August 6, 2018 | David F. Coppedge

Darwin’s Tree Is Dead

How many people have heard that Darwin’s famous branching-tree diagram of universal common ancestry is obsolete? Many scientists haven’t heard yet, either.

The only diagram in Darwin’s Origin was a more formal representation of a drawing he had made earlier, showing how ancestral forms branched out and diversified over time. Diversification undoubtedly occurs, but Darwin assumed that variation under selection would produce “endless forms most beautiful” of higher complexity.

His theory of natural selection, supporting his belief in universal common ancestry, demanded that spontaneous beneficial variations be heritable. Details of how variations were produced by random mutations became incorporated in the 1930s into the modern synthesis known as neo-Darwinism.

Ever since, biologists have been infatuated with building phylogenetic trees of sponges, flowering plants, mammals and all kinds of other groups, believing that all these would stitch together nicely into tree of universal common ancestry, related by a single trunk from some primeval LUCA (last universal common ancestor). We regularly encounter evolutionary biologists doing this. Now comes a new book blowing it all up.

In Nature, John Archibald has just reviewed David Quammen’s latest book The Tangled Tree: A Radical New History of Life (Simon & Schuster, 2018). He titles his review, “The band of biologists who redrew the tree of life.” They didn’t redraw it as much as cut it down:

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.

If organisms have been exchanging genes, what happens to the tree of common ancestry? It evaporates. Information sharing is closer akin to intelligent design than evolution. The information was already there; it’s just getting passed around. The vision of a “tree” becomes a phantom, a misrepresentation of reality.

Archibald begins his review with a photo of Carl Woese (1928-2012), who began the radical revolution by positing the existence of a third domain of life, the Archaea. The complexities found by Woese, Lynn Margulis and other prominent biologists in the 1960s and beyond started scrambling the tree image. The “tree thinking” that had been ingrained in biologists (14 Nov 2005) began to give.

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.

So radical was the new view, Quammen writes of some proponents as “’the four horsemen’ of the gene-transfer apocalypse: William Martin, Jeffrey Lawrence, Peter Gogarten and Ford Doolittle.” If Darwin’s tree is gone, what could be left but a tangled bush, or a lawn, or an orchard, that suggests common design arising at once, rather than a gradually developing tree? Archibald ends by reminding that the “tree” picture is not out there in nature, but rather in the heads of philosophers.

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.

Incidentally, we learn two surprises about Woese in this review: (1) he believed in a deity (this surprised Archibald), and (2) he disliked Darwin. He started to collaborate with Canadian science historian Jan Sapp for a new book to be titled Beyond God and Darwin, but then,

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.

Archibald describes the older Woese as a “jaded, curmudgeonly legend wracked by a Darwin complex,” trying to get the scientific community to accept his three-domain tree. He died of pancreatic cancer in 2012. His three-domain view is now commonly accepted, and horizontal gene transfer continues to unravel Darwin’s tree.

To use Woese’s own term, the ‘bastard’ Darwin deserves less substance and more repugnance for all the harm he caused for leading biology on a 158-year detour. Yes, Carl, there is a deity. We hope you got to know him before it was too late.

So Darwin’s tree is gone. The Darwin holdouts will still try to discern a tree in the dots with their powers of pareidolia, but will see it in spite of the evidence, not because of it. It’s not that Darwinians are unable to conceive of a tree in the scrambled data. They are, after all, skilled divination artists and storytellers (5 Jan 2018). It’s that the data require a story to support a belief.

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