Re: [asa] historical versus experimental sciences

From: Cameron Wybrow <>
Date: Fri Aug 21 2009 - 22:45:18 EDT


Regarding your request for more information about genetic bar-coding:

First, you can read the entire article that I linked to.

Second, there are several good web-sites you can find by searching the web
(I can't remember where I found them, because it's been a while) which give
a good layman's account of the science behind genetic bar-coding, and some
of them specifically deal with the point Hebert was making, i.e., that
contrary to Darwinian expectations, DNA readings for individuals *within* a
species are tightly clustered, and there are consistent and pronounced gaps
*between* species. On the Darwinian model, one would expect much more
blurriness and shading. If you want the reason for that, read Chapters 1-4
of *The Origin of Species*. As Ken Miller says, the core of Darwin's
evolutionary thought is found there.

David Campbell claims that there are good neo-Darwinian reasons (which he
doesn't specify) to expect the results Hebert found, and he therefore
implies that Hebert was unnecessarily alarmed by the implications of his
results. Well, let David take it up with Hebert. He can write to him,
debate with him, and report back to us on the results.

I repeat what I said in another post, i.e., that I have no brief to carry
for the science of genetic bar-coding, and if it turns out that using
mitochondrial DNA to classify species is misguided, it's no skin off my
nose. My point was to provide yet another illustration of how
neo-Darwinians will override apparent evidence for design due to prior
commitments (e.g., we must never explain what we find in nature in terms of
design). This *a priori* attitude does not appear to bother Tim, David
Campbell, or some others here, but it bothers me. As I said before, it is
not the duty of scientists to make sure, by any means fair or foul, that
design explanations are ruled out of court. It is the duty of scientists to
explain nature in a coherent way that is compatible with the empirical data.
When we are dealing with origins, all rationally-based, empirically-based
explanations must be "on the table", including design explanations. If it
isn't obvious why this is the case, people can read Stephen Meyer's new book
to get the detailed argument.


----- Original Message -----
From: "wjp" <>
To: <>; "Moorad" <>
Cc: "Cameron Wybrow" <>; "asa" <>
Sent: Friday, August 21, 2009 9:47 AM
Subject: RE: [asa] historical versus experimental sciences

>A few comments.
> 1) It seems to me that drawing the conclusion of a "close common ancestor"
> is logically impossible without ancillary theory. The matter is worse
> than
> the Humean problem of cause and effect. For in this case we "habitually"
> witness an event and a subsequent one. Whereas in the case of a
> "common ancestor" all we perceive is two effects. The conclusion of a
> "common ancestor" is to interpret or see in the two effects the same
> "cause." Adding the modifier "close" is like relating a cause and effect
> that follow each other perceptually immediately, as in one billiard ball
> striking another. We are more confident in this kind of "causal" link
> than we are with identifying the movement of a butterfly in Mexico with
> the hurricane in India. Nonetheless, all "causal" relationships are
> founded
> upon a close and habitual association of two events (events here taken as
> possibly complex entities).
> The case of a common cause when we have only the effects is more
> problematic.
> To my naive mind it seems that there is no habitual association related to
> this causal assignment. It seems that it is only when some theoretical
> net or story is laid over the effects that the cause appears. Perhaps the
> situation is analogous to a solving a murder mystery. We have laid before
> us all the temporal effects, after the fact effects. We seek a cause, or
> complex of causes, to explain the effects. We begin with the conviction
> that there is a rational explanation for the effects. It is not clear
> to us which of the effects are the "important" ones, and much of the work
> of investigation is involved with clearing away the "irrelevant." We
> have selected a single event, of the myriad of others, to explain, the
> murder itself. Only the rational "causal" chain associated with the
> murder
> is to be unearthed. We additionally operate under the a priori
> presumption
> of the kind of causes that are required to explain the murder. We may
> presume it is human, and so the motivations and reasons must be human,
> which is good, since we understand so little of other motivations.
> Well, I like the analogy. It appears to fit well with what evolutionary
> biology is about. But it does require a complex story, the art of
> the story teller, and a perceived world in which to embed the story.
> More could be said here, but I'll move on.
> 2) Cameron, I did read the piece about Hebert and his mitochondrial
> classification
> of species. My naive understanding of why this has significant
> ramifications is that
> apparently current evolutionary theory expects a more continuous shift in
> genetic
> or molecular differences between species than Hebert finds. Rather he
> finds
> islands of genetic differences.
