The clock is supposed to work by the “steady” accumulation of genetic changes over eons.
So what how does that work for species like sea turtles that are essentially unchanged since they coexisted with dinosaurs? Don’t they disprove the clock analogy?
None of today’s sea turtles are the same species as the ones who lived hundreds of millions of years ago. They change regularly, just like any other animals. The changes are not as visible as some, but gazillions of animals look pretty much the same as they used to.
You’re also confusing a couple of concepts. The genetic clock you’re talking about is calculated by changes in DNA. We don’t have DNA for animals hundreds of millions of years old. Barring a few extraordinary partials, we only have DNA for relatively recent burials, tens of thousands at most, not even millions of years. This clock is use for changes within species not with comparing today’s species to their ancestors.
They may look the same superficially, but they are still accumulating genetic changes.
And the part of the DNA that is usually used for a “clock” is the part that doesn’t code for proteins. Often referred to as “junk DNA”, much of seems to have no purpose at all, so it can easily collect changes that don’t affect the organism (an oversimplification, but good enough for this thread).
Right, we usually want to compare DNA that we know doesn’t code for protein, because we would expect protein-coding DNA to be affected by natural selection, and therefore either conserved or changed in a non-random way.
But if we test non-coding DNA, we have a pretty justified belief that any change in that DNA is random, and therefore really does act as a sort of “clock”, with changes accumulating slowly over time, more changes mean more time, fewer changes mean less time.
So even though present day turtle species look pretty similar to turtle species millions of years ago, and we might expect that their coding DNA would be very similar to those ancient turtles (although it might not be), we DO expect that their non-coding DNA would be pretty different, since there’s no mechanism to select out turtles that have a mutation in non-coding DNA. The mutations pile up over the millenia.
Now, that isn’t to say that the rate of mutation is constant. We know that some species seem to have more mutations over time than others. There are enzymes that repair mutations, changes in the efficiency of those enyzmes means changes in the mutation rate for the species.
No exactly. By looking at the number of genetic differences between two species, one can assess how much time has passed since the last common ancestor of the two contemporary species lived, that is, how long ago the two species separated, assuming that both species change at the same rate. We cannot sequence the genes of this ancestor, but assume that its gene sequence shows more ot less the same number of sequence differences to the two offspring species.
Even if the two species keep looking very similar, this does not mean that their genome sequence stays similar: they still accumulate silent mutations in their DNA, mutations that have no effect on the phenotype.
We don’t need to know that they change at the same rate, just at what rate they change. Mammals and reptiles seem to have different “clocks”, but as long as we have a good idea of what those differences are, then we can still estimate the time of their divergence. Of course, we don’t always know how long the clocks have been different and when they started to change, so there are always going to be errors.
Not quite. The phenotype is a lot more than just what the animal looks like to an untrained biologist. Changes to the immune system aren’t visible, but are still part of the phenotype. It would be odd indeed if the turtles the OP were referring to had not accumulated changes in their immune system over time.