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Monday, February 17, 2014

Scientists should be humble, not arrogant

It's shocking how much venom and bile you can stir up by criticizing Darwin in public. I more or less expected, when I wrote a post critical of evolutionary theory at BigThink.com, there'd be a few heated comments. I didn't expect so many of the 600+ comments to be so heated. Quite a few of the comments were and are just plain ugly. And the most vitriolic attacks came not from the religious right, but from supporters of Darwin!

Looks like I struck a nerve.

Some people jumped to the conclusion that, with my post, BigThink was selling creationism under a thin veneer of science. That's just plain wrong. I am not a creationist. I consider creationism magical thinking. It may be satisfying to others. It's not for me.

More than one commenter suggested I get some biology training before writing about evolution. I guess I should have made clear, up front, that I have two degrees in biology: a B.S. from UCI and a master's in microbiology (summa cum laude) from UC Davis, where I was a Regents' Fellow. I took (and passed) qualifying exams for a Ph.D. One of the specialty areas I was examined in was molecular genetics.

What did I say in my BigThink blog that was so controversial? First let's get clear what I did not say. One of the commenters claimed I said changes in DNA were not responsible for evolution. I never said that. What I said was that point mutations (of the kind the give rise to single-nucleotide polymorphisms) are almost certainly not a major driver of evolution. We know this because it's been demonstrated many times that the majority of non-neutral point mutations are deleterious, leading to loss of function, not gain of function. Spend some time reading about "Muller's ratchet" if you don't believe me.

How, then, does speciation occur? We don't know. No one has seen it occur in the lab. Nature no doubt relies on a variety of tactics, some of which we know a good deal about, many of which we barely understand, no doubt others of which we haven't yet discovered. We know that sexuality (which is probably around a billion years old) has led to an explosion of diversity (and has kept Muller's ratchet from sending countless species into extinction). On a molecular level, there are still many things we don't understand about how chromatin is managed, how micro-RNA is regulated, when and why DNA methylases come into play, the relative importance (or unimportance) of translocases, and much, much more. To assert that we understand how speciation occurs is to assert a half-truth. It's like saying we understand the weather because we can measure atmospheric pressure.

One of the major embarrassments of modern biology is that more than a decade after having sequenced the human genome, we still don't know what most of our DNA does: We can account for 30,000 human genes (which is not even ten times the number of genes in E. coli). Meanwhile our DNA has enough base-pairs to encode 3 million genes. But we're pretty sure the "true number" of human genes is under 50,000. What does all that DNA do? We have some hints at answers, but no more than that. (Note: When the surplus of DNA in the human genome was first discovered, scientists called it "junk DNA." It took years for that unfortunate terminology to disappear.) The honest answer is, we're still not even close to understanding what all our DNA is doing.

It's been my experience that the best scientists are humble, rather than proud. They're willing to concede the immensity of what they don't know. Arrogance and over-confidence are hallmarks of immaturity, in science as well as in life.

If we're humble, and honest, we have to admit that physics is unable to explain where most of the matter and energy in the universe is. (No one knows what "dark matter" is, where it came from, what its properties are, whether it's made of particles, how long it's been around, whether it obeys normal laws of physics, etc.) If we're humble, we have to admit we don't know what most of the human genome is doing. We also have to admit we don't know how or why the Cambrian Explosion happened. (Darwin himself conceded that the Cambrian Explosion posed a major unanswered challenge to his theory.) We have to admit we have no idea how life originated on earth.

The list of things we don't understand is far longer than the list of things we do understand. If we don't understand that, all is lost.

21 comments:

  1. Anonymous8:09 AM

    Did you ever bother to respond to Jerry Coyne (who has way more impressive credentials then you)?

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    1. I also have a degree in biology from UCI. And I remember learning what "fittest" actually means such that I would never make the embarrassingly bad mistake of trying to claim that "survival of the fittest" is a tautology.

