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A Scientific Scandal


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 The full text of this article is available at Commentary’s website.

IN SCIENCE, as in life, it is always an excellent idea to cut the cards after the deck has been shuffled. One may admire the dealer, but trust is another matter.

In a recent essay in COMMENTARY, “Has Darwin Met His Match?” (December 2002), I discussed, evaluated, and criticized theories of intelligent design, which have presented the latest challenge to Darwin’s theory of evolution. In the course of the discussion I observed that the evolution of the mammalian eye has always seemed difficult to imagine. It is an issue that Darwin himself raised, and although he settled the matter to his own satisfaction, biologists have long wished for a direct demonstration that something like a functional eye could be formed in reasonable periods of time by means of the Darwinian principles of random variation and natural selection.

Just such a demonstration, I noted in my essay, is what the biologists Dan-Erik Nilsson and Susanne Pelger seemed to provide in a 1994 paper. (1) Given nothing more than time and chance, a “light-sensitive patch,” they affirmed, can “gradually turn into a focused-lens eye,” and in the space of only a few hundred thousand years–a mere moment, as such things go.

Nilsson and Pelger’s paper has, for understandable reasons, been widely circulated and widely praised, and in the literature of evolutionary biology it is now regularly cited as definitive. Not the least of its remarkable authority is derived from the belief that it contains, in the words of one of its defenders, a “computer simulation of the eye’s evolution.”

If this were true, it would provide an extremely important defense of Darwin’s theory. Although a computer simulation is not by itself conclusive–a simulation is one thing, reality another–it is often an important link in an inferential chain. In the case of Darwin’s theory, the matter is especially pressing since in the nature of things the theory cannot be confirmed over geological time by any experimental procedure, and it has proved very difficult to confirm under laboratory conditions. The claim that the eye’s evolution has been successfully simulated by means of Darwinian principles, with results falling well within time scales required by the theory, is thus a matter of exceptional scientific importance.

And not just scientific importance, I might add; so dramatic a confirmation of Darwinian theory carries large implications for our understanding of the human species and its origins. This is no doubt why the story of Nilsson and Pelger’s computer simulation has spread throughout the world. Their study has been cited in essays, textbooks, and popular treatments of Darwinism like River Out of Eden by the famous Oxford evolutionist Richard Dawkins; accounts of it have made their way onto the Internet in several languages; it has been promoted to the status of a certainty and reported as fact in the press, where it is inevitably used to champion and vindicate Darwin’s theory of evolution.

In my essay, I suggested that Nilsson and Pelger’s arguments are trivial and their conclusions unsubstantiated. I also claimed that representations of their paper by the scientific community have involved a serious, indeed a flagrant, distortion of their work. But in a letter published in the March issue of COMMENTARY, the physicist Matt Young, whom I singled out for criticism (and whose words I have quoted here), repeated and defended his characterization of Nilsson and Pelger’s work as a “computer simulation of the eye’s evolution.” It is therefore necessary to set the matter straight in some detail.

I hope this exercise will help to reveal, with a certain uncomfortable clarity, just how scientific orthodoxy” works, and how it imposes its opinions on the faithful.

HERE IN their own words is the main argument of Nilsson and Pelger’s paper:

[snip.] The full text of this article is available at Commentary’s website.

THE RESULT is a pin-hole eye, which is surely an improvement on no eye at all.

[snip.] The full text of this article is available at Commentary’s website.

HOW MUCH does the initial light-sensitive patch have to change in order to realize a focused camera-type eye? And how long will it take to do so? These are the questions now before us.

[snip.] The full text of this article is available at Commentary’s website.

NILSSON AND Pelger’s work is a critic’s smorgasbord. Questions are free and there are second helpings.

Every scientific paper must begin somewhere. Nilsson and Pelger begin with their assumption that, with respect to the eye, morphological change comes about by invagination, aperture constriction, and lens formation. Specialists may wish to know where those light-sensitive cells came from and why there are no other biological structures coordinated with or contained within the interior of the initial patch for–example, blood vessels, nerves, or bones. But these issues may be sensibly deferred.

