Monday, February 07, 2011

Evolution's Hidden Force


I was really excited (not) when the January 8th edition of New Scientist arrived. The cover story was bound to be something I could use in my course when we discussed modern views of evolution. Even the title was provocative: Uncertainty principle: How evolution hedges its bets.1

The article was written by freelance science writer Henry Nicholls. He lives in London UK and he has a Ph.D. (2007) in Evolutionary Ecology. Here's how the article begins ...
A man walks into a bar. "I have a new way of looking at evolution," he announces. "Do you have something I could write it down on?" The barman produces a piece of paper and a pen without so much as a smile. But then, the man wasn't joking.

The man in question is Andrew Feinberg, a leading geneticist at Johns Hopkins University in Baltimore; the bar is The Hung, Drawn and Quartered, a pub within the shadow of the Tower of London; and what's written on the piece of paper could fundamentally alter the way we think about ... evolution ....
Let's turn this into a quiz.

What did Andrew Feinberg write about on that piece of paper?
  1. the importance of small RNAs
  2. random genetic drift
  3. epigenetics
  4. species sorting
  5. hierarchical theory
  6. evo-devo
  7. evolvability
  8. mutationism
  9. developmental constraints
  10. contingency
  11. alternative splicing
  12. selfish DNA
  13. the demise of the Central Dogma
  14. facilitated variation
  15. group selection
  16. phenotypic plasticity
  17. molecular chaperones
  18. genome complexity and the myth of junk DNA
  19. horizontal gene transfer
  20. the death of trees
  21. molecular drive
  22. endosymbiosis
  23. mass extinctions
  24. punctuated equilibria
  25. genomics
  26. proteomics
  27. systems biology
  28. the high cost of a beer in London
All of these things have been touted as new ways of looking at evolution. Which one did he choose?

Here's a hint ...

Before setting foot in the pub, Feinberg had taken a turn on the London Eye, climbed Big Ben and wandered into Westminster Abbey. There, as you might expect, he sought out the resting place of Isaac Newton and Charles Darwin. He was struck by the contrast between the lavish marble sculpture of a youthful Newton, reclining regally beneath a gold-leafed globe, and Darwin's minimalist floor stone.

As he looked round, Feinberg's eyes came to rest on a nearby plaque commemorating physicist Paul Dirac. This set him thinking about quantum theory and evolution, which led him to the idea that ... XXX ... might inject a Heisenberg-like uncertainty into the expression of genes, which would boost the chances of species surviving. That, more or less, is what he wrote on the piece of paper.
Hmmm ... Hung, Drawn and Quartered ... that gives me an idea. Let me write it down ....


[Photo Credit: Jaunted]

1. Most of you can't follow the link because it's behind a paywall.

15 comments:

  1. Stochasticity? None of the answers you provided seems to fit.

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  2. Amateurism and sensationalism is the major problem with the New Scientist. I have noticed that the contributors on Evolution don't read the scientific papers they cite and offer a very superficial analysis. You can be interesting and stick to good standards of scientific journalism.

    Sure, NS is a science magazine and not a journal, but it should be more critical of what eminent scientists, such as Larry Moran, have to say. Always question, never accept anything when there is even an iota of reasonable doubt: That is my motto.

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  3. The article was about epigenetics and how epigenetic control can maintain diversity in a population. In other words, as Bjørn Østman, commented none of your options seem to fit very well.

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  4. Knowing Larry's trigger points and New Scientist's predilection to getting thngs wrong, that word is probably "epigenetics". So we have "eigenetics might inject a Heisenberg-like uncertainty into the expression of genes".

    Whatever. As Larry pointed for a few zillion times, a good start would be to define the damn term. It's not like an idea that randomness plays a role in many biological phenomena is particularly new. Else, I don't know WTF the analogy to the uncertainty principle might mean.

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  5. The sad thing is that Andy Feinberg isn't a hack--here's the actual science to which this article refers:
    http://www.ncbi.nlm.nih.gov/pubmed/20080672

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  6. Anonymous, thanks for the "the actual science to which this article refers"!

    I read the paper to see what the deal is about. As far as I can see, the relation to evolution is tangential. I can't judge technical side of the massive methylation mapping. What I am missing there is an indication of the noise/errors. I.e., how much of their findings can be reasonably attributed to pure chance? But that's the experimental part and the one that's not directly related to evolution and is not IMHO very linked to the paper's main thesis.

    The rest as I see it:
    1. A hypothesis that an increased variance of the trait's expression increases fitness.
    2. Simulations aimed to prove self-evident propositions that a) when selective pressure favors large X, large X with small variance gets selected, b) when selective pressure favors alternately large X or small X, organisms with large variance of X get selected.

    #2 in no way proves #1. I am very sympathetic to #1 and I am sure there are instances where it is true and where it is false. It will be a lot of fun to think of experiment(s) that can test it most easily. All in all, however, a far cry from "Uncertainty principle: How evolution hedges its bets"!

