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The Tree Of Life: metaphysics vs. metaphor

2019; Wiley; Volume: 35; Issue: 5 Linguagem: Inglês

10.1111/cla.12369

1096-0031

Andrew V. Z. Brower,

Genomics and Phylogenetic Studies

CladisticsVolume 35, Issue 5 p. 600-602 Book ReviewFree Access The Tree Of Life: metaphysics vs. metaphor Andrew V. Z. Brower, Corresponding Author Andrew V. Z. Brower Andrew.V.Brower@APHIS.USDA.GOV orcid.org/0000-0001-6874-3589 USDA-APHIS National Identification Service, Riverdale, MD, USASearch for more papers by this author Andrew V. Z. Brower, Corresponding Author Andrew V. Z. Brower Andrew.V.Brower@APHIS.USDA.GOV orcid.org/0000-0001-6874-3589 USDA-APHIS National Identification Service, Riverdale, MD, USASearch for more papers by this author First published: 05 February 2019 https://doi.org/10.1111/cla.12369Citations: 8 Disclaimer: The opinions expressed in this review do not necessarily represent the policies of the U.S. Department of Agriculture. AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat The Tangled Tree: a radical new history of life. By David Quammen. Simon & Schuster, New York. 2018. 461 pp. U.S. $30 (hardbound), ISBN 978-1-476-77662-0; ebook ISBN 978-1-476-77664-4 The Tangled Tree is a trade book, written by a popular science writer for lay people. Why review it in an esoteric scientific journal? Because it makes sweeping metaphysical claims about the nature of evolutionary history, and argues that one of the central premises of phylogenetic systematics—the bifurcating hierarchy—is a false and obsolete icon of the history of life. I am going to explain why I disagree with that claim, but first I will describe the contents of the book. Quammen is a talented writer, who interweaves his scientific narrative with anecdotes about the personalities and events through which the story unfolds. This makes for quick, entertaining reading. Enhancing this digestibility is the structure of the book, with 84 chapters, averaging less than five pages apiece. The main subjects of the book are horizontal gene transfer, microbial phylogeny (or non-phylogeny) and the discovery of the Domain Archaea. Featured players include W. Ford Doolittle, Lynn Margulis and especially Carl Woese, around whose life, science and immodest character the narrative is framed. As Quammen relates, Woese fancied, and professed to his acolytes, that his scientific contributions were more significant than Charles Darwin's. Honoring Woese's legacy, the University of Illinois named a building after him. Enough said about that. Quammen's narrative proceeds like this: Darwin, in his 1837 “B notebook” drew the famous sketch of a phylogenetic tree, captioned “I think”, and stated, “organized beings represent a tree”. Having consulted Pietsch's (2012) and Archibald's (2000) lavishly illustrated tree books (reviewed in Cladistics by Brower, 2012, 2016), Quammen acknowledges that the tree iconography is ancient and was employed by Lamarck and other pre-Darwinians. Darwin (1859) elaborated the metaphor, and it was reified in actual tree illustrations by Haeckel (1866). Quammen repeatedly refers to tree-like diagrammatic representation as “Darwin's theory”, but this is only an accurate claim if, as Mayr (1942) argued, Darwin's theory is really five theories—one of which states that the natural system is organized as an irregularly bifurcating hierarchy (or, more evolutionarily speaking, living beings are related by descent with modification). Of course, Darwin's most eponymous theory (the mechanism of natural selection) is not affected by the form of biological diversification and, indeed, the evolution of antibiotic resistance via lateral gene transfer among bacterial strains is considered a textbook example of how natural selection operates (and not a falsification of phylogeny). Back to the story. Margulis (1970) published a book popularizing the hypotheses of bacterial endosymbiotic origins of mitochondria and chloroplasts in eukaryotic cells (proposed much earlier by Wallin (1927) and Mérejkovsky (1920), respectively). These two symbioses, subsequently corroborated by phylogenetic analyses identifying bacterial sister taxa of eukaryotic organellar ribosomal DNA sequences, indicate that the pattern of the history of life is not an exclusively divergent hierarchy. Some, such as Woese, held that such events happened infrequently and long ago—the exceptions that prove the rule, and that the subsequent history of life has been mainly divergent, with major lineages going their separate ways (otherwise Woese's claim to fame, the Domain Archaea, would vanish in the tangle). Casting further shade upon the tree, Quammen invokes the discoveries of microbial transformation, transduction and conjugation, each of which allows the incorporation of exotic