Happy New Year, ID movement! (ID and Evol. Immunology)

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The new PNAS article “The descent of the antibody-based immune system by gradual evolution,” blogged by Carl Zimmer (“The Whale and the Antibody”) and Reed Cartwright at PT, brings to mind a famous old declaration by Michael Behe in his 1996 book Darwin’s Black Box:

“We can look high or we can look low, in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system.” Darwin’s Black Box, p. 138

This wasn’t true in 1996, as was documented when PT contributor Matt Inlay reviewed Behe’s immune system argument in 2002 (see “Evolving Immunity” at TalkDesign.org and the hilarious response of ID advocates when challenged). It is even less true now, due to the new PNAS article and other evolutionary immunology research published in 2004 and before. In fact, the ID movement is in total denial about this body of literature, yet ID advocates continue to parade around as if they have some shred of scientific credibility behind their rhetoric. They even have the gall to claim that the scientific mainstream is dogmatically oppressing them – it’s rather like a geocentrist arguing for a stationary earth without considering Foucault’s Pendulum.

I’ll take the liberty of making some predictions for 2005:

Predictions about Intelligent Design and Evolutionary Immunology for 2005

  • Several major new articles increasing our understanding of the evolution of the vertebrate adaptive immune system will be published.
  • Several more major new articles increasing our understanding of the evolution of the invertebrate/vertebrate innate immune system will also be published.
  • If the genome sequence of a new basal chordate is sequenced, several new articles reviewing the evolution of the vertebrate blood-clotting system in the light of this new data (which is related to the innate immune system) will be published.
  • These articles, and all of the other research on the evolution of the immune system, will continue to be ignored by the ID movement. Any response will amount to no more than variations on “You haven’t provided an infinitely detailed explanation yet, so you should accept our ‘explanation’ invoking a completely vague, magical, ‘designer’ instead.”
  • ID advocates will never let on to their loyal supporters that the scientific discipline of evolutionary immunology exists and has far more Ph.D. participants actively conducting research and publishing articles in this one subfield of immunology than the whole ID movement has doing biological research of any sort.
  • The ID movement will continue to boldly pronounce the downfall of evolutionary biology, the inability of evolution to explain “irreducibly complex” systems, and the oppression of ID by the Dogmatic Darwinian Establishment.
  • ID advocates will continue to argue that ID deserves to be treated with kid gloves by the scientific community
  • Despite their almost complete unwillingness to engage the scientific literature on the evolution of the immune system, the origin of new genetic information, or many other topics, ID advocates will continue to argue that the fake “scientific debate” over ID and bogus “criticisms of evolution” deserves attention in public schools.
  • Anyone new to “intelligent design” (such as scientists, parents, teachers, school boards, judges, and reporters) who investigates the topic in detail will become aware of these kinds of gaping holes in ID. They will therefore see ID for what it actually is: a fake scientific movement, designed for the purpose of slipping theological apologetics past the Supreme Court and into public school science classes, in order to support a certain subset of protestant evangelical Christianity that considers special creationism to be crucial support for the faith.

Oh, and I almost forgot: 10. The Panda’s Thumb will be here to point these things out as they occur.

Happy New Years, everyone!

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Evolutionary biologists face a challenge that's a lot like a challenge of studying ancient human history: to retrieve vanished connections. The people who live in remote Polynesia presumably didn't sprout from the island soil like trees--they must have... Read More

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Wow, a top ten list that has ten items in it; who would have thought?

If Bush gets to stack the Supreme Court with Scalia clones as he has promised, they won’t have to ‘slip past’. Hopefully some moderate Republicans will join the Democrats and not allow that to happen.

“Anyone new to “intelligent design” (such as scientists, parents, teachers, school boards, judges, and reporters) who investigates the topic in detail will become aware of these kinds of gaping holes in ID. They will therefore see ID for what it actually is: a fake scientific movement, designed for the purpose of slipping theological apologetics past the Supreme Court and into public school science classes, in order to support a certain subset of protestant evangelical Christianity that considers special creationism to be crucial support for the faith.”

Sadly I feel this may be an optimistic prediction.

You know, it (facetiously) occurs me that if creationists want us to point out evolutionary theory’s shortcomings in the science classroom, it’s only fair that they should have to point out creationism’s shortcomings in bibleschool.

More seriously, this is an awesome discovery. More gap-filling to point out to the pro-ID people.

