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Response to Dr. Joan Roughgarden's Review of Michael Behe's The Edge of Evolution

By Casey Luskin

In her online response to Michael Behe's book The Edge of Evolution, "A matter of mutation," Joan Roughgarden, an evolutionary biologist at Stanford, makes some standard--though misplaced--objections to intelligent design (ID). She also misunderstands some of Michael Behe's core arguments in The Edge of Evolution and misconstrues the nature of evolutionary biology.

Precursors to the Flagellum?
Dr. Roughgarden opposes irreducible complexity, writing: "The structures thought to be irreducibly complex aren't; precursor structures can be identified whose modification can lead to a flagellum—or any other trait, for that matter."

So, what exactly are those precursors? Dr. Roughgarden doesn't say, but she probabably has in mind the type III secretory system (T3SS). But leading biologists argue that phylogenetic data implies the T3SS could not have been a a precursor to the flagellum. As Miltaon Saier writes: Fla systems have been able to diverge in structure so as to span either one membrane or two in the envelopes of Gram-positive and Gram-negative bacteria, respectively. So why haven’t TTSSs? The most plausible explanation considers that TTSSs arose late from pre-existing Gram-negative bacterial Fla systems.

(Milton H. Saier, Jr., Evolution of Bacterial Type III Protein Secretion Systems, Trends in Microbiology, Vol. 12:113 (2004).)
Flagella are thought to exist in some of the earliest known bacteria, long before the existence of eukaryotes. Given that T3SSs are used by bacteria to infect Eukaryotic cells, it makes sense that they would not arise as a precursor to flagella. They would seem to necessarily predate flagella.

Misunderstanding the Scope of Intelligent Design
Dr. Roughgarden then critiques ID as follows: "Furthermore, ID advocates don't offer any hypothesis about what happened in the evolutionary past—where, when and how did the designer give bacteria their flagella?"

Dr. Roughgarden’s critique is ironic given that evolutionary biology has also told us virtually nothing about where, when, and how bacteria got their flagella. As a paper in Nature Reviews Microbiology stated in 2006, “the flagellar research community has scarcely begun to consider how these systems have evolved.” That rhetorical rebuttal aside, Dr. Roughgarden overstates the scope of ID if she expects the theory of ID to answer all of those questions.

ID is a theory about detecting design, and ID is very good at determining whether a structure arose as a result of intelligent causation. Some questions about the deep past—such as exactly where, when, or how flagella arose—may be difficult to assess. But it’s a logical fallacy to state that a theory’s non-answering of one question implies that the theory doesn’t answer another question, or that the theory is worthless. ID theorists can answer the question of whether the flagellum was designed.

Thus, Roughgarden is making a cheeky and fallacious objection to design based upon the false premise that if ID does not answer all questions, then it’s worthless. IDEA’s FAQ: FAQ: How or When did the designer do the designing? explains this as follows: Intelligent design theory can only detect that which is empirically detectable via the scientific method. Epistemological theory limits the explanatory scope of any scientific theory. It may (or may not) be possible to determine exactly "how" or "when" the designer did the designing--it just depends on what is theoretically possible to empirically determine. But we don't have to be able to answer these questions to know that the object in question was indeed designed. Nonetheless, the reality is that ID can lead to advances in a variety of different fields, and is useful for explaining a wide variety of data, including in fields such as:
  • Biochemistry, where ID explains and predicts the presence of high levels of complex and specified information in proteins and DNA;

  • Genetics, where ID predicts and explains function for so-called “junk” DNA while neo-Darwinism stifles such research;

  • Systematics, where ID explains why there are similarities between living species, including examples of extreme genetic “convergence” that severely conflict with conventional evolutionary phylogenies;

  • Cell biology, where in the words of Jonathan Wells, ID explains why the cell resembles “designed structures rather than accidental by-products of neo-Darwinian evolution,” allowing scientists to better understand the workings of molecular machines;

  • Systems biology, where ID encourages biologists to look at various biological systems as integrated components of larger systems that are designed to work together in a top-down, coordinated fashion, which is what biologists are finding is the case;

  • Animal biology, where ID predicts function for allegedly “vestigial” organs, structures, or systems whereas evolution has made many faulty predictions here;

  • Bioinformatics, where ID explains the presence of new layers of information and functional language embedded in the genetic codes, as well as other codes within biology;

  • Information theory, where ID encourages scientists to understand where intelligent causes are superior to natural causes in producing certain types of information;

  • Paleontology, where ID's prediction of irreducibly complexity in biological systems explains paleontological patterns such as the abrupt appearance of biological life forms, punctuated change, and stasis throughout the history of life;

  • Physics and Cosmology, where ID encourages scientists to investigate and discover more instances of fine-tuning of the laws of physics and properties of our universe that uniquely allow for the existence of advanced forms of life.
  • Miscasting ID as a Mere Negative Critique Against Neo-Darwinism
    Rougharden then tries to cast ID as a purely negative argument against evolution, stating: "The ID position wound up being a litany of complaints against Darwin rather than a scientific hypothesis in its own right."

