Original author's comments on this response.
Abstract: Dr. Behe argues that a protein performing a given function in the complex environment of the cell is such an improbable thing that it could not be expected to arise in the time span available on earth. The problem with his formulation is this: the process he models is not the same process described by the theory of evolution. Evolution requires inheritance, mutation, and selection. Dr. Behe's process involves only inheritance and mutation. Once you have a simple replicating structure (inheritance) that from time to time suffers changes in its replication code (mutation), and particular mutants arise that out-multiply others (selection), then the mutant type becomes common, forming the background population in which the next winning mutation occurs. In this way, each stepwise "gain" (in light of the final result) is consolidated.
A PROTEIN HAS BEEN PRESENTED as a complex thing. It is. There are limited ways it can be modified and still function in the cell. That is true. The exact ways a particular protein can differ without destroying function have been investigated experimentally with exquisite technique. A protein is in essence a chain of discrete beads or elements of finite number and of describable relative availability for stringing. Therefore all possible ways of randomly constructing a chain of equivalent length can be simply calculated. The elements in a protein chain are viewed as steps that have to have occurred.
In such a model, with a chain of any appreciable length, and an amino acid soup of any appreciable diversity, the probability of getting one of the few possible chains that "work" quickly gets exceedingly small, so small, that for our minds to grasp the unlikelihood, we must resort to metaphor. All this is true.
The process Professor Behe describes-a process of stepwise amino acid substitutions adding up to an improbable product; a process extended in time but with a probability of occurrence analyzed no differently than had it all been assembled in "one fell swoop"-is not analogous to the process of evolution by natural selection. Yes, like organic evolution, there are replication and mutation. But what has been left out are the filters, the sieves that at every generation sift the outcomes. The sieve is natural selection. No discerning selector is implied.
Selection is a way of describing the fact that, in the environment in question, some of the variants will be more successful than others in populating the next generation with their sort. These variants are better at lasting long enough to make copies, and better at making relatively many of these copies. No selector is implied, but "sense" does build itself into the process. Which variants do relatively well is not entirely haphazard. On average, successful variants surmount the complex challenges of their environment by happening to be a bit more complex themselves in the effective sorts of ways.
As this mechanical process is iterated, and variants of differing success continue to pop up, the diversity in the total collection rises. Rising diversity means that the environment in which the variants exist and replicate gets more complex over time. So, yet more complex ways of existing and replicating are the ones that work relatively better in later generations. Viewed overall, the unfolding scenario has the look of progress.
The analogy between typing monkeys and evolution has a flaw, which is teleology. Teleology is a goal toward which something is working, In the monkey example, the goal is the character string that spells "Drop the anchor in one hour." The monkey types character strings of lengths similar to the goal. Every time the random product gets the same letter in the same place as the goal, that character is inserted in that site with each succeeding string of letters the monkey types. Naturally, by and by, the goal is reached. The teleology is not in the mind of the monkey, it is true, but is present because the game is rigged.
A little less teleological is the transmogriftcation of everyday food preparation into a practical, delicious showpiece of regional cuisine. Night after night throughout the region, meals are prepared. Haphazard elements affect the product: what's in season, what's on hand, what's convenient at the time. Children poke at it, husbands mumble over it, but once in a while someone says, "Hey, that's delicious-write it down!" A recipe appears. The recipe gets replicated whenever a guest or a relative asks to have it, and it is replicated even more when it is included in the PTA fundraiser cookbook. Each new owner of the recipe is likely to alter it a bit, leaving out a disliked ingredient, adding a radish rosette. New environments affect what is made: microwave ovens, say, or the Surgeon General's recommendations. A recipe that is really successful in leaving descendants bears a name everyone recognizes- fajitas, ginger beer, bubble-and-squeak.
So, with somewhat accidental variation, "filters" that operate every time the dish is made, and replication, we have an outcome: a regional dish that could not have been specified at the outset in the cabins of the first local settlers. The analogy, however is flawed. Design does creep in. Food preparers do think, and have short-term goals in mind.