There is a nice article on the immune system in this month’s Scientific American

Immunity’s Early-Warning System:

The innate immune response constitutes the first line of defense against invading microbes and plays a role in inflammatory disease. Surprising insights into how this system operates could lead to new therapies for a host of infectious and immune-related disorders

11. ID theorists will not produce an ID model that can even remotely be described as “detailed” or “testable” for the origin of the immune system, or any other IC system for that matter.

This fairly extensive list can be boiled down to only two predictions, which subsume all the ramifications:

1) Continuing research will keep discovering ever-clearer refutations to creationist doctrine.

2) Since evidence is irrelevant to doctrine, creationist tactics won’t change.

Cary Wrote:

You know, it (facetiously) occurs me that if creationists want us to point out evolutionary theory’s shortcomings in the science classroom, it’s only fair that they should have to point out creationism’s shortcomings in bibleschool.

Actually it is the anti-evolutionists who should be demanding that, wherever creationism or ID is taught, there should be equal time devoted to their shortcomings. That they rarely if ever do so speaks volumes.

That they rarely if ever do so speaks volumes.

If we’re listening carefully, of course. Some of the ID positions, as presented, come a great deal closer to evolution as we know and love it than to any of the creationist positions. Why, some IDists accept common descent, deep time, even natural selection. Yet even these people are never, ever found even hinting at disagreement with even the most glazed-eyed YEC fanatic. What a striking contrast with genuine evolutionists, who engage in acrimonious battles with one another. The fireworks among Wright, Gould, Dawkins, Cosimedes and Tooby, etc. would singe your hair, yet these people are arguing only about relatively minor issues of emphasis, pacing and the like.

Why is this? Because even though the various creationist natural histories have such wide variation, their *goals* are the same - to convert the non-believer. In their view, you are either for God or against him. Now, God Himself can be a bit ambiguous, saying now this and now that, producing the appearance of age sufficient to fool the unsophisticated, and speaking into different hearts with forked tongue. But all of this can be written off as human limitation and original sin. What can NEVER be written off is the denial of God, and abiogenesis followed by natural hereditary mechanisms denies God. It leaves Him out!

Directly challenged, any random IDist might allow as to how he disagrees with another on some of the details (like a few billion years, a common ancestor, macroevolution, and other trivia), but these aren’t important enough to be raised outside of a direct challenge. Meanwhile, back to the important focus of attacking those whose theories omit God. Intolerable.

I’ll be more impressed about the kind of immune systems that dinosaurs have if someone can first tell me whether their T-cells and such were floating in warm or cold blood.

LOL! Amazing. We don’t know whether creatures just a few tens of millions of years old had warm or cold blood but we’re claiming to know what kind of immune cells were in creatures hundreds of millions of years old?

Gimme a break.

I know, right? We don’t even know if they breathed helium, or were made out of antimatter, or had the power of invisibility, but these scientists want to say they had immune cells? Those dorks.

I’ll be more impressed about the kind of immune systems that dinosaurs have if someone can first tell me whether their T-cells and such were floating in warm or cold blood.

LOL! Amazing. We don’t know whether creatures just a few tens of millions of years old had warm or cold blood but we’re claiming to know what kind of immune cells were in creatures hundreds of millions of years old?

Gimme a break.

DaveScot: You are clearly misunderstanding the way comparative immunology works. It doesn’t study the immune system of organisms that died millions of years ago, but that of their living descendents today. Since all jawed vertebrates (cold- and warm-blooded) have similar (though not identical) T cells, B cells, antibodies, T cell receptors and major histocompatibility antigens, however, we can infer that their last common ancestor did.

Within the general frame of the vertebrate “adaptive” immune system, we also see a pattern of nested hierarchy, also predicted by common descent, in the distribution of some secondary features. For instance, only tetrapods (amphibians and “up”) display multiple types of antibodies that become expressed by a new kind of gene recombination mechanism (“switch” recombination), warm-blooded, but not cold-blooded animals have structures called “germinal centers” in which the immune response “matures”, only mammals have certain kinds of antibodies (e.g. IgA), and only in the great apes you find dupicated genes for those antibodies (IgA1 and IgA2).

So infer for me whether dinosaurs had warm or cold blood. If you can infer the kind of immune cells they had surely you can infer whether they were warm or cold blooded.

You boys do an awful lot of inferring in evolutionary science, huh? Almost like it’s a forensic science with no hard proofs about anything - just a bunch of guesswork with more or less chance of being correct guesses.

