Legacy route: /cs/theft_over_toil/ The advantages of theft over toil: the design inference and arguing from ignorance John Wilkins and Wesley R. Elsberry examine the claims made by "intelligent design" advocate William A. Dembski for his "explanatory filter". This is an online version of the 2001 Biology and Philosophy peer-reviewed paper, one of the few papers in the peer-reviewed literature that is explicitly about "intelligent design". John S. Wilkins 1 , Wesley R. Elsberry 2 Unedited version. Published as: Wilkins, John S, and Wesley R Elsberry. 2001. The advantages of theft over toil: the design inference and arguing from ignorance. Biology and Philosophy 16 (November):711-724. Abstract Intelligent design theorist William Dembski has proposed an "explanatory filter" for distinguishing between events due to chance, lawful regularity or design. We show that if Dembski's filter were adopted as a scientific heuristic, some classical developments in science would not be rational, and that Dembski's assertion that the filter reliably identifies rarefied design requires ignoring the state of background knowledge. If background information changes even slightly, the filter's conclusion will vary wildly. Dembski fails to overcome Hume's objections to arguments from design. Keywords Intelligent design, Bayesian inference, natural selection, Darwin, Dembski Sam Spade enters his office to find "Fingers" Finagle, a reformed safecracker, standing in front of his open safe holding the priceless artifact the Cretan Sparrow that Spade was looking after for a client. "Fingers" insists he did not crack the safe, but merely spun the combination dial a few times idly, and it opened by itself. Spade knows from the promotional literature that came with the safe when he bought it at the Chump end-of-season sale that is has over 10 billion (1010) possible combinations, and that only one of these will open it. Moreover, he knows that the dial must be turned in alternating directions, not - as "Fingers" claims he did - in the same direction repeatedly. What does Spade know about this situation? Is the safe open by design, or by accident? William Dembski (1998) thinks he can answer this question definitively. Dembski has proposed an "explanatory filter" (EF) which, he claims, enables us to reliably distinguish events that are due to regularities, those that are due to chance, and those that are due to design. Such a filter is needed, he believes, to determine the reason for cases like Spade's safe, the discrimination of signals by the Search for Extra-Terrestrial Intelligence project (SETI) that are due to intelligent senders from those that are caused by ordinary phenomena like quasars, and most critically, whether all or some aspects of the biological world are due to accident or design. In other words, Dembski's filter is a reworking of Paley's design inference (DI) in the forensic manner of identifying the "guilty parties". We will argue that Dembski's filter fails to achieve what it is claimed to do, and that were it to be adopted as a scientific heuristic, it would inhibit the course of science from even addressing phenomena that are not currently explicable. Further, the filter is a counsel of epistemic despair, grounded not on the inherent intractability of some classes of phenomena, but on the transient lacunae in current knowledge. Finally, we will argue that design is not the "default" explanation when all other explanations have been exhausted, but is another form of causal regularity that may be adduced to explain the probability of an effect being high, and which depends on a set of background theories and knowledge claims about designers. Spade's immediate intuition is that "Fingers" has indeed burgled the safe, but Spade is no philosopher and he knows it. He has, however, read The Design Inference by the detective theoretician, Dembski, and so he applies the filter to the case in hand (literally, since he has "Fingers" by the collar as he works through the filter on the whiteboard). The EF is represented as a decision chart (p37): HP events are explained as causal regularities. If it is very likely that an event would turn out as it did, then it is explained as a regularity. IP events are events which occur frequently enough to fall within some deviation of a normal distribution, and which are sufficiently explained by being between those extremes. The rolling of a "snake eyes" in a dice game is an IP event, as is the once-in-a-million lottery win. SP events come in two flavours: specified and unspecified. Unspecified events of small probability do not call for explication. An array of stones thrown will have some pattern, but there is no need to explain exactly that pattern, unless the specifiable likelihood of a pattern is so small that its attainment calls for some account. If an array of stones spells out a pattern that welcomes travellers to Wales by British Rail, then that requires explanation; to wit, that the stones were placed there by an employee of British Rail, by design. The minuscule probability that a contextually significant message in English would occur by chance is ruled out by the specified complexity of that sentence. This Dembski calls the Law of Small Probabilities - specified events of small probability do not occur by chance. 3 Spade, though not given to deep reflection, nevertheless studied statistics at the Institute of Forensic Studies, and so he wishes to be thorough. He traverses the filter step-by-step. E: the safe door is open. HP? No, the door regularly remains locked without intervention, and "Fingers" did not know the combination. IP? No, there is no significant chance that random spinning of the dial would happen on the combination. Even had "Fingers" chanced to spin the dial the right directions - an IP event - the chance is one in ten billion (10-10) that he would have happened on the combination. The chance is effectively zero, using the Law of Small Probabilities. SP? Yes, the event has a very small probability. sp/SP? Yes, the prior probabilities are exactly specified in addition to being very small. Conclusion: "Fingers" opened the safe by design, not by accident. "Fingers" is duly charged and arraigned for burglary. He engages the renowned deep thinking lawyer, Abby Macleal, and she defends him with skill. Before we get to the courtroom scene, however, let us go back in time, over a century, to the musings of a young naturalist. This naturalist - call him Charles - is on a voyage of discovery. He has read his Paley; indeed, he might almost have written out Paley's Evidences with perfect correctness by memory. Although he has not heard of Dembski's filter, he knows the logic: whatever cannot be accounted for by natural law or chance must be the result of design. Young Charles encounters some pattern of the distribution and form of a class of organisms - let us suppose they are tortoises - on an isolated archipelago and the nearest large continent. Each island has a unique tortoise most similar to the autochthon of the neighboring island and the island closest to the continent is most similar to that species. On the basis of the biological theories then current, he knows that there is no known process that can account for this pattern. It is so marked that one can draw a tree diagram from the continental form to the islands, and it will match a diagram showing the similarity of each form to the others. What should Charles rationally infer from this? Let us assume for comparative purposes that Charles is in possession of the filter; he will therefore reason like this: E: Species are distributed such that morphological distance closely matches geographic distance. HP? No, there is no regularity that makes this distribution highly probable. IP? No, the likelihood of such a distribution is extremely low. SP? Yes, it is a very small probability (made even smaller as more variables are taken into account). sp/SP? Yes, the problem is (more or less) specified. Conclusion: The tortoises have the biogeographic distribution and formal distribution they do by design. By Dembski's framework, Rational Charles should have ascribed the tortoises' situation to intelligent agency, and his subsequent research should have been directed to identifying that agency, perhaps by building balsa rafts to test the likelihood that continental sailors might have taken varieties now extinct on the continent and placed them each to an island according to some plan. An even more parsimonious explanation, and one more agreeable to the Rev. Paley's natural theology, might be that a single agent had created them in situ, along a plan of locating similar species adjacent to each other, which has the added virtue of explaining a large number of similar distributions known throughout the world, as Alfred, a later young voyager, was to note. Unfortunately for the progress of rational science, Actual Charles is not rational in this manner. He infers that some unknown process accounts for this distribution as a regularity, instead of inferring design. He irrationally conjectures that all the variants are modified descendants of the continental species, and that the morphological and geographical trees are evidence of a family tree of species evolution; and thus the theory of common descent is born. Charles is, rightly, castigated by his friends for irrationality and lack of scientific rigor. His leap to an unknown process is unwarranted, as is his subsequent search for a mechanism to account for it. Were his ideas to be accepted, perhaps out of fashion or irreligion, science would be put back for more than a century until Dembski came along to put it right. Lest this seem to be a parody of Dembski's views, consider his treatment of the evolution versus creation debate and the origins of life. Dembski (wrongly) conflates the two, treating the origins of life as a test case for the validity of evolutionary theory (it isn't - even if the major groups of living organisms had separate origins, or were created by an