Darwin's Black Box
The Biochemical Challenge to Evolution
Meeting Darwin's Wager How biochemist Michael Behe uses a mousetrap to challenge evolutionary theory: "During the fall of 1996, a series of cultural earthquakes shook the secular world with the publication of a revolutionary new book, Michael Behe's Darwin's Black Box.... The reviewer in the New York Times Book Review praised Behe's deft analogies and delightfully whimsical style, and took sober note of the book's radical challenge to Darwinism. Newspapers and magazines from Vancouver to London, including Newsweek, the Wall Street Journal, and several of the world's leading scientific journals, reported strange tremors in the world of evolutionary biology. ...
"Encouraging the nonscientists in the audience to stay tuned, Behe explained briefly what he meant by the phrase 'When I say that something is irreducibly complex, I simply mean it is a 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 cease functioning." With his characteristically impish grin breaking through a full beard, Behe flashed on the screen a diagram of the humble mousetrap, his trademark illustration of "irreducible complexity."
"After pointing out the five parts necessary for mousetrap function, he added, "You need all the parts to catch a mouse. You can't catch a few mice with a platform, then add the spring and catch a few more, and then add the hammer and improve its function. All the parts must be there to have any function at all. The mousetrap is irreducibly complex.'...
"Michael Behe is the father of six children, three boys and three girls ranging in age from two through eleven, with a seventh on the way. ... Behe's wife, Celeste, has a teaching career as well; she home schools four of the Behe children."
Evolution is a flexible word. it can be used b y one person to mean something as simple as change over time, or by another person to mean the descent of all life forms from a common ancestor, leaving the mechanism of change unspecified. In its full-throated, biological sense, however, evolution means a process whereby life arose from non-living matter and subsequently developed entirely by natural means. That is the sense that Darwin gave to the word, and the meaning that it holds in the scientific community. And that is the sense in which I use the word evolution throughout this book.
Like many great ideas, Darwin's is elegantly simple. He observed that there is variation in all species: some members are bigger, some smaller, some faster, some lighter in color.... He reasoned that since limited food supplies could not support all organisms that are born, the ones whose chance variation gave them an advantage in the struggle for life would tend to survive and reproduce, outcompeting the less favored ones.... [Pages 3-4]
Almost a century and a half after Darwin proposed his theory, evolutionary biology has had much success in accounting for patterns of life we see around us. To many, its triumph seems complete. But the real work of life does not happen at the level of the whole animal or organ; the most important parts of living things are too small to be seen. Life is lived in the details, and it is molecules that handle life’s details. Darwin’s idea might explain horse hoofs, but can it explain life’s foundation? [Page 4]
Shortly after 1950 science advanced to the point where it could determine the shapes and properties of a few of the molecules that make up living organisms. Slowly, painstakingly~ the structures of more and more biological molecules were elucidated.... The cumulative results show with piercing clarity that life is based on machines -- machines made of molecules! Molecular machines haul cargo from one place in the cell to another along “highways” made of other molecules, while still others act as cables, ropes, and pulleys to hold the cell in shape. Machines turn cellular switches on and off.... Thus the details of life are finely calibrated, and the machinery of life enormously complex.... [Page 4-5]
...if you search the scientific literature on evolution, and if you focus your search on the question of how molecular machines—the basis of life—developed, you find an eerie and complete silence. The complexity of life’s foundation has paralyzed science’s attempt to account for it; molecular machines raise an as-yet-impenetrable barrier to Darwinism’s universal reach. [Page 5]
Black box is a whimsical term for a device that does something, but whose inner workings are mysterious -- sometimes because the workings can’t be seen, and sometimes because they just aren’t comprehensible. Computers are a good example of a black box. Most of us use these marvelous machines without the vaguest idea of how they work, processing words or plotting graphs or playing games in contented ignorance of what is going on underneath the outer case. ... There is no simple, observable connection between the parts of the computer and the things that it does.... [Page 6]
The box is opened
....This level of discovery began to allow biologists to approach the greatest black box of all. The question of how life works was not one that Darwin or his contemporaries could answer. They knew that eyes were for seeing—but how, exactly, do they see? How does blood clot? How does the body fight disease? The complex structures revealed by the electron microscope were themselves made of smaller components. What were those components? What did they look like? How did they work?... 