So infer for me whether dinosaurs had warm or cold blood. If you can infer the kind of immune cells they had surely you can infer whether they were warm or cold blooded.

Why? They are two entirely different issues, based on entirely different sets of evidence. You seem to believe that an “inference” is the same as a “guess”, but it isn’t. Anyone with a barely adequate scientific education should know that.

That said, as I understand it (I am no paleontologist), the current data do not allow a clear inference regarding non-avian dinosaurs’s warm- or cold-bloodedness. However, technically speaking, all existing avian dinosaurs, and by inference their extinct ancestors to the last common ancestor, are (and were) warm-blooded.

You boys do an awful lot of inferring in evolutionary science, huh? Almost like it’s a forensic science with no hard proofs about anything - just a bunch of guesswork with more or less chance of being correct guesses.

All sciences do a lot of inferring, DaveScot. We never went outside our solar system, but we know quite a bit about what’s going on in the rest of the universe. Ever wondered why? Again, inferences are not guesses.

“All sciences do a lot of inferring, DaveScot. We never went outside our solar system, but we know quite a bit about what’s going on in the rest of the universe. Ever wondered why? Again, inferences are not guesses.”

No, I never wondered why because we can directly observe the sky. The sky isn’t something that happened in the past. It’s there right now. Just go outside at night and look up at it if you don’t believe me. Evolution on the other hand is something that happened in the past. I can’t observe an amoeba as it turns into a rhinoceros as I can look at the moon rising and setting and waxing and waning.

And yes, inference IS a guess. It may be an arbitrarily good or bad guess but it is still a guess. Direct observation is not guesswork.

I guess you think we can directly observe clouds of dust turn into stars, planets orbiting distant suns, the universe expanding, or what’s inside black holes, uh?

Well, at least we have a real live example of what it means to have absolutely positively NO grasp of what science means, whatsoever.

Do you suppose it’s worth pointing out that when we look up at the stars, we are seeing the past and inferring that stars shone in the past? We sure aren’t seeing them in the present. Do you suppose it’s worth pointing out that evidence means anything, that inferences are based on evidence and guesses are not? Do you suppose we might infer that our educational system is being demonstrated to have totally failed in at least this case?

Nick Matzke wrote:

In fact, the ID movement is in total denial about this body of literature, yet ID advocates continue to parade around as if they have some shred of scientific credibility behind their rhetoric. They even have the gall to claim that the scientific mainstream is dogmatically oppressing them — it’s rather like a geocentrist arguing for a stationary earth without considering Foucault’s Pendulum.

With all due respect to the authors of this paper, it is you and they who are in denial. This paper contributes nothing towards the explanation of the origin of the immune system. The authors quite correctly state: “This seemingly sudden appearance of a complex (and highly organized) body system presents a challenge to evolutionary biology”. That’s a colossal understatement. What it does is to falsify the mechanism of evolutionary biology that relies on random, accidental, fortuitous occurrences and denies the importance of intelligent input. The authors go on to say: “Here we sketch out some of the changes that the emergence of the AIS entailed and speculate how they may have come about.” This is an admission that there is not one shred of empirical evidence, either experimental or observational, to back up their argument. I think that they may have watched too much Sesame Street when they were kids. Remember Sherlock Hemlock, always making up wild explanations to explain clearly obvious events? In their conclusion they state: “The evolution of the AIS itself must have begun long before the divergence of agnathans and gnathostomes from their common ancestor.” Why do they say this? Because it is required to support their evolutionary weltanschauung. The darwinian paradigm is so deeply rooted in their psyche that they cannot imagine any other explanation. Their adherence to this false paradigm has clouded their scientific objectivity and rendered them blind to the actual data: that the immune system appeared very suddenly in the early vertebrates and in no other lineage. Here’s the rest of their howler: “The evolution consisted initially of changes unrelated to immune system response that were selected to serve other functions. The different functions may have been unrelated to one another, but ultimately, (now here’s where the magic comes in. Cue the evolution pixies!) a combination of these functions arose by chance, which presented the potential for the development, in a not too large number of steps, of a qualitatively new system. The actualization of the potential required integration of the different functions into one whole.” How was this integration accomplished without intelligent input? How can random events have the insight to “integrate” (use different structures and different processes together in such a way that they not only support each other, but support the overall function of the system) components into a working system? And how does this process decide if the system is working? They completely gloss over this incredible gap in their scenario and move right on to: “once the critical steps were accomplished in the gnathostome lineage, the integration created the illusion of a sudden, explosive change, a big bang. However in reality, the entire process was gradual, consisting of accumulation of small changes over an extended period.”

