On Evolutionary Monographs

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For some years now, we have been hearing about Paul Nelson's forthcoming monograph On Common Descent, which one assumes will stem from his now nearly seven year old PhD in philosophy Common Descent, Generative Entrenchment, and the Epistemology in Evolutionary Inference. As the DI/CSC website notes, "[h]is forthcoming monograph, On Common Descent, critically evaulates the theory of common descent, and is being edited for the series Evolutionary Monographs." The Wedge document notes:
William Dembski and Paul Nelson, two CRSC Fellows, will very soon have books published by major secular university publishers, Cambridge University Press and The University of Chicago Press, respectively. ... Nelson's book, On Common Descent, is the seventeenth book in the prestigious University of Chicago "Evolutionary Monographs" series and the first to critique neo-Darwinism.
Ignoring that the book has been in press for nearly seven years now (surely a record!), these references had been puzzling me for some while. Though trained as an evolutionary biologist, I had never read "the prestigious University of Chicago 'Evolutionary Monographs' series" and had never seen it referred to in research papers. Indeed, I had - wrongly - assumed that the Evolutionary Monographs series had something to do with the University of Chicago Press. Checking the UCP website revealed no such series. So, off to the library I went.

Read more at Stranger Fruit.

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Over at the Panda's Thumb, Paul Nelson has offered an informative reply to my post regarding On Common Descent. You may want to check it out. Read More

For some years now, we have been hearing about Paul Nelson's forthcoming monograph On Common Descent, which one assumes will stem from his now [eight] year old PhD in philosophy Common Descent, Generative Entrenchment, and the Epistemology in Evo... Read More

93 Comments

John,

The adjective “prestigious” was inserted by a long-departed publicity staffer at the Discovery Institute, as was the error about the U of C Press. Both disappeared from the Discovery webpage after Leigh Van Valen complained to me about it. As for your other gripes about Evolutionary Monographs, I don’t care about “prestige” or looks and neither does Leigh. His own journal, Evolutionary Theory, has been a simple affair since it first appeared in 1976: no fancy typesetting or binding (to keep costs down), but very provocative ideas nonetheless. Tom Frazzetta, Soren Lovtrup, Mae Wan Ho, and other rebels have published there; as I recall (need to check this), Leigh’s “Red Queen” hypothesis made its first appearance in Evolutionary Theory.

The story of On Common Descent runs as follows. Late in 1997, as I was preparing to defend my dissertation, Leigh and I were talking in his office one afternoon, and – quite unmotivated by me – he said, “You know, I could publish this” (referring to the dissertation MS as it stood at the time). The plan was then for me to revise the dissertation in the light of my committee’s comments, and to turn it in for additional editorial review.

But a funny thing happened on the way to the printer. A topic that (in 1997) was largely the province of one lonely ID philosopher of biology, namely, How would we know if the theory of universal common descent were false? began to bubble away in the literature. Carl Woese published his broadside “The universal ancestor” in PNAS in 1998, saying there never was such an organism, and then the hydrant opened. (I’ve compared trying to revise and edit On Common Descent to standing in front of a wide-open fire hose.) W. Ford Doolitle, Michael Syvanen, Elliott Sober, Malcolm Gordon (at UCLA), and others said, in major publications, “Hey, what if there never was a single Tree of Life? What then?” And the genomics revolution turned up an array of anomalies wholly unanticipated when I started on my dissertation (e.g., the appearance of widespread lateral gene transfer, and so-called ORFan sequences). Back to the computer keyboard.

All that would have been manageable, however. What really slowed me down was my finding (actually, my increasing certitude) that two widely-held theses about Common Descent were false. Moreover – I learned this in lecturing on the topic around the country and in Europe – most bench biologists were completely unprepared to rethink those theses. If I wanted those biologists to think as they were reading my monograph, and not simply react, I needed to restructure the whole argument in a way that they could follow. Back to the computer keyboard once more.

Leigh Van Valen has been very patient throughout this whole process. Others have not: I regularly receive email from people badgering me for the MS or a publication date. But as I’ve said elsewhere on this blog, I have one chance to get this right. Common Descent is not a minor theory tucked away in some quiet corner of biology. It is the geometry or topology that gives structure to what Leigh calls “the evolutionary half of biology,” and (boy have I learned this from my lecture audiences) widely identified with empirical or biological reality itself by scientists.

