If a theory claims to be able to explain some phenomenon but does not generate even an attempt at an explanation, then it should be banished. Michael J. Behe, DBB p.186

Table of Contents Click on titles

This website is made up of posts made on Behe Fails Weblog. Even though it is made up of separate posts, the posts were written to relate to each other sensibly.

1. Behe is incoherent on what design and evolution are
2. "Design" for Behe is merely an attempt to redefine biochemistry as designed
3. In criticizing Dawkins, Behe conflates Paley's "design" with his own
4. Behe brings up physical precursors, then fails to acknowledge their ubiquity in organisms
5. What are the odds that designed entities would be comprised only of "physical precursors"?
6. Behe is misleading about textbooks
7. Design in life is easy to detect--look for breaks in evolution
8. Large questions are fine--if it's the Big Bang
9. Blood clotting's dependency on Vitamin K leaves us vulnerable
10. With causes of evolution of clotting given, Behe declares otherwise
11. The primary issue at stake is the foundation of knowledge
12. Endosymbiosis shows how some cell transport evolved
13. Science is about evidence of occurrence, not mere possibility
14. Evidence for the complex evolution of oxygenic photosynthesis is strong
15. Photosynthesis facilitated the "Cambrian explosion"
16. So, why were Ediacaran fauna, and Hallucigenia, designed?
17. So why were the Ediacaran fauna designed, then annihilated?
For more, click here

Links to other sites

Behe Fails blog
Electric Consciousness
Consciousness as Electric Field Dyanamics

1. Behe is incoherent on what design and evolution are

Behe tends to define terms as he desires, and then to redefine them again, with no consistency, reason, or scientific justification for doing so. For instance, he apparently just makes up his own definition of "macroevolution":
Roughly speaking, microevolution describes changes that can be made in one or a few small jumps, whereas macroevolution describes changes that appear to require large jumps. DBB 14.
That simply isn't true. Roughly speaking, microevolution involves changes within species, macroevolution occurs when species evolve. There is no difference in size of "jumps" inherent in the definitions at all. Here Behe seems (if witting--which is by no means certain) to be trying to change the discussion by shifting terms from what they mean.

Parenthetically, I suggested above that Behe might be unaware of his redefinition of microevolution and macroevolution (which remains a good possibility), and yet in his preface he would seem to suggest that "Darwinism" explains only microevolution, as it is known to science. There he writes:
Darwin was ignorant of the reasons for variation within a species (one of the requirements of his theory), but biochemistry has identified the molecular basis for it. DBB x.
He does not write that Darwin only explains variation within species, I would emphasize. Yet the context involves his continuous claims about how complex life is and how this complexity is not explained by Darwin. Your average creationist might be comforted by the quote above--which is in the preface, I repeat--for it seems to suggest that evolution might be very limited indeed.

Nevertheless, Behe rather quickly allows that larger scale evolution might happen by Darwinian means. On page four of DBB he writes that "Darwin's idea might explain horse hoofs, but can it explain life's foundation?"

Much of the rest of Behe's argumentation seems to suggest that only complex metabolic pathways are really a problem for evolution. Paley had argued that the eye is so well-made (with "relational" parts) that it must be designed, while Behe's argument against the evolution of the eye moves directly to the "black box" of the biochemistry of the eye (DBB, 18 and on).

Biochemical pathways are what require "large jumps" in his view, so he focuses on these. Nevertheless, he returns to granting very little to evolution by stating that Darwinism "explains microevolution very nicely" (DBB, 22). To most evolutionists and creationists, that allows very little evolution, in fact. And even if we were to accept his "definition" of microevolution, what does it even mean? What is a "large jump"?

At one point he even states that, "The behavior of hemoglobin can be achieved by a rather simple modification of the behavior of myoglobin..." and he states that therefore the case for design (he considers doubt regarding evolution to be evidence of design) of hemoglobin is weak (DBB, 207). And since hemoglobin apparently evolved prior to our split from lampreys, that would suggest that an enormous amount of evolution could occur. Mostly his "unevolvable" systems in DBB date back to the Cambrian or earlier.

As I have previously stated, I have not yet read Edge of Evolution. Nevertheless, reviews of the book give evidence that, as implied in DBB's preface, he may not allow for much unassisted evolution. Here is a quote from Edge of Evolution:
"If two mutations have to occur before there is a net beneficial effect - if an intermediate state is harmful, or less fit than the starting state - then there is already a big evolutionary problem." (Edge of Evolution, p.106
Of course various evidences are against that conclusion (many disadvantageous mutations persist in populations), including the fairly recent report of the evolution of citrate transport in E. coli in extremely small populations (compared to the world, that is) and in a fairly short time. That's not the point I wish to make with today's entry, however. Currently I wish to demonstrate what extremely variable and mostly useless "criteria" he uses in these discussions, at least prior to Edge of Evolution. How anyone is to make sense of his incoherent usage of terminology and concepts, I do not know.

His use of the word "design" is equally reprehensible in intellectual terms, but I will leave discussion of that for tomorrow's entry. These discussions of terms are not especially interesting, in my view, but they are essential to start off the discussion of the remainder of the issues in Behe's writings. For, it is difficult to make sense of Behe, and one might end up criticizing what he wrote in one area, when he does not make the same error in another area.

Because Behe really has little or no idea of what is possible in evolution (the complexity that does make particular evolution more difficult in isolation also increases the material with which evolutionary processes may proceed, a fact that he does not adequately consider), and even less idea of what meaningful criteria for design are, he shifts the meaning of terms with little regard for scientific precision and accuracy. Yet it seems likely that anyone who thinks "anything might have been designed" (DBB, 205) is essentially uninterested in what terms and concepts mean--especially the most central word in his "explanation", the word "design."