> I confess I don't understand this. If we are to have a classification
> system
> at all, it seems we must have islands of distinctions, even if those
> classes
> are fuzzy in places. Why is it surprising, then, that such differences
> are
> reflected at the molecular and genetic level?
> Thanks,
> Bill
> On Thu, 20 Aug 2009 18:44:36 -0400, "Alexanian, Moorad"
> <> wrote:
>> Sorry for butting in. However, how does one know that two entities “share
>> a close common ancestor?” Through experimentation, that is
>> how---knowledge of DNA and so on; or, else, through morphology.
>> Therefore,
>> one can never supplant experimental work no matter what the theory is. Of
>> course, if the theory makes predications, which evolutionary theory
>> cannot
>> unambiguously do, then one can possible relate tow entities that at first
>> do not appear to be closely related.
>> Moorad
>> ________________________________________
>> From: [] On Behalf
>> Of
>> Cameron Wybrow []
>> Sent: Thursday, August 20, 2009 6:30 PM
>> To: asa
>> Subject: Re: [asa] historical versus experimental sciences
>> David:
>> I don't think we going to get any further on this question because you
>> still
>> are not focusing on the logical structure of your argument. The further
>> examples and arguments you are giving here suffer from the same weakness
>> as
>> your earlier ones. In particular, this statement:
>> "aha! these belong to the x group (possibly even
>> a previously unknown species) and therefore, because they share a
>> close common ancestor, are likely to be similar in vulnerabilities to
>> the better-known closely related species."
>> shows that you do not grasp the redundancy of evolutionary classification
>> for the kind of practical matters we are talking about. The line of
>> argument you are using runs this way:
>> features in common -- implies both A and B belong to group x (an
>> evolutionary classification) -- therefore they share a close common
>> ancestor -- therefore they will have other features in common
>> The middle two steps are unnecessary. Either the features you are using
>> to
>> assign A and B to the same evolutionary classification are very broad
>> general features which need have no relevance to pheromone biochemistry
>> (for
>> example --and I'm just making this up so don't jump on it and correct me
>> pedantically, because it is the point, not the exact facts that matter
>> here -- suppose that [for reasons that seem good to evolutionary
>> biologists]
>> all "broad-winged" fruit flies are classed in the same evolutionary
>> group,
>> but that breadth of wing is no indicator whatsoever of pheromone
>> chemistry
>> in fruit flies), in which case proving that A and B are evolutionary
>> relatives will have *no* practical relevance to solving the agricultural
>> problem; or the features you are using to assign A and B to the same
>> evolutionary classification are very narrow and focused on exactly the
>> sort
>> of things that could well be relevant to pheromones (for example -- and
>> again I'm making it up -- both fruit flies have a certain genetic
>> sequence
>> related to pheromone production which always yields pheromones of a
>> certain
>> chemical family, and frequently yields exactly the same pheromone), in
>> which
>> case you can jump directly from the genetic similarity to the probable
>> pheromone similarity without discussing evolutionary theory at all. So
>> either the evolutionary classification is an *unreliable* guide to
>> probable
>> pheromone chemistry (in which case it would be a *worse* method to use
>> than
>> the pragmatic rule of thumb I would use), or evolutionary classification
>> is
>> a *redundant* guide to probably pheromone chemistry (in which case it
>> would
>> be *no better than* my pragmatic rule of thumb).
>> I can't make my point any clearer than this, so I will drop it.
>> On some other points you raise:
>> A. I agree with you that predicting what would happen to a rabbit in the
>> Amazon would involve fearsomely complex reasoning. In that respect, your
>> comparison with the satellite pieces is apt. But you are neglecting the
>> huge difference, i.e., that we *do* understand, with very great
>> precision,
>> the laws of physics which make objects fall, bounce off each other, etc.,
>> and it is *only* the sheer number of interacting objects that makes exact
>> prediction in some cases difficult; whereas in the evolutionary case, not
>> only are there a very large number of factors, but their operation is
>> (beyond safe generalities) poorly understood. In fact, to be honest, we
>> have no "laws" of evolution at all, but only vague general principles of
>> almost infinite explanatory elasticity -- mutation, drift, selection.
