Blood-clotting expert Russell Doolittle simply asserts that the required proteins in the system were produced by gene duplication and gene shuffling. But gene duplication just produces a duplicate of an already existing gene. Doolittle does not specify what mutations have to take place in this duplicated gene to give the protein it produces a new function useful in some evolving blood clotting system. Gene shuffling is based on the idea that each gene is made of several subsections. Sometimes in the course of reproduction the sections of genes break apart and combine back together in a new order. The reshuffled gene would produce a different protein. But the odds against getting the right subsections of genes to come together to form a new gene that would produce a protein useful in the blood-clotting cascade are astronomically high. One protein in the system, TPA, has four parts. Let us assume an animal existed at a time when the blood clotting system was just starting to form, and there was no TPA. Let us further assume that this animal had 10,000 genes. Each gene is divided into an average of three subsections. So this means 30,000 gene pieces are available for gene shuffling. The odds of getting the four parts that make up TPA to come together randomly are thus one in 30,0004—not very likely. But the main problem is getting all the parts together into a working system. Only such a system, which contributes to the fitness of the organism, can be acted on by natural selection. Isolated parts of a system do not really contribute to fitness, and therefore there is no natural selection possible. So, in order to explain the presence of today’s human blood clotting system, evolutionists first have to show the existence of a simple blood clotting system and show step by step how changes in the genes could produce more and more effective systems that work and contribute to the fitness of an organism. That has not been done in any detailed way (Behe 1996, pp. 90–97). To escape this criticism, some scientists suggest that the parts of such a complex system could have had other functions in other systems before coming together in the system in question. But that further complicates an already complicated question. In this case, scientists would then have to show how these other systems with different functions arose in step by step fashion and how parts of these systems were co-opted for another purpose, without damaging those systems.
The Dna Replication System
When a cell divides, the DNA in the cell also has to divide and replicate itself. The DNA replication system in humans and other organisms is another system that is difficult to explain by evolutionary processes. DNA is a nucleic acid. It is composed of nucleotides. Each nucleotide is composed of two parts. The first is a carbohydrate ring (deoxyribose), and the second is a base attached to the carbohydrate ring. There are four bases: adenine (A), cytosine (C), guanine (G), and thymine (T). One base binds to each carbohydrate ring. The carbohydrate rings join to each other in a chain. At one end of the chain is a 5’OH (five prime hydroxyl) group. At the other end of the DNA chain is a 3’OH (three prime hydryoxyl) group. The sequence of base pairs in a strand of DNA is read from the 5 prime end to the 3 prime end of the strand. In cells, two strands of DNA are twisted together in a helix. The bases in the nucleotides of each strand join to each other. A always bonds with T, and G always bonds with C. The two strands are thus complementary. One of them can replicate the other. If you know the base sequence of one strand of DNA you know the base sequence of the second strand in the helix. For example, if part of the sequence of bases in one strand is TTGAC, then you know that the same part of the second strand must have the bases AACTG. So each of the two strands can serve as a template for producing the other. The end result is two new double strands of DNA, matching the parent double strand. Therefore, when a cell divides into two cells, each one winds up with a matching double strand of DNA (Behe 1998, p. 184).
For DNA to replicate, the two coiled strands of DNA have to be separated. But the two complementary strands of DNA in the parent cell are joined by a chemical bond. The replication occurs at places on the DNA strand called “origins of replication.” A protein binds to the DNA at one of these places and pushes the strands apart. Then another protein called helicase moves in, and taking advantage of the opening starts pushing down the strand (like a snowplow). But once the two DNA strands are pushed apart, they want to rejoin, or if they don’t rejoin, each single strand can become tangled as hydrogen bonding takes place between its different parts. To solve this problem, there is SSB, the singlestrand binding protein, which coats the single strand, preventing it from tangling or rebonding with the other DNA strand. Then there is another problem. As the helicase moves forward, separating the two strands of coiled DNA, the two strands of DNA in front of the advancing helicase become knotted. To remove the knots, an enzyme called gyrase cuts, untangles, and rejoins the DNA strands (Behe 1998, p. 190).
The actual replication of a DNA strand is carried out principally by the polymerase enzyme, which binds itself to the DNA strand. The polymerase is attached to the original DNA strands by a ring of “clamp proteins.” There is a complex system of proteins that loads the ring onto the DNA strand. A special kind of RNA starts the replication process by linking a few nucleotide bases together forming a short chain of DNA. The polymerase then continues adding complementary nucleotide bases to the
3 prime end of the new chain. For example, if on the original DNA strand there is a G base the polymerase adds a complementary C base to the new strand. The adding of nucleotide bases takes place at the “replication forks,” the places where the two original DNA strands are pushed apart (Behe 1998, p. 188).
As a replication fork moves along one strand from the 5 prime end to the 3 prime end, the polymerase enzyme replicates this strand, called the leading strand, continuously. DNA can be replicated only in this direction, toward the 3 prime end. But the two DNA strands that make up a DNA double helix face in opposite directions. So how is the second strand replicated? While the polymerase enzyme is replicating the leading strand in the continuous manner just described, moving always toward the leading strand’s 3 prime end, it simultaneously replicates the second, or lagging strand, in a discontinuous manner, adding groups of nucleotides to its new complement in the opposite direction. The process starts with a short segment of RNA, which serves as a primer. A few nucleotides are then added to this piece of RNA, going backwards towards the 3 prime end of the lagging strand. After adding these few nucleotides going backwards, the polymerase replication machinery is unclamped and moves forward and is reclamped at the new position of the replication fork, which is continually moving toward the 3 prime end of the leading strand and away from the 3 prime end of the lagging strand. The polymerase continues replicating the leading strand by adding more bases to its new complementary strand going forward and at the same time continues replicating the lagging strand by adding to its new complementary strand another set of bases going backwards. To the lagging strand’s new complement, the polymerase adds another piece of RNA primer and a few more nucleotides going backward until they touch the previous set of RNA primer and nucleotides. Each set of nucleotides replicated on the lagging strand’s complement is called an Okazaki fragment. To join the new Okazaki fragment to the previous one, a special enzyme has to come in and remove the RNA primer between the two fragments. Then the two Okazaki fragments have to be joined by an enzyme called DNA ligase. Then the polymerase replication machinery has to be unclamped, moved forward to the replication fork, and clamped again. The process proceeds until both the leading and lagging strands have replicated completely (Behe 1998, p. 191). There is also an elaborate proofreading system that corrects any mistakes in the replication process.