How does subjective experience arise from matter? Forgive me for lacking rigor, but if what I know is correct, it is established that consciousness and other higher functions characteristic of humans are a consequence of our cortex, specifically neocortex. However, what has always puzzled me is the neurobiological basis that gives rise to the phenomenon that we associate our bodies with ourselves – i.e., why does my brain think of my physical body as "me" and make me care for it? In other words, why is me me at this particular point in time and not some other body living e.g. centuries ago? Why do I not associate "me" with multiple bodies living at the same time, or have identity at all? 

A naive, materialist answer would perhaps be that given our nervous system etc., "me" is only a sort of an illusion created by the brain which acts as a kind of "least thinkable unit" that has no neural connections to other physical bodies. Still, what is the process that "picks" precisely my brain and my body to become "me" – why have I not sensed reality from the viewpoint of e.g. Albert Einstein or Brad Pitt?

I wonder if any empirical answers to such questions can be given, or at least if these questions have been reformulated to a set of more well-defined questions in the light of modern neuroscience.



UPDATE:
A better way to form this question would be: if two bodies come to exist at the same time, and consciousness is an emergent, materialistic phenomenon of the body, why do I experience the emergence of consciousness in one specific body (i.e. the one I call my own) and not in another?
This is partially an aspect of the binding problem.


  Sensory information arrives in parallel as a variety of heterogeneous hints, (shapes, colors, motions, smells and sounds) encoded in partly modular systems. Typically many objects are present at once. The result is an urgent case of what has been labelled the binding problem. We must collect the hints, bind them into the right spatial and temporal bundles, and then interpret them to specify their real world origins. (2003, 97)


http://plato.stanford.edu/entries/attention/

The bottom line is that our senses are integrated and some of our most important senses (smell, sight, hearing) all have their organs located very close together.  Spatial perception is (at least partially) stored in the parietal lobes. The parietal lobes integrate information from somatosensors like muscle spindles to relay the body's position in space as well as the eyes (and ears), which help form a perspective of the environment.

You might also consider Tononi's framework for consciousness: integrated information theory which presumes:


  (i) the quantity of consciousness corresponds to the amount of integrated information generated by a complex of elements; (ii) the quality of experience is specified by the set of informational relationships generated within that complex. Integrated information (Phi) is defined as the amount of information generated by a complex of elements, above and beyond the information generated by its parts. Qualia space (Q) is a space where each axis represents a possible state of the complex, each point is a probability distribution of its states, and arrows between points represent the informational relationships among its elements generated by causal mechanisms (connections). Together, the set of informational relationships within a complex constitute a shape in Q that completely and univocally specifies a particular experience.


I think the deeper question we need answered before we get to your specific question is "how does a subjective experience arise from matter in the first place?".  Other than that, your question is no different than "why did that rock not get this rock's blemish?".  It was mostly likely just a matter of chance in initial conditions.