Not so the issues that remain. Nilsson and Pelger treat a biological organ as a physical system, one that is subject to the laws of theoretical optics. There is nothing amiss in that. But while theoretical optics justifies a qualitative relationship between visual acuity on the one hand and invagination, aperture constriction, and lens formation on the other, the relationships that Nilsson and Pelger specify are tightly quantitative. Numbers make an appearance in each of their graphs: the result, it is claimed, of certain elaborate calculations. But no details are given either in their paper or in its bibliography. The calculations to which they allude remain out of sight, if not out of mind.

The 1-percent steps: in what units are they expressed? And how much biological change is represented by each step? Nilsson and Pelger do not say. Nor do they coordinate morphological change, which they treat as simple, with biochemical change, which in the case of light sensitivity is known to be monstrously complex.

Does invagination represent a process in which the patch changes as a whole, like a balloon being dimpled, or is it the result of various local processes going off independently as light-sensitive cells jostle with one another and change their position? Are the original light-sensitive cells the complete package, or are new light-sensitive cells added to the ensemble as time proceeds? Do some cells lose their sensitivity and get out of the light-sensing business altogether? We do not know, because Nilsson and Pelger do not say.

Biologists commenting on Darwin’s theory have almost always assumed that evolution reflects what the French biologist Francois Jacob called bricolage–a process of tinkering. Biological structures are put together out of pieces; they adapt their function to changes in their circumstances; they get by. This suggests that in the case of eye formation, morphological change might well purchases less visual acuity than Nilsson and Pelger assume, the eye being tinkered into existence instead of flogged up an adaptive peak. But if, say, only half as much visual acuity is purchased for each of Nilsson and Pelger’s 1-percent steps, twice as many steps will be needed to achieve the effect they claim. What is their justification for the remarkably strong assertion that morphological transformations purchase an optimal amount of visual acuity at each step?

Again we do not know, because they do not say.

More questions–and we have not even finished the hors d’oeuvres.

[snip.] The full text of this article is available at Commentary’s website.

WE ARE at last at the main course. Curiously enough, it is the intellectual demands imposed by Darwin’s theory of evolution that serve to empty Nilsson and Pelger’s claims of their remaining plausibility.

[snip.] The full text of this article is available at Commentary’s website.

FINALLY, THERE is the matter of Nilsson and Pelger’s computer simulation, in many ways the gravamen of my complaints and the dessert of this discussion.

A computer simulation of an evolutionary process is not a mysterious matter. A theory is given, most often in ordinary mathematical language. The theory’s elements are then mapped to elements that a computer can recognize, and its dynamical laws, or laws of change, are replicated at a distance by a program. When the computer has run the program, it has simulated the theory.

Although easy to grasp as a concept, a computer simulation must meet certain nontrivial requirements. The computer is a harsh taskmaster, and programming demands a degree of specificity not ordinarily required of a mathematical theory. The great virtue of a computer simulation is that if the set of objects is large, and the probability distribution and fitness function complicated, the computer is capable of illustrating the implications of the theory in a way that would be impossible using ordinary methods of calculation. “Hand calculations may be sufficient for very simple models,” as Robert E. Keen and James Spain write in their standard text, Computer Simulation in Biology (1992), “but computer simulation is almost essential for understanding multi-component models and their complex interrelationships.”

Whatever the merits of computer simulation, however, they are beside the point in assessing Nilsson and Pelger’s work. In its six pages, their paper contains no mention of the words “computer” or “simulation.” There are no footnotes indicating that a computer simulation of their work exists, and their bibliography makes no reference to any work containing such a simulation.

Curious about this point, I wrote to Dan-Erik Nilsson in the late summer of 2001. “Dear David,” he wrote back courteously and at once,

You are right that my article with Pelger is not
based on computer simulation of eye evolution.
I do not know of anyone else who [has]
successfully tried to make such a simulation either.
But we are currently working on it. To
make it behave like real evolution is not a simple
task. At present our model does produce
eyes gradually on the screen, but it does not
look pretty, and the genetic algorithms need a
fair amount of work before the model will be
useful. But we are working on it, and it looks
both promising and exciting.

These are explicit words, and they are the words of the paper’s senior author. I urge readers to keep them in mind as we return to the luckless physicist Matt Young. In my COMMENTARY essay of last December, I quoted these remarks by Mr. Young:

Creationists used to argue that … there was
not enough time for an eye to develop. A computer
simulation by Dan-Erik Nilsson and Susanne
Pelger gave the lie to that claim.

