Another Big Failure
Evolution predicts that more distant species should have greater differences in their genomes. After all, species in distant limbs of the evolutionary tree likely have different evolutionary pressures and have been evolving independently for millions of years. This genome difference should be all the more obvious for DNA changes that are functionally unimportant. Such changes can accumulate independently in the different evolutionary lineages, as they go unchecked by evolution’s selection process.
When DNA changes do influence function then the prediction becomes more complicated. These DNA changes may be selected for, or against, depending on how they affect the function, and ultimately the reproductive advantage, of the organism. But for DNA segments that are not functionally constrained, the theory of evolution predicts divergence across different species. Or in other words, for functionally unconstrained DNA, similar sequences should not be found in distant species. The corollary to this prediction is that similar DNA sequences found in distant species must be functionally constrained.
This prediction has been falsified in the many examples of functionally-unconstrained, highly similar stretches of DNA that have been discovered in otherwise distant species. For instance, thousands of so-called ultra-conserved elements (UCEs), hundreds of base pairs in length, have been found across a range of species including human, mouse, rat, dog, chicken and fish. Evolutionists were astonished to discover these highly similar DNA sequences in such distant species. In fact, across the different species some of these sequences are 100% identical. Species that are supposed to have been evolving independently for 80 million years were certainly not expected to have identical DNA segments. “I about fell off my chair,” remarked one evolutionist. 
Evolutionists assumed such highly preserved sequences must have an important function. But even if true, it would be difficult to see how so little sequence variation could be tolerated. The results were not what evolutionists expected, but this was just the beginning. Subsequent laboratory studies failed to reveal any phenotype effects. A variety of knockout experiments were done to determine the function of these sequences that evolution was supposed to have preserved. But in many of the regions no function could be found. One study knocked out several UCE regions, including a stretch of 731 DNA base pairs that was hypothesized to regulate a crucial gene. Evolutionists expected the knock out to result in lethality or infertility but instead found normal, healthy mice. Months of observation and a battery of tests found no abnormalities or significant differences compared to normal mice.  As one of the lead researchers explained:
For us, this was a really surprising result. We fully expected to demonstrate the vital role these ultraconserved elements play by showing what happens when they are missing. Instead, our knockout mice were not only viable and fertile but showed no critical abnormalities in growth, longevity, pathology, or metabolism. 
Another study knocked out two massive, highly conserved, DNA regions of 1.5 million and .8 million base pairs in laboratory mice and, again, the results were viable mice, indistinguishable from normal mice in every characteristic they measured, including growth, metabolic functions, longevity and overall development.  “We were quite amazed,” explained the lead researcher. 
Extensive tests have failed to find a function for many of the UCEs and these results were surprising to evolutionists. Perhaps some mysterious functions will be discovered in the future, but the years of research at this point indicate evolution’s prediction is false. The best information we have to date, and it is extensive, indicate that the genomes of distant species include highly similar and even identical stretches of DNA that otherwise are not functionally constrained.
It is worth noting that problems posed by this evidence will not all disappear even if some mysterious function is discovered in the future. Highly similar sequences in distant species, functional or not, are simply not consistent with evolution. Because such sequences are in distant species, according to evolution such sequences must date back to a very distant ancestor. In other words, these sequences not only must have important function in the extant organisms in which they are found, but they must have evolved early in the history of life, and they must have been important in a very different organism, under very different conditions.
And whatever the mysterious function is, it must be incredibly sensitive to every detail in the DNA sequence. But how could the sequence initially evolve if little or no variation is allowed? Evolution requires a functional pathway to arrive at the sequence in the first place but the highly restricted UCEs would have none. We would have to believe that functionally important stretches of DNA, hundreds of base pairs in length, just happened to form and then were preserved by evolution. The odds against this are astronomical.
“It can’t be true” was one evolutionist’s reaction to the UCE findings in recent years.  The findings falsify predictions of evolution, but they are true and they have been verified independently. Some evolutionists considered the possibility of sequence armoring. That is, perhaps these highly conserved sequences are a consequence of a strong, local, resistance to mutations at certain locations in the DNA. But it is difficult to imagine how such localized DNA protection could occur, and in any case empirical observations have ruled out this explanation.
Evolutionists have also considered the possibility of functional redundancy. In this case, no deleterious effects are observed in the knockout mice because other DNA regions perform the same function as do the deleted UCE regions. But then this would not explain why the UCE are so highly conserved.
On the other hand, perhaps the deleterious effects of removing an apparently functionless UCE are observed only in subsequent generations. But again, this idea has difficulty explaining why the UCEs are so highly conserved.
Perhaps the most common hypothesis is that many of the UCEs have functions that are difficult to detect. This is certainly possible, but it raises the problem of how evolution could select for such rare sequences and subtle function.
UCEs are another example of how the theory, rather than the evidence, drives evolutionary thought. The DNA must have a function, even though myriad tests have found none. If we cannot detect the function, then there must be a problem with the tests. There must be a function which otherwise is undetectable to us. It is a perfect example of how metaphysical certainty resists falsification as Antony Flew once illustrated in his gardener parable:
Once upon a time two explorers came upon a clearing in the jungle. In the clearing were growing many flowers and many weeds. One explorer says, “Some gardener must tend this plot.” The other disagrees, “There is no gardener.” So they pitch their tents and set a watch. No gardener is ever seen. “But perhaps he is an invisible gardener.” So they set up a barbed-wire fence. They electrify it. They patrol with bloodhounds. (For they remember how H. G. Well’s The Invisible Man could be both smelt and touched though he could not be seen.) But no shrieks ever suggest that some intruder has received a shock. No movements of the wire ever betray an invisible climber. The bloodhounds never give cry. Yet still the Believer is not convinced. “But there is a gardener, invisible, intangible, insensible, to electric shocks, a gardener who has no scent and makes no sound, a gardener who comes secretly to look after the garden which he loves.” At last the Sceptic despairs, “But what remains of your original assertion? Just how does what you call an invisible, intangible, eternally elusive gardener differ from an imaginary gardener or even from no gardener at all?”
For evolutionists evidence such as the UCEs cannot pose a problem for the theory. There must be an explanation. And as in Flew's parable, sometimes evolutionists have creative explanations for why the evidence does not seem to reveal their gardener.
1. Karen Lurie, “Junk DNA,” ScienCentral July 20, 2004.
2. N Ahituv, Y Zhu, A Visel, A Holt, V Afzal, LA Pennacchio, EM Rubin, “Deletion of ultraconserved elements yields viable mice,” PLoS Biol 5 (2007): e234.
3. DOE/Lawrence Berkeley National Laboratory, “Mice thrive missing ancient DNA sequences,” ScienceDaily 6 September 2007.
4. M. A. Nobrega, Y. Zhu, I. Plajzer-Frick, V. Afzal, E. M. Rubin, “Megabase deletions of gene deserts result in viable mice,” Nature 431 (2004): 988-993.
5. S. Pagán Westphal, “Life goes on without ‘vital’ DNA,” New Scientist June 3, 2004.
6. E. Pennisi, “Disposable DNA puzzles researchers,” Science 304 (2004): 1590-1591.