What did the Discovery Institute get up to in 2010? Part 1: Research

2010 has come and gone: the year of the iPad, the year of the drama surrounding Wikileaks, the year I first gained university access to scientific papers… But what happened in the intelligent design movement during that fateful year? Did anything important happen to the Discovery Institute, the infamous Seattle-based ID think tank?

I’ll be going back through the Internet archives to find out what 2010 held for the ID movement, what “research” was published, what books were released, what lawsuits exploded, among other things. I wrote a similar piece on 2009 a year ago, but this one will be slightly different – I won’t be going through the year by month, I won’t be touching on everything that happened, only the important things, and I’ll be breaking the piece into a series of blog posts, not just one massive one.

So, where shall we begin? Ah yes, the research.

Research

It’s important to note here that none of the papers published by intelligent design proponents in scientific and philosophical journals in 2010 were actually proper pro-ID papers, in that they didn’t offer positive evidence for intelligent design and instead all attacked evolutionary theory, which is a useless tactic in the scientific community, where competing hypotheses must stand up on their own independent from each other.

The biggest research news, arguably, from the Discovery Institute in 2010 was the opening of a new pro-ID, peer-reviewed online journal: BIO-Complexity. I did some research last year into its board of editors, the people designated the task of peer-reviewing articles wanting to be published in the journal, and found that all of them (with one vague exception – a scientist from Europe whose ID views I couldn’t discover) were at the very least sympathetic to intelligent design, with a lot of them outright active proponents of ID. Unbiased peer-review? I don’t think so.

However, as biased as the editorial board turned out to be, BIO-Complexity published only four papers in 2010, all of them, as mentioned, failing to provide positive evidence for ID, deciding to attack evolution as a substitute.

Douglas Axe authored the first paper, entitled The Case Against a Darwinian Origin of Protein Folds, and argued that known evolutionary mechanisms can’t account for the adaptive, functional evolution of proteins. But there is no explicit mention of ID anywhere in the paper, raising questions about why Axe couldn’t have simply tried to get the paper published in a proper journal, which would have increased the scientific credibility of his conclusions. No one in the anti-ID community felt that the paper should be taken seriously, given the context in which it was published, lacking proper scientific checks and balances.

The same goes for the second paper, Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness, authored by Ann Gauger, Stephanie Ebnet, Pamela F. Fahey and Ralph Seelke, about a population of E. coli with a doubly-mutated tryptophan synthesis gene failing to evolve back tryptophan synthesis even given a gradual pathway for that evolution. Of course, the paper has nothing to do with intelligent design, with the ID community relying on the implication that, because evolutionary mechanisms failed this apparently simple task, ID is the only other logical alternative.

But the Gauger et al.’s paper isn’t all that revolutionary, it simply demonstrated that evolution sometimes doesn’t work the way you would expect or would like it to, dumping what we would intuitively expect to be the most desirable outcome – regaining tryptophan synthesis – for an immediate fitness gain – inactivating the non-functional tryptophan gene because of over-expression. But again, it’s unclear why it wasn’t submitted to a real journal, given that it doesn’t mention ID.

The third paper published in BIO-Complexity in 2010 was A Vivisection of the ev Computer Organism: Identifying Sources of Active Information, authored by George Montañez, Winston Ewert, William Dembski and Robert Marks, a critique of the evolutionary algorithm ev. I’m not familiar with evolutionary computing at all so I can’t really comment on the paper’s contents, but again: it doesn’t mention intelligent design, so why wasn’t it published in a proper journal? Dembski’s previous work on evolutionary algorithms wasn’t exactly held in any high regard, so it’s hard to imagine the authors justifying their decision by appealing to the sense of prestige the paper would bring to the new journal.

The fourth and final paper was The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Population, authored by Douglas Axe, bringing the proportion of BIO-Complexity papers written by the managing editor up to 50%. The paper is a critique of Michael Lynch and Adam Abegg’s 2010 paper1 on the population genetics of complex adaptation. Like I’ve said before, there’s no real reason I can think of for Axe to publish this in a 0 Impact Factor journal like BIO-Complexity, especially when he’s critiquing the work of major names in the field. However, I have had personal confirmation from Michael Lynch that he will be responding to Axe’s paper in the near future, and I look forward to what wil result.

