Tuesday, July 29, 2008

This is a review I wrote a while back; due to popular demand (a friend's request), I'm posting it here, for all to read, love, and enjoy. It's a review of Sahotra Sarkar's book, Doubting Darwin?, a critique of Intelligent Design "theory," as well as an all-out attack on Michael "Irreducible Complexity" Behe's strange notions of biology. There is thinly masked disdain, dry humor, and gratuitous flighty/outright insulting rhetoric. It's kind of long. But anyone who gets a kick out of the depravity of creationists just might like it...

Doubting Darwin? by Sahotra Sarkar: Commentary & Review

“That the creationists have resorted to this subversion should surprise none of us, for the ethical poverty of their actions matches the intellectual poverty of their beliefs.” -- Peter Atkins

American author and social reformer Upton Sinclair once said, “It is difficult to make a man understand something when his salary depends on his not understanding it.” Likewise, it is difficult for a man to follow evidence to its logical conclusion when the conclusion demands he abandon his primary source of earthly comfort: his faith. Throwing up a web of fancy words and pseudoscience, man will do whatever he can, for as long as he can, to protect himself and his way of life. Intelligent Design (ID) supporters will exalt any succor they can muster, even if logical flaws, false assumptions and gaping holes riddle its landscape. Few authors have so clearly and decisively dissected these flaws as Sahotra Sarkar in his recent book, Doubting Darwin? Creationist Designs on Evolution.

Doubting Darwin is at once different from and superior to many of the newly popular books on atheism. It addresses the affront of Intelligent Design with patient clarity, covering thoroughly the various historical, biological, philosophical, and social perspectives of evolutionary theory. Sarkar begins by very succinctly outlining the assumptions and arguments, and providing clear definitions for discussion. ID creationism is defined as the fundamental claim that “complex adaptations could not have been produced by natural selection or any natural processes. Their emergence requires the intervention of an extra-natural designer” (Sarkar 2). The Central Argument of ID creationism is then divided into four parts: (1) Evolutionary theory allows only (i) the inheritance of traits, (ii) the occurrence of blind variation, and (iii) natural selection. (2) According to this argument, evolutionary theory cannot yet explain many natural phenomena, particularly, the emergence of biological complexity. (3) This failure is so great, that it demonstrates the lack of evolutionary theory’s conceptual resources to explain the emergence of complexity. (4) There is good reason to believe that the required conceptual resources must include some mechanism of intelligent design. These four points make up what Sarkar describes as the central argument of ID, and are the focus of his book. He proceeds to dismantle these points, and explain how such fallacies emerge. After decapitating the creationist argument, he provides a wealth of evidence – biological, historical, philosophical, and logical – for natural selection as the mechanism of evolution.

It might be interesting to note that Sarkar always refers to Intelligent Design as, “ID creationism,” clearly drawing no boundary between the two. This is justified by his explanation of their existence in the same metaphysical framework, thus subject to the same logical critiques. Sarkar addresses, importantly, the philosophical heart of the matter: ID creationists do not object to natural selection or evolution per se; they object to the entire naturalist framework in which it exists. Naturalism, Sarkar rightly claims, is the true target of ID creationism. Thus, Doubting Darwin is also an explanation and defense of naturalism, or the claim that “the methods of science and its extensions are enough to guide us through the enterprise of obtaining knowledge of the world” (Sarkar 3).

Sarkar explains that ID creationism, cannot survive so long as scientific thought depends upon naturalism – ID creationists do not want to merely get rid of evolution, they wish to eradicate naturalism altogether in order to allow their theory to survive.

Sarkar quotes Michael Ruse in his explanation of what naturalism is, distinguishing between methodological and metaphysical naturalism: “The methodological naturalist is the person who assumes that the world runs according to unbroken law; that humans can understand the world in terms of this law; and that science involves just such understanding without any reference to extra or supernatural forces like God… Metaphysical naturalism argues that the world is as we see it and that there is nothing more.” The difference, Sarkar argues, should be obvious: unlike the metaphysical naturalist, for the methodological naturalist, “whether or not there are supernatural forces or beings is another matter entirely and simply not addressed by methodological naturalism.” This is a strain of positivism in the philosophical environment itself; if it cannot be observed, it should not be commented upon. This approach was popularized by SJ Gould, and (expectedly, given their relationship) rejected forcefully by Richard Dawkins, in his recent and popular attacks on religion. Sarkar, however, brings much more to light about the philosophical troubles with ID creationism; while Dawkins takes a rather ad hominem approach, Sarkar describes exactly the difference in method between evolutionary science (naturalism) and ID creationism (teleology). He is careful to explain that naturalism is as much about the nature of epistemology as it is a thesis within epistemology.

