Over the past decade, evolutionists have touted the existence of alleged "junk" DNA as near indisputable evidence for evolution. Junk DNA is exactly what the name would imply: DNA sequences that appear to be extraneous, and therefore serve no purpose in the cell. It can consist of repeated DNA sequences, failed retroviral insertions, or introns, which are segments of DNA that are cut out during DNA to RNA transcription. Basically any DNA that does not code for a specific protein (or in a few cases codes for an apparently useless protein) is considered junk DNA, although more recently the term "non-coding DNA" has come into favor as it has been discovered that much of the DNA previously regarded as junk DNA does in fact serve in many important functions.
The existence of junk DNA found in the human genome is used to support evolution in a number of different ways. Many argue that it is a remnant of discarded evolutionary tools. This claim is very much akin to the vestigial organs argument. It basically holds that as a species population evolves, certain "primitive" DNA sequences may not be used, but will still be maintained in the species' genome for at least some period of time. Similarities in some junk DNA sequences between certain organisms are also used to support the idea of common ancestry.
The second major argument for common ancestry through junk DNA concerns what are called endogenous retroviral insertions. Retroviruses are viruses that, rather than inserting their own RNA into the host cell to carry out the viral protein synthesis, prefer to "reverse transcribe" their RNA into DNA, which is then spliced into the host cell's genome. Scientists have found DNA in humans as well as in many other organisms that shares a very striking similarity to modern day retroviral DNA. These retroviral DNA sequences appear in the human genome quite often, making up about 1% of the total human genome, and they represent about 30,000 different kinds of ERV's.
These supposedly useless DNA sequences appear to be the result of retroviral insertions where a particular virus has attempted to insert its own viral DNA into the host cell, but for some reason or another, the attempt failed. This failed insertion leaves something of a genetic "scar" on the DNA of the host cell, and if that cell happens to be a germ cell, this "scar" will be passed on through reproduction. It is therefore postulated that if an ERV is found in the genome of two species in the same loci on identical DNA sequences, then they must have evolved from the common ancestor that originally carried on the scar.
ERV's, or in the case of humans, HERV's, are used to support common ancestry from chimpanzees, as well as most other members of the primate family. Because similar ERV's have been found in similar loci in both the chimp and human genome, evolutionary biologists have inferred that chimps and humans share a common ancestor. Scientists have also discovered similar ERV sequences in other primates.
One of the major problems with the junk DNA argument is that it fails to take into account the possibility of the DNA in question actually having a designated function. If a particular DNA sequence is found that appears to have no function, it makes sense under an evolutionary interpretation of the evidence that that DNA will have no function, so it is very rare that further investigation will follow. Yet when scientists have examined such apparently extraneous DNA sequences carefully, they are often very surprised.
For example, a recent study demonstrated that certain DNA sequences called LINE-1 elements, formerly regarded as junk DNA, actually serve to repair broken strands of DNA. This DNA was previously thought to be the remnant of ancient DNA left in the human genome by evolution. It is curious to think what could have happened if someone had not questioned the original assumptions.
Another example demonstrating the usefulness of "junk" DNA is the recent discovery of a particular sequence's importance to vertebrate development. This DNA was previously regarded as irrelevant due to the fact that it did not code for any protein. What it did code for however was what is known as "microRNA", although until recently this particular type of RNA's function remained a mystery. It was later discovered however that microRNA actually play a diverse role in any organism, ranging from silencing and regulating gene expression to development and disease control.
Scientists were also surprised in 2004 when a study led by the Cell Press conclusively established the usefulness of more than 1/3 of previously regarded "junk" DNA in the mouse genome. It was once thought that the retrotransposons (self-replicating, mobile DNA sequences) found in the mouse genome were useless, parasitic DNA sequences. The new research suggests however that these transposable elements actually play an important role in the embryo development.
All of these examples run contrary to the evolutionary assumption that junk DNA is simply evolutionary leftovers. They also bring to light a very large problem with evolutionary assumptions regarding junk DNA, namely in that if the scientists who conducted these studies had accepted the evolutionary interpretation of apparently non-coding DNA, no further inquiry would have been pursued. It is also highly likely that more functions will be discovered for this "junk" DNA as scientists are realizing that although some gene functions may not be immediately apparent, many play subtle roles in such areas as embryo development, disease control, and the regulation of gene expression, duplication, and transcription.
This is not to say that all DNA is completely functional. Mutations do of course render much DNA useless, yet this in no way serves to support evolution. There are certainly corrupted strands in the genome of probably every organism on earth, but it is usually very apparent when a segment of DNA has mutated.
ERV's present somewhat of a more difficult challenge to opponents of evolution. The existence of identical ERV's in the same location on similar DNA strands in both the chimp and human genome does seem argue for common descent. The evidence may indeed seem to be convincing, but there are major flaws in the argument.
The first issue regards the usage of evolutionary assumptions involved in the interpretation of the data. There is no way of scientifically proving that heritable ERV's found in the chimp and human genome are in fact the result of failed retroviral insertions. In fact, the evidence seems to suggest just the opposite.
The origin of viruses has always been somewhat of a mystery, but most scientists generally agree that they were likely the result of mutated transposons or plasmids, which are notoriously unstable segments of motile DNA capable of splicing into the genome of other cells. It is therefore very likely that retroviruses actually originated from these transposable elements, rather than the transposable elements associated with ERV's originating from the retroviruses. What this implies is that rather than ERV's being genetic "scars" that we can trace back through our hominid ancestry, they are merely shared segments of transposable elements that later gave rise to retroviruses.
This conclusion is also supported by the numerous functions now being discovered for ERV's. A recent study confirmed that certain DNA sequences found in ERV's called LTR's actually signals the transcription of mRNA from certain parts of DNA. Numerous other studies have shown that many ERV's previously regarded as being extraneous actually play important roles in gene expression.
Of course, many evolutionists would still argue that homologous DNA sequences such as ERV's shared between chimps and humans supports common ancestry, but this is somewhat of a circular argument. If similarity implies common ancestry and common ancestry implies some genetic similarity, then this argument just begs the tar out of the question. It is just as valid to claim that homologous DNA sequences are the result of a consistent, intelligent Creator. This would not be inconsistent with the creation model, or the nature of the Creator.
If junk DNA is truly junk DNA, then it seems problematic that scientists would be finding many different uses for DNA previously thought of as useless. It is not unreasonable to extrapolate that many more uses will continue to be found for this junk DNA. A major problem with assuming junk DNA to be the "leftovers" of millions of years of evolution is the hindrance such an assumption can have on further scientific inquiry as relating to the usefulness of DNA sequences. Although this is what evolution predicts, it is not consistent with many recent studies. It is however consistent with an able Creator who planned for His creation to have the necessary genetic flexibility to cope in an ever-changing world.