8.12.08                                           To top
Glen Davidson

2. "Design" for Behe is merely an attempt to redefine biochemistry as designed

Ought it then to be said, that, though we have little notion of an internal mold, we have not much more of a designing mind? The very contrary of this assertion is the truth. When we speak of an artificer or an architect, we talk of what is comprehensible to our understanding, and familiar to our experience. William Paley Natural Theology chapter 23.

Prior to the quote above, Paley was criticizing metaphysical ideas of "internal molds," which according to some were responsible for the forms of organisms, as being vacuous. In that quote, he fends off any notion that his "designer" would be meaningless, or something much different from what we understand about human artificers and architects. We don't know what a designing mind is? Perish the thought, is Paley's response.

Contrast this comparatively scientific viewpoint (to which Paley only partly adheres) with biochemist Behe's decidedly unscientific claims about design. He writes:
What is "design"? Design is simply the purposeful arrangement of parts. With such a broad definition we can see that anything might have been designed. DBB 193
To support the last sentence of that quote he points out that an accident might be staged, apparent chance meetings might have been arranged, art may be made to look "random".

Could anybody come up with a less useful notion of "design" than that one? Importantly, he has nothing that shows design in the manner that Paley suggests is reasonable, so he claims that anything could be designed. Of course that is as meaningful as saying that any and every scientific measurement might be faked, that it is designed to produce desired conclusions, rather than to actually measure a given phenomenon.

What may be even more important is that there he essentially concedes that his oft-repeated definition of design as the "purposeful arrangement of parts" has no rigor, and basically no meaning. And of course it does not. In the first place, a "purposeful anything" indicates design in the broader meaning of "design," so adding "arrangement of parts" does nothing other than to attempt to deflect questions of how to discover "purpose" and to prejudice people into supposing that arrangments of parts indicates design.

Even he knows that evolution produces "arrangements of parts." So does the wind. And if one recognizes that he has absolutely no means of discovering purpose at all (though he often conflates purpose and function), clearly he's trying to redefine "arrangement of parts" as design.

Of course he's doing more than just that in DBB. He's trying to demonstrate that some aspects of life cannot have evolved. Yet cleric Paley even had the sense to recognize that merely showing that the other ideas don't work isn't good enough, that the word "design" has to refer to something limited and meaningful, and that life has to yield up evidence that is "comprehensible to our understanding, and familiar to our experience," if life is to be rightly identified as being the result of design. One cannot criticize another's ideas for being vacuous, if one's own idea has no limits, nor criteria for adducing positive evidence in favor of one's claims.

Paley the cleric was trying (if not succeeding) to do what Behe the biochemist does not attempt, or even seem to understand to be part of science: To come up with actual evidence of design that is claimed to be evident.

In order to be more specific and meaningful than Paley himself was, I would note that an "artificer or an architect"--in other words, a designer--is rational, purposeful, able to take an idea from one context and to put it into another one, and (one hopes) is capable of novelty. These aspects are basically missing from life, although one might excuse Paley for thinking that these attributes exist in biology.

"Design" will be revisited in many future entries. I wanted to make a more general criticism of Behe's (non) concept of "design" near the beginning, because his lack of a meaningful design concept undermines everything that he states regarding design, and evolution.

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3. In criticizing Dawkins, Behe conflates Paley's "design" with his own

About a year and a half ago, I heard two lectures by Behe, and went to a question and answer session, at a religious college. Behe said at one point that ID was not, in fact, a dead end, for if one found some designed machines on a planet somewhere with none of their creators in sight, one would still be interested in trying to figure out why the machines were made, and who the designers were. This begs a good many questions, like how he can compare the alien designs that we could hope to understand, with his supernatural "design" that he insists cannot be understood regarding purpose and means of designing. However, the question I wanted to ask him was, how does he even distinguish between machines and life, considering that his lectures suggested that he saw life as a collection of machines which are quite analogous with our own designed machines.

I didn't get to ask that, though, because the college students were allowed first dibs on asking questions, and one ignorant loudmouthed "social work" student ranted on for a considerable period about how dishonest scientists were to deny design when, as Behe had claimed, all scientists admit that aspects of life appear to be designed. Unsurprisingly, not all scientists do so:
However, where a creationist sees a design or plan, a scientist sees merely order, or regular arrangement.… The fact is, order in nature is no evidence of design.

Douglas Futuyma. Science on Trial. New York: Pantheon Books, 1983. p. 114
How many scientists do or do not agree that aspects of life appear designed I wouldn't presume to even guess, but a lot of Behe's "argument" for design rested on the "fact" that all agree with that claim. Hence a single example (of a well-known evolutionary biologist) suffices to demonstrate that Behe confuses the universal with the specific, as well as relying on Dawkins's authority (a fallacy onf Behe's part) to make his generalization. It is, indeed, true, as one reads in Darwin's Black Box, that Dawkins does understand life to have the appearance of design. Here is one of Dawkins's strongest statements on the issue:
Biology is the study of complicated things that give the appearance of having been designed for a purpose. p. 1 Dawkins The Blind Watchmaker New York: Norton, 1987
In light of the quote above, I would have to ask Dawkins, along with Behe, for what purpose do liver flukes appear to have been designed? Aristotle, thanks to his philosophical viewpoint, could believe that the organism is the end or telos of the parts of which it is made, but it makes no sense in the philosophy of science nor in Christian philosophy to make the same assumption of "purpose" of parts when the whole organism (or ecology) has no discernable purpose. Paley waffled on this issue, sometimes suggesting that "design of the parts" was sufficient evidence of design, yet always looking for a purpose beyond mere metabolism and reproduction.

