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<font size="-1"><font face="Arial">Thanks Greg. No matter what method
is used, be it 'parsimony,' quasi-Bayesianism, etc., I would never
accept the results when I know there are other relevant data that need
to be considered. In lieu of even publishing a cladogram using the
sequence data, it would have been appropriate to wait on the formal
phylogenetics until the relevant data are compiled. </font></font><font
size="-1"><font face="Arial">There is no such thing as 'total
evidence' analyses - an inference either considers one's available
relevant evidence for the sake of maximizing rationality of
explanation, or they opt
for accepting that the results are going to be more irrational.</font></font><br>
<font size="-1"><font face="Arial"><br>
But since you mention it, I'm also deeply concerned at the fact that
systematists routinely publish phylogenetic hypotheses using a variety
of different methods, often with contradictory results, regardless of
what data are used. Why do it? We can't compare the results because
they're inferred from very different assumptions regarding theories,
and no one has ever provided any good empirical arguments for the
practice. It seems we've lost sight (or maybe never had it) of why
those trees are produced in the first place, and are too enamored with
the fact that computers can produce branching diagrams whenever we want
'em.<br>
<br>
I'm sorry for coming across so critically, but, we have to face the
fact that a critical attitude toward phylogenetics is just plain
absent. It's a dangerous situation when a field of science becomes so
complacent that any sort of method is acceptable and in fact condoned.<br>
<br>
Kirk<br>
</font></font><br>
Greg Rouse wrote:
<blockquote cite="mid:42EC96C3-03DA-429A-8CF1-045E56909472@ucsd.edu"
type="cite">Kirk,
<div>Please consult the Supplement for details on a maximum parsimony
analysis that I assume you would not find dubious. A total evidence
analysis (i.e., a "limited set of sequence data", plus what must also
be called a "limited set" of morphological data) will appear in due
course that may alleviate your other concern.
<div>greg<br>
<div><br>
<div>
<div>On Aug 23, 2009, at 7:15 AM, J. Kirk Fitzhugh wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div bgcolor="#ffffff" text="#000000"> <font size="-1"><font
face="Arial">The phylogenetic hypotheses are only 'solid' insofar as
they explain a limited set of sequence data. Given that the authors
must know they are actively avoiding considering all sorts of other
relevant data that are in need of being explained in the same context,
e.g. the setae as Jim Blake noted, and the use of Bayes Theorem is not
meant for the inference of hypotheses, then Torsten's endorsement is
ill-founded at best.<br>
<br>
But then, let's not quibble with the fine points of doing good science
- it's more important to impose blind acceptance of methods by even
more blind endorsement.<br>
<br>
Kirk<br>
</font></font><br>
Struck, Torsten wrote:
<blockquote
cite="mid:263E84B5DC854F4C92307908F8E054FD4EEF00@XCH.biologie.Uni-Osnabrueck.DE"
type="cite">
<pre wrap="">Indeed, it is a nice discovery and very interesting. Moreover, the
phylogenetic hypotheses are very solid (not at all "dubios at best") and
good in comparison to several other analyses out there.
</pre>
<blockquote type="cite">
<pre wrap="">Nice discoveries indeed. It's unfortunate that the scientific merits of the
phylogenetic hypotheses are dubious at best. But then, it *is* published in
Science. ;-)
Kirk
-----Original Message-----
From: <a moz-do-not-send="true" class="moz-txt-link-abbreviated"
href="mailto:annelida-bounces@oat.bio.indiana.edu">annelida-bounces@oat.bio.indiana.edu</a> on behalf of Geoff Read
Sent: Sat 8/22/2009 12:54 AM
To: <Annelida list
Subject: [Annelida] Swima the swimmer
Swima bombiviridis named (new genus, new species of acrocirrid)
Abstract: "By using remotely operated vehicles, we found seven previously
unknown species of swimming annelid worms below 1800 meters. Specimens were
large and bore a variety of elaborate head appendages. In addition, five
species have pairs of ellipsoidal organs homologous to branchiae that produce
brilliant green bioluminescence when autotomized. Five genes were used to
determine the evolutionary relationships of these worms within
Cirratuliformia. These species form a clade within Acrocirridae and were not
closely related to either of the two known pelagic cirratuliforms. Thus, this
clade represents a third invasion of the pelagic realm from Cirratuliformia.
This finding emphasizes the wealth of discoveries to be made in pelagic and
deep demersal habitats."
Nice discovery. I want to know what they feed on, and how.
------ CONTACT INFORMATION ------
PD Dr. habil. Torsten H. Struck
University of Osnabrück
Department of Biology/Chemistry
Zoology
Barbarastrasse 11
D-49069 Osnabrück
Germany
