Darwin's Black Box: The Biochemical Challenge To Evolutionby Michael J. Behe
Virtually all serious scientists accept the truth of Darwin's theory of evolution. While the fight for its acceptance has been a long and difficult one, after a century of struggle among the cognoscenti the battle is over. Biologists are now confident that their remaining questions, such as how life on Earth began, or how the Cambrian explosion could have produced… See more details below
Virtually all serious scientists accept the truth of Darwin's theory of evolution. While the fight for its acceptance has been a long and difficult one, after a century of struggle among the cognoscenti the battle is over. Biologists are now confident that their remaining questions, such as how life on Earth began, or how the Cambrian explosion could have produced so many new species in such a short time, will be found to have Darwinian answers. They, like most of the rest of us, accept Darwin's theory to be true.
But should we? What would happen if we found something that radically challenged the now-accepted wisdom? In Darwin's Black Box, Michael Behe argues that evidence of evolution's limits has been right under our noses but it is so small that we have only recently been able to see it. The field of biochemistry, begun when Watson and Crick discovered the double-helical shape of DNA, has unlocked the secrets of the cell. There, biochemists have unexpectedly discovered a world of Lilliputian complexity. As Belie engagingly demonstrates, using the examples of vision, bloodclotting, cellular transport, and more, the biochemical world comprises an arsenal of chemical machines, made up of finely calibrated, interdependent parts. For Darwinian evolution to be true, there must have been a series of mutations, each of which produced its own working machine, that led to the complexity we can now see. The more complex and interdependent each machine's parts are shown to be, the harder it is to envision Darwin's gradualistic paths, Behe surveys the professional science literature and shows that it is completely silent on the subject, stymied by the elegance of thefoundation of life. Could it be that there is some greater force at work?
Michael Behe is not a creationist. He believes in the scientific method, and he does not look to religious dogma for answers to these questions. But he argues persuasively that biochemical machines must have been designed either by God, or by some other higher intelligence. For decades science has been frustrated, trying to reconcile the astonishing discoveries of modern biochemistry to a nineteenth-century theory that cannot accommodate them. With the publication of Darwin's Black Box, it is time for scientists to allow themselves to consider exciting new possibilities, and for the rest of us to watch closely.
He then presents a modern-day version of the kinds of anti- Darwin arguments adduced a century ago: How could so intricate an organ as the vertebrate eye evolve through step-by-step chance mutations? Clearly there must be a designer at work, an eye-maker of an eye, just as there is a watchmaker for a watch. Behe's contemporary examples are a biochemistry student's nightmare: How do you make a cilium? Cilia are those fine hairs that stick out from cells lining the lungs and sweep out debris or, when attached to a bacterium, allow the bug to swim. The fine structure and molecular motors that power a cilium are awesome. And what Behe does for the cilium he does in spades in describing the biochemical events that occur when you cut yourself and a clot forms, or when your immune system takes arms against an invader. He emphasizes how each molecular actor must come on stage and go off in precise order or else the process won't work. Allusions to Rube Goldberg inventions pale by comparison. But where is it written that because science can't explain the origins of complex phenomena, the only answer is design? The history of science is replete with enigmas that have succumbed to new concepts, new tools, new paradigms. Complexity theory is in its infancy; Darwinian theory undergoes revisions departing from gradualism. Nonlinear system theory, self- organizing systems, newly discovered developmental and regulatory genes are contributing profound insights into the development of complex organs and systems.
Belief that "irreducible complexity" implies design may comfort the faithful (Behe is a Roman Catholic), but it is neither necessary nor sufficient for many other practicing scientists.
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Darwin's Black BoxThe Biochemical Challenge to Evolution
By Michael J. Behe
Free PressCopyright © 1996 Michael J. Behe
All right reserved.
Chapter OneROW, ROW, ROW YOUR BOAT
As strange as it may seem, modern biochemistry has shown that the cell is operated by machines - literally, molecular machines. Like their man-made counterparts (such as mousetraps, bicycles, and space shuttles), molecular machines range from the simple to the enormously complex: mechanical, force-generating machines, like those in muscles; electronic machines, like those in nerves; and solar-powered machines, like those of photosynthesis. Of course, molecular machines are made primarily of proteins, not metal and plastic. In this chapter I will discuss molecular machines that allow cells to swim, and you will see what is required for them to do so.
