In Praise of Flukes

I have an article in tomorrow’s New York Times on a provocative theory about our origins. Humans, other animals, plants, fungi, and protozoans are all eukaryotes. We all share a distinctive genome compared to other organisms (prokaryotes, which include bacteria and archaea). Our genes are more versatile: they can be switched on an off in more complex patterns than in prokaryotes, and one gene can make many different proteins, depending on which parts of the gene our cells look at. Some scientists would like to say that this distinctiveness must be the product of natural selection. But Michael Lynch, a biologist at Indiana University, is here to remind us that natural selection is not the whole story when it comes to evolution. By this he doesn’t mean that the rest of the story involves aliens manufacturing everything we don’t yet understand. He means genetic drift and neutral evolution–processes that dont’ get much attention in the popular press. In writing this article, I figured out why: they’re hard to write about. There are few good metaphors in easy reach for these processes, so you’re left swinging around blunt weapons of statistics. Yet ultimately this is very provocative stuff: it suggests that a great deal at the core of our biological existence emerged in large part thanks to flukes of probability, not thanks to the fine craftsmanship of the blind watchmaker known as natural selection.

The new paper is here. You need a subscription to read it. But a paper Lynch published earlier this year that describes one piece of the puzzle is free.

Update, 1/4 10:30: I’ve posted the full text on here.

Update, 1/4 10:40 am: John Travis, deputy news editor at Science comments that he’s surprised that the article did not include comments from other scientists. Actually, it originally did, but in the merciless squeeze to fit on the newspaper page, those quotes had to come out. I contacted four experts in the field, and three had high praise for Lynch’s ideas and one remained skeptical. It’s certainly a controversial idea, since so many efforts in the past to explain the eukaryote genome have proposed that its features emerged as adaptations favored by natural selection.

0 thoughts on “In Praise of Flukes

  1. Carl,
    You wrote in yesterday’s NYT

    “Evolutionary biologists generally agree that humans and other living species are descended from bacterialike ancestors. But before about two billion years ago, human ancestors branched off.
    This new group, called eukaryotes, also gave rise to other animals, plants, fungi and protozoans.”

    With all due respect, there is not a shred of empirical evidence, either observational or experimental that supports the audacious claim that eukaryotes “evolved” from prokaryotes, much less that drift and/or selection was the mechanism.

  2. Carl wrote:

    “Re Charlie Wagner’s comments: There are quite a few “shreds,” for those who would actually like to consider them. See here for starters.”

    Instead of asking people to wade through dozens of journal articles, (a tactic often used to dissuade people and create obfuscation) why don’t you just take a moment and summarize the key pieces of evidence that supports the claim you made?
    Since you made the claim, It seems to me that it’s your responsibility to defend it yourself instead of asking me to prove to myself what I don’t believe is true.
    After all, you are a science writer and popularizer of science topics and you generally write for laypersons, surely you can state your points in a simple and understandable manner for anyone with a reasonable intelligence to understand.

  3. With Charlie’s bait and switch above, he has clearly demonstrated that he doesn’t actually want to be bothered with investigating the evidence. If he needs someone to summarize this information for him, then perhaps he should refrain from making blanket statements about it.

  4. I’m with Charlie on this one, although I strongly suspect Charlie and I agree on little else. For those of us who are not formally trained in biology the material you have referenced is heavy going. I have long thought that the appeal of fundamentalist religion is that it requires little thought or analysis – there is, after all, only one book to read. By contrast, even a narrow area of science such as cellular biology requires years of study just to understand the basics. Some of us, though seriously interested, don’t have the time or dedication for that education and need summaries of the most important points.

  5. Carl wrote:

    “With Charlie’s bait and switch above, he has clearly demonstrated that he doesn’t actually want to be bothered with investigating the evidence. If he needs someone to summarize this information for him, then perhaps he should refrain from making blanket statements about it.”

    Your conclusion that there is a component of laziness involved is misguided. I’ve read dozens of articles on this subject, including many that are on your list by Woese, Doolittle, Margulis and others. I have come to the conclusion by analyzing the evidence that there is no credible reason to believe that eukaryotes “evolved from” prokaryotes.
    Perhaps you are confusing relatedness with phylogeny. Because forms have similar structures and processes, doesn’t mean they are necessarily phylogenetically linked.
    I don’t think it’s asking to much for you to summarize the reasons why you are making this claim. I’ve looked at the same evidence that you have and obviously reached a different conclusion. It’s up to you to clarify your thinking on the matter. You’re the one making the blanket statements.

  6. Michael, I’m happy to write about this sort of stuff for those who don’t want to wade through a lot of scientific papers. That’s my job, and I’m grateful for it. But in this case, I’m responding to someone who has made a sweeping statement about the lack of evidence for the origin of eukaryotes from a bacteria-like ancestor.

  7. Carl,

    I do like this argument about drift having a bigger role in evolution. This argument has its origins in the development of neutral theory by Kimura and Nei. Recently, this is coming to the fore in human evolutuion, viz, which model better accounts for the diversity DNA research uncovers in humans a result of adaptations (regional selection) or simply neutral variability? I am inclined to think ‘isolation by distance’ and drift have played a significant role in human evolution.
    Carl, what information have you on this topic? Are there any papers supporting modeling key human characteristics by non-selective forces: say, upright walking, enlarged brains etc. These key features have always been interpreted as arising from purely selective forces. Not to mention population specific diseases and loci, which may themselves be simple effects of non-selective forces.

  8. I’m some three years into reading the Bible. I suspect that most professional theologians have not finished it. It is slow going. It has been translated several times and suffers on clarity. It meanders. There is enormous repetition. The content density is quite low, especially if there is something specific you want to learn from it. I’d much rather read biology journals even though I have little formal biology training. At least if there’s a term I don’t know, it is possible to look it up. With the Bible, it isn’t at all clear if I’ve missed a point entirely, unless I also study several additional references.

    The term ‘laziness’ typically has judgmental overtones. It is nearly always a good thing to look for a short cut.

  9. Hi Carl,

    I enjoy your writing.

    I have a question about one sentence you wrote. (I’m a biologist, but I’m pretty ignorant about evolution or splicing, so treat me as an amateur.)

    You wrote:
    “Once an intron was wedged into the middle of a gene, a cell had to be able to recognize its boundaries in order to skip over it when making a protein.”

    You sound like saying that an intron is a random sequence of DNA inserted into a previously-intronless gene. Is there evidence for this? I’m asking this because:
    1) I know cases when genes lose introns (for example when genes are integrated into retroviruses) but I didn’t know about reverse cases.
    2) Self-splicing introns (which are admittedly minority of introns) are hardly random sequences and I recall that even splicing of the majority of introns that are not self-splicing is catalyzed by a similar mechanism.

    Basically, I’m curious, as a non-expert, about the origin and evolution of introns and they relate to divergence of prokaryotes and eukaryotes. And how about archea?

    Anyway, keep up the good work!

  10. Carl
    I enjoyed your story but, as a science journalist myself, I was surprised that you didn’t include comments about Lynch’s theory from others in the field. I don’t think every story needs the “outside comment” but this was one that left me wondering how Lynch’s ideas have been received.

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