BOOKS AND ARTS

The band of biologists who redrew the tree of life

John Archibald praises a compelling guide to the past 3 billion years — and its molecular historians.
John Archibald is a professor in the Department of Biochemistry & Molecular Biology at Dalhousie University in Halifax, Canada, and the author of One Plus One Equals One: Symbiosis and the Evolution of Complex Life.
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Carl Woese, a white man with grey hair and holding a pair of glasses, looks up towards the camera from a lightbox.

Carl Woese discovered the ‘third domain’ of life — the Archaea.Credit: Jason Lindley/LAS, Univ. Illinois at Urbana-Champaign

The Tangled Tree: A Radical New History of Life David Quammen Simon & Schuster (2018)

In The Tangled Tree, celebrated science writer David Quammen tells perhaps the grandest tale in biology: how scientists used gene sequencing to elucidate the evolutionary relationships between living beings. Charles Darwin called it the ‘great Tree of Life’. But as Quammen reveals, at the molecular level, life’s history is more accurately depicted as a network, a tangled web through which organisms have been exchanging genes for more than 3 billion years. This perspective is indeed radical, and he presents the science — and the scientists involved — with patience, candour and flair.

Centre stage in Quammen’s narrative is Carl Woese (1928–2012), the US microbiologist best known as the discoverer of the Archaea (Archaebacteria) — the ‘third domain’ of life. Inspired by the visionary musings of Francis Crick, Linus Pauling and Emile Zuckerkandl, Woese committed himself to molecular phylogenetics at a time when this powerful approach to the study of evolution was in its infancy. During the 1960s and 1970s, the Woese Laboratory at the University of Illinois at Urbana–Champaign developed and refined techniques for deriving sequence information from molecules of ribosomal RNA (core components of the cell’s protein-synthesizing factory, the ribosome). Sequences were painstakingly obtained from diverse microbes and used as molecular yardsticks to infer how the organisms were related to one another and to animals and plants. Through the following two decades, as molecular sequencing got easier and cheaper, Woese’s ‘three-domains’ tree — comprising archaea, bacteria and the nucleus-containing eukaryotes — served as the definitive road map for the field of comparative genomics. In many ways, it still does.

But life is complicated, and so are the scientists who study it. In his breezy, conversational style, Quammen shepherds us up and down life’s vast timeline, and across 150-plus years of exciting, often controversial discoveries. He handles the complexities with humour and clarity (he’s right: some ribosomes do look like rubber ducks). We learn about the seeds of “tree thinking” in biology, before and after Darwin’s 1859 On the Origin of Species. We learn of a time when a natural classification of microorganisms was considered impossible (they were deemed morphologically too simple, physiologically too variable). We learn how molecular sequencing helped test and eventually prove the endosymbiont hypothesis for the origin of mitochondria and chloroplasts; these eukaryotic organelles are now known to have evolved from once free-living bacteria.

And we learn that although molecular phylogenetics provided the means with which to build a universal tree of life that includes microbes, it also provided the data that ultimately led us to question the precise nature of the tree. From the late 1990s onwards, with dozens and eventually thousands of complete genome sequences in hand, biologists began to realize that the horizontal exchange of genes between distantly related organisms is an important evolutionary force. (Quammen also reminds us that, as early as 1963, medical microbiologist Tsutomu Watanabe and colleagues provided evidence for horizontal gene transfer as a mediator of antibiotic resistance in bacteria.) Because genes have “moved sideways”, not all genes in a given genome share the same history. Current evidence suggests that this is also true for at least some macroorganisms (such as plants). The tree of life is tangled, some branches hopelessly so.

At times, this master storyteller’s book reads like a travelogue. It brims with revelations from dozens of interviews with key players in their native habitats: the late Lynn Margulis, US champion of endosymbiotic theory; former Woese Lab members George Fox, Mitchell Sogin and Linda Bonen; and the environmental-DNA-sequencing legend and three-domains defender Norman Pace. Here too are “the four horsemen” of the gene-transfer apocalypse: William Martin, Jeffrey Lawrence, Peter Gogarten and Ford Doolittle.

Some of the stories are laugh-out-loud funny. In one, Woese’s collaborator Charles Vossbrinck — an “openhearted bear of a man” — picked up a tipsy, pontificating Woese at a barbecue and threw him into the bushes. (Their friendship survived.) Other tales are shockingly intimate. Woese’s last months and weeks with pancreatic cancer, as revealed by those closest to him, make for painful, albeit illuminating reading. I was surprised, for instance, to learn that Woese believed in a deity.

The Tangled Tree traces the full arc of Woese’s life and career. We see the fiercely determined young scientist struggling to collect the data that he intuited would be important, and the brooding, combative mid-career professor fighting to have his beloved archaea and three-domains tree accepted by the scientific community. Finally, there is the jaded, curmudgeonly legend wracked by a Darwin complex. None of the accolades showered on Woese seemed to matter (he and many others clearly felt he deserved a Nobel prize, but he never got one). Around 2010, Woese and Canadian science historian Jan Sapp began to collaborate on a book tentatively entitled Beyond God and Darwin. The project never moved beyond Sapp’s draft introduction, on which Woese wrote: “Jan, you accord Darwin so much more substance than the bastard deserves.”

Above all, Quammen reminds us that science is an imperfect, highly social activity. It happens in labs — but also in hallways and airports, over pizza or coffee. And as with any other human endeavour, egos and reputations play a huge part. Friendships are forged, broken and mended over perceived or actual slights in the literature or at conferences. The actual data matter less often than we would like to admit.

To what extent is the tree metaphor still ‘useful’? On this thorny question, Quammen is clear: among practising scientists, opinions differ greatly. Horizontal gene transfer is here to stay — it’s now a question of how, how much, how important and between which organisms. And it is here that our twenty-first-century science connects back to the centuries-old struggle to classify and make sense of the world around us. At root, science and philosophy are interwoven in ways that many of us fail to realize, a fact to which Quammen is wisely alert.

Nature 560, 26-27 (2018)

doi: 10.1038/d41586-018-05827-1
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