Decay Indices - summary

Joe Felsenstein joe at evolution.genetics.washington.edu
Mon May 1 00:45:23 EST 1995

In article <DEernisse-2604950950410001 at deernisse.fullerton.edu>,
Doug Eernisse <DEernisse at fullerton.edu> wrote:
>... I am happy to also respond to Joe Felsenstein's
>comments on my comparison of SI and bootstrap values, because I should
>have anticipated that my comments might have been posted to this
>news group as well as to their intended recipient.
>Concerning my comparison of SI and bootstrap values, it was not my
>intention to be overly critical of the bootstrap. A bootstrap value
>might be a useful heuristic, even if not a precise confidence interval,
>for node robustness. I happen to prefer SI values for reasons given.
>It is true that neither high bootstrap or SI values will necessarily
>mean that a node is robust because the node reflects historical truth.
>Other systematic biases in the data set (e.g., frequent T->C 
>transitions at sites free to vary) could be an alternative explanation.
>>>SI values vs. Bootstrap values:
>>>A high SI generally corresponds to a high bootstrap value (with some
>>>infrequent exceptions)
>>This seems true but little is yet known about statistical properties of
>>SI.  Perhaps Doug would argue that statistical inference is not the right
>>framework for thinking about this anyway ...
>[Text that might suck me into a sticky methodological and political debate 
> respectfully deleted for now.]
>Yes it is true that many do not view historical inference as a problem
>of statical inference. The arguments against applying statistics to
>historical reconstruction usually concern the difficulty of generalizing
>about how historical events occur. You mentioned Farris, but he must not be 
>totally against bootstrap estimations because he provides very efficient
>calculation of them in his program RNA. Of those I know who prefer 
>viewing historical reconstruction as a problem of statistical inference, 
>who might for example prefer maximum likelihood to parsimony, several are 
>extremely critical of the bootstrap as either a measure of reliability or 
>repeatability. You have already discussed why it gives high values when a 
>method is inconsistent.

Sorry, Doug, I didn't mean to harass you about these things.  I'm just being
a bit frustrated by the absence of discussion of which view ...
hypothetico-deductive, logical-parsimony, or statistical, underlies inferring
phylogenies.  My interpretation of the position of the original founders of
the Hennig Society is that they started with the first, have moved to the
second (without ever writing a paper saying that this was now their view)
and may be in the process of moving on to the third, all the while
putting out that they have always been right about all this.  I was just
trying to see if you knew of anywhere that people like Kluge and Farris
have stated their logical-parsimony view in print.  But these matters are

For the rest of our differences about SI and bootstraps, well we just
have different views about what is "intuitive", and whether omitting some
characters in particular replicates of bootstrap sampling is a serious

>The SI is difficult to confuse with a statistical measure of confidence.
>That is all I meant. You will have to admit that there are countless
>articles in molecular biology journals where authors have assumed that
>the bootstrap is a confidence statement for the reality of a node,
>never considering the possibility that other factors besides similarity due
>to history might account for the node robustness (i.e., they did not read
>your articles on bootstrap calculations).

[about whether SI advocates should also try bootstraps and vice versa]

>I  just suggested trying both, even though they are largely redundant.
>Journals such as MBE demand in their instructions to authors that all figured
>trees should include bootstrap estimations. Am I alone in thinking that this
>is  a bit severe when SI values are an acceptable alternative? I may have
>been the only author to so far get away with publishing only SI values on
>my trees in MBE, but it wasn't easy.

Well, I agree that bootstrapping is being done too mechanically and without
adequate consideration of its assumptions (this is true for likelihood too, and
for parsimony).  I would like to see the same examination of the statistical
properties of SI that has recently gone into bootstrapping -- that would
make me happier about considering it an "acceptable alternative".

>>Sorry about the theological warfare here, but the literature on things
>>like foundations of inferring phylogenies and criticisms of bootstraps
>>is in a funny state right now, with a lot of oral tradition and not
>>many clear treatments in journal articles.
>I agree, but please don't discourage people from trying something that is
>relatively new as I believe that you have by framing this as theological

In using the phrase I was being sheepish about introducing all this
discussion of foundations, etc. into another discussion.  I did not mean
to label advocacy of SI as "theology".  Sorry if that's how it cam off.

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