Re: There was never a moment in time when

Perplexed in Peoria <jimmenegay@xxxxxxxxxxxxx> wrote or quoted:
> "Tim Tyler" <tim@xxxxxxxxxxx> wrote in message news:d8t4j7$6cb$1@xxxxxxxxxxxxxxxxxxxxxx
> > Perplexed in Peoria <jimmenegay@xxxxxxxxxxxxx> wrote or quoted:

> > > I'm not sure I understand what you are saying here. By a "cycle ...
> > > not involving the correct positioning of a unit", do you mean a
> ^^^
> > > cycle which adds a unit correctly, then removes it (incorrectly)?
> >
> > No: in the same terms, I would describe that as a cycle which /does/
> > involve the correct positioning of a unit (though it is subsequently
> > undone).
>
> Whoops. My mistake. The marked "not" should not have been there.
>
> [snip yet another go-around of the same disagreement]
>
> > If it helps at all, here's Cairns-Smith describing the process
> > that leads to error correction during crystal growth:
> >
> > ``Even then, new units will come and go meny times: the difference
> > between crystal growth and crystal dissolution is not absolute
> > under such circumstances: both happen, it is a question of which
> > is marginally faster. And mistakes are frequent, perhaps usual.
> > That is no matter since a crystal with a mistake in it is less
> > stable - more soluble than a more perfect crystal: the crystal
> > will tend to redissolve until the mistake has been eliminated.
> > Trial and error - and error correction - are the secrets to success.''
> >
> > - Genetic Takeover, p.156.
> >
> > You may perhaps discount Cairns-Smith's testimony. However, I cite
> > him, since he's a *much* greater expert in crystallography than I am.
>
> AFAIK, Cairns-Smith has correctly described the crystal growth process.

That's good - it seems you at least now recognise that crystals
contain a built-in error correction mechanism - which seems a
bit of a turn around from:

``I realize that you frequently wax rhapsodic regarding the "error
correcting" abilities of crystal growth, but you are wrong.'' - JM.

> AFAIK, Cairns=Smith has NOT described "kinetic proofreading".
> I don't see why you continue to misunderstand what I am saying.

As far as I can tell, we are in violent areement over what
constitutes "kinetic proofreading" - but for some reason -
we disagree over whether crystal growth processes represent
an instance of it :-|

If attachment was as likely as detachment - for both
correctly and incorrectly positioned units (i.e. everything
was reversible) then crystal growth would *completely* break
down as a high-fidelity process.

The problem area still seems to be whether energy can be dissipated
during a cycle of attachment and detachment of units.

I've explained that crystals are dissipative structures - and
do not act completely reversibly. In particular, the mechanics
of crystal growth processes results in units precipitating from
more dense regions and dissolving into less dense ones - and so that
attaching and detaching an equal number of units tends to
result in entropy increasing - by increasing the homogeneity
in the surrounding liquid.

Also, I've explained how variations in saturation can arise
naturally through commonplace events - such as erosion, or
evaporation followed by turbulent fluid flow.

The result of this is that the detachment of a correctly positioned
unit is *less* likely than its attachment (under appropriate
supersaturated conditions) - because the conditions in the liquid
that would encourage detachment arise less frequently - and there's
an asymmetry when this case is compared with the case of the
incorrectly positioned unit - since the magnitude of the
energies involved in attachment/detachment is greater.

Another analogy might help at this stage:

Imagine that a vibrating surface has some large and small holes on it.
Particles bounce around on the surface.

What happens here is that the particles tend to accumulate in the large
holes - for the simple reason that particles tend to bounce out of
the small holes - but when they land in a large hole, the vibrations
don't have enough energy to bounce them out again - and the energy
that they had when they fell in in the first place gets dissipated
when they hit the bottom of the hole - so they are stuck there.

The analogy with crystal growth is as follows: large holes are
like correctly-posisioned units - small holes are like
incorrectly-positioned ones. The landscape can be thought of as
an energetic landscape - and the vibrations are thermal noise.

Once an unit becomes correctly positioned, it's too "deep" in an
energy well for thermal noise to shake it out again. Why doesn't
the unit bounce right out of position again - if all its bonds
are reversible ones? The answer is much the same as in the case
of the hole - when the unit "hits the bottom", it often *doesn't*
"bounce" out again - since the some of the energy it had on the way
in is not bond energy, but kinetic energy - and that energy
dissipates radially through the crystal lattice, and into the
surrounding medium in an irreversible manner.

If somehow the lattice could supply a radial burst of energy
concentrated on the unit - and the surrounding liquid could
conspire to have a low level of saturation again - then maybe
the unit *could* leap free again.

....but that's about as likely as the mud particles at the bottom of the
hole all convulsing simultaneously - and the air vibrations made when
the particle fell into the hole all precisely reversing themselves.

That's an exaggeration - but *hopefully* it illustrates where the
loss of energy takes place - and how it can happen despite the
presence of bonds that are classically regarded as being reversible.

Of course, that the forward reaction is harder to reverse in the
case of a correctly positioned unit than it is in the case of an
incorrectly positioned unit (plus the ability to iterate to allow
multiple chances to eliminate mistakes) is precisely what is
needed to make kinetic proofreading work.

About the only place I can see the discussion going from here,
is into quantitative realms - how *much* usable energy is involved
in these irreversible processes - and what kind of fidelety of
error correction in crystals results from it in practice.

I sumbit again that real crystals illustrate that it is substantial.

Kinetic proofreading is the only game in town worth playing - in the
primitive-chemical-error-correction area - nothing else could
be producing the high-fidelity effects seen in real crystals.
--
__________
|im |yler http://timtyler.org/ tim@xxxxxxxxxxx Remove lock to reply.

.

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