      Fittest means "leaves the most progeny which can then have progeny" not "survives." Wow, actually, I learned that in high school biology. I distinctly remember my teachers pointing out how "fit" does not mean "big, buff, and lives longer" like we may colloquially think. An organism that dies in 30 days can be much more "fit" than an organism that lives for 30 years. The key is producing offspring that are themselves capable of producing offspring. So two organisms could produce equal numbers of progeny and live exactly the same length of time, but if one has progeny that are very unsuccesful at mating and reproducing then it is less fit!

      So no, Mr. Thomas, "survival of the fittest" is NOT a tautology, despite what the common creationist tropes would have us believe. And rather than pulling a Deepak Chopra, indignantly claim your right to argument of authority, and then flounce off, perhaps actually addressing the plethora of errors you made as pointed out by an *actual* evolutionary biologist like Dr. Coyne would be in order?

      But when you open your "Big Think" piece with such an incredibly poor error that my high school biology teacher would cringe that you have a high school diploma let alone your other degrees (which you obviously never use, as you yourself stated) I don't hold out much hope.

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  2. Thomas has not responded to my substantive scientific criticisms. Despite his calls for humility, he's not humble enough to admit he was wrong. I've written a further post outlinine the errors in the one above, and you can find it here: http://whyevolutionistrue.wordpress.com/2014/02/18/kas-thomas-replies-if-you-can-call-it-that/

    Jerry Coyne

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  3. given the title you have chosen for this article, one would think you might have been humble enough beforehand not to write the badly informed article you did at The Big Think. Amateurs in a field, even those with some credentials, if those credentials are never used, have much to be humble about, generally.

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  4. Scientists should share correct and accurate knowledge. They also have a duty to correct their errors and misstatements. You sir have failed miserably to do any of the above.

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  5. Anonymous9:50 AM

    About thirty examples of speciation being observed can be found here. The observations go back to the 1900's (though they really start snowballing in the 50's-60's).
    I don't know where you got your information about speciation never having been observed, but you should stop trusting that source.

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  6. Dave Wisker10:00 AM

    "What did I say in my BigThink blog that was so controversial? First let's get clear what I did not say. One of the commenters claimed I said changes in DNA were not responsible for evolution. I never said that. What I said was that point mutations (of the kind the give rise to single-nucleotide polymorphisms) are almost certainly not a major driver of evolution."

    What you also said was this: "When I was in school, we were taught that mutations in DNA are the driving force behind evolution, an idea that is now thoroughly discredited. "

    Sorry, but no biologist worth his salt would ever say this. My genetics profs at UC Berkeley (is that university good enough for you. BTW?) enever said anything near that, so forgive me if I don't buy that statement. As others have pointed out, mutations provide variation upon which forces like natural selection and genetic drift can act. A layman reading your article could be seriously mislead by what you wrote.It is your duty then, as someone who claims to be interested in science, to take the serious criticism (like Dr Coyne's) like a man and admit you may have gotten a considerable portion of your article wrong.

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  7. Possibly relevant to this is PZ's recent post, "The state of modern evolutionary theory may not be what you think it is" (http://freethoughtblogs.com/pharyngula/2014/02/14/the-state-of-modern-evolutionary-theory-may-not-be-what-you-think-it-is/). He reprises the differences between classic Selection Theory, Neutral Theory, and Nearly-Neutral, lists a number of propositions of classic theory and how they are regarded today, and gives some useful references. Net: it's a lot more complicated than "survival of the fittest," and much closer to the "survival of the luckiest".

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  8. Kas Thomas, the reason more than one commenter suggested you get some biology training before writing about evolution is because you not only demonstrated ignorance regarding evolutionary biology, you trotted out the hackneyed, repeatedly-debunked creationist arguments and fallacies.

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  9. Kas Thomas, the reason more than one commenter suggested you get some biology training before writing about evolution is because you not only demonstrated ignorance regarding evolutionary biology, you trotted out the hackneyed, repeatedly-debunked creationist arguments and fallacies.

