Posted June 13, 2003
Has Commentary become a platform for evolution denial? Is there no more pressing issue than Berlinski's penchant for insulting scientists over his misunderstandings? Or is it just that we need relief from the relentless seriousness of events? Even in that case I must protest the publication of Berlinski's bizarre charge of fraud against a list of names seemingly pulled out of the hat. Granted the charge is absurd, but in these anti-intellectual times I'll not be surprised if someone writes to commend it.
I'm sure others will write to help Berlinski understand Nilsson and Pelger's paper. But I doubt that an entire issue of Commentary could hold an adequate tutorial for that purpose. This is not Berlinski's fault; that's the way it is with technical papers not in one's field.
What may be behind this interest in biology bashing is "intelligent design", or ID, a subject that wants clarification. Current ID 'theory' comes down to two things: one is 'irreducible complexity' (IC), ID's one connection with biology, and the other involves probability of a sort. IC is a relation among 'parts', especially proteins, that exists yet allegedly cannot come from evolution. In reality IC can easily evolve, but is unlikely in just the highly complex situations that IDists have emphasized .
The probability part works like this; when you want to apply it to something, declare that it is 'specified', e.g. it is a circular formation, and that you know no natural cause. Then note that it is highly improbable as a random collection of particles, as nearly everything is. Then you may infer that it was Designed. Examples that would have passed the test until their cause was discovered include circular craters on the moon, and circular rock formations found in Alaska. Are you thinking "It can't be that silly"? It can be, although it is only applied selectively, to a bacterium's flagellum for instance.
Is ID good theology? It is God of the Gaps at best and when you get down to cases (the flagellum again) the Designer is a direct cause of serious diseases. Thank Darwin for freeing theology from this miserable mess .
What more need one know about an idea lacking both rational and spiritual merit? It is politics, without which we would not be discussing it. Unlike other creationists who form strictly creationist organizations, IDists are Senior Fellows or better in a political club called the Discovery Institute. They have been working for years to publicize their odd ideas, putting articles anywhere they can and if possible writing to praise one another e.g. recently in Commentary.
This brings us full circle. Perhaps the names Berlinski chose to falsely insult in his article were not random picks after all. They happen to be people who say things the ID Fellows don't like. True, Berlinski's charge is absurd. But in politics, the charge not the details is what sticks.
 Irreducible Complexity Demystified, online at talkdesign.org and talkreason.org.
Berlinski's attack on Nilsson and Pelger's work contains clear signs of misunderstanding key elements of that work. He claims that:
A precise formulation of the N-P's premises will eliminate most objections.
Evolution is presumed incapable of coordinating the development of devices, such as the eye structure, made up of several seemingly unconnected components. For this reason N-P phrased their question in precise terms: in what way can the evolutionary process form this marginal "surplus value" - i.e. create an eye structure.
The "patch" constitutes a normal part of the animal phenotype, and as such is subject to morphological changes. Each group of "patch-possessors" should contain individuals whose patch deviates from the group average.
In order to measure a fluctuation, N-P designed a metric that would serve as a reasonable gauge of the degree to which one patch differs from another. This enabled them to build a continuous trajectory of change from a patch toward the eye, using only morphological changes that occur in nature on a daily basis. The main feature of this trajectory is the continuous increase of the eye's optical capabilities. According to N-P's calculations, the entire process takes 1,829 1-percent steps.
In order for this model to acquire evolutionary reality, three conditions must be fulfilled: the eye's development must not cause biological "losses", the acquired traits must be set in the population, and the entire process must not take too much time.
The first condition can be provided with empirical commentary. By all indications, the visual ability constitutes a great advantage which outweighs any eye disorder. Absolutely blind individuals, regaining mere percents of vision, say that they have gained an entire world. A reasonable assumption is that this also held true in the intermediate stages of the process.
The crucial point in the second condition is that this is not our problem. To put it simply, in this regard the eye behaves like the giraffe's neck. Those who accept the evolution of the giraffe's neck already possess a positive answer.