Other analogies avoid the problem of teleology. You and I are the highly improbable outcomes of all the chance meetings, feelings of love, mutual attractions, rapine roughness, release of particular ova, and plain old fluid dynamics of all the couplings of all our ancestors since the dawn of history. We were not envisioned in our glorious uniqueness by any of the players in our past. But this analogy, too, is imperfect. We are, arguably, no more complex than our ancestors in Mesopotamia, or wherever.
It is Tom Ray's computer program that makes the best analogy I know of to the process of organic evolution. The elements of replication, production of new variation, and non-teleological. automatic selection are present. These elements produce novelty, complexity, diversity.
The best example, of course, is the real thing: organisms surviving and reproducing in environments in which some types do better than others. Successful variants tend to be those good at acquiring whatever the needed resources are, converting them efficiently into growth and offspring, lasting long enough to do so, and helping organisms with genotypes most like one's own. For those wanting to understand what evolutionary biologists mean by evolution, organismal biology merits careful study.
To touch on something else, the production of new variants is sometimes equated with point mutation. A point mutation is an altered nucleotide in the genetic material. An analogy to this is a substitution in a typed character string. When evolutionary biologists speak of mutation, they mean point mutation and more. Mutations are Spontaneous gene changes, including point mutations at one or several nucleotides, changes in chromosome number or structure, and shuffling of parts of genes, as, for example, transposition of gene segments.
All this becomes significant when we seek to understand evolutionary attainment in groups as different as bacteria, fungi, green plants, and mammals. Biochemically, it looks as if all life started from one basic kind a long time ago. During diversification, rather different modes of organization were achieved, such as unicellularity, cellular differentiation, or development that proceeds by induction. These modes of organization put constraints on what further kinds of innovation were likely to occur.
Evolution in bacteria, for example, tends to involve minor changes in the code, RNA, which in turn affects metabolic pathways. Flowering plants are developmentally simple and morphologically plastic, and often speciate by multiplication of chromosome number. They are essentially constrained from evolving nervous systems by the cellulose walls that enclose each cell. Mammals have complex, interactive development. Their evolution frequently involves regulatory genes that affect developmental timing and differential sensitivity of different parts of the neuroendocrine system. A small difference early leads to a big difference in adult structure and function.
This means that evolution can be expected to occur with differing tempo and mode at different times during the history of life and in different taxonomic groups. As we learn more and more about molecular genetics and developmental biology, we can make more and more refined predictions about which groups are likely to speciate a lot and under what circumstances, and what sorts of novelty will appear in the daughter species. Deepened understanding will permit new tests of the validity of the theory.
Darwinism has met the challenge of the explosion of new information generated by the growth of molecular biology, and is becoming integrated with it in ways that get richer with the passage of each publishing day. The theory is healthy.
True, one can find practicing scientists who are skeptical about evolution. Without having conducted a survey, I will brazenly hypothesize that such skeptics will be drawn disproportionately from technology fields and fields that focus on more physicochemical levels of organization. These fields have principles of organization of their own which need not be much perturbed by the parade of life. Such principles include quantum mechanics or electron orbital theory.
The big theory for biologists, however, especially those who work at the most emergent levels of organization (such as social behavior), is evolution by natural selection. As an organizing principle that is bolstered by, tested against, and modified according to evidence, it has tremendous explanatory power.
Take one small set of biologists, those who work on amphibians, a minor group of animals. Since 1970, amphibian biologists have been producing more than 1,000 titles per year, according to the Zoological Record. Topics include vocalization, larval traits, endocrinology, the fossil record, reproductive strategies, development, the musculoskeletal system, sensory reception, molecular evolution, cytogenetics, biogeography, and digestion. William Duellman and Linda Trueb produced a big new book, The Biology of Amphibians. The framework into which they fit all this stuff is evolution. This would be true as well if they made an Encyclopedia of Amphibians.
With evolution as an organizing scheme, such an encyclopedia would be compelling and understandable. Without evolution, it would be as exciting as a fourteen-volume set of urban telephone books.
This is why evolution works for me and for my fellow biologists.