Thursday, April 01, 2010

Things You Didn't Know

Patricia J. Wittkopp is a Professor in the Department of Ecology and Evolutionary Biology at the University of Michigan in Ann Arbor. She got her Ph.D. in 2002 with Sean Carroll.

Anything found to be true of E. coli must also be true of elephants.

-Jacques Monod (1954)
Wittkopp has just published a paper in PLoS Biology: Variable Transcription Factor Binding: A Mechanism of Evolutionary Change. The second paragraph tells you something you didn't know.
During the last decade, researchers have discovered that the collection of proteins found in different animals is remarkably similar. In fact, many proteins are found not only in animals, but also in fungi and plants; some are even shared with bacteria. This unexpected—and truly astounding—finding has changed scientists' thinking about how biological diversity evolved ...
Isn't that cool? Before 1990, researchers didn't know that many animal proteins had homologs in fungi, plants, and even (gasp!) bacteria.

I presume she means that she didn't know this because she was still in high school.


10 comments :

  1. Even worse than that: "during the last decade" to me means during the last ten years; that is, since 2000,, not 1990. I guess my college professors were extremely prescient to predict that proteins like DNA polymerase were homologous across kingdoms...

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  2. Jeez, I will need to pull and read the paper. I hope that she meant something more subtle and it came out wrong. It wasn't the physicist Sean Carroll by chance was it???

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  3. It's actually a lot older than 1954. Albert Jan Kluyver, one of the fathers of microbiology, said "From the elephant to the butyric acid bacterium — it is all the same" as early as 1926. What Jacques Monod did was to rephrase it in a more catchy way.

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  4. Actually, wasn't the Monod quote in the context of the operon? In which case he was incorrect

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  5. It seems like an editorial oversight to me. Here's the entire paragraph:

    During the last decade, researchers have discovered that the collection of proteins found in different animals is remarkably similar. In fact, many proteins are found not only in animals, but also in fungi and plants; some are even shared with bacteria. This unexpected—and truly astounding—finding has changed scientists' thinking about how biological diversity evolved; while it was once believed that changes in the sequences of proteins were primarily responsible for phenotypic differences within and among species, it is now clear that changes affecting the production (i.e., “expression”) of proteins also play a prominent role [1]. This evolutionary potential of gene regulation was recognized long before the molecular mechanisms controlling this process were understood [2],[3], but only recently have researchers begun to identify regulatory changes that contribute to the evolution of specific traits (e.g., [4]–[8]).

    Both refs 2 and 3 make reference to evolutionarily conserved sequences and predate the "last decade" claim. What the author is probably referring to is the fact that, in the last decade, the number of whole-genome sequences has increased drastically allowing us to better understand the extent of the inter-taxon conservation. Granted, that is not what the author said, but given that two of her citations predate the last decade and discuss inter-taxon conservation, she probably knows that such ideas have been around for much longer than a decade.

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  6. Michael, I started graduate school in the 1960s and I can't remember a time when my colleagues didn't think that changes in gene expression were very prominent causes of differences in phenotypes.

    This was common knowledge by the time Gould wrote Ontogeny and Phylogeny in 1977. Here's what he says when discussing the differences between humans and chimpanzees.

    What, then, is at the root of our profound separation. King and Wilson argue convincingly that the decisive differences must involve the evolution of regulation: small changes in the timing of development can have manifold effects upon a final product "... The organismal differences between chimpanzees and humans would then result chiefly from genetic changes in a few regulatory systems, while amino acid substitutions in general would rarely be a key factor in major adaptive shifts."

    Wittkopp implies that all of this is a recent insight. I don't count four decades ago as recent.

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  7. I guess what the article had in mind is that the transcription factors and signaling cascades involved in development are largely the same and it is changes in their levels, timing and place of expression that cause the differences in phenotype we observe between phyla.

    It does not at all come out sounding like this, and you are absolutely correct to call it out for that, but the above isn't a meaningless insight. Of course, with the caveat that I haven't been around in the 60's (neither the 70's, 80s or 90's) and all the people who have taught me developmental biology have either also not been around for very long or were evo-devo biologists themselves; or both.

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  8. That is exactly the sort of thing I expect someone who studied under Sean Carrol to write. I am an outsider with regard to the evo devo and so I very well might be confused about it but many papers from Carroll's lab left an impression on me that they report something rather mundane under the guise of a great discovery.

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  9. My point was that Wittkopp most probably misspoke (or miswrote). She has written several reviews on the evolution of gene regulatory networks in which it is quite clear that she know that literature on homologous gene regulatory networks didn't suddenly begin in 2000.

    Thus, it seems much more appropriate to take her to task for poor prose rather than a deficiency in he knowledge.

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  10. No one wants to stand on the shoulders of giants anymore.

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