Note: this is for the lurkers. WG can just ignore it.

On a couple of threads, Intelligent Design has been bandied about, but has not been discussed or described thoroughly. I have been reading up on it and I would like to do a brief piece with some references for further reading—

First, a quote from Richard Dawkins (2004: 549) describing the basic philosophy of Intelligent Design— “This is the ancient ‘Argument from Design,’ also called ‘Argument from Paley’s Watchmaker,’ or the ‘Argument from Irreducible Complexity.’ I have less kindly called it the ‘Argument from Personal Incredulity’ because it always has the form: ‘I personally cannot imagine a natural sequence of events whereby X could have come about. Therefore it must have come about by supernatural means.’ Time and again scientists have retorted that if you make this argument, it says less about nature than about the poverty of your imagination. The ‘Argument from Personal Incredulity’ would lead us to invoke the supernatural every time we see a god conjuror whose tricks we cannot fathom.”

There are number of proponents if ID, but the key figures are Michael Behe and William Dembski. Both of them accept the current age of the earth and will argue that ID is compatible with common descent. “The central issue, therefore, is not the relatedness of organisms, or what is typically is called common descent. Rather, the central issue is how biological complexity emerged and whether intelligence played an indispensable (which is not to say exclusive) role in its emergence.” (Dembski, 2004: 323). Therefore, young earth creationists, like William Morris, are critical of ID.
Ruse (2003: 315-16) gives a succinct description of Behe’s key concept: “The biochemist Michael Behe, in his best-selling book Darwin’s Black Book, most fully articulated the empirical case. He focused on “irreducible complexity,” which he defined as “a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of these parts causes the system to effectively cease functioning” (p. 39). Behe added that any “irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on” (p. 39). Behe’s examples of irreducible complexity are cited over and over by other proponents. He proposes that a 5-part mousetrap is a good model because if any part is removed it will no longer work as a mousetrap. Behe’s most cited biological examples are: 1) the bacterial motion using a flagellum which is driven by a kind of rotary motor and which has a number of parts including several ring structures in the base and 2) the cascade of biochemical reactions, which are sequentially involved in human blood clotting.

I. I’ll deal with each of these in turn. Prof. John McDonald of the University of Delaware has posted drawings on a web site that show how a mousetrap may be constructed with just three, two, or even just one part. McDonald's mousetrap plans are available at: [udel.edu]. Further Behe (2004: 320-21) states:
“Rather more significant though, is that Behe’s mousetrap shows a misunderstanding of the way natural selection works. No Darwinian would deny that in organisms there are parts which, if removed, would lead at once to malfunctioning or nonfunctioning of the systems in which they occur. The point is not whether the parts now in place could be removed without collapse but whether they could have been put in place by natural selection.
To counter Behe’s artifactual analogy we can think of other artifactual analogies that show precisely how the apparently impossible could be achieved. Consider an arched bridge made from cut stone, without cement, held in place only by the force of the stones one against another. If you tried to build the bridge from scratch, upward and then inward, you would fail—the stones would keep falling to the ground. Indeed the whole bridge now would collapse if you were to remove the keystone or any stone surrounding it. What you must do to construct an arch is, first, build a supporting structure (possibly an earthen embankment) on which you lay the stones of the bridge, until they are all in place. Then you remove the structure, which is no longer needed and in fact is in the way of walking under the bridge. Likewise, one can imagine a biochemical sequential process with several stages, on parts of which other processes piggyback, as it were. When the here to nonsequential parasitic processes link up and start functioning independently, the original sequence is eventually removed by natural selection because it is redundant or drains resources.
Moving from the pretend to the actual, today’s Darwinians have many examples of the most complex of processes that have been put in place by selection. Take as an example the process whereby energy from food is converted into a form that can be used by the cells. This process, called the Krebs cycle, occurs in the cell’s mitochondria and centers on two molecules, ATP (adenosine triphosphate) and ADP (adenosine diphosphate). The former is more energy-rich than the latter and is degraded by the body when it needs power. Not only are the molecules themselves complex but so also is the Krebs cycle that makes ATP from other sources of energy. There are almost a dozen sub-processes in the cycle, each making a new product from an earlier one. Every one of these sub-processes demands its own enzyme (these are molecular substances that prior chemical reactions). Do not think that the cycle appeared out of thin air, complete and entire as it were. Each part of the cycle started life doing something else and then (in true Heath Robinson fashion) was grabbed by the cells and put to a new use. Although, when they set out, the scientists who found all of this out certainly did not have Behe and his “irreducible complexity” in mind, one could imagine that they did, especially from the way they set up the problem. “The Krebs cycle has been frequently quoted as a key problem in the evolution of living cells, hard to explain by Darwin’s natural selection: How could natural selection explain the building of a complicated structure in toto, when the intermediate stages have no obvious fitness functionality?” (Meléndez-Hervia et al. 1996:302). A Behe-type problem but no Behe-type answer. To the contrary, the various parts of the Krebs cycle had their original uses, and then these were taken over for the whole.