With that caveat out of the way for now, here is what Behe makes of Dawkins's various statement about the "appearance of design":
A crucial, often-overlooked point is that the overwhelming appearance of design strongly affects the burden of proof: In the presence of manifest design, the onus of proof is on the one who denies the plain evidence of his eyes. DBB (copyright 2006) p. 265
Of course Dawkins is not saying that design is manifest, particularly with close study. What really makes Behe appear hypocritical, however, is that Dawkins's various statements regarding the "appearance of design" are largely focused on Paley's macro-scale "case for design" ("The analogy between telescope and eye, between watch and living organism, is false. All appearances to the contrary..." The Blind Watchmaker, p.5) and Behe himself warns against assuming design on the macro-scale:
So those who labor in the fields of paleontology, comparative anatomy, population genetics, and biogeography should not invoke design until the molecular sciences show that design has an effect at those levels. DBB 230
Behe himself is saying there that Paley's examples, to which Dawkins is referring in the main, should not be accepted as having been designed, unless molecular science indicates that it was (by confusing function and purpose, in Behe's scenario). Behe himself is stating that Dawkins is wrong to infer design in Paley's examples, and yet in the earlier quote he was placing the burden of evidence on Dawkins (the context for the quote from page 265) to show that Paley's examples are not designed. Talk about double-speak!

I am not claiming that Dawkins does not also accept that the appearance of design exists at the molecular level, for evidently he does. My only point on this specific matter is that Behe hypocritically chides Dawkins for denying that the "appearance of design" indicates design, when Dawkins is mostly discussing examples in which Behe himself denies that the "appearance of design" actually indicates design--until it is "shown" to exist on the molecular level.

I will not speculate on whether Behe deliberately confuses the "appearance of design" that Dawkins discusses, with his own "proof of design," or if he is simply that bad at arguing evolution and ID. It suffices to say that he is wrong on this, as he is on most issues (at least regarding some aspect or another of an issue). He has no business trying to make a big deal about Dawkins's claim that life "appears designed," since he himself denies that most of the examples of "appearance of design" to which Dawkins refers actually do (by themselves) indicate design.

Again, I make this post not only because this issue matters in Behe's case, but also because it indicates how sloppy (at best) he really is in his argumentation. There is little point in moving on to more specific problems of DBB before demonstrating how contradictory, incoherent, and just plain wrong his argumentation is in general.

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4. Behe brings up physical precursors, then fails to acknowledge their ubiquity in organisms

"...Can we evolve a bicycle into a motorcycle? ...A motorcycle depends on a source of fuel, and a bicycle has nothing that can be slightly modified to become a gasoline tank. And what part of the bicycle could be duplicated to begin building a motor?" DBB, 44

"A bicycle thus may be a conceptual precursor to a motorcycle, but it is not a physical one. Darwinian evolution requires physical precursors." DBB, 45

The fact is that in DBB Behe hits on a very important phenomenon in determining whether or not evolution occurs, which is that evolution requires, and predicts, that any complex organ or system needs physical precursors. A designed object, like a motorcycle, does not. He carefully avoids generalizing what he says in the quote, and, as predictably, he avoids testing evolution on the availability of "physical precursors of systems and organs. Yet it is there, he does tell us that a motorcycle cannot evolve because it does not have the beginnings of components that are necessary for an evolution.

And what does he do in the rest of the book? He assiduously ignores or minimizes the importance of the fact that life is made up of modified parts, which he recognizes in the quote above is not the case in designed entities like motorcycles. Right there is a crucial difference between designed and evolved objects, and even though he is willing to bring up the difference in yet another of his ill-suited analogies, he will not mention the importance of the fact that most of his "irreducibly complex" systems are made up of components that, totally unlike a gas tank for a motorcycle, are known to have uses in other systems and pathways (he does point out a few biochemicals that do not have related molecules in other systems--though biomolecules lacking known relatives would not be unexpected in evolved organisms).

For instance, does Behe bring up the fact that the complement cascade is shared by both the adaptive and the innate immune systems, and that there is evidence that these molecules evolved first for the innate system? Certainly not, he writes as though adaptive immunity arose with no antecedents. Does he discuss the fact that adaptive immunity may have arisen to spare symbionts? No. And although I do not know if that hypothesis was well known when DBB was written, his lack of imagination is no argument against evolution. He does in fact bring up "an alternative pathway," the innate immunity, on p. 134 of DBB, which he notes can active the "membrane-attack complex." Yet he does not admit that adaptive immunity would therefore indeed have the innate immune system upon which to piggyback the evolution of adaptive immunity (such evolution still has a great many gaps, as might be expected of such an old system, but Behe's clearly not stating the matter fairly).

I intend to discuss the points in the above paragraph in more detail in a later entry.

Getting back to his pathetic bike to motorcycle "analogy" with evolution, clearly adaptive immunity did have a "gas tank" or "an engine" from which it could evolve step by step. No matter what problems remain, this completely undermines this particular analogy, which is really quite a misleading bit of rhetoric. Notably, there is no meaningful analogy between the designed objects that humans make, which very frequently have components which are taken from an entirely different sort of "conceptual evolution," and biological evolution, which in many lineages is almost totally incapable of using anything but "physical precursors" coming from direct ancestors.

Other examples are much the same, like the clotting cascade. When I heard him speak, he did admit that many of the molecules involved in clotting do indeed have relatives acting in other pathways, but in DBB this fact is generally smothered over. For, if he were to honestly face up to his own proclamation that "Darwinian evolution" requires physical precursors, while design evolution can make do with conceptual precursors, he would be stuck admitting that Darwinian evolution typically has evidence of such precursors in biochemical (and morphological) relatives--and to the degree that it does not, there are reasonable explanations for this (like the extinction of biochemical relatives--extinction being a prediction of any real evolutionary scenario).