So that’s all the papers from BIO-Complexity out of the way, but what about other papers that the Discovery Institute promoted as ID breakthroughs into the academic literature?

Michael Behe made waves in the ID community (and nowhere else) when he published a literature review in The Quarterly Review of Biology about adaptive evolution in bacteria and viruses, entitled Experimental evolution, loss-of-function mutations, and “the first rule of adaptive evolution”. The paper didn’t mention ID (of course, as it was published in a proper journal), but was nonetheless trumpeted by ID proponents everywhere as the best thing since sliced bread. It was also widely criticised by the anti-ID community, with some pointing to Behe’s omission of eukaryotic evolutionary mechanisms, others to his omission of some bacterial evolutionary mechanisms, and others taking a holistic approach to his failures.

Behe clearly tried to extrapolate far too much from his literature review, something that the ID community has not yet admitted. And the fact that it didn’t mention ID? “Bah, inconsequential!” they most likely exclaimed.

William Demsbki, Winston Ewert, George Montañez and Robert Marks authored a paper back in April of 2010 in Proceedings of the the 42nd Meeting of the Southeastern Symposium on System Theory (a very obscure journal) entitled Efficient Per Query Information Extraction from a Hamming Oracle, investigating Richard Dawkins’s WEASEL evolutionary simulation from his 1986 book The Blind Watchmaker. Needless to say, it wasn’t pro-ID, or even anti-evolution, taking issue only with Dawkins’s simulation. If the WEASEL simulation doesn’t properly map to real evolution by natural selection (which it doesn’t) then Dembski et al.’s paper wasn’t really news to anyone. And guess what? Nobody paid any attention to it, for at least two reasons – I’m sure you know what they are.

Wolf-Ekkehard Lönnig published a paper (accepted March 2010) in the journal Floriculture and Ornamental Biotechnology entitled Mutagenesis in Physalis pubescens L. ssp. floridana: Some Further Research on Dollo’s Law and the Law of Recurrent Variation, which mentioned ID in a positive light, but failed to justify said light. I’m actually not going to talk about it in any detail, because I already have. Also, the title of that post is my favourite pun of 2010 – I still don’t know how I came up with it.

The last paper I’m going to mention is Information and Entropy — Top-Down or Bottom-Up Development in Living Systems?, authored by Andy McIntosh in the International Journal of Design & Nature and Ecodynamics. Along with Lönnig’s paper, it is one of only two supposedly pro-ID papers from 2010 that explicitly mentioned intelligent design. It’s a silly paper about “intelligence”, “engineering”, “top-down processes” and the like. No wonder no one in the anti-ID community took it seriously. In fact, no one really mentioned it. Was it because of its appalling quality, or because we’re all scared of its implications and hope it will fade away? You decide.

So, that’s all the papers that were published within the intelligent design movement last year. If there were any more, the Discovery Institute didn’t mention them, and if they didn’t mention them then they really don’t matter, to be honest. If Casey Luskin thinks a “pro-ID” paper isn’t worth writing about, he probably found it scrawled on the wall of a public toilet behind a church.

None of the papers made a proper case for intelligent design, most of them were published in obscure journals, and most of them were anti-evolution, not pro-ID. The intelligent design community really didn’t accomplish a lot in terms of research in 2010.

In the next post in this series, I’ll be looking at the lawsuits that took place around intelligent design in 2010. Fun times!

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  1. Lynch and Abegg. The Rate of Establishment of Complex Adaptations. Molecular Biology and Evolution (2010) vol. 27 (6) pp. 1404-1414

21 thoughts on “What did the Discovery Institute get up to in 2010? Part 1: Research

  1. Part 1

    You wrote:

    "I did some research last year into its board of editors, the people designated the task of peer-reviewing articles wanting to be published in the journal, and found that all of them (with one vague exception – a scientist from Europe whose ID views I couldn’t discover) were at the very least sympathetic to intelligent design, with a lot of them outright active proponents of ID. Unbiased peer-review? I don’t think so."