Further, as Dawkins (2004:550-552 )points out:
“Kenneth Miller of Brown University deals with the whole question in a tour de force of cleat exposition. As Miller shows, the allegation that the component parts of the flagellar motor have no other functions is simply false. As one example, many parasitic bacteria have a mechanism for injecting chemicals into host cells called the TTSS (Type Three Secretory Apparatus). The TTSS makes use of a subset of the very same proteins that are used in the flagellar motor. In this case they are used not for providing rotatory motion of a circular hub, but for making a circular hole in a host’s cell wall. Miller summarizes:
Stated directly, the TTSS does its dirty work using a handful of proteins from the base of the flagellum. From the evolutionary point of view, this relationship is hardly surprising. In fact, it’s to be expected that the opportunism of evolutionary processes would mix and match proteins to produce new and novel functions. According to the doctrine of irreducible complexity, however, this should not be possible. If the flagellum is indeed irreducibly complex, then removing just one part, let alone 10 or 15, should render what remains ‘by definition nonfunctional.’ Yet the TTSS is indeed fully functional, even though it is missing most of the parts of the flagellum. The TTSS may be bad news for us, but for the bacteria that possess it, it is a truly valuable biochemical machine. The existence of TTSS in a wide variety of bacteria demonstrates that a small portion of the ‘irreducibly complex’ flagellum can indeed carry out an important biological function. Since such a function is clearly favored by natural selection, the contention that the flagellum must be fully assembled before any of its component parts can be useful is obviously incorrect. What this means is that the argument for intelligent design of the flagellum has failed.”

And, finally Ruse (2003: 321-322) points out: “Behe’s position does not seem plausible, given what we know of the nature of mutation and stability of biological systems over time. When exactly does the Intelligent Designer supposedly strike to do its work? In Darwin’s Black Box Behe suggests that everything might have been done long ago and then left to its own devices. “The irreducibly complex biochemical systems that I have discusses.. . did not have to be produced recently. It is entirely possible, based simply on an examination of the systems themselves, that they were designed billions of years ago and that they could have been passed down to the present by the normal processes of cellular reproduction (pp. 227-228). Although Behe ignores the history of the preformed genes from this point between their origin (when they would not have been needed) and today (when they are in full use), we should not. According to the biochemist Kenneth Miller (1999:162-163), “As any student of biology will tell you, because these genes are not expressed, natural selection would not be able to weed out genetic mistakes. Mutations would accumulate in these genes at breathtaking rates, rendering them hopelessly changed and inoperable hundreds of millions of years before Behe says that they will be needed.” There is a mass of experimental evidence showing this to be the case. Behe’s idea of a designer doing everything back then and leaving matters to their natural fate is “pure and simple fantasy.”

