Mutations can be neutral for various reasons. The DNA code is a ‘degenerate code. This is a technical term meaning that some code ‘words’ are exact synonyms of each other. When a gene mutates into one of its synonyms, you might as well not bother to call it a mutation at all. Indeed, it isn’t a mutation, as far as consequences on the body are concerned. And for the same reason it isn’t a mutation at all as far as natural selection is concerned. But it is a mutation as far as molecular geneticists are concerned, for they can see it using their methods. It is as though I were to change the font in which I write a word, say kangaroo to kangaroo. You can still read the word, and it still means the same Australian hopping animal. The change of typeface from Times New Roman to Arial is detectable but irrelevant to the meaning.

Not all neutral mutations are quite so neutral as that. Sometimes the new gene translates into a different protein, but the ‘active site’ of the new protein remains the same as the old one. Consequently, there is literally no effect on the embryonic development of the body. The unmutated and the mutated form of the gene are still synonyms as far as their effects on bodies are concerned. It is also possible (although ‘ultra- Darwinists’ like me incline against the idea) that some mutations really do change the body, but in such a way as to have no effect on survival, one way or the other.

So, to sum up on the neutral theory, to say that a gene, or a mutation, is ‘neutral’ doesn’t necessarily mean that the gene itself is useless. It could be vitally important to the animal’s survival. What it means is that the mutated form of a gene – which might or might not be important for survival – is no different from the unmutated form with respect to its effects (which might be very important) on survival. As it happens, it is probably true to say that most mutations are neutral. They are undetectable by natural selection, but detectable by molecular geneticists; and that is an ideal combination for an evolutionary clock.

None of this is to downgrade the all-important tip of the iceberg – the minority of mutations that are not neutral. It is they that are selected, positively or negatively, in the evolution of improvements. They are the ones whose effects we actually see – and natural selection sees’ too. They are the ones whose selection gives living things their breathtaking illusion of design. But it is the rest of the iceberg – the neutral mutations, which are in the majority – that concern us when we are talking about the molecular clock.

As geological time goes by, the genome is subjected to a rain of attrition in the form of mutations. In that small portion of the genome where the mutations really matter for survival, natural selection soon gets rid of the bad ones and favors the good ones. The neutral mutations, on the other hand, simply pile up, unpunished and unnoticed – except by molecular geneticists. And now we need a new technical term: fixation. A new mutation, if it is genuinely new, will have a low frequency in the gene pool. If you revisit the gene pool a million years later, it is possible that the mutation will have increased in frequency to 100 per cent or something close to it. If that happens, the mutation is said to have ‘gone to fixation’. We shall no longer think of it as a mutation. It has become the norm. The obvious way for a mutation to go to fixation is for natural selection to favor it. But there is another way. It can go to fixation by chance. Just as a once proud surname can die out for lack of male heirs, so the alternatives to the mutation we are talking about can just happen to disappear from the gene pool. The mutation itself can become frequent in the gene pool, by the same tuck as has led ‘Smith’ to emerge as the commonest surname in England. Of course it is much more interesting if the gene goes to fixation for a good reason – that’s natural selection – but it can also happen by chance, given a large enough number of generations. And geological time is vast enough for neutral mutations to go to fixation at a predictable rate. The rate at which they do so varies, but it is characteristic of particular genes, and, given that most mutations are neutral, this is precisely what makes the molecular clock possible.

It’s fixation that matters for the molecular clock, because ‘fixed’ genes are the ones that we look at when we compare two modern animals to try to estimate how long ago their ancestors split apart. Fixed genes are the genes that characterize a species. They are the ones that are all but universal in the gene pool. And we can compare the genes that have become fixed in one species with the genes that have become fixed in another, in order to estimate how recently the two species split apart. There are complications, which I won’t go into because Yan Wong and I discussed them fully in ‘The Epilogue to the Velvet Worm’s Tate’ with reservations, and with various important correction factors, the molecular clock works.

Just as radioactive clocks tick at hugely variable speeds, with half-lives ranging from fractions of a second through to tens of billions of years, so different genes provide a marvelous spread of molecular clocks, suitable for timing evolutionary change on scales ranging from a million to a billion years, and all stages in between. Just as each radioactive isotope has its characteristic half-life, so each gene has a characteristic turnover rate – the rate at which new mutations typically go to fixation by random chance. Histone genes characteristically turn over at a rate of one mutation per billion years. Fibrinopeptide genes are a thousand times faster, with a turnover of one new mutation fixed per million years. Cytochrome-C and the suite of hemoglobin genes have intermediate turnovers, with times to fixation measured in millions to tens of millions of years.

Neither radioactive clocks nor molecular clocks tick in a regular fashion like a pendulum clock or a watch. If you could hear them ticking, they’d sound like a Geiger counter, the radioactive clocks literally so since a Geiger counter is precisely what you would use to listen to them. A Geiger counter doesn’t tick regularly, like a watch; it ticks at random, the ticks coming in strange, stuttering bursts. That’s how mutations, and fixations, would sound, if we could hear them on the immensely long timescale of geology. But, whether stuttering like a Geiger counter or ticking metronomically like a watch, the important thing about a timekeeper is that it should tick at a known average rate. That’s what radioactive clocks do, and that’s what molecular clocks do.

I introduced the molecular clock by saying that it assumes the fact of evolution and therefore can’t be used in evidence of it. But now, having understood how the clock works, we can see that I was too pessimistic. The very existence of pseudogenes – useless, untranscribed genes that bear a marked resemblance to useful genes – is a perfect example of the way animals and plants have their history written all over them.

Excerpted from ‘The Greatest Show on Earth’ by Richard Dawkins