Behe's Irreducible Complexity Is Refuted

DNAUnion,I am not surprised that Behe excludes macroscopic systems. That being said, the only reason that he seems to exclude them is that they are at a "higher level". I see no reason why higher level systems can not show us how evolution can occur to result in IC systems. From one of the Behe quotes "The fossil record has nothing to tell us about whether the interactions of 11-cis-retinal with rhodopsin, transducin, and phosphodiesterase could have developed step-by-step." I argue that the fossil record can and does. Again, co-aptation as an indirect evolutionary pathway that is viable both at the macro and biomolecular level. The development of the middle ear ossicles is a result of selection on individual changes in protein expression. Unless you want to suggest that phenotype is not caused by genotype, the middle ear ossicles are the direct result of protein expression, as is the flagella and blood clotting pathway. Therefore, both are under the same selection pressure, natural selection. New variation is brought about by random mutation.Secondly, what do the interactions of proteins/molecules in one system tell us about another system in their current configurations? Nothing. What does 11-trans-retinal and rhodopsin tell us about fibrinogen in the clotting cascade? Nothing. What does the evolutionary pathway seen in the fossil record, and the middle ear ossicles in particular, tell us about the history of fibrinogen in the clotting cascade? That it could have been previously used in another system and has since become integral in the clotting cascade. I would contend that the pathways in the fossil record tell us MORE than looking at current and unchanging configurations of molecular machines. This is the trap that Behe falls into. He looks at the current configuration of the bacflag and thinks it has been that way throughout history. He should look at the fossil record and learn a few things.Look at post #115 again. Notice that I pose two problems with Behe's proposition for IC via ID. If he claims that the bacflag came about through steps that are contrary to observed evolutionary mechanisms, then HE MUST SHOW HOW THOSE STEPS OCCURRED BY OBSERVATION. With the lack of observation, why should we posit a mechanism (ID, large and quick steps) which has not been observed for one that has been observed (co-aptation, slow and step by step). He still hasn't made a case, so there really isn't anything to refute as of yet. In other words, the need for an outside designer other than natural selection is not warranted, nor is it needed to understand the development these structures over time.[This message has been edited by Loudmouth, 03-10-2004]

So are we all in agreement yet that the ossicles don't refute Behe because they don't form an IC system?

Not if we use the original, simple sounding definition of Behe's.Now it seems that IC systems can only be biochemical. Let me try to rephrase what the defnition of IC systems are that you want to use. Please correct it for me.An irreducibly complex system is a biochemical system at the lowest possible chemical level that we are able to proble in which the removal of any one chemical component causes that system to fail to function completely.If this is what we are talking about then, by definition, the ossicle are not BIC (biochemically IC ).Now since biochemical evolution may, or may not, be harder to trace Behe has, as has been pointed out, no evidence for the nature of it's evolution at all. It may also be true, or may not, that the evolutionary theorists have no evidence either.That leaves us with nothing to hang our hats on.I understand that many, if not all of Behe's original BIC systems have been shown to be evolvable. Is that true?Are there any new suggestions for non-evolvable BIC systems? Do any of these have any evidence to show that they are, in fact, non-evolvable since some of those original BIC systems that were claimed to be non-evolvable were incorrectly designated as such?Of course, if we do find a non-evolvable BIC system(though I don't know how we would know), all that does is suggest we need to figure out additional evolutionary mechanisms that may allow for the evolution of these systems.These additional mechanisms may be a minor modification of what we understand the ToE to be or may be a major shake up. They do not force a leap to a sentient designer.The reason Behe gets to the designer so fast is that is where he wanted to go in the first place. It does not follow from the lack of evidence he has so far.

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I understand that many, if not all of Behe's original BIC systems have been shown to be evolvable. Is that true?

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That's what I was getting at when I first started in this thread (either my first or second post). Why would someone rely on ossicles - which don't even meet Behe's usage of IC - when some of his actual examples have supposedly been refuted?

