Random responses to Luskin on evolution of creationism, quotes, and information

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(Note: I got off on some tangents in this post – big tangents, not having written a Luskin-rebuttal in awhile. In some cases – most of them, probably – I may be the only person in the world who would bother to rebut these points. But, hey, everyone needs a summer vacation, and Luskin usually takes lack of response as evidence that he must be right. This is hilarious, but it’s funniest when he relies on an argument for many years, getting more and more confident in it. But, eventually someone has to pop the bubble. I really have to stop now so please point out errors, which must exist, and I will fix when I get a chance.)

Casey Luskin has responded to my recent article “The Evolution of Creationist Movements” in Evolution: Education and Outreach. My article is freely online, so you should read it and all of the other great pieces in that issue, which was a festschrift for Eugenie C. Scott (only a few of the articles are currently open access, however).

Luskin raises 3 issues. I will answer in 3 parts:

Part 1: Luskin claims I only “sneer” at the information argument:

Pop quiz: Did the following quote come from (A) Panda’s Thumb, or (B) An article in a scholarly journal published by Springer science publishing?

“An especially good example of silliness is the ID assertion that natural processes cannot create new genetic information. ID advocates have recently been pushing this line heavily as of late (Meyer 2009)…”

If you answered (A), then…

…you’re wrong. It came from a recent article former by NCSE staff-member Nick Matzke in the journal Evolution: Education and Outreach – an NCSE-aligned outfit, where apparently such language passes for scholarly argument. In the words of Jay Richards “a sneer is not an argument.”

Hmm. Well, in the first place, my article was primarily a work of history, and an attempt to correct some mis-perceptions about the history and character of the ID movement that are ubiquitous among ID advocates and somewhat common even amongst pro-evolution writers, journalists, historians, scientists, and other commentators. It was explicitly not an attempt to give detailed rebuttal to ID arguments. Instead, I referred readers to numerous other works. As I did in the very passage Luskin partially quotes as being a sneer:

An especially good example of silliness is the ID assertion that natural processes cannot create new genetic information. ID advocates have recently been pushing this line heavily as of late (Meyer 2009), even in the science standards of some states (see Matzke and Gross 2006, for discussion and refutation of the information argument),

Whoops! Just read the next line, Luskin!

Now, Luskin may be annoyed because Matzke & Gross (2006) primarily relies on Long et al. (2003), a long review in Nature Reviews Genetics handily entitled “The origin of new genes” (free online in many places). The article is handy because Table 1 lays out the various mutational mechanisms that copy and rearrange DNA, and Table 2 lists dozens of examples known in 2003 (many more are known now) where publications in the literature reconstructed the origin of various “young” genes.

It’s a great article, and we’ve been pummeling the ID movement’s information argument with it ever since it came out. You can see some discussions using it on PT (for example in “Meyer’s Hopeless Monster” in 2004), it was cited in 2005 by expert testimony in Kitzmiller v. Dover (with no rebuttal whatsoever from the ID side – your fault, ID fans, not ours!), it was officially entered into the court record as exhibit P-245, and was subsequently cited in the decision.

As far as I know, despite all of us using Long et al. (2003) as a club with which to beat the helpless baby seal that is the ID “evolution can’t produce new genetic information!” argument, no ID advocate ever even acknowledged the existence of the article, much less the entire subfield of research which it reviewed, until 2006, when Luskin finally got around to realizing what a huge problem it was. Even then, his only response – from 2006 until 2010! – was to complain that the word “information” doesn’t appear in the article, as if that was a response which should be taken seriously. ID advocates have yet to provide any objective definition of “genetic information” – a crashing, horrific, scandalous, head-exploding flaw in their argumentation, given just how much they love to talk about “information” – but if we know only one miniscule thing about what ID advocates mean when they the words “genetic information”, they mean that functional gene sequences contain information. They say that gene sequences contain information all the time, every chance they get. And if this is true, then new gene sequences with new functions contain new information. It’s simple deduction, it’s as crashingly obvious as that, and any response to Long et al. or similar works that relies on hairsplitting like “but the word ‘information’ wasn’t used!” is just not serious. [1]

Luskin has, very recently, finally at long last realized that a more serious response to Long et al. is needed, and has produced some huge document arguing that every single example in Long et al. actually fails, for various randomly chosen and inconsistently-applied reasons. He’s not even willing to concede that high sequence similarity implies copying, not even in overwhelmingly obvious cases like the below example of Sdic, aka Sperm dynein intermediate chain of Drosophila, and he’s not even willing to concede the high plausibility of selection for something like a sperm dynein intermediate chain, nor the wildly impressive evidence for natural selection (in the form of a selective sweep). So it’s hard to see what the point is in even arguing with him. It’s easier to just put up the detailed scientific explanation of the origin of Sdic (see graphic below) and tell ID to put up or shut up and give us a better explanation.

An explanation of the origin of sdic that, I’m sure, is “not detailed enough” for IDists:

Ponce_Hartl_2006_sdic_evolution_pt1.png

Ponce_Hartl_2006_sdic_evolution_pt2.png

Fig. 6. Model for the evolution of the Sdic gene cluster. (1) In the ancestral situation, Cdic and AnnX genes were adjacent. (2) A first duplication event duplicated both Cdic and AnnX while maintaining their original orientation. (3) Several deletions occurred in the duplicated region and the new chimeric gene Sdic was formed; around this time a retrotransposon was inserted upstream of the Sdic gene. (4) A second duplication event duplicated both the new gene and the intergenic region between Sdic and Cdic; the two copies of Sdic diverge. (5) A third duplication event duplicated the whole cluster in which the two existing Sdic genes and the intergenic region between them and Cdic was duplicated. (6) The four Sdic genes diverged by point mutations and deletions becoming distinguishable Sdic genes.

From: R Ponce, DL Hartl (2006). “The evolution of the novel Sdic gene cluster in Drosophila melanogaster.” Gene 376(2), 174-183.

