S2Focus

...and at the end, there aren't any big pieces (of Wells) left! The post is quite long, so I'll just reproduce the juiciest half. (The entire post can be found at this <a href="http://groups.google.com/groups?dq=&hl=en&lr=&ie=UTF8&oe=UTF8&group=talk.or igins&selm=74227462.0206150054.51b15ecd%40posting. google.com" target="_blank">google link.</a>)


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Wells responds to reviewers

But not "Icons of Obfuscation"

Here is the article:

<a href="http://www.discovery.org/viewDB/index.php3?command=view&id=1180&program=CRSC%20Res ponses" target="_blank">http://www.discovery.org/viewDB/index.php3?command=view&id=1180&program=CRSC%20Res ponses</a>

I recommend that anyone who has their blood-pressure raised enough to
write commentary on a section or quote, attempt to do it in "copyable"
style that could be included in a potential multiauthor response.
We've already got the The Worlds Biggest Icons FAQ so it's not
crucial, but often people are inspired to write after the first-read
through of an ID article while they are still feeling provoked, and we
might as well make use of that.

I quote the intro. for reference, and the geochemistry section as I
will be providing an example commentary on it (or really, just a small
section of it)

...........

(extensive quotation of Wells' article snipped here. See the google link above to read it -- S2Focus)

............


First off, Wells criticizes Padian & Gishlick for citing a "freelance
science writer" on the oxygen "controversy". But nowhere does Wells
give his readers the reference to the paper in question, which was in
fact:

Copley, J. (2001). "The story of O." Nature, V410: 892-864. Link:
<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=113095 82&dopt=Abstract" target="_blank">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=113095 82&dopt= Abstract</a>

[note to self, I copied this citation from the Wells FAQ and the page
numbers should be 862-864; there are a few other typos I've noticed in
the FAQ but I never remember to write 'em down]

In other words, the article is indeed by a freelance science writer,
Jon Copley -- but he is a freelance science writer writing in Nature,
*specifically* reviewing the question of oxygen in the early
atmosphere, a task which he performs by a combination of reviewing the
recent literature (citing 14 articles) and further by interviewing the
principal scientists examining the question. In other words, this is
just the kind of article one wants to examine if one wants to get a
sense of "the state of scientific opinion" on the question of oxygen
in the early atmosphere.

And what is "the state of scientific opinion" according to Copley? He
writes, in the very first sentences no less,

"Take a deep breath. A fifth of the air that fills your lungs is
oxygen. But it was not always like this. Around 3.5 billion years ago,
the Earth's atmosphere contained almost no oxygen. Simple
microorganisms had evolved, but they were adapted for an atmosphere
rich in nitrogen, carbon dioxide and the sulphurous gases poured forth
by volcanoes.

Thankfully for us, cyanobacteria evolved. These primitive
microorganisms, descendants of which survive to this day, were
probably the first to photosynthesize, harnessing light from the Sun
to power their own growth and generating oxygen as a by-product. As a
result, they started a momentous evolutionary change ? adding oxygen
to the atmosphere and paving the way for the eventual evolution of
multicellular life."

There is, to be sure, a controversy to be discussed in the article;
this is the kind of thing that Wells regularly latches onto and quotes
(or more accurately quote-mines). Copley's next sentences:

"Up in the air

But as geologists and geochemists studying the early Earth know, the
story is not quite so simple. Fossil evidence for cyanobacteria can be
seen in rocks dating from as far back as 3.5 billion years ago."

This sentence, taken alone, might appear to support Wells' argument.
In his response to reviewers he writes:

"My claim in Icons of Evolution, however, was that the issue of
primitive oxygen remains controversial--a claim amply supported by the
article Padian and Gishlick cite. [5] The problem with biology
textbooks is that they routinely ignore the controversy and tell
students that because the Miller-Urey experiment doesn't work in the
presence of oxygen there must not have been any oxygen on the early
Earth. This is putting the cart before the horse: Demonstrating the
absence of oxygen is necessary to establish the relevance of the
experiment; assuming the relevance of the experiment doesn't
demonstrate the absence of oxygen."

But if we return to Copley (2001), we find that *the very next
sentence* ***directly contradicts Wells!!!***. Copley writes:

"But there is a host of evidence suggesting that oxygen remained a
trace element in the atmosphere until about 2.5 billion years ago."