    Ever think of applying that kind of critique to the journals that publish non-ID papers? Do you think you will find bias there? Ceratainly not! They are all so objective and scientific and stuff. Everyone knows that. Right?

    Then you wrote regarding Ann Gauger, et al.'s paper:

    " …it simply demonstrated that evolution sometimes doesn’t work the way you would expect or would like it to…."

    Of course, we know that evolution is a fact, therefore when experiments show that it 'doesn't work the way you would expect' the theory (sorry, fact) says it will — well, sometimes 'stuff' happens, doesn't it? We can't deny the facts, can we? If the fact of evolution is a fact, and other facts just happen to contradict it, then who cares for facts anyhow. We have our theory (ehhh… fact) and all other facts are — well, just unexpected!

    Or else, things just don't act the way we 'would like it to.' This is another scientific principle that Bacon never mentioned when he originally developed the scientific method that we still use today. Must be because he believed in Christ and all that superstitious/supernatural stuff. The principle we use today states: "If you don't like it, it's just plain pseudo-scientific nonsense!" Yeah science! We have to make sure our kids all learn this modern stuff, otherwise they the original founders of science seriously. Then think of how much trouble we will be in if people start believing in God! God forbid!

    Finally you end your "critique" of the paper with:

    "…it’s unclear why it wasn’t submitted to a real journal, given that it doesn’t mention ID."

    You obviously see some merit in the paper, and plus it doesn't mention the pseudo-scientific term "ID." And everyone knows that real journals are governed by unbiased and objective peers and boards. While automobiles are certainly the product of intelligent design, and therefore (1) its influence obviously has a real, detectable and effective existence, and (2) it is possessed and deployed by an intelligent organism (Man), wqe must conclude that ultimately it is merely the result of an unintelligent process of electricity produced by the neruonic activity of the organism. How do we know this? Well, science doesn't know everything. But we can't let anyone doubt that, so we have to come up with some sorry story and state it with unshakeable conviction. Thank God, we can go on to the next issue!

    A third paper on evolutionary computation is again "critiqued" in the same way:

    "… it doesn’t mention intelligent design, so why wasn’t it published in a proper journal?"

    If these papers don't mention ID but are published in the journal of Biocomplexity, then maybe "Biocomplexity" isn't really different from other journals that don't mention ID. That means the only difference that could possibly make a difference is the biased board that makes up "Biocomlexity." Proper journals have completely non biased boards made up of scientists who accept the fact of evolution. All others are improper. QED.

    The fourth paper challenging Jack's idol, Michael Lynch, again receives the same critique:

    "…there’s no real reason I can think of for Axe to publish this in a 0 Impact Factor journal like BIO-Complexity, especially when he’s critiquing the work of major names in the field."

    Gee, I just thought of a reason! Duh! What if Biocomplexity is a real, proper journal and is just trying to establish itself as such in the field of biocomplexity! Imagaine the gall of all those silly IDers!

    [continued part 2]

  2. Paret 2 (cont)

    Regarding Behe's paper, Jack tells us, "It was also widely criticised by the anti-ID community…." Of course, that community is the elite bunch of sophisticated scientists at Panda's Thumb, a completely unbiased and objective group dedicated tooth and nail to Darwin's finches. Of course, we would be amiss if we did not mention as well peppered moths, Haeckles embryos, missing links, etc., etc. Of course we all know how the giraffe gots its long neck by natural selection, even if its young would have died off in that scenario, knowing that giraffe's don't feed their young like birds do. Shhh… we don't want to give away the shop!

    Then we get some brilliant comments about the author's favorite "laughable" scientist, William Demsbki [sic] (or Dembski) as he mentions: "William Demsbki, Winston Ewert, George Montañez and Robert Marks authored a paper" — we can't correctly figure out the spelling of his name, so how can you expect us to ever correctly figure out the mathematics of this Harvard graduate. So for these two reasons, that you all know, we just give a nervous laght out to him!

    Then he comes to some real fodder in Lonning's paper where he "mentioned ID in a positive light, but failed to justify said light."

