Regarding reductionism and quarks-- Recently physicists have become more interested in 'complexity'. From Physics World survey Dec. 1999-

"Reductionism has failed in a grandiose manner," Itamar Procaccia Giorgio Margaritondo, (the challenge for physics is) "... to develop a general theory of complex systems, in particular of living systems, without relying on the 'reductionist' approach, which is based on the illusion that complex systems can be explained based on an understanding of their more elementary components."

I mention this because sometimes people think that the reductionist appproach is argued on philosophic grounds only.