agent, their subsequent history could and would have an explanation in terms of "undesigned" evolution). Creationists - the actual ones that do reject evolutionary theories in the way that Rational Charles should have in the 1830s - challenge what Dembski putatively does not, that species share common ancestors with their closest relatives and that natural selection accounts for adaptation. As an adjunct to their arguments, they also, along with Dembski, give credence to the "calculations" of the probability that prebiotic processes would spontaneously form the building blocks of life (the LIFE event), especially of genetic molecules, that various authors have given. Dembski discusses Stuart Kauffman's (and others') blocking of the design inference (Kauffman 1993, 1995) with the following argument: Premise 1: LIFE has occurred. Premise 2: LIFE is specified. Premise 3: If LIFE is due to chance then LIFE has small probability. Premise 4: Specified events of small probability do not occur by chance (the Law of Small Probabilities). Premise 5: LIFE is not due to a regularity. Premise 6: LIFE is due to regularity, chance, or design (the filter). Conclusion: LIFE is due to design. Of Dawkins' arguments (Dawkins 1986: 139, 145-146) that there is a lot of "planetary years" available because there are a very large number of planets in the universe in which LIFE might have occurred and a lot of time available on each, Dembski says "... because Dawkins never assigns an exact probability to LIFE, he never settles whether LIFE is a high probability event and thus could legitimately be attributed to a regularity" (p58, italics added). Therefore, he says, we may infer that Dawkins accepts Premise 5! But what Dawkins actually says is that the improbability of life occurring had better not exceed the probability that it arose by chance on any one of the available number of planets on which it might have done. This sets a minimum bound to the probability of life, and Dawkins says that on (then) current knowledge, he doesn't know how probable life is. For all he knows, life is indeed due to a regularity. Kauffman's work on the dynamics of autocatalytic polymer sets supports the notion that the upper bound to the probability of life occurring is very high indeed, and life is to be "expected" in appropriate conditions. Dembski's comment? This is a "commitment". The implication is that it is a mere belief or act of faith on Kauffman's part. In fact, it is considerably more than that, and the real problem for origins of life researchers is not to find a possible scenario, but to decide which of a growing number of them holds the most promise, or which combination. But Dembski's filter makes it unnecessary to even try. 4 So, let us return now to the courtroom drama in time to hear Abby Macleal rebut prosecutor Pearl E. Mason's case. Abby calls retired Chump engineer Lachlan (Locky) Smith to the stand, and elicits from him the information that the Chump safe Spade owns has an inherent design flaw. If the tumbler is spun five times or more, centrifugal force will cause the lock to spontaneously open. Spade suddenly realizes why he got it so cheap. "Fingers" is acquitted, and initiates civil action for mental anguish and loss of reputation. Clearly, the background information has changed the probability assignments. At the time Spade found "Fingers" at the open safe, he was in possession of one set of background information, Bi. The probability of the event E requiring explanation led to a design inference. After Smith's testimony, a different set of background information, Bj, comes into play, and so the filter now delivers a "regularity" assignment to E. Suppose, though, that Smith had delivered yet another background set, Bk, by testifying that the model in question only actually used two of the five cylinders in the lock. Given that there are 100 possible numbers that might match the successful open state for each cylinder, the probability of a random opening is now 10-4, which is a much higher probability, given the number of Chumps of that model in use in the Naked City (particularly after Chump's massive sell-off of that model to clear the faulty stock). Now the same filter delivers us a chance explanation given Bk. The point is that Dembski's filter is supposed to regulate rational explanation, especially in science, and yet it is highly sensitive to the current state of knowledge. One single difference of information can change the inference from design to regularity to chance. This goes to the claim that Dembski's explanatory filter reliably finds design. Reliability, Dembski tells us, is the property that once an event is found to have the property of "design", no further knowledge will cause the event to be considered to have the property of "regularity" or "chance". What the filter lacks that real-world design inferences already have is a "Don't know" decision. If we can say of a problem that it is currently intractable or there is insufficient information to give a regularity or chance explanation now, then the Filter tells us we must ascribe it to design if it is specifiable. But it can be specifiable without the knowledge required to rule out regularity or chance explanations. This is clearly a god of the gaps stance, and it can have only one purpose: to block further investigation into these problems. Supposing we do insert a "don't-know" branch: where should it go? There is an ambiguity in Dembski's treatment of his argumentative framework. The Explanatory Filter is written about as if it describes a process of analysis, but Dembski's further argumentation is cast in terms of a first-order logical calculus. In a process, we would come to a "don't-know" conclusion after some evaluation of alternatives, but in a logical framework, there is no temporal dependency. We will here ignore the demands of process and concentrate on the logic. As Dembski's filter eliminates hypotheses from high probability to low probability, clearly an inability to assign a probability in the first place makes the decision the first branch point. So if, on Bi, the probability of E is undecidable, that needs to be worked out first: Undecidable probabilities lead us to a blocking of the inference at all. No further inferences can be drawn, and no design is required to explain any event for which there is no assignment. However, even if E is decidable on Bi, that in no way licences the expectation that on Bj or Bk those probabilities will remain fixed. For example, when Dawkins wrote in 1986, the state of knowledge about prebiotic chemical reactions was sparse; the range of possible RNA codes and molecular alternatives was not properly understood. As knowledge has grown, our estimate of the probability that some ribonucleotides, or perhaps ribonucleoproteins, or even polyaminoacids, might enter into protobiotic autocatalytic cycles has become much higher. Some even think that in a geologically short time after the cooling of the earth's surface, with the right conditions (themselves now expected to be of reasonably high probabilities on earth) life is almost certain to arise. Perhaps, then, we need another branching at each decision, leading to "Don't-know-yet". As Dembski's probabilities are Bayesian assignments made on the basis of a set of prior knowledge and default hypotheses, this seems to be a perfectly reasonable move. However, it has one glaring problem - it blocks any inferences of design, and that is too much. There are well attested cases of design in the world: we humans do things by design all the time. So an explanatory filter had better not exclude design altogether. How can it be included here? When is a design inference legitimate? The problem with a simple conclusion that something is designed, is its lack of informativeness. If you tell me that skirnobs are designed but nothing else about them, then how much do I actually know about skirnobs? Of a single skirnob, what can I say? Unless I already know a fair bit about the aims and intentions of skirnob designers, nothing is added to my knowledge of skirnobs by saying that it is designed. I do not know if a skirnob is a good skirnob, fulfilling the design criteria for skirnobs, or not. I do not know how typical that skirnob is of skirnobs in general, or what any of the properties of skirnobs are. I may as well say that skirnobs are "gzorply muffnordled" 5 , for all it tells me. But if I know the nature of the designer, or of the class of things the designer is a member of, then I know something about skirnobs, and I can make some inductive generalizations to the properties of other skirnobs. The way we find out such things about designers is to observe and interact, and if we can, converse, with them. In this way we can build up a model of the capacities and dispositions of designers. Experience tells me that a modernist architect will use certain materials to certain effect. Lacking any information about modernist architects leaves me none the wiser knowing that an architect is modernist (in contrast to other architects). Once we have such knowledge of designers, though, what we can say about them is that they generate regularities of outcomes. We know, for example, what the function of the Antikythera Device, a clockwork bronze assembly found in an ancient Greek shipwreck, was because we know the kinds of organisms that made it, we know the scientific, religious and navigational interests they had, we know about gears, and we know what they knew about the apparent motions of the heavens. Hence we can infer that the Antikythera Device is an astrolabe, used for open sea navigation by the stars, or a calendrical calculator, or both (de Solla Price 1974). But suppose it was found by interstellar visitors long after humans went extinct. What would they know about it? Unless they had simil


Theory Is As Theory Does