    What is that failure you may inquire? You have to see his other entry on this topic (the one with the 'witty' title). Simply enough: "What positive evidence does he have for it?" "ID is the default hypothesis for the origin of biological traits, and evolutionary hypotheses must be not just rendered plausible but explicitly demonstrated if they are to falsify it."

    Of course, we all know that evolution is the defalut hypothesis. How dare those nauty IDers try to default the defaulters. Everyone knows how evolution has been positively proven. We've all seen how at least amoebas can crawl out of a population of evolving bacteria. Haven't we? Haven't we? Or have we not? Well, at least bacteria have been shown to evole into other bacteria. If bacteria can evolve into mutated bacteria, then certainly they can evolve into ameobas, plants, insects, animals and man. Why now: Where is your positive prooof that it can't. Show me, and then I will believe you. Give me the evidence that it can't happen that way, or hasn't happened that way, then we will accept your non-evolutionary ideas. Otherwise shut up, accept our default hypothesis as the only scientific explanation, and don't dare question us unless you want our condemnation and contemptuous tounge lashing. Boooh!

    In conclusion, your fair and balanced writing on this subject is to be admired. I am sure that if you exchanged your use of ID with Evolution, and evolution with ID, the paper would come out sounding exactly the same. Just see how balanced it is!

    Good job Jack. XOXOXO

  3. In another post, Jack wrote that if you throw a coin, it is possible to land 10 times in a row with heads up. But why stop at ten? What about heads 20, 100, 1000, or 50 billion times in a row? For him, everything is possible. That's his (mis?)understanding of probability! If that is the kind of authority you defer to, then there is a bridge I would like to sell you.

    • Okay, I'm not entirely sure what you're getting at here.

      Strictly speaking, it IS possible to throw 50 billion times in a row. The probability of doing so is vanishingly small (i.e. I'd bet everything I own in the world, plus all my future earnings, that it wouldn't happen in real life small), but that doesn't stop it from being possible.

      Of course, that's from a theoretical point of view. From a 'real life data' point of view, we'd quickly start to be suspicious of such a long run of heads. That's why there are statistical tools we can use that give us some sort of idea as to whether or not the coin is fair or biased.

      That said, I'm really not sure what your point is — it doesn't seem to have anything to do with anything I said.

      • OK DBP. You got the point when you wrote: "That's why there are statistical tools we can use that give us some sort of idea as to whether or not the coin is fair or biased. "

        If we see a pattern/design arising it is only rational to think that some cause is behind the design. Either we can search out the cause in impersonal laws of nature, or a personal designer/agent. If we choose laws as the cause, however, we have to further investigate why those laws are there, and then it is natural to ask who is the lawmaker.

        Such a situation cries out for an Intelligent Designer. We can no longer claim there is just contingent/ accidental chance at work. We may not be able to prove it by any experiment, but our reason would force us to such a conclusion. So which is the more scientific conclusion about the origin of the universe and Man: gradual evolution by chance, or creation by design? If it is the latter, how is science in any way affected?

        The original founders of science believed in a rational creator, and therefore believed that rational order could be found in nature. Without the first belief, the second was impossible. every scientist has that faith that nature can be rationally explained because it has a rational cause behind it. This is the meaning of science. It takes what appears chaotic and makes some intelligent sense out of it. To claim that everything is due to chance is anti-scientific, against everything that science tries to overcome.

        Hope you get it now.

        • Doesn't the existence of an Intelligent Designer scream out for the existence of an Intelligent Designer designer?

          • Not necessarily. Once our ability in synthetic biology increases to a certain point, we would fit the definition of "Designers" in the ID sense of the term. Do we, at that point, require a Designer to explain our existence? Of course not, the two things have nothing to do with each other.

            • I'm aware of that Jack, I was being facetious. Infinite regression and all that.

            • Excuse me, but you are both making an error because of lack of proper philosophical education. This is not only your poor training, but many of the major scientists as well.

              1. The argument of who made the Designer, is a false one for anyone who has studied even introductory philosophy. The original Designer is God, or the Absolute, which means that God is independent. Therefore God cannot be caused by anything other than God. We or any creature (aliens, angels, etc.) are Relative or fully dependent upon something other than ourselves. for our being or existence. God does not, nor does God ever have such dependence. Thus God is called Absolute – meaning being without condition. Rather all being derives its existence from God.

