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Genome as Program II: b-galactosidase chart

Gary Welz gwelz at panix.com
Sun May 7 18:11:16 EST 1995


Readers,
In an earlier posting I proposed that it could be valuable to consider 
the genome as a computer program and analyze it with flow charts of the 
type used in writing software.  Since that time I have received some 
very helpful email concerning how this might be done.

Several readers said that the genome's program must be a highly parallel 
one and that we must think of flow charts as diagrams representing the 
processes involved in gene expression.  These would not be charts of a 
program that is written in the gene, so much as they are descriptions of 
the processes that can be observed.
 
As a sample of the kind of chart I have in mind, below is a flow chart 
for the expression of the beta-galactosidase gene in E. coli.  This is 
obviously a well known process, though perhaps not previously 
represented in this kind of programming schematic.  

***********

Flow Chart of the process of beta-galactosidase 
gene expresssion in E. coli


      |
      |__________________________________________
      |                                         |
     / \                                        |
    /   \                                       |
   / if  \           ___________                |
  /glucose\____yes_| b-gal not |                |
  \present/        |transcribed|                |
   \     /         |___________|                |
  (activator shows                              |
  small molecule                                |
  present)                                      |
      |                                         |
      |no                                       |
      |                                         |
      |                                         |
      |                                         |
    /   \         _________________             |
   / if  \        |repressor binds |            |
  /lactose\--yes--|to operator     |            |
  \present/       | b-gal not tran-|            |     
   \     /        |scribed         |            |
    \   /         |________________|            | 
      |no                                       |
      |                                         |
  ____|_________________                        |
  |RNA Polymerase       |                       |
  |transcribes          |                       |
  |gene, b-gal made     |                       |
  |_____________________|                       |
      |                                         |
      |                                         |-- glucose 
      |                                         |   feedback
  ____|_______________________________          |   loop 
  |b-gal enzyme breaks down lactose  |          |
  | into galactose and glucose       |__________|
  |__________________________________|


********

Please suggest other processes that could be expressed in this way.

I want to extend this method to larger parts of genomes and ultimately 
entire genomes.  A crude picture of the entire genome of some virus or 
bacteria would be a good start.  On the macro-scale it must look 
something like this:


                  |            |   ____     
        ..... ___/\-----------/\___|  |......
													/\	 \/           \/   |__|
             \/   |     |     |
              |   |    /\-----|
              .   .    \/     .
              .   .     |     .
     
There would be many processes running concurrently with some dashed 
lines representing connections between them.  

The two main subroutines would be a developmental subroutine and a "life 
function" subroutine.  The developmental routine would handle all the 
gene expressions involved in organism development, the life function 
routine would handle all the gene expressions involved in eating, 
breathing, excretion, reproduction and so forth.  Initially the 
developmental round would dominate, later the functional routine would.

My first article dealing with this topic is scheduled to appear in the 
July issue of a new computer magazine called "The X Advisor" - I will 
post an early draft here during the coming weeks.

Comments are welcome.

Gary Welz
Dept. of Mathematics
John Jay College
City University of New York





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