II. blood clotting. This will be shorter. Behe’s claim is easily dealt with. As Ian Musgrave (2005) states : ”Miller has pointed out to Behe that whales and dolphins lack the contact pathway (Factor XII or Hageman Factor) (5). Furthermore, puffer fish don’t have the pathway either (3). So two groups of vertebrates can live happily without a major arm of the clotting cascade. Behe has not addressed this.” The evolution of the clotting cascade is detailed in Miller (n.d). Musgrave also describes experiments with knockout mice that show that clotting can proceed when mice with different parts of the cascade genetically eliminated are interbred and compensate for the missing parts of the clotting cascade. As described above, the evolution of a much more complex biochemical system, the Krebs cycle, has been described arising from the putting together of simpler components that originally had different functions.
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William Dembski

William Dembski is the theoretician of the movement. His books are full of abstruse and complicated mathematical formulas. He claims to be using information theory to derive his conclusions. His basic claim is that “complex specified information (CSI)” cannot be generated by natural selection and therefore must be due to an “intelligence.” In his interesting review of Dembski (2002), Orr (2002) puts it this way: “An object, event, or structure exhibits specified complexity if it is both complex (i.e., one of many live possibilities) and specified (i.e., displays an independently given pattern). A long sequence of randomly strewn Scrabble pieces is complex without being specified. A short sequence spelling the word "the" is specified without being complex. A sequence corresponding to a Shakespearean sonnet is both complex and specified.” Dembski has designed a “filter” which eliminates the possibility that a piece of information is due to chance or following a law and thus is truly “complex specified information.” He also calculates the possibility of the elements coming together simultaneously and sets a lower limit of 10^150 to assert that something is due to design. Dembski’s prime “real-life” example is Behe’s bacterial flagellum.

Mark Perakh (2004: 27), who works on statistical physics and is thus qualified to cut through the smog, has this to say about Dembski’s use of mathematical formulations: “Actually, The Design Inference contains little of genuine mathematics, but is full of mathematism, that is, the use of mathematical symbolism as embellishment, often only to create an impression of a scientific rigor of the discourse. And again (2004:38)”Actually all these convoluted notions of detachability, tractability, and delimitation seem superfluous and the criterion of specification seems to boil own to the simple requirement that can be expressed as: an event is specified if it displays a recognizable pattern. Of course, if Dembski limited his discourse to such a brief and easily comprehensible assertion he would not be able to write a whole book with its seemingly sophisticated mathematical apparatus. What does recognizability entail? To recognize a pattern we must have in mind some image, independent of the pattern actually observed, to which we compare the observed pattern. That is actually the idea of “detachability,” stripped of its sophisticated embellishments.. .”

What really drove the point home to me was Perakh’s description of the various information theories that Dembski claims to be using. The seminal papers are by Shannon (1948). Perakh 92004: 64-67)” In fact, what information theory studies is the communication process, viewed as the transmission of information, regardless of the presence or absence of a meaningful message in that information.. . Information has no relation either to the semantic contents of the message or to the particular appearance of the symbols used to record it. It is essential for our discussion to note that the more random the transmitted text, the larger the amount of information it carries.. . One of the measures of information according to information theory, is a quantity named entropy. To all intents and purposes, it behaves like its namesake in thermodynamics. The entropy of a text quantitatively characterizes the level of disorder in that text. The total entropy of a text as a whole is proportional to the text’s length and is therefore an extensive quantity. A more interesting quantity is the specific entropy, which is the entropy of a unit of text, and therefore is an intensive quantity. Usually it is expressed in as entropy per character and measured in bits per character. In the following discussion, unless indicated otherwise, the term entropy will mean the specific entropy. There exists a hierarchy of texts in regard to their entropy For example, consider a string of the same letter (like A) repeated, say, a million times: AAAAAAA.. .etc. This meaningless text is perfectly ordered. The entropy of the text is practically zero. Now consider a text obtained , for example, by what we cal the urn technique .[BOM completely random]. . Let a text in an “urn language” be, say, a million letters long. This string is almost always gibberish (there is some, extremely small probability that a string of an urn language happens to be a piece of a meaningful message). If, as is overwhelmingly the case, this string is gibberish, in an overwhelming majority of situations there is no or very little order in that string. We call it a random string. The entropy of that meaningless random string is large, and so is the information carried by that string. Meaningful texts are located somewhere in the middle of the entropy scale, their entropy being much larger than in perfectly ordered texts of very low entropy (like AAAAA. ..) but much smaller than in the meaningless random texts. Here are some typical numbers. The entropy of a normal meaningful text in English (as was estimated already by Shannon) is about 1 bit per character. On the other hand, the entropy of a text written in urn language, that is the entropy of a randomized sequence of 27 symbols (26 letters plus space), may be as high as 4.76 bits per character.”
Perakh (2004: 67) concludes “Reading Dembski’s treatment of information, including his alleged law, leaves the impression that when discussing CSI he does not notice how inconsistently he switches back and forth between the concepts of information in the sense of information theory and complex specified information (which actually means a meaningful message and hence is not information in the sense of information theory). The mathematical apparatus of information theory, which Dembski uses in The Design Inference, is not applicable to meaningful messages, i.e., to what he refers to as CSI. In my view this makes Dembski’s entire treatment of information largely off the mark.”