Legacy route: /cs/theory_is_as_theory_does/ Theory Is As Theory Does Ian F. Musgrave, Steve Reuland, and Reed A. Cartwright examine the claims of the Michael Behe and David Snoke paper published in Protein Science in 2004. While the goal of the Behe and Snoke paper is to generate impressive-looking improbabilities for the evolutionary development of a class of biochemical features, it turns out that use of biologically realistic numbers in their model shows that evolution is almost certain to develop them. Posted by Reed A. Cartwright on October 11, 2004 11:06 AM by Ian F. Musgrave, Steve Reuland, and Reed A. Cartwright “There’s precious little real biology in this project,” Mr. Behe said. For example, he said, the results might be more persuasive if the simulations had operated on genetic sequences rather than fictitious computer programs. Michael J. Behe was commenting in The Chronicle of Higher Education (Kiernan 2003) on a paper reporting that digital organisms could evolve irreducibly complex systems without intervention (Lenski et al. 2003). Ironically, Behe has just coauthored a theoretical paper with David W. Snoke on the evolution of complex molecular adaptations that has “precious little real biology” in it. William Dembski has already stated that Behe and Snoke’s research “may well be the nail in the coffin [and] the crumbling of the Berlin wall of Darwinian evolution” (Dembski 2004). Despite the common claim made by “intelligent design” activists that evolution is in trouble, they have so far been unsuccessful in presenting their arguments to the scientific community. Is this the long-awaited peer-reviewed publication which will finally do it? No. Although some in the “intelligent design” community tout Behe and Snoke’s paper as the long-awaited theoretical paper (Discovery Institute 2004) , it contains no “design theory”, makes no attempt to model an “intelligent design” process, and proposes no alternative to evolution. In reality Behe & Snoke (2004) is an unmemorable investigation of neutral drift in protein and nucleic acid sequences. As we will show, the paper cannot even support the modest claims it does make. Behe has argued that certain biochemical systems or structures have a property he calls “irreducible complexity” (Behe 1996). Irreducible complexity is an update on the old anti-evolutionist argument of “What good is half a wing?” Simply put, the idea is that all the components of a system must be present before the system can accomplish its current function, and, therefore, there is no gradual, step-by-step way for natural selection to construct the system being considered. Behe’s arguments have attracted significant criticism , and Behe has recast his definition of “irreducible complexity” from time to time to attempt to deal with these criticisms. One of these re-definitions of “irreducible complexity” introduces the notion of unavoidable gaps in a stepwise progression of adaptive evolutionary intermediates of a system, such that the only means of bridging the gap is via neutral evolution (Behe 2000). The current paper is apparently an attempt to quantify just how improbable this process of bridging gaps via neutral mutation might be, and thus we may expect that when Behe makes arguments along these lines in the future he will point to this paper as the justification for saying that evolution does not have the time available to fashion “irreducibly complex” structures. Although Behe and Snoke are “skeptical” of the ability of “Darwinian processes” to account for the evolution of complex biochemical systems (Behe & Snoke 2004), there is substantial scientific evidence for the conclusion that complex biochemical systems can and have evolved on earth. There is direct experimental research (Hall 2003). There are observed instances of it occurring in nature (Copley 2000, Seffernick & Wackett 2001, Johnson et al. 2002). There is also much evidence from comparative studies (Melendez-Hevia et al. 1996, Cunchillos & Lecointre 2003 as two examples). However, we don’t have enough space to fully explore the large amount of data that Behe and Snoke’s “skepticism” must overcome. We have our hands full just explaining some of the manifold ways in which Behe and Snoke’s model fails to represent molecular evolution. The flavor of Behe and Snoke’s paper may be gauged by the fact that the authors are skeptical of Darwinian processes to produce complex structures, yet use a model which largely ignores Darwinian processes. In the following sections we will examine some of the more questionable aspects of Behe and Snoke’s paper. Contents Contents One True Sequence? Evolution of DPG Binding Subfunctionalization vs. Neofunctionalization Rho-Oh! How unlikely is the evolution of MR features? Applying Behe & Snoke’s equations to the DPG binding site example Conclusion Acknowledgements References One True Sequence? Theory is rather hard to review, and it is not uncommon for problematic theory to get published. For this reason, post-publication review is very important to sifting good theory from bad. We cannot emphasize this enough. The theoretician among us only trusts theory that either has withstood the test of time or has been satisfactorily replicated by him. (This paper satisfies neither.) There are two issues in creating good theory: (1) getting the modeling right and (2) using assumptions relevant to nature. Sometimes the former dooms theory, but in most instances it is the latter. We believe there are some issues with the modeling in the paper, but investigating them is too complex for this essay. However, even a rough reading of the paper makes it clear that Behe and Snoke’s work and the conclusions they draw are not relevant to nature. Behe and Snoke are attempting to estimate how long and how large of a population it would take for a protein in the absence of selection to evolve a new binding site or other complex feature. They assume up-front that multiple amino acid substitutions would be required before the new feature can be preserved by natural selection. They call this a “multiresidue” feature (MR). Behe and Snoke are modeling the formation of a completely new binding site in a duplicated protein. While this process is important in generating some kinds of new function, in the majority of duplicated proteins, existing binding sites are either modified to act on new substrates (for example the expansion of the protein kinase (Manning et al. 2002, Caenepeel et al. 2004, Waterston et al. 2002) and G-protein coupled receptor families in vertebrates) or new catalytic mechanisms (the TIM family of proteins; Schmidt et al. 2003, Gerlt & Babbitt 2001). (See Musgrave 2003 for more discussion about the evolution of binding sites. See Musgrave 2004 for a discussion on disulfide bonds.) Duplication of enzymes and modification of their existing binding sites can produce quite complex pathways; for example the clotting cascade is due to duplication of proteolytic enzymes with a subsequent change in substrates (Miller 1999 and the references therein). Behe and Snoke use five parameters to model the neutral evolution of their sequences: the number of mutations needed for the multi-residue feature (λ), the ratio of null mutations (ones that create a pseudogene) to needed mutation (ρ), the number of duplicate genes in the population (N), the selection coefficient of the multi-residue feature (s), and the instantaneous rate of point mutation per site (ν). (Contrary to what Behe and Snoke claim, ν is not a per generation rate of nucleotide mutation.) In the model, selection only acts upon a duplicate gene’s multi-residue feature when it has acquired the particular λ “compatible” mutations and none of the λρ mutations that would nullify it. Behe and Snoke implement nullification by assuming that the duplication is deleted when the first “compatible” mutation (forward or backward) occurs after the first null mutation occurs. The deleted duplication is instantly replaced by a new gene that has no compatible and no null mutations. We call this “reset on null.” After a bit of math and some simulations Behe and Snoke estimate the average time to first appearance (T f ) and the average time to fixation (T fx ) of a multi-residue trait under various parameter sets. They use these results to conclude that point mutations plus selection cannot explain the evolution of multi-residue traits. However, the model has many restrictive assumptions that prevent it from supporting the conclusion that Behe and Snoke make. In reality, the paper says that if you have a protein function that requires two or more specific mutations in specific locations in a specific gene in a specific population, and if the function is not able to be acted on by natural selection until all mutations are in place and if the only form of mutation is point mutation, and if the population of organisms is asexual, then it will take a very large population and very long time to evolve that function. This is not unexpected. Furthermore, this paper follows the fallacious fascination with the “one true sequence” that is popular in the “intelligent design” community (for example Meyer 2004). Behe and Snoke end their paper with the following conclusion: Although large uncertainties remain, it nonetheless seems reasonable to conclude that, although gene duplication and point mutation may be an effective mechanism for exploring closely neighboring genetic space for novel functions, where single mutations produce selectable effects, this conceptually simple pathway for developing new functions is problematic when multiple mutations are required. Thus, as a rule, we should look to more complicated pathways, perhaps involving insertion, deletion, recombination, selection of intermediate states, or other mechanisms, to account for most [multi-residue] protein features. (Behe & Snoke 2004 p11) No matter how much Behe and Snoke want to make this conclusion, it is simply not warranted by any work presented in the paper. The evolution of new functions is not a process that requires a certain target to be hit. There can be multiple new functions that any starting protein can acquire. Likewise, there can be multiple ways of acquiring