And what about the time-span? Here N-P employed formulas obtained for selection models. Their sole nontrivial parameter is that of "selection intensity". Judging by other data (or by references provided by N-P), the ratio of 0.01 seems reasonable.
We must keep in mind that N-P's theory basically can be experimentally verified. If we blind a seeing animal genetically (by taking away its capacity for growing eyes), providing it instead with a genetically determined "patch" of light-sensitive cells, then, according to N-P's theory, it will create a new eye at the ideal pace. Can a biologist be found willing to comment on this experiment?
To the Editor:
"A Scientific Scandal" (Commentary April, 2003) is a scientific scandal: the continued publication, in a political-cultural opinion journal, of David Berlinski's uninformed bellyaching about evolutionary biology. What the editors hope to accomplish thereby escapes me. Commentary is not the place for quasi-technical arguments against Darwinism, or for reprinting the scientific papers or textbook chapters that disprove them.
Mr. Berlinski has several times found fault with me. The method is characteristic; and it is salient in "A Scientific Scandal." I had written earlier that Berlinski's disparagements are old and naïve, that they are refuted in the literature. Responding in March, 2003, he dismissed this airily as an unanswerable gripe. But it is not a gripe. Nor was it meant to be answered in Commentary. It is just a fact about the scientific literature. Any reader can check for himself. 
Only once, in the eleven years since the start of their anti-evolution PR-blitz, have any arguments of Berlinski's colleagues at the Center for Science and Culture appeared in the primary literature. That once was an early, philosophical monograph by the Christian apologist, William Dembski. Berlinski (in Commentary, December, 2002) has now rejected that argument as applied to biology, although he gave the book a glowing blurb. The rest of their anti-evolution kvetching has been in trade books mainly from religious publishers, in nonscience journals, testimony to legislators, interviews, speeches and rallies for the faithful. Not in the scientific literature.
Thereto, I called attention. Berlinski gave the inevitable crank excuse: conspiratorial prejudice of scientists. Then came his coup de main. He quoted in triumph an essay of my own, published in 1986: "Being right isn't enough. What you say, however right, must be said in a currently acceptable language, and must not violate too brutally currently acceptable taste, and must somehow signify your membership in a respectable club." Touché, yes?
No. My essay was about L. V. Heilbrunn, Professor in the University of Pennsylvania who discovered the critical role of calcium ions in cellular signaling. But he insisted on presenting his findings in the obsolete language of colloid chemistry. Hence they were not adequately appreciated. He died young. Heilbrunn was the antithesis of a crank. Esteemed scholar and teacher, author of scores of papers in peer-reviewed journals, he wrote the major textbook in English of general physiology. So Berlinski's quoting me was not only irrelevant, but deceptive, a dishonor to that good scientist. In fact Berlinski's entire argument rests on the fallacy ignoratio elenchi: arguing to conclusions beside the intended point.
Why? Because the obvious purpose of this "Scandal" piece, like Berlinski's other adventures in evolution, is to belittle Darwinism. He starts by citing Darwin himself, worried that his theory might not be able to account for the eye. Berlinski's real case, then, is that Darwin's fears were justified: evolutionary theory can't explain the eye; and there is a cover-up. But Darwin's fears are ancient history: a century and a half have passed. Darwin was still haunted by Paley's 1802 version of the argument from Design.
This is the twenty-first century. There is no question that eyes, endlessly varied in structure and quality, have evolved. Most of the intermediates between a primitive patch of photosensitive cells and the camera eye of a fish or a mammal exist. Many more have existed in the past, during the 540 million years or so since there have been eyes. There were no fishes or mammals 540 million years ago, and no squid or fish or bird or mammalian eyes either. Those have all appeared on Earth since then.
