Woese, the Darwinian Threshold and Intelligent Design

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Intelligent Design Creationists like Bill Dembski have argued that Woese’s work contradicts evolutionary theory or more specifically common descent and Darwinian theory. See for instance “Woese: Life could have started “millions of times”” or this old posting of mine.

Since many creationists have come to misunderstand Woese’s arguments, the impact on Darwinian evolutionary theory, let’s start exploring Woese’s argument

Dembski’s article which references (and fully reproduces) an article by Ronald Kotulak claims that Woese commented in 2002 that life could have started “millions of times”, a statement I have not been able to track back to his scholarly work.

The 2002 paper is likely: Carl Woese On the evolution of cells PNAS June 25, 2002 vol. 99 no. 13 8742-8747

Woese recognizes a pre-Darwinian period, a Darwinian threshold and a Darwinian period. In the pre-Darwinian period massive horizontal gene transfer made it impossible for individual species to evolve however the Darwinian processes of “amplification, variation and selection” still played a role (See for instance “Gene duplication and other evolutionary strategies: from the RNA world to the future” by Jürgen Brosius published in Journal of Structural and Functional Genomics 3: 1–17, 2003).

In other words, pre-Darwinian referred to a period in which speciation was impossible, not a period in which the Darwinian processes did not play a role. From this gene pool, Woese believes that the three Kingdoms arose.

As Woese reminds us in “Evolving Biological Organization” that first of all Darwin’s theory did not depend on common descent

There was never a universal common ancestor. The Doctrine of Common Descent has deceived us. But we are deceived, too, if we think Darwin is responsible for this doctrine. Yes, Darwin did conjecture that “all the organic beings which have ever lived on this earth may be descended from some one primordial form,” but in the same discussion,he said: “this inference … is chiefly grounded on analogy and it is immaterial whether or not it be accepted. No doubt it is possible … that at the first commencement of life many different forms were evolved.”

Furthermore, there still exists a universal tree, however its roots start at the Darwinian threshold, not at the beginning of life.

The root of the universal tree denotes the beginning of this transition phase. The tree’s root denotes the point at which the first of the cell designs crosses its Darwinian threshold.

Both from: Evolving Biological Organization CARL R. WOESE published in “Microbial Phylogeny and Evolution: Concepts and Controversies” by Jan Sapp - Science

This is yet another good example of how it pays off to check the primary sources.

Woese himself has corrected Intelligent Design Creationists’ claims before as I outlined in Icons of ID: Carl Woese the final word?

Woese scoffs at Meyer’s claim when I call to ask him about the paper. “To say that my criticism of Darwinists says that evolutionists have no clothes,” Woese says, “is like saying that Einstein is criticizing Newton, therefore Newtonian physics is wrong.” Debates about evolution’s mechanisms, he continues, don’t amount to challenges to the theory. And intelligent design “is not science. It makes no predictions and doesn’t offer any explanation whatsoever, except for ‘God did it.’” Ratcliffe as quoted by PZ Myers

Similarly to Meyers, Dembski also made claims about Woese that are erroneous

Dembski argues that in a 2002 paper Woese rejects common descent

There is a question about the extent of evolution, but that is a question being raised by non-ID scientists. Carl Woese in the Proceedings of the National Academy of Sciences just a few weeks ago published a piece where he explicitly rejects common descent. What ID proponents want is to teach is the evidence for evolution as well as whatever evidence places limits on evolutionary change (like Carl Woese’s idea of lateral gene transfer). Scott and Branch are here merely playing on fears of school boards and educators. Dembski in “Darwin’s Predictable Defenders”

I reported on this on September 26, 2004 and yet in 2006, Dembski’s posting suggests that he has learned little.

For those interested in exploring this issue further, I point you to a recording by Radiolab first aired on March 14, 2008. (Radiolab is an excellent resource btw for people interested in fascinating science topics. The same show has a fascinating topic on Chimeras, including a woman whose sons were not related to her but were related to her husband, and Geeps, the real story about Goat/Sheep chimeras.)

Steve Strogatz, an applied mathematician at Cornell, tells us about a radical theory that says that way back at the beginning of life, 3 billion years ago, life was a big commune of gene swapping. Nigel Goldenfeld, one of the scientists who came up with this theory, says that the idea of different species, and consequently Darwinian evolution, simply didn’t apply for the first billion years of life on Earth.

