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The headline on the MSNBC Web site proclaimed, "Darwin Vindicated!" In the article that followed, Arthur Caplan, a nationally noted professor of bioethics and molecular and cellular engineering, proclaimed what he thought was the most important finding to emerge from human genome research: "The genome reveals, indisputably and beyond any serious doubt, that Darwin was right-mankind evolved over a long period of time from primitive animal ancestors. . The response to all those who thump their Bible and say there is no proof, no test and no evidence in support of evolution is, 'The proof is right here, in our genes.'"
Of course, Caplan's was only latest of several such pronouncements. Last summer, when the Human Genome Project and Celera Genomics jointly announced that they had mapped the human genome, Nobel laureate David Baltimore wrote in The New York Times that the breakthrough "confirms something obvious and expected, yet controversial: our genes look much like those of fruit flies, worms and even plants. Should there be any doubt . the genome shows that we all descended from the same humble beginnings and that the connections are written in our genes. That should be, but won't be, the end of creationism."
Although such pronouncements are the stuff of "strong" editorials, they're about as wrong as they can be. Far from supporting Darwin's theory of evolution, genetic research is posing bigger and bigger problems for it. Caplan's and Baltimore's remarks testify not to the truth of Darwin's theory, but to the tenacity and ingenuity of its adherents.
To understand what recent genetic research means for Darwin's theory of evolution, we must first understand the theory itself.
Contemporary Darwinism holds that all living organisms descended from a single "universal" ancestor. All the plants, animals, and other organisms that exist today are products of random genetic changes and natural selection.
According Darwinism, nature acts like a breeder, carefully scrutinizing every organism. As useful new traits occur, they are preserved and passed on to the next generation, while harmful traits are eliminated.
Though each change is small, these changes eventually accumulate to produce new tissues, organs, limbs or other parts. Given enough time, organisms may change so radically that they bear almost no resemblance to their original ancestor-or to their distant cousins alive today. Thus, humans, squids and dragonflies differ dramatically from their alleged single-celled ancestor. And they differ almost as dramatically from each other. Most importantly, all this happens without any purposeful input-no Creator, no Intelligent Designer. Chance and nature run the whole show.
So what's that got to do with human genome research?
If Darwinism is true, all living organisms are physically related to each other. Since we all descended from the same universal ancestor, we are literally members of the same family. As a result, every organism should share some family resemblances, however faint. These resemblances are marks of our common ancestry.
Since Darwinian evolution is driven by genetic changes, evolutionary biologists have long desired to document family resemblances at the genetic level. And this is supposedly what recent genetic research has done.
For example, scientists have shown that we have 223 genes that are similar to those found in bacteria. We also share similar genes with nematode worms, fruit flies, sea urchins, spiny worms, mice and other organisms.
These genetic similarities are taken as hard evidence that humans once shared a common ancestor with these organisms-and that Darwin was essentially correct. Hence the excitement of Caplan, Baltimore and others.
If that sounds a bit flimsy, it is.
Berkeley law professor Phillip Johnson, a noted critic of Darwinism and the author of Darwin on Trial and Defeating Darwinism by Opening Minds, has spent many years analyzing Darwinist arguments.
"Darwinists consistently confuse the existence of a pattern with the process that produced itnamely, common descent guided by natural selection," Johnson said. "Whenever they see anything that seems to confirm the existence of the pattern, they think that it confirms their specific theory about how the pattern came about. Of course, it doesn't."
The reason it doesn't confirm their theory is that it doesn't rule out competing explanations, such as intelligent design.
"A lot of things show similarities," Johnson said. "For example, there's a pattern in the symphonies of Beethoven or the opinions of the United States Supreme Court. One Darwinist used various models of the Corvette as an example of an evolutionary pattern. But in all of those cases, the pattern existed in the mind of a designer. The mind is responsible for both the pattern and the variations on the pattern."
The Corvette example is particularly telling. In his book, Evolution and the Myth of Creationism, biologist Tim Berra used different models of Corvettes to show how evolutionary biologists could use similarities among organisms to construct an evolutionary "family tree." What he unwittingly demonstrated, however, was that designed objects could also be forced into an "evolutionary tree."
Thus, demonstrating the existence of similarities is useless for proving that Darwinism is correctand that random genetic changes and natural selection are capable of producing wholesale evolutionary change. That can only be proved with other evidence. But this "other evidence" has posed problems right from the start.