Evidence of selective sweep:

sdic_selective_sweep.png

From: D Nurminsky, DD Aguiar, CD Bustamante, DL Hartl (2001). “Chromosomal effects of rapid gene evolution in Drosophila melanogaster.” Science.

Part 2: Luskin says I garbled a quote from Meyer’s 2009 book:

But exactly how does Meyer allude to the “purpose-driven life”? Matzke’s paper garbles a passage from Signature of the Cell (SITC) as follows:

As a teenager in the mid-1970s, I sensed this absence of meaning in modern life…What heroism, thought or feeling, labor, inspiration, genius, or achievement will last, if impersonal particles are all that ultimately endure? …Though the theory of intelligent design does not identify the agent responsible for the information–the signature–in the cell, it does affirm that the ultimate cause of life is personal…The case for intelligent design challenges the premise of the materialist credo and holds out the possibility of reversing the philosophy of despair that flows from it. Life is the product of mind; it was intended, purposed, “previsioned.” Hence, there may be a reality behind matter that is worth investigating.

If the conscious realities that comprise our personhood have no lasting existence, if life and mind are nothing more than unintended ephemera of the material cosmos, then, as the existential philosophers have recognized, our lives can have no lasting meaning or ultimate purpose. Without a purpose-driven universe, there can be no “purpose-driven life.” (Meyer 2009)

Using Matzke’s quote as a guide, the second paragraph in this quote is extremely difficult to locate in SITC because it appears two pages before the first paragraph. Of course, this reflects the fact that Matzke took the liberty of engaging in a significant amount of re-arranging of Meyer’s words, leaving out much context.

Here I have to plead a little bit guilty. Somewhere between my final draft and the proofs, Springer’s copy-editors (I think) took out all of the page numbers – which I had originally included for every single quote in the article. Either that or I got the idea somewhere that this was the house style and re-ran the Endnote formatting without page numbers. All of the involved files exist in multiple version, most with file save times of approximately 6 a.m. (which for me, means that was about when I went to bed). Anyway, this then left these two paragraphs, each with a (Meyer 2009) reference. In another round of editing, the first (Meyer 2009) was helpfully (@#$*!) copy-edited out as redundant, producing an apparent two-paragraph quote with the paragraphs out of order. For good measure, here’s screenshots from the different drafts, so you can see them:

Matzke_2010_EEOquote_v1.png

Matzke_2010_EEOquote_v2.png

Matzke_2010_EEOquote_v3.png

Anyway, for the interests of posterity, I’ve put up a PDF of my plain-text final draft, formatted with page numbers. This is not quite identical to the published version since there were copy-edited and an abstract added. But it is useful if anyone wants the page numbers.

But, it should be pointed out that (a) nothing hangs on the order of the two paragraphs, and I didn’t imply anything based on the order – they are just two striking examples from this section of Meyer’s book; and (b) Luskin’s actual complaint is that I nefariously left out a relevant passage:

Had Matzke continued with the actual context after the first paragraph, as his quote wrongly implies the second paragraph ought to be, one would have discovered the following prose from Stephen Meyer:

These implications of the theory are not, logically speaking, reason to affirm or reject it. But they are reasons–very personal and human reasons–for considering its claims carefully and for resisting attempts to define the possibility of agency out of bounds. (p. 451)

The context of Meyer’s discussion indicates that he’s is talking about the larger implications of ID, and not the arguments for ID. But Matzke’s argument implies that discussing larger philosophical or theological implications or alluding to religious topics is inappropriate for “any standard scientific book on the origin of life.” Ironically, Matzke is doing exactly what Meyer warns against: trying to define ID as “out of bounds” without actually addressing the argument. Hence, Matzke is reduced to calling SITC’s arguments “silliness” and making irrelevant complaints about Meyer’s discussion of theological implications.

But I didn’t allege that Meyer said these were logical reasons to affirm ID. I said, quite specifically: “Finally, it doesn’t take much looking before virtually any ID advocate will let down their guard and admit that the real point of studying ID is to return God and purpose to the culture.” Thus, I quoted from the concluding section of Meyer’s book – the one right before “Conclusion”, explicitly entitled “Why It Matters” – and even noted that “Why It Matters” this was the section heading! (Actually, looking at the book now, “Why It Matters” is the heading on each page of the section, and “It Gets Personal: Why It Matters” is the full title of the section. Even better, for my point.)

It’s not like I’m misrepresenting Meyer. Meyer is proud of his motivations for studying ID – justifiably so, from his perspective – and he owns his concerns about religion and purpose, and he says them again in the last two paragraphs of the “Why It Matters” section:

These implications of the theory are not, logically speaking, reasons to affirm or reject it. But they are reasons – very personal and human reasons – for considering its claims carefully and for resisting attempts to define the possibility of agency out of bounds. Is intelligent design science? Is it religion? Perhaps these are not the right questions. How about, “Is there evidence for intelligent design?” “Is the theory of intelligent design true?” And, if so, “What does it imply?”

Indeed, for me, far from wanting to avoid the philosophical or theological questions that naturally arise from a consideration of the evidence for intelligent design, these questions have done much to sustain my long interest in the scientific controversy surrounding the origin of life. And why not? If there is evidence of design or purpose behind life, then surely that does raise deeper philosophical questions. Who is the designer, indeed? Can the mind that evidently lies behind life’s digital code be known? Can we as persons know something of the agent responsible for the intricacies of life? Is there a meaning to existence after all? I have asked these questions for many years. What excites me about the theory of intelligent design and the compelling evidence now on display in its favor is not that the theory answers these questions, but instead that it provides a reason for thinking that they are once again worth asking. (Meyer 2009, p. 451)

Whether or not having these kinds of motivations is a bad thing is a different question, one I don’t address at length in the article. I was primarily trying to give readers insight into creationist history and the creationist mind, and thus was mostly being descriptive. I do think that the idea that science can give proof of the existence of God and show that there is a purpose to life is tremendously seductive. (Just imagine for a moment that you are a scientist in some science fiction movie, and you discover deep in your lab proof positive of the existence of alien life, good enough that it ought to convince all the skeptics. Now replace “aliens” with “God.” Throw in the scene where Indiana Jones finds the Holy Grail and you’re there. That’s what I mean by seductive.) I do think that the seductiveness of this kind of finding, both to ID leaders and their worshipful, noncritical fans and funders, is a large part of the reason why creationists/IDists are so amazingly sloppy with their science. But to make this argument rigorous would require a detailed demonstration of huge flaws in ID’s arguments about evolution, which I didn’t do here. Such arguments are found in, let’s see, most of my other friggin’ publications and posts about ID, many of them cited in the E:EO piece – but oh well, Luskin forgot about those.