In other words, speciation did not happen although all the Darwinian mechanisms were still present and playing an important role. Read more about Carl Woese and Nigel Goldenfeld’s Essay About Gene Swapping and Early Life

Its special role in any form of life leads inexorably to the rather striking prediction that early life must have evolved in an inherently Lamarckian way, with vertical descent marginalised by the more powerful early forms of HGT[23]. Such gradual refinement through the horizontal sharing of genetic innovations would have led to the generation of a combinatorial explosion of genetic novelty, until the level of complexity, as exemplified perhaps by the multiple levels of regulation, required a transition to the present era of vertical evolution. Thus, we regard as rather regrettable the conventional concatenation of Darwin’s name with evolution, because there are other modalities that must be entertained and which we regard as mandatory during the course of evolutionary time.

Even Richard von Sternberg seems to have been confused by Woese’s arguments

You have leaders in the field like W. Ford Doolittle presenting evidence that there is no “Tree of Life” but, instead, a complex web of gene sharing. Likewise, Carl Woese, one of the fathers of molecular phylogenetics, thinks the data support multiple, independent origins of organisms—that the notion of a Universal Common Ancestor is erroneous. Then again, evolutionary developmental biologists like Stuart Newman have performed experiments that suggest that animal body plans originated before genomes to “encode” them. I know it sounds radical, but he and other leaders in the field of “evo-devo” think that genes support development, but they don’t provide the blueprint. Embryos self- organize, and genes provide the building materials. Finally, even the specter of Lamarck has reappeared. Lamarck’s idea was, of course, that acquired traits can be passed on to offspring. None other than “Darwin Day” organizer Massimo Pigliucci is giving second thought to Lamarckism—after all, he notes, Darwin was a Lamarck

Source: Sternber South Carolina Talk

Of course, none of the above mentioned work has ANY relevance to ID which remains powerless in explaining anything in biology.

Carl Woese Interpreting the universal phylogenetic tree. Proc Natl Acad Sci U S A. 2000 Jul 18;97(15):8392-6.

C. R. Woese A New Biology for a New Century Microbiol. Mol. Biol. Rev., June 1, 2004; 68(2): 173 - 186.

Creationist responses

Behe is not impressed what better endorsement.

Bill Dembski’s Review of Darwin’s Gift to Science and Religion. By Francisco J. Ayala. Washington, DC: Joseph Henry Press, 2007. ISBN-13 978-0-309-10231-5. US$24.95.

For instance, he cites a 2000 article by molecular phylogenetics pioneer Carl Woese, claiming that Woese’s research supports common descent (81). Yet Woese’s most recent work casts doubt on common descent by arguing for multiple origins of life (“Collective Evolution and the Genetic Code,” PNAS, 2006).

6 Comments

If no one has done it yet, consider this a direct question for every DI fellow. If they are serious about ID being science, I would expect at least a few of them to show up right here and offer their personal answers to these questions (and debate their internal differences if any):

1. Do Woese’s conclusions support a 6-day Creation model (old or young Earth version)?

2. Do Woese’s conclusions support concluding that the human lineage originated independently of all the others, as in a unique life-from-nonliving matter event?

Given the level of sophistication of these massive HGT models for early epochs of evolution, is it even possible for someone who continues to be willfully ignorant of basic evolutionary theory to comment/quote these authors correctly?

JGB:

Given the level of sophistication of these massive HGT models for early epochs of evolution, is it even possible for someone who continues to be willfully ignorant of basic evolutionary theory to comment/quote these authors correctly?

In my opinion? Not really. But then again that has never stopped them before. They misuse and misrepresent the scientific work of others constantly as it is so why would they stop now? Even when it is clear to people who do actually know the scientific literature that many of the Creationists are either deliberately misrepresenting others work or are simply in way over their heads.

Another useful historical lesson for recent PT arrivals such as I. And rather timely considering the recent re-creo-action on Woese’s work.

Dembski’s article which references (and fully reproduces) an article by Ronald Kotulak

But this indicates that the last part of the article, with a timeline of cosmology, astronomy and evolutionary history, was dropped. That would be logical as dating is considered farting in the Big Tent.