>> This
>> is why debates between evolutionary biologists about possible
>> evolutionary
>> pathways and so on much more resemble the debates of medieval theologians
>> than they resemble the debates of chemists and physicists. You can no
>> more
>> predict an outcome with such vague and general notions as drift,
>> mutation,
>> and selection than the scholastics could predict physical outcomes by
>> speaking of exemplary causes, formal causes, concurrence, effluents, etc.
>> Of course, once evolutionary biologists have such a firm grip on their
>> subject matter that they can explain, in detail, how the eye, the lung,
>> etc., evolved, they will have much more success in predicting future
>> evolutionary events. But, I am assured by our discussion here, that day
>> is
>> still far away.
>> B. Regarding the water strider, I took the time to look at the article.
>> It
>> does *not* contain any argument, as far as I can see,
>> about "exactly what genes changed when". (If I missed the argument,
>> please
>> point out where it is.) The article is almost entirely about the genes
>> themselves and their putative effects on leg length (not all of which
>> even
>> the authors regard as yet proved). There are, however, the usual
>> gratuitous
>> speculative remarks which have no demonstrative force, e.g.:
>> "Therefore, within hemimetabolous insects, Ubx has evolved a new
>> expression
>> domain but maintained its ancestral elongating function in L2, whereas
>> Ubx
>> has maintained its ancestral expression domain but evolved a new
>> shortening
>> function in L3. These changes in Ubx expression and function may have
>> been
>> a
>> key event in the evolution of the distinct appendage ground plan in water
>> striders."
>> Note that, without a record of the genome of the purported ancestors, the
>> term "ancestral" is a loaded term, implying the evolutionary relationship
>> which the article purports to establish; yet the article provides no data
>> about the alleged ancestors. Were there once water striders that could
>> not
>> skim the water? When did they live? What were their genomes like? How
>> do
>> we know any of that? The article is silent about these things. Rather,
>> it
>> assumes, just because it has located a gene which appears to be
>> responsible
>> for the difference in leg length, that this result should be interpreted
>> in
>> terms of an evolutionary change. But the evolutionary framework is
>> brought
>> to the data; it does not follow from the data. It would only follow from
>> the data if we had reliable genomic and morphological data from the
>> putative
>> ancestors. I would therefore expect the authors to trot out a
>> 100-million-year-old water strider trapped in amber, and show us the
>> different leg lengths in comparison with today's water striders, and show
>> us
>> from the preserved genome that the precisely the predicted gene is
>> missing
>> in the fossil specimen. But there is no such evidence in the article.
>> There almost never is, in the evolutionary literature. Present genetic
>> and
>> morphological data is simply given an evolutionary interpretation, and
>> everyone is supposed to accept that interpretation without troubling
>> their
>> brain to ask for the relevant data from past organisms. Evolutionary
>> biology counts on reader laziness. But some readers are not lazy.
>> To be fair to the authors, they do use the subjunctive "*may* have been a
>> key event". This shows appropriate scientific reserve. But note how the
>> news story was written up -- without the caution. And that's always the
>> way. The scientists exaggerate somewhat, and then the science
>> journalists
>> make the tale quite a bit taller. I would think that the evolutionary
>> biology community should take some responsibility for reining in these
>> Darwin-worshipping science reporters, perhaps by not giving interviews in
>> the future to reporters who in the past have over-claimed things for
>> evolution.
>> All in all, the water strider story is at best mere Darwinian
>> speculation,
>> with no demonstrative force, and in its popular presentation, it's badly
>> hyped. And this happens so many times, that it is no wonder the public
>> regards evolutionary biologists as the boy who cried wolf.
>> C. Your dismissive remarks about Hebert's motives and training are
>> unresearched and clearly ad hoc. I don't buy them. Neo-Darwinian theory
>> makes a prediction about what we should find in the mitochondrial DNA.
>> Hebert, a neo-Darwinian, candidly admits (to his credit) that the data do
>> not support the prediction. Your answer is to refer vaguely to other
>> factors which might explain why the Darwinian prediction is falsified.
>> That's the problem with neo-Darwinian explanation. It is too elastic.