But first, some necessary details. In order to understand the molecular basis of life one has to have an idea of how proteins work. Those who want to know all the details - how proteins are made, how their structures allow them to work so effectively, and so on - are encouraged to borrow an introductory biochemistry textbook from the library. For those who want to know a few details - such as what amino acids look like, and what are the levels of protein structure - I have included an Appendix that discusses proteins and nucleic acids. For present purposes, however, an overview of these remarkable biochemicals will suffice.
Most people think of proteins as something you eat. In the body of a living animal or plant, however, they play very active roles. Proteins are the machines within living tissue that build the structures and carry out the chemical reactions necessary for life. For example, the first step in capturing the energy in sugar and changing it into a form the body can use is carried out by a catalyzing protein (also known as an enzyme) called hexokinase; skin is made up mostly of a protein called collagen; and when light strikes your retina, the protein called rhodopsin initiates vision. You can see even by this limited number of examples that proteins are amazingly versatile. Nonetheless, a given protein has only one or a few uses: rhodopsin cannot form skin, and collagen cannot interact usefully with light. Therefore a typical cell contains thousands and thousands of different kinds of proteins to perform the many tasks of life.
Proteins are made by chemically hooking together amino acids into a chain. A protein chain typically has anywhere from about fifty to about one thousand amino acid links. Each position in the chain is occupied by one of twenty different amino acids. In this they are like words, which can come in various lengths but are made up from a set of just 26 letters. As a matter of fact, biochemists often refer to each amino acid by a single-letter abbreviation - G for glycine, S for serine, H for histidine, and so forth. Each different kind of amino acid has a different shape and different chemical properties. For example, W is large but A is small, R carries a positive charge but E carries a negative charge, S prefers to be dissolved in water but I prefers oil, and so on.
When you think of a chain, you probably think of something that is very flexible, without much overall shape. But chains of amino acids - in other words, proteins - aren't like that. Proteins that work in a cell fold up into very precise structures, and the structure can be quite different for different types of proteins. The folding is done automatically when, say, a positively charged amino acid attracts a negatively charged one, oil-preferring amino acids huddle together to exclude water, large amino acids are pushed out of small spaces, and so on. Two different amino acid sequences (that is two different proteins) can fold into structures as specific and different from each other as an adjustable wrench and a jigsaw.
It is the shape of a folded protein and the precise positioning of the different kinds of amino acid groups that allow a protein to work (Figure 3-1). For example, if it is the job of one protein to bind specifically to a second protein, then their two shapes must fit each other like a hand in a glove. If there is a positively charged amino acid on the first protein, then the second protein better have a negatively charged amino acid; otherwise, the two will not stick together. If it is the job of a protein to catalyze a chemical reaction, then the shape of the enzyme generally matches the shape of the chemical that is its target. When it binds, the enzyme has amino acids precisely positioned to cause a chemical reaction. If the shape of a wrench or a jigsaw is significantly warped, then the tool doesn't work. Likewise, if the shape of a protein is warped then it fails to do its job.
Modern biochemistry was launched forty years ago when science began to learn what proteins look like. Since then, great strides have been made in understanding exactly how particular proteins carry out particular tasks. In general, the cell's work requires teams of proteins; each member of the team carries out just one part of a larger task. To keep things as simple as possible, in this book I will concentrate on protein teams. Now, let's go swimming.
Suppose, on a summer day, you find yourself taking a trip to the neighborhood pool for a bit of exercise. After slathering on the sunblock, you lie on a towel reading the latest issue of Nucleic Acids Research and wait for the adult swim period to begin. When at long last the whistle blows and the overly energetic younger crowd clears the water, you gingerly dip your toes in. Slowly, painfully, you lower the rest of your body into the surprisingly cold water. Because it would not be dignified, you will not do any cannonballs or fancy dives from the diving board, nor play water volleyball with the younger adults. Rather, you will swim laps.