One example of inconvenient evidence is the fossil record. Although textbooks say that the fossil evidence is a bulwark of support for Darwinian evolution, it has always been a liability.
If Darwinism is true, the history of life should look like a spreading tree-with species slowly branching off from one another as small differences accumulate into larger ones. The fossil evidence should reflect this history, showing lots of gradual change. In fact, the change is so gradual that it should be hard to tell just when a new species begins.
But that's not what the fossils show.
As Darwin himself noted, "The number of intermediate varieties, which have formerly existed on the earth, [must] be truly enormous. Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graded organic chain; and this, perhaps, is the most obvious and gravest objection which can be urged against my theory." 
That problem remains with us today. Most fossil species appear all at once, fully formed, and change very little throughout their stay in the fossil evidence.
Several years ago, this situation led noted paleontologist Niles Eldredge to lament, "Either you stick to conventional theory despite the rather poor fit of the fossils, or you focus on the [data] and say that [evolution through large leaps] looks like a reasonable model of the evolutionary processin which case you must embrace a set of rather dubious biological propositions." 
That problem reaches dramatic proportions with what paleontologists call the "Cambrian explosion," which occurred about 530 million years ago. Over a period of only five to 10 million years, a flash of geological time, virtually every major animal group (or phylum) appears in the fossil evidence.
This is precisely the opposite of what contemporary Darwinism would lead us to expect. Instead of small differences accumulating into large ones, we see the largest differences right up front. As even Oxford zoologist and arch-Darwinist Richard Dawkins was led to remark, "It is as though they were just planted there, without any evolutionary history."
Thus, far from being a bulwark of support for Darwinism, the fossil evidence is something that must be explained away.
Of course, Darwinism has more problems than the fossil evidence. Ironically, one of those problems springs from similarities scientists found where they weren't supposed to: in genes that control embryonic development.
Darwinists maintain that the evolution of an organism's physical features is caused by underlying changes in its genes. The more these genes change, the more the organism changes. When you see large differences between two organisms, you should find corresponding differences in their genes. This is especially true of genes that control embryonic development, because they determine how the organism is built.
For years, then, Darwinists predicted that different organisms would have different genes controlling development.
But according to embryologist Jonathan Wells, author of Icons of Evolution, that's not what genetic researchers found. To the contrary, "the genes that have major effects in early development turn out to be strikingly similar across a wide range of [organisms]."
Scientists found, for example, that the gene controlling the development of limbs in fruit flies is very similar to the genes controlling the development of limbs in mice, tube-feet in sea urchins and spines in spiny worms-all of which are vastly different structures that have nothing in common. Indeed, according to evolutionary biologists, each of these structures evolved independently.
Yet the genes are so similar, Wells said, "that developmental genes from mice-and even humans-can replace their counterparts in flies."
What's more, such crossovers are legion. Indeed, many organisms seem to share not just one gene, but an entire suite of genes. And researchers say this seems to be the rule rather than the exception.
Now, if you believe that living organisms were designed by a creative intelligence, these similarities make sense. Just as humans use dipswitches in a variety of electronic devices, a designer could use genetic switches in a variety of organisms. For Darwinists, however, it's a different story.
"This discovery shocked the pants off Darwinists," Wells said. "But then they quickly choked back their surprise and declared that they expected it all along." According to the new story, Wells said, the reason these genes are so widespread is that they came from a common ancestor. "But the evidence indicates that the common ancestor lacked the features that these genes now control. That's a serious problem."
In the Darwinist view, complex genes arise through the slow accumulation of advantageous mutations. But what's the advantage of evolving a gene if the feature it controls doesn't exist?
Some might reply that the gene controlled some unknown feature in the ancestral organism. But that's little more than wishful thinking-and a tacit admission that these findings are not an asset to Darwinism, but a problem to be explained away.
As vexing as those similarities may be, they're not the worst problem. Though you may not know it from press accounts, one of the most striking discoveries of recent genome research is the extent to which organisms differ from each other.
As the genomes of more species are deciphered, researchers are finding that about 30 to 40 percent of each species' genes are unique to that species.  For humans that figure is a little above that. 
