Another uncritical review of David Quammen’s new book

David Quammen, an acclaimed science writer, recently published the book below (click on screenshot to go to Amazon site). It’s basically a three-part book, dealing with Carl Woese and his discovery of the Archaea, a major branch of life; telling the story of Lynn Margulis and her revival of the theories that mitochondria and chloroplasts, essential parts of eukaryotic cells, came about via endosymbiosis of bacteria; and recounting the discovery of horizontal gene transfer (HGT) between unrelated species.

 

These three bits aren’t obviously connected, except that they are major discoveries about biology that weren’t anticipated, though no major discoveries ever are. And none of them overturn either evolutionary theory or our view of humanity, though Quammen says they do. And that, I suppose, is the hook for the book: how our view of life, evolution, and even ourselves was overturned by these discoveries. Darwin was wrong!

But it’s Quammen who is wrong: endosymbiosis is a new brand of symbiosis; the domain of Archaea just shows that there’s another branch on the tree of life that we didn’t know about (there may be more!); and HGT, far more pervasive in prokaryotes than eukaryotes, may have confused some microbial evolutionary trees but doesn’t efface or eliminate the tree of life, which is based on the branching of populations, not single genes, and is reconstructed by looking at many genes, not just a few. In fact, it is the use of multiple indicators of ancestry that convinced Woese and now us that Archaea is a new domain of life. If HGT were that pervasive in microbes, we wouldn’t be able to discern a whole new domain of organisms.

As I said, HGT isn’t all that common in multicellular organisms or other eukaryotes, and some scientists doubt that it’s occurred more than very rarely. If it were as pervasive as Quammen says, we wouldn’t have any idea what is related to what. We wouldn’t know, for instance, that our closest relatives are the chimpanzees and bonobos, nor that falcons are more closely related to parrots than they are to other raptors like hawks.

Finally, the discovery that our guts are full of bacteria, and our DNA is full of dead retroviruses, hardly overturns the notion of “what it means to be human”—a question I find both ambiguous and boring.

While Quammen’s book is well written, and I did learn a lot from reading it (mostly about the history of science), the science itself is overblown and misleading to the public, especially its major theme: that the tree of life is “wrong.” I concentrated on this theme, expressed by the book’s title and cover, in my review of the book in The Washington Post. You can read that at the link, but my point was that HGT, endosymbiosis, and other things, do not overturn Darwin’s branching “tree of life”. (The “Darwin was wrong” trope was another hook used to sell the book.)

A short while back, I dissected three other reviews of the book, two from the New York Times and one from the New Republic. The common thread of all of these was that they were totally uncritical of Quammen’s there-is-no-tree-of-life theme, though there were other criticisms (one NYT reviewer, for instance, decried Quammen’s portrayal of women). One reviewer was a literary critic, one a science journalist, and one a physician. None of them appeared to have any deep acquaintance with evolutionary biology, and apparently none were equipped to critically appraise the book’s thesis.

Why I dissected the other reviews—something I don’t often do—was to make the point that reviewing science “trade books” (the term for “popular science books”) requires reviewers who are acquainted with the science. Otherwise all you get is a canned summary of the book’s contents and perhaps some irrelevant or misguided remarks, as with the NYT reviewer who indicted Quammen, mistakenly, for short-changing women in his narrative.

And so we have another review, this time from the Boston Globe (click on the screenshot to read it). The reviewer, Thomas Levenson, is identified as “a professor of science writing at MIT.” He appears to write mainly about physics, the subject of three of his five books. And when he comes to Quammen, he’s done no better than the others.

The first thing he does is parrot Quammen’s thesis that new discoveries have overturned the tree of life:

That image, the tree of life, proved such a powerful metaphor, that in the 20th century it morphed from being a map of evolution into an origin story.

These modern trees showed a single line up the page — the trunk — representing the earliest bacteria, simple, single-cell creatures, known formally as prokaryotes. That trunk continued upward to all modern microbes; while, over billions of years, a branch emerged that would eventually produce all other life forms, the multicelled eukaryotes, which pack their DNA into a compartment within the cell called the nucleus.

The only problem with that picture? In crucial ways, it’s wrong.