These, too, are forthright words, but as I have just shown, they are false: Nilsson and Pelger’s paper contains no computer simulation, and no computer simulation has been forthcoming from them in all the years since its initial publication. Sheer carelessness, perhaps? But now, in responding to my COMMENTARY article, Matt Young has redoubled his misreading and proportionately augmented his indignation. The full text of his remarks appears in last month’s COMMENTARY; here are the relevant passages:

In describing the paper by Nilsson and Pelger …,
I wrote that they had performed a computer simulation
of the development of the eye. I did not
write, as Mr. Berlinski suggests, that they used
nothing more than random variation and natural
selection, and I know of no reference that
says they did.

… The paper by Nilsson and Pelger is a sophisticated
simulation that even includes quantum noise;
it is not, contrary to Mr.
Berlinski’s assertion, a back-of-the-envelope
calculation. It begins with a flat, light-sensitive
patch, which they allow to become concave
in increments of 1 percent, calculating
the visual acuity along the way. When some
other mechanism will improve acuity faster,
they allow, at various stages, the formation of
a graded-index lens and an iris, and then optimize
the focus. Unless Nilsson and Pelger
performed the calculations in closed form or
by hand, theirs was, as I wrote, a “computer
simulation.” Computer-aided simulation might
have been a slightly better description, but not
enough to justify Mr. Berlinski’s sarcasm at my

And here is my familiar refrain: there is no simulation, “sophisticated” or otherwise, in Nilsson and Pelger’s paper, and their work rests on no such simulation; on this point, Nilsson and I are in complete agreement. Moreover, Nilsson and Pelger do not calculate the visual acuity” of any structure, and certainly not over the full 1,829 steps of their sequence. They suggest that various calculations have been made, but they do not show how they were made or tell us where they might be found. At the very best, they have made such calculations for a handful of data points, and then joined those points by a continuous curve.

There are two equations in Nilsson and Pelger’s paper, and neither requires a computer for its solution; and there are no others. Using procedures very. much like Nilsson and Pelger’s own, Mr. Young has nevertheless deduced the existence of a missing computer simulation on theoretical grounds: “Unless Nilsson and Pelger performed the calculations in closed form or by hand, theirs was, as I wrote, a computer simulation.” But another possibility at once suggests itself: that Nilsson and Pelger did not require a computer simulation to undertake their calculations because they made no such calculations, their figure of 1,829 steps representing an overall guess based on the known optical characteristics of existing aquatic eyes.

Whatever the truth–and I do not know it–Mr. Young’s inference is pointless. One judges a paper by what it contains and one trusts an author by what he says. No doubt Matt Young is correct to observe that “computer-aided simulation might have been a better description” of Nilsson and Pelger’s work. I suppose one could say that had Dan-Erik Nilsson and Susanne Pelger rested their heads on a computer console while trying to guess at the number of steps involved in transforming a light-sensitive patch into a fully functioning eyeball, their work could also be represented as computer-aided.

MATT YOUNG is hardly alone in his lavish misreadings. The mathematician Ian Stewart, who should certainly know better, has made virtually the same patently false claims in Nature’s Numbers (1995). So have many other prominent figures.
(3) But misreadings are one thing, misrepresentations another. More than anyone else, it has been Richard Dawkins who has been responsible for actively misrepresenting Nilsson and Pelger’s work, and for disseminating worldwide the notion that it offers a triumphant vindication of Darwinian principles.

In a chapter of his 1995 book, River Out of Eden, Dawkins writes warmly and at length about Nilsson and Pelger’s research. (4) Here is what he says (emphasis added throughout):

[Their] task was to set up computer models of
evolving eyes to answer two questions … [:] is
there a smooth gradient of change, from flat
skin to full camera eye, such that every intermediate
is an improvement? … [and] how
long would the necessary quantity of evolutionary
change take?

In their computer models, Nilsson and Pelger
made no attempt to simulate the internal
workings of cells.

… Nilsson and Pelger began with a flat
retina atop a flat pigment layer and surmounted
by a flat, protective transparent layer. The
transparent layer was allowed to undergo localized
random mutations of its refractive index
They then let the model transform itself at random,
constrained only by the requirement that
any change must be small and must be an improvement
on what went before.

