Computer Metaphors for Biochemistry

The metaphor of the computer represents in some crude fashion the chemistry of life. Nowadays one may assume that the average citizen of an industrialized country is at least as familiar with computers as with rain forests. The idea of using the computer as a metaphor is a natural one. A computer is a device for handling information according to a program which it is able to remember and execute. A living cell, to remain in control of its vital functions in a variable environment, must also possess a program of chemical reactions which it is able to remember and execute. The control system of the cell must be capable of storing and handling the large amount of information that is needed to keep a large number of complicated chemical reactions in balance.

Everyone who works with computers knows that two essential components are needed to make them useful. The components are hardware and software. Hardware is the computer itself, the box full of electronic circuits which carry out logical or mathematical operations. Software is the floppy disk on which instructions and information are written. You feed the software into the hardware in order to tell the hardware what to do. Likewise, every living cell has two dominant components, two kinds of large chemical molecules called proteins and nucleic acids. The discoveries of the last fifty years have revealed that proteins behave like hardware, acting as catalysts to make other chemicals react in highly specific ways. And nucleic acids act like software, organizing the proteins and telling them what to do. The decisive event which started the modern era in biology was an experiment done by Oswald A very and his colleagues in New York in 1944. A very took bacteria of one variety and fed them nucleic acid from another variety. The bacteria were transformed into the variety from which the nucleic acid came. If computers and floppy disks had existed in 1944, Avery might have said that the change of nucleic acid was affecting his bacteria just as a change of disk affects a computer.

The computer metaphor has been enormously fruitful as an aid to the understanding of living processes. Like the metaphor {57} of the rain forest, it is not exact. It is only a metaphor. One should not push metaphors too far. One should not think that a molecule of nucleic acid is really an inert object like a floppy disk. In reality, a molecule of nucleic acid can do many other things besides serving as a passive container of information. Recent experiments have shown that under some conditions nucleic acids can act as catalysts just as proteins do. The separation between hardware and software in a living cell is not absolute. There is no law of nature which forbids proteins to carry information and forbids nucleic acids to process information. Nevertheless, the metaphor is a good one to describe the overall organization of a cell. Most of the time, proteins are busy chopping and splicing while nucleic acids are quietly telling them what to do.

he computer metaphor can be extended a little further. Living cells have two primary functions which are given the names "metabolism" and "replication." Metabolism means eating and digesting and excreting. Metabolism maintains the integrity of the cell by a continual reshuffling of chemical components, converting raw materials from outside the cell into the substances required for its continued existence. Replication means making exact copies of molecules so that a cell can reproduce itself. Replication allows the copying of hereditary information so that the characteristics of a cell can be precisely inherited by its offspring. The two functions of metabolism and replication are again well described by the metaphor of hardware and software. Metabolism is the business of protein, replication is the business of nucleic acid. Metabolism is a hardware function because it requires constant activity. Replication is a software function because it requires stability and legibility. Nucleic acids, like floppy disks, are easily read and copied. Proteins, like computers, are made by following instructions and not by copying.