Re: Stereotypes and reputations

Pim van Meurs wrote:

> Cornelius Hunter wrote:
>
>
> [quote]
> The stunning degree of match between even the most incongruent
> phylogenetic trees found in the biological literature is widely
> unappreciated, mainly because most people (including many biologists)
> are unaware of the mathematics involved (Bryant /et al/. 2002
> <http://talkorigins.org/faqs/comdesc/section1.html#Bryant_etal2002>;
> Penny /et al/. 1982
> <http://talkorigins.org/faqs/comdesc/section1.html#Penny_etal1982>;
> Penny and Hendy 1986
> <http://talkorigins.org/faqs/comdesc/section1.html#PennyHendy1986>).
> Penny and Hendy have performed a series of detailed statistical
> analyses of the significance of incongruent phylogenetic trees, and
> here is their conclusion:
>
> "Biologists seem to seek the 'The One Tree' and appear not to be
> satisfied by a range of options. However, there is no logical
> difficulty in having a range of trees. There are 34,459,425 possible
> [unrooted] trees for 11 taxa (Penny /et al/. 1982
> <http://talkorigins.org/faqs/comdesc/section1.html#Penny_etal1982>),
> and to reduce this to the order of 10-50 trees is analogous to an
> accuracy of measurement of approximately one part in 106 ." (Penny and
> Hendy 1986
> <http://talkorigins.org/faqs/comdesc/section1.html#PennyHendy1986>, p.
> 414)
>
> For a more realistic universal phylogenetic tree with dozens of taxa
> including all known phyla, the accuracy is better by many orders of
> magnitude.
> [/quote]
>
> From:
> http://talkorigins.org/faqs/comdesc/section1.html#independent_convergence
>
> All CH had to offer was "You might want to go read the Penny (1982)
> paper to see how meaningless it really is."
>
> well tell us...
>
>

Douglas even addresses Hunter's claims

      Confusion about Evolutionary Theory

Camp goes on to quote Hunter concerning this point:

    Hunter illustrates the point this way:

        Penny obtained his trees by culling those that were most
        parsimonious--that is, he selected the trees that showed the
        least amount of evolutionary change to represent the history of
        life. The first problem is that Penny's method works perfectly
        fine on things we know did not come about via Darwinian
        evolution. For example, Penny's method would also claim that
        automobiles evolved from one another.

As pointed out above, Hunter is incorrect. Hunter makes the bold claim
that "Penny's method would also claim that automobiles evolved from one
another" in the absence of any evidence to support that claim.
Automobiles might give a most parsimonious tree (though this is not
assured), but even if they do, the resulting tree will be bunk. It will
not satisfy the mathematical requirements for nested hierarchies, and
the reasons are explained in Prediction 2
<http://www.talkorigins.org/faqs/comdesc/section1.html#pred2>. If Camp
and Hunter think otherwise, they should determine a phylogenetic tree of
cars, using standard phylogenetic programs, that has statistically
significant high values of cladistic hierarchical structure. To really
drive the point home, they could derive two trees independently, and
then show that they match with statistical significance. If they are
correct, they could easily prove their point--but in reality they will
be unable to do so.

      A False Analogy <http://www.intrepidsoftware.com/fallacy/falsean.htm>

Camp continues with Hunter's quote:

    Consider a group of vehicles, beginning with a small economy car and
    increasing in size to larger cars and to minivans and large-sized
    vans. One could quantify several aspects of the vehicle designs,
    such as tire size, steering mechanism, engine size, number of seats
    and so forth. Presupposing the evolutionary paradigm and searching
    for parsimonious relationships, we would find that most of the
    design measures suggest the same relationship. The smaller vehicles
    have smaller tires, manual steering, smaller engines, and fewer
    seats. The larger vehicles have larger tires, power steering, larger
    engines, and more seats. In other words, the groupings suggested by
    the different design measures (tire size, steering mechanism, engine
    size, etc.) tend to be similar. But of course, the family of
    automobiles did not evolve from one another via random mutations.
    The groupings of the design measures are a natural result of
    engineering and have nothing to do with Darwinian evolution. How
    then can Penny's results provide "strong support" for evolution?
    (Hunter, 40.)

Hunter's example is erroneous for another reason--he has chosen
characters that are not independent. This is a big "no-no" in cladistic
analysis, and it is a rudimentary issue that is addressed early on in
any introductory text on phylogenetic analysis. When using characters of
organisms in a cladistic analysis, biologists attempt to use characters
that are as functionally and developmentally independent of one another
as possible. For instance, the size of an animal is only one character.
Of course larger animals will in general have larger bodies, larger
legs, and larger heads, just as in Hunter's example larger cars have
larger tires, larger engines, etc. To be valid, "largeness" cannot be
counted more than once. The very easy solution, which is regularly used
by biologists, is to measure the /relative/ sizes of different
characters. For instance, having a femur/tibia ratio of 3 is a different
character from having a femur/tibia ratio of 1/2, regardless of the
overall length of the bones. Biologists know that they must normalize
for size, and instead they concentrate on structural details. Hunter's
example is thus a straw man.

Penny's analysis (Penny /et al/. 1982
<http://www.talkorigins.org/faqs/comdesc/camp.html#Penny_etal1982>) used
five genes, four of which are functionally independent; thus, the result
that trees made from several different independent genes match with
statistical significance is indeed extremely strong support for common
descent. For Hunter's analogy to be valid, he would have to claim that
phylogenetic trees made only with cars' steering wheels will match
phylogenetic trees made only with cars' tires and trees made only with
cars' headlights and trees made only with cars' engines and trees made
only with cars' transmissions. Such a claim would be false, since cars
with similar tires (e.g. similar width/diameter ratio, manufacturers,
tread, color, materials, etc.) do not generally also have similar
engines (e.g. similar manufacturer, injection systems, cylinder
arrangement, orientation, etc.), or headlights (e.g. similar shape,
brightness, manufacturer, bulb type, position, number, etc.), or
transmissions, or steering wheels.

Thus, Hunter's analogy is false
<http://www.intrepidsoftware.com/fallacy/falsean.htm> for multiple
reasons. Hunter's example of how cars' characters can be analyzed to
infer a phylogeny is quite different from how real organisms' characters
are analyzed by biologists when inferring a phylogeny.
Received on Fri Aug 5 13:07:06 2005