Embarrassing J. Wells quote
John Harshman
context. It's from Jonathan Wells' book Icons of Evolution, p. 51. Wells
is attempting to cast doubt on the efficacy of molecular systematics, by
pointing out how silly some of the results are:
"Even when different molecules can be combined to give a single tree, the
result is often bizare: A 1996 study using 88 protein sequences grouped
rabbits with primates instead of rodents; a 1998 analysis of 13 genes in
19 animal species placed sea urchins among the chordates; and another 1998
study based on 12 proteins put cows closer to whales than to horses."
Of course the last example is the funniest, given the wealth of molecular
and fossil data showing that cows and whales are indeed related.
See:
Gatesy, J., P. O'Grady, and R. H. Baker. 1999. Corroboration among data
sets in simultaneous analysis: Hidden support for phylogenetic
relationships among higher level artiodactyl taxa. Cladistics 15:271-313.
Matthee, C. A., J. D. Burzlaff, J. F. Taylor, and S. K. Davis. 2001.
Mining the mammalian genome for artiodactyl systematics. Syst. Biol.
50:367-390.
Naylor, G. J. P., and D. C. Adams. 2001. Are the fossil data really at
odds with the molecular data? Morphological evidence for Cetartiodactyla
phylogeny reexamined. Syst. Biol. 50:444-453.
Gingerich, P. D., M. ul Haq, I. S. Zalmout, I. H. Khan, and M. S. Malkani.
2001. Origin of whales from early artiodactyls: Hands and feet of Eocene
Protocetidae from Pakistan. Science 293:2239-2242.
and older references therein.
Of the other two examples, the first (rabbits) is a real example of
improper results arising from poor methodology, which I will gladly
explain to anyone who asks. The second, though, just like the whale-cow
example, is correct; the study didn't find sea urchins to be nested within
chordates, it found them to be the sister group of chordates, which of
course they are.
Wells read a lot of the primary literature for his book, but not enough.
He was just quote-mining on a large scale, and didn't grab enough context
to realize the cow-whale claim wasn't bizarre, even in 1998.
For the record, Wells was citing these:
Graur, D., L. Duret, and M. Gouy. 1996. Phylogenetic position of the order
Lagomorpha (rabbits, hares and allies). Nature 379:333-335.
Naylor, G. J. P., and W. M. Brown. 1998. Amphioxus mitochondrial DNA,
chordate phylogeny, and the limits of inference based on comparisons of
sequences. Systematic Biology 47:61-76.
Cao, Y., A. Janke, P. J. Waddell, M. Westerman, O. Takenaka, S. Murata, N.
Okada, S. Paabo, and M. Hasegawa. 1998. Conflict among individual
mitochondrial proteins in resolving the phylogeny of eutherian orders.
Journal of Molecular Evolution 47:307-322.
--
*Note the obvious spam-defeating modification
to my address if you reply by email.
Ronald Okimoto
John Harshman wrote:
You'd think that Wells would have learned from the creationist debacle of
complaining about the Whale - cow relationship in the early 1980s. Gish
would go around in debates with his half cow half whale. He dropped that
slide in a debate on campus that he gave in 1992 because all the evidence
indicated that he had made a stupid blunder, but then a few days later at a
back to genesis revival he troted out the slide for the ignorant masses
without telling them what a fool he had been for using it all those years.
Creationists also were caught up in the bird-aligator-turtle relationship.
For some reason they thought that it was rediculous.
Guys like Wells and Gish are just stupid or purposely deceptive. They could
be insane as a third option.
Ron Okimoto
TomS
<harshman.diespamdi...@user-2ivfm9s.dialup.mindspring.com>,
harshman....@sjm.infi.net stated..."
>
>I can do quote mining too. The difference is that this quote isn't out of
>context. It's from Jonathan Wells' book Icons of Evolution, p. 51. Wells
>is attempting to cast doubt on the efficacy of molecular systematics, by
>pointing out how silly some of the results are:
>
>"Even when different molecules can be combined to give a single tree, the
>result is often bizare: A 1996 study using 88 protein sequences grouped
>rabbits with primates instead of rodents; a 1998 analysis of 13 genes in
>19 animal species placed sea urchins among the chordates; and another 1998
>study based on 12 proteins put cows closer to whales than to horses."
