Re: There was never a moment in time when


"Tim Tyler" <tim@xxxxxxxxxxx> wrote in message news:d8n48d$18lf$1@xxxxxxxxxxxxxxxxxxxxxx
> After some reflection, I think you need to look again at crystal growth
> processes.
[snip]

I have looked again, as you requested, and have reached the same conclusion
as before. Accuracy, in crystal growth, is limited by Boltzman's formula.
Accuracy, in kinetic proofreading, is not. We seem to be at an impass.

> However the crystal growth processes under discussion are not *exactly*
> reversible, and *do* wind up dissipating energy - on average.
>
> To see why, consider one step "forward" and one step "backwards" -
> which consists of one unit crysatallizing onto the surface and then
> dissolving off again.
>
> How is this process /not/ symmetrical and reversible?
>
> The asymmetry lies in the degree of saturation of the surrounding liquid.
> When the unit crystallizes, the chances are it did so because the
> surrounding liquid had slightly more units in solution than could be
> supported without precipitation. And when it dissolved, the chances are
> that it did so because it was in a region that was slightly less
> heavily saturated.
>
> So: one forward cycle and one reverse cycle is likely to have had the side
> effect of moving a unit from a point in the liquid where there were
> slightly more units than usual to one where there were fewer free units -
> i.e. energy is dissipated and the cycle is not reversibile (except in
> the simple sense that all the laws of physics are thought to be
> reversible).
>
> If you are poetically inclined, you could invoke this dissipated energy as
> "paying" for the resulting error correction process.

Your pleading in this passage does suggest that I should add one more condition
to my list:

4. The energy-dissipating net result of a futile cycle is kinetically
inhibited from occurring in any other way than through the cycles.

So, even if you see small microscopic fluctuations in concentrations as
constituting an energy gradient (and I'm pretty sure you shouldn't) there
is no kinetic inhibition of the relaxation of that gradient by processes
that don't make use of the cycle. Simple diffusion, for example.

It can thus be seen that kinetic proofreading is the perfect archetype of
a living process - if you chose to define life in terms of its thermodynamic
status as an open system. What Nature (wearing her hat as the implementor
of the 2nd law) "really wants" is to dissipate energy as rapidly as possible.
And, the most rapid way to do that is to run through a bunch of futile
cycles. But, at the same time, Nature (wearing her hat as an "anti-entropic"
creative force) parasitizes some of that energy flux for the creative
function of copying genetic information.


.

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