Why is it wrong? Because Woese found a new domain of life, the Archaea. But the finding of Archaea through molecular phylogeny, as I said in my review, undercuts Quammen’s very thesis: that interchange of genes among species makes reconstruction of the tree of life impossible. Indeed, Levenson should have realized that when he wrote this (my emphases in all excerpts below):

Beginning in the 1960s, Woese and his collaborators performed a series of laborious experiments that compared chemical structures in different microbes to see how closely each bug was related to the next. What they found was shocking: There wasn’t just one broad category of microbes, the bacteria. There were two. Ultimately Woese realized they represented not just a new subset of bacteria, but a wholly separate domain of life, now know as Archaea.

The result was startling, initially controversial, and ultimately a vindication of the molecular approach to evolution: tiny creatures that looked very much alike through a microscope were shown to have different and wholly distinct evolutionary histories.

Well, the “molecular approach to evolution” has, in the past several decades, been the main way scientists reconstructed the history of life.

Levenson goes on to cite HGT as another finding that dooms the tree of life, implying that the problem is ubiquitous and not just limited to microbes:

To complete his saga of intellectual revolution, Quammen looks at one last molecular epiphany, the discovery of a phenomenon called horizontal gene transfer, or HGT. Observed first in the 1920s in a bacterium that causes pneumonia, HGT performs what Quammen calls “infective heredity”: one organism passing useful genetic material straight into the genome of another microbe.

HGT matters for brutally practical reasons: It can kill us. The spread of antibiotic-resistant “superbugs” is, in large measure, the result of HGT. When any bug comes up with a way to disarm a drug, HGT can rapidly transfer that trick to other infectious microbes, who then don’t have to figure it out themselves. That contributes to the spread of antibiotic resistance that kills tens of thousands of people every year.

Even with that toll, the crucial realization for Quammen is that HGT radically redraws the conventional tree of life. That image cannot capture the messy reality of one organism handing off genes to very different ones — which isn’t just confined to the realm of microbes. It can happen between animals of wildly different species as genes travel complex journeys through multiple organisms. HGT doesn’t overturn the fundamental logic of evolution by natural selection, but it vastly complicates it.

Well, antibiotic resistance, often passed between bacteria by plasmids, is interesting, but insufficient to overturn molecular trees.  And in fact Levenson simply doesn’t know enough to counter his own statement that the “conventional tree of life” doesn’t work for both microbes and eukaryotes. So he just parrot’s Quammen’s claim and moves on.

Not only that, but HGT isn’t even said by Quammen to “overturn the fundamental logic of evolution by natural selection”; Quammen says it overturns the notion of evolutionary trees, but not evolution by natural selection. Conflating these two is a big mistake, for Quammen of course accepts evolution by natural selection. Further, HGT doesn’t even “vastly complicate” that: transferred genes will either proliferate in their new host or be eliminated, and that will depend on whether they enhance or hurt their bearer’s fitness; that is, via natural selection.  Here Levenson is misleading his readers.

It irks me that newspapers run these kinds of uncritical reviews of science books when they wouldn’t do that for, say, books on sociology, literature, or history (viz., the critical [and to mind mostly misguided] reviews of Pinkers Enlightenment Now). Science gets a pass in the quality-criticism department because not many writers know enough about science to cast a cold eye on popular science writing, and because many scientists who could do that can’t write well enough to create a lively review. I’d urge editors to ferret out those scientists who can, as well as those journalists —Carl Zimmer and Faye Flam come to mind—who have taken the time to understand the science they write about. Sadly, I don’t think either Carl or Faye do much book reviewing, as they’re science journalists.

Finally, Levenson buys uncritically into Quammen’s “this stuff overturns our notion of what it means to be human” theme, a theme running through the last chapters of his book. Levenson:

In “The Tangled Tree,’’ David Quammen unpacks that error [JAC: the notion that there’s a branching tree of life], offering an elegant and accessible account of a revolution in knowledge and perspective, one that has advanced without much public fanfare but has accumulated into a fundamental change in our view of life — and what it means to be human.

Nope. I still wake up each day with my load of E. coli and my DNA riddled with the remnants of ancient retroviruses, and think, “Yes, I’m still Jerry Coyne.” And everyone else thinks so, too. I don’t see philosophers musing about how these new findings affect our concept of humans and humanity. In other words, that statement, which appears in so many science books, is pretty much garbage. But it does sound good, doesn’t it? What it means to be human. 

So my message to science editors (except mine!): get off your bums and ferret out reviewers who know something about science!