              Spinoza, with mathematical technique of axioms, postulates, and proofs showed that the Absolute is (in Latin) causa sui – self caused. This means that God is not caused by anything outside of or other than God Himself. This is the very meaning of the Absolute Godhead. This also explains God's free will. Whatever causes itself to move is endowed with free will, and therefore Personality. We also have free will, and therefore we are persons. but we are dependent persons. That is the prime difference between us and God who is independent Person.

              This conclusion is not only found in Spinoza, it is also found in one of the oldest writings in the world, Brahma Samhita, where the Sanskrit says about the Absolute that God is sarva karana karanam, meaning the 'cause of all causes.'

              2. The second philosophical misunderstanding is from Jack who thinks that synthetic biology can create a living organism from its constituents. Kant showed that this can never happen (he summarized his conclusion by stating, "There will never be a Newton of a blade of grass,") In other words, Life is categorically different from mechanical or chemical systems of non-living Matter, Just like cartography and book binding are categorically different from authoring a book. How much time, money and effort is being wasted on the simple fact of scientists not being educated in philosophy.

              Consider the difference between a dead bird and a living bird. A dead bird can be shot our of a canon and its trajectory can be traced using the laws of mechanics. Now try to trace the trajectory of a living bird. It can't be done. Its movement can't be predicted by any of the laws of mechanics, because it is possessed of free will. There is a difference between Life and Matter that can not be bridged by any mechanical or chemical means. Scientific law causes Matter to move by external causes applied to Matter. Life has its own cause within itself, as we mentioned above.

              Self replicating systems are not alive because they are simple chemical reactions. They possess no free will.

              • 1. Is there independent verification for that property of God, because you seem to be defining it into existence. You can't just postulate something without evidence and expect everyone to agree with you.

                2. Do bacteria have free will? If so, how? If not, are they alive? Are single eukaryotic cells alive? Are plants alive? Defining "living" as "having free will" seems to exclude a lot of things we consider to be alive, unless your definition of "free will" is substantially different to what the phrase usually means.

                • 1. I have given the reference to Spinoza and his term 'causa sui.' His book on this subject is called "Ethics." Perhaps you have heard of Google? You can look it up. The proof is well known. The axiomatic framework of his system is found in the first part of his book. It is a great misfortune that scientists today know nothing of philosophy. Why do they still call a PhD a doctor of philosophy?

                  • 2. The concept of a living organism as distinct from a mechanical or chemical system is found in Kant's 'Critique of Judgement.' On what basis do we judge an organism as living as opposed to non living matter? This is a question of epistemology as well as ontology. Without knowledge of these ideas how can you have a rational understanding of experience? I am sure you are innocent. It is your teacher's responsibility to educate you about such things. Unfortuantely your science teachers have a poor fund of knowledge, so what could be expected of their students.

                    All life is necessarily characterized by free will, even cells. The exercise of that freedom, however, may be restricted. For example, if you put a man in prison, his freedom is restricted compared to that of a law abiding citizen. If you ride a bicycle your speed will be slower than that of a man riding in a car. In other words, free willed the living entity (soul) is restriced by the body it occupies. The free will is there, but it can be conditioned by the circumstances. God does not face this type of restriction. That is the difference between God and the finite living entity or soul.

                    • Much work has been done on celluar sentience. I was going to send you some references on this subject, but you never answered my last email to you. Maybe you didn't get that message. If you are ready to get up to speed on cutting edge biological research, outside the restricitve and outdated viewpoint of Victorian science (Darwinism), I will be happy to send you all the references you could want on the new concepts that biologists are turning toward for explaining even the simplest living bacteria.

                      I appreciate the respectful dealings you and the others here show on your blog to those who may disagree with you. This is a rare and admirable quality. So I am quite willing to share with you as much as I know about these subjects.

  4. A few stray observations from a Voice of Reason:

    1. Constantly comparing 'theory' with 'fact' in reference to evolution: sooo 1980s. I don't think even Kirk Cameron trots out that old chestnut anymore. You really should be past that. Is ID a theory, or a fact?

