Protein as an indicator

[dttom]

It is believed that mutation occurs at a steady and slow rate (I know this from book), however, I doubt the point. As everyone knows, innumberous disaster occurs in the history of life, during disasters, for example, an explosion of cosmic ray, may increase the number of mutations in a great degree, so at these times, the so called 'steady and slow' mutation rate is disturbed.

 

So, todays, people uses protein as an indicator to find out the time for two species being apart form the life tree. For instance, if an amino acid difference between corresponding protein in two species represents 50 thousand years (i.e. one amino acid changes from one to another for each 50 thousand years), so people would believe that two species with 3 amino acid difference in their corresponding protein represents that they went apart from the life tree 1.5 million years ago. While, if apply the point that mutation does not occur at a steady rate mentioned above, such calculation might be incorrect, as, if the two species just departed from the life tree 25 thousand years ago, while a disaster occur changing three amino acid constituents in their corresponding protein, we might believe the two species under concern departed from each other 1.5 million years ago, which is not the fact in the assumption.

 

I don't know whether the point I mentioned is correct or not, so I would like to have some suggestions, or someone may point out what's wrong in the view I stand.