"Thus, I maintain that science studies the whole of human life--there is no metaphysically distinct part of us that is immune from scientific investigation. However, science gives us an incomplete account of human life, an account that can only be put into perspective by a religious point of view" (Nancey Murphy, Bodies and Souls, Or Spirited Bodies, page 120).
Hence, Murphy believes that the scientific perspective must be corrected or adjusted by religion. She is a non-reductive physicalist, who is convinced that not only do bottom-up processes account for higher-level conscious states but top-down processes also exert causal force on microbiological processes: "It is not the body qua material object that constitutes our identities, but rather the higher capacities that it enables: consciousness and memory, moral character, interpersonal relations, and, especially, relationship with God" (Bodies and Souls, Or Spirited Bodies, page 132).
Murphy also invokes the study by David Wiggins entitled Identity and Spatio-Temporal Continuity which helps one to appreciate the importance of "covering concepts" within the context of discussions on numerical identity.
On the other hand, substance dualism begs the question about a "soul" or res cogitans. Neuroscience, modern philosophy of mind, and the Kantian assault on the soul have shown us that we have no need of the immortal soul hypothesis; furthermore, substance dualism (notably exemplified by Descartes) is highly problematic in light of the mind-body problem. Conversely, reductive materialism is possibly not all that satisfying either. That is particularly the case when it comes to the view that one's body is identical with his/her persona.
The one particularly controversial aspect of Murphy's thought is what she writes about non-reductive physicalism or top-down causation. She argues that we need to consider the potential effect that environmental conditions possibly have on lower-level entities; for example, the role that the environment seems to have on the formation of "neural nets" or cell assemblies. One could evidently say that it is not only the random growth of dendrites and synaptic connections that lead to the formation of neural nets, but a "co-presentation of stimuli" to neurons that might also explain these assemblies. What top-down causation further suggests is that self-direction or freedom may result from an initially deterministic system. Another example that Murphy gives is the gradual emergence of self-direction in prokaryotes. Her account of what makes us human ultimately can be articulated in natural terms; however, she does not exclude the work of God or the holy spirit nor does she deny the incarnation or the resurrection of the body.