From: Chris Taylor (Christopher.Taylor@man.ac.uk)
Date: Fri 20 Jun 2003 - 22:26:01 GMT
Dace wrote:
>>From: Chris Taylor <Christopher.Taylor@man.ac.uk>
>>
>>>How do they do that when every cell has precisely the same genes
>
> (including
>
>>>the homeobox genes)? Clearly the answer comes from its spatial
>
> position,
>
>>>i.e. the "field" effect. Blah yadda etc. <snip>.
>>
>>Ffs man give it up ;) I admire your tenacity, and your grasp of the raw
>>facts, along with your dedication to micro-questioning assumptions, but
>>not every assumption is a hazard sign. The fields that determine
>>developmental patterns are gradients of chemicals, some of which are
>>metabolites, some are RNAs blah blah blah. Genes are induced at a rate
>>determined by the chance that a molecule that fits a promoter will bump
>>up against it in the right way (paraphrasing a little to save pain). The
>>concentration of those signal molecules in a region of a cell (often
>>localisation is via the train network of microtubules where that other
>>nutter Penrose's conciousness lives lol), and across sheets of cells,
>>switches on cascades of genes, that express proteins and RNAs that do
>
> stuff.
>
> And what determines the concentration of signal molecules-- genes or fields?
> I know you believe the former, but why? Let me save you the bother of
> explaining. You subscribe to the notion that reality is essentially matter.
> This is a meme, a culturally-shared habit of thought. Needless to say,
> memes do not make good science.
>>Also just cos a theory (like MR) 'explains' most stuff _so_far_
>>doesn't make it a winner. It is at best a competing explanation which if
>>valid will eventually be accepted by the usual route. The problem is
>>that it predicts less, and has less explanatory power, than the stuff I
>>believe.
>
>
> The thrust of Gibbs' 8/01 Sci-Am article was that many biochemists are
> abandoning mathematical models that rely on the "central dogma" because
> these models aren't helping develop new drugs. Nobelist Alfred Gilman
> claims that new modeling that avoids genetic reductionism will become a
> "drug discovery engine." So this has nothing to do with "explanatory
> power."
I'd assume you don't mean 'the' central dogma, cos we've known about all
sorts of routes back to the genes for ages (reverse transcriptase,
transposons etc.).
Biology is undergoing a bit of a revision at the moment when it comes to
our view of exactly how goddamn complex organisms are, but it hasn't
gone completely dark, and won't, because we know the kinds of answer we
will get, just not the specifics. I just saw a guy at ASMS who gave a
plenary about intefering with protein-protein interactions (tricky cos
the active sites are so broad). Based entriely on theory (chemical
mostly) with some knowledge of protein interfaces (like they tend to
have a hydrophobic zone in the middle, making them a bit like a pair of
[erm, oppositely oriented] fridge magnets) he built synthetic scaffolds
with sticky-outy bits in a few choice places (predicted by molecular
modelling software) and showed several times overthat his chemicals
interfered really severely with bonding between the parts of the
complexes. Theory, prediction, result.
> By the way, it's nice to hear from you again, Chris.
Cheers. It's good to have a dedicated opposition :)
I just wish I had more time for this.
>>>The genes contain the information that instructs the developing cells to
>>>differentiate based on their relative position in the developing embryo.
>>
>>Ted:
>>How do they do that when every cell has precisely the same genes
>
> (including
>
>>the homeobox genes)? Clearly the answer comes from its spatial position,
>>i.e. the "field" effect.<
>>
>>How does a cultural studies major know which part of the library to use?
>
> As
>
>>cells differentiate they turn off inappropriate genes. One known
>
> mechanism
>
>>is methylation of the phosphate backbone. This change in structure makes
>
> it
>
>>impossible for DNA transcriptase holoenzyme to unzip the helix, thus the
>>gene cannot be expressed.
>
>
> What determines cell differentiation? Chemical signals? Okay. What
> determines chemical signals? How could it be genes when they're the same in
> all the cells?
>
>
>>Weiss:
>>"...One can readily understand how this has led to the illusion that
>>character is nothing more than a bunch of characters. An individual thus
>
> had
>
>>to appear to genetic analysis not as a subject, but as a conglomerate of
>>attributes. Thus one identified, for example, genes bearing on black vs.
>>blond hair and called them, for short, genes for "black" or "blond"...and
>
> so
>
>>forth. What one had actually established was a correlation between gene
>>differences on the one hand and *differences* between entities on the
>
> other.