>
>Of course the last example is the funniest, given the wealth of molecular
>and fossil data showing that cows and whales are indeed related.
And, of course, the recent fossil finds as published in Nature
and Science.
In the latest issue of Discover magazine, there is a letter to
the editor citing "Icons of Evolution" about "gill slits" in human
embryos.
Tom S.
Andy Groves
> I can do quote mining too. The difference is that this quote isn't out of
> context. It's from Jonathan Wells' book Icons of Evolution, p. 51. Wells
> is attempting to cast doubt on the efficacy of molecular systematics, by
> pointing out how silly some of the results are:
>
> "Even when different molecules can be combined to give a single tree, the
> result is often bizare: A 1996 study using 88 protein sequences grouped
> rabbits with primates instead of rodents; a 1998 analysis of 13 genes in
> 19 animal species placed sea urchins among the chordates; and another 1998
> study based on 12 proteins put cows closer to whales than to horses."
>
> Of course the last example is the funniest, given the wealth of molecular
> and fossil data showing that cows and whales are indeed related.
<snip>
Here's another Wells quote, of buttock-clenchingly embarrassing proportions:
"At the end of the Washington Monument rally in September, 1976, I was
admitted to the second entering class at Unification Theological
Seminary. During the next two years, I took a long prayer walk every
evening. I asked God what He wanted me to do with my life, and the
answer came not only through my prayers, but also through Father's
many talks to us, and through my studies. Father encouraged us to set
our sights high and accomplish great things.
He also spoke out against the evils in the world; among them, he
frequently criticized Darwin's theory that living things originated
without God's purposeful, creative activity. My studies included
modern theologians who took Darwinism for granted and thus saw no room
for God's involvement in nature or history; in the process, they re-
interpreted the fall, the incarnation, and even God as products of
human imagination.
Father's words, my studies, and my prayers convinced me that I should
devote my life to destroying Darwinism, just as many of my fellow
Unificationists had already devoted their lives to destroying Marxism.
When Father chose me (along with about a dozen other seminary
graduates) to enter a Ph.D. program in 1978, I welcomed the
opportunity to prepare myself for battle. "
It's from his page at
http://www.tparents.org/Library/Unification/Talks/Wells/DARWIN.htm
Andy
syvanen
> context. It's from Jonathan Wells' book Icons of Evolution, p. 51. Wells
> is attempting to cast doubt on the efficacy of molecular systematics, by
> pointing out how silly some of the results are:
>
> "Even when different molecules can be combined to give a single tree, the
> result is often bizare: A 1996 study using 88 protein sequences grouped
> rabbits with primates instead of rodents; a 1998 analysis of 13 genes in
> 19 animal species placed sea urchins among the chordates; and another 1998
> study based on 12 proteins put cows closer to whales than to horses."
>
> Of course the last example is the funniest, given the wealth of molecular
> and fossil data showing that cows and whales are indeed related.
Who first proposed the affinity between whales and ungulates? Was it
a paleontologist or a molecular biologist?
Mike Syvanen
Rodjk
> John Harshman wrote:
>
> > I can do quote mining too. The difference is that this quote isn't out of
> > context. It's from Jonathan Wells' book Icons of Evolution, p. 51. Wells
> > is attempting to cast doubt on the efficacy of molecular systematics, by
> > pointing out how silly some of the results are:
> >
>
> You'd think that Wells would have learned from the creationist debacle of
> complaining about the Whale - cow relationship in the early 1980s. Gish
> would go around in debates with his half cow half whale. He dropped that
> slide in a debate on campus that he gave in 1992 because all the evidence
> indicated that he had made a stupid blunder, but then a few days later at a
> back to genesis revival he troted out the slide for the ignorant masses
> without telling them what a fool he had been for using it all those years.
> Creationists also were caught up in the bird-aligator-turtle relationship.
> For some reason they thought that it was rediculous.