Discovery has been unhappy with my slow and pointedly deliberate pace: I was demoted from “Senior Fellow” to “Fellow” a couple of years ago because the monograph hadn’t yet been published. But given the choice of demotion at DI and mockery at blogs like this, versus carefully doing a good job with a rich and difficult topic, I’ll take the latter option every time. I’m trying to write something that is (a) readable (even fun), (b) biologically accurate, and (c) makes a difference to the actual practice and content of historical biology.

If readers say, “Well, that was worth waiting for,” I’ll be pleased. Anything worth doing is worth doing right.

Will ‘On Common Descent’ contain positive evidence for intelligent design?

As an aside, I take it that we can conclude that the Wedge blurb quoted above is a bit of spin in the PR war?

If the idea is valuable, if one does not wish to be dogmatic about it and one actually works against dogmatism, one may find that there are many opportunities to “get it right.” Look at Hawking. Look at Edison. Look at Darwin, whose range of writings on how things really work, from coral atolls through speciation, the workings of insectivorous plants, and the importance of worms, demonstrates that one may constantly rethink in the light of new information and more careful observation.

Linus Pauling won a Nobel in chemistry, was close to one in physiology and won a second in Peace. An interviewer once asked him what one does when one wins a Nobel. “Change fields,” Pauling said.

Get the idea out there. If it floats, it floats.

P.S. – There is a fellow Paul Nelson should be aware of at the University of Kentucky who points out that we have solid evidence that some viruses could not share common ancestors. He’s got the lab results to show it.

The difficulty is, of course, that this does nothing for intelligent design, really, and also does nothing against Darwinian evolution.

I’m trying to write something that is (a) readable (even fun), (b) biologically accurate, and (c) makes a difference to the actual practice and content of historical biology.

That’s nice.

Does your, uh, magnum opus contain a scientific theory of intelligent design, a description of how this scientific theory of intelligent design explains the origins and diversity of life, and how we can test this scientific theory of intelligent design using the scientific method?

Why not?

I can see where Paul’s difficulty lies: it starts with the conflation of “universal common descent” sensu strictu (the fact that the every extant living organism must be linearly and wholly descended through a single, identifiable genealogy from a single identifiable common ancestor), with the more general theory of common descent, which says that known life forms on this planet are the product of a mechanism of descent with modification (as opposed to, say, special creation, or continuous spontaneous generation) and therefore are related, to various degrees, to other extant and extinct organisms all the way back to the beginning of life. The latter is in fact what Darwin himself claimed his theory to be about at the end of The Origin of Species (leaving even the door open for the possibility of a few independent lineages!), and that what it still is, in its essential nutshell.

To falsify common descent (sense 1) one would just have to show some even minimal, but reproducible incongruence of gene trees, or that the organismal tree could in principle not be rooted. But of course biology has a way to confound simplistic models: Woese’s theory of a communal common ancestor and the discovery of horizontal gene transfer showed that common descent (sense 2) holds even when one includes the stage of evolution in which the concept of species and even separate organisms did not apply (which, in retrospect, was almost an inescapable necessity of the abiogenesis process - how stupid not to have thought of that, uh?), and warned us not to confound common descent of organismal lineages with common descent of genetic lineages (is that Dawkins giggling from the back of the room?).

So Paul’s difficulty now is that to falsify common descent, at this point, we would have to imagine a world very different from the one we live in: a world of organisms with many independent inheritance systems, genetic codes and biochemistries, a world that - as far as we know - does not exist. It seems almost as absurd as imagining a world in which heliocentrism, or atomic theory, could be “falsified”. There is a conclusion to be drawn from this, but Paul is not ready to draw it. So, it’s back to the computer keyboard for him, again and again.

PS: I don’t think it is fair to demand from Paul to include evidence for, or a comprehensive theory of ID in his book, that’s not what the book is about. He has already enough of a sisyphean task on his hands.

Paul’s on the right track. If it could be shown that not every single organism shared a common ancestor, the evil Darwinism would crumble. Oh wait

There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

Glad that wasn’t a decade of My life.

Three of the four comments above ask if Nelson plans to offer a theory of intelligent design in his book. It seems clear that’s not the topic of the book, and Nelson has in the past been honest about the lack of such a theory. I’m as willing as anyone to hammer ID for its lack of an actual explanatory theory (the bullshit one reads about ID being an “inference to the best explanation” is just that: vacuous bullshit), and I’ve personally fought the wars on the ground both locally and at the state level with time and money. But it’s also incumbent on us to recognize what Nelson’s object in the book is, and not badger him for not doing something else.