    Again, Dr. Roughgarden misunderstands ID. As stated in the IDEA FAQ, “ FAQ: Does intelligent design make predictions? Is it testable?,” ID makes the following testable predictions: (1) High information content machine-like irreducibly complex structures will be found. (2) Forms will be found in the fossil record that appear suddenly and without any precursors. (3) Genes and functional parts will be re-used in different unrelated organisms. (4) The genetic code will NOT contain much discarded genetic baggage code or functionless "junk DNA". Thus, Dr. Roughgarden has tried to recast ID according to her own false misconceptions about the theory, not according to how ID proponents have actually formulated it.

    For example, at the Dover trial, ID proponents were extremely clear that ID is not merely a negative argument against evolution but uses a strong positive argument, as Michael Behe testified, “This argument for design is an entirely positive argument. This is how we recognize design by the purposeful arrangement of parts.” (Day 10 AM Testimony, p. 110.) Behe also made this clear in the afterward to Darwin’s Black Box, stating: “[I]rreducibly complex systems such as mousetraps and flagella serve both as negative arguments against gradualistic explanations like Darwin’s and as positive arguments for design. The negative argument is that such interactive systems resist explanation by the tiny steps that a Darwinian path would be expected to take. The positive argument is that their parts appear arranged to serve a purpose, which is exactly how we detect design.” (Darwin’s Black Box, pp. 263-264 (2006).)

    Scott Minnich and Stephen Meyer also explain the positive argument for design: “Molecular machines display a key signature or hallmark of design, namely, irreducible complexity. In all irreducibly complex systems in which the cause of the system is known by experience or observation, intelligent design or engineering played a role the origin of the system … in any other context we would immediately recognize such systems as the product of very intelligent engineering. Although some may argue this is a merely an argument from ignorance, we regard it as an inference to the best explanation, given what we know about the powers of intelligent as opposed to strictly natural or material causes.” (“Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic Bacteria,” in Proceedings of the Second International Conference on Design & Nature, Rhodes Greece (2004).)

    ID is thus not merely a negative argument against evolution but is based upon finding in nature the types of complexity which in our experience derive from intelligent causes. Stephen Meyer makes this point clear in a scientific paper published in Proceedings of the Biological Society of Washington: “Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source from a mind or personal agent.” This specified complexity, also called complex and specified information (CSI), is a tell-tale indicator that intelligence was at work. Meyer explains why this makes for a positive—not negative—argument for design: “by invoking design to explain the origin of new biological information, contemporary design theorists are not positing an arbitrary explanatory element unmotivated by a consideration of the evidence. Instead, they are positing an entity possessing precisely the attributes and causal powers that the phenomenon in question requires as a condition of its production and explanation.”

    Thus, it seems that ID does not simply state itself as a negative critique of evolution, but tries to formulate a positive hypothesis that can be tested.

    Misconstruing Behe’s Argument
    In Roughgarden’s critique, she writes: "Behe's new book recasts the ID position. Gone is the focus on irreducibly complex structures; in its place is a concern for the rate and randomness of genetic mutation. Most of the book is about the implications of genetic mutation," later saying "he has replaced his early naive claims about irreducible complexity with a more sophisticated argument about whether sufficient genetic variation exists upon which natural selection can act."

