I've published two books where I have explored the links between physiology and evolution. I have a third in progress.
My first book, The Extended Organism. The Physiology of Animal Built Structures (2000, Harvard University Press) examines how artefacts built by animals, such as nests, webs, burrows and so forth, are actually examples of "extended physiology", where these are adaptive devices between living systems and the physical environment. Among the logical outcomes of "extended physiology" is the "extended organism" where the distinction between living system and physical environment becomes hazy and blurred. This has some interesting implications for how we think about evolutionary adaptation.
My second book, The Tinkerer's Accomplice. How Design Emerges from Life Itself (2007, Harvard University Press) looks at the phenomenon of biological design, and asks whether design is a real phenomenon, or is it, as is commonly said, just an illusion. We see design because our minds wish to see it, but it is only apparent. Rather, blind and non-designing natural selection explains it all. In this book, I argue that design is a quite real phenomenon, and that it is the product of agents of homeostasis-"Bernard machines", that create new living environments and impose homeostasis upon them. This leads to some radical conclusions about the sufficiency of modern Darwinism as a coherent explanation for life.
I have a third book, in progress, with the working title Biology's Second Law. Evolution, Purpose and Desire. This book takes up where The Tinkerer's Accomplice left off, and builds the case that a coherent theory of biology rests upon two fundamental and independent laws. The First Law is Darwinian selection of living systems (not genes). The Second Law is homeostasis, which is a profound statement about the nature of life. The writing of this book is funded through the generosity of the John Templeton Foundation.