any given function. And finally, evolution doesn’t happen in a single population; it happens in multiple populations at the same time. Calculating that it would take a long time for a specific new function to evolve from a specific gene with a specific set of mutations in a specific population in no way suggests that it would take a long time for any new function to evolve in any gene from any set of mutations in any population. Behe and Snoke’s work attempts to show the former, but in their discussion they conclude the latter. Their conclusion simply does not follow. Behe and Snoke do mention this early in their discussion: … because the simulation looks for the production of a particular MR feature in a particular gene, the values will be overestimates of the time necessary to produce some MR feature in some duplicated gene. In other words, the simulation takes a prospective stance, asking for a certain feature to be produced, but we look at modern proteins retrospectively. Although we see a particular disulfide bond or binding site in a particular protein, there may have been several sites in the protein that could have evolved into disulfide bonds or binding sites, or other proteins may have fulfilled the same role. For example, Matthews’ group engineered several nonnative disulfide bonds into lysozyme that permit function (Matsumura et al. 1989). We see the modern product but not the historical possibilities. (Behe & Snoke 2004 p11, emphasis original) Unfortunately Behe and Snoke ignore their own caveat in the rest of their discussion, resulting in an entirely unjustified conclusion. At the very least, it biases their estimates of population sizes and generations considerably upward. A more realistic scenario, in which multiple targets could be reached, would result in a much smaller number of generations and/or smaller required population sizes. (To be fair, it would be more difficult to model such a scenario.) At worst, the fact that they only consider specific changes at specific locations makes their model meaningless because it assumes a fundamentally different process than the one that occurs in nature. The rest of this essay will be divided into two parts. The first part will explore the assumptions that Behe and Snoke use to build their model, and why those assumptions bias their model toward their favored conclusion. The second part will discuss the likelihood of MR features evolving, and will include a calculation for Behe and Snoke’s flagship example using realistic parameters. Evolution of DPG Binding Let us now look at one of Behe and Snoke’s own examples, the evolution of β-hemoglobin’s 2,3-diphosphoglycerate binding site. Hemoglobin is the protein that caries oxygen in vertebrate blood. In most vertebrates, hemoglobin is a tetramer composed of two α and two β protein chains. There is much evidence that the α and β chains evolved from duplicates of an ancestral globin chain (Li 1997 pp289-292). In mammals, frogs, and reptiles there is a small pocket which binds the organic phosphate molecule 2,3-diphosphoglycerate (DPG) at the interface between the two beta chains. (Reptiles use inositol pentaphosphate (IPP) as the physiological modulator, but their site binds DPG very effectively.) If a molecule of DPG is bound to hemoglobin, it helps stabilize the tetramer, reducing the hemoglobin’s affinity for oxygen. Therefore, DPG regulation allows hemoglobin to release more oxygen in capillaries. DPG is produced by a shunt pathway that prevents glycolysis (the pathway that “burns” glucose to produce energy) from producing the energy molecule ATP when levels of ATP are high. This means that DPG levels are positively correlated with the oxygen levels. When oxygen levels are high, ATP levels are high, and DPG levels are also high. When oxygen levels are low, ATP levels are low, and DPG levels are also low. Therefore, low levels of oxygen favor increased oxygen affinity of hemoglobin. In sum, DPG regulation ensures that hemoglobin can work efficiently even when oxygen levels are low. Behe and Stoke refer to DPG binding as an example of a function that must have involved multiple neutral mutations, citing Li (1997). At the beginning of their discussion, Behe and Stoke state: Some features of proteins, such as disulfide bonds and ligand binding sites, … are composed of multiple amino acid residues. As Li (1997) points out, the evolutionary origins of such features must have involved multiple mutations that were initially neutral with respect to the MR feature. (Behe & Snoke 2004 p7, emphasis added) However, this is simply not supported by Li (1997): The emergence of a new function in a DNA or protein sequence is supposedly advantageous and is commonly believed to have occurred by advantageous mutations. However, acquiring a new function may require many mutational steps, and a point that needs emphasis is that the early steps might have been selectively neutral because the new function might not be manifested until a certain number of steps had already occurred. (Li 1997 p427, emphasis added) Note the change from “might have been” to “must have involved.” Li (1997) in fact never says early mutational steps “ must have been.” He points out that at least one mutation to form the DPG binding site was selectable, the one that generated histidine at position 2. He also says “Of course one cannot rule out the possibility that either Lys82 or His143 or both have evolved because of a selective advantage other than DPG binding” (p 428). As we shall see below, this is in fact the case. Behe and Snoke overemphasize must , creating a misleading impression that there is authoritative support for the concept that all amino acids of a site must be in place for a selectable function to occur. This is exactly the opposite of current knowledge. It is interesting to point out that in their introduction Behe and Snoke actually quote from this section of Li (1997), yet manage to misread it. As Li (1997) noted, the binding site for diphosphoglycerate in hemoglobin requires three residues. The population size required to produce an MR feature consisting of three interacting residues by point mutation in a duplicated gene initially lacking those residues would depend on the number of nucleotides that had to be changed—a minimum of three and a maximum of nine. (Behe & Snoke 2004 p10) This gives the misleading impression that Li (1997) states that the DPG binding site requires all 3 amino acids, and only those amino acids, in place before selectable binding occurs. Unfortunately for Behe and Snoke, the DPG binding site is a good example of plasticity and redundancy which highlights a key flaw in their “one true sequence” assumption. Li (1997), the very article they quote, gives examples of alternate sequences that work well, thus invalidating the assumption that only their “one true sequence” will have that function. The modern mammalian DPG binding site is formed from 3 amino acids on the beta chain. Histidines (H in the single amino acid code ) at position 2 and 143, and lysine (K in the single amino acid code) at position 82. All these amino acids are basic; we can call these amino acids responsible for DPG binding the HKH triad. Behe and Snoke imply that you must have the HKH triad in place for both binding and selection to take place. Now, while all of these sites are required for good binding, there are mammals without these 3 that do quite nicely. You can replace basic histidine with basic arginine ® and a functional DPG binding site is obtained at either position 2 or 143 (Bonaventura et al. 1975). So you can have R KH and HK R and still get DPG binding with selectable function. There are even more variants with selectable function. Mice have an asparagine (N) at position 2, giving an N KH triad. Lemurs make do with leucine ( L KH). Ruminants have methionine (M) at position 2. The M KH variant is much less sensitive to DPG, but still has binding and selectable function (Angeletti et al. 2001). Even with a limited number of vertebrates, we can show that the actual example cited by Behe and Snoke, the DPG binding site, does not in fact follow their “one true sequence” model. But it gets more interesting than that. As one example, Li (1997) has argued that the precursor to modern hemoglobins that can bind diphosphoglycerate did not have any of the three amino acid residues involved in the interaction. (Behe & Snoke 2004 p11) This is true, but highly misleading. DPG binding is at the end of a sequence of development of allosteric modulation by anions and organic phosphates paralleling the development of tetrameric hemoglobin. While most vertebrate hemoglobins are α 2 β 2 tetramers, most species of hagfish, a primitive jawless fish, have monomeric hemoglobin. In other species of hagfish, the oxygenated form of hemoglobin is a monomer, and the deoxygenated form is a dimer. In all known species of lamprey, another primitive jawless fish, the oxygenated form of hemoglobin is a monomer, and the deoxygenated form is either a dimer or tetramer. In sharks, the oxygenated form is the αβ dimer, and the deoxygenated form is a tetramer. In bony fish, frogs, lizards and mammals hemoglobin is the familiar α 2 β 2 tetramer. In most vertebrates, organic phosphates modulate the oxygen affinity of hemoglobin, but most vertebrates use ATP, the energy bearing phosphate produced by oxidative metabolism, to modulate hemoglobin oxygen affinity (Nikinmaa 2001, Coates 1975a). Mammalian DPG binding evolved not from scratch, as implied by Behe and Snoke, but from an ATP binding site. Lamprey hemoglobin is not modulated by organic phosphates, it has PSS (proline, serine) at the equivalent posit


Legacy route: /cs/wein_nfl_review/ Not a Free Lunch But a Box of Chocolates: A critique of William Dembski's book No Free Lunch Richard Wein's review of No Free Lunch argues that Dembski's case is nothing more than a god-of-the-gaps argument dressed up in misleading pseudoscientific mumbo jumbo. Read the full article PDF (off-site) .


Response? What Response?

