Molecular taxonomy: on way out?

[John Grehan]

> From: Richard Jensen [mailto:rjensen at saintmarys.edu]
> Sent: Tuesday, July 19, 2005 11:43 AM

> Once the sequence data are generated, it is simply not reasonable to
ask
> that the researcher examine every sequence visually to verify putative
> homologies and apomorphies.  

Oh how I wish I could use that excuse for the rest science. Would it not
be wonderful if I did not have to justify every element of my data but
assert that it is true because I have so much. That seems to be the
message here.

First, visual inspection is in all
> probability
> more likely to result in errors and the amount of data is just too
great.

If there is too much data for empirical testing character by character
then I'm not sure its something that I would like to hang my hat on. 

> A good computer algorithm is simply much more efficient and reliable.

Good for sorting out conflicting patterns of relationship yes, but
figuring out which characters are derived and which are not apart from
an artificial device of outgroup polarity being imposed upon the data I
would say no.

any use of
> any
> computer program for any task that a human can do by hand is is
mimicry
> because the algorithms cannot study the data. 

Agreed. But one mimicking does not necessarily mean the same.

 I suppose that, if the data
> set generates multiple solutions, you also do not rely on the computer
> algorithm to find all of them - it's better done by hand to make sure
that
> nothing is overlooked. 

No I never said any such thing.

 In fact, I'm surprised you use e-mail; after all,
> the mindless computer algorithms that make all of this possible have
no
> knowledge of the real intent of your words.  All the algorithms do is
> concatenate a series of keystrokes, with no understanding of what any
of
> it
> means.

Agree completely which is why I would not rely on the algorithm to
compose my email in the first place.


> For the most part, people I know who employ cladistic algorithms to
infer
> phylogenies based on molecular data are probably just as careful about
> generating their data as are those of us who examine morphological
data.

Its not a matter of being careful, but a matter of whether one restricts
the data set to characters that can be individually assigned a derived
status.

> Your comments certainly infer that you don't trust them to be
responsible,
> thoughtful scientists who gather data  and analyze it with care.  

You can make any inference you like. That is your right.

You
> apparently learned cladistics in an "old school" setting (as many of
us
> did)
> in which we had to choose appropriate outgroups for our study and
> carefully
> examine character state distributions in the outgroup to determine
> putatively plesiomorphic states.  

Yes I am old.

What you seem unwilling to accept is
> that,
> regardless of the nature of the data, a computer algorithm can perform
> that
> task for you.  All that is required is that you, as the person
> constructing
> the data matrix, are confident that your are working with homologous
> characters and that you have properly interpreted the character states
and
> made no errors in scoring the states for each OTU. 

Right. But in molecular methods one uses the algorithm to do that.

 Once you have created
> your data matrix, you are certainly free to go through and examine the
> patterns for each character individually to determine what the
> plesiomorphies are. 

Is this another way of saying that the algorithm can't do that?

 For small data sets, this is easily done.  But for
> large data sets with hundreds of OTUs and thousands of characters, it
is
> simply a tremendous waste of time when the computer algorithm can do
it
> for
> you.

No, because the algorithm cannot study the actual character and have any
way of constructing an argument in defense of the choice other than a
recipe already built in. 

> 
> One thing you seem to overlook is this: if you claim I am wrong, it it
not
> up to me to prove I'm right; it's up to you to prove I'm wrong.

No - there are no such obligations in science.

Cheers, John Grehan

> 
> Cheers,
> 
> Dick J.
> 
> 
> --
> Richard J. Jensen              | tel: 574-284-4674
> Department of Biology      | fax: 574-284-4716
> Saint Mary's College         | e-mail: rjensen at saintmarys.edu
> Notre Dame, IN 46556    | http://www.saintmarys.edu/~rjensen
> 
>