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  7. DK says,

    I read the paper to see what the deal is about. As far as I can see, the relation to evolution is tangential.

    I haven't read the article but what you're saying can't be true.

    We were told that, "what's written on the piece of paper could fundamentally alter the way we think about ... evolution ...."

    New Scientist wouldn't lie to me, would it?

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  8. "The sad thing is that Andy Feinberg isn't a hack--here's the actual science to which this article refers:
    http://www.ncbi.nlm.nih.gov/pubmed/20080672"

    I don't agree; one can publish an article in a respectable journal and still do poor science and be labelled a hack. I'm not commenting on Dr. Feinberg here, but merely noting that your assertion is not necessarily correct. The journal that published Dr. Feinberg's article is PNAS, and there have been occasions where bizarre papers have made it in (e.g. search Margulis and PNAS).

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  9. DK says:"I read the paper to see what the deal is about. As far as I can see, the relation to evolution is tangential."

    Exactly. Even Feinberg himself is quoted in NS article (full text online here) saying that methylation is not typically transmitted between generations, so doesn't have much to do with long term genetic or morphological change.

    But - he is arguing that proneness to methlyation (i.e. CpG dinucleotides) is non-randomly distributed in the genome, making for a mechanism of sorts that may enhance fitness in variable environments.

    Let's say that it probably won't be an idea that shakes the world of evolutionary biology to its very core.

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  10. Although not disputing an important contribution of Lamarkcian inheritance, ..

    Not the most lucky expression!

    In quantitative genetics good theoretical studies on variances exist. Feinberg did not even try to find out whether anybody had done a model more or less like this before.

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  11. Larry, what the article actually said was:

    "What's written on the piece of paper could fundamentally alter the way we think about epigenetics, evolution and common diseases."

    I think cutting out key parts of the quote and then criticising the mutilated version, rather than the ours, is unfair. It's not the sort of thing you'd take to kindly if creationists did it.

    Further down in the piece, we clearly state:

    "As surprising as Feinberg's idea is, it does not challenge the mainstream view of evolution."

    The piece also reflects some of the scepticism expressed here:

    Jerry Coyne, an evolutionary geneticist at the University of Chicago, is blunter. "There is not a shred of evidence that variation in methylation is adaptive, either within or between species," he says. "I know epigenetics is an interesting phenomenon, but it has been extended willy-nilly to evolution. We're nowhere near getting to grips with what epigenetics is all about. This might be a part of it, but if it is it's going to be a small part."

    I'm sorry if you feel we lied to you. But Henry and I (the editor of the feature) worked hard to try to ensure the piece was balanced and put Feinberg's ideas in context for a general readership, and I still think we did a pretty good job.

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  12. Michael Le Page says,

    Larry, what the article actually said was:

    "What's written on the piece of paper could fundamentally alter the way we think about epigenetics, evolution and common diseases."

    I think cutting out key parts of the quote and then criticising the mutilated version, rather than the ours, is unfair. It's not the sort of thing you'd take to kindly if creationists did it.


    Gimme a break. My posting was supposed to be a quiz and including the word "epigenetic" would have sort of given it away, no?

    Besides, if you check your cover page you'll see that criticizing you for overblown statements about evolution isn't exactly out of line.

    I'm sorry if you feel we lied to you. But Henry and I (the editor of the feature) worked hard to try to ensure the piece was balanced and put Feinberg's ideas in context for a general readership, and I still think we did a pretty good job.

    I didn't say you lied but you sure did try and turn a molehill into a mountain. Are you aware of the fact that we've known about methylation of DNA sequences for 35 years? Mutations that affect methylation in bacteria and bacteriophage have been well-studied for decades and natural variants of methylation in bacterial strains are hardly new.

    There was even a Noble Prize in 1978.

    It's too bad the bartender didn't have a copy of a microbiology textbook. :-)

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  13. OK, here's a challenge. Conduct a straw poll of some of your biologist colleagues who haven't read the article. Ask them what causes the variation in phenotypes seen within any species.

    I bet the majority will say it is a combination of genetic variation and environmental variation - and the interaction between the two. A few might mention developmental noise. If they mention epigenetics at all, they probably have in mind adaptative changes that are genetically programmed.

    What Feinbergy is claiming, by contrast, is that a lot of the variation is due to random epigenetic changes, and that this is not mere "noise" in the system, but that there is actually a special mechanism for producing it.

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  14. I gave up my long time subscription to New Scientist (off and on since the sixties) after the 'Darwin was Wrong' article. I realised that the New Scientist was now featuring opinion and entertainment rather than science.

    The epigenetics article was another example of this trend.

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  15. "Ask them what causes the variation in phenotypes seen within any species."

    Right, we've never encountered terms like penetrance or even bothered to enumerate what mechanisms could possibly be behind phenomena like that...

    And don't say 'random'; use the term 'stochastic'.

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