>> It
>> can always call upon other vaguely understood possible factors to rescue
>> the
>> theory when the data doesn't match. That is why I maintain that
>> Darwinian
>> theory can never be falsified, and is not good science. A robust, manly
>> scientific theory puts its neck on the line, and when it's wrong, admits
>> it's wrong. It doesn't need to always be pleading special excuses, as
>> neo-Darwinism does.
>> Note also Hebert's own rather pathetic explanation to try to get out of
>> the
>> consequences of his research: he postulates an evolutionary cleansing
>> mechanism for which he has *absolutely no empirical evidence*, merely
>> because without such a mechanism he does not see how he can fight off
>> "creationist" conclusions. Sadly, that's the neo-Darwinian way of doing
>> science. When the facts are against you, postulate undocumented
>> mechanisms,
>> forces, factors, etc. Do *anything* but admit that the evidence may be
>> more
>> in favour of intelligent design than of accidental mutations and
>> fortuitous
>> selections. In neo-Darwinism, empiricism goes out the window in favour
>> of
>> maintaining *a priori* commitments to chance and necessity. This is why
>> neo-Darwinism is an embarrassment to science. It does not meet the
>> minimum
>> requirements of intellectual honesty, which dictate that when opponents
>> score a point, it should be granted to them.
>> Cameron.
>> ----- Original Message -----
>> From: "David Campbell" <>
>> To: "Cameron Wybrow" <>
>> Cc: "asa" <>
>> Sent: Thursday, August 20, 2009 12:55 PM
>> Subject: Re: [asa] historical versus experimental sciences
>>> In your examples below, you are granting more knowledge about the
>> species
>>> (some knowledge of the biochemistry, some knowledge of mitochondrial
>> DNA,
>>> etc.) than we originally supposed in our scenario. (Or at least, than I
>>> supposed.) All of my argument was based on the assumption that we had
>> *no*
>>> genetic or physiological knowledge of the new fruit fly, but knew only
>>> what
>>> it looked like, and its eating habits and such behavioural
>> characteristics
>>> as were obvious to the despairing farmers whose crops were being
>>> destroyed.
>>> My complaint, based on that assumption, was that you would not have
>> enough
>>> information to determine evolutionary relatives, and your line of
>>> diagnosis
>>> and prescription would thus be stopped in its tracks. Of course, if you
>>> have more information, then I understand how you could arrive at
>>> evolutionary relationships.
>> If you have whatever information has been adequately studied to be a
>> pointer to evolutionary relationships, whether it is a DNA sequence or
>> the configuration of hairs or stripe pattern or mantle flap shape,
>> then you are able to tell what group it belongs to. [Knowing the
>> genome means we have the entire thing sequenced, as opposed to having
>> one or some genes.]
>> By looking at one feature, we can, on evolutionary grounds, predict
>> similarities in unrelated features due to common descent. Some
>> features of practical interest are not as easy to determine directly
>> as others of less immediate practical interest. For example, if you
>> capture a few flies in LA, that isn't likely to be enough to
>> extensively test what attracts them. However, it is easily enough to
>> generate some DNA sequences. Using the sequence (or possibly the
>> configuration of hairs or stripes or some other morphological
>> feature), we can say "aha! these belong to the x group (possibly even
>> a previously unknown species) and therefore, because they share a
>> close common ancestor, are likely to be similar in vulnerabilities to
>> the better-known closely related species."
>>> However, then the *second* part of my argument would kick in, i.e.: even
>>> if
>>> you could determine the evolutionary relationships, it would be
>>> superfluous
>>> to do so. The similarities in DNA and/or and/or general biochemistry
>> would
>>> point the scientists and policy-makers in the direction of the solution.
>> Why? If they were created separately, there would be no reason why
>> the creator could not mix and match physically unrelated attributes to
>> create a range of forms. There's nothing about similarity in
>> mitochondrial genes that functionally connects them to what bait
>> attracts a fly.
>> It is, of course, empirically true that living things that are similar
>> in certain ways are often similar in other ways. But if you want to
>> explain that pattern, evolution is the only model that has worked.
>> That's why living versus non-living makes a difference.
>>> I see no benefit in arguing "Often close evolutionary relatives have
>>> similar pheromones", if you cannot determine close evolutionary
>>> relationship without *first* determining genetic, biochemical or
>>> morphological similarity<
>> Well, determining evolutionary relationship is based on the evidence,
>> so it is difficult to determine without a consideration of the
>> evidence. But without evolution you have no explanation for why
>> similar mitochondrial DNA and similar pheromones (or whatever other
>> feature you like) go together.
