One problem encountered when physicists talk to philosophers of science is that we are, to quote George Bernard Shaw out of context, divided by a common language. A prime example concerns the word “reductionism”, which means different things to the two communities.
In the 20th Century the Logical Positivist philosophers were engaged in a highly normative program of specifying how they thought academic enquiry and science should be conducted. In 1961, Ernest Nagel published “The Structure of Science”, in which he discussed how high-level explanatory concepts (those applying to complex ensembles, and thus as used in biology or the social sciences) should be related to lower-level concepts (as used in physics). He proposed that theories at the different levels should be closely related and linked by explicit and tightly specified “bridge laws”. This idea is what philosophers call “inter-theoretic reductionism”, or just “reductionism”. It is a rather strong thesis about linkages between different levels of explanation in science.
To cut a long story short, Nagel’s conception does not work; nature is not like that. Amongst philosophers, Jerry Fodor has been influential in refuting Nagel’s reductionism as applied to many sciences. He called the sciences that cannot be Nagel-style reduced to lower-level descriptions the “special sciences”. This is a rather weird term to use since all sciences turn out to be “special sciences” (Nagel-style bridge-law reductionism does not always work even within fundamental particle physics, for which see below), but the term is a relic of the original presumption that a failure of Nagel-style reductionism would be the exception rather than the rule.
For the above reasons, philosophers of science generally maintain that “reductionism” (by which they mean the Nagel’s strong thesis) does not work, and on that they are right. They thus hold that physicists (who generally do espouse and defend a doctrine of reductionism) are naive in not realising that.
“The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble.” — Paul Dirac, 1929 
The problem is, the physicists’ conception of reductionism is very different. Physicists are, for the most part, blithely unaware of the above debate within philosophy, since the ethos of Nagel-style reductionism did not come from physics and was never a live issue within physics. Physicists have always been pragmatic and have adopted whatever works, whatever nature leads them to. Thus, where nature leads them to Nagel-style bridge laws physicists will readily adopt them, but on the whole nature is not like that.
The physicists’ conception of “reductionism” is instead what philosophers would call “supervenience physicalism”. This is a vastly weaker thesis than Nagel-style inter-theoretic reduction. The physicists’ thesis is ontological (about how the world is) in contrast to Nagel’s thesis which is epistemological (about how our ideas about the world should be). Continue reading