Biochemistry has pushed Darwin’s theory to the limit. It has done so by opening the ultimate black box, the cell, thereby making possible
our understanding of how life works. It is the astonishing complexity of subcellular organic structures that has forced the question, How
could all this have evolved? ...
In The Origin of Species Darwin dealt with many objections to his theory of evolution by natural selection. He discussed the problem of the eye in a section of the book appropriately entitled “Organs of Extreme Perfection and Complication.” In Darwin’s thinking, evolution could not build a complex organ in one step or a few steps; radical innovations such as the eye would require generations of organisms to slowly accumulate beneficial changes in a gradual process. He realized that if in one generation an organ as complex as the eye suddenly appeared, it would be tantamount to a miracle. Unfortunately, gradual development of the human eye appeared to be impossible, since its many sophisticated features seemed to be interdependent. Somehow, for evolution to be believable, Darwin had to convince the public that complex organs could be formed in a step-by-step process.... 
Darwin convinced many of his readers that an evolutionary pathway leads from the simplest light-sensitive spot to the sophisticated camera-eye of man. But the question of how vision began remained unanswered. Darwin persuaded much of the world that a modem eye evolved gradually from a simpler structure, but he did not even try to explain where his starting point—the relatively simple light-sensitive spot — came from. On the contrary, Darwin dismissed the question of the eye’s ultimate origin: “How a nerve comes to be sensitive to light hardly concerns us more than how life itself originated.”
He had an excellent reason for declining the question: it was completely beyond nineteenth-century science. How the eye works—that
is, what happens when a photon of light first hits the retina—simply could not be answered at that time.... 
To Darwin, vision was a black box, but after the cumulative hard work of many biochemists, we are now approaching answers to the question
of sight. [a biochemical explanation follows].... 
The relevant steps in biological processes occur ultimately at the molecular level, so a satisfactory explanation of a biological phenomenon — such as sight, digestion, or immunity — must include its molecular explanation....
Each of the anatomical steps and structures that Darwin thought were so simple actually involves staggeringly complicated biochemical processes that cannot be papered over with rhetoric. Darwin’s metaphorical hops ... are now revealed in many cases to be huge leaps between carefully tailored machines....
Anatomy is, quite simply, irrelevant to the question of whether evolution could take place on the molecular level. So is the fossil record. It no longer matters whether there are huge gaps in the fossil record.... The fossil record has nothing to tell us about whether the interactions of 11-cis-retinal with rhodopsin, transducin, and phosphodiesterase could have developed step-by-step.... This is not to say that random mutation is a myth.... 
It is not just paleontologists looking for bones, though, who are disgruntled. A raft of evolutionary biologists examining whole organisms wonder just how Darwinism can account for their observations. The English biologists Mae-Wan Ho and Peter Saunders complain as follows:
"It is now approximately half a century since the neo-Darwinian synthesis was formulated. A great deal of research has been carried on within the paradigm it defines. Yet the successes of the theory are limited to the minutiae of evolution, such as the adaptive change in coloration of moths; while it has remarkably little to say on the questions which interest us most, such as how there came to be moths in the first place."
University of Georgia geneticist John McDonald notes a conundrum:
"The results of the last 20 years of research on the genetic basis of adaptation has led us to a great Darwinian paradox. Those [genes] that are obviously variable within natural populations do not seem to lie at the basis of many major adaptive changes, while those [genes] that seemingly do constitute the foundation of many, if not most, major adaptive changes apparently are not variable within natural populations."
Australian evolutionary geneticist George Miklos puzzles over the use fullness of Darwinism:
"What then does this all-encompassing theory of evolution predict? Given a handful of postulates, such as random mutations, and selection coefficients, it will predict changes in [gene] frequencies over time. Is this what a grand theory of evolution ought to be about? 
Jerry Coyne, of the Department of Ecology and Evolution at the University of Chicago, arrives at an unanticipated verdict:
"We conclude—unexpectedly—that there is little evidence for the neo-Darwinian view: its theoretical foundations and the experimental evidence supporting it are weak."
And University of California geneticist John Endler ponders how beneficial mutations arise:
"Although much is known about mutation, it is still largely a “black box” relative to evolution. Novel biochemical functions seem to be rare in evolution, and the basis for their origin is virtually unknown."