RBH

Well, there were only four comments when I started writing my previous comment.

RBH

Paul,

Thanks for the information. I, too, would like to echo RBH’s comment regarding folks realizing what your manuscript is - and is not - about.

I have no problem with you working on the manuscript since 1997 in an attempt to get the argument right. I guess the main gist of what I was saying was actually that On Common Descent should have been sent to another publisher - particularly if it stemmed from your UC PhD. Frankly, the appearance of your critique in Evolutionary Monographs is not likely to change anyones mind. I would also hope that you have a group of hostile peers reading what you write :)

PS: I don’t think it is fair to demand from Paul to include evidence for, or a comprehensive theory of ID in his book, that’s not what the book is about.

OK. Which ID book **IS** about that.

Oh, wait — NONE of them are.

I wonder why that would be . … .

His backpeddaling to explain why he hasn’t published yet doesn’t wash.

he could have easily published his thesis “as is”, because that’s all it frickin’ is: A THESIS!!!!

Is Paul trying to tell us he is turning his thesis into some kind of grand unification theory??

ridiculous.

if he were serious about publishing anything, he would have published his thesis, then released further articles as “new evidence” or trends appeared that affect his original conclusions.

bah.

“I’m trying to write something that is (a) readable (even fun), (b) biologically accurate, and (c) makes a difference to the actual practice and content of historical biology.”

well, i seriously doubt Paul will be able to address (b) and (c) with any degree of credibility, which leaves (a).

uh, to be “readable” one actually has to be able to READ it to begin with.

better hurry up, Paul.

As others have pointed out already, the idea that common descent should trace back to a single common ancestor rather than multiple common ancestors, is a common strawman found in ID creationist arguments (check out Salvador or the IDEA club webpages for instance). Add to this the misunderstanding of the Cambrian explosion and we notice how ID’s thesis becomes “phyla arose independently in the Cambrian” without any further explanation. Since however science is not constrained by faith, it has uncovered how phyla are related and trace back to pre-cambrian periods. While ID loves to refer to Valentine, they even have a DVD where Valentine discusses the origin of phyla, they do not represent Valentine’s position which is that the origin of phyla can be well understood in Darwinian evolutionary terms. Yet the quote mining of Valentine seems to continue. Not very original but that is all ID has to offer, a ‘critique’ of evolutionary theory based on random quotes without any coherent explanation to offer.

To amplify on Andrea Bottaro’s excellent comment (#27556)…

The notion of strong common descent from a single ancestor and without lateral transfer of genetic information is not, of course, necessary to any part of the neodarwinian modern synthesis. The essential elements are mutation, particulate inheritance, and selection among individuals within a population. As a result, the genotypes of the organisms in a population change over time.

The finding that horizontal gene transfer is an important source of evolutionary novelty means only that there is additional mechanism that can accelerate the accumulation of genotypic diversity within populations. In other words, the wheel need not always be reinvented. On one level, this is electrifying. On another, it’s not at all surprising.

The importance of horizontal gene transfer in bacteria has been clear for decades; the availability of genomic sequences has allowed the detailed exploration of horizontal transfer, but this aspect of the genomic data surprised few among those of us who were actually paying attention to microbial molecular genetics. By the time that the extent of horizontal genetic transfer in microbial populations was understood, the molecular mechanisms of these transfer events (transformation, transduction, conjugation, recombination, transposition) were pretty thoroughly understood.

To cite just one example: my dissertation advisor, Maggie So, reported the first clear case of a bacterial virulence factor on a movable DNA element in 1979 (So M. et al., The E. coli gene encoding heat stable toxin is a bacterial transposon flanked by inverted repeats of IS1. Nature 277:453-6). As it happens, this was the very first virulence factor to be cloned using recombinant DNA techniques. It soon became clear heat labile toxin, shiga toxin, and cholera toxin had all originated from a single gene that had moved into new populations by lateral transfer.

In this context, I find Nelson’s suggestion that something fundamental changed twenty years later with Woese’s 1998 paper to be strangely naive. It’s as though he’s unaware of the last forty or fifty years of work on DNA transformation, transposition, transduction, etc. (In fairness, some of the more classically-minded evolutionary biologists took too long to acquaint themselves with this literature, too; but Nelson still seems to be surprised!)