>
> Guys like Wells and Gish are just stupid or purposely deceptive. They could
> be insane as a third option.
I vote for purposely deceptive.
Rodjk #613
>
> Ron Okimoto
Ian Musgrave & Peta O'Donohue
Address altered to avoid spam, delete RemoveInsert
On 10 Oct 2001 13:14:10 -0400, harshman....@sjm.infi.net (John
Harshman) wrote:
>I can do quote mining too. The difference is that this quote isn't out of
>context. It's from Jonathan Wells' book Icons of Evolution, p. 51. Wells
>is attempting to cast doubt on the efficacy of molecular systematics, by
>pointing out how silly some of the results are:
[snip rather hilarious example]
>Of the other two examples, the first (rabbits) is a real example of
>improper results arising from poor methodology, which I will gladly
>explain to anyone who asks.
I'll ask then, could you please explain it to me.
[snip rest]
Cheers! Ian
=====================================================
Ian Musgrave Peta O'Donohue,Jack Francis and Michael James Musgrave
reyn...@werple.mira.net.au http://werple.mira.net.au/~reynella/
Southern Sky Watch http://www.abc.net.au/science/space/default.htm
Ron Okimoto
Gish used to cite a Scientific American Article from 1968, but I don't
know the exact reference. The first morphological article that I saw
that made the artiodactyl-whale comparison was in the early 1990s in
Science. It cited some earlier work, but none going back into the
60's so it could have been the old hemoglobin comparisons that Gish
was citing. They were sequencing a lot of globin molecules from
different taxa in the early days of molecular comparison. I don't
recall cyt c from whales being sequenced in the early data set, but I
could be wrong.
Ron Okimoto
James Acker
: harshman....@sjm.infi.net (John Harshman) wrote in message news:<harshman.diespamdi...@user-2ivfm9s.dialup.mindspring.com>...
Boyden and Gemeroy, Zoologica, 35, p. 145 (1950), on the basis
of immunological precipitin tests that showed higher cross-reactivity
for Ceteacea to Artiodactyla than other with other extant orders.
The problem was, the available fossils (at the time) didn't match
up well with this relationship, so Van Valen (1966) proposed that
whales originated from mesonychid condylarthds, while modern artiodactyls
originated from arctocyonid condylarths. (Adapted from Gingerich
et al., "Origin of Whales from Early Artiodactyls: Hands and Feet
of Eocene Protocetidae from Pakistan", Science 293, p. 2239.
The problem ever since then until the last couple of years
(and particularly until this and a related article were published)
was that the morphology favored the mesonychids while the molecular
data favored the artiodactyls. But the recent discoveries definitively
indicated that whales are the descendants of artiodactyls.
Jim Acker
*** *** *** *** *** *** *** *** *** *** *** *** *** *** *** *** ***
Jim Acker
jac...@gl.umbc.edu
A second flood, a simple famine, plagues of locusts everywhere,
Or a cataclysmic earthquake, I'd accept with some despair.
But no, you sent us Congress! Good God, sir, was that fair?
--- John Adams, "Piddle, Twiddle, and Resolve", from the
musical "1776"
Brian L
<jac...@linux1.gl.umbc.edu> wrote:
Have there been other cases in which paleontologists and molecular
biologists disagreed? Have the paleontologists ever "won" ?
John Harshman
<do...@spam.me> wrote:
I think the "guinea pigs are not rodents" controversy would qualify there. See:
Graur, D., W. A. Hide, and W.-H. Li. 1991. Is the guinea-pig a rodent?
Nature 351:649-652.
Novacek, M. J. 1992. Mammalian phylogeny: shaking the tree. Nature 356:121-125.
Novacek, M. 1993. Mammalian phylogeny: morphology and molecules. Trends
Ecol. Evol. 8:339-340.
Sullivan, J., and D. L. Swofford. 1997. Are guinea pigs rodents? The
importance of adequate models in molecular phylogenetics. J. Mammal. Evol.
4:77-86.