All told, Darwin’s theory has generated dissent from the time it was published~ and not just for theological reasons. In 1871 one of Dar-
win’s critics, St. George Mivart, listed his objections to the theory, many of which are surprisingly similar to those raised by modem critics.
"What is to be brought forward (against Darwinism) may be summed up as follows: That “Natural Selection” is incompetent to account for the incipient stages of useful structures. That it does not harmonize with the co-existence of closely similar structures of diverse origin. That there are grounds for thinking that specific differences may be developed suddenly instead of gradually. That the opinion that species have definite though very different limits to their variability is still tenable. That certain fossil transitional forms are absent, which might have been expected to be present. . . . That there are many remarkable phenomena in organic forms upon which “Natural Selection” throws no light whatever."[30
It seems, then, that the same argument has gone on without resolution for over a century. From Mivart to Margulis, there have always
been well-informed, respected scientists who have found Darwinism to be inadequate.
...we should note the obvious: if a poll were taken of all the scientists in the world, the great majority would say they believed Darwinism to be true. But scientists, like everybody else, base most of their opinions on the word of other people. Of the great majority who accept Darwinism, most (though not all) do so based on authority. Also, and unfortunately, too often criticisms have been dismissed by the scientific community for fear of giving ammunition to creationists. It is ironic that in the name of protecting science, trenchant scientific criticism of natural selection has been brushed aside. It is time to put the debate squarely in the open, and to disregard public relations problems. ... 
Irreducible complexity and the nature of mutation
Darwin knew that his theory of gradual evolution by natural selection carried a heavy burden:
"If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down."
It is safe to say that most of the scientific skepticism about Darwinism in the past century has centered on this requirement. From Mivart’s
concern over the incipient stages of new structures to Margulis’s dismissal of gradual evolution, critics of Darwin have suspected that his
criterion of failure had been met....
What type of biological system could not be formed by “numerous, successive, slight modifications”? Well, for starters, a system that is irreducibly complex. 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 cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. ...
Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on.... 
What does the box tell us?
The scientific problem then becomes, how do we confidently detect design? When is it reasonable to conclude, in the absence of firsthand knowledge or eyewitness accounts, that something has been designed? For discrete physical systems—if there is not a gradual route to their production—design is evident when a number of separate, interacting components are ordered in such a way as to accomplish a function beyond the individual components....
Suppose that you and your spouse are hosting another couple one Sunday afternoon for a game of Scrabble. When the game ends, you leave the room for a break. You come back to find the Scrabble letters lying in the box, some face up and some face down. You think nothing of it until you notice that the letters facing up read, “TAKE US OUT TO DINNER CHEAPSKATES.” In this instance you immediately infer design, not even bothering to consider that the wind or an earthquake or your pet cat might have fortuitously turned over the right letters. You infer design because a number of separate components (the letters) are ordered to accomplish a purpose (the message) that none of the components could do by itself.
Furthermore, the message is highly specific; changing several of the letters would make it unreadable. For the same reason, there is no gradual route to the message: one letter does not give you part of the message, a few more letters does not give a little more of the message, and so on. 
The Chemistry of Life
Cellular DNA is found as a double-stranded molecule — two intertwined polynucleotides (the famous double helix) that are strongly held together by hydrogen bonding. ... 
DNA, the repository of genetic information, is a polynucleotide. But the information it carries tells the cell how to make polypeptides -- proteins. How does the information get translated from one polymer "language" to the other? Shortly after the discovery of the double helical structure of DNA physicist George Gamow proposed the very non-chemical idea that genetic information is stored in coded form.... 
During the early 1960s the code was broken. Nobel laureates Marshall Nirenberg, Severo Ochoa, H. Gobind Khorana, and their associates showed that in the genetic code three contiguous nucleotides correspond to one amino acid (Figure A—5). Since there are sixty-four possible combinations of four bases taken three at a time, there are more than enough permutations to code for all twenty amino acids....
The large number of steps involved in extracting the information contained in DNA can be divided into two conceptual categories called transcription and translation. 
Posted with permission
See also Origin of life and What Darwin didn't know and The Wonder of Life
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