The rarity of oxygen on the early earth is not what is in doubt:
rather, the real question that is discussed by Copley is,

"So if cyanobacteria were pumping out oxygen for at least 1 billion
years before it reached detectable levels, what kept the concentration
of oxygen so low?"

To repeat: geochemists *know* that the concentration of oxygen was low
on the early earth. The phenomenon is agreed upon. The question
geochemists are currently investigating is the usual scientific
question, "why?"

If the short quotes of Copley above don't convince you that Wells is
completely misrepresenting Copley (2001) and generally the state of
the oxygen question, a longer quote of Copley shows that Copley
actually discussed the numerous lines of evidence for the absence of
oxygen on the early earth:

"Much of this evidence comes from palaeosols ? rocks formed by the
compression of ancient soils. The air and water of the early Earth
would have left its mark on these soils and the palaeosols that formed
from them, so geochemists use these rocks to test whether or not
oxygen was present billions of years ago. The key to tracking oxygen
is the way it reacts with iron. If there was little oxygen on the
early Earth, minerals known as iron silicates would have dissolved in
any water that was present, and washed straight through the soil. But
oxygen converts iron silicates into insoluble iron hydroxides, which
would have been trapped in the ancient soils.

Iron hydroxides have so far only been found in palaeosols younger than
2.3 billion years old5, indicating that before this time, the
atmosphere did not contain much oxygen. Other mineral indicators in
palaeosols seem to tell a similar story. A 2.5 billion-year-old
Canadian palaeosol has been shown to contain the element cerium6. Had
oxygen been present it would have reacted with the cerium to produce
cerium oxide ? but none of this oxide was found."

Copley cites -- count 'em -- one scientist who thinks that all of the
above evidence might be wrong, and in fact oxygen levels were higher.
But Copley explicitly points out that pretty much everyone else in the
field *disagrees*:

"But if Ohmoto is going to convince other researchers that he is
right, he will have to account for a range of other evidence that
points to low oxygen levels before 2.5 billion years ago. At that
time, minerals such as pyrite and uraninite were being washed around
by rivers. Contact with oxygen would have altered their composition,
but sediments from 2.75 billion years ago and earlier contain the
minerals in their unreacted form9.

More evidence comes from deposits that cannot form if oxygen is
present. Examples of one of these ? banded iron formations ? seem to
be confined to rocks dating from more than 2.3 billion years ago,
indicating that oxygen was not present at that time. But Ohmoto points
to a similar banded iron formation dating from 1.8 billion years ago
as evidence that such structures can form in the presence of oxygen.
Other researchers argue that this formation is probably an anomaly,
arising in water that contained little oxygen.

A new approach to the problem has further strengthened the case for
the late emergence of oxygen. Developed by James Farquhar of the
University of California, San Diego, the technique takes advantage of
a quirk in the behaviour of different isotopes. Biological reactions
such as photosynthesis leave clear signatures in rocks by selecting
for lighter isotopes. Now it appears that some non-biological
reactions also select for certain isotopes, although here, mass is not
the governing factor. Although the selection mechanism ? known as
mass-independent fractionation ? is not fully understood, the effects
of it can be seen in the geological record.

Sulphur gases in the Earth's early atmosphere were subject to both
biological and non-biological fractionation. Microorganisms that fed
on sulphur preferred the lighter of the element's three isotopes and
the resulting rocks reflect this. But some of the non-biological
processes involved in the formation of other rocks can cause
mass-independent fractionation of sulphur. Such rocks contain isotopes
of sulphur in distinctive ratios that do not fit with those generated
by biological processes.

Crucially, this mass-independent selection of sulphur is driven by
ultraviolet (UV) light from the Sun. As oxygen appeared in the
atmosphere it would have slowed the reaction down by forming a layer
of ozone ? a molecule containing three oxygen atoms ? which blocked
out much of incoming UV light. Oxygen would also have combined with
sulphur and removed it from the atmosphere. Together, these effects
would have stopped the mass-independent selection of sulphur. And
according to Farquhar, evidence for mass-independent fractionation in
the geological record ceases at 2.45 billion years ago10.

