Positivism in evolutionary science

[Tom DiBenedetto]

James Francis Lyons-Weiler wrote:

>> Tom DiBenedetto wrote:

>>.... Whether that pattern is formed by "most of the traits" aquired
>> through descent does not seem to really be an issue, as far as I see.
>
>       Really?  On what grounds?  Is there something intrinsic
>       in the vast possibilities of past and present evolutionary
>       processes that would guarantee that most of the evidence
>       left by those processes is signal, and not noise (wrt
>       shared geneaological relationship)?

Sorry, I was unclear. When I said "does not seem to be an
issue", I meant it is irrelevant, I did not mean it was true or
false. The pattern need only rise above the noise; it need not be
formed by "most of the traits".

>> It seems to me that parsimony methods are quite efficient at
>> distinguishing the hierarchical signal from the incongruent noise.
>
>       I disagree.  I think they are efficient at portraying
>       signal when signal is there and noise is rare and
>       evenly distributed,

If there is no signal, there is no pattern to explain. And there are
plenty of instances of consistent signals shining through lots of
noise.

>        and they are efficient at summarizing
>       nonsense when the preponderance of "pattern" they tap into
>       does not reflect evolutionary relationships.

An organism-wide consistent pattern demands explanation. I dont know
of any which have been proposed beside descent.

>        Parsimony
>       methods can do no more than provide an overall picture of
>       the APPARENT signal in the distribution of states among
>       organisms.  Occasionally, under a restricted set of
>       conditions, MP will summarize true evolutionary
>       signal - and sometimes they will not.

What criterion do you use to distinguish when it is and when it
isnt? How do you know if it ever is?

>       When homoplasy is localized, the hierarchy in the matrix
>       is distorted.

The hierarchy in the matrix? That is the pattern in the data,
mahn,,it is not distorted by the various processes which could have
given rise to it.

>       When homoplasy is not rare, the hierarchy in
>       the matrix is displaced noise - which with varying states
>       MUST assume (by definition) some type of "pattern".

How do you know that? There are cladograms out there that strike me
as quite believable even though they have lots of homoplasy. How do
you know they are not true signal?

>       To say that the pattern in the matrix is reflective of evolutionary
>       relationships is a MAJOR assumption.

I know some preacher types who would agree with you there!  :)

>       The reason why there
>       will always be some finite degree of "pattern" in discrete
>       matrices with varying states is that the matrix is finite;
>       the state must be distributed this way or that.

Look, would you agree that historical descent does pattern the
distribution of characters? If yes, then the question is whether the
noise is SO ubiquitous that it can drown out that pattern. I am sure
that you can do a simulation in which non-descent similarities are
programmed in, such that few descent similarities remain. If
evolution
really worked that way, then how do you propose that any method could
be accurate? How can you model a set of processes when you can never
know which factor, or set of factors are yielding the pattern?

>       When the pattern or implied hierarchy in a matrix has not
>       been caused by informative shared geneaological processes,
>       parsimony will go right on and summarize the major emergent
>       pattern.

true

>        I have focused on independent means to determine
>       when and if the patterning in the distribution of states
>       among organisms looks like it (1) indicates a significant
>       degree of hierarchy ,

which is not the issue here,,,,

>       and if (2) the amount and type of implied hierarchy is the type that does not
>       mislead algorithms that lead to trees.

why dont you just take up some morphological studies? :) Seriously,
the more the field of molecular phylogenetics proceeds, the more
problematical this system of endlessly cycling states seems. Sequence
data is inherently unhierarchical, and I sense that it really will
turn out to be the least useful data source we have.
Of course I admit that there is lots of it!

>       Parsimony will reflect the preponderant or major pattern - and
>       it is hit or miss as to whether that pattern is, in fact,
>       predominantely reflective of shared geneaological relationships,
>       or something else.

Hit or miss? Sorry, but that does imply the existence of causal
factors which can produce patterns consistent on the same scale as
does descent.

>        That something else includes a mix of signal caused by
>       shared genealogical,
>        noise caused by common genealogy (organisms inherit homoplasy for
>       deeper relationships from their progenitors),
>        high rates of anagenetic evolution between speciation events,
>        non-binary fission of species,
>        non-independent anagenesis among characters in the same lineage,
>       inheritance of ancestral polymorphism,
>       concerted evolution (among lineages),
>       high frequencies of convergence (adaptive or random)
>       relative to the frequency of non-convergence,
>       unequal distribution of homoplasy among lineages,

Nice list. Here is not the time or place to argue each one. Some are
legitimate sources of error, many I would argue are not necessarily
confounding at all. But in general, unless many of these factors were
all working in a concerted way, I dont  think you would get false
patterns on the scale of the descent pattern.

>       In light of all these possible sources of noise, the central tenet
>       of phylogenetics should not be that evolution is, in general
>       or in detail, a parsimonious process.

OOhhh, low blow James. I *know* that you are sufficiently well-read
in the subject to know that parsimony is not justified by an
assumption of "parsimonious evolution", and never has been.

>        It is, as I indicated in
>       the second post in this particular thread, positivistic to presume
>       that parsimony will result in an accurate accounting of which
>       characters correctly indicate homology that indicates shared
>       relationships, rather than the alternative, namely, that
>       parsimony may be mislead by "something else".

Parsimony approaches are not  focussed on "accuracy", for that is
unknowable. They are focussed on finding the order which is prevelant
in the data.
What standard external to pattern analysis (or the process models
which explain patterns) do you propose to turn to in order to assess
the accuracy of phylogenetic results?





Tom DiBenedetto                 http://www-personal.umich.edu/~tdib/
Fish Division                                   tdib at umich.edu
University of Michigan Museum of Zoology