So what is the fuss about? In a 1994 theoretical paper, Nilsson and Pelger modeled one possible evolutionary pathway to the geometry of a fish-like eye from a patch of photo-responsive cells. There were already such cells-among the oldest organisms on Earth-a billion years before there were eyes. Nilsson and Pelger used pessimistic estimates of the relevant parameters (such as the intensity of selection) for their number-crunching. The point was to determine how many plausible, populational micro-steps of variation would be needed, under minimal assumptions, for very weak selection to yield a fish-like eye-and then under reasonable assumptions to convert micro-steps into generations and years. The order of magnitude answer was 350,000-a geological blink of the eye. But this answer is just one of many to the failed nineteenth-century creationist complaint of insufficient time.
In his acount of it, Berlinski misunderstands or misinterprets critical elements of the paper. Then he quibbles ponderously about terms and assumptions used in it-and in glosses of it by Richard Dawkins and some of Berlinski's critics. He accuses the latter of fraud (!)-for having failed to denounce Dawkins's use in a trade book of certain of those terms. Berlinski's arguments are quibbles. I leave it to the author(s) of the original paper so to explain at necessary length, in print. I trust some part of that will appear in Commentary.
But these quibbles are beside Berlinski's real point, which is that we lack grounds for believing that eyes evolved. That is false. Eyes, like anything else, could have been invented at a stroke by a supernatural designer. But there is no evidence of it. Neither can it ever be disproved. The only explanation, however, that we have for the structure of eyes-as solid as any explanation in science-is Darwinian evolution. Like the Intelligent Design group as a whole, Berlinski seems unable or unwilling to understand the newest branch of biology: evolutionary developmental biology-genetics. It is there, with discovery of the remarkable developmental regulatory genes, that we have learned how subtle, how versatile, and yet how simple the mechanisms can be for transforming one biological structure to another.  A reader whose view of science comes only from Berlinski will never know of such things.
While Berlinski should be congratulated for pointing out Dawkins' inaccurate popularization of Nilsson and Pelger's article on eye evolution as a stochastic computer simulation (it was actually a mathematical model), Berlinski should remove the plank from his own (discussion of the) eye. In "A Scientific Scandal" he asserts that one of the problems for eye evolution that Nilsson and Pelger did not consider was how the skull would be "reconstructed" to include eye sockets.
But as any decent student who has taken even high school biology would know (at least as long as evolution was not expunged due to creationist political arm twisting), eyes evolved before bones! Cephalochordates, the closest invertebrate relatives of vertebrates, have primitive eyes but no bones. In fact, based on genetic evidence many biologists now think that vertebrate eyes share a common ancestral eyespot with insect eyes, the common ancestor being a perhaps millimeter-long, nearly transparent but eyespot-equipped worm.
Unfortunately, it is a typical creationist strawman to envision eye evolution as occurring on some kind of mythical ancestral eyeless fish with a fully formed skull, brain, etc. On the contrary, biologists (who actually know some biology) know that all manner of gradations of eye complexity exist in extant organisms, from creatures with an "eye" consisting of a single photoreceptor cell, through all of the various stages that Nilsson and Pelger depict, to the "advanced" camera eyes of mammals and cephalopods. Sometimes the whole sequence from eyespot to advanced eye with lens can be seen in a single group (e.g. snails), yet another thing which Berlinski would have known if he'd followed the reference that Nilsson and Pelger gave to the actual classic work on eye evolution, a monster 56 page article by Salvini-Plawen and Mayr in the journal Evolutionary Biology (volume 10, 1977) that reviewed hundreds of papers on eyes across the animal kingdom, and with the fairly clear title "On the evolution of photoreceptors and eyes". The paper answers many of the questions which Berlinski asserts are unanswered or unanswerable. Complex eyes with lenses have even evolved in single-celled dinoflagellates, which have no blood vessels, brains, or numerous other features Berlinski is concerned about.