Final thought: This kind of thing is one of the common ways that quotes – both creationist quote mines and other quotes – evolve over time. Quote metadata seems to be highly vulnerable to loss…

Part 3: Luskin cites a bunch of popular-science books by the likes of Sagan and Hawking making metaphysical-ish statements in their concluding pages. He then accuses me of using a double standard. Apparently I was supposed to review the history of everything anyone had ever said that was vaguely connected to science or evolution. But no, my article had a specific topic: creationists. If you want to learn something about creationists and why they think and act like they do, despite the scientific dubiousness of their arguments (which, as I said, I just assume for the purposes of this article; see my other articles for why creationist arguments are scientifically silly), then read my article. If you want to learn about evolutionists, read something else.

I also didn’t say that all evolutionists were as pure as snow in keeping metaphysics out of their science. For what it’s worth, my considered position is that popular science books, or I guess really a certain subgroup of popular-science books (written by “scientific visionaries”) are rife with metaphysics, most of which ranges from poorly-supported argumentation connected to the scientific facts through some form of emotion-based free-association, all the way over to sheer delusion and future worship. I’m a fan of Mary Midgley and her books Evolution as a Religion and Science As Salvation, for chrissakes (these books examine some of silly, even crazy stuff that gets written at the end of certain popular-science works).

And if I’m talking about it, I might as well give my opinion, which is that we’d be better off with less of that kind of thing, and if everyone had a lot more humility about drawing any kind of metaphysical or moral conclusions from scientific facts about the Universe, evolution, etc.

However, there are some key distinctions between this sort of stuff and ID/creationism metaphysical motivations:

(1) Evolution has a vast professional scientific literature, almost entirely devoid of metaphysical concerns (annoyingly, not quite entirely devoid of it, thus giving the Luskins of the world a job), whereas ID/creationism is just about the opposite (mostly metaphysics, with occasional scattershot collections of random objections to evolution, and very very occasionally some very simplistic and silly attempt at a positive empirical argument)

(2) Prominent evolutionary scientists come from all over the map, from atheists to traditional Christians, whereas ID figures are almost all conservative theists, and the vast majority of them are conservative evangelicals)

(3) Most importantly, there is a world of difference between those who start from diverse metaphysical perspectives and really genuinely put the data and the biology and the empirical work and the testing of hypotheses first and leave the metaphysics out of it (the vast majority of scientists and evolutionary biologists, I would say) – versus those who begin by saying there is a life or death (or eternal fate or Meaning Of Life!) question in the balance, and one of the answers (evolution) means meaninglessness and despair and falsity of their whole worldview (e.g. the Biblicist Christian worldview). The latter is extremely problematic.

Another way to say it:

* With evolution, there is a vast community of thousands of scientists doing biology every day, a few of whom end up becoming popularizers, and some of those become advocates of atheism, omega man, or whatever.

* With creationism, there is a vast community of (millions!) of believers who are deeply disturbed by challenges to Biblicist/literalist Christianity. Supporting/defending/being funded by that community of millions is a subgroup of thousands (literally) of professional apologists, apologetics groups, and ministries devoted to defending this worldview. Within that there are maybe a hundred who have specialized on the science/evolution issue full time (if we count the YECs and IDers together), and they serve as a resource to the wider community of apologists and ministries that have to deal with evolution along with abortion, homosexuality, and everything else (there are similar evangelical specialists for each of these), and they serve as the primary authorities on the evolution issue in the world of conservative evangelical/fundamentalist schools, home-schooling, radio shows, magazines, conferences, TV, etc. It’s not an exageration to say that creation science & ID are fingers on the apologetics arm of the body of fundamentalist Christianity.

(Occasionally members of this group get confident enough to think they can take on the science/education establishment, and then we have the news stories and court cases and other fun. Eventually it becomes evident that they can’t really compete in the big leagues: they weren’t really trying to do science in the first place, after all, so they aren’t very good at it – and eventually, so far at least, they are defeated, go back to home turf, and the cycle repeats. Although a few of them, like Casey Luskin, keep trying to re-fight the old battles. ;-) )

Final thought: It appears that my article has struck a chord with the IDists. So far we’ve had outraged responses from Cornelius Hunter and Casey Luskin. The Hunter thread has gotten 482 comments. Interestingly, neither of them makes major counterarguments, rather both of their responses amount to “but you evolutionists do it too!”, and then accuse me of hypocrisy. I think this is pretty good evidence that I’ve got a bead on creationist history and motivations.

I will re-post my comment on Hunter’s thread on my article, which is a good summary of my feelings about IDist discussions thus far:

Well, this is quite a thread. I’m not sure what Hunter’s objection to my article was, he doesn’t seem to disagree with my statements about creationists, he just seems to be saying “evolutionists do these [presumably bad?] things too!”

I would disagree that this is true as a general matter – evolution as a science relies on no religious assumptions not also used throughout science, including many sciences Hunter and other creationists completely accept. It is true that some popularizers and creationism-rebutters argue against creationism by taking the *creationists’* assumptions about God’s actions and showing evidence that doesn’t comport with these ideas. This is a legitimate activity as long as those ideas are in circulation; but they are not a necessary part of the argument for evolution. But, if you don’t like such assumptions, you can also declare that you have no idea how God would do things, and then note that “God did it but we can say nothing about how/why/when/etc.” is completely worthless as an explanatory hypothesis, whereas evolutionary hypotheses have provoked and survived all kinds of research and tests, and made many successful predictions. And that’s why evolution is science, and “God did it” ain’t.