Pushing off from the side, you bring your right arm up over your head and plunge it into the water, completing one stroke. During the stroke, nerve impulses travel from your brain to your arm muscles, stimulating them to contract in a specific order. The contracting muscles tug against your bones, causing the humerus to rise and rotate. At the same time other muscles squeeze the bones of your fingers together, so that your hand forms a closed cup. Successive nerve impulses provoke other muscles to relax and contract, pulling in various ways on the radius and ulna, and directing the hand downward into the water. The force of the arm and hand on the water propel you forward. After completion of about half of the actions listed above a similar cycle begins, this time with the bones and muscles of the left arm. Simultaneously, nerve impulses travel to the muscles of your legs, causing them to contract and relax rhythmically, pulling the leg bones up and down. Slicing through the water at a stunning two miles per hour, though, you notice that it's getting hard to think; there's a burning sensation in your lungs; and, even though your eyes are open, things start to go black. Ah, yes - you forgot to breathe. It was said of President Ford that he couldn't walk and chew gum at the same time; you find it difficult to coordinate the turning of your head to the water's surface and back again with the other motions required for swimming. Without oxygen to metabolize fuel your brain starts to shut down, preventing conscious nerve impulses from traveling to the distant regions of your body.
Before you pass out and suffer the humiliation of being rescued by a Generation X lifeguard you stop, stand up in the four feet of water, and notice that you're only about twenty feet from the side. To get around the breathing problem, you decide to do the backstroke. The backstroke involves most of the same muscles as freestyle swimming, and allows you to breathe without coordinating neck muscles with everything else. But now you can't see where you're going. Inevitably you drift off course, come too close to the volleyball game, and are smacked in the head by an errant overhand smash.
In order to get far away from the apologetic volleyballers, you decide simply to tread water in the deep end of the pool. Treading water uses your leg muscles, giving you the exercise you want. It also allows both easy breathing and clear vision. After a few minutes, however, your legs begin to cramp. Deep inside your flabby limbs, unknown to you, your seldom-used muscles keep on hand enough fuel for only short bursts of activity, followed by long periods of rest. During the unusually prolonged exercise they quickly run out of sustenance and cease to function effectively. Nerve impulses frantically try to provoke the motions necessary for swimming, but with the muscles malfunctioning, your legs are as useless as a mousetrap with a broken spring.
You relax and remain still. Fortunately, the large region of your body around the waist has a density less than that of water, and so it keeps you afloat. After a minute or two of bobbing in the water, your cramped muscles relax. You spend the rest of the adult swim period floating serenely around the deep end. This doesn't provide much exercise, but at least it is enjoyable - until the whistle blows again, and you are pummeled by the cannonballs of undignified kids.
WHAT IT TAKES
The neighborhood pool scenario illustrates the requirements for swimming. It also shows that efficiency can be improved by adding auxiliary systems to the basic swimming equipment. To take the last scene first, floating requires only that an object be less dense than water; it does not require activity. The ability to float - to be able to keep a portion of the body out of the water with no active effort - can certainly be useful. Yet because the floater simply drifts along with the current, the ability to float is not the same thing as the ability to swim.
A direction-finding system (such as eyesight) is also useful for swimming; however, it is not the same thing as the ability to swim. In the story you could do the backstroke for a while and still advance through the water. Eventually, an inability to sense the surroundings can lead to accidents. Nonetheless, one can swim sighted or one can swim blind.
Swimming clearly requires energy; cramped, useless muscles immediately cause the system to fail. But you traveled twenty feet before running out of oxygen, and then treaded water for a short while before cramping set in. Although they certainly affect the distance a swimmer can go, the size and efficiency of the fuel reserve system thus are not parts of the swimming system itself.