The next point to consider is Dembski’s arguments of extreme unlikeliness of complex events. This is just a different version of the creationist calculations of the improbability of a hurricane assembling a B-52 bomber. As mentioned above, no Darwinian has ever argued that organisms came together in a single event. Ruse (2003: 325-27) writes: “Natural processes producing adaptation is about as likely as a monkey randomly typing a play by Shakespeare, these antievolutionists have claimed. Famously, Richard Dawkins has scotched this kind of argument. Selection decimates the ever-increasing randomness factors. Choosing a line from Shakespeare—METHINKS IT IS A WEASEL—Dawkins shows that one can set up a computer program that produces letters (or blanks) randomly in all twenty-eight spaces that this sentence occupies. It can produce UMMMK JK CDZZ F ZD DSDSKSM, for instance, or S SS FMCV PU I DDRGLKDXRRDO. If one were working randomly, the chances of producing the target sentence in one try is about 1 in 10,000 million, million, million, million, million, million against. Just impossible in fact. Now rejig the program so that it remembers a successful move, in this case getting a little closer to the target sentence. With this constraint added into a system for producing random letters, the target can be reached in less than fifty moves. So much for all this multiplication. “There is a big difference, then, between cumulative selection (in which each improvement, however slight, is used as the basis for future building), and single-step selection (in which each new “try” is a fresh one.” (Dawkins 1996:49). The Intelligent design people do not give this example much weight, pointing out (correctly) that it has many dis-analogies with real-life situations, beginning with the fact that Dawkins specified the end-point, whereas in nature there is supposedly no such fixed goal. Even a progressivist like Dawkins is not going to say that the Cambrian led inevitably to Englishmen. But Dawkins himself conceded this as soon as he gave his example. He was not trying to simulate nature in every respect. He was simply showing that arguments which multiply randomness to a point beyond possibility can be countered simply by factoring in selection.

Dembski criticizes Dawkins’ example, from Orr’s (2002) review:
“The apparent success of Dawkins's algorithm at getting to METHINKS… must therefore be just that, an appearance. If Dawkins tried reaching his target when averaging over all fitness functions, he'd find he does no better than blind search. So why does Dawkins's algorithm seem to work? The answer is that it subtly cheats: it starts not only with a target but also with a fitness function that leads straight to it. Everything's been cooked into the fitness function. Algorithms like Dawkins's thus "fail to generate specified complexity because they smuggle it in during construction of the fitness function."

Hence Dembski's big claim: "Darwinian mechanisms of any kind, whether in nature or in silico, are in principle incapable of generating specified complexity." At best, Darwinism just shuffles around preexisting specified complexity, using up that available in the fitness function to give the appearance of producing it de novo.

