Re: 'not an artist' article

[Pierre Phaneuf <pp@ludusdesign.com>]

Erik wrote:

> I'd imagine that quite a few of the 'simpler' have very limited
> sets of genes, and fairly controlled patterns. Take atomic assembly
> at the first state of excitation, there is a very simple and definite
> way that atoms are put together, and given just 2 numbers you can
> accurately model a stable atom. You can also easily model interactions
> between atoms that create molecules. There're a lot of different atoms
> (check a periodic table), and a HUGE number of molecules. But with a
> small amount of 'control' data you can accurately construct atoms
> and molecules.

I am in the high performance supercomputing area (supporting NEC SX-4
and SX-5 vector machines, one of them with 128 gigabytes of RAM), and my
girlfriend is a microbiologist doing a master related to molecular
biology (genes and proteins).

This is so far away from being possible, you can't possibly have an
idea.

Proteins are a chain of amino acids tied together to form a single long
molecule (a polymer). DNA is transcribed into RNA, which then goes into
a ribosome to be translated into a protein by assembling the smaller
molecules. Proteins are NOT straight, they are twisted all over
themselves because of various atomic forces that attract and push away
other atoms. The shape of the resulting protein is called its
conformation, and it determines what the protein will actually do, by
having various "activation sites" at specific places in its structure.
For example, the hemoglobin protein is shaped like a ring, with iron
atoms along the inside part of the ring, which binds with oxygen atoms
to carry them.

Determining what amino acids will be produced by the translation process
is easy. Determining their conformation (which is what determine their
function, remember) is amazingly hard. Even the largest and most
powerful supercomputers can barely predict how two or three amino acids
will conform, and there are hundreds or even thousands of amino acids in
proteins!

When this will be possible, we will have attained a very important
milestone of molecular biology. Currently, we find out what genes do by
trial and error, passing them through ribosomes and checking out what
protein comes out of it, but when this problem will be solved,
scientists will be able to say "okay, I'd need to create a protein with
this and this feature" and have a computer tell them what string of DNA
will given them what they want. It is the difference between finding
something and using it as well as you can to do what you want, and
designing something specifically made to solve the problem at hand.

In the meantime, we suck. ;-)

-- 
"Unix is the worst operating system; except for all others."
 -- Berry Kercheval

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