Two of my favourite philosophers, Ingo Brigandt and Alan Love, have just published an extremely useful and relatively complete summary essay on "Reductionism in Biology" at the Stanford Encyclopedia. They clearly identify the issues and confusions, which is what an encyclopedia article ought to do.
If I have a criticism, it is that they do not attend, as most modern philosophy doesn't, to the nineteenth century origins of this debate. I mean not only Mill, but Whewell, Jevons and all those who debated the relationship between scientific theories. Those who began the twentieth century debate knew that literature well. But then the nineteenth century is my milieu, so much so that I sometimes think I should retitle this blog Fin de Siecle Thoughts.
Criticism at Evolving Thoughts is good, but criticism at the discussion thread on the "Reductionism in Biology" SEP entry is even better. Alan Love and I set up this discussion thread at the Philosophy of Biology Cafe to gather feedback on our SEP entry, which we will consider when we revise the article the next time.
Your suggestion is quite relevant (and pertains to our section 2). May I ask that you repost it at the discussion thread, so that we can keep track of who made particular suggestions. And everyone else is encouraged to comment at the discussion thread on our SEP entry!
If I had sufficient data or knowledge to do so, I would. But displaying my ignorance is what this blog is for...
I'll keep a record of what I encounter, and let you guys know on that thread. For a start, though, obviously Mill's System is a place to delve.