Legacy route: /cs/wein_what_response/ Response? What Response? Richard Wein replies to William Dembski's reply to Wein's Not a Free Lunch But a Box of Chocolates. How Dembski has avoided addressing my arguments by Richard Wein Copyright © 2002 Version 1.1 [Last Modified: May 28, 2002; change to section 5.1, concerning the LCI] Permission is given to copy and print this page for non-profit personal or educational use. Contents 1. Preamble 2. Peer Review 3. Argument from Ignorance 4. Tornado in a Junkyard 5. Short Responses 5.1 Uniform Probabilities 5.2 The No Free Lunch Theorems 5.3 Specification 5.4 Algorithmic Information Theory 5.5 Predictive Power of Darwinian Evolution 5.6 Explanatory Power 5.7 Wein's Acknowledgment 6. Conclusion he Talkorigins Archive recently posted my critique of William Dembski's book No Free Lunch , entitled Not a Free Lunch But a Box of Chocolates , in which I thoroughly analyzed and refuted his arguments. Dembski quickly responded with an article entitled Obsessively Criticized But Scarcely Refuted: A Response To Richard Wein . Although that article purports to be a response to my critique, it is in fact largely a recapitulation of arguments from No Free Lunch which ignores my refutations of them. In the few instances where Dembski has made a serious attempt to address my arguments, he almost invariably misconstrues them. Not one of my arguments has been satisfactorily addressed. I invite any skeptical reader to cross-check my original critique with Dembski's response. To facilitate such a cross-check, this article uses the same section names and numbers as Dembski's and I provide links to the relevant sections of my critique. All quotations labelled " Wein: " are from my critique and those labelled " Dembski: " are from his response, unless otherwise indicated. 1. Preamble I begin, like Dembski, with some peripheral issues, before getting down to the technical issues in section 3 below . Since he thinks it will work to his advantage here, Dembski makes some appeals to authority. He correctly points out that I have little authority, possessing only a humble bachelor's degree (in statistics). I am happy to let my arguments be judged on their merit, and would not ask anyone to accept them on my authority. Dembski should be wary of casting stones, however, since he himself criticizes experts in fields where he has no qualifications at all, such as biochemistry. He also asks how the eminent endorsers of No Free Lunch can "think NFL is the best thing since sliced bread" if it is as bad as I argue it is. Perhaps he should ask himself how the far more eminent and numerous supporters of evolutionary theory can be so convinced by it if it is as bad as antievolutionists say. The antievolutionist is ill-placed to make appeals to authority when the overwhelming weight of scientific authority is against him. Regrettably, advanced academic qualifications are no safeguard against falling into the trap of pseudoscience, especially when powerful dogmatic convictions are at stake. 2. Peer Review For all the length of his discussion of peer review, Dembski fails to refute any of the facts that I presented ( critique section 8 ). Most important, he is unable to name even one statistician or information theorist who approves of his work in their fields, confirming my suspicion that there are none. While remaining completely silent on the subject of information theorists, Dembski attempts to explain the lack of support from statisticians by suggesting that his statistical claims are more appropriately judged by philosophers of science. I do not dispute that some philosophers have expertise in the field of statistics. But I note that he preferred to claim the support of statisticians when he thought he could get away with it: Interestingly, my most severe critics have been philosophers (for instance Elliot Sober and Robin Collins...). Mathematicians and statisticians have been far more receptive to my codification of design inferences. [NFL, p. 372n2, and " Intelligent Design Coming Clean "] Will he now retract his claim that statisticians have been receptive to his work? In his article, Dembski claims that his method of calculating perturbation probabilities constitutes "a contribution to the applied probability literature." Has he submitted it to a journal of applied probability? Or is this yet another claimed contribution to a technical field that is best judged by philosophers? 3. Argument from Ignorance Dembski begins this section by repeating the claim that his eliminative method of design inference is "inductively sound", based on the same absurd argument which I have already refuted ( critique section 3.6 ). He makes no attempt to address my argument. Next, he repeats his claim that it is possible to rule out unknown material mechanisms: Dembski: Specified complexity can dispense with unknown material mechanisms provided there are independent reasons for thinking that explanations based on known material mechanisms will never be overturned by yet-to-be-identified unknown mechanisms. In No Free Lunch an attempt to dispense with unknown material mechanisms was known as a "proscriptive generalization", but that term appears nowhere in Dembski's current article. It is unclear whether this is just a matter of inconsistency, or whether he now feels the term was an unwise one, suggesting a degree of certainty that he cannot justify. Since he has not acknowledged any change in his argument, I will continue to use his old term for the sake of consistency. I will also assume that his "material" mechanisms are synonymous with the "natural" mechanisms of No Free Lunch . Dembski's frequent unacknowledged changes of terminology do nothing to enhance the clarity of his arguments. The proponent of an argument from ignorance always believes he has sufficient reasons for thinking that his explanation will not be overturned by a yet-to-be-identified unknown mechanism. So the fact that such reasons exist does not save the argument from being one of ignorance. It is an argument from ignorance because it is based not on evidence for the proposed explanation but on the purported absence of any other explanation. In No Free Lunch , Dembski defined arguments from ignorance as being arguments of the form "not X therefore Y" (p. 111). But this is just the type of purely eliminative argument that he is making: not material, therefore design. Whether he eliminates material mechanisms by eliminating known mechanisms individually or by trying to rule out unknown mechanisms through proscriptive generalizations, this is still a purely eliminative argument. Dembski continues by giving an example of a proscriptive generalization against alchemy. But the point is made needlessly, since I have already agreed with Dembski that proscriptive generalizations can be used to rule out some categories of possibilities ( critique section 3.2 ). The point is irrelevant, since these are arguments against possibilities not arguments for a hypothesis. In terms of Dembski's "not X therefore Y", they are a "not X"; they are not a "therefore Y". Scientists did not argue "not alchemy, therefore modern chemistry". Next, we have the example of a combination lock, which I did not discuss in my critique, so I'll consider in some detail here. Dembski argues as follows: Dembski: The geometry and symmetry of the lock precludes that material mechanisms can distinguish one combination from another--one is as good as any other from the vantage of material mechanisms. Not at all. There may be a flaw in the mechanism which causes it to favour some combinations over others. Or the lock may be flawed in some other way. No matter how carefully the lock has been inspected, we cannot completely rule out that possibility. Consider an imaginary scenario in which a safe's combination dial is randomly rotated by natural forces. Let's say the safe is on a rowing boat at sea, and the rolling of the boat is sufficient to make the dial rotate. Now suppose that, while the sole occupant of the boat looks on, the safe springs open. For good measure, suppose that the rower is a locksmith who has thoroughly inspected the lock, found it to be flawless, closed the safe, and thoroughly randomized the dial, all since he has been alone on the boat. How will he explain the spontaneous opening of his safe? Let us say that he appreciates the sheer improbability of the safe opening by pure chance if it was operating to specification, and he rejects that explanation. Does he infer design? Or does he infer that, despite his thorough check, there was a flaw in the mechanism that caused it not to operate correctly? Even though it may seem implausible that the safe sprang open spontaneously, he will surely consider it even more implausible that someone boarded his boat and opened the safe while he was watching it, without him noticing, and he will prefer the former explanation. This is an "inference to the best explanation", or comparative inference. I discussed such inferences at some length ( critique section 3.5 ). Dembski has completely ignored that discussion, and continues to insist that his eliminative inferences are the only option. According to Dembski's logic, the rower should have inferred design, no matter how certain he was that no human agent could have been responsible, even if it required him to posit an unembodied designer. Dembski may respond that the hypothesis of a flawed mechanism is another relevant chance hypothesis which must be eliminated before inferring design. If he does so, he admits the fallacy of his argument that it is possible to "guarantee the security of the lock." I should add that this discussion of proscriptive generalizations has no relevance to Dembski's argument for design in biology, since I have refuted his claim of a proscriptive generalization against Darwinian evolution of irreducibly complex systems (more on this below ). The remainder of Dembski's section is not a response to my critique at all, but is a long passage cut and pasted from one of his articles, with trivial changes. The article in question is the text of his recent talk at the American Museum of Natural History, which he has posted to the Internet under the title " Does Evolution Even Have a Mechanism? " Most of this is a rehash of arguments from No Free Lunch , and does not even belong in a section which purports to be addressing the "Argument From Ignorance" issue. I will address only the parts dealing with that issue. Dembski: Isn't arguing for design on the basis of specified complexity therefore merely an argument from ignorance? Two comments to this objection: First, the great promise of Darwinian and other naturalistic accounts of evolution