This is a monograph about how natural selection shapes adaptation and biological design. It focuses on microbes, both because of their importance and because they are experimentally tractable, allowing biologists to test hypotheses about diversity and design that may not be possible in other systems. More specifically, comparison is key -- if scientists can predict how biological traits change when comparing different conditions, then they can reasonably say that they understand the fundamental evolutionary forces of design. The book is divided into two parts. The first part provides a theoretical foundation, showing how to study biological design through comparative predictions and how to formulate comparative predictions based on foundational aspects of biological theory. The second part applies the concepts and theories from part I to a specific biological trait, that of microbial metabolism. Ultimately, the book makes a case for how to study adaptation and biological design, a major problem in biology"--