For Jim Kasting, a geochemist at Pennsylvania State University,
Farquhar's evidence is "the real clincher". Heinrich Holland, a
geologist at Harvard University, agrees and says he will argue so when
he reviews the evidence at a joint meeting of the Geological Societies
of London and America to be held this summer in Edinburgh. "Every time
somebody looks at something different, it's one more piece of evidence
for low oxygen before 2.3 billion years ago," he says.

But Ohmoto is not willing to give up the fight just yet. He says that
recent work11 from Don Canfield of the Danish Center for Earth System
Science in Odense backs his early oxygen theory. Canfield has found
evidence for sulphate-devouring microorganisms at around 3.5 billion
years ago. Oxygen in the atmosphere promotes the production of
sulphate in the oceans, leading Ohmoto to argue that evidence of the
microbes is evidence of oxygen. But other researchers, including
Canfield himself, are not convinced that one implies the other,
reasoning that other mechanisms could have produced the sulphate.

Into the black
But if the evidence does favour the late emergence of oxygen ? and
most geochemists believe it does ? the original question remains
unanswered: why did oxygen take so long to build up after
cyanobacteria first emerged? The answer may lie not in the processes
that create oxygen, but in the ones that mop it up. "It's like
continually having your spending exceed your income ? it does not lead
to wealth," explains Holland."

At his point the article returns to the discussion of the various
processes that can mop up oxygen and explain why it took a billion
years to rise above trace levels. But having now quoted half the
article for you, you can see just how astoundingly deceptive Wells is
being by claiming that the question of "primitive oxygen remains
controversial--a claim amply supported by the article". Rather --
just as on most scientific questions -- there is a scientist or two
questioning the dominant view. But to imply that having a lone
questioner *changes* what the dominant view is is pure chicanery. The
dominant view *among geochemists* *based on the geochemical evidence,*
(and **not** "because the Miller-Urey experiment doesn't work in the
presence of oxygen") is that oxygen was vanishingly rare in the
atmosphere before about 2.5 billion years ago.

I have here analyzed just a few sentences of a Jonathan Wells piece.
As you can see it took time, access to journal articles and enough
background in the topic to know what kinds of games Wells was playing
with Copley (2001). Refuting a substantial portion of Wells' essay in
this kind of detail would either take a lot of time or multiple
authors; but hopefully I have shown just what kind of a "scholar"
Jonathan Wells really is.

[Hopefully this will stir up more replies on t.o. -- if we had a just
a coupla commentaries illustrating Wells' tactics on various topics
we'd have a suitable response FAQ in no time flat...]

nic

[ June 15, 2002: Message edited by: S2Focus ]</p>

pangloss

"One high priest of Darwinism..."

Hmmm - does that make Wells a low-priest of Moonie-flavored IDcreationism?

KC

One odd thing in Wells's reply is his lambasting Padian and Gishlick for stating he produced no published work while a post doc at Berkeley. He cites the following two papers as proof:

Larabell,Rowning, Wells, Wu & Gerhart, "Confocal microscopy analysis of living Xenopus
eggs and the mechanism of cortical rotation," DEVELOPMENT 122 (1996),
1281-1289

Rowning, Wells, Wu, Gerhart, Moon & Larabell,
"Microtubule-mediated transport of organelles and localization of B-catenin
to the future dorsal side of Xenopus eggs," PROCEEDINGS OF THE NATIONAL
ACADEMY OF SCIENCES USA 94 (1997), 1224-1229.


What is interesting about both of these is that they seem to have been done in John Gerhart's lab (Wells studied for his PhD under Gerhart).In fact, Gerhart himself submitted the PNAS paper Yet Wells was supposed to have done his post doc work in Michael Strohman's lab. No mention of Strohman anywhere, not even in the PNAS paper's acknowledgement section.

One wonders what he did in Strohman's lab for five years.

Cheers,

KC

pangloss

Hmmm.... I was co-author on three pubs by the time I was a 3rd year grad student. Pretty piss-poor performance for a Berkeley grad, no?

Also, I wonder which one of those contains Wells' 'work' in embryology that he touts so often that speels doom for Darwinism?

lpetrich

One of Jonathan Wells's claims is truly bizarre:
With homologies between species, the evidence points in the opposite direction -- in many cases, the molecular mechanisms are also homologous, with the homologies sometimes extending remarkably far. This is a very important discovery of the last few decades; here are some highlights:

The "Hox" genes are well-known across the bilaterally-symmetric members of the animal kingdom, where they control front-to-rear identity. Their arrangement in the genome even matches their position of expression.