We can now complete the Dembskian Syllogism: Organisms show specified complexity; Darwinism can't make it; therefore, something else does. You won't be surprised to learn that that something else is intelligence. Indeed the "great myth of contemporary evolutionary biology is that the information needed to explain complex biological structures can be purchased without intelligence."
Nice answer, wrong question

The problem with all this is so simple that I hate to bring it up. But here goes: Darwinism isn't trying to reach a prespecified target. Darwinism, I regret to report, is sheer cold demographics. Darwinism says that my sequence has more kids than your sequence and so my sequence gets common and yours gets rare. If there's another sequence out there that has more kids than mine, it'll displace me. But there's no pre-set target in this game. (Why would evolution care about a pre-set place? Are we to believe that evolution is just inordinately fond of ATGGCAGGCAGT…?) Dembski can pick a prespecified target, average over all fitness functions, and show that no algorithm beats blind search until he's blue in the face. The calculation is irrelevant. Evolution isn't searching for anything and Darwinism is not therefore a search algorithm. The bottom line is not that the NFL theorems are wrong. They're not. The bottom line is that they ask the wrong question for what Dembski wants to do. More precisely, the proper conclusion isn't that the NFL theorems derail Darwinism. The proper conclusion is that evolutionary algorithms are flawed analogies for Darwinism.

The astonishing thing is that Dembski knows all this. In a remarkable revelation—and one that follows two hundred pages of technical mumbo-jumbo—Dembski suddenly announces that Darwinists won't find his NFL objection terribly relevant. And why not? For the very reason I just gave. Dembski even quotes Richard Dawkins at length, who, it turns out, warned all along that his METHINKS… example is

…misleading in important ways. One of these is that, in each generation of selective "breeding," the mutant "progeny" phrases were judged according to the criterion of resemblance to a distant ideal target, the phrase METHINKS IT IS LIKE A WEASEL. Life isn't like that. Evolution has no long-term goal. There is no long-distance target, no final perfection to serve as a criterion for selection…. In real life, the criterion for selection is always short-term, either simple survival or, more generally, reproductive success (Dawkins 1996: 50).

Ruse (2003) 327-328 deals with a remaining Dembskian objection— that no new complexity can be generated by selective forces:
“The real question is whether more sophisticated computer models can show that selective forces can generate genuine complexity—the kind that we associate with real adapted organisms— without having to put in such complexity into the pool in the first place. And the answer is that they can.
A beautiful example was devised by the biologist Thomas S. Ray. Tierra—an artificial world he created—lives in Ray’s computer; the “organisms” who inhabit it are self-replicating programs of an initially fixed length (80 instructions long). “Having determined the address of its [the organism’s] beginning and end, it subtracts the two to calculate its size, and allocates a block of memory of this size for a daughter cell. It then calls the copy procedure which copies the entire genome into the daughter-cell memory, one instruction at a time” (Ray 1996). Other than being self-replicating, these creatures (as we might neutrally call them) have no functions built in. They exist in a kind of memory pool, and each creature has a chunk of this memory. They cannot write into the program of other creatures, but they can read the information from other creatures and use this information. Time is limited for each creature, and when it has a block of time, it can use it to self-replicate. It then goes to the end of the queue and has to wait its turn for more time. There is a process (the “reaper”) by which the creatures get eliminated, but creatures can put off extinction by performing tasks (like reproduction) more efficiently than their fellows. Mutations are introduced into the mix by making the information of the creatures, and their replication, subject to random changes.

What happens when you set things in motion (Ray 1996: 124)?
“Once the soup is full, individuals are initially short-lived, generally reproducing only once before dying; thus, individuals turn over very rapidly. More slowly, there appear new genotypes of size 80, and then new size classes. There are changes in the genetic composition of each size class, as new mutants appear, some of which increase significantly in frequency, sometimes replacing the original genotype. The size classes which dominate the community also change through time, as new size classes appear.. . some of which competitively exclude sizes present earlier. Once the community becomes diverse, there is a greater variation in the longevity and fecundity of the individuals.
In addition to the raw diversity of genotypes and genome sizes, there is an increase in the ecological diversity. Obligate commensurable parasites evolve, which are not capable of self-replication in isolated culture, but which can replicate when cultured with normal (self-replicating) creatures. These parasites execute some part of the code of their hosts, but cause them no direct harm, except as competitors. Some potential hosts have evolved immunity to the parasites, and some parasites have evolved to circumvent this immunity.”

