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Re: protein folding and relational space...



 
-----Original Message-----
From: ROSEN Forum [mailto:***On Behalf Of Judith Rosen
Sent: Thursday, March 18, 2004 5:30 PM
To: ***
Subject: protein folding and relational space...

Tim,

I'm somewhat puzzled... how did we get from "scientifically proving the existence of" something unperceivable to what you have below:

Tim Gwinn wrote:
Going back to the original thread, if we take the hypothesis that there is
an unperceivable primary structure and unperceivable conformation which is
causally responsible for phenomena, and we build a formal representation of
that primary structure and conformation, then I think that we have created a
metaphor, not a model. Because they are both unperceivable, there is no way
to do any encoding from the primary structure or conformation to the formal
side of the modeling relation. Thus, we do not have a commuting modeling
relation, and our formal representation is not a model, but a metaphor. How
does that sound?
 
Once you know something exists , you can study it further to try and learn the hows and whys of it. Why would you need to model it from the start? Clearly, if you don't know enough about a system to model it in any useful way, you would have to keep working to learn more about it, right?
 
As I understand it, you were proposing that something which we cannot perceive (primary structure + conformation) exists. I don't know what it means to say we know something exists other than to have observables of that something in a commuting modeling relation with a model of that something. Outside of that, as has happened in science many times, we might have phenomena whose behaviors suggests that there is some unknown causal factor at work. We may hypothesize that the unknown causal factor is some particular thing called "X", for example. But I do not think science can or wants to say "we know X exists" until we have that commuting modeling relation.
 
But I find it hard to believe that you won't accept the notion that it is possible to prove, indirectly but scientifically, the existence of something that is beyond our current abilities to perceive directly. Am I misunderstanding your point of view?
 
I think this kind of indirect "proof" is in large part responsible for the morass of confusions and interpretations known as quantum mechanics. We draw inferences from experiments and create formalisms that can predict behaviors, but if and how we can impute the elements and entailment structures in those formalisms back to material reality is, to me, an open question in quantum mechanics.
 
Regards,
Tim