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Monophyly vs. Polyphyly and Christian Schwabe

One theme of Explore Evolution (EE) addresses differing views among evolutionary biologists about Darwin's Tree of Life, i.e., the theory of the universal common ancestry of all organisms on Earth: more precisely, the monophyly of terrestrial life, rooted in the Last Universal Common Ancestor, or LUCA. While the majority position within evolutionary biology endorses monophyly, a growing minority of workers argue for multiple independent origins, or polyphyly (see below). It's an important controversy, well worth the attention of textbooks.

But John Timmer accuses EE of a "bait-and-switch" move in describing this controversy. By "lumping...together in a single footnote" several scientists with very different views about the overall pattern of life's history, he argues, EE tries for "borrowed credibility," misleading its readers about the true outlines of the current monophyly versus polyphyly debate.

Timmer is particularly exercised by EE's inclusion of the ideas of Professor Christian Schwabe of the Medical University of South Carolina, whose publications he calls "borderline deranged." Given the space Timmer uses to criticize Schwabe, one might think that the latter's ideas receive significant attention in EE.

No, actually: the book mentions Schwabe exactly once, in a single footnote (which cites three of his papers). Timmer claims that EE lumps Schwabe together with other, better-known scientists, such as National Academy of Sciences member Carl Woese, as advocates of the polyphyletic view, without informing the reader about the different number of separate origins postulated by their respective theories.

But here is the actual EE footnote (p. 11):

Scientists who support a polyphyletic view differ on how many trees one should expect to find in the "orchard" of life. Some, such as microbiologist Carl Woese of the University of Illinois, argue that life on earth is descended "not from one, but from three distinctly different cell types" ("On the evolution of cells," Proceedings of the National Academy of Sciences 99 (2002):8742- 77; 8746). Others, including Malcolm Gordon of UCLA and Christian Schwabe of the Medical University of South Carolina, think there might be a greater number of separate trees.

And that's it. No misdirection or lumping: Woese says three independent origins; Schwabe and Gordon say more. Anyone who reads the EE footnote should grasp that scientific opinions about polyphyly differ.

Let's go back, however, to Timmer's charitable label for Schwabe, "borderline deranged," as it gives us our first opportunity to address the catechism versus data dilemma in more depth.

Timmer acknowledges that "every couple of years, [Schwabe] publishes a paper in which he argues in favor" of his "borderline deranged" ideas. These, however, "are not scientific controversies," Timmer claims, but "actually opinions that have barely registered within the wider scientific community."

Really? To see how Schwabe's research raises challenges to monophyly and universal common ancestry, consider this excerpt from one of his papers cited in EE:

Against this background of high variability between relaxins from purportedly closely related species, the relaxins of pig and whale are all but identical. The molecules derived from rats, guinea pigs, man and pigs are as distant from each other (approximately 55%) as all are from the elasmobranch's [shark's] relaxin. ... Insulin, however, brings man and pig phylogenetically closer together than chimpanzee and man. (Schwabe 1994, 171-2)

According to Timmer's catechism, however, none of this is worth talking about, because Schwabe's ideas are just too crazy for serious consideration.

But someone forgot to tell journal editors and referees. Schwabe's "deranged" ideas--coming from a tenured professor of biochemistry, and based in part on the puzzling features of relaxin (not "reflexin," as Timmer writes), and its phylogenetic distribution-- have cleared editorial review at the following journals:

• Christian Schwabe and Gregory Warr, "A Polyphyletic View of Evolution: The Genetic Potential Hypothesis," Perspectives in Biology and Medicine 27 (1984):465-85.
• Christian Schwabe, "On the validity of molecular evolution," Trends in Biochemical Sciences 11 (1986):280-3.
• C. Schwabe and E.E. Büllesbach, "Relaxin: structures, functions, promises, and nonevolution," FASEB Journal 8 (1994):1152-60.
• Christian Schwabe, "Theoretical limitations of molecular phylogenetics and the evolution of relaxins," Comparative Biochemistry and Physiology 107B (1994):167-77.
• Christian Schwabe, "Genomic Potential Hypothesis of Evolution: A Concept of Biogenesis in Habitable Spaces of the Universe," The Anatomical Record 268 (2002):171--179.
• Christian Schwabe, "Chemistry and Biodiversity," Chemistry and Biodiversity 1 (2004):1584-9.