>> Yes, you can empirically observe that similarity in particular
>> features often goes together and rely on that without bothering to ask
>> why the pattern should exist. You can also use Kepler's laws without
>> ever bothering to formulate a general law of gravity. But the
>> practice of science is to try to find general common principles that
>> explain a large number of things. Again, you are making exactly the
>> same error as the atheists who claim that we shouldn't believe in God
>> if the laws of science are able to explain science. God provides a
>> comprehensive explanation of everything, both science and non-science,
>> and it is no more unreasonable to invoke evolution as explaining the
>> shared similarities of organisms or to invoke God as behind all the
>> natural laws than it is to invoke electroweak theory as explaining
>> both electric/magnetic forces and the weak nuclear force. (Of course,
>> in each case one must see whether the proposed overarching model works
>> well, but to dismiss a working overarching model as a mere extraneous
>> add on is, reductio ad absurdum, to reject all scientific models.)
>>>But that's exactly what we'd expect if, as Professor Skell has said, as
>> far
>>>as most experimental science is concerned, neo-Darwinism is an
>> interpretive
>>>gloss which is not necessary to conduct the research or validate the
>> Any theory, as far as experimental science goes, is not necessary to
>> conduct an experiment or validate the results. You just go and do the
>> experiment and check your measurements. The theory tells us what
>> experiments are likely to be interesting and what the results mean.
>>> This glossing occurs all the time. The other day, some scientists
>>> discovered the gene that gives the water strider its characteristic mode
>>> of
>>> skimming across the surface of the water, and the news story (perhaps
>>> following the lead of the reporting scientists, I don't know) gave the
>>> matter an evolutionary twist: scientists have discovered the
>> evolutionary
>>> mechanism by which the water strider acquired its ability. In fact, the
>>> *empirical* science had uncovered nothing about evolutionary mechanisms
>> at
>>> all.
>> They discovered the changes in function in one Hox gene that led to
>> the shape and length of legs, which enables the water strider to skate
>> around as it does. In other words, they are providing some of the
>> information about exactly what genes changed when to produce this
>> innovation, a piece of information that you have been requesting for
>> evolution to be validated. Yet now you are saying it is irrelevant
>> for evolution. (Now it is generally true that the news story probably
>> didn't have much useful information, but a quick check of
>> gives the details.)
>>> I find it interesting that you automatically associate "mitochondrial
>> DNA"
>>> with evolutionary theory.<
>> No, I associate it foremost with "relatively well-studied DNA,
>> generally informative at the species level," though it is therefore
>> quite useful for evolutionary analyses (as long as no funny business
>> is going on, such as hybrid polyploid lineages) .
>>> From a non-doctrinaire, non-historical point of view, the mitochondria
>> are
>>> simply organelles in the cell which contain DNA,<
>> Because they evolved from separate free-living organisms
>>> and the sequences in that DNA can be studied, just as the sequences in
>>> nuclear DNA can be studied. One can ask the question "How much different
>>> is
>>> the mitochondrial DNA of *this* species from the mitochondrial DNA of
>>> *that*
>>> species?" without speaking of evolution at all. It's a question for
>>> biochemists to settle.
>> Why should the mtDNA be different? Mitochondria do the same thing in
>> all organisms that have them; as long as the set of genes work
>> together properly, there's no need for our mitochondria to be more
>> like those of apes than mice or even of water striders or land snails.
>> They could function if all of them were identical, or if the DNA
>> similarities were random. But instead there is a regular pattern of
>> degree of difference, and it correlates to other features that we
>> would expect to reflect evolutionary heritage. Why should there be
>> any particular pattern of difference?
>>> By the way, are you familiar with the work of the evolutionary biologist
>>> Paul Hebert at the University of Guelph, who is one of the world's
>> leading
>>> experts on genetic bar-coding? < Yes.
>>> He stated in an interview a few years ago that, to his chagrin, the
>>> results of genetic bar-coding using mitochondrial DNA seem to support
>> the
>>> view of the "creationists". <
>> In the context of overselling his project. Ironically, his example of
>> establishing the provenance of the mouse in the pasta shows that.
