Subject: Re: CCL:orbitals

From: Eric Scerri <scerri(at)chem.ucla.edu>
Date: Fri, 6 Jun 2003 23:37:27 -0700

>On Fri, 30 May 2003 16:07:46 -0700 Eric Scerri wrote:
>
>>
>>
>>  As somebody working in philosophy of science and more specifically
>>  philosophy of chemistry I have found the recent discussion very
>>  interesting.
>>
>
>While for my part, I have always been a "working computational chemist",
>I've studied with great interest the debates between Bohr, Einstein, Bohm
>and others.
>
>>
>>  There is a long-standing debate in philosophy of science going back
>>  for hundreds of years which in modern terminology is referred to as
>>  the realism versus anti-realism debate...
>>
>>  Finally, it should also be recalled that the most widely held
>>  interpretation of quantum mechanics, the Copenhagen interpretation,
>>  is essentially an anti-realistic interpretation regardless of what
>>  people like Einstein and David Bohm may have wanted...
>
>While I agree that this is indeed a long-standing debate, the problem was
>exacerbated by the insistence of some, like Bohr and Heisenberg, that
>science is concerned not with the physical universe ("physical reality")
>per se, but with human knowledge/awareness of the physical universe. While
>we might agree that the latter does fall within the purview of science,
>most scientists today would opine that it falls within the discipline of
>cognitive science rather than physics. Few are the physicists who are able
>to get grants to study human cognition using acceleraters rather than EEGs
>and MRIs!

But far more obviously the anti-realistic view was adopted because so 
many QM concepts seem to defy a realistic interpretation.  Is the 
electron a wave or a particle?  The electron has no definite 
trajectory.  Electron spin is not really spin, Collapse of the 
wavefunction issue etc etc. 

Anti-realism in QM does not depend on holding the view that physical 
theory is somehow concerned with physical awareness. 

>  >
>>  For example
>>  phlogiston was initially quite useful and successful in explaining
>>  many chemical facts.	Some people may even have believed that this
>>  meant that phlogiston was a real physical entity and yet as everybody
>>  knows it turned out to be a mistake.
>
>Perhaps a better example might be the aether and spacetime.

You did not explain why you felt that your example was "better" than 
phlogiston. 

>While most
>people today might say that the aether theory was a big mistake, I regard
>spacetime as simply a modified version of the aether concept, in the same
>way that modern DFT helped reformulate the concepts of hardness and
>electronegativity. So does spacetime "exist"? Or do orbitals have "physical
>reality" (to distinguish it from the real/imaginary/complex
>classification)? To me, questions like this are inherently unanswerable, or
>at least unanswerable at the level of science. Such questions belong in the
>realm of philosophy and religion.
>
>Science can ask: is the phlogiston concept still useful? The answer there
>is no! Is the orbital concept still useful? Here the answer is that, within
>bounds, yes! But is it absolute? Can it explain all observations? Certainly
>not! Now a more difficult question (and one that calls for subjective
>judgements): is it a reasonable working model? Here opinions seem to
>differ.
>
>It is possible to formulate and rationalize most of our observations
>entirely without reference to orbitals. Several successful theories, such
>as the variational formulation of density functional theory and some
>Green's function theories, do just this. Does this make the orbital concept
>any less valid? No, but it does argue against religious beliefs of orbital
>reality. Does this make orbitals any less useful? Again, no. The most
>widely used theoretical formulations (Hartree-Fock, CI, Kohn-Sham DFT) are
>still constructed in terms of orbital expansions. But I would argue that it
>makes little sense to try to "explain" all our observations in terms of
>orbitals, a practice which is still widely prevalent.
>
>>
>>   except in the general sense that all scientific
>>  theories and approaches are eventually refuted.  This view, called
>  > the pessimistic meta-induction, ...
>>
>>
>
>There seems to be an inconsistency here: that of extrapolating beyond the
>known range of validity of the model. I would modify this to say that all
>scientific theories should be, in principle, falsifiable or refutable. A
>theory that isn't so is not science, but religion.

No inconsistency.  I am making a different point from the elementary 
Popperian demarcation criterion between science and pseudo-science 
which you seem to want want to substitute.  Incidentally that 
criterion has been thoroughly criticized by subsequent philosophers 
of science to the point that it is not really a contender these days. 
But that's another story. 

My point is a separate one.  As Popper himself stated, "All theories 
are born refuted", meaning that sooner or later they will all be 
refuted.  Scientific theories are only provisionally useful.  Every 
single one of them will eventually be refuted.  This is a 
meta-induction based on the fate of all past and now defunct theories 
> from the history of science.  This notion in itself should be a 
warning against taking too seriously any of the entities postulated 
by theories, especially those that are unobservable. 

Of course one may argue that induction from past instances is not a 
reliable path to knowledge and that it just so happens that our 
cherished current theories have finally reached the point where they 
are refutable but will never actually be refuted.  But that would be 
plain stupid of course. 

eric scerri
-- 

Dr. Eric Scerri ,
UCLA,
Department of Chemistry & Biochemistry,
607 Charles E. Young Drive East,
Los Angeles,  CA 90095-1569
USA

E-mail :   scerri(at)chem.ucla.edu
tel:  310 206 7443
fax:  310 206 2061
Web Page:    http://www.chem.ucla.edu/dept/Faculty/scerri/index.html

Editor  of  Foundations of Chemistry
http://www.kluweronline.com/issn/1386-4238

Also see International Society for the Philosophy of Chemistry
http://www.georgetown.edu/earleyj/ISPC.html

---

From: Edgar Luttmann <edgar*at*upb.de>
Date: Mon, 02 Jun 2003 13:15:01 +0200

Hi,

I would like to know if there is any method to simulate (at least a 
rough) CD spectrum of a small peptide. I do have a PDB file (so I have 
3D coordinates) and it would be great to predict a spectrum from this.

Any hints are welcome and I will give a summary.

Thanks in advance

Edgar

--
Edgar Luttmann

University of Paderborn, Germany
Department of organic chemistry