From: Chris Taylor (chris.taylor@ebi.ac.uk)
Date: Fri 04 Nov 2005 - 11:33:44 GMT
>> A biology that takes life on its own terms must begin with
>> the whole and its purpose, not mechanisms and their
>> reactions.
>
> Yes, it does begin with the whole, and then we deduce the
> mechanisms and reactions (pleased to see you now agree there
> are mechanisms and reactions).
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.
>> He pointed out that the ability to reverse the orientation of an organ
>> by simply tweaking a gene demonstrates that the gene functions only in
>> the context of a developmental field. The gene flips the field, so to
>> speak, so the organ emerges in one conformation instead of its mirror
>> opposite. It's all about *influencing* development rather than programming
>> it. Nothing you've ever witnessed in a laboratory can establish the latter
>> as opposed to the former. Your view is based on assumption, not observation.
>
> No, again it's more fundamental. The genes controlling left-right are
> expressed very early on, and the pathways are now fairly well
> understood, at the mechanical level.
And just to push this further; what is happening is that one
gene/cistron is contextualising the activity of a sack of other
ones. Nothing trick[s]y there.
>> 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.
>
> Of course, not. I'll bet he doesn't believe in spooky fields or
> dinosaurs signalling to us. And don't try to misrepresent systems
> biology as anti-mechanistic. I was on the scientific advisory board for
> a systems biology conference recently. http://www.biosysbio.com/ I'm
> in the picture on the left. Can you guess which one's me?
Aaaargh! This is the ultimate goal of reductionism (imho); to
understand all the bits to allow them to be _put back together_,
either in the minds of scientists (pre- decent computing
hardware) or explicitly through simulation. Any whole-cell
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!
Just like when I used to take everything to bits as a kid, to
understand the parts; obviously I was aware of their activity as
a whole but you can't just look hard to understand. I have to
admit to less success though in either developing full
understanding, or being able to put the damned things back
together again. Always one bit left... :(
>> With or without a steel plate, termites don't rely on hearing to build
>> their arches. This possibility has already been ruled out
>
> By hearing I mean sensistivity to vibration.
And anyway there is way more to this. If the plate was there
from the start, a pre-existing part of the environment, you'd
have two mounds yes? So something was begun before the plate was
inserted (point one).
Cut now to the complexity people who can offer simulations where
agents (termites, paper wasps, all sorts) follow small sets of
action-reaction rule pairs, only ever having local awareness,
yet building macro (to them) structures that _seem_ to require
some termite stood a hundred yards away with a theodolite, in
nice new wellies (probably near the termite equivalent of a Volvo).
----------------------
I'd still also like to hear thoughts (in this context) on cells;
no cell (iirc) has _ever_ been 'made' from scratch. So to ever
consider genes in isolation is a nonsense. There is no such
thing as an independent part in a cell; one of the best
graphical illustrations of this is when people stain the
cytoskeleton with a fluorescing antibody (aesthetically
beautiful too); this explains a lot in fly dev for example,
where RNAs seem to travel to very specific places in one big fat
polynucleate syncytium (e.g. the periphery). The cell is not a
big bag of stuff requiring guidance from without, it is the
train set of the gods.
----------------------
> I'm in the picture on the left. Can you guess which one's me?
I want to say the silver-haired hippy near the front with the
loosened tie, who I'd probably end up talking to at coffee :)
But if you're aghast at that forget I ever tried to guess...
~~~~~~~~~~~~~~~~~~~~~~~~
chris.taylor@ebi.ac.uk
http://psidev.sf.net/
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