But my paper wasn’t about evolutionists, it was about creationists, and I’m gratified to see apparent agreement from the creationists about my summary of what the real issues are.

For example, this thread is a particularly strong confirmation of one of my summary points:

“The definition of creationism that focuses on divine intervention is the fairest and most accurate representation of not only the historical meaning of the term, but also predominant present meaning. Most importantly, the focus on divine intervention best captures what people have been and are still fighting over.”

Cheers, Nick

Notes

[1] When he’s having a good day, Luskin will remember to connect his “Long et al. didn’t use the word ‘information’” argument to one of the arguments made in Kitzmiller that Plaintiffs made about Behe & Snoke’s 2004 Protein Science article (comprehensively rebutted on PT here), namely that Behe & Snoke (2004) didn’t use the words “intelligent design”.

Luskin says, OK, not using the word “information” isn’t a good argument against Long et al. (well, except when it is; if someone really wanted to, we could use the magic of google to survey the DI blog and the rest of the internet on ‘Luskin “the word information”’ and count the times Luskin thinks it’s a bad argument (like here on the DI blog on July 6, 2010) and the times he thinks it’s a great argument (like here in the Luskin’s March 2, 2010 defense of Explore Evolution from NCSE’s critique of Explore Evolution. But even I have limits.)

But, says Luskin, if using the word “information” isn’t necessary for Long et al., then using the words “intelligent design” shouldn’t have been a damning point against Behe & Snoke 2004, and Judge Jones back in Kitzmiller should have admitted that a scientific article supporting ID existed. Here’s this version of Luskin’s argument:

In his ruling, Judge Jones repeatedly (and wrongly) claimed that ID had not published peer-reviewed scientific articles. A variety of these peer-reviewed scientific articles were documented to him during the course of the trial, including a 2004 paper that Darwin-doubting scientists Michael Behe and David Snoke published in the journal Protein Science. That paper cast doubt on the ability of gene-duplication to produce new functional protein-protein interactions. But Judge Jones dismissed Behe and Snoke’s article paper because “it does not mention either irreducible complexity or ID.”

While Judge Jones is correct that their article does not contain those words, the article does bear directly on those topics as it tests the complexity inherent in enzyme-substrate interactions. Even an anti-ID article in Science acknowledged that the evolution of protein-protein interactions bears on the question of irreducible complexity and the ID argument (See Christoph Adami, “Reducible Complexity,” Science, Vol. 312;61-63 (Apr. 7, 2006).) By Judge Jones’s standards, the lack of the exact phrases “intelligent design” or “irreducible complexity” should preclude one from arguing that the paper supports ID or irreducible complexity. But Judge Jones doesn’t hold evolutionists to the same standard.

What makes this ironic is that Judge Jones claimed that the review paper by Long et al., “The Origin of New Genes: Glimpses From the Young and Old,” accounted for “the origin of new genetic information by evolutionary processes” in a peer-reviewed scientific publication. Yet the body of this article does not even contain the word “information,” much less the phrase “new genetic information.” The word “information” appears once in the entire article – in the title of note 103. This reveals a double standard applied by Judge Jones to pro-evolution versus pro-ID papers as regards peer review.

I’m perfectly comfortable with someone citing Long et al. regarding the origin of new genetic information, even though it doesn’t contain the word ‘information.” Consistently, I think that Judge Jones’ accusation against Behe and Snoke’s paper is fallacious. I’m trying to be fair, and the fact that Long et al. does not contain the word “information” should NOT preclude it from bearing on the topic. Thus, I didn’t dismiss Long et al. but posted a lengthy 10,000+ word analysis of the paper. Wesley Elsberry attacks me for allegedly committing what he considers to be a hasty dismissal of this paper – but why doesn’t he jump on Judge Jones for wrongly dismissing Behe’s paper?

Major problems with this include:

* The word “information” in Long et al. is not something that should be expected. Molecular and evolutionary biologists do not primarily use “information” terminology – it’s not terribly useful in most situations, since crucial biological distinctions, like coding vs. noncoding, selected vs. neutral, and functional vs. nonfunctional, are meaningless in mathematical information theory (I mean real information theory, not woo-based creationist information theory). Biologists have perfectly good words, like “sequence” and “gene”, that they will usually use instead of “information.” Only IDists/creationists obsess about lathering their discussions of biology with nearly meaningless info-babble (which is the result of their having no actual rigorous definition of what they mean by “information”) – biologists are not required to do so.

Nevertheless, as I mentioned in the main post, it is totally impossible to argue that Long et al. does not directly address the evolutionary origin of new genetic information, since the origin of new genes with new functions *is* the origin of new genetic information, since IDists themselves say again and again that functioning gene sequences contain information.

* Furthermore, no one at trial tried to challenge Long et al. by making the “but it doesn’t use the word information!” argument. Probably because these sorts of arguments only seem convincing when you are sitting inside the Discovery Institute offices in Seattle.

* On the other hand, the scientific status of “intelligent design” was definitely a key issue throughout the trial. If the Defense could show that ID was good science, then they might be able to argue that there was an overriding secular purpose and effect of teaching ID in the biology classroom. One way to show that ID was good science would be to enter into evidence support for ID in the peer-reviewed scientific literature. The Plaintiffs definitely entered into evidence articles in places like Nature that supported evolution.

Thus, it really was important whether or not the articles the ID side introduced into evidence used terms like “irreducible complexity” and “intelligent design.” If they don’t, well then, these concepts don’t have support in the scientific literature. Someone could still argue that ID should be considered science despite its lack of literature support – argue that peer-review is a conspiracy, that scientific consensus should be ignored, yadda yadda – and the Defense did this somewhat – but these are tougher arguments to make, and put the court in the position of having to disregard widely-accepted scientific standards in order to rule in favor of ID.