There is little question that Behe slit his own throat by bringing up in DBB the necessity of "physical precursors" in organisms (aside from lateral transfers of genes, that is) under the "Darwinian" scenario, while designed objects like bicycles can make do with "conceptual precursors". Had he properly analyzed the biochemical pathways in his book according to that crucial distinction, he'd have done nothing but to show, first, that they were not designed, and second, that they in fact evolved. Instead, he ignores, or smothers the importance of, the large number of cases where physical precursors do indeed exist for exactly the kind of evolution that he denies happened, and instead he tries to shift the test for evolution away from his very own criterion on page 45 of DBB, instead insisting that we explain the details of an evolution which happened very long ago and without leaving much evidence regarding its pathways. Making up stuff is the very means of "ID science," as most of us already know, but it is not the way that real science operates.

There is much more to be said regarding these issues. At this point, it is sufficient to demonstrate that Behe is completely and utterly oblivious (unless he is wittingly dishonest) to the manner in which his very own distinction between "conceptual precursors" and "physical precursors" destroys his design claims, and bolsters "Darwinian" evolutionary theory. Said distinction is probably the single best scientific test for "Darwinian" evolution, and the cumulative evidence is thus very much in favor of life having evolved sans design. So the truth is that Behe and ID are not completely without an understanding of science--they just know enough in order to refrain from applying such tests whenever and wherever they recognize that ID will fail such tests.

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5. What are the odds that designed entities would be comprised only of "physical precursors"?

Behe does a great job of changing the subject to problems of evolution, and exaggerating them. What he never does at all well is to explain why things look as they do, why even his precious little "irreducibly complex" biochemical pathways are largely composed of demonstrable "physical precursors", and are never demonstrably composed of any merely "conceptual precursors". He produces good PR when he tries to suggest that evolution has questionable odds, but he never touches the odds against life being composed exclusively of physical precursors when it is supposedly designed--and for a very good reason, since that is far less likely than the odds against any evolutionary pathway whose details remain obscure.

Casey Luskin even gave us an ID "prediction" that is testable and falsifiable, and of course, it has been both tested and falsified:

(3) Intelligent agents ‘re-use’ functional components that work over and over in different systems (e.g., wheels for cars and airplanes):

“An intelligent cause may reuse or redeploy the same module in different systems, without there necessarily being any material or physical connection between those systems. Even more simply, intelligent causes can generate identical patterns independently.”

Mostly bogus "predictions" of ID, plus a falsified one

Why yes, C. Luskin and M. Behe, intelligent agents can re-use parts independently of heredity and lateral transfers. So if ID is responsible for life, why don't we see bat wings on pterosaurs, bird wings on bats, or octopus eyes in vertebrates?

Luskin made a very big mistake there, just as Behe did in noting that designed motorcycles are not dependent upon inherited (or laterally transferred) genetic materials. There is absolutely no evidence of independent agents producing similar systems in organisms without there "being any material or physical connection between those systems," unless you consider what humans genetically engineering organisms (although Luskin obviously doesn't recognize that intelligent agents are a part of the "material or physical connection" between such systems).

So come on, Behe, tell us what the odds are that life would have all of the patterns expected of undirected evolution, including a continual reliance upon and limitation to "physical precursors," if in fact life was designed? Astronomically against, is it not? And one can't simply resort to the typical expedient that "we don't know what the designer wants." Clearly the only explanatory or scientific reason to ever bring in a "designer" would be to explain why life has evidence of design, such as organs or systems having some merely conceptual precursors. Both Luskin and Behe fail to come up with a single clear instance of such evidence, hence they owe us an explanation for why design does not immediately fail the test for "conceptual precursors," which ought to exist in designed objects.

I will state more definitely now what is at stake here: Luskin and Behe need to supply the evidence that conceptual precursors (even if these are first principles) exist in organisms, as both of them have indicated that this would be expected from intelligent agents. This is a strong test for their ID claims. And, they need to tell us what the odds are of designed entities having purely physical precursors, as well as these existing in the patterns expected from undirected evolution. This is a strong test (actually, several tests summed up as one) of evolutionary theory.

Unless they can demonstrate that conceptual precursors (or re-used modules without "material or physical connections," using Luskin's botched phrase) exist in organisms, ID fails. And unless they can produce a "designer" that oddly "designs" only by using physical precursors, evolution wins--at least until something else comes along that can explain what evolution does, plus being able to explain even more. That is how science works. ID ends up being falsified using its own predictions, and nevertheless it continues claiming to be a "legitimate science" that is "persecuted" by being treated like every other hypothesis that the evidence has failed to support.

Too many replies to Behe are focused on responding to the framing (that's about all that we get from Behe) that Behe builds in order to avoid the colossal lack of explanatory value, along with avoiding the glaring falsification of genuine prediction, of his own "ID program". There is, in fact, nothing wrong with responding to his questions, for many of these do in fact touch on important remaining questions in evolutionary biology.

However, both Luskin and Behe should have their feet held to the fire over the enormous lacuna that ID is. ID is not something that has gaps, it simply is a gap, one that would like to replace what we do know with the bleat "God did it," or in another version, "the Designer did it."

One can make predictions with an "intelligent design" hypothesis. Both Behe and Luskin have done so (though Behe did so more implicitly than Luskin's explicit prediction), and their predictions have been falsified. Were they actually interested in doing science, they would acknowledge this fact, and drop ID altogether.

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6. Behe is misleading about textbooks

From pages 180 to 183 of Darwin's Black Box, Behe discusses, of all things, biochemistry textbooks with respect to the numbers and types of mentions of evolution in the indexes of these texts. Not molecular biology textbooks, cell biology textbooks, or genetics textbooks, apparently the standard is biochemistry textbooks. Is that perchance a result of his being a biochemist? Possibly?

His point is, of course, that evolution is not discussed much in biochemistry texts, and he disparages many that are there.

There are several rebuttals to make. One is that biochemistry is mostly about unchanging chemical processes, and fairly well conserved biochemistry. Another is that there are many mentions of evolution in at least my old biochemistry text which do not appear in the index. Furthermore, my biochem text uses evolution to justify its discussions of "model organisms". And the last point is that non-biochemistry biology texts of the time did mention evolution a good deal more than his biochemistry textbooks.

