Tuesday, April 18, 2006

The evolution of clots #3

The evolution of clots, Daily Telegraph, April 4, 2006 Intelligent Design is the logic of ignorance - complex life, such as the machinery of blood clotting, can be explained by Darwinism, says Steve Jones [Continued from part #2]

Source: Berg, J.M., et al., "Biochemistry," W.H. Freeman, Fifth edition, 2002.

[I will hold my namesake to his claim that "the machinery of blood clotting, can be explained by Darwinism", that is the natural selection of random micromutations (NSRM). The great French zoologist Pierre Grasse, independently of Mike Behe, came to the conclusion that the machinery of blood clotting, cannot be explained by Darwinism:

"The genesis of control systems with no intervention by the organism is difficult to imagine and postulates Himalayas of chance occurrences that, moreover, could not have happened for lack of time and a sufficient number of generations. Take, for example, regulation of the coagulation of blood, a highly complex phenomenon to which biologists seem to have given little thought. Its normal cause is the opening of a vein, artery, or capillaries; the blood brought into contact with the lip of the wound (damaged tissues) becomes the site of chain reactions ending in the formation of a clot. This is only possible because there preexist in the blood reaction agents or their precursors whose end effect is to coagulate certain proteins of the blood plasma. The organism, ready for all eventualities, bears within itself in the latent state its own protective system. Genes control the elaboration of coagulants, proteins, and enzymes. Such a process forms a single whole; a lack of a substance arises, an enzyme is affected, and the system will not work. One does not see how it can have been formed by successive chance effects supplying a protein or an enzyme in any random order. Besides, we know that the effects of mutations on the system are disastrous and form the lengthiest chapter in blood pathology. The system has become functional only when all its components have come together and adjusted themselves to one another. The Darwinian hypothesis compels us to postulate a preparatory period during which selection acts upon something that does not, physiologically speaking, yet exist. Under the necessary conditions of the postulate, the action can only have been prophetic!" (Grasse P.-P., "Evolution of Living Organisms: Evidence for a New Theory of Transformation," Academic Press: New York NY, 1977, pp.151-152. Emphasis in original)]

Queen Victoria, in an early tilt towards evolution, saw orang-utans as "frightful, and painfully and disagreeably human". She herself had the misfortune to inherit a flaw in a body system much appealed to by the ID crew, for several of her descendants had haemophilia and bled freely after a cut. [This too is false. IDists have not "appealed to haemophilia." ID theorist Mike Behe appeals to the blood-clotting cascade as an example of an irreducibly complex system that could not plausibly arise by the Darwinian mechanism of the natural selection of random micromutations (see long quote of Behe in my "Pierre Grasse and the `irreducible complexity' of the blood-clotting cascade"). Remember that is Behe's mainpoint:

"Darwin knew that his theory of gradual evolution by natural selection carried a heavy burden: `If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.' [Darwin C., 1872, "Origin of Species", 6th ed., 1988, New York University Press: New York, p.154]. It is safe to say that most of the scientific skepticism about Darwinism in the past century has centered on this requirement. From Mivart's concern over the incipient stages of new structures to Margulis's dismissal of gradual evolution, critics of Darwin have suspected that his criterion of failure had been met. But how can we be confident? What type of biological system could not be formed by `numerous, successive, slight modifications'? Well, for starters, a system that is irreducibly complex. 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. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An 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." (Behe M.J., "Darwin's Black Box: The Biochemical Challenge to Evolution," Free Press: New York NY, 1996, p.38. Emphasis original)

This was made even more explicit by Behe in his paper specifically in defence of the blood-clotting cascade, where he revised his definition of "irreducibly complex" to focus on "unselected steps" so that Darwinists cannot (like Jones does here) propose "just-so stories that leap over many steps without comment":

"In Darwin's Black Box I defined the concept of irreducible complexity (IC) in the following way. `By irreducibly complex I mean a single system which is composed of several well-matched, interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning. (Behe 1996, 39)' While I think that’s a reasonable definition of IC, and it gets across the idea to a general audience, it has some drawbacks. Envisioning IC in terms of selected or unselected steps thus puts the focus on the process of trying to build the system. A big advantage, I think, is that it encourages people to pay attention to details; hopefully it would encourage really detailed scenarios by proponents of Darwinism (ones that might be checked experimentally) and discourage just-so stories that leap over many steps without comment. So with those thoughts in mind, I offer the following tentative `evolutionary' definition of irreducible complexity: An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway. That definition has the advantage of promoting research: to state clear, detailed evolutionary pathways; to measure probabilistic resources; to estimate mutation rates; to determine if a given step is selected or not. It allows for the proposal of any evolutionary scenario a Darwinist (or others) may wish to submit, asking only that it be detailed enough so that relevant parameters might be estimated. If the improbability of the pathway exceeds the available probabilistic resources (roughly the number of organisms over the relevant time in the relevant phylogenetic branch) then Darwinism is deemed an unlikely explanation and intelligent design a likely one." (Behe M.J., "In Defense of the Irreducibility of the Blood Clotting Cascade: Response to Russell Doolittle, Ken Miller and Keith Robison," Discovery Institute, Seattle WA, July 31, 2000)

So if a Darwinist (like Jones) comes up with a non-Darwinian explanation of the blood-clotting cascade (including one that "leap[s] over many steps without comment"), then he has conceded Behe's main point!]

