Re: Minimum Cell?


"r norman" <r_s_norman@xxxxxxxxxxxx> wrote in message news:k9pjl3l3ki91tvgsu6uq969c4vh3t4oim8@xxxxxxxxxx
On Sat, 08 Dec 2007 00:12:19 GMT, Tim Tyler <seemysig@xxxxxxxxxxxxxx>
wrote:

r norman wrote:
Tim Tyler <seemysig@xxxxxxxxxxxxxx> wrote:
r norman wrote:
On Fri, 07 Dec 2007 10:14:04 GMT, Tim Tyler <seemysig@xxxxxxxxxxxxxx> wrote:
Error correction is ... the ability to find and fix
copying errors. To quote from my page on the subject:

``There is really only one known example of an error correction
mechanism which occurs in nature outside of biology.

That is the error correction process that is associated with
crystal growth.''

- http://originoflife.net/error_correction/

There's a section there on reversibility. [...]

[snip]
As to why error correction should occur best in near equilibrium
systems, I am at a total loss to understand the motivation for such a
statement.

That was *not* my statement. "Reversibility" != "near equilibrium".

Like you say, you seem to be on a pretty different wavelength.

The link between near-reversibility and natural error correction
is /fairly/ well known:

Yes, and you have the relationship exactly backward. A simple error
correction scheme in an irreversible process can achieve arbitrarily low error
rates, though it must expend (dissipate) energy in doing so. A reversible
process cannot achieve error rates any better than allowed by
Boltzmann's formula, though it can take into account ALL of the delta G
costs of an error. We've been over this before at sci.bio.evolution. I
will again suggest that you read the pair of articles by Yarus on
proofreading which appeared in TIBS. Here is a cite:
Trends Biochem Sci. 1992 May;17(5):171-4.
Proofreading, NTPases and translation:
successful increase in specificity.
Yarus M.

Natural error correction typically requires that incorrect units
can easily become detached and replaced with correct ones.

If the operation attaching "incorrect" units is too strongly
energetically favoured (over the operation that detaches
them again), mistakes are liable to go uncorrected. Similar logic
applies to "correct" units - else the addition of a "correct"
unit would lock an "incorrect" unit in place - leading to another
type of error. For the best chance of success, "correct" and
"incorrect" attachment and detachment operations need to be close
to reversible - allowing a "three steps forward, two steps back"
construction regime - that offers multiple chances to correct any
errors.

http://originoflife.net/error_correction/ offers more details.

Thermodynamic reversibility is closely connected to equilibrium.
Transitioning between stable states is necessarily dissipative.

Error correction can be a late addon to a system, one that requires
significant energy both to detect the error and then to correct it.

I see no reason why it can't be present from day 1. It is quite simple
to implement. All you need is a forward process which kinetically
favors doing it right, a backward process which undoes the forward
process, but kinetically favors undoing a wrong step, and a net
energy cost to the 'futile cycle' of doing something (right or wrong)
and then undoing it. And for a case like nucleic acid replication,
the rules of WC H-bonding automatically give you the favoritism for
doing the good stuff and undoing the bad stuff. In this case, the
error-removal step is actually downhill thermodynamically, though
it yields an unactivated nucleotide removed. So the energy expense
of the futile cycle is paid when you reactivate the 'bad' nucleotide
for later re-use at some other site where it will be 'good'.

Simple mechanically to implement, though it may be a bit tricky
to 'tune'. You need to strike a balance between the kinetic
parameters of two different enzyme activities. 'Improve' the speed
of one of those enzymes without making a corresponding improvement
to the other and you will either be wasting energy or making too
many uncorrected errors.

However, I do agree with rnorman's point of principle. You need
a departure from equilibrium in order to have stable, copyable
information in the first place. Tim's scheme has the nasty property
that the 'template' is just as succeptible to 'correction' as the copy.
You are not going to get natural selection to work if a mutation
that was favored by selection in one generation gets undone
in the next generation because it is disfavored by thermodynamics.

.

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