(And mostly, the important term is “intelligent design.” “Irreducible complexity” has numerous inconsistent definitions, and some of them are uncontroversial and boring, like the idea that some biological systems break if you knock out parts. Luskin tries to argue that Minnich discussing knockout experiments = irreducible complexity = unevolvable irreducible complexity (the interesting kind, if it existed) = support for ID in the scientific literature. But this is a chain of argument (a) not really made at trial (at least not the part about knockout experiments being literature support for ID), and (b) disputing the last two parts of this chain of inference was one of the major points of Plaintiffs’ scientific experts, and of the cross-examinations of Behe and Minnich. To accept this Luskin sub-argument, the Court would have had to agree with Behe & Minnich that “irreducible complexity = unevolvable irreducible complexity (the interesting kind, if it existed) = support for ID” – but it didn’t. The Court found the Plaintiffs’ experts more convincing. And the Court even explicitly concluded in its decision that these two steps of the argument didn’t work, and explained in some detail why not. Tough shakes.)

* Regarding Behe & Snoke (2004), an additional point is worth making, besides the one about not mentioning ID. Luskin says:

Judge Jones repeatedly (and wrongly) claimed that ID had not published peer-reviewed scientific articles. A variety of these peer-reviewed scientific articles were documented to him during the course of the trial, including a 2004 paper that Darwin-doubting scientists Michael Behe and David Snoke published in the journal Protein Science. That paper cast doubt on the ability of gene-duplication to produce new functional protein-protein interactions. But Judge Jones dismissed Behe and Snoke’s article paper because “it does not mention either irreducible complexity or ID.”

This isn’t quite the whole story. Behe & Snoke 2004 was the best article the ID side could come up with at trial – the other articles Luskin thinks Judge Jones should have considered mostly weren’t even entered into evidence. As the best article available (cited by both Behe & Minnich), the Plaintiffs didn’t just dismiss it based on it lacking the words “intelligent design” – rather, they subjected it to a detailed cross-examination, and got key admissions from Behe on the stand. See footnote 17 of the Kitzmiller decision:

17. The one article referenced by both Professors Behe and Minnich as supporting ID is an article written by Behe and Snoke entitled “Simulating evolution by gene duplication of protein features that require multiple amino acid residues.” (P-721). A review of the article indicates that it does not mention either irreducible complexity or ID. In fact, Professor Behe admitted that the study which forms the basis for the article did not rule out many known evolutionary mechanisms and that the research actually might support evolutionary pathways if a biologically realistic population size were used. (22:41-45 (Behe); P-756).

Whoops! A whole chunk of the Behe cross was devoted to the Behe & Snoke’s article, it’s online here. Given what the Court concluded about the best article the ID guys could muster, why should anyone think additional articles would help?

* As for the other scientific articles Luskin thinks Judge Jones scandalously ignored – what evidence was there for them in the trial? Luskin has scoured the entirety of the testimony and evidential exhibits put before the Judge at trial, and the very best thing he could come up with was this quote from Minnich’s testimony:

I think yesterday there was, as I mentioned, there were around, between, I don’t know, seven and ten. I don’t have the specific ones. But Dr. Axe published one or two papers in the journal Biological Chemistry that were specifically addressing concepts within intelligent design. Mike Behe had one. Steve Meyer has had one. So, you know, I think the argument that you’re not publishing in peer reviewed literature was valid. Now there are a couple out there. How many do we have to publish before it is in the literature and being evaluated? I mean, do we have to have 25? 50? I mean, give me a number.

(Minnich Testimony, Day 21, AM, pg. 34)

…and that’s it. The IDists own witness could do no better than making a vague reference to “between…seven and ten. I don’t have the specific ones”, and then only vaguely listing 4, one of which was either Behe’s philosophy article or the Behe & Snoke 2004 article, two were Axe articles that don’t mention ID articles either, and one was Meyer (2004). Neither the Axe articles, nor the Meyer 2004, were ever entered as exhibits and subjected to cross-examination. Compare this to the Plaintiffs’ experts, who cited things like cover-article Nature articles, put them into evidential exhibits, and quoted them into the record, making strong, unambiguous pro-evolution statements; and did similarly with numerous scientific societies condemning the validity of ID.

Luskin seems to think that Judge Jones should have given these articles strong consideration. But there were colossal problems with asking the court to do this.

* Most of Luskin’s alleged pro-ID scientific articles were not actually entered into evidence, and thus were (a) not even citable in the decision, if the judge had wanted to (he didn’t have the references in the exhibit list!), and (b) were not opened up to cross-examination during sworn testimony, like all evidence should be at trial. Articles not entered into evidence include Meyer 2004, Axe’s articles, and Jonathan Wells’s Rivista di Biologia article – if I recall correctly, the only alleged pro-ID articles entered into evidence were the Behe & Snoke 2004 Protein Science article, and Behe’s pieces in philosophy journals). If they had been entered into evidence, the Plaintiffs would have been happy to rebut them – since none of them except Meyer 2004 actually constitute an instance of an (allegedly) peer-reviewed article that actually concludes ID is correct.

* Meyer 2004, if it had been introduced into evidence, had numerous problems, including:

- a statement of lack of support from the very journal that published it;

- the fact that it wasn’t a research article or even a review of pro-ID research, instead it was a review of pro-evolution research that attempted to spin out of that a case for ID;

- entering the article into evidence would have opened up the process by which it was published to things like subpoenas, which many of us strongly suspected would have revealed fishy business

- Stephen Meyer himself had been signed up as an expert witness, and then withdrew, thus avoiding the cross-examination which all of testifying experts were subjected to

- Meyer and the DI attempted to get Meyer’s evidence and the list-of-allegedly pro-ID publications into the court’s back door via a friend-of-the-court brief which initially included Meyer’s expert witness report. This was a sneaky manuever, and just made the court mad.

* Minnich’s only published “pro-ID” piece was Minnich & Meyer 2004, a conference proceedings article which Minnich himself admitted during deposition was not submitted to standard peer-review, because it was a conference proceedings submission. And didn’t mention ID explicitly either.