These differences are so profound that microbiologists may have to adopt new methods for their research. Until recently, microbiologists have assumed that by studying one or two "model" organisms, such as E. coli (the most studied bacterium) and S. cerevisiae (yeast), they could learn about many other organisms. But that assumption may be about to topple.
In a commentary published in 1997, Craig Venter, the lead scientist for Celera Genomics, and three of his colleague wrote, "With such a small set of common genes, and so many unique genes, we are led to question the concept of S. cerevisiae or E. coli as model organisms . In a real sense, organisms that contain unique constituent parts cannot be models for one another. Having several whole genomes spread out for our examination underscores how different from one another these organisms are." 
According to philosopher of biology Paul Nelson, "This is a remarkable, remarkable result." If it turns out that these unique genes have important functions and can't be altered without harming the organism, this would be a major blow to Darwinism.
"If that's the case," Nelson said, "then these genes have no evolutionary predecessors, and naturalistic evolution is in deep, deep trouble-and not because somebody wants the Bible to be true."
As we saw earlier, Darwinian evolution works by accumulating small genetic changes. Large jumps are anathema because they are too improbable and look too much like miracles. Each gene, then, had to be crafted one small step at a time. But if a gene can tolerate little or no change, there can be no line of evolutionary predecessors.
The reason you probably haven't heard about this is because evolutionary biologists, driven by Darwinist assumptions, have jumped to the conclusion that these genes evolved very quickly-so quickly that they bear no resemblance to any predecessor genes. And instead of calling them "unique" genes, they call them "rapidly evolving" genes, substituting a Darwinian interpretation for the facts.
One example of this is a recent study reported in the Proceedings of the National Academy of Sciences. The study examined certain proteins found on the outer coating of mammal's eggs. Two of the proteins allow sperm cells to dock and fuse with eggs. These proteins (and the genes that produce them) differ greatly from species to species-even closely related ones. They're also very picky: If a sperm cell doesn't have just the right proteins on it's own surface, it can't dock with the egg. Thus, there's no way that, say, sperm cells from a rat could fertilize a rabbit's egg. 
Intelligent-design theorists could point to this as a blue-ribbon example of design: Each species has its own reproductive lock and key. What's more, the proteins are so important, so diverse and so picky that they defy a Darwinian explanation. If the genes for these proteins were to pick up random mutations, the key would no longer fit the lock and fertilization would become impossible.
But what did the researchers conclude after examining these and other genes?
"These are among the 10 percent fastest evolving genes in the genome," the lead investigator told a New York Times science writer.
Unfortunately, this kind of reasoning is rife within evolutionary biology.
"I have to tell you that I really can't trust much of what I read from these guys," Nelson said. "Everything is filtered through the assumption that all life descended from a common ancestor. This study is a perfect example. Rapid evolution of this kind has never been directly observed. It's based entirely on the assumption of common descent and the absence of similarity."
And evolutionary biologists get away with this all the time because Darwinism is so widely accepted.
From a nonbeliever's perspective, though, it's clear that Darwinism has survived not because of the evidence, but in spite of it. Its proponents simply assume that it's true and interpret the evidence accordingly.
But that's getting harder to do. The more we learn about genetics and biology, the more Darwinists must hide behind such flimsy notions as "similarities," "rapidly evolving genes" and "unknown features on ancestral organisms."
Sooner or later, though, these notions will collapse under the weight of evidence, and there will be nowhere left to hide.
 Darwin, C. (1979). The Origin of Species. (Reprint of first edition.) New York: Avenel Books, p. 292.
 Eldredge, N. (1985). Time Frames: The Evolution of Punctuated Equilibria. Princeton: Princeton University Press, p. 75.
 Gerald M. Rubin, "The draft sequences: Comparing species," Nature 409, 820 - 821 (2001). Gerald M Rubin et. al., "Comparative genomics of the eukaryotes," Science 287 (24 Mar 2000):2204-15.
 J. Craig Venter et al., "The Sequence of the Human Genome," Science 291 (16 Feb 2001):1304-1351.
 Rebecca Clayton, Owen White, Karen A. Ketchum, and J. Craig Ventner, "The first genome from the third domain of life," Nature 387 (29 May 1997):459-462; p. 462.
 Willie J. Swanson et. al., "Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals," Proc. Natl. Acad. Sci. USA 98 [27 February 2001]:2509-2514.
Copyright 2001 Mark Hartwig. All rights reserved. International
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