John Harshman
reyn...@RemoveInsert.werple.mira.net.au wrote:
> G'Day All
> Address altered to avoid spam, delete RemoveInsert
>
> On 10 Oct 2001 13:14:10 -0400, harshman....@sjm.infi.net (John
> Harshman) wrote:
>
> >I can do quote mining too. The difference is that this quote isn't out of
> >context. It's from Jonathan Wells' book Icons of Evolution, p. 51. Wells
> >is attempting to cast doubt on the efficacy of molecular systematics, by
> >pointing out how silly some of the results are:
> [snip rather hilarious example]
> >Of the other two examples, the first (rabbits) is a real example of
> >improper results arising from poor methodology, which I will gladly
> >explain to anyone who asks.
>
> I'll ask then, could you please explain it to me.
> [snip rest]
Dan Graur is fairly famous for doing 4-species comparisons. (He's also the
one responsible for making guinea pigs into non-rodents, or so he
thought.) In this case he took a rabbit, a rodent, a primate, and an
outgroup (sometimes different species for different genes, but always only
4) and compared the 3 possible trees. The one in which rabbits and
primates go together fit the data better under his analysis. But 4-species
comparisons, when branches are long, which they are here, are especially
vulnerable to long-branch attraction problems. Rodents, for example, tend
to have long branches, and would thus tend to be attracted to the
outgroup. And that's where they show up. The proper way to do this would
be to use lots more species to construct a tree. People who have done this
find rodents and rabbits going together more often than not.
Herb Huston
}biologists disagreed?
Yes, and rather close to home, too, viz., _Ramapithecus_. Only it turned
out not to be so close to home. The "rock guys" were Elwyn Simons and
David Pilbeam, and the "molecule guys" were Vincent Sarich and the late
Allan Wilson. See pages 77-9 of Richard Leakey's _Origins Reconsidered_
for a brief account.
} Have the paleontologists ever "won" ?
"I know my molecules had ancestors, but you paleontologists can only hope
your fossils had descendants." -- Vincent Sarich, as quoted by Richard
Leakey.
--
-- Herb Huston
-- hus...@radix.net
-- http://www.radix.net/~huston
syvanen
> In article <p4pbst8nlin0fn01r...@4ax.com>, Brian L
> <do...@spam.me> wrote:
>
> > On 11 Oct 2001 14:23:35 -0400, James Acker
> > <jac...@linux1.gl.umbc.edu> wrote:
> >
> > >syvanen <syv...@ucdavis.edu> wrote:
> > >: harshman....@sjm.infi.net (John Harshman) wrote in message
>
> > >: Who first proposed the affinity between whales and ungulates? Was it
> > >: a paleontologist or a molecular biologist?
> > >
> > > Boyden and Gemeroy, Zoologica, 35, p. 145 (1950), on the basis
> > >of immunological precipitin tests that showed higher cross-reactivity
> > >for Ceteacea to Artiodactyla than other with other extant orders.
1950??
> > >The problem was, the available fossils (at the time) didn't match
> > >up well with this relationship, so Van Valen (1966) proposed that
> > >whales originated from mesonychid condylarthds, while modern artiodactyls
> > >originated from arctocyonid condylarths. (Adapted from Gingerich
> > >et al., "Origin of Whales from Early Artiodactyls: Hands and Feet
> > >of Eocene Protocetidae from Pakistan", Science 293, p. 2239.
> > >
> > > The problem ever since then until the last couple of years
> > >(and particularly until this and a related article were published)
> > >was that the morphology favored the mesonychids while the molecular
> > >data favored the artiodactyls. But the recent discoveries definitively
> > >indicated that whales are the descendants of artiodactyls.
> >
> > Have there been other cases in which paleontologists and molecular
> > biologists disagreed? Have the paleontologists ever "won" ?
>
> I think the "guinea pigs are not rodents" controversy would qualify there. See:
>
> Graur, D., W. A. Hide, and W.-H. Li. 1991. Is the guinea-pig a rodent?
> Nature 351:649-652.
>
> Novacek, M. J. 1992. Mammalian phylogeny: shaking the tree. Nature 356:121-125.
>
> Novacek, M. 1993. Mammalian phylogeny: morphology and molecules. Trends
> Ecol. Evol. 8:339-340.
