On Tue, 17 Jun 2003 03:52:12 +0000 (UTC), ragland37{at}webtv.net (Michael
Ragland) wrote:

>Mr. Norman, I'm not a biologist but don't try to pull the wool over my
>eyes. Where do the proteins come from? The genetic code consists of 64
>triplets of nucleotides. These triplets are called codons.With three
>exceptions, each codon encodes for one of the 20 amino acids used in the
>synthesis of proteins. That produces some redundancy in the code: most
>of the amino acids being encoded by more than one codon. Proteomics
>complements genomics and extends functional analysis. Here is a
>definition of functional genomics:
>
>[Functional genomics] is characterized by high throughput or large-scale
>experimental methodologies combined with statistical and computational
>analysis of the results. The fundamental strategy in a functional
>genomics approach is to expand the scope of biological investigation
>from studying single genes or proteins to studying all genes or proteins
>at once in a systematic fashion. Computational biology will perform a
>critical and expanding role in this area: whereas structural genomics
>has been characterized by data management, functional genomics will be
>characterized by mining the data sets for particularly valuable
>information. Functional genomics promises to rapidly narrow the gap
>between sequence and function and to yield new insights into the
>behavior of biological systems."  
>
>In brief, the "central belief embedded in functional genomics is that
>the complete sequence of the genomes of many organisms, including
>humans, will change the way we do biology" towards a more holistic view
>of biological systems which is significantly different from the
>classical idea of investigating 'one (or a few) gene at a time'
>
>
>You mentioned how you liked my analogy of removing a cover and seeing
>the genes but now we have to identify their functions. How do you like
>this analogy: "The human genome has often been compared to a book in
>which the letters are nucleotides. We can now look at all of the pages
>of this book, but we lack the ability to fully understand the letters
>and words we observe. One of the major concerns of Statistical Genomics
>is to provide researchers with the tools that allow them to decipher the
>language of the human genomic book."
>http://www.biom.cornell.edu/Homepages/Rasmus_Nielsen/interests.html.
>
>Or, how about this for functional genomics:
>
>"We hope to be able to develop methods that can answer important
>evolutionary questions and provide methods that may establish links
>between variation at the level of the DNA and variation in organismal
>form and function. For example, what are the important genetic factors
>that cause phenotypic differences between humans and our close relatives
>the chimpanzees? Or what are the genetic factors the cause certain
>heritable diseases? These are among the most important genomic questions
>that we are trying to answer."
>http://www.biom.cornell.edu/Homepages/Rasmus_Nielsen/interests.html.
> 
>You write, "In a few decades (or a few years), we may discover that the
>"silent" and "junk" and "non-transcribed"
regions of DNA really do have
>a major functional role in the cell. When that happens, I'll change my
>tune. That is the way science works. We change with the times. But the
>smart money, for the time being at least, is with the proteins."
>
>Mr. Norman, you're a dying breed. It seems to me you're against genetic
>engineering of human beings. Although you state, "And I already cited
>speculation on creating modifications of the code with genetic
>engineering. It is not fixed and immutable! However, nature can really
>no longer do any significant tinkering with it for eukaryotic nuclear
>genes because such an elaborate system has been built around the
>existing code" what you're saying is "nature" (Darwinian
evolution?) can
>no longer do any signifigant tinkering. Theoretically, I don't think
>this is true. I think given enough evolutionary time (millions of years)
>"nature" could gradually do signifigant tinkering with the
genetic code.
>The question is do we as a species have the luxury of millions of years?
>I don't think so. 
>
>There is no question an elaborate system has been built around the
>existing code but that doesn't mean its not flawed and needs to be
>improved. Currently, we can't change the code without disastrous results
>but functional genomics and the complementary field of proteomics are in
>their infancy. Ultimately, genetic engineering will enable us to make
>changes in our genetic code which would have taken Darwinian evolution
>millions of years.  
>
>I'm a "dying breed" too except I acknowledge it. The current human race
>of some 6 billion people is extinct. Either it will be exterminated by
>idiots or gradually through genetic engineering it will become extinct.
>Which do you prefer?
>
The two of us are just looking at the same thing with somewhat
different perspectives.  You say that "Proteomics complements genomics
and extends functional analysis" and then go on to laud "functional
genomics" (after a short detour on elemantary genetics).  What I am
emphasizing is that proteomics is exactly that functional analysis
which you say is so important.  For example, this is from the
e-Proteomics page of the ALtruis Biomedical Network
(http://www.e-proteomics.net/)

"With the completion of the Human Genome Project, the emphasis is
shifting to the protein compliment of the human organism. This has
given rise to the science of proteomics, the study of all the proteins
produced by cell type and organism. As sequencing of the entire
genomes of many prokaryotes and eucaryotes has been completed, we are
seeing a revival of interest in proteomics."

"The term proteome refers to all the proteins expressed by a genome,
and thus proteomics involves the identification of proteins in the
body and the determination of their role in physiological and
pathophysiological functions. The ~30,000 genes defined by the Human
Genome Project translate into 300,000 to 1 million proteins when
alternate splicing and post-translational modifications are
considered. While a genome remains unchanged to a large extent, the
proteins in any particular cell change dramatically as genes are
turned on and off in response to its environment."

My point is that the genome is like a massive cookbook with recipes
for everything that you could ever make.  Unfortunately, the cookbook
was never edited and all the previous drafts and rewrites and
crossed-out material plus massive quantities of every piece of scrap
paper that any cook every owned is mixed in with the recipes.  So the
actual valid recipes form only a tiny fraction of the work and are not
marked or identified in any way we can tell.  The problem is that
cooks actually use the book to prepare fine meals!  The point is that,
given the cookbook, there is no way to tell whether you are eating a
cheap breakfast in a greasy spoon or the finest dinner in the best
epicurean restaurant -- its all in the cookbook somewhere.  The real
significance is in the meals that are served, in the expression of the
genes, not in the list of recipes.  Now imagine that a cryptographer
got hold of the book and substituted a "V" for every
"A", a "T" for
every B, etc.  It would still be the same cookbook with the same
recipes, provided you decoded it properly when you cooked the food.
That exactly what would happen if the genetic code was changed.  And
that is why I say that the code, itself, is irrelevant. Are you sure
you are not confusing the concept of the genetic code with the actual
seqence of the genome?  Changing the genes is important, changing the
genetic code is not.

Two other points.  Yes, I am opposed to human genetic engineering.  I
am all for fixing things that are broken, but I am opposed to
"improving" the species -- eugenics.

Second, you say that :given enough evolutionary time (millions of
years) "nature" could gradually do signifigant tinkering with the
genetic code."  Sorry, nature has had several billions of years and
has only managed to come up with a few very small modifications.
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