Naturalism, Sarkar maintains, is as fallible as any other claim in science. Naturalism requires a minimal ontological commitment to the primacy of the physical world, and is accepted essentially because the laws of science, so far as we know, also assume the primacy of physical matter. Similarly, he points out that no philosophical or scientific theory will be a “theory of everything,” thus all correlations and connections in which things exist are contingent – not the embodiment of (logically) necessary links (Sarkar 145). A priori justification is not needed or desired; it is perhaps not even possible. Therefore, naturalism does not include other philosophical frameworks on a priori grounds. However, crucial to the defense of naturalism, the warrant for belief within this framework is derived exclusively from the evidence specific to the proposition – and evidence has been historically and generally effective in yielding reliable knowledge (Sarkar 145). Because ID creationism asserts that there is more than the primacy of material, they fit into a framework of super-naturalism, and so cannot contend with scientific ideas in the world of science.

Sarkar further distinguishes himself from many popular critiques of ID by explaining the history of metaphysical changes caused (or forced) by advances in science. Each generation feels as though its intellectual landscape has always been, or that the metaphysics they assume have always been held (at least by all “reasonable” people). We forgive historical figures for their strange views, but we do not always think about how their views came to be, and how they themselves helped dismantle the assumptions that led to those views. Sarkar provides us with a chance to hope for a permanent shift in metaphysics – a genuine end to ID creationism and super-naturalism. There is a likelihood, Sarkar maintains, that a metaphysical shift nearer to naturalism will be inevitable as evolutionary biology advances. He provides compelling historical parallels, from the initial response to revolutionary theories, to the last-ditch attempts to modify a dying metaphysics. He describes the response, for instance, to Newton’s laws of mechanics: laws such as gravity implied a strange sort of “action at a distance,” which was completely foreign to contemporary metaphysics. The mechanical philosophy of his time necessitated that all interactions were mediated by local contact between impenetrable particles of matter. Leibniz referred to Newtonian mechanics as “occult,” or “absurd.” However, it soon became clear that mechanical philosophy lacked the conceptual resources to explain phenomena such as gravity. There were several attempts to resuscitate the mechanical philosophy by slight changes in its central arguments, but eventually Newtonian mechanics forced a change in metaphysics. This is an obvious parallel to the shift from creationism to ID – an attempt to revive creationist theory through the supposedly more scientific Intelligent Design. The surest sign of a metaphysical shift is this last-ditch effort tweaking of the central argument – an argument that finds itself in an increasingly hostile environment must migrate (from the laboratory into the church), adapt (by modifying the explicitly Christian nature of creationism), or die (as Sarkar suggests has happened, and will happen, to dissonant metaphysics and their resultant thoughts).

Sarkar goes on to describe more empirically successful theories once deemed metaphysically impossible. The success of these theories forced changes in metaphysics – in addition to Newtonian mechanics, Sarkar describes general relativity and quantum mechanics, comparing the response to these theories to the response to natural selection. By putting evolutionary theory in its proper historical context, Sarkar enables the reader to envision a world where the teleology of ID creationists is as foreign as other dead metaphysical paradigms. To Sarkar, this is not a unprecedented or unexpected struggle; it was as inevitable as the change in metaphysical perspective that will someday be complete.

The arguments of two prominent ID creationists feature in Sarkar’s analysis. Michael Behe, a biochemist and author of Darwin’s Black Box, describes “irreducibly complex” biological systems, which he maintains could not have emerged through the processes of natural selection, and so must require a designer. Sarkar provides Behe’s definition of an irreducibly complex system (ICS): “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.” Examples of such ICSs include the bacterial flagellum, the blood clotting cascade, and the complement cascade. Indeed, the flagellum is so popular with ID creationists that it features as the chosen emblem (on book covers and blog pages) of Sarkar’s next target: William Dembski. We will return to Sarkar’s critique of Behe’s argument, as well as an extensive look at one of the more serious charges against Behe – an insufficient command of cell and molecular biology. To do so, we will stray from a direct analysis of Sarkar’s criticism, as he could not possibly address the abundance of factual errors present in Behe’s argument in a single book. However, the elaborate dissection of one facet of Behe’s book is necessary to demonstrate the severity of its flaws. In the meantime, we will return to Sarkar’s discussion of William Dembski.