Behe makes a sloppy case in just about everything he discusses (with relation to ID, anyway). It is impossible to know how much of this is due to ignorance, and how much is due to lack of concern for the facts. However, I can show how meaningless his little table of numbers of mentions of evolution in biochemistry textbooks is, by listing a considerable number of mentions in my biochemistry textbook. Behe has a table of 30 biochemistry textbooks (many are different editions of single textbooks) on page 182 of DBB, many of which have zero mentions of evolution in their indexes, and none of which has more than 22. The textbook I used in my biochemistry course is in the median, at 12 index entries. This textbook is titled Biochemistry, written by Moran, et al., 2nd edition, published by Neil Patterson, and copyrighted in 1994 by Prentice Hall.

In the first place, even the count of 12 entries is misleading, since there are 16 places in the text indexed, since some entries have multiple text references. That's still not a lot, however.

When we consider mentions that are not in the index, however, the number doubles, just using the ones that I found by scanning. I couldn't have found all of the times evolution was brought up, but here are the ones I found fairly quickly which are not in the index, with representative text (so you know it's really about evolution):

1. 2-2 "The basic plan of the ancestor cell has been elaborated upon with spectacular inventiveness by billions of years of evolution."

2. 2-4 "Yet evolution has produced tremendous diversity..."

3. 27-4 "The distribution of antigenic determinants in the B components of DNA-dependent RNA polymerases of archaebacteria, eubacteria, and eukaryotes suggests the primeval character of the extremely thermophilic archaebacteria." [the accompanying figure compares RNA polymerases across the three domains of life]

4. 27-23 "The deduced amino acid sequences show considerable similarity in spite of their distant evolutionary relationships"

5. 29-7 "In plant mitochondria and in chloroplasts, the standard genetic code is used. But in mitochondria of all other organisms, there are some deviations from the standard code (...). ...And it has been suggested that the altered genetic code allows translation to proceed efficiently..."

6. 29-12 "Conservation of the nucleotide sequence in the D arm is more pronounced among eukaryotes than between prokaryotes and eukaryotes."

7. 32-8 "These parallels suggest that bacterial transposons and retroviruses might be distantly related. As we will see in the next section, eukaryotic transposons and retroviruses are even more intimately related."

8. 32-17 "Most mammals appear to be descended from a common ancestor that lived approximately 100 million years ago, indicating that the organization of genes can be preserved for a considerable time."

9. 32-19 "Closely related species, such as mouse and rat, which diverged only 30 million years ago, can differ significantly in the amount of repetitive DNA."

10. 32-20 "These pseudogenes share a common ancestor with a corresponding intact gene."

11. 32-22 "This is probably because the various genes that make up each family were generated by localized gene duplications that occurred relatively recently."

12. 32-33 "Any theory concerning the evolutionary origin of introns must satisfactorily explain why the vast majority of prokaryotic genes do not contain introns."

13. 32-25 "As is the case in bacteria, there has likely been selection for a small genome in this organism."

14. 32-27 "We have seen that the organization of the genome can change as a result of evolution, but large-scale reorganizations are only evident after millions of years."

15. 32-33 "The available evidence suggests that introns in protein-encoding genes arose late in evolution."

The best mention of evolution not in the index explains why model organisms are useful in general:
16. 2-31, 2-32 "How do we use knowledge gained from biological systems as evolutionarily remote from us as E. coli? As we probe deeper into the chemistry of life, we find that at the molecular level diversity gives way to unity, and themes emerge that pertain to all life. Knowledge gained from studies on an accommodating organism like E. coli can be applied to more recalcitrant model systems, such as the rat. With educated intuition developed from studies of simpler systems, researchers can devise experiments that coax more complex systems to reveal their own intricate mechanisms.

A proper appreciation of the balance between unity and diversity is essential when assessing results of biochemical studies. It is highly unlikely that glycolysis in E. coli will be regulated in exactly the same way as glycolysis in rat liver cells. Yet with experience, patterns of regulation are detectable."
Granted, these do not bring the total up to anything enormous. Yet the authors recognize the importance of the relatedness of all life in the study of biochemistry, since evolution is responsible for relatedness, and for divergence. Note #9, evolution is mentioned when it has to be, such as where closely related organisms diverge in the amount of repetitive DNA.

Of course, evolution is a theory of biology, and biochemistry is, in the main, about chemistry. The explanation for why evolution is not dealt with greatly in a biochemistry text like mine is given in the first chapter of the same text:
One might at first assume that biochemistry is merely a combination of two major sciences, chemistry and biology. However, the defining feature of biochemistry is that it uses principles and language of one science--chemistry--to explain the other science--biology--at the molecular level (chapter one, page one, of Moran et al.)
Of course biochemistry texts aren't especially heavy on evolution, as in many ways it's an extension or application of organic chemistry to life. Even so, a text like the one I own does invoke evolution not infrequently, since design is hardly responsible for either the unity or divergence found in life. At the beginning of chapter 32, this is written:
Until now, we have assumed that a gene is unchanging, static over time. We have implied that a gene exists at a fixed locus in a chromosome and that its structure and function are not affected by rearrangement or recombination....

This gradual change in genetic information is the basis of evolution. (Chap. 32 p. 1 of Moran et al.--this, by the way, is found under "evolution" in the index).
Why would they ever treat the gene as if it were static? The answer is quite obvious to anyone who understands the issues, biochemistry is dealing with the chemistry of what is found, not being particularly interested in evolution as such. The basics are being taught, and then these basics can be applied to dynamic systems.

So as usual, Behe is misleading in DBB. While this is not an especially important matter, it goes to show that once again Behe has distorted the issues, particularly for the many naive people who are likely to read his book.

