Considering how I am one of the authors of the paper in question, I think I know what we were looking at, and rates - average or otherwise - had nothing to do with it. You are confusing the comparison of total changes in branch lengths to glean differences in rates of mutation accumulation to some sort of statement about the average rates of mutation.
So when you wrote: "...and then give us average rates of change for each segment in between while saying that these are the actual rates of change in those groups for those periods." you were totally off base. Nowhere did we say anything about average rates at all, in terms of absolute rates per lineage.
So when you say "rate" you don't mean rate as in X/Y, but the total change? If I misunderstood your use of terms then I apologize for that. You can put me down as totally confused by your use of "rate" to mean "total".
(you quoting the paper)
"We further utilized the percentages of nucleotide change on the branches of the phylogenetic trees in Figs. 3 and 4 along with the estimated ages of the branch points (Table 4) to obtain estimates of evolutionary rates for noncoding DNA. These results are presented in Table 5. They indicate that noncoding DNA accumulated change at a slower rate."
"It has been observed that during primate evolution the rate of accumulation of nucleotide substitutions in noncoding DNA markedly slowed in anthropoids and..."
Now when I substitute "total" for "rate" I am even more confused. "Total" does not make any sense. If you do mean "rate" as in X/Y, I have no idea what your Y is anymore if it does not refer to the length of time for the branch.
See? We were concerned with rates of accumulation, we were not postulating anything about the rate of occurrance
It simply does not matter when the rates of occurrance might have been faster or slower. We were looking at the total - the end results.
Now you are drawing a distinction between all mutations and accumulation (fixation) of mutations, point taken, and if I misrepresented that
mea culpa because I should (do) know better. Obviously you could not know what the number of mutations would be, as only the fixed ones are remaining in the DNA of today.
(you quoting me}
Again the rate of fixing selected mutations would be de facto different under punctuated versus stasis conditions.
See? Fixed mutations. You can put me down for not being specific in talking about mutations in other places then.
However ... if anything, this just changes (refines) the X, and I am having a
real hard time understanding what your Y is, for if you are talking about an X/Y rate of change, and if it is
not the time period of the branch, then what is it? Substituting total for rate does not make any sense.
(you quoting me back at the start of this issue):
Now when we compare "molecular clocks" for mtDNA Eve and yChrom Adam what do we see? More change in Eve than in Adam? Longer change in Eve than in Adam or slower change in Adam than in Eve? We don't know. There is no connection to fossils, hard data, to be able to say at this point.
In my reply, I wrote:
"Again, that is not always the case. Local molecular clocks use fossil divergence dates as calibration points. This paper, for example, employs such clocks and its results are quite congruent with dates inferred from fossil data when applicable. "
So, I think it pretty clear why I introduced it and in reference to what, and it was not inreference ot criticisms about knowing when mutations took place of whether or not the mutations were in coding DNA or not and whether they were beneficial or not, etc..
So your whole point was that in some studies the "molecular clock" is calibrated against the fossil record? I have not questioned that in any way, and am actually impressed by it. Good work etc etc. I think it was a great study and we need more like it.
I also noted that you showed different rates of accumulation of mutations in different lineages -- assuming (as I did) that you meant number of fixed changes per time period of each branch as the "rate" of change. This supports my criticism of "molecular clocks" for assuming constant or average rates of change rather than noting that there is a lot of variation in rates of change.
I further noted that your study is subject to the same problem, and you readily admit that this is the case:
quote:
quote:
(you) Yes. Since local molecular clocks do not rely on any assumptions about mutation rates or rate differentials, a sufficiently large data set will not suffer from potential short term bursts of mutation and selection or the lack thereof.
(me) Nor will it be able to identify short term bursts or conditions under which they may apply.
(you) Totally insightful! And here is more shocking news - shovels don't work well when you want to chop down trees...
What's the big deal? It's not like you were capable of finer resolution of the data, you only had a certain small number of fossils that could be used. So let's agree that the study could not possibly have measured any instantateous rates of accumulation of mutations at any time in the whole study. I am not criticising you for failure to do that.
No, it does not. If for the sake of discussion we adopt your forced position that we were assigning average rates, the very term 'average' means that such differences have been taken into account. That is how one gets averages. Again, for the purposes of the paper in question, such criticisms are superfluous and irrelevant.
Precisely. And
my point was that
not using "average" in the terminology leads to the impression that there are no significant changes in rates of accumulation of change inside those periods. You have valid reasons for this in the limitations of the study. Why the fuss over using average if that is in fact what you were ending up with? Particularly if it is the correct terminology?
Perhaps an analogy is in order.
I am in the business of starting with endpoints and trying to figure out starting points, or stops along the way to the end point, say for cars in a road race. When the cars get to the finish line, I try to figure out where they started from (crazy road race). Upon discerning a starting point for the race, we can observe that car A took much longer than car B to reach the end, even though they started from the same place. I might then conclude that car A drove more slowly than car B. Now, car A might have gone full speed for several miles, then pulled off the side of the road for a rest, then coasted for a time, etc., while car B drove at a steady pace for the entire race.
Would that really matter if my only concern was how long it took each car to get to the end? Regardless of car A's driver's habits, it still took longer to get to the end, even if car A drove super fast for a long tiome and only then slowed down.
Your complaint seems to be that because I did not map out when and for how long car A went super fast then slow, that I cannot draw conclusions about who won the race.
No, my point is that you don't know what maximum speeds the cars are capable of or what kind of sustained high speed they can travel at, and thus if you are looking at a shorter or less intensive race course, or just any different race course, you have no idea whether car A or car B will win. You have no real predictive ability, because all you have is the average speed of each car from that one race. You may have an educated guess, but that is the best it is.
They may well be for some, but it is a mistake to presume that all researchers are interested in and will devote time to all things that appear to be of interest.
That may well be, but such understanding is not required when doing analyses in which such differentiations are irrelevant.
Until you do deal with the variability of rates of accumulation of mutations, you will not have any real predictive ability.
That was my criticism of "molecular clocks" in general and the "adam" and "eve" studies in specific -- that they were making predictions of their age on insufficient information and assumptions of uniformity that don't necessarily apply -- and I see absolutely no reason (yet) to change my mind on this issue.
But it seems that your whole problem is over the use of average in the terminology, and I really have to wonder what the big deal is on this issue.
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