Dembski’s argument for ID begins with what he calls his “explanatory filter.” For Dembski, design is a “logical rather than causal” category, which he attempts to support using plenty of examples of design resulting from conscious human agency. If we ignore the flaw obvious in this logic, we can still be surprised at the flimsy nature of the filter itself. Sarkar breaks the filter down into seven parts: 1) Assume that 3 explanations, Regularity (R), Chance (C), and Design (D), are mutually exclusive and jointly exhaustive explanations of E. 2) Assume that we have a method for determining if E is specified or not. 3) Assume that we should only consider C and D after we reject R, and that we should only consider D if we reject C. 4) If E has a high probability, we should accept R; if not, we should consider C and D. 5) If C does not confer a low probability on E (or if E is not specified), we should accept C, otherwise we should reject C and consider D. 6) Since we have rejected both R and C, we should accept D as the explanation of E. In other words, we never reject D.

According to Dembski’s filter, design is supposed to be inferred if we cannot explain something by regularity or chance (Sarkar 51). The immediate problem is, we are never once invited to consider the probability that D attributes to E – we are never even told what design means, or what a design hypothesis says. Furthermore, Dembski’s filter never addresses the probability that R attributes to E; instead we look only at the probability of E itself. Moreover, the filter provides no threshold filter at which we must reject R, or what probability C must be in order to reject it. The filter never directly addresses the questions at hand.

With Dembski’s filter out of the way, Sarkar turns to one of his even more embarrassing arguments for Intelligent Design. Dembski, himself a mathematician, was very excited by the No Free Lunch (NFL) theorems, proved by David Wolpert and William Macready in 1997. These theorems state that no algorithm (given the set of all possible optimization problems) outperforms any other over the whole set. The first theorem establishes this result for the siuation in which an algorithm only tracks performance during the last generation (as is the case for many genetic/evolutionary algorithms). The second theorem establishes the same result when there is temporal change in the optimization problem and we average over all possible changes (Sarkar 82). In the proofs of these theorems, whether an algorithm is deterministic or stochastic is irrelevant.

The moral of these theorems is beautifully captured by Malcolm Foster’s “toy universe” model: consider a universe in which, on each day, only one of two possibly objects may exist: a sphere (S), or a cube (C). Suppose this universe lasts for exactly two days. If this is the case, the universe has exactly four possible histories: (S, C), (S, S), (C, S), and (C, C). The algorithm used here is supposed to predict what happens on the second day, given knowledge of the first. There are exactly four possible deterministic algorithms: 1) “Same” (same on both days), 2) “Different” (different on both days), 3) “Sphere” (sphere on the second day, regardless of the first), and 4) “Cube” (cube on the second day, regardless of the first). Since each history is equally probable (1/4), each algorithm is equally probable of predicting the second day correctly (1/2). This, when expanded to fit much more general scenarios than this toy universe, is what the NFL theorems mean. Essentially, Forster asserts that we can devise a better algorithm only if we know something empirical about the universe – there is no a priori path to a successful epistemology (Sarkar 84).

These are powerful theorems, and Dembski was certainly impressed, even entitling his book on the subject, No Free Lunch. Unfortunately, as Sarkar illustrates, he is far more impressed with his misinterpretation than their reality. Wolpert himself, who initially proved the NFL theorems, writes in his review that Dembski’s book “is written in jello. There is simply not enough that is firm in his text, not sufficient precision of formulation, to allow one to declare unambiguously ‘right’ or ‘wrong’ when reading through the argument” (Sarkar 86).

But let us ignore, for the moment, what others have said, and examine Dembski’s argument itself. In his own words, Dembski aims to demonstrate the inadequacy of the Darwinian mechanism to demonstrate complexity… By assimilating the Darwinian mechanism to evolutionary algorithms, [Darwinists] have invited a mathematical assessment of the power of their mechanism to generate life’s diversity. Such an assessment, begun with the No Free Lunch theorems of Wolpert and Macready, will be taken to their logical conclusion. The conclusion is that Darwinian mechanisms of any kind, whether in nature or in silico, are in principle incapable of generating specified complexity.

The problem with Dembski’s argument is, it lacks any mathematical or technical relevance at hand; the book, Sarkar claims, is “lacking in technical result, while replete with mathematical formalism well designed to impress the book’s likely readers, who are neither mathematicians nor evolutionary biologists” (85). To use the timeless words of Wolfgang Pauli, “It’s not right. It’s not even wrong.”

To achieve the result he claims to, Dembski would have had to establish that evolution can be viewed formally as an optimization problem (or else, the NFL theorems do not even apply). Since natural selection is very basically not the only factor involved in evolution, there is no optimization problem at hand. To this, Sarkar justifiably dismisses Dembski’s argument as “an exercise in irrelevance” (85).

Sarkar’s book is one of the best critiques of Intelligent Design available; he expertly and forthrightly cuts away at insufficient argument – his most remarkable feat is perhaps the comprehensiveness with which he calmly strips away the superfluous claims to reveal the untenable nature of the ID creationist position. There is little retort Dembski, Behe, or other ID creationist could make to put a dent in Sarkar’s analysis. There is little left to argue with, once Sarkar is through. However, there is one characteristic of ID creationism that Sarkar could not possibly have covered in a single book – the multiplicity of factual errors in – not just evolutionary logic – but in simple cell biology – made by the most prominent biological refutation of evolution by natural selection.