>
> Sullivan, J., and D. L. Swofford. 1997. Are guinea pigs rodents? The
> importance of adequate models in molecular phylogenetics. J. Mammal. Evol.
> 4:77-86.
I don't think this question is yet resolved, at with respect to the
monophyly of the rodents if guinea pigs are included.
Mike Syvanen
syvanen
Long branch attractions are a real problem. But that does not
invalidate 4 taxa comparisons. A better solution to the problem is to
exclude taxa that have demonstrably faster molecular clocks than the
rest. These can be identified using the relative rate test (against a
fifth taxa that is an outgroup to the four under comparison).
Mike Syvanen
James Acker
: harshman....@sjm.infi.net (John Harshman) wrote in message news:<harshman.diespamdi...@user-2ivfjqi.dialup.mindspring.com>...
:> In article <p4pbst8nlin0fn01r...@4ax.com>, Brian L
:> <do...@spam.me> wrote:
:>
:> > On 11 Oct 2001 14:23:35 -0400, James Acker
:> > <jac...@linux1.gl.umbc.edu> wrote:
:> >
:> > >syvanen <syv...@ucdavis.edu> wrote:
:> > >: harshman....@sjm.infi.net (John Harshman) wrote in message
:> news:<harshman.diespamdie-1010011313270001@user-
:>
:> > >: Who first proposed the affinity between whales and ungulates? Was it
:> > >: a paleontologist or a molecular biologist?
:> > >
:> > > Boyden and Gemeroy, Zoologica, 35, p. 145 (1950), on the basis
:> > >of immunological precipitin tests that showed higher cross-reactivity
:> > >for Ceteacea to Artiodactyla than other with other extant orders.
: 1950??
Yeppers. This is five years after G.G. Simpson had trouble
classifying mammals with any other mammalian group. Further research
has led to a resolution of this quandary after only 55 years!
Jim Acker
*** *** *** *** *** *** *** *** *** *** *** *** *** *** *** *** ***
Jim Acker
jac...@gl.umbc.edu
"Since we are assured that an all-wise Creator has observed the
most exact proportions, of number, weight, and measure, in the
make of all things, the most likely way therefore, to get any
insight into the nature of those parts of the creation, which
come within our observation, must in all reason be to number,
weigh, and measure." - Stephen Hales
John Harshman
syv...@ucdavis.edu (syvanen) wrote:
This is helpful, but I maintain that cutting long branches is more
helpful. Also, I'm not sure that you could find a rodent with a slow
clock.
James Acker
: :> In article <p4pbst8nlin0fn01r...@4ax.com>, Brian L
: :> <do...@spam.me> wrote:
: :>
: :> > On 11 Oct 2001 14:23:35 -0400, James Acker
: :> > <jac...@linux1.gl.umbc.edu> wrote:
: :> >
: :> > >syvanen <syv...@ucdavis.edu> wrote:
: :> > >: harshman....@sjm.infi.net (John Harshman) wrote in message
: :> news:<harshman.diespamdie-1010011313270001@user-
: :>
: :> > >: Who first proposed the affinity between whales and ungulates? Was it
: :> > >: a paleontologist or a molecular biologist?
: :> > >
: :> > > Boyden and Gemeroy, Zoologica, 35, p. 145 (1950), on the basis
: :> > >of immunological precipitin tests that showed higher cross-reactivity
: :> > >for Ceteacea to Artiodactyla than other with other extant orders.
: : 1950??
: Yeppers. This is five years after G.G. Simpson had trouble
: classifying mammals with any other mammalian group. Further research
AUGH! Brainlock.
"had trouble classifying WHALES in any other mammalian
group."
That's much better.
: has led to a resolution of this quandary after only 55 years!
John Harshman
syv...@ucdavis.edu (syvanen) wrote:
I think you're letting your delight in horizontal transfer affect your
judgment there. All analyses of the past several years have found rodents
monophyletic. (I'm talking about nuclear gene data sets with large taxon
samples.) Just at the Evolution meeting in June there were two more such
phylogenies. No data set that I know of supports polyphyly.