Berlinski on the other hand has a brain as well as eyes, but apparently does not see when it comes to biology. He is not a creationist but he certainly seems to hang out with them and uncritically repeats many of their arguments, unaware of the biological facts that contradict them. If Berlinski is going to declare as bunk the central organizing theory of biology, he should be taking the matter up with biologists in the professional literature, rather than in forums like Commentary, wherein elementary questions like "which came first, skulls or eyes?" can be botched and yet still get published.
In the April issue of Commentary magazine David Berlinski attacks my paper with Susanne Pelger from 1994 (Nilsson D-E, Pelger S (1994) A pessimistic estimate of the time required for an eye to evolve. Proc R Soc Lond B 256: 53-58). I generally do not debate pseudo-scientists because it gives them credibility, but I have decided to make an exception here.
His essay starts with an attempt to describe the original paper, Nilsson and Pelger (1994). Apart from a mix up in sequence chronology and some minor peculiarities, the only major flaw is his misunderstanding of the response R, which he quotes as a measure of visual acuity. It is not, and the original paper does not say so. This is the first serious mistake and it gets worse in the remainder of the essay.
Berlinski's next move is to list important information, which he claims is missing in the original paper. At regular intervals he repeats the phrase: "they do not say". But all the necessary information is there. Given only 800 words to respond, I cannot reply individually to every point here, but two examples will do: Berlinski claims that there is no unit for morphological change and that we do not explain how we arrive at a sum of 1829 steps of 1%. Explanations to both are given on page 56 of the original paper, starting with the bottom line of the left column. He further claims that we do not explain how morphological change relates to improvements in visual acuity, although most of pages 54 through 56, including graphs and legends of Figures 1 and 3 deals with exactly that, in great detail.
He continues for the rest of his essay on other issues where he believes he has detected logical flaws. He is not right in a single case, and instead reveals an insufficient background in visual optics, sampling theory, basic evolutionary theory, and more. Nor does he seem to have read the key references such as Warrant and McIntyre (1993), Falconer (1989) or Futuyma (1986). Without such knowledge I understand that it is hard to grasp the details of the Nilsson and Pelger paper, but it is standard scientific practice not to repeat lengthy reasoning when a short reference can be given.
But there is more to Berlinski's misconception of our paper. He has a problem with definitions. "Morphological change" becomes "biological change". Spatial resolution (visual acuity) becomes sensitivity of vision. He does not distinguish between selection and intensity of selection. He is obviously confused between the 1% steps which we use as a unit of measure for morphological change, and the 0.005% change per generation which is our conservative estimate of evolutionary rate.
Later in the essay, he attempts a peculiar probability argument with random substitutions of letters. He does not realize that his example implies a single individual in the population, and then there can of course be no selection at all. Again, he badly needs to read Falconer's standard work (1989).
Contrary to Berlinski's claim, we calculate the spatial resolution (visual acuity) for all parts of our eye evolution sequence. The functions in Figure 1 display the results. These plots are computer generated, using small increments. Values and units are given on the axes of the plots, and procedures are explained in the legend. The underlying theory is explained in the main text, including the important Equation 1 and a reference to Warrant and McIntyre (1993) where this theory is derived. Yet, Berlinski insists that "Nilsson and Pelger do not calculate the visual acuity of any structure". It would be much simpler for Berlinski if he went just a tiny step further and denied the existence of our paper altogether.
Had these and all his other points been unfortunate misunderstandings, I would have been only too happy to help, but I get the distinct impression they are deliberate attempts to eliminate uncomfortable scientific results. Why does Berlinski not read up on the necessary scientific background? Why does he so obviously misquote our paper? Why has he never asked me for the calculation details he claims to want so badly? It is simply impossible to take Berlinski seriously.
Berlinski is right on one point only: my paper with Pelger has been incorrectly quoted as containing a computer simulation of eye evolution. I have not considered this to be very serious, because a simulation would be a mere automation of the logic in our paper. A complete simulation is thus of moderate scientific interest, although it would be useful from an educational point of view.