Behe, a biochemist by occupation, produced a biology-heavy work in 1996, claiming that the principles of cell biology did not support accepted theories of evolution. He returns, again and again, to the notion of “irreducible complexity” – although his book is stunningly full of both biological and logical errors and omissions. As Sarkar explains, “Many of [Behe’s] critics – though Johnson and Behe try to deny this – also questioned Behe’s command of the relevant biology. Behe’s recent criticisms of evolutionary theory have also been met with serious – and devastating – response from biologists” (Sarkar 96). Although the fallacies in Michael Behe’s Darwin’s Black Box are vast and easy to spot, there are still many who hail his work as proof of the Bible itself. The multiplicity of errors present in Behe’s work could not be properly responded to without the equivalent of another book. However, we may select one facet of his argument, and examine the biology itself a little more closely, in order to understand the quality of information – and alarmingly bland imagination – being supplied by ID creationists. Sarkar dismantles Behe’s discussions of the bacterial flagellum, the citric acid cycle, and the blood clotting cascade. We will now turn to a study of Behe’s discussion of the human immune system.

In chapter six of his anti-Darwinist crusade, Behe attempts to use immunological arguments to support ID creationism. He launches a three-pronged attack on the unlikely evolution of three complex immunological systems: clonal selection, V(D)J recombination, and the complement cascade. Behe amasses his evidence, carefully building his argument that the human body is filled with biochemical processes that are irreducibly complex, and therefore impossible to evolve. Recall his definition of an ICS: “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 stop functioning(Behe 39). The only way such complicated systems could have arisen, Behe asserts, is through careful and Intelligent Design. Fortunately for Darwin, Behe’s analysis is filled with fatal mistakes and pitiful logic, exhibiting from a lack of background in evolutionary biology, and a tragic deficiency in critical thinking and reasoning skills.

He poses as one providing the reader with expert biological analyses, which are in fact filled with errors, omissions, and outright untruths. His careful misportrayal of the function of antibodies is as almost as convincing as it is inaccurate.

He compares antibodies to toy darts, claiming them to serve only as markers for macrophages, which will then know what to destroy. He goes on to describe the complement system, and the complex set of genes that make up the adaptive immune system’s massive repertoire. Each is dependent on the other, Behe argues; the system is irreducibly complex. Spanning several pages, Behe elaborates on his notion that antibodies serve no purpose other than to mark something for death, and can harm nothing on their own. The most amazing thing about this statement is, it’s just plain wrong. An counterexample coming immediately to mind is hemolin, a protein found in moths. It is almost identical in sequence to antibodies found in higher vertebrates. It binds, generically, to bacteria, causing lysis or precipitation out of the hemolymph (Beck 63). Furthermore, antibodies often serve as catalysts in biochemical reactions. These are widely-known facts that one assumes – for the sake of Behe’s dignity – have been intentionally ignored.

It is also the role of antibodies to neutralize toxins; by binding to the active site of a molecule of poison, the antibody can effectively deactivate it and render it harmless. This is the principle that allows the DPT vaccine to work; the vaccine stimulates the production of the antibodies that can neutralize the relevant toxins (Robison 8). Moreover, antibodies are capable of binding to and disabling viruses, by wedging themselves into the virus’s molecular “hinge” which allows it to infect a cell (Robison 5). Lastly, antibodies are well-known to precipitate targeted bacterial or viral proteins out of solution; if enough antibodies bind to a structure, it will lose its structure, and by extension, its function.

Behe is also not being entirely truthful when he claims that we have no hypotheses on how the enormous repertoire of antibody diversity could have possibly evolved. The V(D)J-C (Variable, Diversity, Joining - Constant) gene schematic is the mechanism for antibody assembly in gnathostomes through primates. In humans, antibody genes are mixed and matched; a little bit of each kind (V, D, and J) DNA is needed to be complete. An antibody gene consists of one V-segment, one D-segment, one J-segment, and one C-segment, each of which are drawn from huge pools of DNA segments. A human antibody can be labeled as V3(D2)J7-C, or V21(D17)J34-C.

But in sharks, the VDJ segments are already assembled; that is, the antibody genes are V5(D5)J5-C, or V21(D21)J21-C. The genes are prearranged in long strings of such assembled genes, called tandem arrays. Our understanding of tandem arrays and the genetic processes that can generate them is well-developed. From these tandem arrays, it is just a short step in evolutionary time to generate the arrangement found in man. Deletions, working in conjunction with secondary expansions caused by tandem duplication, can easily lead to the V(D)J system present in humans (Litman 73). And even if Behe were intelligent enough to argue that this arrangement is useless without the splicing machinery, the presence of a V(D)J system in sharks indisputably disproves Behe’s notion that antibody diversity requires splicing machinery in the first place.

