An analogy for the genome

Once upon a time the genome was likened to a blueprint. Nowadays it often likened to computer code. The trouble with the computer code analogy is that it is quite misleading. The computer code analogy suggests that the cell is a passive machine that does nothing in its own right, a machine whose every action, form, and function is spelled out in the genome. This depiction is quite wrong. The genome contains the specifications of sundry chemicals needed for effecting the actions, forms, and functions of life. Life itself is the specification for life. The following, adopted from a prior essay, may make this clearer:

Life is structured so that it runs by itself; it doesn’t need an intelligence intervening and making things happen. This is, if you like, a miracle but that’s the way it is.

One obvious question is: How can there be what appears to be purposeful change without there being someone to have the purpose. The answer, very roughly, is that all living things have an implicit purpose; they must live and reproduce. This purpose comes from necessity rather than conscious decision.

A second obvious question is: How can complexity arise if DNA is a sequence of coded instructions specifying the structure of the cell and the behaviour of life? Applying the mutation/selection process to computer code does not produce complexity because computer code is too fragile. Very simply, the answer is that DNA does not specify the structure of the cell and the behaviour of life. The living cell is a collaboration between the DNA and the processes in the rest of the cell. Complexity is enabled by the genes; it emerges from the interactions in the processes of life.

Organisms, even the simplest living cell, are complex collections of chemical reactions that effect organized functionality. Here is an analogy which may serve as explanation.

Imagine a small walled town. Within it there is a diversified population of people performing different tasks. There is a butcher and a baker and an undertaker, guards at the gate and a refuse collector. The people in the town are good at their tasks but they are quite stupid so anything novel is a real problem for them. Fortunately there is a library in the town, a library which contains instructions for dealing with unusual situations.

Whenever one of the residents runs into a problem they can’t handle they send a runner to the library to find out what to do. There is a catch; there is no librarian and the runners aren’t very smart either. There is a solution; the books in the library have tokens stamped on them. The runners carry tokens; they search the library until they find a book that matches their token; they then make a copy of the book. The books are very short and they aren’t filled with text; instead they contain blueprints of tools

Once runner finds a book he takes it the town blacksmith. (There isn’t any point in taking the books to the town residents; they can’t read.) The town blacksmith isn’t very bright either, but he can follow a blueprint. Once he has made a tool he hands it off to another runner who wanders about the town until he finds someone who wants the tool.

The whole system is a little bit more complicated than that but it is all organized around the principle that the residents are good at their tasks but that they are very stupid.

Now it happens from time to time that some towns fail – the crops fail in the surrounding countryside or a plague sweeps through – and that other towns prosper. The towns that prosper have a problem; the population becomes too great to hold within the walls. They have a solution; they divide the town up into two towns with separate walls and separate communities. This is a special situation and a very complicated task. In the library are a set of books devoted just to the instructions for how to divide the town into two towns. One of the things that happens, and this is important, is that each town gets a copy of the library. Now it happens to be the case that the copyists, although they are very careful, sometimes make mistakes. This makes for a problem; if there is an error in a book in the library then there will be a problem when that book is called upon. Fortunately, and this is critical, there is a lot of slop in the system. Just because the people in the town are doing things one way doesn’t mean that they can’t do it some other way that is slightly different; it may be better or it may be worse but it is different. The key is that the library doesn’t tell people what to do; it only supplies blueprints for tools that people need. The people do the work; if the tools are slightly different then they do things in a different way. Sometimes an altered blueprint is useless; some towns die because one little piece of information about one little task is gone. Most of the time, however, things go on as they always have, only in a slightly different way. Over time these differences accumulate. The way of life centuries ago is quite different from that of today.

Sometimes an altered tool may be an enabler. That is, its use by one worker allows several workers to collaborate in a way that they hadn’t previously collaborated. The tool doesn’t tell the workers how to collaborate; it just makes collaboration possible. If collaboration is a good thing (it may not be – the workers do not know) then the town will prosper and better versions of the tools needed for the collaboration will come into vogue.

There are no books for complex behaviour in the library. Complexity arises from a series of events. First there are enabler tools – tools that permit collaboration in new ways. Then there are adaptations as the new behaviour is refined.

My analogy is a bit long winded for which my apologies. The whole point is that genes are not blueprints for the cell and the processes of life; they are blueprints for “tools” that the life processes use. There is no master blueprint for the cell in the sense that we think of blueprints. The cell itself is the blueprint for itself, a case of the territory being the map, so to speak. Cells replicate by making copies of themselves.