The results were swift and derisive. A trajectory
of steadily mounting acuity led unhesitatingly
from the flat beginning through a shallow
indentation to a steadily deepening cup, as
the shape of the model eye deformed itself on the
computer screen
… And then, almost like a conjuring
, a portion of this transparent filling
condensed into a local, spherical region of
higher refractive index.

… This ratio is called Mattiessen’s ratio.
Nilsson and Pelger’s computer-simulation model
homed in
unerringly on Mattiessen’s ratio.

How very remarkable all this is–inasmuch as there are no computer models mentioned, cited, or contained in Nilsson and Pelger’s paper; inasmuch as Dan-Erik Nilsson denies having based his work on any computer simulations; inasmuch as Nilsson and Pelger never state that their task was to “set up computer models of evolving eyes” for any reason whatsoever; inasmuch as Nilsson and Pelger assume but do not prove the existence of “a smooth gradient of change, from flat skin to full camera eye, such that every intermediate is an improvement”; and inasmuch as the original light-sensitive patch in Nilsson and Pelger’s paper was never allowed to undergo “localized random mutations of its refractive index.”

And how very remarkable again–inasmuch as there are no computer “screens” mentioned or cited by Nilsson and Pelger, no indication that their illustrations were computer-generated, and no evidence that they ever provided anyone with a real-time simulation of their paper where one could observe, “almost like a conjuring trick,” the “swift and decisive” results of a process that they also happen to have designed.

And yet again how very remarkable–inasmuch as Nilsson and Pelger’s “computer-simulation model” did not home in unerringly on Mattiessen’s ratio, Nilsson and Pelger having done all the homing themselves and thus sparing their model the trouble.

Each and every one of these very remarkable asseverations can be explained as the result of carelessness only if” one first indicts their author for gross incompetence.

FINAL QUESTIONS. Why, in the nine years since their work appeared, have Nilsson and Pelger never dissociated themselves from claims about their work that they know are unfounded? This may not exactly be dishonest, but it hardly elicits admiration. More seriously, what of the various masters of indignation, those who are usually so quick to denounce critics of Darwin’s theory as carrying out the devil’s work? Eugenic Scott, Barbara Forrest, Lawrence Krauss, Robert T. Pennock, Philip Kitcher, Kelly Smith, Daniel Dennett, Paul Gross, Ken Miller, Steven Pinker–they are all warm from combat. Why have they never found reason to bring up the matter of the mammalian eye and the computer simulation that does not exist?

And what should we call such a state of affairs? I suggest that scientific fraud will do as well as any other term.

The full text of this article is available at Commentary’s website.

DAVID BERLINSKI is the author of A Tour of the Calculus, The Advent of the Algorithm, and Newton’s Gift. His new book, Secrets of the Vaulted Sky, is forthcoming from Harcourt later this year.

(1) “A Pessimistic Estimate of the Time Required for an Eye to Evolve,” Proceedings of the Royal Society, London B (1994) 256, 53-58. In my essay I twice misspelled Susanne Pelger’s name, for which I apologize.

(2) A graded-index lens is a lens that is not optically homogeneous; the figure of 1.52 is “the value close to the upper limit for biological material.”

(3) Among those who, by contrast, have raised (on the Internet) points similar to my own, I would single out especially Brian Harper, a professor of mechanical engineering at Ohio State University.

(4) A version of the same material by Dawkins, “Where D’you Get Those Peepers,” was published in the New Statesman (July 16, 1995).

David Berlinski

Writer, Thinker, Raconteur, and Senior Fellow, Discovery Institute
David Berlinski received his Ph.D. in philosophy from Princeton University and was later a postdoctoral fellow in mathematics and molecular biology at Columbia University. He is currently a Senior Fellow at Discovery Institute's Center for Science and Culture. Dr. Berlinski has authored works on systems analysis, differential topology, theoretical biology, analytic philosophy, and the philosophy of mathematics, as well as three novels. He has also taught philosophy, mathematics and English at such universities as Stanford, Rutgers, the City University of New York and the Universite de Paris. In addition, he has held research fellowships at the International Institute for Applied Systems Analysis (IIASA) in Austria and the Institut des Hautes Etudes Scientifiques (IHES) in France.