Hox genes specify rearward identity; if a Hox gene fails to be active, then its associated part will develop like a forward one. Thus, if a fruit fly's "Ultrabithorax" (Ubx) Hox gene fails to be active, it will try to develop a pair of legs for each abdominal segment. The interesting thing is that the homologous gene in a shrimp (Artemia) does not suppress abdominal legs -- the shrimp has such legs, and putting the shrimp version into a fly makes it try to grow abdominal legs. Here's a <a href="http://www.cosmiverse.com/science02250202.html" target="_blank">nice story on that</a>.

Thus the fly version of Ubx has some difference from shrimp Ubx that suppresses abdominal legs.

Interestingly, Jonathan Wells himself has stumbled over this issue.

Hox-mutation limb suppression also happens in vertebrates; snakes lost their front limbs as a result of some Hox-gene changes.

Also, dorsoventral or belly-to-back patterning has confirmed an old speculation about shared anatomical patterns: Geoffroy St. Hilaire and dorsoventral inversion. It would be advocated every 20 years, and then picked apart. Here's a summary:

Arthropods and annelids:

Ventral, CNS, Gut, Heart, Dorsal

Vertebrates:

Dorsal, CNS, Gut, Heart, Ventral

CNS = Central Nervous System

But molecular development-pathway evidence has turned out to be exactly consistent with that hypothesis, with the ventral-side gene in fruit flies being homologous with the dorsal-side gene in frogs, and vice versa. A hypothesis that has been tested by checking if the frog genes do the appropriate things in fruit-fly embryos.

So Jonathan Wells is dead wrong; he ought to be challenged to provide examples of this alleged molecular non-homology.

[ June 16, 2002: Message edited by: lpetrich ]</p>

KC

I understand the DI Wunderkind is writing a new book explaining it to us.

Cheers,

KC

lpetrich

I've found <a href="http://www.arn.org/docs/odesign/od182/hobi182.htm" target="_blank">Jonathan Wells on evolutionary developmental ("evo-devo") biology</a> He makes numerous mistakes, which even I, someone only an amateur in this field, can detect.

He claims that "The underlying assumption that a genetic program directs embryonic development has been seriously questioned by developmental biologists (For a review, see Wells, 1992)." and after some convenient quotes, "Clearly, the genetic explanation for homology is inadequate. As an alternative, some biologists have suggested that homology results from complex developmental mechanisms which are not reducible to a genetic program."

It's not clear how JW thinks that a genetic program is expected to work. Does he expect specification of every little detail or something? And what does he think is going on? Some little elf steps in and does what the genes are incapable of doing?

Here are <a href="http://zygote.swarthmore.edu/evo4.html" target="_blank">some illustrations</a> of how simple changes in growth algorithms can cause drastic changes in appearance. A snail shell can be specified with only a few parameters! JW ought to read D'Arcy Thompson's classic On Growth and Form; here is <a href="http://www-gap.dcs.st-and.ac.uk/~history/Miscellaneous/darcy.html" target="_blank">some of his work</a>.

JW makes several elementary mistakes. He claims that that the vertebrate gut develops from different predecessor cells in different species, but that does not keep the genetic mechanisms of gut development from being homologous. In fact, ectopic (out-of-place) development happens by some development inducer being applied to some inappropriate cells. He is perplexed at why similar-looking embryos and larvae can grow into very different-looking adults; the genetic programming for those differences can simply get a later start.

He also stumbles over indirect vs. direct development in frogs and sea urchins. The solution is simple. In both cases, the usual route of development is through a larval stage, followed by a remodeling into the adult stage. However, if that remodeling can be made to happen early enough, it can happen inside the egg, with the larva becoming vestigial or nonexistent.

Related to that is his stumbling over how homologous mechanisms can produce non-homologous parts, such as arthropod vs. vertebrate Hox genes (whole body vs. spinal cord and hindbrain), and Pax-6 inducing the growth of different sorts of eyes. The answer here is that different genetic mechanism are controlled in each case.

For someone who had gotten a Ph.D. in developmental biology, JW looks remarkably incompetent.

MrDarwin

Could Wells be confusing "homologous" with "homoplasious"?