If there were a designer, he/she/it had to be extremely sloppy and inefficient because less than 5% of the human genome codes for genes. Miller (1994) points out that: “ In fact, the human genome is littered with pseudogenes. Gene fragments, “orphaned” genes, “junk” DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design. If the DNA of a human being or any other organism resembled a carefully constructed computer program with neatly arranged and logically structured modules, each written to fulfill a specific function, the evidence of intelligent design would be overwhelming. In fact, the genome resembles nothing so much as a hodgepodge of borrowed, copied, mutated, and discarded sequences and commands that has been cobbled together by millions of years of trial and error against the relentless test of survival. It works, and it works brilliantly; not because of intelligent design, but because of the great blind power of natural selection to innovate, test, and to discard what fails in favor of what succeeds. The organisms that remain alive today, ourselves included, are evolution’s great successes.”
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There are a number of philosophical and logical problems associated with ID which I won’t discuss. ID articles have not been published in per reviewed journals in the relevant disciplines. In almost ten years, ID has not developed any further examples or “irreducible complexity” than the flagellum and the clotting cascade—not a very good testimony to its productivity as a research strategy. In a Kuhnian sense, any theory seeking to replace another has to be able to explain everything than the previous theory has explained plus be able to explain areas that the theory it seeks to replace has not. Even posing the question, makes the position of ID versus the modern synthetic theory of evolution laughable.



[I put () around htpp// so that the url's would not be truncated]

Behe, M. 1996. Darwin’s Black Box: the Biochemical challenge to Evolution. New York: Free Press.

Dawkins, R. 1996. The Blind Watchmaker New York: Norton.

Dawkins, R. 2004. The Ancestor’s Tale New York: Houghton Mifflin

Dembski, Wm. 2002. No Free Lunch: Why Specified Complexity Cannot Be Purchased without Intelligence. New York: Rowman & Littlefield

Dembski, Wm. 2004. “The Logical Underpinnings of Intelligent Design,” in Wm. A. Dembski and M. Ruse, eds.Debating Design. From Darwin to DNA, pp. 311-329 Cambridge: Cambridge Univ. Press.

Meléndez-Hevia, E. et al. 1996. “The Puzzle of the Krebs Citric Acid Cycle: Assembling the Pieces of Chemically Feasible Reactions, and Opportunism in the Design of Metabolic Pathways During Evolution,” Journal of Molecular Evolution 43: 293-303.

Miller, K.R. n.d. “The evolution of the clotting system” (http://)biocrs.biomed.brown.edu/Darwin/DI/clot/Clotting.html

Miller, K. R. 1994. “Life’s Grand Design,” Technology Review 97 (#2):28-29.


Miller, K.R. 1999. Finding Darwin’s God. New York: Harper and Row

Miller, K.R. 2004. “The flagellum unspun: the collapse of ‘irreducible complexity,” in Wm. A. Dembski and M. Ruse, eds.Debating Design. From Darwin to DNA, pp. 81-97 Cambridge: Cambridge Univ. Press.

Musgrave, I. 2005. “Clotted rot for rotten clots.”
(http://)www.pandasthumb.org/pt-archives/000884.html

Orr, H.A.2002. review No Free Lunch: Why Specified Complexity Cannot Be Purchased without Intelligence
(http://)www.bostonreview.net/BR27.3/orr.html

Perakh, M..2004. Unintelligent Design Amherst, NY: Prometheus Books.

Ray, T.S. 1996.”An Approach to the synthesis of Life,” in The Philosophy of Artificial Life, ed. M.A. Boden. Oxford: Oxford Univ. Press

Ruse, M. 2003. Darwin and Design.Cambridge: Cambridge Univ. Press

Shannon, C.E,. 1948. “A Mathematical Theory of Communication.” Parts 1 and 2. Bell System Technology Journal(July 1948: 379-90; (October 1948: 623-37).

Other resources
[www.talkreason.org]
[www.talkorigins.org]
[www.ncseweb.org]

Bernard