🚀 go-pugleaf

In article <DnIxD5.qs@ncifcrf.gov>, toms@kaylor.ncifcrf.gov (Tom Schneider) writes:
|> SproutsRad (sproutsrad@aol.com) wrote:
|> : In bionet.info-theory John Baez (baez@guitar.ucr.edu) writes:
|> 
|> : >So what I'm wondering is this: given the complete genome of an organism,
|> : how
|> : >much *additional information* would you need to give someone for them to
|> : >be able to build a living copy of that organism? 
|> 
|> : I don't see how there could be a general answer to this question.
|> 
|> Of course there has to be an answer, at the very minimum it would be
|> the additional information needed to specify the locations of the atoms
|> within their vibrational "cloud" of possible positions.
|> 

  Maybe I misunderstood the question, but I would think that one needs very 
  little additional information, namely the concentration of the molecules 
  in the cell that are not encoded in the genome and information about the cell
  wall.
  Let's restrict the discussion to a bacterial cell:
  The vibrational state is not important because the system would equilibrate
  quickly (as long as the initial postions and momenta were within reasonable
  bounds.)
  Alternatively, we could run a molecular dynamic simulation for each species of 
  molecule in water at 300 k and 'measure' the equilibrium positions and
  vibration amplitudes.
  Now for the macromolecules : Their primary structure is encoded in the DNA, 
  if we know the genetic code used.
  If we had a general folding algorithm which would allow us to predict from
  the primary structure the secondary, tertiary and quartery structure, we
  would have to know only the number of each species of molecule 
  present in the cell.
  Of course, today such a general algorithm is not available, but regarding
  the number of smart people working on that, I would guess that it's only
  a question of time until this problem is solved.
  Maybe we could even compute the number of each macromolecular species in the 
  cell, if we could compute the interaction strength of the repressor and
  activator molecules with the the promoter and operator sequences in front of 
  each operon and the resulting rate of initiation of translation.  

  Maybe I'm unusually optimistic today :-)

  Regards

  Hendrik Tiedemann 
II. Institute for Theoretical Physics
    of the University of Hamburg
Luruper Chaussee 149
22761 Hamburg 
Germany
E-mail : tiedeman@x4u2.desy.de