i would suggest reading some stuff by francisco varela, a biologist who was also quite interested in philosophy, whose work runs across the boundaries that have been troubling people here.
the basic outline of this approach--biological autonomy i suppose one could call it---- is in a text he coauthored with his teacher muratana. it is called "the tree of life" and is a great place to start.
a later text, "the embodied self" addresses directly the questions raised above.
the same concerns animate his work on husserl's accounts of internal time consciousness, which seems to be a level of thinking where one can find a degree of recursion linking the processes that you would experience as staged via "subjectivity" (the nature and parameters of which are thoroughly ideological) and the patterns that shape that experience at what you might call the "hardware" level (the formation and activities of neural networks)---patterns which cannot be understood if you take the boundaries of the skull as determining the boundaries of interrogation.
the approach varela developed is fascinating, both in itself and in its philosophical implications. best to chase down some of his stuff for a potted summary than to rely on one attempted here.
for a jump-off:
http://web.ccr.jussieu.fr/varela/
varela died in 2000, but curiously enough his homepage still floats in netspace.
the husserl essay can be downloaded from the site.
it is technical, in that i assumes you have a working knowledge of husserl--but you might be able to work out the general direction of his work by having a look in any event.