If this is supposed to be as much about a specific application as it is about generally learning about microcontrollers/digital signal controllers/dsps, start with an ARM chip, e.g. one of the new Cortex-M3 parts.

Once you're familiar with the general concepts (even just things like "what's an emulator and how do I use one"), you can move to microcontroller architectures that are more suited to your specific application if necessary.

Oh, one more thing: Hardware design for biomedical applications does come with its own pitfalls, and those can be somewhere between painful and fatal. You will need a working knowledge of the concepts (isolation, etc) well before you connect any of your creations to an actual person.