* On top of all this, we had Behe’s devastating admission:

Q. And, in fact, there are no peer reviewed articles by anyone advocating for intelligent design supported by pertinent experiments or calculations which provide detailed rigorous accounts of how intelligent design of any biological system occurred, is that correct?

A. That is correct, yes.

(Behe Testimony, Day 12 AM, pg. 22-23)

* Finally, friend-of-the-court briefs, even if they don’t attempt sneaky things like the Discovery Institute did, are going to be much less influential that courtroom testimony subjected to cross-examination. Anyone can say anything they want in such a brief, without fear of contradiction or informed criticism. So Luskin’s argument that the publications were found in the DI’s amicus brief is also not very credible, even apart from the problems with the publications themselves.

As an aside: throughout his posts over the 5 years since the Kitzmiller trial, Luskin again and again fails to realize that court decisions are based on what evidence is entered at trial, where both sides have equal opportunity to enter evidence and testimony, and subject it to cross-examination. This is really surprising, considering Luskin is supposed to be a lawyer. Decisions are not based on things not entered into evidence, dreamed up via obsessive wishful thinking long after the trial, published by witnesses who withdrew from the trial and thereby avoided cross-examination, or published in friend-of-the-court briefs which are also not subject to cross-examination. I don’t want to help Luskin, but given Luskin’s belief in the credibility of the allegedly “pro-ID” articles that should have been entered into evidence, he would be better off arguing that the Defense did a bad job defending ID, than he would be arguing that the Court should have made a different decision, given the actual evidence actually put before it.

I don’t think that argument would be much better, of course: the Defense actually followed the ID literature closely, talked to its biggest experts, and got ID’s two most credible academics to testify. They did a credible job presenting ID as it was available “off the shelf” in 2005. But there just wasn’t that much on ID’s shelf, especially compared to evolution’s shelf – heck, evolution had a bigger shelf devoted just to the single topic of the evolution of the vertebrate immune system!

Everything I’ve said above is made even worse by the fact that the issue at trial was not “is there some marginal chance that ID might have the tiniest smidgen of credibility, if you squint just right, if you ignore everything inconvenient, and if the wind is blowing the right direction and the moon is in the correct phase.” Rather, the issue was “is this ID stuff on the level of what is typically expected to be taught in public school biology classrooms and textbooks?”

279 Comments

This is why I come to PT. My degrees are in History and Politics, but with a eclectic mix of interests well beyond these humanities.

When I read about actual scientists negating this crap I am instinctively warey of, I feel the world hasn’t quite gone to hell in the proverbial ‘handcart.’ Thanks Nick, RBH and others for making science accessible. Something liars are incapable of. If I had a penny for all the misleading, psuedo-scientific claptrap I have read at UD, AIG, and CMI I would have $4.75:)

I can, just, follow the science here, and that to me is as it should be; knowledge, specifically knowledge which is of relevance to humanity as a whole, should be accessible, understandable. I have now become anaesthetized to ID jargon, and, ever since I could identify it, have come to loath its erzatz science.

How will Luskin respond to this science based example, easy, with a predictable mish-mash of scientese, and jargon, half truths, lies of ommission, lies and statistics. Or as the great British PM Disreali said with, ‘Lies, Damn Lies, and Statistics.’

Sorry! Benjamin Disraeli.

Nick,

Excellent summary and overview of creationism in the USA and where it might be leading. Wish that entire issue was available for public access, merely as a pedagogical tool I could have used last night when I met two young supporters of Ken Ham on the subway, apparently visiting New York City on some Christian youth movement. Had an interesting chat in which I politely, but firmly, explained why evolution is scientifically valid and creationism, especially Intelligent Design, isn’t.

Let me mildly dissent on one point. You don’t need to show new genes arising to show evolution putting new adaptive information into the genome. In Meyer’s (and Dembski’s) terms new “specified information” can be put into the genome by natural selection choosing a better allele out of those available in a population. If we have (say) 4 alleles, A, C, G, and T, at one site in a DNA sequence, and each is equally frequent, and their fitnesses are equal, except for one which has a higher fitness, then natural selection in a large population will preferentially pick the good one and fix it.

The result is an increase in the genome of precisely the kind of “specified information” Meyer is talking about, an increase in fitness, in the degree of adaptation. (To the local Information Police, let me add that we don’t necessarily have to relate this to either the Shannon or the Kolmogorov definitions of information, if instead we just talk about whether the population has increased its degree of adaptation, i.e. its fitness). That is really the point at issue in Dembski’s and Meyer’s arguments – can natural selection increase fitness and make the organism better adapted?

I gave exactly such an example in my article (which you can see here) 3 years ago (see the section on Generating Specified Information). It is unfortunate that so many biologists miss the point – they implicitly concede the point that if no new locus arises, new information cannot have arisen. They should not concede that – it isn’t true.

BTW note that I have phrased this as natural selection “putting information into” the genome to avoid getting tangled in the later Dembski/Marks disputation about whether the information is really new, or whether having the four alleles have different fitnesses means that the information is somehow already there lying around in the shape of the fitness surface. That is in any case not really the issue.

Oh no, the return of the Luskito … a creature with the body of an insect and the head of a creationist.

For once I am impressed with creationists, since we have proof that they have developed a matter transporter.

Joe Felsenstein said: The result is an increase in the genome of precisely the kind of “specified information” Meyer is talking about, an increase in fitness, in the degree of adaptation.

To nitpick, this definition itself is problematic, as it defines information as a relational quality with the environment, and thus the “specified information” in a genome could change without the genome itself changing, if the environment altered to reduce fitness. Unless I’m mistaken, this approach would have to say that the “specified information” in a fish species genome reduces to zero if the pond the species is in dries up. That is definitely contrary to the Shannon notion of information, and I’d argue to any sensible notion as well.

A most excellent article. I’m in awe of the effort that went into it. I always take the easy way out and ignore Casey’s more convoluted postings because: (a) from long experience I’m confident they’re worthless; (b) it’s way too much work to dig in and refute them; and (c) only creationists pay attention to his writings anyway.

