David M. writes: 
I think that it would be quite right to argue that the
SOM"
and positivist dominated science of the early/mid 20th
century
has eased off and is now less open to Pirsig's
criticisms,
but it is only less so and not completely so. For
example,
on-going ideas of value-free objective science still
hints at a denial
of metaphysics as per positivism and a SOM dismissing
of
values as somehow subjective and contaminating
science,
whereas values are always present even if
unacknowledged. But some scientists are more free of
these particular prejudices than others"

Jorge: I tend to agree with you in the use of  "it is
only less so and not completely so". It would be a
mistake to think of scientists opinions and beliefs as
uniform; especially on general matters like causality,
"the meaning of truth" and "reality" one would find a
wide range of opinions. But this is no reason to pick
up on one extreme sector of this range and ignore all
the rest. I'll try to phrase it like this: 

 In the course of the last century 'causality' lost
its central role in Physics and moved to a secondary
role (which doesn't mean that we don't keep using
causality here and then whenever it comes handy).
 
 By the end of last century the notion that
"scientific truth" corresponded with "absolute truth"
was largely abandoned by most scientists. The same
could be said about the notion that the part of the
world  subject to scientific enquiry is "the real
world" or "reality".

Re, yours "value-free-objective Science", and the SOM
influence,  I'd rather leave for later if you don't
mind.  They require a rather long introduction. 

David M. (continued): 
. Other prejudice is the idea that higher level must
be
reducible to lower ones, for which there is little
evidence for
as the philosopher of science John Dupre argues in
'The Disorder of
Things'.

Jorge: I am not quite sure of what do you mean by 
"higher levels reducible to lower ones." If by that
you mean the technique of describing complex systems
in terms of their elements, I wouldn't call it a
prejudice but the use of a certain technique
(analysis) which gives good results in many cases.
With highly complex systems the same technique works
very poorly and holistic techniques seem to give
better resultsÂ… but we might be talking of different
things. 
     



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