Junk DNA

"Junk DNA" is any material within a lifeform's genome that is not used in any cell process. It makes up the vast majority of the genetic material in most organisms. A common misconception is the synonymous use of the term "junk DNA" and "non-coding DNA", popularly used by uninformed journalists to make small discoveries of a few new transcription factors seem like genetic revolutions. "Non-coding DNA" refers to portions of the genome that don't code for proteins. These sections do, however, have many other utilities in cell processes, including rRNA/tRNA genes, 5'UTRs and 3'UTRs in exons, centromeres, introns, telomeres, scaffold attachment regions, and transposons. Protein-coding and non-coding DNA (known functional DNA) make up about 8.7% of the human genome, and 65% of the rest is known junk. It is assumed that the unknown 26.3% is most likely junk &mdash; geneticists and ENCODE project members differ in that ENCODE tends to assume functionality as a null hypothesis (ironically, so do creationists) and real scientists assume non-functionality.

Creation
Junk DNA is produced by a few different processes:
 * Viral DNA is sometimes interpolated into a cell's genome (endogenous retroviral insertion); while the cell generally ignores it, it sometimes leads to the creation of new genetic traits when the "commenting-out" process fails. These genetic patterns can also be used to approximate a date of divergence between two closely related species.
 * Copying errors can duplicate sections of the genome, the result of which may or may not be functional.
 * A large proportion of non-coding DNA is made up of pseudogenes, which no longer have any biological function but were once functional genes. Some of them were originally formed by the previous process. The rest of them were most likely formed by mutation.

Creationism
My problem is that junk DNA does not equal noncoding or nontranscribed DNA, and I am sort of sick to see junk DNA being buried, dismissed, rendered obsolete, eulogized, and killed twice a week. After all, your findings have no bearing on the vast majority of the genome, which as far as I am concerned is junk. Turning the genome into a well oiled efficient machine in which every last nucleotide has a function is the dream of every creationist and IDiot (intelligent designer), so the frequent killing of junk DNA serves no good purpose. Especially, since the evidence for function at present is at most 9% of the human genome. Why not call noncoding DNA noncoding DNA? After all, if a DNA segment has a function it is no junk.

The trope that Junk DNA does not exist &mdash; or rather, that it is "not really junk" &mdash; is a common PRATT when it comes to creationism. It was the subject of a book by Jonathan Wells, The Myth of Junk DNA, which has been reviewed and extensively debunked by Larry Moran at his blog Sandwalk. Other examples abound in the creationist "literature."

The reasoning behind this denialism is that a Designer would not produce a flawed creation. The idea of 'junk' in a divinely created world is anathema to such a creationist. The most common evidence cited in support of this position is the occasional discovery of kinds of Junk that actually do things. However, the problem here is that these discoveries only account for the tiniest portion of the material consigned to Junk status. Junk DNA is not going anywhere fast.

There is, however, at least the one species which is not believed to have junk DNA of any kind:  which has the smallest genome out of all free-living bacteria.

Relevance
All insects or all amphibians would appear to be similarly complex, but the amount of haploid DNA in species within each of these phyla varies by a factor of 100. There are various reasons why we think that Junk DNA exists. For one, the amount of DNA in different species varies wildly without rhyme or reason (excluding a few organisms that may be adapted to circumstances which require very small genomes). Also, almost all of the genome can be mutated without an effect on fitness.

Some regions of noncoding DNA form important structural portions of the DNA molecule: for example, as binding sites for histones (proteins that help to wrap up the DNA molecule in eukaryotes) and for "scaffold" proteins that hold the entire chromosome into its characteristic shape. Although these regions are noncoding, they are generally not considered "junk DNA", as they are evolutionarily conserved: that is, changes in them will upset the organism's survival. Noncoding structural DNA also makes up the telomeres (long structures at the end of eukaryotic chromosomes and an important part of the replication, aging, and cancer formation processes). Telomeres may mutate extensively without harm to the organism (in fact, gradual truncation of the telomere is one sign of cellular aging, and inappropriate lengthening of the telomere is a risk for a cell turning cancerous), and so could still be put under the umbrella of "junk" even though they serve a major role.

Finally, we do know that only a small part of the genome codes for proteins, along with an even smaller amount that is classified as 'regulatory DNA' in that it it involved with the function of the genes but is not directly functional itself, so to speak. However, the typical creationist argument tends to claim that Junk DNA is also regulatory DNA, which is false.

Note that evolution itself makes no prediction on the existence of Junk DNA; if it did turn out to be a 'myth,' per Wells, that would not falsify the theory in any way.

Evolutionary role of junk DNA
While the existence of "junk" DNA may be problematic for creationists, it's actually useful for evolutionary theory. Nonconserved, noncoding DNA inside the chromosome, ie. what we classically think of as "junk", can mutate rapidly and extensively without harm to the organism. It has been hypothesised, and extensively researched, that these noncoding regions can serve basically as sandboxes for gene evolution, where changes can occur randomly without altering the organism, and then be brought into play all at once, producing entire new amino acid sequences in an existing protein. To express this as an example: if an intron (a noncoding segment sandwiched inside a functional gene) mutates wildly (as introns are apt to do) and then is reintroduced into the coding system of the protein by a mutation that removes the bit that says "I am an intron, ignore me", this would result in the introduction of a new string of amino acids into the protein structure. This might result in the protein becoming dysfunctional, but many proteins are surprisingly resilient to such changes: if the protein remains functional it could be significantly altered by this mechanism. This is a subset of Motō Kimura's neutral theory. Some organisms even possess noncoding regions known as "pseudogenes" which are believed to exist solely for this reashon.

And that is why studying genetics is cool.

Research uses for junk DNA
Just because we don't know what, if anything, sections of DNA are for, does not make them useless for research. One example is much of the male-specific Y-chromosome, which largely has no coding function. Slow changes over time on the Y (such as single nucletoide polymorphisms), however, help construct a phylogenetic tree of human male lineages leading back to Y-chromosomal Adam, potentially useful for disciplines such as anthropology, history, and genealogy.