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!

19 Comments

  1. Posted September 2, 2018 at 11:58 am | Permalink

    Quammen is more of a journalist than a “science writer” and, as I suggested earlier, is better at essays than book-length theses. My impression is that he’s an honest and conscientious thinker and would probably appreciate your contacting him personally to discuss your concerns re his thesis. I know I would if I were in his place. He could, of course, read your review and contact you, but that might seem defensive on his part. In any case, he can be reached at dq@davidquammen.com.

  2. steve b
    Posted September 2, 2018 at 12:07 pm | Permalink

    I was starting to read the book when I read Jerry’s review. Then I returned it to the library.

    • Posted September 2, 2018 at 12:08 pm | Permalink

      Well, I’m not sure you should have returned it. There are things to learn in the book, lots of history of science, for instance, and after all it is just my personal opinion.

      • Posted September 2, 2018 at 2:01 pm | Permalink

        A agree. Enjoyed the history and narratives of scientists ar work and at war.
        Did not get upset about suspicions of role of HGT. As a retired surgeon who lived through the bacteria getting resistance to antibiotics I appreciate how this happened and how slow we were to accept care in antibiotic use, if we have.

  3. ThyroidPlanet
    Posted September 2, 2018 at 12:16 pm | Permalink

    Sub

    • ThyroidPlanet
      Posted September 2, 2018 at 12:18 pm | Permalink

      … this is me – getting old.

  4. Posted September 2, 2018 at 12:29 pm | Permalink

    I do think Quammen has a point but he is overstating it. The Tree of Life is more reticulated than we thought, although the general pattern is still tree-like. The advent of genomic data has shown that gene flow between species (by hybridization or HGT) is relatively common. I have been studying this phenomenon in birds and I have advocated the use of phylogenetic networks (to complement phylogenetic trees). If you are interested, you can check out my publications here: https://jenteottenburghs.wordpress.com/publications/

  5. Steve Pollard
    Posted September 2, 2018 at 12:37 pm | Permalink

    Thanks (again…and again!) for an interesting and informative review.

    The only comment I might take issue with is that newspaper reviews on popular books about sociology, literature and history are usually more critical. Literature and history, maybe, although (anyway in the UK) they’re a pretty mixed bag. But many reviews of popular sociology just seem to reflect the uncritical prejudices of the reviewer. Perhaps that’s because most popular sociology is pretty superficial in itself.

  6. fvisser3
    Posted September 2, 2018 at 12:52 pm | Permalink

    DOMAINS = Woese
    KINGDOMS = Margulis
    SPECIES = Darwin

    There should not be conflict as long as we take the level into account.
    I have never understood why Margulis claimed that endosymbiosis works at the level of species as well. And why were Archaea and Bacteria not treated as kingdoms within the prokaryote domain?

    • Posted September 4, 2018 at 12:08 pm | Permalink

      I’m no expert by any means but I think the idea is that Archaea and Bacteria are as far apart from each other as either is to eukaryota, so …

      • Torbjörn Larsson
        Posted September 11, 2018 at 10:28 am | Permalink

        It appeared so, and if you sequence all the genetic material including the mitochondria and its bacterial genes that has moved into the nucleus, eukaryotes are “half and half”.

        But looking at the original speciation, it happened pre-mitochondria and eukaryotes branched off from within Archaea – the TACK archaea clade specifically. The latest results have the best labs (IMO, of course) argue for the two domain hypothesis.

  7. fvisser3
    Posted September 2, 2018 at 1:08 pm | Permalink

    Perhaps it is more the form of the Tree we should debate and not the Tree as such? More a chestnut than a cypress? But no big deal?

  8. Posted September 2, 2018 at 6:32 pm | Permalink

    Does Quammen give the impression that HGT occurs in the typical bacterial cell division? Because it doesn’t — it messes up, but does not totally obliterate, the bacterial tree of life. The impression of ubiquity comes from the lengths of the branches of the tree being hundreds of millions of years. HGT can be fairly rare and still tangle the bacterial tree.

  9. Posted September 2, 2018 at 6:53 pm | Permalink

    One tangential question: to what extent is a book’s cover and/or title determined by the publishing house rather than author? (I’m reminded of the parallel issue in media, where the title and lede is usually owed to the (sub)editor, not the journalist.)

    I’ve looked at an excerpt from the book (https://www.theatlantic.com/science/archive/2018/08/tangled-tree-species-individuals-evolution/568036/). I’m a harsh critic, but there are claims I think at least could have been made more clearly.

  10. rickflick
    Posted September 2, 2018 at 8:22 pm | Permalink

    It’s depressing that the key motives involved in the making of Q’s book and many others is money. Basically, in order to sell lots of books these folks seem to think you have to lie through your teeth(which is what he’s doing here). They can see that if the book is written truthfully it might be a fine piece of literature but destined for a small audience of connaisseurs.
    Those critics who agree to take on the task of reviewing a book they probably cannot understand simply means they are eager for a paycheck even though they don’t deserve it.
    This scenario is little different from a sports hero promoting a product she has no use for, except we’re talking about the failure of what should be science education.
    The only positive effect of the charade is that it might get people who wouldn’t read anything to give it a go.

  11. Leigh Jackson
    Posted September 3, 2018 at 1:38 pm | Permalink

    Endosymbiosis and HGT are fascinating 20th Century discoveries which any self-respecting science buff should know about. Indeed, they are important enough to be more widely recognised. Books to inform the public about these discoveries are welcome.

    A sympathetic exegesis of the relationship of these discoveries within a context of a general theory of evolution would not pitch Darwin against his successors.

    Einstein held Newton in the highest respect, saying that nobody could have done better than Newton was able to do at the time he was working. Even Einstein’s theory does not entirely uproot Newton’s, but reveals the latter to be a picture of more limited scope.

    Darwin’s Tree of Life is well rooted. Woese and Margulis add unanticipated branches, they do not uproot it.

  12. Posted October 14, 2018 at 5:24 pm | Permalink

    I wouldn’t read this book. There may be a lot of useful information in it, but it would get on my nerves. I become furious just from Prof. Coyne’s reviews!


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