Still, it’s very good to have a professional take-down. Well done!

Nick, your article kinda reminds me of the Clinton Whitehouse.

Tulse said:

Joe Felsenstein said: The result is an increase in the genome of precisely the kind of “specified information” Meyer is talking about, an increase in fitness, in the degree of adaptation.

To nitpick, this definition itself is problematic, as it defines information as a relational quality with the environment, and thus the “specified information” in a genome could change without the genome itself changing, if the environment altered to reduce fitness. Unless I’m mistaken, this approach would have to say that the “specified information” in a fish species genome reduces to zero if the pond the species is in dries up. That is definitely contrary to the Shannon notion of information, and I’d argue to any sensible notion as well.

I agree that using “infomation” by itself in this sense would be problematic. However, as Joe pointed out, the ID term “specified information” is used in exactly that sense (WHEN it is actually used in any sort of coherent sense, which is rare enough): information that serves a specific adaptive purpose, i.e. makes a species or individual better adapted to it’s current environment. Thus, the fact that this “specified information content” must be environment specific is not surprising - and the fact that a fish who is in a drying up pond loses all it’s SI reveals the hilarious stupidity of the “Specified Information” concept in the first place!

One of the problems with “specified information” – there are many – is that it is possible to identify information associated with a function, but not so easy to identify information without knowing what the function is.

For example, a file of 100 numbers. Specified information? On the fact of it, one might say yes. If it is then explained that the 100 numbers were all randomly generated, would it no longer be specified information? One might agree. However, if it was then said that the file was a test set to exercise a number-crunching routine – I used to produce such files to validate routines I wrote for customers – then would it be specified again?

But in any case, would there be anything in the file to distinguish it from a “real world” data set? No, it would still be a file of a hundred numbers.

And, following the creationist argument, if the dataset was from a natural phenomenon, would the specified complexity argument hold that it is intelligently designed? MEANING that it is unexplainable by science, it’s just “magic pooferism” at work? And that would cover ANY natural phenomenon.

The specified complexity argument has no core and so it can be used to make any point desired.

My take on “specified” is that it was introduced to avoid the “Texas sharpshooter fallacy” (see the Wikipedia article http://en.wikipedia.org/wiki/Texas_[…]oter_fallacy). That allows the ID advocate to say that he’s taken that into account - without having to go through the work of taking that into account.

It’s worth noting the number of articles that use “evolution” as a keyword. This obviously dwarfs intelligent design publications. I might point out that over 700 articles use the key phrase “cold fusion.”

BTW note that I have phrased this as natural selection “putting information into” the genome to avoid getting tangled in the later Dembski/Marks disputation about whether the information is really new…

“information,” as used by IDists, is a classic example of equivocation. The word starts as a metaphor for a gene sequence (or allele). The design proponent then applies some selected definition of information to argue that some abstract condition cannot be met.

Then the metaphor is reified and voila, an observable physical phenomena becomes impossible because in the metaphorical world it violate some abstract rule.

It doesn’t even matter what the rule is, because the point is to obfuscate rather than to argue.

As far as I’ve seen, there’s only one rule, the “Law of Conservation of Information”, though it gets manipulated in different forms – always ending up as “only an intelligence can create information.”

It is no more than a rephrasing of the Paley fallacy: “complexity equals Design”.

I’ve seen it expressed as “random mutation plus natural selection cannot crete complex specified information.”

I forget why. I suspect it’s just because.

It comes in many forms. “But if it can’t, then what can?”

“Only an intelligence!”

Oh, silly me, I did have to ask.

One of the more enlightening questions that can be asked of ID/creationists is if “information” interacts with matter. Does it form mutual potential energy wells with other information or with matter? Can it scatter off matter? Can particles of information form orbits around matter, or vice-versa?

In other words, how does information influence or determine the spatial arrangements of matter?

MrE, useful but maybe a bit too arcane for them.

Personally, I’ve got quite a bit of mileage in asking them how I would calculate the “information” in an arbitrary computer program.

So far the response has been sheer RESENTMENT. I’m catching them flat-footed – they haven’t been able to get their heads together and come up with a baloney answer yet, so they just cry “UNFAIR!”

midwifetoad said:

I’ve seen it expressed as “random mutation plus natural selection cannot crete complex specified information.”

I forget why. I suspect it’s just because.

Well, didn’t you know that it’s because randomly spewing letters on a piece of paper will not likely produce a Shakespeare sonnet? How dumb are you! :o)

Change the smiley from “:o)” to “:poe)”.

MrG said:

Change the smiley from “:o)” to “:poe)”.

sorry, I haven’t been around long enough yet to know what “poe” refers to?

How about “loki troll”?

Poe’s law (religious fundamentalism) — “Without a winking smiley or other blatant display of humour, it is impossible to create a parody of fundamentalism that someone won’t mistake for the real thing.”

Wikipedia

And Loki troll: prankster postings, named in honor of the Norse trickster demigod Loki.

thanks - I’m with the Poes and Lokis!

MrG said:

MrE, useful but maybe a bit too arcane for them.

Indeed; that is exactly the point.

They either avoid the question completely, or they accuse you of not understanding information.

And when you follow up by asking them to give the definition of information, you still won’t get an answer.

MrG said:

MrE, useful but maybe a bit too arcane for them.

Personally, I’ve got quite a bit of mileage in asking them how I would calculate the “information” in an arbitrary computer program.

So far the response has been sheer RESENTMENT. I’m catching them flat-footed – they haven’t been able to get their heads together and come up with a baloney answer yet, so they just cry “UNFAIR!”

hilarious!

I had a similar experience when I engaged kairofocus on UD a little while ago: when he was spewing some random numbers out of his usual garbled repertoire of information theory as alleged proof that evolution couldn’t happen, I asked what event exactly was he calculating the probability for in his number juggling. He resorted to pouting, accusing me of changing the subject of the thread, and descending into “fever swamps of distortion”…

MrG said:

MEANING that it is unexplainable by science, it’s just “magic pooferism” at work?