>> What he is saying is that there is little variation within a species
>> and a lot between species, and he claims that the reason is unclear
>> evolutionarily but implies that it would fit well with a model
>> invoking separate creation of species or the like. In fact, there are
>> good evolutionary reasons to expect the pattern to be common, and
>> plenty of exceptions to the pattern (with the caveat that pseudogenes
>> and similar confounding factors that might create the appearance of
>> greater variation in the barcode are rarely firmly ruled out). Like
>> myself, he seems to be a morphological taxonomist who got into
>> molecular work because that was a good source of additional data and a
>> better way to get funded. As such, he may not have as much background
>> in population genetics, which provides the evolutionary explanation.
>> I previously mentioned that one of the things that I ought to be doing
>> is working on a paper on snails of the genus Juga. As a matter of
>> fact, the specific bit of the paper that is calling (not loud enough)
>> right now is to compile a table of the level of "barcode" percent
>> differences. In these snails, sometimes there is minimal difference
>> in the barcode (cox1) between species, sometimes there is the good
>> barcode pattern of slight variation within the species and significant
>> variation between species, and sometimes there is high variation
>> between species. The presence of enough variation within house mice
>> mtDNA to identify where the mouse in the pasta came from shows that
>> sequences are not, in reality, invariant within species.
>> Consider a species. There is some degree of variation in the cox1
>> sequence within it. Divergence within the population eventually leads
>> to separate species. Because these are finite samples of a finite
>> population, the original cox1 variation will almost certainly not be
>> evenly distributed between the two daughter species, especially given
>> that evolutionarily, there will probably be some degree of correlation
>> between the general genetic variation in the population and the
>> distribution of the key feature(s) that promote speciation. Also, the
>> separation of daughter species often involves some geographic
>> separation, and the original variation in cox1 probably was not
>> totally uniform geographically.
>> As the two daughter species become reproductively isolated from each
>> other, there is less and less exchange of mitochondrial DNA (although
>> the occasional hybridization event can throw things off). Within a
>> reproductively isolated population, alleles will be lost and new ones
>> will arise due to genetic drift. If the population is small, the loss
>> or fixation of alleles can happen rapidly (exact rates depend on the
>> mutation rate, the population size, and the reproductive
>> pattern-generation time, the proportion of the population that
>> actually breeds, and the relative contribution of each individual).
>> If a species has fairly high levels of genetic mixing within it,
>> fairly low mutation rates, not too large a starting population, and a
>> long period since splitting off from the ancestor (relative to
>> generation time), then it ought to have relatively low genetic
>> variation within the species but medium difference between the
>> species.
>> The prime exemplars for barcoding are birds, bats, and insects. But
>> they are very likely to have relatively long times between speciation
>> events and good intraspecies mixing, because they can fly and
>> disperse. If the climate changes at natural rates, they don't have to
>> speciate to adjust-they can often simply move. Almost none of the
>> insects known from the Pleistocene glacial periods are extinct today
>> (prime exception was a specialist mammoth parasite). Birds also are
>> exceptionally well-studied. They are big, often showy, and and
>> mostly diurnal. Thus, the chances that we've noticed morphological or
>> behavioral differences are generally pretty good (except for patterns
>> only visible with UV).
>> Additionally, barcoding often gets a bit circular-here are two birds,
>> currently considered to be the same species, but they have high cox1
>> differences, so it must be two species according to a barcode paper.
>> Maybe they are overlooked species, but maybe there's high variation
>> within the species-you need to go back and see if 1) is the difference
>> clear and abrupt when you have data for several individuals across the
>> range, or does it become a continuum? 2) can you find other features
>> that correlate with the difference?
>> If you want a genuinely simple evolutionary system, analogous to the
>> two body problem of launching a satellite, you need something like the
>> studies that put two kinds of flour beetles into a lab enclosure and
>> see which one wins out. Depending on precise conditions (especially
>> moisture), you can indeed predict which one will still be around after
>> many generations. Predicting what will happen to a lagomorph or a
>> rodent in the Amazon over millenia is more akin to using the laws of
>> gravity and motion to predict the exact fate of all the pieces from
>> the recent satellite-satellite collision.
>> --
>> Dr. David Campbell
>> 425 Scientific Collections
>> University of Alabama
>> "I think of my happy condition, surrounded by acres of clams"
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Received on Fri Aug 21 22:46:21 2009

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