Most developmental biologists would attribute ear-bone evolution to developmental regulatory changes. That is, no new material was/is employed. Instead, the same old material was simply reshaped. And this could occur because of changes in the timing of expression of certain genes. Yet such regulatory/timing schemes seem largely irrelevant to Behe's focus. Proteins do not change because of the time when they are expressed. To change a protein, you need to change the amino acid sequence. To create a molecular IC system, we need to account for the various parts without the help of a developmental program. Thus, unlike the ear-bones, evolution of the cellular systems involve changing the material and coming up with new material.Behe constrains his IC considerations to "discrete molecular systems" and explains why on pg. 41. I happen to think molecular machines are well-situated for IC considerations. For any machine is a conglomeration of parts. The parts can exist separately in a non-functional state and are then assembled into a system in which function emerges somewhat like a phase transition. And this is why middle ear bones are irrelevant. During embryological development, how are middle ear bones formed? Is there a "bone-synthesizer" that manufactures 200-or-so different human bones separately and then they are all assembled into a functioning skeleton? The answer is NO. If bones were formed like this, then yes, I think their IC state would pose a problem for non-teleological explanations.Yet molecular machines are built like this. Here, the "parts" correspond to specific gene products (polypeptide chains). The parts are individually brought together by the ribosome and then assembled (often with the help of chaperones) through their complementary conformations. Upon assembly, function emerges (in fact, one way cells use to turn off function is to disassemble the machine partially or completely).When dealing with molecular machines, defining parts and systems is easy. In fact, IDers don't have to define these, the scientific community has already done it (or in the process of doing it, depending on the machine).[This message has been edited by Warren, 03-10-2004]

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NosyNed: Not if we use the original, simple sounding definition of Behe's.

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I already pointed out that there is more to IC than a one-sentence definition.Same goes for other things dealing with science, such as evolution. One of the most-used definitions of evolution is "changes in allelic frequencies in a population". If we stick to just that definition then we can't legitimately state that dinosaurs or trilobites evolved because we don't have access to their alleles.[This message has been edited by DNAunion, 03-10-2004]

I'd be tempted to argue that we do have access to the alleles since they show up in the phenotypes.However, I agree that things can be oversimplified. But I don't see more in Behe's definition of IC (other than restricting it to biochemical systems). Is there more to it?[This message has been edited by NosyNed, 03-11-2004]

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DNAunion: I already pointed out that there is more to IC than a one-sentence definition.

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Same goes for other things dealing with science, such as evolution. One of the most-used definitions of evolution is "changes in allelic frequencies in a population". If we stick to just that definition then we can't legitimately state that dinosaurs or trilobites evolved because we don't have access to their alleles.

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NosyNed: I'd be tempted to argue that we do have access to the alleles since they show up in the phenotypes.

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But then you’d be bringing in a new concept; one that is not part of the one-sentence definition of evolution. How is that materially different from bringing in the concept of minimal function into Behe’s usage of IC, which he mentions several times in his book?Also, it is possible for a phenotype to change without there being an associated change in allelic frequencies. This can happen if the number of each allele in the population remains constant but their distribution — between heterozygotes and homozygotes — changes.PS: I am not arguing against evolution, just making a point about the inadequacy of many one-sentence definitions.

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NosyNed: However, I agree that things can be oversimplified. But I don't see more in Behe's definition of IC (other than restricting it to biochemical systems). Is there more to it?

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Yes. Here is something I wrote up several years ago, back when I was an IDist (if one must pigeonhole). Even it is not complete (minimal function is not mentioned, nor are other things).PS: I should point out that I am posting this as is, without updating it.3) IRREDUCIBLE COMPLEXITYIrreducible complexity is best defined by Dr. Michael Behe, who coined the term in his 1996 book Darwin’s Black Box: The Biochemical Challenge to Evolution. On page 39 of that book, he states:

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By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.

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So any system that has all 6 of the following attributes is IC:(1) SINGLE SYSTEM
The system must be a single system. It cannot be a composite system, such as an automobile. Even though the reciprocating, four-stroke, internal-combustion engine of a car is probably IC, the car itself is not because its sound system and its air conditioning system can be removed without the car losing its function. These systems that could be removed without the car losing function are subsystems of the car (which means that a car is not a single system, but is rather an aggregate system composed of multiple systems). Not even the eye — which many people would simply assume counts as a single system — meets this criterion, as Behe points out.

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Both Hitching and Dawkins have misdirected their focus. The eye, or indeed almost any large biological structure, consists of a number of discrete systems. The function of the retina alone is the perception of light. The function of the lens is to gather light and focus it. Tear ducts and eyelids are also complex systems, but separable from the function of the retina.

