It may be the case that every process is purely chemical and physical, and it most probably is, but it is not a useful way to understand the world. Even if merely conceptual, a metaphysical side to our essence does exist. What's trancendental might indeed be an illusive physical phenomenon, but we're sort of trapped into it, even if we understand it one day, the subjective experience that is, our understanding will happen within our subjective experience, so why try to deny it? I think it's better to embrace it. Karen Armstrong has produced some very interesting reading on the topic [1], though I do not agree her on each and every point she makes.

BTW, when I say metaphysical and trancendental, I do not refer to religion and divine existence. I am a bit close to Sartre, though not completely, I'm adding this just to clarify my stance a bit more.

[1] https://en.wikipedia.org/wiki/Karen_Armstrong