Are species real?

Richard Zander Richard.Zander at MOBOT.ORG
Wed Apr 12 08:39:43 CDT 2006


Anyone who thinks arguing about what is "real" is a waste of time should
be wary of his/her assumptions. It is easy, especially in phylogenetics,
to fall prey to confirmation bias (what supports your ideas is
acceptable, what doesn't is not scientific), cognitive dissonance
(holding mutually contradictory cognitions and liking it), and mumbo
jumbo. 

Want examples? 

Confirmation bias: To consider as meaningful branch arrangements of more
then 50% bootstrap while discounting arrangements less than 50% (i.e.
data supporting hard polytomy as an alternative). The data should be
combined, or Bayes Theorem used to combine the two.

Cognitive dissonance: A cladogram or subclade with various bootstrap or
BPP values on branch arrangements is entirely correct at a probability
that is the product of the reliability values of the individual branch
arrangements; Bonferroni correction of multiple tests is almost never
used in evaluating subclades of interest. 

Mumbo Jumbo: Make a 4 taxon data set out of one sequence duplicated 4
times. Change 2 of the sequences (not the outgroup) so that, say, 10
sites are different from the original nucleotide but also different from
each other. Thus, two of the sequences differ from the rest at the same
10 sites but share no phylogenetically informative traits. With maximum
parsimony, you will be informed by PAUP that there are no
phylogenetically informative traits, the number of steps joining the two
"taxa" is 1 through 10, and the branch length actually assigned will be
the maximum, 10 steps. (Lots of cladograms are published with number of
steps given to arrangements that have bootstrap proportions less than
50%.) Bayesian analysis will give you a low BPP with a proportion of
sites invariant, and a high BPP with all sites equal in chance of
change. Thus, absolutely no shared traits can contribute to the apparent
reliability of a cladogram.

This may seem small potatoes, but it adds up to a "real" phylogeny that
is a house of cards.

******************************
Richard H. Zander
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166-0299 USA
richard.zander at mobot.org
Web sites: http://www.mobot.org/plantscience/resbot/
and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
For FedEx and UPS use:
Missouri Botanical Garden
4344 Shaw Blvd.
St. Louis, MO 63110
******************************

-----Original Message-----
From: Thomas G. Lammers [mailto:lammers at UWOSH.EDU]
Sent: Tuesday, April 11, 2006 7:38 AM
To: TAXACOM at LISTSERV.NHM.KU.EDU
Subject: Re: [TAXACOM] Are species real?

At 11:53 PM 4/10/2006, Don.Colless at CSIRO.AU wrote:
>Anyone silly enough to get involved in this thread will soon find 
>himself arguing about the meaning of "real"

THAT precisely what I have always wondered about this question.  What
does
"real" mean?  Why is it important that they be so?   It smacks too much
of
metaphysics for my taste.




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