was precisely to show how known material mechanisms operating in known ways could produce all of biological complexity. So at the very least, specified complexity is showing that problems claimed to be solved by naturalistic means have not been solved. Biologists have never claimed to know precisely how every biological structure evolved. So Dembski is attacking a straw man. Dembski: Second, the argument from ignorance objection could in principle be raised for any design inference that employs specified complexity, including those where humans are implicated in constructing artifacts. An unknown material mechanism might explain the origin of the Mona Lisa in the Louvre, or the Louvre itself, or Stonehenge, or how two students wrote exactly the same essay. But no one is looking for such mechanisms. It would be madness even to try. Intelligent design caused these objects to exist, and we know that because of their specified complexity. Once again, Dembski assumes that all our inferences of design use his eliminative approach. I have already addressed this claim ( critique section 3.5 ). He has not responded. I note that this section of Dembski's article contained not one direct response to any argument of mine. He made no attempt at all to refute my argument that his method of design inference is a purely eliminative argument, an argument from ignorance, and a god-of-the-gaps argument ( critique section 3.3 ). He did not provide definitions of these terms and attempt to show that his method does not match them. He did not even attempt to challenge my definitions of these terms. Nor did he address my argument that the term "specified complexity" is an unnecessary middleman. Let me make that argument even simpler: why not replace all relevant chance hypotheses eliminated --> specified complexity --> design with all relevant chance hypotheses eliminated --> design ? 4. Tornado in a Junkyard I pointed out ( critique section 4.1 ) that Dembski's only probability calculation for a biological system is based on a hypothesis of purely random combination, or what I called a "tornado in a junkyard" scenario. Since such hypotheses are already universally rejected by biologists, I argued that the calculation was addressing a straw man hypothesis, and was therefore irrelevant. Dembski responds: Dembski: Wein therefore does not dispute my calculation of appearance by random combination, but the relevance of that calculation to systems like the flagellum And why does he think it irrelevant? Because co-optation is supposed to be able to do it. Dembski has not read my article carefully enough. I wrote: Wein: No biologist proposes that the flagellum appeared by purely random combination of proteins--they believe it evolved by natural selection--and all would agree that the probability of appearance by random combination is so minuscule that this is unsatisfying as a scientific explanation. Therefore for Dembski to provide a probability calculation based on this absurd scenario is a waste of time. There is no need to consider whether Dembski's calculation is correct, because it is totally irrelevant to the issue. There is nothing here about co-optation. I did not mention co-optation until the following section (where I called it "change of function"). So Dembski has entirely failed to address my argument. Nevertheless, I thank him for confirming that his calculation is based on a hypothesis of random combination. At this point, let me interject a passage from Dembski's talk at the American Museum of Natural History, which he included in his section 3: Dembski: Convinced that the Darwinian mechanism must be capable of doing such evolutionary design work, evolutionary biologists rarely ask whether such a sequence of successful baby-steps even exists; much less do they attempt to quantify the probabilities involved. I attempt that in chapter 5 of NFL (to which I'll return shortly). There I lay out techniques for assessing the probabilistic hurdles that the Darwinian mechanism faces in trying to account for complex biological structures like the bacterial flagellum. The probabilities I calculate--and I try to be conservative--are horrendous and render natural selection utterly implausible as a mechanism for generating the flagellum and structures like it. There is no mention here that the probabilities were calculated under a hypothesis of random combination. On the contrary, there is a distinct implication that they were calculated under a hypothesis involving natural selection. We know this to be untrue, but listeners at the AMNH may have been misled by it. A reader unfamiliar with the tactics of antievolutionists might have thought that it did no harm to include an irrelevant calculation in No Free Lunch . But those of us familiar with antievolutionist rhetoric foresaw that it would be abused in the way we see here. In my next section ( critique section 4.2 ), I refuted Dembski's claim to have found a proscriptive generalization against the Darwinian evolution of irreducible complexity. Since this is an important point, I'll repeat the passage here: Wein: Let us accept, for the sake of argument, that Dembski's definition is tight enough to ensure that IC systems cannot evolve by direct pathways. What has he said on the vital subject that Behe failed to address--the subject of indirect pathways? The answer is nothing. The crux of his argument is this: Dembski [NFL]: To achieve an irreducibly complex system, the Darwinian mechanism has but two options. First, it can try to achieve the system in one fell swoop. But if an irreducibly complex system's core consists of numerous and diverse parts, that option is decisively precluded. The only other option for the Darwinian mechanism then is to try to achieve the system gradually by exploiting functional intermediates. But this option can only work so long as the system admits substantial simplifications. The second condition [that the irreducible core of the system is at the minimal level of complexity needed to perform its function] blocks this other option. Let me stress that there is no false dilemma here--it is not as though there are other options that I have conveniently ignored but that the Darwinian mechanism has at its disposal.[p. 287] Wein: But there is indeed an option that Dembski has overlooked. The system could have evolved from a simpler system with a different function. In that case there could be functional intermediates after all. Dembski's mistake is to assume that the only possible functional intermediates are intermediates having the same function. For once, Dembski appears to have read and understood my argument, but he makes no attempt to refute it. His proscriptive generalization is therefore dead. That leaves him with only appeals to ignorance and red herrings: Dembski: For Wein to account for systems like the flagellum, functions of precursor systems must co-evolve. But that means the space of possible functions from which these co-evolving functions are drawn is completely unconstrained. This provides yet another recipe for insulating Darwinian theory from critique, for the space of all possible biological functions is vast and there is no way to establish the universal negative that no sequence of co-evolving functions could under co-optation have led to a given system. Dembski is not required to establish a universal negative. He just needs to show that a design hypothesis is better, given the available evidence, than the hypothesis of purely natural evolution. But he rejects inferences to the best explanation, insisting on a purely eliminative mode of inference, and that puts him in the unenviable position of either establishing a "universal negative" or admitting there is a category of possibilities he has not eliminated. Since he cannot do the first and does not wish to do the second, he equivocates, first claiming that he has ruled out all Darwinian possibilities (his proscriptive generalization) and then, when it is shown he has not done so, complaining that the expectation was unreasonable. In short, he wants to have his lunch and eat it too! Dembski: Let me suggest that there are further reasons to be deeply skeptical of Wein's co-optation scenario. First, specified complexity is used to nail down design in cases of circumstantial evidence, so if there should happen to be design in nature, specified complexity is how we would detect it. Thus, my probability calculation for the flagellum, in the absence of a counter-calculation by Wein, is prima facie evidence of biological design. This may not provide sufficient reason for convinced Darwinists to abandon their paradigm, but it gives evolution skeptics reason to consider other options, including design. This is the crude argument from ignorance: having eliminated the absurd hypothesis of purely random assembly, we must infer design unless biologists can give an alternative hypothesis detailed enough to allow a probability calculation. Dembski: Second, there is a whole field of study developed by Russian scientists and engineers known under the acronym TRIZ (Theory of Inventive Problem Solving) that details patterns of technological evo


A Presentation Without Arguments