There are many more fascinating clues to possible evolutionary origins to the adaptive immune system which are conveniently absent from Behe’s arguments. The intriguing similarities in molecular structure of antibodies to those involved in immune recognition, and especially those involved in cell-to-cell (non-immune) recognition. Why the resemblances? The recombination machinery which builds antibodies is, interestingly, active in vast regions of the brain; could antibodies have evolved from cell-to-cell recognition molecules? It certainly seems likely.

After reviewing Behe’s lack of immunological understanding, it is easy to conclude that his ideas about Intelligent Design are just as unsound. However, even if his biology was accurate, his central argument is hopelessly flawed, his logic doomed; even if his descriptions of the “irreducibly complex” systems were correct, even if there were no misleading omissions or subtle manipulation of the facts, his pretenses still, inevitably, collapse.

Sarkar reminds us that all of these cases are attempts by Behe to demonstrate the irreducible complexity of the immune system. Behe uses his favorite example, the mousetrap, to illustrate: a mousetrap has a clearly defined function (squashing mice), and is composed of several interacting parts (platform, spring, bait, metal bar for squashing, etc). Behe describes this system as irreducibly complex; if you remove any one of the interacting parts, the mousetrap will no longer be able to perform its function, and no mice will be squashed by that particular mousetrap.

This metaphor, Behe maintains, extends into the biochemical processes that keep us alive. Behe’s claim is that the adaptive immune system is so complex, with each antibody binding perfectly to its antigen, that there is no way it could have evolved. “There are billions of different kinds of antibodies… Could this system have evolved step-by-step? … In a simplified scheme, we are left with three critical ingredients: (1) the membrane-bound form of the antibody; (2) the messenger; and (3) the exported form of the antibody. If any of these parts is missing, the system fails to function” (Behe 124). As Behe rightly states, we gain nothing by replacing a problem with a miracle, so it is best to disregard statistically impossible explanations. In so doing, Behe rejects any possible Darwinian explanation for the evolution of such a complex system. This, however, is a fatal error: a solution does exist.

Ignoring the possible but highly unlikely chance that all genetic mechanisms to produce the immune system arose at the same time, or the idea that the parts of this “irreducibly complex” system evolved separately for other purposes and then joined together by accident to create adaptive vertebrate immunity, there is a very simple, and very Darwinian, explanation.

A system deemed irreducibly complex can be built step-wise, through the gradual addition of parts that are, initially advantageous, but become, because of later changes in the system or environment, essential for proper functioning. Sarkar quotes biologist H. Allen Orr’s response to irreducible complexity:

An irreducibly complex system can be built gradually by adding parts that, while initially just advantageous, become – because of later changes – essential. The logic is very simple. Some part (A) initially does some job (and perhaps not even very well). Another part (B) later gets added because it helps A. This new part isn’t essential, it merely improves things. But later on, A (or something else) may change in such a way that B now becomes indispensable. This process continues as further parts get folded into the system. And at the end of the day, many parts may all be required.

This applies also to the example at hand. Imagine that gene X encodes a protein that performs a certain function. Somehow, gene Y is acquired through mutation, and is selected for because it coincidentally helps with the function of gene X. Gene Y is not, at first, crucial, it simply improves upon what already occurs. Eventually, whether through changes in the organism or environment, gene Y becomes an essential part of the function initially only performed by gene X. This compounds over time, and can easily, over billions of years, become “irreducibly complex.” This step-wise refutation of irreducible complexity originates in 1918, refined later in 1939, with the writings of H. J. Muller, giant in genetics, and winner of the 1946 Nobel Prize in medicine for his work on artificially-induced mutations and genes.

This is also one of the thrusts behind the Red Queen Theory of Evolution, named after Lewis Carroll’s character in Through the Looking Glass. In her world where the landscape was a treadmill, the Red Queen said, “It takes all the running you can do, to keep in the same place.” It suggests that a species may have to evolve quickly just to hold on to its particular niche, which would plausibly explain the emergence of “irreducibly complex” systems.