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  10. I think you've made your point. Thank you for your opinion.

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    Replies
    1. Mr Thomas, your article has increased my knowledge of evolution's '"problems" almost as much as Kirk Cameron has.

      Well done, sir!!

      Delete
  11. Anonymous4:34 PM

    Kas, in the face of overwhelming criticism with cited eveidence, perhaps you could address the glaring deficiencies in your article?

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  12. I look at this from another angle...the way people react when anyone disagrees with them / has a different opinion from theirs.

    I know how I feel when someone has a different opinion from mine - my heart speeds up, I'm nervous, maybe scared. I don't know, but I have a feeling, if most people were honest, they'd say it's the same for them. I'd love to chat with a psychologist to find out why this happens to us.

    What I do know for sure though is this...I don't have to react in an abusive manner.

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  13. "One of the major embarrassments of modern biology is that more than a decade after having sequenced the human genome, we still don't know what most of our DNA does"

    Why, exactly, is this a "major embarrassment of Modern Biology"? What are you trying to say? - that we don't know the full answer but we should? That scientists have made no progress in this area? That you know the answer but scientists don't? That scientists think they know the answer but you know they are wrong?

    It seems to me that an "embarrassment to Modern Biology" would be to make claims for which there is no evidence, or make claims for which there is evidence but you have been too lazy to read and consider. Manufacturing controversy might drive traffic to your website, but it contributes absolutely nothing to the public understanding of science and evolutionary biology in particular - this isn't an embarrassment to modern biology as much as it is a personal and professional embarrassment for you. You likely won't have the humility to admit your error and this will compound your embarrassment. And on this point your scientific credentials cease to help you because you are no longer behaving like a scientist.

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  14. "What I said was that point mutations (of the kind the give rise to single-nucleotide polymorphisms) are almost certainly not a major driver of evolution. We know this because it's been demonstrated many times that the majority of non-neutral point mutations are deleterious, leading to loss of function, not gain of function."
    what you actually wrote is, "When I was in school, we were taught that mutations in DNA are the driving force behind evolution, an idea that is now thoroughly discredited." If you meant "mutations" to refer only to point mutations, then why didn't you say so?

    It's easy to demonstrate that the inference you're making in the above quote is faulty. If most non-neutral point mutations are deleterious, then some rare ones will be beneficial (given that beneficial, neutral, and deleterious are the only options, this conclusion is obvious). Those rare ones will give their possessors a fitness advantage which allows them to outcompete their neighbors, leading to a selective sweep. http://en.wikipedia.org/wiki/Selective_sweep It's hard to see how the cause of a selective sweep could be described as "not a major driver of evolution."

    (part 1)

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    1. "How, then, does speciation occur? We don't know."
      um, http://en.wikipedia.org/wiki/Speciation yeah, we know a lot

      "On a molecular level, there are still many things we don't understand about how chromatin is managed, how micro-RNA is regulated, when and why DNA methylases come into play, the relative importance (or unimportance) of translocases, and much, much more. To assert that we understand how speciation occurs is to assert a half-truth. It's like saying we understand the weather because we can measure atmospheric pressure."
      What you're saying is like saying that even though we can predict storms and have a strong understanding of whether to expect hail or snow, we don't understand the weather because we don't understand how cloud boundaries are maintained. Cloud boundaries are difficult to model, but if we have good, predictive models of weather that ignore them, then what's the problem?

