On Wed, 18 Jun 2003 02:35:29 +0000 (UTC), ragland37{at}webtv.net (Michael
Ragland) wrote:



Some basic biology:  First, the genome seems to be filled with a lot
of "junk" that looks very clearly like it serves no function.  Second,
it is filled with a lot of stuff for which can discern no function,
but which may later turn out to be important in some way.  Third,
there are actual coding regions that seem to actually be used to code
for something.  And fourth, there are control regions involved in
determining just which sections are to be transcribed when.  Virtually
all of the genome is in the first two categories -- very little is in
the last two.

My metaphor of the genome as a very badly edited cookbook is based on,
first, the idea that most of the genome seems to be non-functional.
That is the lack of editing -- there are tried and failed recipes,
partially copied recipes, little pieces of ideas for recipes, and an
awful lot of just plain scribbling in between and even in the middle
of the good recipes.  

Second, it is based on the idea that the genome describes the basic
ingredients for every protein that any cell in that species is capable
of making.  It lists all the possibilities.  No one ever makes all the
recipes in a cookbook.  You have to pick and choose just which ones
you want for any particular type of meal.  The cell does the same --
picking and choosing just which genes to express.  The picking and
choosing is NOT in the genome -- it is in the the functioning of the
complex organization of the cell machinery, itself.

Third, just knowing the ingredients for a dish doesn't mean that you
can make it properly.  It takes a trained chef using the right tools
and with a lot of experience to prepare and mix and cook and finally
present a dish.  Similarly, the genome describes a basic sequence of
amino acids to make a protein, but the "chefs" in the cell then cut
and splice different pieces of protein together, throwing away some
parts, and most importantly folding the protein into the proper shape
and relocating it to the proper location in the cell before it is
functional. That post-translational processing is NOT in the genome --
it is in the functioning of the complex organization of the cell
machinery.

That is why I downplay the significance of the genome.  In one sense,
it is everything.  But in another sense, it really is only a very
small part of a functioning cell.  Molecular biologists naturally
emphasize the first interpretation.  Cell biologists and organismal
biologists emphasize the second.  As an organismal biologist, I
emphasize the complex organization of the living cell as being
absolutely essential to understand how the genome is expressed.  That
is why, now that we "know" the complete human genome, we really still
don't know much.  Interpreting the genome is the goal.

You really do need to get a good basic education in biology -- you
need a good basic grounding in biochemistry, molecular biology, cell
biology, and organismal physiology, not to mention ecology and
evolution.  You are trying to put together in your own mind a fairly
complex story, integrating pieces from here and from there to see how
it all fits together.  However, when you do have a better sense of
what is going on, you will also get a very different impression and
much improved notion of how it all hangs together.  I think that is
why, when Larry Moran and Lilith and I try to explain things to you,
you come back with more "naive" questions.  There is nothing wrong or
inappropriate with your questions -- they are just what you would hope
for from a student with burning curiosity and intense imagination but
not a lot of the basic facts.  Still, geting a good biology background
would help you understand things like Lilith's point about the basic
question of just what a "gene" really is and even in how to use some
of the basic tools of molecular biology and bioinformatics like
GenScan.
---
þ RIMEGate(tm)/RGXPost V1.14 at BBSWORLD * Info{at}bbsworld.com

---
 * RIMEGate(tm)V10.2áÿ* RelayNet(tm) NNTP Gateway * MoonDog BBS
 * RgateImp.MoonDog.BBS at 6/18/03 3:03:01 PM