The Nilsson and Pelger (1994) paper remains scientifically sound, and it has not been challenged in any scientific journal with a peer review system. I do not intend to take any further part in the meaningless debate with Berlinski. But if his essay was an April fools' joke I must congratulate the editors and others involved.
To the Editor:
It is funny that Commentary, which by no measure is a scientific publication in biology or computer science, has allocated so much space to several articles by Mr. Berlinski. With no record of scientific research, either in biology or in computer science, he set out to pronounce judgment on certain topics of these two sciences. In his latest such endeavors (answering readers' letters in the March 2003 issue of Commentary and in the article A Scientific Scandal, Commentary, April 2003) Berlinski expends a lot of ammunition to annihilate all those who have sent critical letters regarding his preceding paper (in the December 2002 issue) as well as those scientists who disagree with him regarding Nilsson and Pelger's article.
Contrary to all of Berlinski's rhetoric, the alleged scandal in science related to Nilsson and Pelger's article occurred only in Berlinski's imagination.
Nilsson and Pelger report an estimate of the time necessary for the development of an eye, a calculation which entails certain assumptions but which is viewed by many scientists as sufficiently sound. (According to the Science Citation Index, Nilsson and Pelger's article has been positively referenced in at least 25 peer-reviewed scientific publications.)
Berlinski, however, unlike all these scientists, does not like Nilsson and Pelger's conclusion indicating that an eye could have developed in a geologically short time.
In fact, Berlinski obfuscates the essence of the dispute by delving into discussions of the distinctions between computer simulation, computer models, and computer calculations. These semantic exercises are inconsequential to the real question. The issue at hand is whether an eye could have developed in a geologically short time (as Nilsson and Pelger, and with them scores of biologists familiar with their work, think), or (as the advocates of Intelligent Design and Berlinski insist) it could not have happened via Darwinian mechanism.
A reader cannot fail to notice an especially appalling feature of Berlinski's escapade found at the end of his newest article. He accuses ten respected scientists of a "scientific fraud." The reason for that preposterous accusation is that they did not repudiate Nilsson and Pelger's work. Berlinski apparently cannot imagine that these ten scientists, among them professional biologists and physicists with a record of substantial achievements in science, can have an opinion of Nilsson and Pelger's work different from his own. His accusation sounds even odder coming from a man who provided rave blurbs for books by Dembski and Behe even though, as is clear from his article in the December 2002 issue, he is actually in disagreement with them regarding essential parts of their assertions. Maybe by his standards this is a manifestation of integrity, but for many observers it may look more like an expediency whose roots are not exactly in the search for a scientific truth.
Connoisseurs of pseudoscience will recognize in David Berlinski's latest essay all of the standard tropes of the crank's playbook: The smug sarcastic tone. The barrage of bullet-point criticisms to create the illusion that something truly rotten is being exposed; criticisms he knows will be answered by nothing more formidable than a few indignant letters. The crude baiting of scholars of vastly greater accomplishment than he. The presentation of minor errors as tantamount to fraud. David Berlinksi has no interest in bringing clarity to difficult scientific issues. If he did, he would not have made so many misrepresentations of his own in describing Nilsson and Pelger's work. Two examples: Mr. Berlinski's claim that their model eyes were simply "flogged up an adaptive peak" ignores the fact that establishing the existence of such a peak was one of the primary accomplishments of the paper. That there is a smooth gradient of increasing visual acuity linking a light-sensitive spot to a lens-bearing eye is a discovery that they made; it was not a foregone conclusion. And his claim that "in their paper there is no mention whatsoever of randomly occurring changes" falls flat considering that the need for such changes is mentioned explicitly in the discussion section of the paper, and is plainly implied throughout. In addition, Mr. Berlinski would not have unloaded so many spurious criticisms. For example, his query as to "why is selection pressure held constant over the course of 300,000 years" is easily answered by noting that it was held constant at a value that was ludicrously low for almost any environment.