Behe depends upon his “irreducibly complex” argument to attack biochemical cascades, in particular the blood-clotting and the complement cascades. He states, “Because of the nature of a cascade, a new protein would immediately have to be regulated. From the beginning, a new step in the cascade would require both a proenzyme and also an activating enzyme to switch on the proenzyme at the correct time and place. Since each step necessarily requires several parts, not only is the entire blood-clotting system irreducibly complex, but so is each step in the pathway” (Behe 87). This statement is earlier contradicted by Behe himself, when he describes how the blood-clotting cascade is capable of starting on its own: “it seems there is always a trace of thrombin in the bloodstream. Blood clotting is therefore auto-catalytic, because proteins in the cascade accelerate the production of more of the same proteins” (Behe 83). (Interestingly enough, it is often the hypothesis of an auto-catalytic set that would bolster the idea of our primordial soup origins, as complex systems analysis grows as a field, we uncover more and more data illuminating the evolution of auto-catalytic biophysical systems (Waldrop 87).)

Behe’s skill at manipulation is not to be underestimated; his gentle, confident tone and tactically humble encouragement of the reader to double-check the facts are handy tools to maintain the illusion of his authority. Behe does not hold a degree in evolutionary biology; he is a biochemist by education and practice. Evolutionary biologists have openly questioned his knowledge of basic evolutionary concepts such as soft selection, Muller’s ratchet, or the Fundamental Theorem of Natural Selection (Orr 7). The problem with his reasoning is that it is an “argument from ignorance” (Robison 2); Behe is saying that because we don’t know how the “irreducibly complex” immune system evolved, it didn’t evolve. This painful, pseudo-logic has led Behe to arrive at a conclusion based on a lack of information. It takes a remarkable lack of imagination to believe in irreducibly complex systems; any healthy mind with biological training may conceive of how these systems may have evolved.

Even if Behe had provided us with an interesting and valuable critique to evolution, which closer evaluation reveals is not the case, his reasoning falls apart when he tries to use arguments against evolution as support for intelligent design. This deceptive logic is another of Behe’s traps; it is like trying to argue for the health benefits of Coca-Cola, using evidence that Pepsi is unhealthy. This sort of negative argumentation is utterly useless without an alternative and testable hypothesis.

This trap, along with the deliberate omission of information about the function of antibodies, misleading metaphors, and unfounded assumptions, whether tactical or sincere, are quite suspicious when viewed alongside stunningly false statements, such as the one appearing on page 179: “There has never been a meeting, or a book, or a paper on details of the evolution of complex biochemical systems.” Ignoring papers such as the four published by a single lab (Melendez-Hevia) in 1985, 1988, 1990, and 1994 on the evolution of the pentose phosphate pathway, and a 1993 paper on glycogen biosynthesis, which cite other analyses of Krebs cycle evolution, published in 1981, 1981, 1985, 1987, 1987, and 1992. Furthermore, there were two entire books published on the subject within three years of his writing. Behe also decides to ignore the paper published a month before Darwin’s Black Box, entitled, “The puzzle of the Krebs citric acid cycle: Assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution” (Mendelez-Hevia 1996).

Behe’s brand of criticism consists of disregarding relevant facts, pretending that data does not exist, and claiming that the lack of the data he intentionally ignores proves his theory. Convinced of his own brilliance, Behe writes, of his own part in the “discovery” of intelligent design, “It is so significant that it must be ranked as one of the greatest achievements in the history of science… rivaling those of Newton and Einstein, Lavoisier and Schrodinger, Pasteur, and Darwin.” The rest of the scientific community can only shake their heads in amazement, wondering how a scientist with a clear creationist agenda, who is very untrained in evolutionary biology, can get such a fancy publication deal on a subject he clearly knows nothing about.


1. Sahotra, Sarkar. Doubting Darwin? Blackwell Publishing. 2007.

2. Behe, Michael. Darwin’s Black Box: The Biochemical Challenge to Evolution. The Free Press. 1996.

3. Litman, Gary. “Sharks and the Origins of Vertebrate Immunity.” Scientific American. November 1996; 60-66.

4. Beck, Gregory. Habicht, Gail. “Immunity and the Invertebrates.” Scientific American. November 1996; 67-71.

5. Melendez-Hevia, Waddell & Cascante. “The puzzle of the Krebs citric acid cycle: Assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution.” Journal of Molecular Evolution, Sep 1996, 43: 293-303.

6. H. J. Muller, "Reversibility in Evolution Considered from the Standpoint of Genetics". Biological Reviews 14 (1939): 261–80.

7. Orr, Allen H. “Darwin v. Intelligent Design (Again)”. Boston Review. Jan 1997.

8. Robison, Keith. “Darwin's Black Box: Irreducible Complexity or Irreproducible Irreducibility? Dec 11 1996.

9. Waldrop, Mitchell. Complexity: The Emerging Science at the Edge of Order and Chaos.

Simon & Schuster. 1992.

Friday, July 25, 2008

There are an incredible number of things happening in the world, and we can read about them on the Internet. For instance, did you know that some Portuguese researchers created paper-based transistors? Yeah, pretty soon, we'll be writing code literally.

