, if selection does not suffice).  Therefore their size differences are easy to explain.

What independent evidence do you have for the molecular mechanisms (regulating body size) at work in the extinct groups -- therapsids, etc. -- featured in the reptile-to-mammal sequence?

In what natural populations of canids, JAM, do we observe size differences on the scale seen in domesticated dogs?

Date: 2008/07/03 09:55:02, Link
Author: Paul Nelson
Hi Alb,

Bob Richards, the author of the Haeckel biography, served on my dissertation committee at the U of C.  I was a member of his graduate seminar on Haeckel, 1989-90, and more recently have exchanged correspondence with him about Haeckel's diagrams.

I didn't realize The Tragic Sense of Life was out, however.  (I've read some of the chapter drafts.)  Thanks for the tip -- I'll have to order a copy.  And I would be interested in seeing your review for Choice.

Date: 2008/07/10 00:39:34, Link
Author: Paul Nelson
Hi Gary,

Morse Peckham's variorum edition of the Origin shows "by the Creator" added by Darwin in two places (both in reference to the origin of life, after the verb "breathed").  This addition occurs, if I recall correctly -- don't have the book with me at the moment (I'm in Oxford at a conference) -- in the second, not the sixth, edition, and is retained by Darwin from the second ed. forward.  (He did grumble in private correspondence about making the addition, but never took it out.)

Alb, my copy of The Tragic Sense of Life arrived.  We'll be citing it in the new edition of Explore Evolution.

 

 

 

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