From: Chris Taylor (chris.taylor@ebi.ac.uk)
Date: Mon 28 Nov 2005 - 11:19:29 GMT
Hi.
>>Protein folding (again): Fine, there are many stable
>>configurations for some proteins to fold to (cf. prion disease
>>for a nasty one) but that is managed by (1) a whole suite of
>>stuff during manufacture (chaperones, pauses in translation
>>etc.) and (2) a really thorough misfold-spotting machinery that
>>recycles anything remotely dodgy.
>
> How do the chaperones know what to do? Are they guided by genetic
> instructions? Is it mechanical necessity? How does misfold-spotting
> machinery know which is folded right and which is wrong?
We've been over this. Proteins are most often localised close to
where they need to be, where that us an issue, then stochastic
bumping does the rest (in part why Q10 issues arise when the
temperature is changed). Almost all of the chemistry of life is
based on complementary shapes that fit together given the chance
without any need of guidance. Self-assembling. Simulations have
shown this to be perfectly feasible.
As for the misfold-spotting machinery; that is quite complex and
a survey of the literature will answer your question better,
without my needing to spend more time here. Basically the ER is
a clever bugger.
>>Cell 'manufacture': Who exactly is looking at making cells from
>>scratch? I'll wager statistically nobody. Everyone is looking at
>>actual biological processes, which have no start.
>
> I'm not sure how you got the idea that I was saying anything about making
> cells from scratch.
>>> Instead of finding out how DNA
>>> serves to differentiate individuals within a common theme, scientists are
>>> trying to find out how DNA builds bodies from scratch (a single cell).
Okay misquote maybe. So we can at least agree that 'cells from
scratch' is not an issue (cf. your combinatorial 'nightmare')?
>>Clouds(?): This is just nonsensical. Structure in cells is
>>elaborate.
>
> Yes, structure in cells is far more elaborate than in a cloud of gas.
> That's the problem. According to thermodynamics, the behavior of free
> molecules is indeterminate, and only at the large-scale does a gas reveal
> certain patterns of behavior. But the patterned behavior found in cells,
> which are composed of free molecules, is vastly more intricate and complex
> than the patterns found in a gas. How do we account for this discrepency?
Exactly what proportion of these molecules do you assume are
'free'? I'll tell you; very few indeed. Most are tethered or
localised by all sorts of mechanisms. This 'randomised bag of
stuff' idea bears no resemblance to the reality.
And by the way the 'laws' of thermodynamics to which you refer
are not specific about the behaviour of free molecules because
the theory is approximate. There is no indeterminacy when you
look at the level of individual molecules (apart from difficulty
[for us only, not for the system] in calculating the outcome of
multiple-body collisions.
>>As for 'free will': This is just bizarre. Does a motion sensor
>>have the 'will' to sound an alarm when it is triggered? Does
>>chemotaxis qualify as something different (no)? Does a bee have
>>a 'desire' to remember a route using that special neural
>>structure it has (no)? There is a sliding scale for awareness to
>>be sure, but it drops off pretty rapidly and is reliant on
>>having something that can process _large amounts of information
>>at once_. Action-reaction pairs are _not_ thought. Without
>>thought there can be no 'desire' for anything.
>
> If organisms are machines, then even among humans free will is impossible.
> If organisms are not machines but merely contain mechanical elements within
> a holistic context, then free will can exist at any level of development.
> The meaning of evolution is that species are self-created in conjunction
> with natural selection. Thus human free will is only the individualization
> of what ordinarily manifests at the species level.
Bingo. You're one of them -- just like all the people desperate
for something 'quantum' to get them out of the problem that
_no-one has free will_!
This is the nub of it. This illogical insistence that we are
somehow more than the outcome of mixing our experiences in our
heads then living in a context of stimuli provides the big
irrational hole through which you are poking this argument.
Holism is your preferred (erroneous) argument for free will,
based on the fact that you generously grant it to everything.