(Credit: CENIMAT)

There are also excellent comedians in the field of 12-tone music. Read what might have happened had Schoenberg had made cereal instead of compositions. Alternatively, re-live your favorite moments from the Second Viennese School. Music not your thing? Perhaps that's because it's witchcraft, plaguing our youth and disparaging our culture.

Welcome to the Internet, where insanity reigns.

Whilst mopping the kitchen at 5:00AM on this lovely evening, I was struck by an idea so brilliant, so perfect -- so obviously the result of divine inspiration -- I simply had to share. It is possible that I've been inhaling too many cleaning products, but I've come across a way to reverse that unfortunate trend of everything looking hotter while you're drinking:

Thursday, July 24, 2008

I'd like to begin the day by asking the reader to take a moment and imagine all the potential abuses of this technology: slydial.com. "I don't understand, I called you in advance to tell you I was sick..." Will we ever trust voicemail again? This is akin to a real version of Google's Custom Time prank, sans the self-restraint even Google's prank squad displayed ("Our researchers have concluded that allowing each person more than ten pre-dated emails per year would cause people to lose faith in the accuracy of time, thus rendering the feature useless"). How long will it be before the upper echelons of the corporate hierarchy get wise to this scheme, this latest friend of the Internet-surfing slacker? How long will it be before we ourselves begin hating it? I'm glad I ignore all my voicemails anyway; now I can ignore them for a reason.

Before I hightail it over to the lab, I'd like to share something I'd buy if I had $25 that I needed to get rid of. They are tablet-versions of the Miracle Fruit (Synsepalum dulcificum) -- flavor-tripping berries. These berries, from West Africa, are supposed to make sour foods sweet, distorting your tongue's sour receptors for 20-30 minutes. Evidently, this results in a bunch of sophisticated people chugging hot sauce, remarking on its saccharine qualities. These tablets, however, are supposed to last up to six hours. Sadly, I have not yet tried these berries, but I just might have to throw an unusual (flavor-tripping) birthday party this year...

Wednesday, July 23, 2008

Friday, July 18, 2008

Louis Untermeyer, ed. (1885–1977).

Modern American Poetry. 1919.

GOD, though this life is but a wraith,

Although we know not what we use,

Although we grope with little faith,

Give me the heart to fight—and lose.

Ever insurgent let me be,


Make me more daring than devout;

From sleek contentment keep me free,

And fill me with a buoyant doubt.

Open my eyes to visions girt

With beauty, and with wonder lit—


But always let me see the dirt,

And all that spawn and die in it.

Open my ears to music; let

Me thrill with Spring's first flutes and drums—

But never let me dare forget


The bitter ballads of the slums.

From compromise and things half done,

Keep me with stern and stubborn pride;

And when at last the fight is won,

God, keep me still unsatisfied.

Platform Planning Meeting: "This is Democracy"

This Saturday, July 19, 2008, from 2:00-4:00PM, come to an official Barack Obama Platform Planning Meeting in Hyde Park. Details and RSVP through this link. Hope to see you there!

Tuesday, July 15, 2008

I has a kitteh!! And she is love.

Stopping by Digg on a Work-Filled Evening (with apologies to Robert Frost):

Whose dreams these are I think I know,
Her boss is on the campus, though;
He will not see me stopping here,
To bask in this screen's pale blue glow.

My little cat must think it queer
To ignore life year after year,
But between downtown and the lake,
All the world exists right here.

Her tranquil mind cannot partake
In hours spent alive-asleep;
Was ARPA's child a mistake?
This online world I cannot break.

The web is vast and talk is cheap,
But I have promises to keep,
And hours to go before I sleep,
And hours to go before I sleep.

Wednesday, July 09, 2008

It's been over two years since this blog was born, and over five months since my last post. I should correct that... What shall I talk about? Ah, I know.

Religion. Religion is still as misguided as ever, but atheists have risen spectacularly to the task of proving that "reasonable" folk, too, can be utterly moronic. The point of atheism is to maintain a healthy skepticism, an honest humility, and an acceptance of what one does not and cannot know. The point is not to jump down the throat of those who are as ignorant of their views as you are of yours. A bad atheist is just as dangerous, just as pathetic, and just as stupid as a bad theist.

I'm reminded of a conversation I had just over a year ago with Leon Kass. As I tentatively made clear my transhumanist tendencies, he expressed -- to my surprise -- a form of relief, instead of the hostility I was expecting. He said he'd rather deal with people who were aware of technology's potential -- for good and for bad -- than those who were completely in the dark about the possibilities. This, I think, is a good stance to take. It's better to face an enemy who is educated in his weapon of choice; such people exhibit intelligence, caution, respect, and skill, and are far more worthy of triumph or defeat.

