Given a choice between philosophy and my fingertips, I bet on the second. That decision may represent a philosophy but it also reflects the order in which we assembled ourselves. JB
----------

A: "I'm coming from a naturalist / materialist philosophy perspective where philosophy is on a continuum with the natural sciences, and the relationship between philosophy and science is reciprocal."

We differ, I wish you well. I view words and philosophy as derivatives of physics and some juicy stuff (chem & bio) in between. Check Pinker, Blank Slate, for his case that our verbal apparatus is a "spin doctor." (You might enjoy a paper by Lehn on evolution in soups of complex chemicals. Orig published in Science or Nature about two years ago, available at www.pnas.org/cgi/doi/10.1073/pnas.072065599) Also remember Geoff Miller's concept (2000, The Mating Mind: How Sexual Choice Shaped the Evolution of Human Nature. NY: Doubleday) that our thoughts are ornaments that serve sexual selection: expensive, blossoms in early puberty, is disproprotionate the environmental necessities, and is easy to learn and fun to do!

As for "reciprocal," environments and genes modify each other (eg Lewontin, R., 1998/2000, Triple Helix: Gene, Organism, Environment. Cambridge, MA, Harvard, and another eg, Richerson, P, & Boyd, R (2005) Not by Genes Alone: How Culture Transformed Human Evolution. Chicago: University of Chicago Press, or Odling-Smee & his tribe [Odling-Smee F.J., Laland, K.N., & Feldman, M.W. (2003) Niche Construction. The Neglected Process in Evolution. Monographs in Population Biology. Princeton, NJ: Princeton University Press] but I view philosophy as usually having local effects within clusters and most of it superstitions that serve to increase compliance with local traditions and to suppress individual variation. (omigod.)

I know, however, that your interest is more persistent than mine and you may enjoy some of the arcana that Christian Perring assembles along with members of the NYAssoc for Adv Philos & Psychiatry. You can find him on Google...
----------

A: "it may assist us in working out the function of mental states (belief, desire, emotion etc)"

A hot area: check David Smith's group on cognitive psychology and evolution. You might also get into Barabasi's "Linked" (about $15, paper, very clear, almost revolutionary as well as evolutionary. The cognitive people pretend that they discovered networks! Network physics gives us a revised, even-PC definition of "fitness"!) Please hold onto Stu Kauffman's idea (Kauffman, S. (2000) Investigations. NY: Oxford.) that emergent organizations discover self-interest when they discover resources. That is, my love for a bike competes with and shows no mercy to my other responsibilities. Such networks also recruit allies. Similar to Dawkins's 1976 metaphor but with a different level of detail and explanation.)
---------

A: "My current area of interest is emotion. Are emotions natural kinds? How are emotions different to / the same as / related to other cognitive states such as belief and desire?"

Fred shared this obsession two years ago. He LOVED LeDoux's work. ("J" not "Chris"! LeDoux, J. (1996) The Emotional Brain. NY: Simon & Schuster.) Check also Bob Wright (Wright, R. (1994) The Moral Animal. The New Science of Evolutionary Psychology. New York: Pantheon.) and Trivers Trivers, R. (2002) Natural Selection and Social Theory: Selected Papers of Robert Trivers. NY: Oxford). I find Trivers to be compelling with his concept of emotions as enforcers for the reciprocity system. Can also be related to Stu Kauffman's ramblings about chaos and stasis (Kauffman, S., 1995, At Home in the Universe: The Search for the Laws of Self Organization and Complexity. NY: Oxford.) Implication: we go through life doing one of two things from instant to instant...we "simplify" or "complicate" our niche by means of emotions and according to content that we assemble or encounter (Brody, 2002, From Physics and Evolutionary Neuroscience to Psychotherapy: Phase Transitions and Adaptations, Diagnosis and Treatment. In G. Cory & R. Gardner (Eds.) The Evolutionary Neuroethology of Paul MacLean: Convergences & Frontiers, Praeger-Greenwood, pp. 231-259)

An individual can be thought of not only as an explorer and builder but as the meeting point between past and future. Past and future are more chaotic than present and present is the phase transition between them. I envy the years that you have ahead. Never think that you're just another F'n phase transition...every damned one of us is unique.

JB