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Hitching’s argument is vulnerable because he mistakes an integrated system of systems for a single system, and Dawkins rightly points out the separability of the components. (Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p38)

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(2) SEVERAL PARTS
The single system mentioned in (1) must be composed of several (i.e., at the absolute minimum, three) parts. A two-part system that requires each part - such as a natural lever system formed by one pine tree falling perpendicular to and on top of an already fallen pine tree - is not an IC system (note that such a fallen-tree-lever system also fails the criterion of parts having to be well matched, which will be discussed next). Everything else being equal, the greater the number of (interacting) parts in a system, the greater the system’s complexity; and the underlying concept of Behe’s book and argument is irreducible complexity, not irreducible simplicity.(3) WELL-MATCHED PARTS
The several parts mentioned in (2) must be well matched. That is, the parts should physically fit together (and work together) so well that a change in one part’s size and/or shape would require compensatory changes in at least one other part’s size and/or shape. In addition, a well-matched part must be a solid, not a fluid.For example, for a standard mouse trap (the object Behe uses to explain his concept of irreducible complexity), decreasing the length of the holding bar by half would necessitate an equivalent reduction in the size of the hammer as well as a large-scale adjustment in the position of the catch and probably the spring also. Similarly, doubling the length of the hammer would also necessitate concomitant changes in other parts: the holding bar’s length would need to be doubled, and its girth may need to be increased in order to handle the additional load, the catch would need to be repositioned, the length of the base would need to be increased, and a repositioning of the spring may be required. For an IC system, the parts’ sizes and shapes should be somehow specific to each other: generic parts are not well matched to each other.

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The appearance of the modifier "well-matched" in the definition I constructed reflects the fact that complexity is a quantitative property. A system can be more or less complex, so the likelihood of coming up with any particular interactive system by chance can be more or less probable. As an illustration, contrast the greater complexity of a mechanical mousetrap with the much lesser complexity of a lever and fulcrum. Together a lever and fulcrum form an interactive system which can be used to move weights. Nonetheless, the parts of the system can have a wide variety of shapes and sizes and still function. Because the system is not well-matched, it could easily be formed by chance.

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Systems requiring several parts to function that need not be well-matched, we can call "simple interactive" systems (designated 'SI'). Ones that require well-matched components are irreducibly complex ('IC').

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let me first illustrate a well-matched system using the blood-clotting cascade (Stubbs and Bode 1994). The active form of one protein of the cascade is called thrombin, which cleaves the soluble protein fibrinogen to produce fibrin, the insoluble meshwork of a blood clot. The chemistry catalyzed by thrombin is simply the hydrolysis of a certain fibrinogen peptide bond. However, all proteins are made of amino acid residues joined by peptide bonds. A typical protein contains several hundred peptide bonds. There is nothing remarkable about the bond in fibrinogen that is cleaved by thrombin. Yet thrombin selects that particular bond for cleavage out of literally hundreds of thousands of peptide bonds in its environment and ignores almost all others. It can do this because the shape of thrombin is well-matched to the shape of fibrinogen around the bond it cleaves. It "recognizes" not only the bond it cuts, but also a number of other features of its target. The other proteins of the clotting cascade (Stuart factor, proaccelerin, tissue factor, and so on) have similar powers of discrimination. So do virtually all of the components of the molecular machines I discussed in Darwin's Black Box. (http://www.discovery.org/viewDB/index.php3?program=CRSC%2... )