Although I have shown that at least my textbook finds evolution to be important despite its emphasis on applying chemistry to biology, I also took a look at my old cell biology book from around the same time period. It is Molecular Biology of the Cell, 3rd edition, by Bruce Alberts, et al., New York, Garland Publishing, 1994. I counted 81 entries for evolution in the index, many of which have multiple page listings. There are three more entries under "Evolutionary Relationships." I didn't bother even looking for mentions not found in the index.

Molecular biology is a lot more like what biochemistry is not, a combination of chemistry and biology. Is it at all surprising that it deals much more heavily in the biological theory of evolution?

8.20.08                                           To top

7. Design in life is easy to detect--look for breaks in evolution

Since Dawkins agrees that biochemical systems can be designed, and that people who did not see or hear about the designing can nonetheless detect it, then the question of whether a given biochemical system was designed boils down to simply adducing evidence to support design. DBB, 203

Behe gets that much right. But how do you adduce evidence to support design? Well, a rationally thought out system would indicate design, and so would some actual purpose in living organisms, to bring up two important criteria. Less precisely, "conceptual precursors" instead of "physical precursors," would fit the bill, as Behe pointed out, and as I discussed previously. Or another way of putting that fairly inchoate (but usable) conception--and extending it somewhat--would be that we would look for arrangements that do not fit evolutionary patterns.

In other words, probably one of the best ways of looking for design candidates would be to find something that does not fit with evolutionary predictions. After all, what would be a better potential marker for intelligent design than something that wouldn't occur via natural processes (now using the definition "natural" which means "not caused by humans")? One would probably still have to check to see if rational thought was used, and if the putative "design" serves a likely purpose, but merely breaking the mold of evolutionary expectations would tend to suggest that something has intervened in the natural processes of evolution.

Behe himself brings up the subject, writing, "...The work does show that an intelligent agent can design a system exhibiting biochemical-like properties without using the biochemicals known to occur in living systems." DBB 202.

Yes, finding something like that would indeed be a pretty good first indication of design. For instance, find an malaria strain that has a completely new protein, which also has novel amino acids in it. But we wouldn't have to be that exacting in our demands, a completely new protein would certainly flag researchers that this strain of P. falciparum likely was engineered.

By the way, I used Plasmodium falciparum for an example quite on purpose, since it does not normally share genes with other organisms (not so far as I know, anyway), like anthrax does. Since sharing genes is "natural" for anthrax, and not for malaria, a new protein in the latter would break the evolutionary expectations rather better than a new (or unknown) protein in anthrax would.

There are less clear examples of design, those which simply take a gene from one organism and insert it into a very distantly related organism. Interestingly, these also are relatively easy to find, at least so long as we have their genetically unmodified relatives around. I really do not think that aliens that came to earth would have any difficulty discovering that many of our food crops have been genetically modified by injecting the Bt gene (which produces an insect-killing protein) into these crops, even though the Bt gene has evolved naturally.

Aliens could discover design of Bt crops because, of course, Bt in corn breaks the evolutionary patterns of inheritance and change. Corn, like P. falciparum, does not typically receive genes from other species, while intelligent humans know how to insert Bt genes into the corn genome. To be sure, there are other tell-tale marks of genetic engineering, although many of these are also taken from nature and placed in "unnatural" contexts (like viral promoters are). Nevertheless, even if the genes were entirely "natural," the fact that evolution would not be expected to produce corn plants with Bt toxin (and liverworts are not) would tend to give the game away. The other "unnatural" components only enhance the notion that Bt genes and other deliberately introduced genes were "designed" to at least a degree.

So why doesn't Behe drive home the point that he delicately prompts, namely the easy manner in which human designs in nature could be detected (though generally they are detected by looking for known specific patterns of "engineered" genes), by recognizing their breaks from the evolutionary patterns? There is only one reason, this being the fact that he can produce nothing that does not fit the expected evolutionary patterns (aside from our own interventions). He wants to suggest in DBB that there is really no problem with deciding that life was designed because we can do it, while he pointedly ignores the fact that our interventions do not follow the (evolutionarily-produced) taxonomic patterns of nature, and also need not rely upon physical precursors (although we often do--yet we produce unnatural patterns even then).

The fact is that, in both of Behe's books, he avoids integrating knowledge. That is unsurprising, since said lack would be expected in a creationist. He'll happily bring up human modification of life as an analogy, but he will not discuss the fact that quite obviously our designs purposefully break the evolutionary patterns, unlike what we see in wild-type organisms. He insists that design can be detected in life (which almost all of us have agreed was possible from the beginning), but he avoids the fact that design would not follow evolutionary patterns, nor would it rely upon physical precursors, as empirically-known evolution does.

The one thing that we would expect almost any kind of biological design to do--step in where evolutionary limits prevent a desired capability--is absent from biology. And even more absurdly, Behe insists that evolution cannot produce complex biology--which conforms to evolutionary limitations--but he insists that design nudged evolution along without producing any of the evidence of genetic modification that even humans have done with their decidedly limited late 20th and early 21st century capabilities. Intelligent intervention is supposed to have occurred, and yet that intelligence didn't dare to break the rules of evolution, or to deviate from evolutionary patterns.

Instead of breaking the evolutionary patterns, as we would expect of design, Behe insists that design is responsible for complex evolutionary patterns. Has any other crank scientist ever worked so hard to avoid the meaningful tests of his claims as Behe has with his "intelligent design"?

8.21.08                                           To top

8. Large questions are fine--if it's the Big Bang

Behe finds fault with scientists who do not accept the evidence when large questions remain:

It is impossible to deny that the Big Bang has been an enormously fruitful physical model of the universe and, even though large questions remain (as they inevitably do in basic science), that model was justified by the observational data. Scientists such as Einstein, Eddington, and Hoyle fudged and twisted in their efforts to resist a scientific theory that flowed naturally from the data because they thought they would be forced to accept unpleasant philosophical or theological conclusions. DBB, 45.