Nevertheless, we’re still dealing with the usual mechanisms of selection, mutation, gene flow and recombination, and genetic drift, all occurring within (and now to some limited but important extent, between) populations of individual organisms. It’s only the relative importance of gene flow that has changed, and it has done so in ways that would make classical neodarwinian mechanisms more, not less, efficient.

Does this somehow make invocation of a Designer more (or less) important? If it does, I’ve not seen anyone try to make that case, and I can’t see how it could be made.

Maybe that’s what is taking Nelson so long?

I agree that it is slightly unfair to ask Paul to add to his already weighty workload. However it is frustrating to see the bulk of the ID case involving attacks on Darwinism and not positive evidence for ID. Paul seems to be one of the brightest of the ID bunch; given this I personally would have like to have seen him devote his talents to pro ID (directly) rather than anti evolution (ID indirectly).

Just my 3 penneth (aka 2 cents).

PS; as a genuine suggestion, why doesn’t Paul write something a little less lengthy. Something thats conceptually the same but shorter and could be submitted to a journal like TREE.

What I find frustrating is not just ID’s refusal to offer a concrete theory. What I find equally frustrating, if not more so, is the absolute refusal of ID proponents to even develop a valid critique of Darwinism.

As I read Paul Nelson’s defense it struck me (as other posters point out) that there could very well be multiple trees and Darwinism would be expanded, not destroyed.

It also struck me that no one was ever claiming, as far as I could tell, that we were all literally descended from **one organism**. I always assumed that it was a group of organisms.

Everything I read in ID seems intent on exaggerating the minor and yet very fascinating developments in evo-devo, or mechanisms like lateral gene transfer, or endo-symbiosis to try and falsify Darwinism.

Maybe my problem is that I don’t know enough biology yet know too much philosophy of science. It strikes me that Darwinism might (and I say this speculatively) be on the verge of another synthesis of the type that occurred with the work of Haldane, Fisher, Wright, Mayr and Dobzhansky when a clear mechanism of heredity was added to Darwin’s theory of natural selection. Perhaps we are about to broaden the hard core of Darwinism (then again, perhaps not).

But if so, that does not refute Darwinism or lead to ID.

Ahh, the mischief that Thomas Kuhn has wrought…

Nelson Wrote:

And the genomics revolution turned up an array of anomalies wholly unanticipated when I started on my dissertation (e.g., the appearance of widespread lateral gene transfer, and so-called ORFan sequences). Back to the computer keyboard.

One of my committee members works on genomics and lateral gene transfer. According to her, the initial reportings of “widespread” lateral gene transfer have been discounted because the trees lacked enough resolution to detect lateral gene transfer. In other words, because taxa were often unrepresented, missing data was being reported as lateral gene transfer.

Nelson’s “work” does not seem to relate to any ID theory. Is anybody over at the DI working on an actual theory of ID? After the beatings they’ve taken, have they just given up?

What’s their position on the existence of ID “theory”? Do they say it exists, or do they say it will soon exist?

When I contacted someone in Leigh Van Valen’s department at UChicago about this monograph several years ago, they wrote back saying that a new volume in the series hadn’t been published in years, that there were certain financial problems with the journal, and that the University has forbidden any more issues to be published until these financial matters are sorted out.

I’m sure I told Paul about this when I briefly spoke with him in Boston in 2003. Has anything changed, Paul?

I don’t understand how certain viruses not having a common ancestor has any bearing on common descent. I would think that viruses WOULD NOT HAVE a common ancestor with cellular organisms of any kind, that they are a so different from prokaryotes and eukaryotes that biologists are unclear as to the validity of even calling them life forms. Viruses are very simple and utterly dependent on a more complex host to reproduce (a cell.) It seems that viruses could have, like certain organismic traits, evolved multiple times in symbiosis with different cells throughout biological history. Anyone with a biology background feel free to correct me. I may be completely wrong in my understanding.

Mark this, I’m no viral genetecist, but i’ll take a shot at it.

hmm. well as i recall, the argument might come from folks using the postion that non-lytic viral DNA can be encoded as oncogene content, which can then be normally transcripted by the host cell, and can also undergo meiotic recombination, and mutation, along with the host DNA. at any given time (depends on the trigger) the viral DNA (provided it didn’t get busted somewhere along the way, i guess) could “reactivate” and start a whole new lytic cycle of the virus again, possibly taking new mutated copies of itself, along witht the host DNA, and infect other individuals.