DNA into the genome of bacteria horizontally, rather than by errors in endogenous DNA replication. He also discusses the discovery of transposable elements of viral origin in eukaryotes (of course, viruses themselves are not a natural group, but a hodgepodge of parasitic bits of the genomes of other organisms). Some have suggested that lateral gene transfer is more Lamarckian than Darwinian, but although the passage of genes from one organism to another, whether horizontally or vertically, can be viewed as “acquisition of characters”, the expression of those genes follows the Central Dogma. Thus, a more important Darwinian vs. Lamarckian distinction is whether those features are teleologically beneficial for the solution of future evolutionary challenges. It is unlikely that bacteria acquire plasmids in order to gain antibiotic resistance—those that do are fortuitous, not gifted with foresight, and it is Darwinian selection that permits their differential survival and reproduction. Now I am going to depart from describing the book and nitpicking its lesser shortcomings, to offer my argument about its major flaw. Quammen evidently does not grasp the simple philosophical principle that the irregularly bifurcating hierarchy is not a picture of evolutionary history that is true or false, but an epistemological framework or model through which we understand patterns of relationship, and without which, the notion of horizontal transfer is meaningless. The tree-like pattern is an a priori assumption of phylogenetic analysis, albeit corroborated by more than two centuries of empirical data (Brower, 2000). The fact that we can recognize gene x as “foreign” to the genome of a species means that we must have a pre-existing notion of what “native” DNA for that species is. The irregular bifurcating hierarchy is not a metaphysical statement that (as Quammen repeatedly asserts) is false. It is a null hypothesis that the weight of the evidence has failed to reject. As Popper (1968) said, we do not discard a hypothesis simply because some falsifying evidence contradicts it until we have a better hypothesis to replace it. A mass of spaghetti is not a better hypothesis—a reticulated network is rather a collection of ad hoc singular statements that by their nature are unfalsifiable without the epistemological framework provided by the tree. It is only through the lens of systematics that such patterns may be discovered: horizontal transfer, be it between bacterial lineages or hybridizing eukaryote species, is only recognizable once we conceive of such lineages or species as entities which exhibit patterns of apparent homology that are incongruent with the expected phylogenetic pattern, based, at least under the cladistic paradigm, on the preponderance of pertinent evidence. As a science writer and reporter of the “facts” that he was told by the interested scientists he interviewed, perhaps Quammen can be forgiven for failing to appreciate the subtleties of systematics. But then again, perhaps not. This is the writer who describes bacterial taxonomy as “an exercise in arcana, a marginal activity of risible triviality beside which stamp collecting looks like an adventure sport” (p. 71). Now to be fair, he offsets this calumny by describing how ecologically and materially important bacteria are to humans, but the pungency of the comparison lingers nonetheless. Taxonomy is boring minutia—“no one makes Hollywood movies about bacterial taxonomists” (p. 72). There are pronouncements about how some significant percentage of the human genome is composed of foreign DNA from various sources. Perhaps so, but again, we need to know what is “native” before we can determine what is foreign—such claims implicitly presuppose that taxa have a priori discrete genetic identities. Another problem is Quammen's superficial treatment of species concepts. On p. 380, he states that the category of species is “a collective entity but a discrete one, like a club with a fixed membership list. The lines between this species and that one don't blur.” He says that this concept, too, is false. And so would most evolutionary biologists and systematists for the past 150 years (Quammen notes that Darwin rejected essentialism). He goes on to quote Ernst Mayr's (1970) Biological Species Concept (BSC) and its criterion of interbreeding. He says the BSC is inapplicable to bacteria both because they reproduce asexually (so there is no way to assess interbreeding), and because of horizontal transfer, which he suggests equates to a lack of reproductive isolation (of course, conjugation, etc., are not “reproduction”). These seem like contradictory reasons why the BSC fails. He then suggests that the BSC is also inadequate to cope with the “hybridization” of Homo sapiens with H. neanderthalensis. Of course