Quantum jiggery-pokery is everyone elses'. Get over it people --
this flawed scrabble for some semblance of specialness is
misguided. You have the appearance/feel of free will cos you are
too complex to know as a whole (like the weather), but you are
deterministic as hell; firmly part of this clockwork universe.
So BZZZ, sorry. No free will exists 'even' in us.
>>(1) What controlled experiments have _directly tested_ what you
>>et al. suggest as possible, rather than everything relying on
>>rationalised passive observations?
>
> I guess you haven't read Hill's paper. There are many experiements
> demonstrating holistic effects, but this is a good place to start. Hill
> demonstrates that the mutations occurring in an isolated population are
> nonrandom insofar as they reflect the mutations of a closely related but
> physically separated population undergoing exposure to toxic chemicals or
> high temperatures. This has profound implications for evolution. If a
> given species is divided into two populations, and a new threat to its
> survival hits one population before the other, then the second population
> has time to adapt to the threat before it hits.
Yes I see the potential benefit (just as I do for marsupials
untangling their reproductive plumbing, which they can't, or for
herbivorous mammals to be able to make themselves green, which
they can't [unless they are so slow they get mossy]).
But how do you know that the influence of a neighbouring colony
_is_ relevant in your own microclimate? Seems a double-edged
sword to me -- I'd rather have the facility to respond myself if
I were one of them -- do you postulate an editorial procedure on
this influence or is it universal (in which case why only Hill
as witness?)?
Anyway I'm defering to Derek on the critical appraisal of that
one, as he is far better qualified. What was that other paper
though that you mentioned a week or two ago? I was interested to
read that one.
>>(2) What is the origin of life in the morpho world?
>
> I'm with Cairns-Smith. Why do you ask?
Okay so Cairns-Smith postulated claymation followed by RNA
world. I raise it because I want to know how the morpho thing
bridges the gap from non-life to life? Firstly, can non-alive
(whatever that means) things influence each other through fields
(crystals would seem to be a good example, also relevant to your
cloud objections above)? Secondly, what influenced the first
thing anyone could acknowledge as life, as by definition there
was no template? This keys into the next one too -- how perfect
is the field-based copying? Is it copy-with-error (i.e.
neo-Darwinian)?
>>(3) What is the mechanism of evolution, in full? All Lamarckian?
>
> Lamarckian evolution is theologically guided. God started the process and
> guided it with the intention of producing H sapiens. Darwin dropped
> Lamarck's theology but kept his emphasis on the inheritance of traits
> developed through use and disuse. Such traits cannot be inherited
> genetically and must rely on holistic memory which, according to Sheldrake,
> operates via the resonance of current forms with prior, similar forms.
Right. So why do we never _see_ Lamarckian (or any variant)
evolution? Why in so many cases where it would seem to be a
_sitter_ for an easy way out of a 'dead end niche' is it _not_
resorted too? It should be _rife_ if it is so straightforward!
So many organisms use other tricks to solve what L.-style
field-based systems would allow very straightforwardly. So why
might it not work for all (or even the vast majority)?
And I don't mean do you support evo as laid out by Lamarck
himself! Obviously neither would I offer Darwin as a provider of
good theories on the mechanism (pangenes ffs). What I mean by
Lamarckian v Darwinian is the modern take where Lamarckian means
inherited lifetime changes, Darwinian means inherting germ plasm
and a few little other bits (methylation patterns, some
cytoplasmic stuff).
>>(4) What is a 'lethal' gene for you (i.e. knockout/mutant =
>>never develops or dies very early)?
>
> Again, why do you ask? What's your point?
Because if something is far more dependent on fields for
existence, why do so many gene knockouts die so thoroughly?
Surely if genes are not hugely important ('individuation' rather
than fundamental development) there should be no such thing?
They can't all be involved in channeling the field can they?
Cheers, Chris.
~~~~~~~~~~~~~~~~~~~~~~~~
chris.taylor@ebi.ac.uk
http://psidev.sf.net/
~~~~~~~~~~~~~~~~~~~~~~~~
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