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So what does well-matched mean? I’ll give it a shot.3a. Strong sensematch = to fit together (related to proper size and shape)well = (1) to a high degree, and/or (2) to a large extent or degree, and/or (3) to an extent approaching completeness, and/or (4) without doubt or questionWell-matched: Physically fitting together both precisely and specifically due to having exactly the correct sizes and shapes (tailor made). A change in the size and/or shape of (at least the interacting portion of) one part would necessitate a compensatory modification to the size and/or shape of (at least the interacting portion of) the other part.Example: An enzyme possessing great specificity for its substrate (due to their complementary, three-dimensional, recognition surfaces), or the moving, interlocking gears of either a transmission or a mechanical clock (they mesh together perfectly).3b.Weaker sensematch = to fit together (related to proper size and shape)well = (1) in a good or proper manner, or (2) satisfactorily with respect to conduct or actionWell-matched: Physically fitting together properly - that is, satisfactorily enough to perform a particular action — due to having appropriate sizes and shapes. Though the two parts may not interlock or have large areas of complementary surface contact as they do in the strong sense, the size and shape of (at least some region of) each part are still constrained to being within certain fairly narrow parameters. If the size and/or shape of one part were changed by more than a trivial amount, a compensatory change in the size and/or shape of the other part would be required.Example: The holding bar on a mechanical mouse trap that restrains the hammer from moving.So what does well-matched not mean?Argument: If a system is able to function, then its parts must be well matched.Counter: A functioning lever system made of non-well-matched parts can be produced by numerous different-sized and/or different-shaped objects (diving board, refrigerator, bookshelf, tree branch, car, etc.) coming to lie perpendicularly across a fallen pine tree.Argument: If a system is able to function well, then its parts must be well matchedCounter: A functioning lever system consisting of non-well-matched parts (such as was just described) can perform its function well.Argument: In a water-channel system, water is a well-matched part as it perfectly fits the specific three-dimensional contours of the other parts (the two sides and bottom)Counter: Fluids do not fit Behe's usage of "well-matched". His usage of "well-matched" pertains to solid objects that physically fit together well due to their shapes and sizes. If a fluid (liquid or gas) is poured into a cylindrical container, it will immediately conform to that particular shape (becoming cylindrical). If that very same fluid were then poured into a cubic container, it would immediately conform to that particular shape (becoming cubic). If that very same fluid were next poured into a container of irregular shape, it would immediately conform that that particular shape (becoming irregular). And if a liquid were poured out onto the floor, it would immediately conform to the floor's particular contour (becoming flat). A single fluid (liquid or gas) conforms to whatever shape it is contained in. As such, it cannot be considered a well-matched part according to Behe's usage. The reason? Lack of specificity: fluids are the ultimate conformers. In the following quote, Behe explains that the components of the BZ reaction are not well matched because those parts are generic and fit a wide range of other parts that are not components of the system under consideration.

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BEHE: Let's contrast this biochemical specificity [of the specificity of the blood-clotting enzymes] with a comparable chemical reaction lacking such specificity. The peptide bonds of proteins can also be cleaved by simple chemicals. A typical procedure calls for incubating the protein in 6N hydrochloric acid at 110C for twenty four hours. If fibrinogen were incubated under those conditions, the peptide bond that thrombin leaves would be broken, but so would every other peptide bond in the protein. It would be completely reduced to amino acids. If thrombin were in the mix, it too would be completely destroyed. If the other proteins of the clotting cascade were there, no clotting would take place, even though the peptide bonds that are cleaved in the cascade would be cleaved, because all other peptide bonds would be hydrolyzed too. There is virtually no specificity to the chemical hydrolysis beyond the type of bond that is cleaved.

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Similarly, the reactants of the BZ reaction are small organic or inorganic chemicals that show little specificity for each other. One ingredient, sodium bromate, is a general purpose oxidizing reagent and is capable of degrading a very large spectrum of chemicals besides the ones used in BZ reactions (thus its transport aboard airlines is forbidden). Another requirement of the reaction is simply for a transition metal that can change its oxidation state, and a number of such metals are known, including iron, cerium, and manganese ions (Field 1972). A third requirement is for an organic molecule that can be oxidized. Many candidates could fulfill this role (ones that have been used include malonic, citric, maleic, and malic acids), and organic molecules can be oxidized by many reagents other than bromate. The last ingredient is simply a high concentration of sulfuric acid. As Field (1972, 308) noted, setting up BZ reactions "is an exceedingly easy task as they will occur over a wide range of concentrations and conditions."
(http://www.discovery.org/viewDB/index.php3?program=CRSC%2...)

