Re: Is evolution really the central theory for all of biology?

From: Cornelius Hunter <>
Date: Thu Sep 22 2005 - 14:49:08 EDT


This is a knowledge-based approach that does not require evolution, per se. We call it an evolutionary approach in normal science because evolution is the paradigm, not because evolution is required, per se. This is an excellent example of what Phil is talking about. You can, for example, replace "evolutionary" with "design" and have the same paper.


  ----- Original Message -----
  From: Hofmann, Jim
  To: Bill Hamilton ; Dick Fischer ; ASA
  Sent: Thursday, September 22, 2005 8:19 AM
  Subject: RE: Is evolution really the central theory for all of biology?

  Published online before print September 19, 2005
  Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0501046102
  Cell Biology
  An evolutionary proteomics approach identifies substrates of the cAMP-dependent protein kinase
  ( Ras proteins | sequence conservation | stationary phase )

  Yelena V. Budovskaya *, Joseph S. Stephan *, Stephen J. Deminoff, and Paul K. Herman

  Department of Molecular Genetics, Ohio State University, Columbus, OH 43210

  Edited by Anthony J. Pawson, University of Toronto, Toronto, ON, Canada, and approved August 12, 2005 (received for review February 7, 2005)

  Protein kinases are important mediators of much of the signal transduction that occurs in eukaryotic cells. Unfortunately, the identification of protein kinase substrates has proven to be a difficult task, and we generally know few, if any, of the physiologically relevant targets of any particular kinase. Here, we describe a sequence-based approach that simplified this substrate identification process for the cAMP-dependent protein kinase (PKA) in Saccharomyces cerevisiae. In this method, the evolutionary conservation of all PKA consensus sites in the S. cerevisiae proteome was systematically assessed within a group of related yeasts. The basic premise was that a higher degree of conservation would identify those sites that are functional in vivo. This method identified 44 candidate PKA substrates, 5 of which had been described. A phosphorylation analysis showed that all of the identified candidates were phosphorylated by PKA and that the likelihood of phosphorylation was strongly correlated with the degree of target site conservation. Finally, as proof of principle, the activity of one particular target, Atg1, a key regulator of autophagy, was shown to be controlled by PKA phosphorylation in vivo. These data therefore suggest that this evolutionary proteomics approach identified a number of PKA substrates that had not been uncovered by other methods. Moreover, these data show how this approach could be generally used to identify the physiologically relevant occurrences of any protein motif identified in a eukaryotic proteome.

  size=2 width="50%" align=left>
  Author contributions: Y.V.B., J.S.S., S.J.D., and P.K.H. designed research; Y.V.B., J.S.S., and S.J.D. performed research; Y.V.B., J.S.S., S.J.D., and P.K.H. contributed new reagents/analytic tools; Y.V.B., J.S.S., S.J.D., and P.K.H. analyzed data; and Y.V.B., J.S.S., and P.K.H. wrote the paper.

  *Y.V.B. and J.S.S. contributed equally to this work.

  To whom correspondence should be addressed.

  Paul K. Herman, E-mail:

  Jim Hofmann


  From: [] On Behalf Of Bill Hamilton
  Sent: Thursday, September 22, 2005 6:18 AM
  To: Dick Fischer; ASA
  Subject: RE: Is evolution really the central theory for all of biology?

  Before we leave this topic, at the risk of saying something that has already been said, here's my take:

  I'm probably biased because I'm trained as an electrical engineer -- meaning that my view of the sciences is the so-called "hard" sciences -- chiefly physics. To an individual with a physics bbackground, evolution looks "messy". If we could have more fossils and could recover more genetic material from ancient life forms, perhap it wouldn't be so messy. An article in a now defunct magazine called Scientific Research ~1967 dealt with the Wistar Symposium in which Professor Murray Eden brought up some mathematical challenges to the theory of evolution. They interviewed Eden and among other things he mentioned a paper submitted to one of his colleagues for review. The paper discussed the evolutionary implications of the dominance of a particular variety of rodent (I believe) in a particular location. To see what would happen, Eden changed the variety and circulated the paper to colleagues for comment. Soon evolutionary explanations came back. The article implied that t his pointed out a flaw in the theory of evolution. I think it just points out that evolution is an incomplete model, but still very useful for understanding how life has developed in a systematic way and for making some kinds of predictions. It does not now have the precision of say classical physics, but it is still a useful model. (And we all know that classical physics is an approximation of relativistic physics (at high gravity/high speed) and quantum mechanics (at the quantum level))

  Dick Fischer <> wrote:

    Cornelius brought this up:

    . a paper out of Doolittle's lab has called for a "relaxation of tree thinking."

    This is a good example of scientists doing what scientists do and the great unwashed, not steeped in science, reaching errant conclusions. The "tree of life" with more and more fossils having been found has developed into more of a "bush." Richard Leakey pointed this out in his book, Origins Revisited. Note the title of his book. With new discovery of fossil evidence, branches are reshaped when the evidence accumulates. No one with any sense denies the interconnectedness of life, but exactly where and wh en branching occurred gets revised with new discovery as it should, that's how science works.

    ~Dick Fischer~ Genesis Proclaimed Association

    Finding Harmony in Bible, Science, and History

  Bill Hamilton
  William E. Hamilton, Jr., Ph.D.
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Received on Thu Sep 22 14:54:21 2005

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