    2. It is hard to understand what you are alluding to in your tortured automobile metaphor but I suspect it's a variation on the old 'tornado through a scrapyard' bit. If there's one thing Creationists are screaming out for (apart from some sort of evidence on which to base their belief) it is originality. I wish that all evolution critiquers would begin their spiels with “Stop me if you've heard this one before" but they never do.

    3. If Biocomplexity is a real, proper journal they may want to consider encouraging contributors from outside of small and extremely infamous cadre of pseudo-scientists whose lack of scientific rigour is a matter of public record.

    4. Your statement regarding giraffes is the least coherent thing I have read all year. Kudos.

    5. Jack's misspelling of Dembski was clearly a typo which could happen to anyone. For example, you misspelt Biocomplexity in one of your paragraphs and I was too classy to mention it.

    6. The fact that Dembski went to Harvard is irrelevant to the fact that his conclusions about evolution are absolute scribble.

    Will, you will do better at debating on this topic if you do two things: Firstly you haven't actually addressed any of Jack's original points. You make vague sarcastic opening statements and then kind of ramble off into obscurity – it is hard for the reader to understand what point you’re actually trying to make in most of your paragraphs. Secondly, you haven't actually shown any positive evidence that would suggest that ID is a legitimate theory. This is why evolution is the currently accepted model; there is positive evidence for evolution by natural selection as it is currently understood. There is no positive evidence for ID whatsoever which is why it is so overwhelmingly, and justifiably, derided by people who are knowledgeable about biological science.

    • Hi Jack Cambrian. You wrote: "The fact that Dembski went to Harvard is irrelevant to the fact that his conclusions about evolution are absolute scribble. "

      You obviously don't have much faith in Harvard educated graduates. I wonder what university you went to that could leave you with such an impression? Or are you just a dilettante? Perhaps you can show us the mathematical proof of your statement if not.

      Dr Dembski seems to me a very nice, gentle and highly intelligent scholar. The books and articles he has written show a sincere and very serious attempt to explain things in probability theory that have not been explored in such depth before. I haven't seen anyone apply equal sweat in trying to disprove what he has written, only some superficial swipes at his impressive mathematical skills and conclusions.

      Anyone can take an a priori stand against anything to do with ID, and then easily dismiss it by repeating the usual unceremonious banter found in evolutionist's circles on this issue. Those who take a more objective view, however, are hardly impressed.

  5. I am merely saying, Will, that Dembski's opinions should stand or fall on their merits not just assumed to be sound because he went to a prestigious school. I would suggest that the vast majority of Harvard graduates accept the fact of evolution. Does their high education impress you enough to assume that they are correct about this?

    • That is not what you are "merely saying." Look at the sentence that was quoted from you. It contains not only a statement about Harvard education, but a judgement about Dembski,s work being "absolute scribble." It seems you don't even understand what you are saying, what to speak about what Dembski is saying.

      Please don't take this negatively. The hope is that you may be more diligent in your appraisal of others work in the future.

  6. I understand perfectly well what I'm saying. I've referred to two points: 1. Dembski went to Harvard. 2.Dembski's conclusions about evolution are gibberish. Both of these facts are entirely independent and verifiably true. Dembski's work has been refuted and rebutted many times over by competent scientists. For example David Wolpert: http://www.talkreason.org/articles/jello.cfm or Jeffery Shallit: http://ncse.com/files/pub/legal/kitzmiller/expert….

    My opinion on Dembski's work being absolute scribble is not exactly a rash judgment, just an honest appraisal of the evidence at hand.

    • I am not in position to judge who is correct in the debate over Dembski's mathematical conclusions. But I object to the pettiness of those who dismiss his serious work with mere slurs. He may or may not be wrong in his calculations, but that can be intelligently stated without condescension. Wolpert felt that Dembski did not rigorously prove his inference to design, but never called his work jibberish. The criticisms of Shallit, who was Dembski's teacher in '87-'88, were countered in Dembski's book "The Design Revolution," and also, at http://www.iscid.org/boards/ubb-get_topic-f-6-t-0

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