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(4) INTERACTING PARTS
The several parts mentioned in (2) must interact. A system that is composed of non-interacting parts is not IC. This includes:4a. A system in which the components are stationary/static. For example, the pieces of a standard jigsaw puzzle interlock, but they do not interact.4b. A system in which the components are arranged in a simple serial manner, with each one acting upon the next in line (such as a line of falling dominoes). Here the distinction is between acting and interacting.The problem with 4b is that the parts are merely acting on the next in line, as opposed to interacting with multiple other parts in various ways. It is clear that there is a distinction between:4b-1: A system composed of a series of things in which each is merely acted upon by (and/or dependent upon) the next in line (such as a food chain, or an A->B->C->D metabolic pathway).4b-2: A system composed of a group of things arranged into an interacting (and/or interdependent) network, with each of the parts acting/depending upon multiple others such that various linkages run from each part in multiple directions to form a complex meshwork of interacting (and/or interdependent) parts (such as a food web, or a mouse trap).Interactions that are made by forces being applied through direct, physical contact are clearly interactions; in the strong sense of the word. Interactions that occur only logically, or indirectly through intermediaries, are not clearly interactions of the type Behe requires (they are interactions in the weak sense and would need to be examined individually).(5) PARTS CONTRIBUTE TO OVERALL FUNCTION
Each of the several parts mentioned in (2) must contribute to the system’s overall function. An accessory part is a part of the general system that (1) is not required for the functioning of the core IC system or (2) performs a function that does not tie directly in with that of the core IC system. For example, a mechanical mouse trap could have a rubber pad added to its base in order to make the trap easier to grasp or to dampen the sound of the SLAP associated with the forceful impact of the hammer with the base. But the rubber pad would not contribute to the catching of mice and so would serve a function unrelated to the overall function of the device. Any such accessory part does not count as being a part of an IC core system and must be eliminated from the parts mentioned in (2).(6) ALL PARTS REQUIRED
Removal of any one of the several parts mentioned in (2) causes the system to lose function. A system can have an IC core with accessory parts added on. Consider again a rubber pad added to the base of a mechanical mouse trap. We already saw that the pad is an accessory part because it serves a function unrelated to the overall system’s function. But even if that weren’t true, the rubber pad would still be a mere accessory part because it could be removed without leading to the loss of system function. In such a case, the accessory parts are part of the overall system, but they are not part of the *IC* core system, and must be eliminated from the parts mentioned in (2).

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The reason for the conclusion [that a watch must be designed] is just as Paley implied: the ordering of separate components to accomplish a function beyond that of the individual components. The function of the watch is to act as a timekeeping device. Its components are the various gears, springs, chains, and the like that Paley lists.

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So far, so good. But if Paley knows what to look for in his mechanical paradigm, why did he go downhill so quickly? Because he got carried away and started looking to the wrong features of the watch. The problems start when Paley digresses from systems of necessarily interacting components to talk about arrangements that simply fit his idea of the way things ought to be. The first hint of trouble comes in Paley’s opening paragraph, when he mentions that the watch’s wheels are made of brass to prevent rust. The problem is that the exact material, brass, is not required for the watch to function. It might help, but a watch can function with wheels made of almost any hard material — probably even wood or bone. Things only get worse when Paley mentions the glass cover of the watch. Not only is the exact material not required, but the whole component is dispensable: a cover is not necessary for the function of the watch. A watch cover is simply a convenience that has been attached to an irreducibly complex system, not a part of the system itself. (bold emphasis added, italic emphasis in the original, Michae lBehe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p 215-216)

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Note that confusion often arises when people remove what they believe to be a part from a system Behe determined to be IC with the resulting system still being functional (which appears to refute Behe’s claims). The problem is usually that these people are not removing a part of the IC system, but rather are removing either an accessory part (see (5) and (6) just above) or a part of one of the parts of the IC system. For example, consider a system that typically has say 12 copies of a rod-like structure that together form some sort of a barrel that is one of the several parts of the IC system. Someone may find that 1, 2, or 3 copies of the rod-like structure that combine to form the barrel can be removed without the system losing function. They might then claim to have falsified an example of IC, but they would be wrong. The barrel — which was the part of the IC system - is still there, functioning as it was before: it itself just has fewer components now than before. So this would not be the removal of a part of the system, but rather the removal of a part of a part of the system (it would be merely a subpart of the system that was eliminated). The individual parts of an IC system do not have to be IC themselves: parts of a part of the IC system, or copies of a multi-component part, can be taken away from an IC system without the resulting system losing function, without contradicting Behe’s definition/example at all.

but: These two quotes are contradictory. Note especially the emphasis in the first. If Behe determined it to be IC then no parts can be removed without it ceasing to function. But if a part can be removed it is shown to have been miscast as IC.(We have, of course, already noted that IC systems can evolve even if they met Behe's definition in all ways.)It would also be helpful to refer to an example that Behe agrees meets all these various criteria. Which I note have now gone beyound IC. In other words, it is not as you started out to say that IC can't be simplied to a single sentence, you do that again above. It is that there is more criteria added on to make a system one that is to be considered.By the way, I'm not at all sure that we understand what "system" means or is. I've been through this problem before when doing design work (or rather meta-design). A system is a form of abstraction that can be considered at any one of a number of levels.An earlier discussion of yours had Behe moving down to strictly biochemical systems. Why then does he use a mousetrap as an aid to understanding when it is, by definition, outside of what he is considering.We need now to consider an few examples perhaps.