Legacy route: /cs/without_arguments/ A Presentation Without Arguments Mark Perakh evaluates William Dembski's presentation at the CSICOP conference in Burbank, CA on June 21st, 2002. How William Dembski defeats skepticism, or does he? By Mark Perakh [Contributed June 29, 2002, Last Modified July 3, 2002] Starting on June 20, 2002 and through June 23, the 4 th World Conference of Skeptics took place in Burbank, CA. Its main organizer in the USA was CSICOP, which stands for Committee for the Scientific Investigation of Claims of the Paranormal. Although the forum in question was designed as a meeting of skeptics, whose participants are all squarely on the side of genuine science and opponents of all incarnations of creationism regardless of the disguises the latter employs (such as Intelligent Design, Irreducible Complexity, etc) one not quite common feature of that meeting's program was that its organizers invited two prominent proponents of modern modifications of creationism, William Dembski and Paul Nelson, to give talks and to defend their views in an open dispute with two opponents of the anti-evolution movement, Wesley Elsberry and Kenneth Miller. I cannot remember a single conference of creationists wherein the opponents of creationism were scheduled to give talks in an open discussion. The proponents of creationism sometimes accuse their detractors of being doctrinaire adherents of anti-religious bias whose motivation is not pursuing the truth but assaulting the religious faith. Although this may be not the most important point, still it seems worth mentioning that both Elsberry and Miller have asserted that they are not atheists. Professor of biology Miller is a faithful Catholic, and Elsberry, while vigorously defending the theory of evolution, has also said that he is a "theistic evolutionist." Hence, both Dembski and Nelson were given a chance to argue in favor of their position using arguments of substance, based on facts rather than on ideology, in a dispute with opponents who had no reason to assault Dembski's and Nelson's religious beliefs In this brief essay I will discuss only the presentation by Dembski. The text of Dembski's presentation [1] is notable by the almost complete absence of any arguments relevant to the gist of the dispute between ID advocates, like he himself, and the opponents of that theory. Indeed, the only instance of Dembski's touching on the substance of the dispute seems to be a paragraph on page 4 in [1] where Dembski mentions his term of Specified Complexity and unequivocally defines it as a synonym for "specified improbability." Of course, there is nothing new in that statement. Dembski's interpretation of complexity as "disguised improbability" was expressed by him in various forms in many of his articles and books (for example, in [2,3]). This interpretation has been criticized more than once as being contrary to logic and to the accepted mathematical notion of complexity (see the partial list of references at the end of this essay). Dembski's statement illustrates once again his disdainful dismissal of all and every criticism directed at his work. Dembski does not bother to offer any reply to the critique of his interpretation of complexity and steadfastly adheres to his concept which is viewed by many critics as deficient. Continuing in the same vein, Dembski repeats his thesis, suggested by him many times before, that what he calls "specified complexity" is a necessary indicator of design. The fallacy of that statement was demonstrated more than once (for example in [4,5]). Indeed, consider an example discussed several times before. Imagine a pile of pebbles found on a river shore. Usually each of them has an irregular shape, its color varying over its surface, and often its density also varying over its volume. There are no two pebbles which are identical in shape, color and density distribution. I guess even Dembski would not argue that the irregular shape, color and density distribution of a particular pebble resulted from intelligent design, regardless of how complex these shapes and distributions may happen to be. Each pebble formed by chance. Now, what if among the pebbles we find one which has a perfectly spherical shape, with an ideally uniform distribution of color and density? Not too many people would deny that this piece in all likelihood is a product of design. However, it is much simpler than any other pebble, if, of course, complexity is defined in a logically consistent manner rather than in Dembski's idiosyncratic way. A logically consistent definition of complexity is given, for example, in the algorithmic theory of randomness-probability-complexity (and is often referred to as Kolmogorov complexity). Kolmogorov complexity of a perfectly spherical piece of stone is much lower than it is for any other pebble having irregular shape and non-uniform distribution of density and color. Indeed, to describe the perfectly spherical piece one needs a very simple program (or algorithm), actually limited to just one number for the sphere's diameter, one number for density and a brief indication of color. For a piece of irregular shape, the program necessarily must be much longer, as it requires many numbers to reproduce the complex shape and the distributions of density and of color. This is a very simple example of the fallacy of Dembski's thesis according to which design is indicated by "specified complexity." Actually, in this example (as well as in an endless number of other situations) it is simplicity which seems to point to design while complexity seems to indicate the chance as the antecedent cause of the item's characteristics. That is about all Dembski chose to discuss in his presentation with regard to the substance of the dispute. Instead, Dembski dabbles in prophecy. His argument in favor of ID mainly boils down to the references to polls which show that the majority of Americans believe in some form of creationism. This may be true. However, Dembski himself gives an example of astrology which is no less popular in America than ID, but this by no means makes astrology plausible. Dembski is not arguing in his presentation that ID will win the minds because it is true. It will win, predicts Dembski, because the American public is predisposed to believe in ID. The same may be true though for astrology and other fads and fallacies he himself listed as being widespread despite their contradicting scientific data. One more argument by Dembski is that young people are inclined to take the side of innovators, and, since ID-ists are the new guys in town, the sympathy of the younger generation will be with them, thus ensuring their victory. Maybe so. What does it have to do with the merits of ID "theory?" If scientific theories were accepted or rejected by a popular vote, or just by the vote of young people, quantum mechanics, the general theory of relativity and a whole bunch of other great achievements of the human mind would never have had a chance to take their legitimate place in the progress of humankind. On page 4 Dembski argues that his ID theory is "not a crank theory (at least not one that is obviously so)." The sole argument Dembski offers in favor of that statement is that Paul Davies "thinks that it's onto something important," thus disagreeing with those who, like Wesley Elsberry, "think it merely codifies the argument from ignorance." This seems to be a rather weak argument, even by Dembski's standards. The reference to Davies can be interpreted in various ways and is far from endorsing ID as a real scientific theory. Moreover, so what if Davies or any other writer has indeed said something which can somehow be interpreted charitably regarding Dembski's ideas? The position whose strength can be sustained only by such ambiguous references is weak indeed and can be suspected of being crank science with a high degree of likelihood. If all Dembski can say in support of his views is that somebody thinks it has "something to it," it raises a suspicion that he has no factual evidence favoring his suppositions. To show that certain ideas or theories indeed belong in real rather than crank science, one has to subject those ideas to merciless tests, wherein evidence supporting these ideas can be reproduced and independently verified. Dembski and his colleagues in the ID "movement" not only did not ever produce such evidence which could be independently verified, but in fact offered no evidence at all despite having a substantial financial support and a substantial fighting force at their Discovery Institute of Seattle. Instead of supporting his theory by factual evidence and arguments of substance, all Dembski was able to do was to resort to a dubious reference which proves nothing and is largely irrelevant. That is the tenor of Dembski's entire presentation. In a similar manner, Dembski plays with other quotations allegedly supporting his thesis, like a quotation from Mencken on page 2, juxtaposed with a quotation from Gould, which, Dembski implies, contradict each other. These two quotations may or may not contradict each other (and actually they were relating to different situations and therefore their juxtaposition was meaningless). It is, however, always possible to mine a host of quotations on every subject and pretend that they prove something even if they are not relevant to each other in any way. Such play with mutually irrelevant quotations confirms the suspicion that Dembski has no real arguments which would be necessary in a talk to an audience not consisting of such ID adherents who would happily swallow anything seemingly confirming their already held preconceptions. One the main points stressed by Dembski in his presentation is the assertion that Intelligent Design, unlike such fringe pseudo-science as astrology and the like, has by now become firmly "mainstream" in science. In this, Dembski depicts the desired as if it is real. So far, the overwhelming majority of mainstream scientists ignore ID as can be seen by searching through the scientific literature. Practically no scientific magazine has published articles by scientists wherein a discussion of ID and related matters could be found. No references to ID can be found in the mainstream peer-reviewed scientific publications. The ID advocates either publish their productions as popular or semi-popular books and collections by non-scientific publishers or in their own periodicals mostly connected to their Discovery Institute. The only exception seems to be Dembski's monograph [2] published by the Cambridge University Press. Even this book, reportedly, was Dembski's doctoral dissertation in philosophy rather than in science. Regardless of how many times Dembski will repeat his mantra about "mainstreaming" ID, the scientific community has not and will not accept the claims by ID-ists unless and until he and his colleagues present real data supporting their contentions. So far no such data have been presented. The overall level of Dembski's acerbic assault on skeptics can be exemplified by his comment that the letters COP in the abbreviation CSICOP are "not accidental." Is this so? In the absence of real arguments, they may be sometimes replaced with attempts at being witty by using irrelevant puns. Dembski wants the readers to believe that the organization of skeptics is like police trying to muzzle its opponents. Somehow he does not notice the absurdity of such an accusation given the fact that he and his cohort Nelson are freely presenting their views at the meeting organized by the same CSICOP which allegedly is out to prevent the IDists from presenting their views. Maybe in his actual talk Demski said something beyond the irrelevant discussion of the prospects for ID versus evolution to win the minds of masses? It does not seem to be the case. According to the reports by the attendees of the conference, in his actual talk Dembski did not say anything beyond the immaterial quasi-arguments of his posted piece [1]. (This can also be verified by viewing the video tape of the session in question, available from CSICOP). Let me list some of the items that were discussed by Dembski's critics (a partial list of critical reviews of Dembki's literary