A.N. Whitehead called his process system a “philosophy of organism” thus distinguishing it from the mechanistic picture implicitly assumed in the prevailing scientific worldview. He believed the assumption that objects in the world were made of an inanimate substance was fallacious and undermined science.
While it has long been clear that biological systems are based in chemistry, which in turn is based on (quantum) physics, the notion that living things and all of their remarkable features can be reduced to physics has remained problematic to this day. Philosophers of biology continue to debate the issue (see this Stanford encyclopedia entry). As an example of a paper on the topic by a skeptic of the orthodox view, see the most recent one by Rich Cameron. (Gratitude is owed again to the resource of David Chalmer’s great web site). I differ from Cameron in that I don’t like an emergence model as a solution, but his analysis of the problem is well presented.
Here’s what I think it comes down to. In realizing that biological systems are grounded in the world of physics, we have two options: first, we can picture organisms as made of bits of dead matter and then struggle to recover what makes their qualities so remarkable; or, second, we could expand our view of the world of matter and energy to include features which make life explicable (and by the way quantum mechanics is pointing us there anyway).
Obviously, I prefer option two.