Re: [DIYbio] Advice for a computer scientist who doesn't understand biology

On Fri, Feb 8, 2013 at 3:22 PM, William Heath <wgheath@gmail.com> wrote:
> 3. The biology field and most of the people in the field are not computer
> scientists and are very shocked to discover that cells are actually hardware
> (cells) executing programs (dna).

This has been discussed before in-depth, and it really is a vast
simplification to say DNA is THE program.

See:
Comparing E. coli to Linux
https://groups.google.com/d/topic/diybio/TfhBPXFgl4M/discussion

> 5. Synthetic biologists are the elite of biology.

WHAT? That's a bit preposterous. Synthetic biologists exist because of
the work traditional biologists and chemists have done, don't scoff at
them because their method for uncovering knowledge seems awkward in
hindsight. The paradigms have served well in the past, that doesn't
mean they're fit for the future, but without them we wouldn't have
synthetic biology at all.

Give this a read if you want to understand the biologist/engineer
paradigm differences:
Can a Biologist Fix a Radio? —or, What I Learned while Studying
Apoptosis. Y. Lazebnik. Cold Spring Harbor Laboratory
http://www.protein.bio.msu.ru/biokhimiya/contents/v69/pdf/bcm_1403.pdf

> 6. The fundamental way that innovation/research is done in synthetic
> biology is understanding proteins. The accepted way to understand/analyze
> proteins is to do xray crystallography.

Don't ignore the simple chemistry of the various groups, the shape
only tells you where they are, and gives some indication to the
electronic state of the molecule.

> 8. Understand that synthetic biology is trying to understand the mind of
> God. This is also heresy in the biological community as most are darwinists
> and refuse to acknowledge a creator. When you realize this it helps you
> really think outside the box. For example, understand that nature is using
> quantum mechanics to select for fitness. God wrote DNA and setup all the
> systems that cause life to work. It is not wasteful or inneficient. I
> absolutely did not believe in junk DNA as was later proved right. God
> doesn't make junk and the entire universe is engineered by God to support
> life. Understanding this allows you to make discoveries that normal
> darwinists cannot make as easily in my opinion.

Isn't God a point of factual contention, thus limiting it to the realm
of theory? Doesn't science limit theory from becoming fact until proof
has been established?


>
> 9. Use python not perl when possible. If you use python other biologists
> can use it as it is 10 times easier than perl. Python has a wonderful
> library called biopython (http://biopython.org/wiki/Main_Page). It is not
> as good as perl but could be close enough for what you want to do.
>
> 10. An hour in the library is worth 100 in the labratory. If you can
> simulate or find papers on what your trying to do it is going to save you
> much time and money on accomplishing your goal in synthetic biology.
>
> 11. I am probably one of the only people in the world that can give you an
> accurate comparison of silicon based computing compared to cell based
> computing:

Seems like you're ignoring the folks who had the same idea in that
PNAS paper linked via the DIYbio discussion comparing E.coli to linux,
as well as Anselm who directly engaged you in that discussion. Seems
like you're saying you have secret knowledge that other's in the field
don't have, this sounds like the tenure-track professors you
complained about.

--
-Nathan

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