    This misrepresents Behe’s argument. The Edge of Evolution in no way backs away from the argument for irreducible complexity. Behe makes this very clear in the book: And now the problem of its irreducible complexity has been enormously compounded. Let's reconsider the mousetrap--the paradigm of irreducible complexity I discussed in Darwin's Black Box. A standard mechanical mousetrap needs multiple parts to work. If the spring is removed or a metal bar broken, the trap won’t catch any mice. Despite the imaginative but dubious efforts of Darwin fans over the past decade, it's extremely difficult to see how something like a mousetrap could actually evolve by something akin to a blind Darwinian search process. But now let's move beyond the structure of just the mousetrap itself. Imagine an automated mousetrap factory that assembled the parts of the trap, set it, and reset the trap each time it went off. Clearly the complexity of such a system is much greater than the complexity of the mousetrap alone. And just as the odds against winning a Powerball lottery skyrocket the more numbers you have to match, the difficulty of explaining how a mousetrap-making system could arise by "numerous, successive, slight modifications" (as Darwin required of his theory) rises exponentially the more separate kinds of parts the system contains.

    (Michael Behe, The Edge of Evolution, Pg. 94 (2007).)
    This quote comes from a section in Behe’s book titled “irreducible complexity squared.” (pg. 93) which discusses how when we take into account the need for coherent assembly instructions for irreducibly complex systems, we get Far from abandoning arguments from irreducible complexity, Behe seems to be claiming in The Edge of Evolution that irreducible complexity is far greater than we first imagined. Thus, he says when discussing the cilium that “Despite the amazing advance of molecular biology as a whole, despite the sequencing of hundreds of entire genomes and other leaps of knowledge, despite the provocation of Darwin’s Black Box, in the more than ten years since I pointed it out the situation concerning missing Darwinian explanations for the evolution of the cilium is utterly unchanged.” (pg. 95) It sure doesn’t seem like Behe is abandoning the argument from irreducible complexity. But what he does address in The Edge of Evolution is that evolutionists have responded with outlandish appeals to indirect, non-Darwinian evolutionary explanations that would require mutations that do not necessarily yield any functional advantage. Behe thus calculates how easily complex features requiring multiple mutations can evolve. This leads to Roughgarden’s next misplaced critique.

    Misunderstanding Behe’s Chloroquine Resistance Calculations Dr. Roughgarden alleges that Behe discounts the possibility that mutations involved in the evolution of malarial resistance to chloroquine requires that multiple mutations must occur simultaneously to be effective. She thus writes: ”Behe doesn't spell out exactly what he is assuming in his calculations, but evidently he is supposing that the resistance to chloroquine requires two unique mutations that must occur simultaneously to be effective." But on his Amazon blog, Behe has responded to these sorts of charges, making it clear that in The Edge of Evolution his arguments about obstacles to the evolution of chloroquine resistance requires no such assumptions: The number of one in 1020 is not a probability calculation. Rather, it is statistical data. It is perhaps not too surprising that both Miller and Coyne make that mistake, because in general Darwinists are not used to constraining their speculations with quantitative data. The fundamental message of The Edge of Evolution, however, is that such data are now available. Instead of imagining what the power of random mutation and selection might do, we can look at examples of what it has done. And when we do look at the best, clearest examples, the results are, to say the least, quite modest. Time and again we see that random mutations are incoherent and much more likely to degrade a genome than to add to it — and these are the positively-selected, “beneficial” random mutations. Behe’s point is that, rather than he being the one who presumes that malaria resistance to chloroquine requires two mutations, it is Roughgarden who, in a standard mode of Darwinian thinking, presumes that it can be selected cumulatively. In fact, Behe’s argument is much sounder than Roughgarden's argument. Behe’s point is that the degree to which the mutations confer a cumulative advantage is relatively unimportant, because, as he wrote on his Amazon blog, the 1020 statistic is an empirically derived fact that is valid regardless of the mutational pathway taken: Miller asserts that I have ruled out cumulative selection and required Plasmodium falciparum to achieve a predetermined result. I’m flattered that he thinks I have such powers. However, the malaria parasite does not take orders from me or anyone else. I had no ability to rule out or require anything. The parasite was free in the wild to come up with any solution that might help it, by any mutational pathway that was available. I simply reported the results of what the parasite achieved. … Certainly, there may be several routes, maybe permutations of pathways, too. But whether or not there are several routes, the bottom line is that resistance arises only once for every 1020 parasites. Similarly, Behe says in response to Jerry Coyne: The number I cite, one parasite in every 1020 for de novo chloroquine resistance, is not a probability calculation. Rather, it is a statistic, a result, a data point. (Furthermore, it is not my number, but that of the eminent malariologist Nicholas White.) I do not assume that “adaptation cannot occur one mutation at a time”; I assume nothing at all. I am simply looking at the results. The malaria parasite was free to do whatever it could in nature; to evolve resistance, or outcompete its fellow parasites, by whatever evolutionary pathway was available in the wild. Neither I nor anyone else were manipulating the results. What we see when we look at chloroquine-resistant malaria is pristine data — it is the best that random mutation plus selection was able to accomplish in the wild in 1020 tries. It seems indisputable that Behe’s claim was based upon statistical data, and is not dependent upon an assumption that all mutations must occur simultaneously to acquire resistance. If anything, Behe makes no assumptions, but rather the rarity of this resistance could imply that multiple mutations are required to confer such a resistance advantage. The rarity of such a trait shows how difficult it is to evolve even modest biological complexity under any circumstances. Like many other critics of Behe, Roughgarden has misunderstood Behe’s argument.

