Biologists seek to discover mechanisms. Molecular biologists discovered the basic mechanisms of DNA replication and protein synthesis, and they continue to elucidate the myriad mechanisms of gene regulation. Neuroscientists study the mechanisms of spatial memory, the propagation of action potentials, and the opening and closing of ion channels in the neuronal membrane. Medical researchers probe the genetic basis of cystic fibrosis and how nutrient deficiencies give rise to somatic symptoms. Evolutionary biologists study the mechanism of natural selection and the isolating mechanisms of speciation. Ecologists study nutrient cycling mechanisms and the way imbalances in nutrient cycling produce dead zones in places such as the Chesapeake Bay in the eastern United States. Across the life sciences, the goal is to open black boxes and to learn through experiment and observation which entities and activities are components in a mechanism and how those components are organized together to do something that none of them does in isolation.

        Biologists look for mechanisms because they serve the three central aims of science: prediction, explanation, and control. First, knowing the mechanism usually allows one to predict how the phenomenon will behave. If one knows how a mechanism works, one can say how another instance in similar circumstances would work. Sometimes one can also predict the behavior of the mechanisms if it is placed in different conditions or given different inputs. Second, and related, describing the mechanism for a phenomenon serves to explain the phenomenon. In some cases, one can literally see how the mechanism works from beginning to end. Finally, knowing the mechanism potentially allows one to intervene into the mechanism in order to produce, eliminate, or change the phenomenon of interest. Biological mechanisms, in other words, are of interest because we want to bring them under our control: for production (as in agriculture and farming), for healing (for the purposes of medicine and pharmacology), and for environmental management and protection (in ecology). Examples abound: One's understanding of how a normal mechanism fails in disease can guide one in the search for cures and preventions. One’s understanding of how a natural ecosystem works might suggest interventions to control or ameliorate the effects of an oversupply of nutrients.

        Our goal in this book is to make the central aspects of this mechanistic perspective explicit. Our aim, first, is to answer the question: what is a mechanism? Second, we offer a set of questions, constraints, and strategies that might help people to undertake the search for mechanisms. ...