>
>>Yet, shorthand usage gradually abstracted the differential attributes from
>>their substrata, keeping the characters "black," "blue," and "split" in
>>view, while forgetting about their carriers; i.e., hair, eye, and lip,
>>perhaps in the expectation that they will likewise in the end prove
>>decomposable into a collection of attributes; but attributes of what?"
>>
>>Attributes of the individual cells that make up the anotomical "carrier"
>>which are, in turn, understandable in terms of attributes of the
>
> individual
>
>>chemicals that make up the cells which are in turn...
>
>
> Weiss' point is that genes can explain phenotypes like black hair or blue
> eyes or harelip, but it tells us nothing about morphological structures such
> as hair, eyes, or lips. Genes only explain differences between organisms,
> not the organisms themselves.
>
>
>>Weiss:
>>
>>The Boltzmann theorem and thermodynamics... relate unequivocally the
>>average
>>state of a system at time t1 to its average state at time t2, but realize
>>that tracing an individual molecule through that course is not only
>>unfeasible but would be scientifically uninteresting and inconsequential:
>
> it
>
>>would in each individual instance and instant be of nonrecurrent
>
> uniqueness,
>
>>hence valueless for any detailed predictability of future microevents.<<<
>>
>>Absolutely in paradigm.
>>
>>Ted:
>>
>>>Physics long since abandoned microdeterminism, not merely at the quantum
>>
>>level (quantum indeterminacy) but at the atomic and molecular levels.<
>>
>>I don't know where you get this idea.
>
>
> Determinism (which relies on micro as well as macro-determinacy) was
> abolished from science by Boltzmann. Its continued life since then has been
> entirely due to force of habit. The determinism meme appears to exploit our
> fear of freedom and the responsibility that goes with it. Erich Fromm
> famously referred to this as "the flight from freedom."
>
>
>>I spent years in grad school at
>>Harvard discussing the reaction mechanisms for individual molecules and
>
> was
>
>>successful at predicting the outcome of novel reactions on a "macroscopic"
>>level.
>
>
> Right. That's called macrodeterminacy. But this is merely a statistical
> aggregate. True determinism requires that atoms and molecules also behave
> deterministically, and this is not the case. What we find instead is
> "nonrecurrent novelty."
>
>
>>In other words, I drew pictures of individual reactions on the board
>>and then made macroscopic amounts of product based on those predictions.
>>"Microdeterminancy" was *the* useful theory, certianly not abandoned. I
>>also discovered novel reactions and then investigated their reaction
>>mechanism. Then I used that understanding to develop new reactions. All
>>the while I was assuming that all the molecules did what I thought a
>
> single
>
>>one would do. We were able to get 90% + yields, which (statistically) is
>>pretty good. Who cares if it was true? It worked.
>
>
> I agree. Macrodeterminacy works, despite the fact that there's no genuine
> determinism in the constituents from which it's built up.
>
>
>>>Weiss:
>>>If physics has had the sense of realism to divorce itself from
>>>microdeterminism on the molecular level, there seems to be no reason why
>>>the
>>>life sciences, faced with the fundamental similitude between the
>
> arguments
>
>>>for the renunciation of molecular microdeterminacy in both
>
> thermodynamics
>
>>>and systems dynamics, should not follow suit and adopt macrodeterminacy
>>
>>Chris:
>>WHAT are you talking about?
>
>
> Weiss is referring to the Boltzmann theorem. Physicists long ago gave up on
> micro-level determinism. Macrodeterminism is merely a mirage generated by
> statistical aggregation. There's no underlying, true, determinism for it to
> be based on.
>
>
>>Chris:
>>Are you saying that if you truly (in a
>>thought-experiment God-like manner) knew the state of all the items in a
>>system you still could not predict what would happen?
>
>
> Oh, absolutely. Edward Lorenz demonstrated this mathematically in 1962 and
> thereby unwittingly ushered in the age of chaos theory. See a brief
> discussion of the intrinsic randomness of nature by Stephen Wolfram:
>
> http://www.wolframscience.com/reference/notes/971c
>
> One last note to Reed: Electromagnetic waves do not require a carrier (i.e.
> "ether") in space. This has been known since Einstein published his Special
> Theory of Relativity in 1905. Your refusal to concede your error on this
> point suggests that you're approaching this more as a debate than a
> discussion.
>
> Ted
>
>
>
> ===============================================================
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>
-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Chris Taylor (chris@bioinf.man.ac.uk) http://pedro.man.ac.uk/ »people»chris ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ =============================================================== This was distributed via the memetics list associated with the Journal of Memetics - Evolutionary Models of Information Transmission For information about the journal and the list (e.g. unsubscribing) see: http://www.cpm.mmu.ac.uk/jom-emit
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