Well, a simple experiment would be to take a single cell, culture it through several generations (sequencing a particular gene out of one of the immediate daughter generations), and then examine the content of that gene in subsequent generations. The number of point substitutions divided by the number of cell divisions and the length of the genome is a rough estimate of the number of point substitutions per number of base pair replications, absent any environmental mutagens.
An estimate is all we can get, of course. Mutation is a random, stochiastic process. And obviously we're aware of the fact that some genes mutate more than others. But as a rough estimate it's servicable. I mean, think about it. Any mole or birthmark you have represents a mutation in your skin (that was passed on, as you developed, to the daughter generations of that single skin cell.) Any time you're out in the sun you're accruing mutations, too. Or any time you eat cooked red meat.
It's all but trivial to establish that mutations are occuring. I can't see how this basic scientific point could possibly be under dispute. Once again it's going to be something fairly hard to point to
one paper proving it because it's such a trivially obvious scientific fact that it isn't worth writing a paper on.
Until we determine that the mutations are happening we can't assume that they are the sources of differences.
Where else are the differences coming from? Pluto?
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