In theory, this could create a horizontal transmission mechanism that would complicate tracking direct lineages via DNA.

However, i don’t recall anybody publishing results indicating this in practice. I’m a bit out of the loop on that tho, as i haven’t perused the primary literature on this subject in over 15 years.

cheers

In reply to random people:

Having read Nelson’s PhD., I think it is safe to say that he is not merely trying to argue that common descent is false at the domain level – i.e., the bacteria, archaea, and eukaryotes are specially created. This position is instead held by Julie Thomas/Mike Gene.

Rather, Paul Nelson is trying to find to find a silver bullet to kill common descent arguments in general, from the domains right down to human-chimp ancestry. He started by going after “universal common descent” arguments – i.e. the issue of the near-universal genetic code, but these days he seems to be focusing on development.

(Paul, if you are listening, your only chance is if you can find a way to identify the created “kinds” rigorously and repeatably. Good luck!)

Rather, Paul Nelson is trying to find to find a silver bullet to kill common descent arguments in general, from the domains right down to human-chimp ancestry. He started by going after “universal common descent” arguments — i.e. the issue of the near-universal genetic code, but these days he seems to be focusing on development.

Does Nelson oppose the admissibility of DNA fingerprinting evidence in paternity cases? If not, at what taxonomic level does his opposition kick in?

Harq al-Ada,

I think the idea behind bringing up the lack of common ancestry of different groups of viruses (such as, off the top of my head, those represented by SV40 and tobacco mosaic virus) is that this refutes the oft-heard claim that common ancestry in and of itself is not falsifiable.

Couldn’t a virus evolve from a part of another genome, like jumping gene, if it acquires genes to encapsule itself?

hmm. well bacteria can produce plasmids to exchange DNA, in a certain sense, these plasmids could essentially be classified as viruses.

Plasmids pretty much act in the way you are implying; like “jumping genese”.

in fact, there have been several articles i see that document at least potential gene flow from genetically modified crops into local microorganisms.

one most recently in Nature:

Colin MacIlwain, “Stray seeds had antibiotic-resistance genes,” doi:10.1038/434548a, p 548 v 434, Nature, 31 Mar 2005.

I had forgotten what an interesting topic horizontal gene flow was. I hope someone who is more knowledgeable kicks in with some commentary.

sorry, here is a link to the actual article from nature i referenced:

http://www.nature.com/cgi-taf/DynaP[…]548a_fs.html

cheers

er, not that i want to take away from the topic of the thread. we could take this to “after the bar closes” if John thinks it more appropriate.

Discovery has been unhappy with my slow and pointedly deliberate pace: I was demoted from “Senior Fellow” to “Fellow” a couple of years ago because the monograph hadn’t yet been published. 

Publish or perish.…..

Heddle Clucked:

The only reason I come here is to learn some biology. But since most of what gets posted here is politics and smear campaigns, it really isn’t the best place.

Perhaps not. Do let us know when you find a more appropriate place. Oh, and don’t let the door hit you in the face on the way out!

Anyway, to get back to the discussion about the supposedly upcoming monograph from Paul Nelson. The cryptochristian movement known as ID has been around for two decades now. Several times they’ve put forth arguments which resembled garbled scientific hypotheses, with poorly defined terms (like CSI). Usually they just pick something about the results and practice of evolutionary science, and argue that it’s flawed. Rather than generate a theory to explain data, they argue for ignorance. “I don’t believe that’s ironclad,” they say, “therefore forget it, it’s worthless”. I expect Nelson’s monograph will be cut from this cloth. Maybe something like “Horizontal gene transfer really makes it hard to determine lineage, therefore common descent is not ironclad, therefore it’s worthless, forget it.”

My experience is that, even in the “social sciences,” if there is scholarship afoot, it keeps leaking into real publications.

One can look back at the medical journals in the 1980s to see how many blind paths about HIV/AIDS were pursued, especially before any virus had been explicitly implicated.

Solid science research tends to answer small questions – even if the only answer is, as Edison once lamented, to tell that a particular hypothesis didn’t work (Edison noted that the years of failure to produce a lightbulb had at least produced a list of thousands of things that would not work as a filament).

Steve, I suspect the real problem is that Nelson is not working in a a lab. The problem with the Discovery Institute is that there is no discovery there. Apologies to Gertrude Stein.

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This page contains a single entry by John M. Lynch published on April 30, 2005 10:15 PM.

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