It's now well over a decade since that statement was first made, and still no sign of self-awareness from Behe. In it, he mischaracterizes Einstein's role in the matter as well.

Basic science is not the only type that has many questions left, of course, and it is generally accepted that historical sciences will be increasingly patchy in the details the further back one looks. Not for Behe, though, who blithely demands all of the details. Or rather, he demands all of the details for evolution, but not for geology, for ancient plate tectonics, for the crash of Theia into earth creating the moon, or for the Big Bang. And he certainly does not demand any details regarding his so-called "design," nor even any identifiable causes--instead he resists everything that would be expected from the concept "design," from purpose, to meaning, to rationality, and on to any specific role of intelligence in his supposed "design."

He does thereby implicitly admit, however, that science should be able to come up with answers although ID has absolutely none. There is no way that he can do science with ID to supply any answers, but he can do what every pseudoscientist does to divert attention from the fact that their favorite crank idea has hordes of large questions and no answers, which is to demand that real science supply answers to every question, while completely disregarding the ravages of time on the available evidence:
...Kenneth Miller argued in response [to Behe's "challenge" in DBB] that the two-hundred component cilium is not really irreducibly complex, he offered no Darwinian explanation for the step-by-step origin of the cilium. Edge of Evolution 95
The rank hypocrisy of this is evident by comparing the first and second Behe quotes, above. Behe faults scientists for not accepting the evidence that the Big Bang happened, despite the fact that rather fundamental questions remain about the Big Bang, especially with respect to inflation (without inflation the Big Bang has many unexplained gaps). While the cilium has known precursors homologous with other cellular machinery, is made of the physical precursors that Behe himself states is demanded by evolutionary theory (and is missing the conceptual precursors so common in known design), and is made by genes which have basically the expected relationships and homologies coming from early in eukaryotic evolution.

I will soon deal some with what is known about the evolution of the fundamental biochemistry of biology, not because it is at all fair to judge evolution by its ability to answer the details of long-past evolution for which so little evidence remains as Behe wishes people to believe is a "fair test," but because these are interesting questions which do have rather more answers than Behe admits or addresses. They are interesting in their own right, is what I am saying, and Behe's treatment of them is abysmal. The sound tests of evolution involve the tests of relatedness, not only of organisms, but of the parts ("physical presursors," as Behe notes).

But I thought that, once again, the ground rules have to be in place prior to any such discussions. One of the ground rules is that unanswered questions in science are no show-stopper, and Behe knows this to be the case. He only fully admits it in the latter part of his book when he is criticizing others, though, and not when he is leveling his own illegitimate and almost completely unargued criticisms (he points to complexity, ignores the evidence problems, and points out that questions remain--hardly argumentation in any intellectual sense of the word). I do not doubt that the opening quote appears in the latter part of the book because many people would remember this admission as he tried to make as much as he can of the fact that considerable questions remain from the distant past.

I mean to address some of his questions, not as he demands, but as the available evidence (particularly evolutionary evidence involving various sequencings) actually indicates evolution. Questions remain, but they are not at all as difficult questions as those that continue to vex the Big Bang, or even the collision that is believed to have produced earth's moon. Behe only demands that the hardest evolutionary questions be answered because he has nothing else to throw at it--certainly no evidence in favor of design--and not at all because of any principle of his that science actually requires that the hard questions have to be answered before good explanations are accepted.

8.26.08                                           To top

9. Blood clotting's dependency on Vitamin K leaves us vulnerable

Bleeding disorders also accompany deficiencies in FSF, vitamin K, or α2-antiplasmin, which are not involved directly in clotting. DBB 89

As Behe stresses, the clotting cascade is rather complex, and is vulnerable to a number of disruptions. He wants to make this into an argument against evolution, and yet the dependency of the crucial function of blood clotting on not entirely dependable sources of vitamin K is clearly what would be more expected from the contingencies existing in "Darwinian" evolution, and not of some highly intelligent designer dealing with the issues of complexity and of vulnerability. While vitamin K deficiency is not typically a major threat to human life, in pre-industrial societies vitamin K deficiency is not uncommon precisely when humans are otherwise quite vulnerable, just after birth:
Newborns are especially prone to vitamin K deficiency. A nursing-mother's milk is low in the vitamin; breast milk can supply only about 20% of the infant's requirement. Infants are born with low levels of vitamin K in their body; they do not have any vitamin K-producing bacteria in their intestines. Their digestive tracts are sterile. As a result, a form of vitamin K deficiency, called hemorrhagic disease of the newborn, may develop. This disease involves spontaneous bleeding beneath the skin or elsewhere in the infant's body, and occurs in about 1% of all infants. In rare cases, it causes death due to spontaneous bleeding in the brain.
Source on Vitamin K deficiency

What Behe deliberately tries to do is to blur the differences between evolution and design, mainly because all of the evidence is in favor of evolution. If he really wanted to make a scientific case for design, he'd sharpen the distinctions between the two, pointing out what evolution explains and what design could explain.

Since he dares not discuss the differences, I would like to point out that evolution is what is expected to co-opt already existing pieces into its complexity, so that the result is "good enough." Sure, babies are vulnerable to insufficient blood clotting due to vitamin K deficiency, but most make it without medical intervention. Best of all, vitamin K was available to assist one step of the clotting cascade (p. 84 of DBB). Evolution is often constrained by a lack of needed components to its complexity. Evolution makes do with vitamin K, then, despite the fact that newborns lack crucial sources of vitamin K, and adults can run into deficiencies as well. The point is that already-available vitamin K works much better during evolution than having to evolve something anew from something lacking vitamin K's abilities.

Design, on the other hand, looks ahead to difficulties and tries to make complexity robust against disruptions in nutrition. A designer actually might be quite happy to use vitamin K, then, but would give to mammals the ability to synthesize vitamin K, or otherwise prevent the vulnerabilities that dietary and bacterial supplies of vitamin K pose for us.