If you're a radical atheist, and believe me, I can be, remember your reasons for it. Remember why you became an atheist in the first place. Most atheists I know (e.g., atheists pre-Dawkins et al) became so independently, often secretly, because their intellectual paths forced them there. I, for one, did not want to stop believing in God. The idea of an all-knowing, all-loving, all-merciful God is a great concept -- our lives are guaranteed to mean something. There is an answer, and a fairly simple one at that. This sort of God may very well exist, although I'm inclined to doubt it. As a little girl, I wanted desperately to be like the God-loving heroines I read about in books; I valued very highly the virtues I read about, including the deep piety exhibited by all my childhood heroes. As an almost laughably spiritual kid, I'd skip classes in elementary school (sorry, Mom and Dad) to climb trees and tell God what was on my mind. I very much believed He was listening, although I never once expected him to talk back. I'd often feel guilty for wasting his time with my silly observations, and foolish laments (often over dead birds or wounded snails), so I instead spent hours praying for people I didn't know, generically hoping that everyone would be okay.

I remember finding a book on prayer in the back of a classroom (Mr. Marshall's room, in case anyone who reads this went to Highland Oaks Elementary in the early 1990's). Skimming it led me to believe that this was a secret method for actually communicating with God -- a hotline to the Deity himself! I remember furtively copying the Lord's Prayer into my own notebook, so that I could try it myself later that day. It became almost an obsession; I'd recite it in my head as I walked to school, to classes, as I fell asleep. It didn't matter that He never answered back; He's God, He's not supposed to respond to humans. We were supposed to accept our place happily, and I did. Knowing that God was real, that he was listening, and that I loved Him -- all of these things brought me almost constant elation.

Anyone who says that even theists aren't happy all the time is not a good theist -- if you truly believe, with every breath, that there is an all-forgiving God who loves you, you will always be happy. Moments of unhappiness are moments of weakness that are quickly corrected, when you remember how the universe truly works. This life is important, sure, but it's nothing compared to the totality of God and His plans. Hardships are merely opportunities for you to smile upwards and thank Him for giving you this test. If you are worried about yourself, ever, as a Christian, you're doing it wrong. Needless to say, elementary school was overwhelmingly the happiest time of my life.

I remember, even further back, my mother telling me as a toddler about Karma. I wildly misinterpreted the concept -- I believed that she was describing a physical law, and that there were actual, physical repercussions based on good and evil deeds. This, combined with being told that God and Christ were real, absolute figures, skewed my thinking for years. Of course, this is why most children brought up in a religious household are themselves religious; kids take everything literally, and parents are incapable of telling a lie. Parents are also incapable of not having an answer.

In fourth grade, I switched elementary schools, and had to do my first ever science project. (If this were a Christian blog, you'd insert ominous music here.) Terrified of looking stupid -- I had never done a science project before, and all the other kids had been doing them since first grade -- I tried to learn everything I could about doing science. I found a book on science projects, interestingly (or perhaps not) also in the back of Mr. Marshall's classroom.The first time I read the scientific method, I didn't understand it. The second time, something was involuntarily electrified in my thoughts -- this was a method of knowing truth! Truth! The most important thing possible! Previously, I had constant faith that truth existed, and that it was knowable -- but this was how to actually make it known! I was as excited as I was when I found the book on prayer -- this was a way to communicate with the absolutes, the only things that mattered. I thanked God almost constantly for months. I kept reading.

Thus began my career in science; a desire to learn the Truth at all costs (and let me tell you, being a nerd all your life has its costs. How many people will have to tell their grandkids that they missed their senior prom for an international science fair?). I kept reading, kept questioning, and kept familiarizing myself with increasingly nuanced scientific thought. For a long time, God and science were not incompatible; they were the same thing. And for a lot of people, this is still the case; they managed to understand in a way that I could not. The threads of positivism are so deeply and beautifully woven into the fabric of scientific thought, that I was at long last forced to reluctantly give up my all-consuming belief in the Christian God. This was not desired; it was merely necessary. I do not regret it.

Real revolutions are not those declared -- they are those resigned to, those forced upon the unwilling; they are the uprooting and often unpleasant changes brought to the door of the disinclined yet prepared. If you became an atheist because you consider yourself a rebel, or because your friends are, or because you think PZ Myers is cool, you are not an atheist. You are a child, or an idiot. You owe a great deal of historical debt to religion, whether you like it or not. You must cast off God with reluctance and acceptance of this debt. You must move forward only because you are compelled to, by your own independent and rational thought. You are not an atheist -- just as you are not a theist -- unless you've earned it.