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One of the most fundamental distinctions between organisms is between the prokaryotes and the eukaryotes. Eukaryotes include all vertebrates (like humans) as well as many single-celled organisms, like yeast. The simpler prokaryotes are a distinct class of organisms, including various types of bacteria and cyanobacteria (blue-green algae).

Although the basic mechanisms that underlie cellular biology are surprisingly few, there are many instances and many variations on these mechanisms, leading to an ocean of detail concerning (for instance) how the process of microtubule attachment to a centrosome differs across different species. Cellular-level systems, because they are so small, are also difficult to observe directly, which means that obtaining this detail experimentally is a long and arduous process, often involving tying together many pieces of indirect evidence. Most importantly, cellular biology is hard to understand because living things are extremely complex—in several different respects.

The best way to understand and model complex systems is to obtain detailed information about their behavior. Biologists have developed many ways to obtain information about the workings of a cell. Some of these methods are clever and intricate, and many methods collect indirect evidence of behavior. I will start by discussing the most natural of these methods—the microscope—because, as Yogi Berra is reputed to have said, “you can observe a lot by just watching.” For many purposes, the best way to study a cell is to look at it through a microscope.

A well-worn cliché is that cells are machines, the components of which are molecules. This leads to an important point: in general, molecules are too small to be seen or manipulated directly. How can one study a machine if you can’t look at or manipulate its components? To use a computer science analogy to this problem, imagine trying to reverse engineer a PC from a hundred yards away, with your only tools for manipulation being a collection of bulldozers and excavators and such that you direct by remote control. What sort of things could you do, and what sort of things would you learn?

There is another whole family of approaches to studying very small objects: rather than attempting to study molecular-level processes with the (comparatively) huge and clumsy machinery that we humans can design, let us look for useful molecular-level tools we can find in nature. In particular, living cells are full of useful molecular-level machinery— what can we, as biologists, do with this existing machinery?

There are a number of reasons for wanting to insert foreign DNA into a cell, one of which is simply to amplify (increase) the quantity of foreign DNA by making use of a cell’s natural ability to grow and multiply. However, there is a more direct way to amplify DNA, by using of some of the cell’s DNA replication machinery in vitro. This technique is called polymerase chain reaction (PCR). To explain how it works, I will first review, at a high level, how DNA is duplicated (replicated) in a cell. (The mechanisms for this differ somewhat in prokaryotes and eukaryotes—here I will focus on prokaryotic replication).

As biologists become better and better at collecting data, the problem of managing, analyzing and interpreting the massive amount of data that has already been collected becomes more and more important. The growing field of bioinformatics is focused on this problem; more broadly, it is concerned with using computational methods to solve problems from biology. There are now a number of review articles, books and even complete educational curricula on bioinformatics, so this chapter is not in any way complete: however, it will hopefully give a useful overview of what the most active topics are.

This document is aimed at computer scientists who are trying to acquire a “reading knowledge” of biology. For those that want to learn more about core biology, the gentlest introduction I know of is “The Cartoon Guide to Genetics.” The most comprehensive introduction is “Molecular Biology of the Cell, 4 Edition,” by Alberts et al., which also has the virtue of being freely available on-line at the National Library of Medicine (NLM).