Behe fails to bring up these matters, because they would clearly underline the fact that the constraints on evolution that Behe likes to point to have indeed shaped what we are. The designer is concerned about constraints of operation, while evolution is "concerned about" (constrained by, in the more proper non-anthropomorphic terms) its severe restrictions of biochemicals and adaptive abilities to supply function. Thus evolution often fails to provide the kinds of functions that design could provide (although over time, and with reasonably good adaptive pathways to follow, highly efficient systems often do appear), but it does find its way to function in many cases (although many functions, like radio communications, are essentially precluded from biological adaptation).

Vitamin K was adopted during the course of evolution not because it would ensure the kind of clotting function that vertebrates need throughout their entire lives, but because it was already provided by diet and/or bacterial symbionts. It is a "good enough" solution, certainly, yet it is exactly the sort of "solution" that would be expected from undirected evolution, and not from a designer.

8.27.08                                           To top

10. With causes of evolution of clotting given, Behe declares otherwise
Prothrombin appears in an ancient guise with EGF domain(s) attached, the result of a ... protease gene duplication and ... shuffling. DBB 92 (quoting Russell Doolittle)
The above is only one example of a host of instances of duplications and gene shuffling that Doolittle mentions on pp. 92-93 as causes in the evolution of the clotting cascade. And yet Behe has either the stupidity or the dishonesty to write this:
Now let's take a little time to give Professor Doolittle's scenario a critical look. The first thing to notice is that no causative factors are cited. DBB 93
Except that the causative factors were right there in front of his face. He does actually cite them again in the same paragraph, apparently being too dull to recognize a causal factor even when he is writing about it: Doolittle appears to have in mind a step-by-step Darwinian scenario involving the undirected, random duplication and recombination of gene pieces. (Ibid.) Now it's probably true that Behe does not credit those factors as being adequate causes (and note also that he essentially ignores the role of natural selection), and he could argue against them as such. But it's nothing less than dishonest (or the kind of stupidity that precludes honest discussion) to say that causative factors (ones that are clearly documented in the genome) are not mentioned by Doolittle.

There is little reason to try to meet Behe's demands for all of the desired details from a half billions years or more back. The real point is that the evidence does indicate evolution, as even Behe essentially admits in the clotting chapter, "Rube Goldberg in the Blood." And his various writings become painfully contrary to each other as he continually tries to evade the evidence of unguided evolution. In The Edge of Evolution he writes:
Yet genome duplication...and...time seem not to have given baker's yeast any advantage it wouldn't have otherwise have had. EoE 74
Yes, there needs to be selective pressure for duplications to be of any value. More to the point, in the clotting cascade, as well as in many other cases (plants are particularly known to be "evolvable" due to their frequent genetic duplications), the opportunity to evolve advantage does appear to have come partly from gene duplications.

The more I read Behe, the more I recognize these obvious lacunae. He will generalize from a single example, as with the yeast, while completely ignoring the fact that duplications are not expected to always have a dramatic effect and that sometimes they apparently have allowed for dramatic evolution. Plus, one has to wonder how competent he is at any science when he can list the causes that Doolittle adduced for the evolution of the clotting cascade, then to blithely state that no causative factors were cited.

Furthermore, he is clearly treating similar evidence in completely different ways between duplications involved in the origin of the clotting cascade and duplications in yeast. Since he insists that the clotting cascade did not evolve, the duplications behind the clotting cascade are magical, intelligently caused duplications (the "designer" is revealed as supplier of mutations in EoE), and duplications in yeast are merely accidental. How does he know that? Easy, he had already decided that the clotting cascade did not evolve as it appears to have done.

A real scientist looks at the evidence for common descent and apparently random mutations, plus selection, and asks how the clotting cascade evolved by those causes (among others), since one must match up cause and effect in science. Behe is quite the opposite, because he had already decided that life was designed. He simply looks at the sort of evidence he accepts in the evolution of yeast and tries to come up with a "designer" whose causation does not leave effects different from those of unguided evolution (aside from providing a more efficient supply of beneficial mutations, that is), which is easy to do when one's "designer" was always one that could simply "do anything" at all. Proving only that those who won't give up "design" will shift their concept of "the designer" until it can no longer be distinguished from mindless processes.

8.28.08                                           To top

11. The primary issue at stake is the foundation of knowledge

In this cause, therefore, we ought to rest; in this cause the common sense of mankind has, in fact, rested, because it agrees with that which in all cases is the foundation of knowledge,--the undeviating course of their experience. The reasoning is the same as that by which we conclude any ancient appearances to have been the effects of volcanoes or inundations, namely, because they resemble the effects which fire and water produce before our eyes; and because we have never known these effects to result from any other operation. William Paley Natural Theology Chap. 23 (pp. 232-233 in the link)

Paley actually understood the epistemology of science fairly well. As he mentions there, we have to use our experience, our observations of causes, in order to understand the causes behind anciently produced phenomena. We watch what "fire" and water produce today, and if we see what seems to be the results of these particular "forces" in phenomena from the past, we ascribe "fire" and water as the causes of said phenomena.

To be sure, the context of the above quote makes it clear that he believed that design could be properly inferred to be behind the structure and function of animals in the same manner, something that even in Paley's time strained the meaning of experience, considering how different animals are from our own designs. Nevertheless, the principle he called upon for the foundation of knowledge is sound, and not a few considered design to be a legitimate inference prior to the development of evolutionary theory. Dawkins still writes as if it would be a sound inference without Darwin's insights and subsequent developments of theory, although I myself do not think that inferring from human design to a very different sort of "design" in life was ever as clearcut as either Paley or Dawkins consider it to be in the early nineteenth century (many ancients did not see animals mechanistically, so it ap
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