Were these papers ignored? No: the relaxin puzzles are well-known; as other biologists who study relaxin observe (Wilkinson et al. 2005, 3),

Relaxin evolution has confounded researchers for decades. High sequence variability in relaxins across closely related species is a well-known feature of this peptide, however startling similarities have been observed between very distant species such as pigs and whales.

Nor have Schwabe's heterodox ideas about the evolutionary process escaped critical notice. His 2004 paper in the journal Chemistry and Biodiversity was followed immediately--in the very same issue--with a critical reply, as was the case with Schwabe's 1999 FASEB Journal paper. Hafner and Korthof (2006) argue vigorously against Schwabe's position, and Wilkinson et al. (2005, 9) note that "relaxin evolution has been the centre of much controversy," which they believe their approach has been able to resolve.

"The centre of much controversy"--but Timmer says (falsely) that no one cares, because it's all "borderline deranged" anyway. Thus, what might be an interesting case study, supported by multiple peer-reviewed publications, pro and con, about how to interpret molecular evidence in relation to the tree of life and its origin, would be tossed aside by Timmer, in favor of the catechism: the "fact" of evolution, never mind the data.

As we mentioned above, EE cites Schwabe in a single footnote. His name never appears in the main text. A reader who followed up the Schwabe citations, however, would find a rich controversy, likely to stimulate thinking.

And that's good, all worries about the complicated data notwithstanding.

UPDATE: Two scientists who read the above response complained (one publicly, the other in an email) that I had neglected to inform readers about the refutation of one of Christian Schwabe's claims about the protein relaxin. Their complaints, while in my view misdirected, raise some interesting questions that I'll discuss in my next blog entry.

First, Schwabe's claim, and the testing that challenges it. In this 1999 paper, Schwabe claimed to have isolated the protein relaxin from Ciona intestinalis, a tunicate. Given the usual functional roles of relaxin in vertebrates (e.g., relaxing or widening the birth canal during parturition; hence, its name), this would have been a remarkable discovery, if supported by further research. Ciona doesn't bear live young via a birth canal.

When the complete genome of Ciona was published, however, the sequence for relaxin wasn't there. Thus, Schwabe's 1999 finding was likely the result of contamination.

My correspondent griped that I'd failed to inform readers about this explicitly:

Why didn't you mention in your Schwabe post that his claim of pig relaxin in Ciona is probably due to contamination? It's dishonest not to. Particularly when you lecture your readers on the importance of data, you can't let something like this go unmentioned. A vague reference to Hafner & Korthof just doesn't cut it.

The "vague reference" he mentions is my citation of this paper, which strongly criticizes Schwabe's 1999 FASEB paper. So it seems I needed to do more than cite Schwabe's critics, such as Wilkinson et al. 2005, who also critically evaluated the Ciona claim, and whom I also cited.

Okay: so let's make it really plain: the Ciona relaxin finding was probably the result of contamination. But anyone who followed up my citations would have quickly found this, so...I can't see what I missed.

In any case, the point of my Schwabe reply wasn't to endorse all of Schwabe's arguments or claims, but to illustrate the existence of a genuine controversy about relaxin, which Timmer had denied.

References Cited
Hafner, Martin and Gert Korthof. 2006. Does a "500 million-year-old hormone" disprove Darwin? The FASEB Journal 20:1290-2.

Schwabe, Christian. 1994. "Theoretical limitations of molecular phylogenetics and the evolution of relaxins." Comparative Biochemistry and Physiology 107B:167-77.

Timmer, John. "A biologist reviews an evolution textbook from the ID camp." September 24, 2008. http://arstechnica.com/reviews/other/discovery-textbook-review.ars.

Wilkinson, Tracey N., Terence P. Speed, Geoffrey W. Tregear, and Ross A.D, Bathgate. 2005. "Evolution of the relaxin-like peptide family." BMC Evolutionary Biology 5:14.


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