Re: what is life

From: rem642b_at_Yahoo.Com (RobertMaas_at_YahooGroups.Com)
Date: 09/07/04 

Date: Tue, 7 Sep 2004 04:58:48 +0000 (UTC)

> From: eagleliu@hotmail.com (haiguang)
> those gene materials, DNA and RNA are really life, and all other
> parts are serving for this purpose.

I agree with this way of thinking. Life consists of two parts, the
replicators themselves, and all the stuff the replicators need around
them to be able to replicate, including the replicating machinery
itself (DNA replicase for example). In some sense, only the replicators
themselves are the "true life", the rest is all the ecology in which the
replicators can survive. Some of this ecology is given a priori, such
as sunlight coming to Earth (to be used by photosynthetic organisms),
while some is directly coded by the replicator, such as the particular
proteins within the cell. Some of the ecology is a mix of natural and
replicator-causation, such as essential amino acids in human cells
which must come from outside food sources but which must be broken down
from proteins to individual amino acids to be usable by the cells hence
usable by the replicators. A cell is a tiny ecosystem in which many
different replicators co-exist and co-evolve. An animal body is a
larger ecosystem in which the many replicators in the many cells
co-exist and co-evolve.

> We should rethink about the definition of life: which property is
> more fundamental? I prefer self-replication or reproduction.

I agree with that way of looking at it.

> However, there is no perfect replication; there are always some gene
> mutations or some gene transfer, which causes modification on the
> original 憀ife'.

You are correct about mutations: When a replicator mutates, from that
point onward it's no longer exactly the same replicator going on.

You are incorrect about gene transfer: All that happens is that a new
replicator enters the ecosystem of the cell. Each replicator already
there is just the same as before, just it's now in a slightly different
environment from before.

Note that no individual replicator can replicate all by itself. I'm not
just saying that it needs an environment of food/energy and other
materials available, but also that it needs other replicants in the
same ecosystem to maintain the many biochemical pathways that a single
replicant can't maintain. But any single replicant is dependent only on
the general availablity of products from other replicants, not on any
specific replicant per se. Some other replicant can be modified or
completely replaced, and so long as some modified or new replicant
provides the necessary ingredients, the original replicant of our
discussion can continue to replicate.

Sometimes I like to take the view that each locus along the DNA is a
replicant, which requires all of:
- the context of neighboring loci to form a complete gene,
- the context of other genes to form a sufficient set of biochemical
pathways,
- the context of other cells and/or organisms to provide a sufficient
larger ecosystem.

If the current state (A C G or T) of that single locus cause its gene
to be more effective than any of the three alternatives, then mutations
would tend to be selected away, and if also the overall survivability
of that cell-line is good enough in the larger context, then that
particular state of that particular locus would survive a long time.

> We know that bacterial can move towards food, because they can sense
> the gradient from the solution.

I found this a few weeks ago:
http://brodylab.eng.uci.edu/~jpbrody/reynolds/lowpurcell.html
Apparently bacteria swim just long enough in a straight line to outrun
diffusion, so they get a different sample from where they started, then
either stop and change direction or continue in the same direction
depending on whether the new sample is worse or better than the
original. Does anybody know whether that model is currently regarded as
correct?

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