Molecular Biology for Computer Scientists
“Computers are to biology what mathematics is to physics.” — Harold Morowitz
One of the major challenges for computer scientists who wish to work in the domain of molecular biology is becoming conversant with the daunting intricacies of existing biological knowledge and its extensive technical vocabulary. Questionsabout the origin, function, and structure of living systems have been pursued by nearly all cultures throughout history, and the work of the last two generations has been particularly fruitful. The knowledge of living systems resulting from this research is far too detailed and complex for any one human to comprehend. An entire scientiﬁc career can be based in the study of a single biomolecule.Nevertheless, in the following pages, I attempt to provide enough background for a computer scientist to understand much of the biology discussed in this book. This chapter provides the briefest of overviews; I can only begin to convey the depth, variety, complexity and stunning beauty of the universe of living things. Much of what follows is not about molecular biology per se. In order to
2ARTIFICIAL INTELLIGENCE & MOLECULAR BIOLOGY
explain what the molecules are doing, it is often necessary to use concepts involving, for example, cells, embryological development, or evolution. Biology is frustratingly holistic. Events at one level can effect and be affected by events at very different levels of scale or time. Digesting a survey of the basic background material is a prerequisite forunderstanding the signiﬁcance of the molecular biology that is described elsewhere in the book. In life, as in cognition, context is very important. Do keep one rule in the back of your mind as you read this: for every generalization I make about biology, there may well be thousands of exceptions. There are a lot of living things in the world, and precious few generalizations hold true for all ofthem. I will try to cover the principles; try to keep the existence of exceptions in mind as you read. Another thing to remember is that an important part of understanding biology is learning its language. Biologists, like many scientists, use technical terms in order to be precise about reference. Getting a grasp on this terminology makes a great deal of the biological literature accessible tothe non-specialist. The notes contain information about terminology and other basic matters. With that, let’s begin at the beginning.
1. What Is Life?
No simple deﬁnition of what it is to be a living thing captures our intuitions about what is alive and what is not. The central feature of life is its ability to reproduce itself. Reproductive ability alone is not enough; computer programs cancreate endless copies of themselves—that does not make them alive. Crystals inﬂuence the matter around them to create structures similar to themselves but they’re not alive, either. Most living things take in materials from their environment and capture forms of energy they can use to transform those materials into components of themselves or their offspring. Viruses, however, do not do that; theyare nearly pure genetic material, wrapped in a protective coating. The cell that a virus infects does all the synthetic work involved in creating new viruses. Are viruses a form of life? Many people would say so. Another approach to deﬁning “life” is to recognize its fundamental interrelatedness. All living things are related to each other. Any pair of organisms, no matter how different, have acommon ancestor sometime in the distant past. Organisms came to differ from each other, and to reach modern levels of complexity through evolution. Evolution has three components: inheritance, the passing of characteristics from parents to offspring; variation, the processes that make offspring other than exact copies of their parents; and selection, the process that differentially favors the...