      Like you, Kas, I am trained in biology, and it so happens that chromatin is my specialty. So I can tell you in great detail all that we don't konw about chromatin assembly, remodeling, CpG methylation, etc, but what's more important is that I can tell you just how little all those issues matter when you're talking about speciation. Your entire argument rests on a failure to separate scales, a fundamental issue in complex systems ( http://necsi.edu/guide/concepts/scale_separation.html ). The details of molecular biology just aren't that important when considering the general pattern of speciation. The key to speciaition (among sexual species) is reproductive isolation. The precise mechanism which mediates the reproductive incompatibility basically doesn't matter if the question you want to answer is, "what are the circumstances give rise to speciation?" because those circumstances are external to the organism/population. Note that the various categories, allopatric, peripatric, etc, are all informative regardless of whether we're talking about yams or clams, so how could the details of methyltransferase function matter in the slightest?

      If the question you want to answer is, "what are the underlying mechanisms that makes two philogenetically close species sexually incompatible," well then it's not unlikely that molecular details will be important. But that is just one small part of the larger problem of speciation.

      Likewise, your correct observation that we don't understand nearly all there is to know about DNA function is not evidence that we don't understand evolution, just as our failure to understand the physics behind the standard model (string theory, or whatever) does not suggest that we don't understand the behavior of crystals. These are simply separate areas of concern.

      (part 2)

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    2. "No one has seen it [speciation] occur in the lab."
      This is just special pleading. You know very well* that we do see speciation occur in the lab, it's just that you're throwing up senseless disqualifications so that those observations don't count for you. *I'm not merely telling you what I think you know, or baldly asserting that you're arguing in bad faith (I don't think you're arguing in bad faith, I just think you're terribly mistaken). In your previous article, you write, "unless you want to count plant hybridization or certain breeding anomalies in fruit flies." So you are aware that we have observed speciation in the lab. But you don't "want to count" these observations for some unspecified reason.
      * * *
      If your point is merely to suggest that we don't know everything there is to know about evolution, then it's rather discomfiting that you should present this as "The Trouble with Darwin" or "such an incomplete and unsatisfying theory on purely scientific grounds." The problems with quantum theory (e.g. measurement, non-locality, the ontological status of a waveform, copenhagen vs many worlds, etc) utterly dwarf the problems with evolution, which are more along the lines of "this is a really complex issue, and we haven't got all the information we need to solve it" - compare that to "the basic units in this theory may not actually exist." And yet quantum theory is rightly heralded as one of the most profound and important discoveries of 20th century science. Evolution is a solid a theory as any in science, and your representation of it goes a long way to abet the ignorance that plagues my country (USA).

      (part 3 of 3)

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  15. Anonymous5:07 AM

    I believe Thomas is right. The evolutionists don't know yet how DNA appeared (which is not an unimportant, but rather an essential key, the cornerstone of the neo-darwinian research program) - see the Dawking's hilarious comment about the intervention of the aliens at this point...And about the speciation, can we say that we saw in nature (not in labs) a real case of speciation? An if yes, can we say that the new species is a real progress comparing with the previous? Did we obtain a plus of information, like the incipient appearing of an eye, or ear, or something in this neighborhood? Of course not!
    The Cambrian explosion is still unexplained. That is not a minor problem: on the contrary...And of course, it is today a common place that the so-called junk DNA does not seem to be after all so junk...If so many guys critique Thomas here, they should also try to substantiate their attacks with facts...

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    1. Hey Anon., your post is nonsense.

      Not knowing how DNA appeared does not remotely change the enormous amount of scientific evidence that supports biological evolution.

      And regarding speciation, Jerry Coyne referred to a book that he wrote on that subject. Perhaps you should try actually reading it before you make your ignorance of speciation public.

      And the Cambrian 'explosion' is a problem for evolution how? You made no attempt to explain why this is a problem for evolution so can we safely assume that you are too ignorant of the subject to actually know?

      You probably wouldn't know a 'fact' of evolution if it crawled up your Jebus loving ass.

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    2. The neo-darwinian research program aims to explain the evolution of living things, not the origination of living things. Creationists like to point out the lack of consensus on abiogenesis because they feel it undermines the naturalistic account of our origins. Well, even if it did, it wouldn't help their case against evolution, which does not attempt to explain where the first living things came from.

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