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So are we all in agreement yet that the ossicles don't refute Behe because they don't form an IC system?

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I will agree to that. But I wouldn't be me if I didn't fully agree.You do not have to show the evolution of a biochemical IC system in order to refute Behe's hypothesis. He claims that IC systems, whose existence is not in doubt, came about through developmental steps that can not be ascribed to natural, evolutionary mechanisms. He claims that intelligent design is responsible for these IC systems. To refute Behe, I have cited an evolutionary pathway that could result in IC systems. I think the example of the middle ear illustrates this well. When looking at extant reptillian middle ears, the stapes alone is responsible for sound transmission to the inner ear from the jaw and outer tympanum. In mammals, two bones seem to have been inserted between the outer tympanum and the stapes. Behe argues that, in biochemistry, these type of insertions would result in a period of non-functionality for the biochemical system. Such a period would not allow the natural selection to act upon the now non-functional protein agreggate.However, using the example of the middle ear ossicles, there may be reasons to believe that the period of non-functionality is unnecessary. The biochemical IC systems may have been functional throughout their development to the systems we see today. Behe's contention that natural selection was not able to act upon these IC systems is not evidenced and argued from ignorance. To refute Behe's idea, one must put forth evolutionary pathways that could result in these IC systems, and I think that the co-aptational pathway seen in the middle ear ossicles is a prime example of such a pathway. This knowledge of indirect pathways trumps Behe's argument from ignorance.I argue that this is not an argument from analogy, but rather indirect evidence. I will concede that the middle ear ossicles do not qualify as an IC system as set out by Behe. However, the development of middle ear ossicles does refute Behe's contention that evolutionary mechanisms lack the ability to create biochemical IC systems, and ultimiately refutes the contention that ID has to be involved for IC systems to arise.

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Most developmental biologists would attribute ear-bone evolution to developmental regulatory changes. That is, no new material was/is employed.

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I will disagree with the second part. New DNA sequences are responsible for developmental changes, and changes in DNA sequence are responsible for changes in protein "morphology" as well. Changes in protein shape can result in different specificity and enzymatic function. Changes in morphology can result in better hearing or faster locomotion. All of this is due to changes in DNA sequence.

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And this could occur because of changes in the timing of expression of certain genes.

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Which is under the control of the environment, DNA sequence of cis/trans acting regulator proteins, and promoter sequences. Other than the environment, changes in DNA sequence can and does effect temporal gene expression.

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To create a molecular IC system, we need to account for the various parts without the help of a developmental program. Thus, unlike the ear-bones, evolution of the cellular systems involve changing the material and coming up with new material.

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I could also similarly reduce the parts of a cellular system to the levle of being the same material. All cellular parts are made up of long polypeptides or the products of these polypeptides. Therefore, to make a cellular IC system you do not need new material.

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I happen to think molecular machines are well-situated for IC considerations. For any machine is a conglomeration of parts. The parts can exist separately in a non-functional state and are then assembled into a system in which function emerges somewhat like a phase transition.

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Behe has never shown that the parts making up cellular IC systems were at all times non-functional. He must show how these parts have not evolved or changed overtime. As I have said in previous posts, Behe needs to show the actual development of these cellular IC systems, and how that development can not be attributed to the observed mechanisms of random mutation and natural selection. Simply pointing to extant systems and claiming that evolution was impossible falls short of evidence. Evolution of co-dependence and subsequenct mutation/selection is a very possible, and Behe seems to miss this fact.

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And this is why middle ear bones are irrelevant. During embryological development, how are middle ear bones formed? Is there a "bone-synthesizer" that manufactures 200-or-so different human bones separately and then they are all assembled into a functioning skeleton? The answer is NO. If bones were formed like this, then yes, I think their IC state would pose a problem for non-teleological explanations.

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Is there a separate system that forms each and every protein? No. Then proteins are irrelevant too.