The clotting machinery is an icon of just how complex life may be. [Indeed, Jones gives it as an example in one of his books, noting that "From cut to clot involves several steps. Different proteins are arranged in a cascade which responds to the damage ... A dozen or more different genes scattered all over the DNA co-operate in the production line" (my emphasis):

"Now whole sections of DNA from normal and haemophiliac families can be compared to show exactly what has happened and, just like the genetic map itself, things have got much more complicated. Haemophilia shows how molecular biology has made geneticists' lives more difficult. First, uncontrollable bleeding is not a single disease, but several. This is because clotting itself is a complicated business. From cut to clot involves several steps. Different proteins are arranged in a cascade which responds to the damage, produces and then mobilises the material which makes up the clot and finally assembles it into a tough protective barrier. A dozen or more different genes scattered all over the DNA co-operate in the production line." (Jones J.S., "The Language of the Genes: Biology, History and the Evolutionary Future," [1993], Flamingo: London, 1994, reprint, pp.81-82)

So how did the Darwinian `blind watchmaker' set up a "production line" involving "A dozen or more different genes scattered all over the DNA"? ]

Designers love it: for to staunch the flow needs a cascade of a dozen or more enzymes that work like a row of toppling dominoes. [Great analogy! In fact Jones himself in his "Almost Like a Whale" (aka "Darwin's Ghost" in the USA) gives the blood clotting cascade as a prime example of a system that does not "vary most" because it is "least important," i.e. it varies least because it is so important:

"Perhaps, some say, most of the DNA is an organ of small importance, whose presence is not noticed by Darwin's machine. If so, much of life is neutral ground upon which natural selection enacts its few rare struggles. That view is supported by a surprising fact: that the parts of the body that vary most are those that appear to be least important. Blood clots are made when small proteins link together in response to damage. For much of the time each unit floats in the plasma, its ability to bind checked by a short piece that blocks the crucial site. After a cut, the plug is snipped out, the molecules link up and the clot forms. Most of the protein does not vary at all, but the stopper, with its simple job, is filled with diversity. Natural selection surely cannot act to retain differences in the part of the molecule with the least exacting task. Most of the changes in the stopper probably have no effect on how it works and merely accumulate with time. In the same way, in DNA as a whole, the parts that make no protein vary more than those that do, and the more embedded in the machinery of the cell any protein may be, the less variable its gene. Diversity, it seems, builds up where it does no harm, but is excluded from places where it might cause trouble. The champions of Darwinism find it painful to admit that most variation under Nature is a spectator at the evolutionary play. " (Jones J.S., "Almost Like a Whale: The Origin of Species Updated," Doubleday: London, 1999, pp.142-143) ]

Two interacting pathways meet at a crucial junction point. One is set off by a change in acidity after a cut, while the other acts when it picks up chemical cues from damaged cells. An injury sets off a chain reaction until the job is done and, if any step goes wrong, the whole system collapses. [Indeed. So Darwinism has to explain not just one pathway, but two, and which moreover "meet at a crucial junction point". And how could such a system that "collapses" "if any step goes wrong", be assembled by a Darwinian "step"-by-tiny-"step" mechanism?]

How could such a complicated machine evolve from simple beginnings? [Note how Jones now changes the question. The issue is not how did the blood clotting cascade "evolve from simple beginnings," since both Behe (and I) accept universal common ancestry:

"For the record, I have no reason to doubt that the universe is the billions of years old that physicists say it is. Further, I find the idea of common descent (that all organisms share a common ancestor) fairly convincing, and have no particular reason to doubt it." (Behe, Ibid, 1996, pp.5-6)

and so I (and I presume Behe) expect that the existing system was built on the foundations of a previous system (or systems). The question that Jones needs to answer is: how did the blood clotting cascade "evolve" by the Darwinian natural selection of random micromutations "from simple beginnings"?]

What use is part of a clot? Much better, in fact, than no clot at all. [This also is an attempt to change the question. The issue is not "part of a clot" but part of a blood clotting system. An animal that had blood but "no" clotting system "at all" would not be viable and so would be eliminated by natural selection. And as for "part of a" clotting system, Jones does not specify how much a part. A 99% "part" of a clotting system might be viable but a 1% "part" of a blood clotting system would not be any better than "no" clotting system "at all". In fact, Jones' own quote above about, "parts of the body that vary most are those that appear to be least important" and for "Blood clots ... Most of the protein does not vary at all" is evidence that, apart from the "plug", even a 99% "part" of the existing blood clotting system is not better than "no" clotting system "at all"!

[Continued in part #4]

Stephen E. Jones, BSc (Biol).
"Problems of Evolution"

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