From: Chris Taylor (firstname.lastname@example.org)
Date: Mon 14 Nov 2005 - 23:49:25 GMT
Hiya. Third time lucky...
>>>A biology that takes life on its own terms must begin with
>>>the whole and its purpose, not mechanisms and their
>>You can't use words like purpose for wholes (or even parts).
>>Consider firstly (one take on) functionalism from sociology;
>>things' roles are purely defined by their effects, not by
>>'intent' (which as a full-on meme machinist I'd say can never be
>>freed from those quote marks whatever the context...).
>>This is additionally a solid gold meme point a la Dennet; use of
>>particular language can be a bar to a whole way of thinking.
>>'purpose' as you use it (i.e. for organic form) is only ever
>>discernable with hindsight.
> Purpose, at least in our own lives, is self-evident. As we ourselves are
> organic forms, we may confidently attribute purposiveness to other organic
> forms as well, all the way down to bacteria. We don't have to approach life
> from the outside, as if we were robots unable to comprehend causation except
> in terms of mechanical necessity. When I was six years old, I used to
> pretend I was a robot, and my mission was to save America from evil,
> communist robots. Sometimes I think reductionists have never outgrown that
> stage of development.
Sorry but you _must_ leave your very human perspective behind.
There is no forward planning mode available, even to humans --
this is (shockingly) a ~memetic thing as clearly our ability to
imagine/simulate/plan is based only on our experience (direct or
recombined) and that 'planning' is just a case of rapidly
iterating a series of 'what if' scenarios generated at random
(consider 'drawing a blank'). But I digress...
This is true of organisms: For example; if there is purposive
mode of change available, why the wastage of the normal
distribution in offspring traits? Why are not all offspring
directed towards the 'better' form, or will you come over all
neo-Darwinian now and talk about bet-hedging in an uncertain
world (which is the death knell for Lamarckism btw)? All that
happens is that there is (standing variety allowing of course --
which incidentally is another _major_ problem for you -- what of
the cheetahs that can evolve no more due to loss of
heterozygosity as a result of small N [to their firm detriment
as a parasitised species] or the zero recombination lines in
plants that have formed massive 100% linkage groups -- no
variation, which is actually why they did it cos they don't want
to fall off their narrow fitness peak) a range of phenotypes
generated in offspring (statistically zero-percent of that
variety coming from mutation btw, cf. the cheetahs again, cloned
phasmids etc. that have no answer to change), some of which do
better and survive. This is how species cope so well with
unpredictability -- only after the fact can a species 'know'
what worked, all they can do in advance is spread their bets
(incidentally the only thing one _can_ do as a 'robot'). The process is _inherently_ hindsight-only. To crave purposiveness is understandable but entirely wrong; we cannot know the future and would be fools to place just one bet on it anyway.
In the biosphere generally, there is no planning mechanism.
Acquired characters are not observed to be passed down by any
other than physical mechanisms (i.e. there is nothing rigorously
observed that is not explicable through standard inheritance, be
that genes altered in the germ line by environmental mutagens or
radiation or [very, very rare] uncorrected copying errors, other
DNA-level features like mobile elements or methylation patterns,
parental RNA in gametes, or other gametic-cytoplasmic factors,
or immune inheritance through breast feeding in mammals or
whatever). You are in real danger of painting the picture of the
giraffe straining to reach the leaves and getting a heritably
longer neck as a result...
And generally the idea of purpose is anathema in relation to
organisms that _cannot think_, like bacteria. What sort of
internal dialog are we imagining here..? Could we extend it to
allow gaseous nebulae to 'think' in space?
Incidentally, _do_ you suggest any change within an organism's
lifetime that steps outside the bounds of normal phenotypic
plasticity (i.e. am I an athelete or a couch potato, a shrub or
>>>In his August, 2001 article for Scientific American, "Cybernetic
>>>Cells," by W. Wayt Gibbs noted that "three centures of reductionism
>>>in biology" was giving way to another approach known as whole-cell
>>>simulation. According to James E. Bailey at the Federal Institute of
>>>Technology in Zurich, the confused state of microbiology is much like
>>>astronomy prior to Kepler, when a great mass of data was available on
>>>planetary orbits, but nothing could be predicted. Researchers such as
>>>Bailey are generating useful predictions by modeling whole processes
>>>in cells rather than the effects of individual components, including
>>>genes. No one's accusing Bailey of abandoning science.
>>simulation is just an assemblage of models each built on
>>reductionist analyses, all run in parallel. Reductionism does
>>not forbid interaction; this is not the 'great' Mrs Thatcher
>>denying society in favour of individuals. Reductionism is an
>>analytical technique not a philosophy!
> The point is that describing the parts doesn't necessarily reveal the whole.
> According to Alfred G. Gilman, a Nobel Prize-winning biochemist (quoted in
> Gibbs' article) "I could draw you a map of all the components in a cell and
> put all the proper arrows connecting them." But for even the simplest
> microbe, "I or anybody else would look at that map and have absolutely no
> ability to predict anything." To make predictions, you have to run
> simulations of whole cells until you stumble onto the right model. We don't
> know, just from the parts, what that useful model will be until we hit upon
> it through trial and error. Clearly, there's more to a cell than its parts.
> Reductionism is perfectly fine as a technique applied in conjunction with
> holism. Alas, it's been a philosophy opposed to holism for nearly 400
> years, and that's a deeply ingrained meme not easily uprooted.
What is missing from the above statement is information, which
exists in the present with no requirement to be linked to any
other time or place. Cells, as I have stressed repeatedly, are
_never_ created de novo, there is only one (branching) cell line
in the world and it's LUCA's ancestor was not a cell at all, just some hypercycles in a blob of lipid (most likely -- I didn't really like the life through claymation hypothesis tbh). This raises something I'd like you to answer actually but I'll raise that in a minute...
Basically it is almost impossible to run a cell simluation
because the list of information given above is severly limited.
No mention is made of the state or amounts or locations of the
various molecules that matey boy could join up with all those
arrows (and I bet that list is short of complete anyway); the
The fundamental point is that you just can't kick start a cell
from some set of initial conditions, in the real world or in a
computer, you have to somehow 'drop in' to an ongoing process
with fluxes in action. Cells never 'start' -- _that's_ why it's
hard, not because there's is something else going on that we're
* [Why not coin another eh :) e.g.
although this list sucks as it bizarrely seems not to have the
proteome -- the Gerstein lab one was better but it is apparently
is now a [expletive deleted] commercial product..? ffs!]
The delayed question I mentioned above is on what the origins
story is from your perspective? How did life start from your pov?
[To be continued...]
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