Horsepookey.

You claim that ID’ers are in denial? Physician, heal thyself.

Charlie Wagner http://www.charliewagner.com

Charlie Wrote:

What it does is to falsify the mechanism of evolutionary biology that relies on random, accidental, fortuitous occurrences and denies the importance of intelligent input.

No wonder Charlie is so confused, he does not even get his descriptions of evolutionary theory correct.

In response to Andrea Bottaro who said,“All sciences do a lot of inferring, DaveScot. We never went outside our solar system, but we know quite a bit about what’s going on in the rest of the universe. Ever wondered why? Again, inferences are not guesses.” DaveScot Said:

No, I never wondered why because we can directly observe the sky. The sky isn’t something that happened in the past. It’s there right now. Just go outside at night and look up at it if you don’t believe me.

Well, we don’t directly observe the cheical compounds present in extra solar objects, but based on the optical spectra they radiate, we can infer what the chemical compounds are based on the recorded optical spectra of known chemical compounds. We have never directly opserved an extra solar planet, but we have seen effects such as orbital wobble and gravitational lensing, from which we can infer the existence of planets orbiting other stars. Rutherford never saw the nucleus of an atom, but was able to infer it’s existence based on the angle of scattering of electrons fired at a gold foil. Likewise, we directly observe the relatedness of immune systems in a variety of animals and can infer the evolutionary history of these immune systems.

Andrea Bottaro said “However, technically speaking, all existing avian dinosaurs, and by inference their extinct ancestors to the last common ancestor, are (and were) warm-blooded.” That’s a reasonable inference but I’m not sure that’s a safe one. I mean, if the only evidence for Heterocephalus glaber were a fossil it would be reasonable to think that as a mammal it was warm blooded too. And some of H. glaber’s relations are neither one thing nor the other, I’m told. Although I loved Dr Bakker’s “dinosaur heresies” when it came out, it’s probably safer to say some may have been, than all were.

Interestingly, this article just came out in the most recent issue of Nature:

Transposition of hAT elements links transposable elements and V(D)J recombination

LIQIN ZHOU, RUPAK MITRA, PETER W. ATKINSON, ALISON BURGESS HICKMAN, FRED DYDA & NANCY L. CRAIG

From the conclusion:

It had been suggested that the V(D)J recombination system may have evolved from an ancient transposable DNA element. Our findings here of such a close mechanistic relationship between hAT transposition and V(D)J recombination—that is, a double-strand break via hairpin formation on flanking DNA and 3’ OH joining to the target DNA—and the related active sites of hAT transposases and RAG1 provides strong support for the view that V(D)J recombination evolved from transposable elements.

For those who don’t know, V(D)J recombination is the primary mechanism producing antibody diversity, and is one of Behe’s unevolvable IC systems. The hAT transposase represents one ‘part’ of that system.

Gav: OK, OK, fair enough, though of course naked mole rats’ ectothermy is a derived character. So, I should have said “all known existing avian dinosaurs, and by inference their extinct ancestors to the last common ancestor, are (and were) warm-blooded.”

The point, with respect to DaveScot’s claim that we couldn’t infer the warm- or cold-bloodedness of dinosaurs, is that in fact for many of them we can.

Man, tough crowd… ;-)

Charlie Wagner -

You wrote:

“How was this integration accomplished without intelligent input? How can random events have the insight to “integrate” (use different structures and different processes together in such a way that they not only support each other, but support the overall function of the system) components into a working system? And how does this process decide if the system is working?”

An obvious assumption to make, given the tenor of your remarks, is that you are aware of evolutionary theory. And as it turns out, the paragraph of yours I quoted above is a pretty good layman’s description of evolutionary theory - random events bringing together different processes and structures to support the working system in a different, and perhaps better, fashion than before. Since you know the theory, you know the answer to your question - success is determined by passing on the new arrangement. Congratulations, Charlie! You’ve done such a good job of summing up evolutionary theory that I’ll use it in my class!

MakeMineRed

“The sky isn’t something that happened in the past. It’s there right now.”

Wow. This statement belies an ignorance beyond amazing. Indeed, when we look into the sky, we are looking into the deep past (as well as the recent past and the present); the further the subject of observation, the more distant the event was in the past. Could anything be more basic?

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This page contains a single entry by Nick Matzke published on December 31, 2004 7:56 PM.

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