And really, what would a creationist post be without the obligatory quote-mine?

WD Wrote:

Woese says No — life could have started “millions of times,” and no single cell was ancestral to all organisms on Earth.

Why would the demarcation line between non-cellular and cellular designs or between pre-Darwinian and Darwinian systems be any more resolvable as other demarcation between species? IANAB but I don’t see the fixation to the idea of a first cell as opposed to a first separation of populations into individual species. The quote of Woese leaves that open (“the first of the cell designs”) regardless of Dembski’s claims.

Btw, reflecting on Woese’s bush I saw this paper (with a series of supporting ones) where it seems constraint analysis on structural features of tRNA may tentatively root a bush and belabor on the pre-Darwinian/Darwinian path. It arrives at Woese’s Archaea as root, and Bacteria as a more recent split from Eukarya:

Constraining molecules from Eukarya and Bacteria into a monophyletic group [constraint (EB)] was the most parsimonious solution and was consistent with an early split of two ancient lineages, one of archaeal origin and the other of eukaryal-bacterial origin. When forcing molecules from two of the three superkingdoms individually and as a group into monophyly, the Eukarya and Archaea dichotomy [constraint ((E)(A))] was most parsimonious. This suggests the earliest two superkingdoms to diversify were Eukarya and Archaea. The S values for these constraints indicated that their diversification always preceded the onset of Bacteria. […]

We also explored the origins of viruses by constraining molecules from each individual superkingdom or viruses into monophyletic groups, together [e.g., (AV)] or separately [e.g., ((A)(V))] (Table 2). The most parsimonious scenario always linked the origins of viruses to the archaeal lineage, with S values matching those defining the organismal timeline (Figure 2). […]

Our evolutionary timeline is also remarkable in that it identifies three epochs in the evolution of the organismal world that were analogous to those proposed earlier [16]: (1) an architectural diversification epoch in which tRNA molecules diversified their structural repertoires (light green areas in Figure 2), (2) a superkingdom specification epoch in which tRNA molecules sorted in emerging lineages that specified superkingdoms Archaea, Bacteria, and Eukarya (salmon areas), and (3) an organismal diversification epoch that started when all tRNA coalesced in each superkingdom (light yellow areas).

I guess my layman question to Demsbki would be - if dominating HGT is “a big stumbling block in classical evolution”, how come evolutionary methods result in timelines with relationships and epochs between lineages and their coalescence (Figure 2)?

Sternberg conveniently leaves out that W. Ford Doolittle most certainly accepts a standard ‘tree’ of life for animals (including humans, of course). I heard him say this himself two weeks ago at an evolution conference at Rockefeller (http://www.rockefeller.edu/evolution/). It’s only near the base that you get the ‘network’ topology overwhelming the ‘tree’. Needless to say, he was by no means denying that evolution happens, or asserting that Intelligent Design is its engine.

Btw, one thing that came through strongly at the conference, was that several of the speakers there were not particularly enamoured of Woese’s ‘three kingdoms’ model…to put it mildly.

Life’s Chirality And Circadian Rhythm, Evidence Of Updated Darwinian Evolution (a recompilation)

A. Updated life’s concepts:

http://www.the-scientist.com/commun[…]122.page#423

- Earth life consists of three strata: genes are primal organisms, genomes are evolved 2nd stratum organisms, and cellular organisms are evolved 3rd stratum.

- Life’s evolution started at genesis.

- Life’s evolution is not random. It is biased, driven by culture.

B. Earliest evidences of updated Darwinian evolution:

- Life’s chirality http://www.the-scientist.com/commun[…]122.page#387 http://www.physforum.com/index.php?[…]#entry327715 - Circadian rhythm

http://forum.physorg.com/index.php?[…]#entry301299

Suggesting,

Dov Henis http://blog.360.yahoo.com/blog-P81p[…]BbHgtjQjxG_Q–?cq=1

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This page contains a single entry by PvM published on March 11, 2008 7:07 PM.

NY Times: Expelled from “Expelled”? was the previous entry in this blog.

University of Iowa: public lecture on “Evolution, Intelligent Design and Faith” on March 25. is the next entry in this blog.

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