    Redefining Evolutionary Theory and Rewriting History
    As part of a campaign to convince religious persons to accept both religion and neo-Darwinian evolution, in recent years evolutionists have embarked on a P.R. campaign to de-emphasize the random and undirected nature of neo-Darwinian mechanisms. The purpose here is not to assess whether religion is compatible with a "random" and "undirected" evolutionary proecess, but whether evolutionists are correct to attempt to redefine their theory.

    As part of this campaign, Roughgarden attempts to redefine evolution by claiming that it is neither random nor undirected. Thus, she writes: Contrary to Behe's insistence, the concept of random genetic mutation is not fundamental to evolutionary biology. Darwin never used the term random in the Origin of Species. From its beginning, Darwinism has focused on the natural-selection component of the evolutionary process, and Darwin's theory accommodates whatever information genetics supplies for the mechanism of inheritance. So I'm puzzled by Behe's fervent identifying of Darwinism with "random" mutation, as in sentences such as: "Darwin's proposed mechanism of evolution—random variation and natural selection—. . . sought to explain the development of life explicitly without recourse to guidance or planning by anyone or anything at any time." Behe never claims that Darwin specified a particular mechanism of inheritance or generation of variation--all Behe said was that Darwin's mechanism required "random variation and natural selection." Thus, it seems clear that Behe did not make the mistake Roughgarden accuses him of.

    She goes on to say: Darwin does not say that evolution is unguided. In Darwin's theory, the guidance for evolution comes from the natural-selection component of the evolutionary process, not from the mutation component. What random means in evolutionary theory is that the mutations that occur are independent of whether they might prove subsequently useful; their usefulness is for natural selection to determine. The reality is that Behe is neither miconstruing Darwin nor modern evolutionary biology. As will be seen in the following extensive documentation, evolutionary biologists have been quite clear about both the random and unguided/undirected nature of neo-Darwinian evolution.

    Five editions Kenneth Miller’s textbook, Biology, describe evolution as a purposeless, undirected process, stating: “[E]volution works without either plan or purpose … Evolution is random and undirected.” Both the 1991 and 1994 editions of Miller & Levine’s Biology: The Living Science left readers with a stark passage on the implications of evolution: “Darwin knew that accepting his theory required believing in philosophical materialism, the conviction that matter is the stuff of all existence and that all mental and spiritual phenomena are its by-products. Darwinian evolution was not only purposeless but also heartless--a process in which the rigors of nature ruthlessly eliminate the unfit. Suddenly, humanity was reduced to just one more species in a world that cared nothing for us. The great human mind was no more than a mass of evolving neurons. Worst of all, there was no divine plan to guide us.” Likewise, Guttman’s Biology also teaches that all species—including our own—are the result of “chance,” which is dictated by the “cosmic dice”: “Of course, no species has ‘chosen’ a strategy. Rather, its ancestors—little by little, generation after generation—merely wandered into a successful way of life through the action of random evolutionary forces …. Once pointed in a certain direction, a line of evolution survives only if the cosmic dice continues to roll in its favor. … [J]ust by chance, a wonderful diversity of life has developed during the billions of years in which organisms have been evolving on earth.” Harvard ecologist E. O. Wilson et al.’s textbook Life on Earth argues that many features of life “are accidents of the history of life on this particular planet.” Regarding biological differences between humans and other species, the textbook explains that “No forethought or master planning is implied here, only two different life patterns, both of which confer a high survival value on their species…”