Now let's consider the mechanical requirements of swimming. You used your hands and feet to contact the water and push it, thus moving your body in the opposite direction. Without the limbs, or some substitute, active swimming would be quite impossible. So we can conclude that one requirement for swimming is a paddle. Another requirement is a motor or power source that has at least enough fuel to last several cycles. At the organ level in humans, the motor is the leg or arm muscle that alternately contracts and relaxes. If the muscle is paralyzed; there is no effective motor, and swimming is impossible. The final requirement is for a connection between the motor and the paddling surface: in humans, these are the areas of bones to which the muscles adhere. If a muscle is detached from a bone it can still contract; because it does not move the bone, however, swimming does not take place.
Mechanical examples of swimming systems are easy to find. My youngest daughter has a toy wind-up fish that wiggles its tail, propelling itself somewhat awkwardly through the bathtub. The tail of the toy fish is the paddle surface, the wound spring is the energy source, and a connecting rod transmits the energy. If one of the components - the paddle, motor, or connector - is missing, then the fish goes nowhere. Like a mousetrap without a spring, a swimming system without a paddle, motor, or connector is fatally incomplete. Because the swimming systems need several parts to work, they are irreducibly complex.
Keep in mind that we are discussing only the parts common to all swimming systems - even the most primitive. Additional complexity is frequently seen. For example, my daughter's toy fish has, besides its tail, spring, and connecting rod, several gears that transmit force from the rod to the tail. A propeller-driven ship has all manner of gears and rods redirecting the energy of the motor until it is finally transmitted to the propeller. Unlike the eye of a swimmer, which is separate from the swimming system itself, such extra gears are indeed part of the system - removing them causes the whole setup to grind to a halt. When a real-life system has more than the theoretically minimum number of parts, then you have to check each of the other parts to see if they're required for the system to work.
WHAT ELSE IT TAKES
A simple list of pieces shows the very minimum of requirements. In the last chapter I discussed how a mousetrap that had all the necessary pieces - a hammer, base, spring, catch, and holding bar - still might not work. If the holding bar were too short or the spring too lightweight, for example, the trap would be a failure. Similarly, the pieces of a swimming system must be matched to each other to have at least minimal function. The paddle is necessary, but if its surface is too small a boat might not make enough progress in a required amount of time. Conversely, if the paddle surface is too large, the connector or motor might strain and break when moving. The motor must be strong enough to move the paddle. It must also be regulated to go at an appropriate speed: too slow, and the swimmer does not make physically necessary progress; too fast, and the connector or paddle may break.
But even if we have the right parts of a swimming system, and even if the parts are the right size and strength and are matched to each other, more is needed. The additional requirement - the need to control the timing and direction of the paddle strokes - is easier to see in the example of a human swimmer than in the case of a paddleboat. When a nonswimmer falls into the water he helplessly flails his arms and legs, making no more progress than if he simply floated. Even a beginning swimmer like my oldest daughter, who is just learning the strokes, quickly sinks unless Dad supports her. Her individual strokes are adequate, but their timing is not coordinated, she doesn't hold herself parallel to the water's surface, and she keeps her head out of the water.
Mechanical systems seem not to have those problems. A ship doesn't flail its propeller, and the timing and direction of a paddleboat's strokes are smooth and regular from the beginning. But the argument is deceptive. The apparently effortless abilities are actually built into the shape and connectivity of the paddlewheel, rotor, and motor of the boat. imagine a steamboat in which the paddle boards were not arranged nicely around a circular frame. Suppose the boards went off at various angles and the rotor turned first forward, then backward, then side to side. Instead of taking a scenic tour of the Mississippi the boat would drift helplessly, spastically floating with the current toward the Gulf of Mexico. A propeller with blades set at haphazard angles would churn water, but it wouldn't move a boat in any particular direction. The apparent ease with which a mechanical system paddles - compared to the difficulties of a human non-swimmer - is an illusion. The engineer who designed the system "trained" it to swim, pushing the water in the correct direction with the correct timing.
In the unforgiving world of nature, an organism spending energy to flail helplessly in the water would have no advantage over the organism floating serenely beside it. Do any cells swim? If so, what swimming systems do they use? Are they, like a Mississippi steamboat, irreducibly complex? Could they have evolved gradually?
Excerpted from Darwin's Black Box by Michael J. Behe Copyright © 1996 by Michael J. Behe . Excerpted by permission.
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