Let’s not drag Jesus’ sexuality into this.

Mike Elzinga said:

And when you follow up by asking them to give the definition of information, you still won’t get an answer.

Creationists honestly seem to think they’ve hit the motherlode with information theory, that now they’ve got the real decisive argument. When asked any question that reveals the hollowness of the argument, they tend to react with a certain degree of shock, like it just doesn’t compute.

I think they’ve gone about as far with information theory as they can. Not that they’re about to give it up; it’s just that they can only keep reshuffling the same variations on the argument over and over again. In the meantime, the opposition is gradually accumulating an ever-increasing arsenal of counterarguments that renders the uselessness of creationist information theory increasingly obvious.

madbat.089 said:

thanks - I’m with the Poes and Lokis!

Be careful. No matter how over-the-top you make a Loki troll posting, you will find a real creationist who can over-the-top it.

You’re regurgitating garbage, Joe G -

Joe G said:

Information the “I” in CSI:

http://intelligentreasoning.blogspo[…]-in-csi.html

What is ID:

http://intelligentreasoning.blogspo[…]ve-been.html

Biological evolution- what is being debated:

http://intelligentreasoning.blogspo[…]s-being.html

Evoluion is “directed” in the sense that a population has selective pressures from physical and biological factors. Physical factors include climate and geography. Biological factors include availability of food, potential and actual predators and competition with other species for available resources. Natural Selection could “force” a population to go toward a better “adaptive peak”, and as a result yield either incremental or relatively fast (“sudden” in the fossil record) genomic and morphological shifts that might result in speciation (the production of new species).

These are facts which the “brilliant” Bill Dembski and his colleagues, like the equally intellectually-challenged Robert Marks, seem most incapable of understanding:

So have I. He ducked me in person immediately after the Spring 2002 American Museum of Natural History Intelligent Design debate when I asked him how he could calculate confidence limits for his “Explanatory Filter”. Nor could he answer that question when I received unsolicited e-mails from him in early December 2007. Instead he boasted that he knew scores of Texas high school principals who wanted only Intelligent Design, not evolution taught in their science classrooms.

In reply, I asked him if any of these principals could teach a rigorous freshmen-only introductory physics course, which the current principal of Stuyvesant High School - the premier American high school devoted to mathematics, science snad engineering (one of only two American high schools that have at least four Nobel Prize laureate alumni) - does (And he has taught physics there as a teacher and as the school’s principal for over two decades.). I was greeted with silence. Nor could he answer me when I noted that during a Fall 2005 alumni gathering (as the Kitzmiller vs. Dover Area School District trial was in progress), he pledged that Intelligent Design would never, ever, be taught there as long as he continued serving as Stuyvesant’s principal, since it is not scientific (NOTE TO THOSE WHO MAY BE ROLLING THEIR EYES AT MY MENTION OF MY HIGH SCHOOL ALMA MATER: privately I know of several Pharyngulite posters who agree with me that I am well within my rights to mention Stuyvesant High School for the reasons I have stated. It speaks volumes about your stubborness to concede that I had raised two valid points with Dembski regarding Stuyvesant, and these were points he was unable to answer.):

Joe G said:

Malchus:

No, I believe that Dembski actually claims that ID is not a mechanistic theory. Are you quite sure that you are familiar with his writings?

I have corresponded with him.

Have you?

Saying ID is not a mechanistic theory means it is not about any specific design mechanism…

Anybody can correspond with Dembski.

Get him to admit an error? That’s really rare.

You would have also noted that any attempt to question Joe about the details results in a huge hissy fit.

Malchus said:

I have examined your blog - that’s why I could note its singular lack of traffic; and read both authors. They fail to provide a functional, workable, meaningful definition of “information.” Apparently you are unable to remedy their deficiency. In that case, this discussion isn’t going to last very long.

Joe G said:

Malchus:

I would like to see Joe produce a coherent definition of information that would be useful in this context. The entire ID community has failed lamentably to address this point.

Meyer addresses it in “The Signature in the Cell”.

Dembski has also addressed it-

And I have blogged about it.

And yes fnxtr the debate is that “evolution” is not a blind, undirected process.

This is pathetic- you chumps rail against ID even though it is clear that you don’t have a basic grasp of what ID claims.

Joe G said:

MrG:

I don’t see anything in there about how I would calculate the amount of information in an arbitrary computer program.

The best you can do is count the bits the program contains.

Do you know how to count?

A bad programmer may write twice as much code as a good coder (and visa-versa) are you saying that one program contains twice the information even though they perform the same function? Also you mention that if you duplicate the genes you don’t duplicate the information but there are cases where the two duplicated genes will produce twice as much product.

He also has his other e-mail addresses listed on his CV posted where he teaches at the Southwestern Baptist Theological Seminary in Texas:

Wesley R. Elsberry said:

Anybody can correspond with Dembski.

Get him to admit an error? That’s really rare.

Wesley, I guess he ignored you on that point. Right? Typical mendacious behavior from him IMHO:

Wesley R. Elsberry said:

Anybody can correspond with Dembski.

Get him to admit an error? That’s really rare.

John Kwok said:

Wesley, I guess he ignored you on that point. Right? Typical mendacious behavior from him IMHO:

Wesley R. Elsberry said:

Anybody can correspond with Dembski.

Get him to admit an error? That’s really rare.

Yes, Dembski ignored that piece of information for a while.

Isn’t he still ignoring you? But if he is, that’s his standard operating procedure:

Wesley R. Elsberry said:

John Kwok said:

Wesley, I guess he ignored you on that point. Right? Typical mendacious behavior from him IMHO:

Wesley R. Elsberry said:

Anybody can correspond with Dembski.

Get him to admit an error? That’s really rare.

Yes, Dembski ignored that piece of information for a while.

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This page contains a single entry by Nick Matzke published on July 12, 2010 10:38 PM.

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