Darwin's Black Box: The Biochemical Challenge to Evolution

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9780743290319: Darwin's Black Box: The Biochemical Challenge to Evolution

Darwin’s Black Box helped to launch the Intelligent Design movement: the argument that nature exhibits evidence of design, beyond Darwinian randomness. Today, with the movement stronger than ever, Michael J. Behe updates the book with an important new Afterword on the state of the debate.

—Time

Naming Darwin’s Black Box to the National Review’s list of the 100 most important nonfiction works of the twentieth century, George Gilder wrote that it “overthrows Darwin at the end of the twentieth century in the same way that quantum theory overthrew Newton at the beginning.” Discussing the book in The New Yorker in May 2005, H. Allen Orr said of Behe, “he is the most prominent of the small circle of scientists working on intelligent design, and his arguments are by far the best known.” From one end of the spectrum to the other, Darwin’s Black Box has established itself as the key text in the Intelligent Design movement—the one argument that must be addressed in order to determine whether Darwinian evolution is sufficient to explain life as we know it, or not.

For this edition, Behe has written a major new Afterword tracing the state of the debate in the decade since it began. It is his first major new statement on the subject and will be welcomed by the thousands who wish to continue this intense debate.

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About the Author:

Michael J. Behe is a Professor of Biological Science at Lehigh University, where he has worked since 1985. From 1978 to 1982 he did postdoctoral work on DNA structure at the National Institutes of Health. From 1982 to 1985 he was Assistant Professor of Chemistry at Queens College in New York City. He has authored more than forty technical papers, but he is best known as the author of Darwin's Black Box: The Biochemical Challenge to Evolution. He lives near Bethlehem, Pennsylvania, with his wife and nine children.

Excerpt. © Reprinted by permission. All rights reserved.:

CHAPTER 3: ROW, ROW, ROW YOUR BOAT

PROTEINS

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.

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...

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