production includes, but not limited to [4,5,6,7,8,9,10,11,12,13,14,15,16,17]). To some of his critics Dembski never replied in any form. To some others he responded (for example in his latest book [3]) with superficial and largely irrelevant arguments, but he never really replied to the substance of a number of points listed below, which constitute essential elements of his theory. Dembski asserted that complexity is tantamount to low probability. This assertion was rebuffed more than by one of the listed critics. Dembski never replied to that critique. Dembski asserted that his Explanatory Filter never produces "false positives." This assertion was rebuffed by several of the listed (as well as by some not listed) critics. Dembski never replied to them. (It can be argued though that in his latest book [3] Dembski by implication concedes that false positives can be produced by his Explanatory Filter after all but he still does not admit this explicitly). Dembski announced a supposedly new important law – the so-called Law of Conservation of Information. More than one critic argued that the law in question does not exist. Dembski never replied to those critics. Dembski widely used a concept of what he called Specified Complexity. More than one critic argued that the concept in question is meaningless in the sense it has been used by Dembski. The latter never replied to this critique. The same can be said about Dembski's concept of Complex Specified Information (CSI). Dembski insists that design can be reliably inferred if low probability of an event is combined with its specification. More than one among the listed critics argued that the specification as defined by Dembski has no reasonable interpretation. Dembski never responded to that critique. There are other items claimed by Dembski, subjected to critique to which Dembski never responded while he continues to promote the same criticized concepts and assertions. In his presentation, Dembski condescendingly suggested a program of action for skeptics if the latter wish to defend their position against ID. In his uncompromising self-confidence Dembski seems not to realize that if he suggests a new, allegedly revolutionary theory, the burden of proof is on him and on his colleagues in the ID camp. It is ID-ists who need to provide evidence, any evidence, in support of their position. It is precisely the absence of evidence for the ID theory that makes skeptics (read: mainstream scientists) to reject ID as an unsubstantiated attempt to overturn the facts established by science. If Dembski or any of his colleagues showed any reasonable evidence supporting their views, then, beyond doubts, scientists would be much more receptive in regard to their theory. So far this has not happened. Therefore, rather than suggesting what skeptics should do to defend their views from the assault by ID, Dembski should better think of how to search for any believable proof of his own so far arbitrary and dubious assertions. By inviting Dembski and Nelson to give talks at the 4 th World Skeptics Conference, its organizers offered Dembski a chance to reply to his critics on the matters of substance and to defend his position in front of a diversified audience, mostly not very friendly to his views. By taking the floor at the conference in question, Dembski put himself in an unenviable position of denying a simple fact obvious to all – he was complaining about skeptics suppressing his views while speaking to the same skeptics who provided to him the forum. Acknowledgements I would like to thank Brian Spitzer, Pete Dunkelberg, and Wesley Elsberry for constructive remarks regarding the initial version of this article. References [1] William A. Dembski, [online], Skepticism's Prospects for Unseating Intelligent Design , http://www.iscid.org/papers/Dembski_SkepticismsProspects_062102.pdf , accessed on June 22, 2002. [2] William A. Dembski, The Design Inference , (Cambridge University Press, 1998). [3] William A. Dembski, No Free Lunch – Why Specified Complexity Cannot Be Purchased without Intelligence , (Rowman and Littlefield, Lanham, Maryland, 2002). [4] Mark Perakh, A Consistent Inconsistency, [online], www.talkreason.org/articles/dembski.cfm , accessed on June 22, 2002 [5] Mark Perakh, A Free Lunch in a Mousetrap, [online], www.talkreason.org/articles/dem_nfl.cfm , accessed on June 22, 2002 [6] Richard Wein, [online], http://website.lineone.net/~rwein/skeptic/whatswrong.htm , accessed on November 22, 2001 [7] Richard Wein, Not a Free Lunch But a Box of Chocolate, [online]. www.talkreason.org/articles/choc_nfl.cfm , accessed on June 22, 2002. [8] Matt Young, [online], www.pcts.org/journal/young2002a.html , accessed on March 10, 2002. [9] Victor J. Stenger, [online], http://spot.colorado.edu/~vstenger/Found/04MessageW.pdf , accessed on January 17, 2002. [10] Robert T. Pennock, Tower of Babel (Cambridge, MA: The MIT Press, 2000). [11] Taner Edis, [online], www.csicop.org/si/2001-03/intelligent-design.html , accessed on January 17, 2002. [12] Eli Chiprout, [online], http://members.aol.com/echiprt/dembski.htm . Accessed on July 25, 2001 [13] Wesley R. Elsberry, [online], www.infidels.org/library/modern/science/creationism/dembski.htm , accessed on November 22, 2001 [14] Wesley R. Elsberry, [online], www.talkreason.org/articles/inference.cfm , accessed on June 22, 2002. [15] Thomas D. Schneider, [online], www.lecb.ncifcif.gov/~toms/paper/ev/dembski/claimtest.html , accessed on November 22, 2001. [16] Branden Fitelson, Christopher Stephens and Elliott Sober, Philosophy of Science , 66, (1999): 472. [17] John S. Wilkins and Wesley R. Elsberry, The Advantages of Theft over Toil: The Design Inference and Arguing From Ignorance, Biology and Philosophy, v.16, 711 (2001).


You Missed a Spot, Dr. Dembski

Legacy route: /cs/you_missed_a_spot_dr_dembski/ You Missed a Spot, Dr. Dembski Original: You Missed a Spot, Dr. Dembski William A. Dembski recently published a book, The Design Revolution: Answering the Toughest Questions About Intelligent Design . The subtitle offers a promissory note, and so do several of the blurbs on the dust jacket and front matter to the effect that Dembski covers herein all the criticisms that have been offered about "intelligent design" and Dembski's particular contribution, "specified complexity". This is untrue, as I will attempt to demonstrate. Dembski has gone so far as to challenge critics to find criticisms that he missed entirely. I responded earlier , pointing out various difficulties in proving a negative as Dembski had asked for. At that point, I had not read the whole text of TDR carefully, and thus did not wish to offer something that might be discussed on pages I had not yet gotten to. But now I have read the whole thing, and one rather glaring omission is evident to me. Throughout the book, Dembski touts "specified complexity" as a reliable marker of "intelligent design" and says that certain biological systems, such as the flagellum of E. coli bacteria (please note, Dr. Dembski, that the species name is NOT capitalized) have "specified complexity". This completely sidesteps and ignores a criticism I raised at the CTNS/AAAS "Interpreting Evolution" conference at Haverford College, June 17th, 2001, in a presentation on Dembski's ideas. I pointed out that Dembski's program of submitting events of known design and unknown cause to his "explanatory filter/design inference" were no test at all of the reliability of his apparatus, calling it a "verificationist program". To actually test his methodology Dembski and other ID advocates would have to examine cases where we had biological systems with a sufficiently detailed evidential record that even the ID advocates would agree beforehand that natural causes were sufficient to explain their deveolpment. Only then would running them through Dembski's "explanatory filter/design inference" place the EF/DI at hazard of showing a "false positive" result. I suggested that Dembski and his comrades at the (then) Discovery Institute Center for Renewal of Science and Culture concentrate upon systems like the impedance-matching system of the mammalian middle ear and the Krebs citric acid cycle, which exemplified complex systems for which biologists have accumulated a strong set of empirical data concerning their development. I reiterated the criticism in a web page critiquing Dembski's book, "No Free Lunch". TDR is bereft of any hint that this criticism impinged upon Dembski's mental processes at all. At least, there's no hint that I see. To the contrary, there are still the explicit statements that the EF/DI is somehow verified by Dembski's program of feeding it examples that cannot possibly put it at risk of failure. The bogus and completely unfounded "reliability" that Dembski claims thereby is used in several places in TDR to assert strong claims about the need to incorporate Dembskian notions of "design" into biology. That seems to me to be avoiding a tough question about "intelligent design". Further links: Haverford conference video: William Dembski's presentation My presentation Dembski and Elsberry panel Dembski and Elsberry audience Q&A My PowerPoint file for presentation


ID-Commentaries

A collection of commentaries on ID-texts, written by Morgan Grey.

Legacy route: /people/mgrey/ ID-Commentaries This is a collection of my weekly ID-Commentaries, originally posted on the DebunkCreation discussion group . ID-Commentary: "Who's Got the Magic?" (10/21 2001) ID-Commentary: "Disbelieving Darwin -- And Feeling No Shame!" (10/12 2001) Dembski `retracts' comments about Dennett (10/20 2001) ID-Commentary: "Another Way to Detect Design?" (10/7 2001) ID-Commentary: "Why Evolutionary Algorithms Cannot Generate Specified Complexity" (10/2 2001) ID-Commentary: "Explaining Specified Complexity" (9/16 2001) Other on-line articles. Some of the articles I refer to in my ID-commentaries have been placed on-line here, due to the ever-changing structure of the internet.


ID-Commentaries

Legacy route: /people/mgrey/IDC.html ID-Commentaries This is a collection of my weekly ID-Commentaries, originally posted on the DebunkCreation discussion group . ID-Commentary: "Who's Got the Magic?" (10/21 2001) ID-Commentary: "Disbelieving Darwin -- And Feeling No Shame!" (10/12 2001) Dembski `retracts' comments about Dennett (10/20 2001) ID-Commentary: "Another Way to Detect Design?" (10/7 2001) ID-Commentary: "Why Evolutionary Algorithms Cannot Generate Specified Complexity" (10/2 2001) ID-Commentary: "Explaining Specified Complexity" (9/16 2001) Other on-line articles. Some of the articles I refer to in my ID-commentaries have been placed on-line here, due to the ever-changing structure of the internet.