    Haviland’s Anthropology likewise contends that human origins “was made possible only as a consequence of historical accidents.” In a section titled, “The Nondirectedness of Evolution,” the textbook teaches that an “essentially random event—the collision [of earth] with a comet or asteroid—made possible our own existence.” The textbook goes on to quote Stephen Jay Gould’s explanation of the “fortuitous series of accidents” that led to human beings: "The history of any species is an outcome of many such contingencies. At any point in the chain of events, had any one element been different, the final result would be markedly different. As Stephen Jay Gould puts it, “All evolutionary sequences include … a fortuitous series of accidents with respect to future evolutionary success. Human brains did not evolve along a direct and inevitable ladder, but by a circuitous and tortuous route carved by adaptations for different reasons, and fortunately suited to later needs.” Campbell, Reece, and Mitchell’s popular text Biology: Concepts & Connections likewise attributes life to a series of chance events: “We have documented the role of change in shaping the vast diversity of life. We have also chronicled the role of chance. Chance has affected the evolutionary process in the generation of genetic diversity through mutation. Chance has also played a role at every major milestone in the history of life. Before life began, over 3.5 billion years ago, the chance union of certain small organic molecules ignited a chain of events that led to the first genes. Much later—about 65 million years ago – a chance collision between Earth and an asteroid may have caused mass extinctions. … One of the great wonders of our existence and of life itself is that it has all arisen through a combination of evolutionary processes and chance events.” Helena Curtis and N. Sue Barnes’s text Invitation to Biology explains to students that “[i]t is difficult to avoid the speculation that Darwin, as has been the case with others, found the implications of his theory difficult to confront.” The implications described in this text are striking: “The real difficulty in accepting Darwin’s theory has always been that it seems to diminish our significance. Earlier, astronomy had made it clear that the earth is not the center of the solar universe, or even of our own solar system. Now the new biology asked us to accept the proposition that, like all other organisms, we too are the products of a random process that, as far as science can show, we are not created for any special purpose or as part of any universal design.” Modern evolutionists have also been quite clear that neo-Darwinian evolution is random. Nicholas Barton et al.’s textbook Evolution emphasizes the randomness of Darwinian evolution, asserting that there is “extreme randomness [in] the evolutionary process” and “begin[s] its consideration of the processes for evolution by emphasizing the randomness of evolution.” The text goes on to explain that evolution involves “random genetic drift,” “random mutation,” “random variation,” “random … individual fitness,” and “random reproduction” and the “[r]andom growth of a sexual population” stemming from “the random number of offspring from each individual. The textbook summarizes “Darwin’s view of evolution” as teaching that “there is no overall tendency for progress towards ‘higher’ forms and man has no special place in nature,” and thus “natural selection [which] is based on random death and extinction” has been “widely felt to be an unacceptable mechanism.”

    Perhaps the most blatant example of philosophical materialism in textbooks is found in Douglas Futuyma’s widely used college text Evolutionary Biology. Futuyma makes no mistakes when explaining his view of the anti-religious implications of evolution: "By coupling undirected, purposeless variation to the blind, uncaring process of natural selection, Darwin made theological or spiritual explanations of life superfluous. … Darwin's theory of evolution, followed by Marx's materialistic (even if inadequate or wrong) theory of history and society and Freud's attribution of human behavior to influences over which we have little control, that provided a crucial plank to the platform of mechanism and materialism--in short, to much of science--that has since been the stage of most Western thought." Futuyma goes on to explain how Darwin removed purpose and design from biology, making such a theological foundation “completely superfluous”: “The entire tradition of philosophical explanation by the purpose of things, with its theological foundation, was made completely superfluous by Darwin’s theory of natural selection. The adaptation of organisms—long cited as the most conspicuous evidence of intelligent design in the universe—could now be explained by purely mechanistic causes. … The profound, and deeply unsettling, implication of this purely mechanical, material explanation for the existence and characteristics of diverse organisms is that we need not invoke, nor can we find any evidence for, any design, goal, or purpose anywhere in the world, except for human behavior.” According to various leading biology textbooks of the past few decades, neo-Darwinian evolution is variously a “random,” “blind,” “uncaring,” “heartless,” “undirected,” “purposeless,” “chance” process that acts “without plan” or “any ‘goals’” and requires accepting “materialism” because we are “not created for any special purpose or as part of any universal design” and “a god of design and purpose is not necessary.”

    Joan Roughgarden may wish to accuse Behe of misconstruing evolution by claiming that modern evolutionists say that evolution is random, unguided and undirected, but it would seem that according to what we see in many textbooks, she is the one misconstruing modern neo-Darwinian evolutionary theory in a failed attempt to remake modern evolutionary thinking in the image of her own theistic evolutionary views.