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Yet molecular machines are built like this. Here, the "parts" correspond to specific gene products (polypeptide chains). The parts are individually brought together by the ribosome and then assembled (often with the help of chaperones) through their complementary conformations. Upon assembly, function emerges (in fact, one way cells use to turn off function is to disassemble the machine partially or completely).

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The individual parts are made by the ribosome. The combination of these parts occurs away from the ribosomes. Assembly can happen by just bringing these parts together in a fluid environment without any outside help. However, some systems do need a certain sequence of events to happen in a certain order, just as we see in fetal development. I still don't see how these two entities are qualitatively different.

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NosyNed:

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DNAunion: Note that confusion often arises when people remove what they believe to be a part from a system Behe determined to be IC with the resulting system still being functional (which appears to refute Behe’s claims). The problem is usually that these people are not removing a part of the IC system, but rather are removing either an accessory part (see (5) and (6) just above) or a part of one of the parts of the IC system.
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but:

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Behe: By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.
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These two quotes are contradictory. Note especially the emphasis in the first. If Behe determined it to be IC then no parts can be removed without it ceasing to function. But if a part can be removed it is shown to have been miscast as IC.

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This is an apparent contradiction, not an actual one.A good example of this is the cilium, which Behe states is IC. Kenneth Miller claimed to have refuted Behe by showing that some cilia are missing key parts, such as the central microtubule doublet and the outer dynein arms. Problem for Miller is that Behe doesn’t include them as being parts of the IC cilium: they’re accessory structures. The fact that neither the outer dynein arms nor the central doublet are required for ciliary motion is irrelevant to Behe’s claim of IC and can’t possibly be used to refute him.The problem here is that people don’t try to understand what Behe actually means. If a person reads Behe’s book and tries to understand his argument, they will understand that when Behe says the cilium (or some other system) is IC he means that the cilium contains an IC core. The IC core consists of a subset of the parts of the whole system wherein each element of the subset is required for system function. Accessory parts can be tacked onto such a core. Those other parts, not required for system function, would be parts of the system as a whole but not part of the (core) IC system.

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NosyNed: An earlier discussion of yours had Behe moving down to strictly biochemical systems. Why then does he use a mousetrap as an aid to understanding when it is, by definition, outside of what he is considering.

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He uses a mousetrap for several reasons. First, because most everyday Joes, who know nothing about eukaryotic cilia, are familiar with a mousetrap. Therefore, he can explain the general concepts in the first few chapters and not overwhelm the reader with too many details all at once. Second, he — and anyone else - can pick up a mousetrap, identify the various parts, move them, and see how they interact: that’s not possible with a cilium. Finally, despite what some earlier statements may have led one to believe, a mousetrap is not outside of his definition of an IC system. If you will note, I qualified my statements by saying that Behe rejects macroscopic BIOLOGICAL systems from being IC: macroscopic mechanical systems can be IC if they meet the certain criteria. The key difference is that a macroscopic biological system — such as an organ or organ system — is never a single system: it’s always an integrated system of a multitude of separate systems. On the other hand, a mousetrap is indeed a single system: it’s parts (hammer, spring, holding bar, etc.) are the lowest level one needs to drill down to in order to give a fully satisfactory and detailed explanation for the system’s function.[This message has been edited by DNAunion, 03-11-2004]

I can not understand a mousetrap without drilling down to a lower level than the parts mentioned. If I thought I could I would be mistified when a mousetrap with inadequate friction between some of the parts would fail to 'set' correctly.It is beginning to seem that Behe is being rather arbitrary in just what meets which criteria.If we do take a mousetrap as being IC then, of course, it has been shown that a conventional mousetrap can operate without all the parts. This doesn't mean that taking one part of an existing mousetrap leaves it working. It is just that a mousetrap can exist and work with out all the current parts but with different arrangements and forms of the parts left.It does appear that it is difficult or impossible to even determine what is actually IC. The definition seems to be about as sharp as the edge of a cloud.

Oh, i see, now we find that the cilium isn't IC either. It does get harder and harder to follow just what he is talking about. Perhaps someone has the book and can give the quotes from Behe's book where he makes this distinction between the cilium and the "core" clear. I hadn't heard it expressed that way before.Are there some other examples of IC systems that aren't but that do contain an IC core? What part of the clotting mechanism is IC then?