this is illogical, because, under the BSC, H. sapiens and H. neanderthalensis are conspecific by definition. They can only be separate species if we divide them by alternative criteria. He says, “some experts now consider Neanderthals to have been a subspecies of humans”, but that is the orthodoxy I learned as an undergraduate, and also, if memory serves, from the Time-Life Nature Series “Early Man” book (Howell, 1965) that captivated me as a boy in the 1960s—so, hardly a novel circumscription. Regardless, the BSC is certainly not the only game in town, and it would have been more interesting to contemplate the implications of these issues for other concepts, such as the Simpson–Wiley–de Queiroz Evolutionary Species Concept (Simpson, 1951; Wiley, 1978; de Queiroz, 2005). Also in his discussion of humans, Quammen makes the statement, “some parts of our genome even today look more chimp than human” (p. 382). What can this possibly mean, from a phylogenetic perspective? Among extant species, humans and chimpanzees are sister taxa, and so the null hypothesis is that copies of a gene from each of them would be more similar to each other than it is to copies of the same gene from any other taxon. The only evidence I can imagine that might support such a claim is that perhaps some polymorphism occurs within humans, and that some humans’ alleles are claimed to be phenetically more chimp-like than those of others. The book is generally well produced, with scattered text illustrations (mainly of trees), and a section of halftone portraits of the main characters on a glossy paper insert in the middle. There are no citations in the text—fitting for a trade book, but frustrating if you want to determine the original sources. There are 386 footnotes, but these also are not indicated within the text. Strangely, the format of the citations is idiosyncratic (generally including issue numbers but excluding page numbers for journal articles), and the section seems to have not been edited for consistency. For example, we find citations variously for “Jan O. Anderson” and “Jan O. Andersson”, for “Francis Crick” and “F. H. C. Crick”, and for “Carl Woese”, “C. R. Woese” and “Dr. Carl R. Woese”. In sum, this book, although entertaining, conveys an unfortunate message. Many people who do not know any better will read it and consider Quammen's condemnation of the Tree of Life to be a legitimate criticism of the core epistemological paradigm of systematics. Although science advances by the falsification of old hypotheses and their replacement with new ones, and although iconoclastic evolutionary biologists may build their careers by challenging the status quo, jumping to the conclusion that the classificatory framework that has organized biological diversity for over two centuries is defective and obsolete is counterproductive and demeaning to those whose efforts have contributed to its construction. It is no sin to popularize the idea of horizontal gene transfer as a complicating source of homoplasy for phylogenetic patterns, but this is neither new nor radical, except when wielded as a nihilistic critique of systematics. References Archibald, J.D., 2014. Aristotle's Ladder, Darwin's Tree: The Evolution of Visual Metaphors for Biological Order. Columbia University Press, New York. Brower, A.V.Z., 2000. Evolution is not an assumption of cladistics. Cladistics 16, 143– 154. Brower, A.V.Z., 2012. A picture is worth a thousand words. Cladistics 28, 655– 657. Brower, A.V.Z., 2016. Trees and more trees. Cladistics 32, 215– 218. Darwin, C., 1859. On the Origin of Species. John Murray, London. Haeckel, E., 1866. Generelle Morphologie der Organismen. G. Reimer, Berlin. Howell, F.C., 1965. Early Man. New York, NY, Time Life Nature Series. Margulis, L., 1970. Origin of Eukaryotic Cells. Yale University Press, New Haven. Mayr, E., 1942. Systematics and the Origin of Species. Columbia University Press, New York. Mayr, E., 1982. The Growth of Biological Thought. Belknap Press, Cambridge. Mérejkovsky, C., 1920. La plante considerée comme une complexe symbiotique. Bull. Soc. Nat. Sci. Ouest. (3rd Series), 6, 17– 98. Pietsch, T.W., 2012. Trees of Life: A Visual History of Evolution. Johns Hopkins University Press, Baltimore. Popper, K.R., 1968. The Logic of Scientific Discovery. 2nd English ed. Harper and Row, New York. de Queiroz, K., 2005. A unified concept of species and its consequences for the future of taxonomy. Proc. Calif. Acad. Sci. 56 (Suppl. 1), 196– 215. Simpson, G.G., 1951. The species concept. Evolution 5, 285– 298. Wallin, I.E., 1927. Symbionticism and the Origin of Species. Waverly Press, Baltimore. Wiley, E.O., 1978. The evolutionary species concept reconsidered. Syst. Zool. 27, 17– 26. Citing Literature Volume35, Issue5October 2019Pages 600-602 ReferencesRelatedInformation