Once we have swept the field of Mr. Berlinski's distortions and accusations we are left with a few simple facts.
Creationists often claim, without presenting evidence, that there has not been enough time for a complex organ such as the eye to have evolved. To examine that claim empirically, Nilsson and Pelger devised a scenario by which an eye could have evolved. Each stage through which their eye progresses is known in the animal kingdom today. I described their scenario in my last letter, and Mr. Berlinski has gotten it almost right in his more-recent contribution.
Briefly, Nilsson and Pelger formed an eye by changing various parameters, such as aperture diameter, in 1 % increments, until no improvement could be made. 1 % is an arbitrary number (any small increment will suffice) and does not represent the change in a single generation. Using what they and Richard Dawkins describe as conservative numbers, Nilsson and Pelger calculated an average change of 0.005 % per generation. The relative change in n generations is therefore (1.00005)n, which they set equal to the overall change of morphology in their simulation (1.011829, where 1829 is the number of 1 % steps required to form an eye). The number 1.00005 is not, contrary to Mr. Berlinski, a percentage; it is the relative change of a given parameter in a single generation. Nilsson and Pelger concluded that an eye could have evolved in approximately 350,000 years.
Does anyone claim that an eye evolved precisely as Nilsson and Pelger's simulation suggests? No. But I stand by my statement that they have given the lie to the creationists' claim and firmly made the case that an eye could have evolved within a geologically short time.
Mr. Berlinski argues, for example, that morphological changes of the skull might slow the process. Never mind that only vertebrates have skulls, and Nilsson and Pelger's eye is, again contrary to Mr. Berlinski, an invertebrate eye. The development of an eye will require not only morphological changes but also advancements to the nervous system and the brain. Will these requirements bring evolution to a halt? Cuvier asked the same question in 1812, and the answer is, "No." We now know that evolution progresses modularly, with different systems evolving in parallel and nearly independently. If Mr. Berlinski thinks that various modules could not have coevolved, he needs to support his argument quantitatively, not just proclaim it.
Nilsson and Pelger have shown precisely what they set out to show: that an eye could have evolved in a geologically short time and that the eye itself is not a limiting factor. Mr. Berlinksi holds against them that they did not perform the full-fledged simulation he wants them to do and seems to think that their calculation is therefore somehow faulty.
I will not respond to the disdainful tone of Mr. Berlinski's article, nor to his cheap shots directed at me personally. Nor will I continue the pointless distraction of whether Nilsson and Pelger performed a simulation or a calculation. I am, however, concerned with Mr. Berlinski's contention that reputable scientists have conspired to support a technical paper that he finds "unfounded"; charging specific individuals with fraud is not to be taken lightly. The paper is not unfounded, it has survived peer review, and it has not been shown to be unfounded in any peer-reviewed journal. If Mr. Berlinski thinks the paper is unfounded, let him submit a paper of his own to a peer-reviewed journal and find out what the scientific community thinks of his ideas. Nature has notoriously published a paper by Jacques Benveniste supporting homeopathic "medicine," so I can reasonably assure Mr. Berlinski that it will not conspire to censor his paper out of prejudice.
Matt Young's home page
 Examples: Mark Ridley, Evolution, Second Edition (Cambridge, MA: Blackwell Science, 1996); John Gerhart and Marc Kirschner, Cells, Embryos, and Evolution. (Malden, MA: Blackwell Scientific, 1997); Rudolf A. Raff, The Shape of Life (Chicago: University of Chicago Press, 1996).
 A professional but accessible account: Sean B. Carroll, Jennifer K. Grenier, and Scott D. Weatherbee. From DNA To Diversity: Molecular Genetics and the Evolution of Animal Design. (Malden, MA: Blackwell Science, 2001). Popular, but sound: Richard O. Prum and Alan H. Brush. "Which came first, the feather or the bird?" Scientific American, March 2003, 84-93.