Re: PiP OOL 1 - Origin of Life == Emergence of Biochemistry

On Thu, 29 Nov 2007 17:40:03 -0700, dkomo <dkomo871@xxxxxxxxxxx>
wrote:

r norman wrote:

On Tue, 27 Nov 2007 18:55:43 -0700, dkomo <dkomo871@xxxxxxxxxxx>
wrote:


Perplexed in Peoria wrote:


This is the first of a planned series of postings in which I will present some
details of my vision of an autotrophic, metabolism-first, membrane-centric
account of abiogenesis. As has been the case with previous planned
posting series, this one may not reach completion if my motivation
peters out, but ... here goes. Blame Howard Hershey for getting me
started.

I want to begin by taking a fresh look at that old chestnut of a question:
"What is an appropriate definition of life, for purposes of talking about
the origin of life?". I'm going to provide a somewhat 'flip' answer to
this question. "'Life' originates at the same point in time at which
biochemistry emerges from chemistry." That is, if we were observing
the origin of life by using a time machine, we could say that life has
originated at the stage in the process where a chemist studying the
process would say "This ain't just chemistry anymore. What is
happening here is outside my field. We need to call in a biochemist."
Bear with me on this - my answer may grow on you.


I find this a bit circular. Biochemistry is defined as the study of
substances which occur inside of living things. If life is just
starting to emerge, don't you have a problem defining exactly what
biochemistry is?

The definition of organic chemistry is sharp: it's the study of
carbon-containing substances, and hence biochemistry is a subset of
organic chemistry. Organic chemistry might deal with substances like
plastics and petroleum which are not in the domain of biochemistry.


I think you are being a bit hard on poor PiP. He has a good idea here
to start with (even if his facts are wrong). There is time to jump
all over him when he starts saying something.

The notion is an excellent one that biology and biologists are
concerned with function (in a funny sort of way) because biological
objects including biochemicals are agents in a larger system and their
function is the role they play in that larger system. That indeed is
a really important difference between chemists and biologists.


I'm not so sure. If a chemist is working on synthesizing a complex
molecule requiring 200 derivation steps involving dozens of other
chemicals and using advanced lab equipment, I'd say he'd have to be
quite aware of the functions of all the components and their roles in an
entire synthesis system.

I think the point about life is that there is more to the system than
the reaction sequence, itself. Of course if the chemist is to get
paid for doing that work, he'd better have some awareness of the role
that the result will play in some sort of economic activity (or social
benefit). From my perspective, the "higher" role of all the
components in a biological system is the whole point of biology. But
you need people who investigate the separate components and how they
work regardless of or even uncaring about any such higher order system
and role. This is sort of like arguing in physics which is "more
important", the theorist or the experimentalist. Both are necessary
and they feed off each other.

I think the point PiP is making is that chemical substances become
biochemicals and part of biology when and only when the chemistry
involved becomes part of a larger system so that there is indeed a
proper function or role that the chemicals play in the larger system.
They then become not important in and of themselves, but only as part
of the whole.

The problem is in where to locate the people traditionally called (or
self-identified as) biochemists. Consider that many of them come from
chemistry departments or chemistry backgrounds, not biology. Most
biochemists don't really have the perspective you suggest . You might
be remembering the good old days (a century or so ago) when
biochemistry was originally physiological chemistry. Back then it
was as you describe it.


The Campbell and Reese biology text 6th edition says that "Biochemists
now know the amino acid sequences of more than 100,000 proteins and the
three-dimensional shapes of about 10,000." Imagine how much work was
done to accomplish all this. How many more proteins are still out
there? I'd say biochemistry is a speciality with pretty good job security.

Accountants have pretty good job security but that doesn't make
accounting a vibrant field filled with exciting ideas (fortunately, my
friends who are accountants don't read this group). People who do
good work in their carefully delimited areas are absolutely vital to
the development of biology. I just want to point out that different
disciplines have very different perspectives on what questions are
important enough to spend years and lifetimes working on. And I agree
completely with your point that attention to that "higher" function is
a key to separating biology from the lower and baser sciences (though
workers in those sciences would probably prefer instead to call them
more fundamental and basic).

Several times I co-taught a course with a molecular biologist who had
been trained as a biochemist from within a chemistry department and
had industrial experience in the biochemical industry. It was very
interesting because we would take whatever subject (once it was
receptors and cell signaling, once it was bioinformatics and gene
identification) and she would talk about all the nuts and bolts of
just how the details worked and then I would talk about just what the
stuff was actually doing inside the cell. The perspectives were
actually very different. We thought that having the students see both
sides was really very important as a "capstone" course in our
undergraduate biochem curriculum. But that is not ordinarily how
biochemists teach or how they approach the material. And the strict
departmental structure of most institutions doesn't even allow a
biochemist to meet, let alone talk to or, God forbid, teach with an
actual biologist.



--dkomo@xxxxxxxx


.

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