Junk DNA, put simply, is those parts of the genome (human or otherwise) that have no known function. The human genome has about 19,000 genes. A gene is essentially a sequence of base pairs that code for a protein – there are four difference bases with each triplet being a “word” that either codes for an amino acid or tells the process of transcribing the protein to stop.

Even within genes there are noncoding regions, called introns, which have to be removed from the RNA so that the coding regions can be joined together. Between the genes there are also vast non-coding regions. Some of this non-coding DNA is regulatory and structural – it helps regulate when and how much specific genes are transcribed into proteins.

The burning question is, how much of the non-coding regions between the genes serves any function and how much is completely unnecessary, or “junk”? This is an important question for understanding genetics, but also has implication for creationists. Creationists don’t like the concept of junk DNA because it strongly implies an evolutionary history. Why would a designer sloppily insert so much unneeded junk into our pristine genome? Why are genes clogged with non-coding regions that need to be removed? So they claim that all DNA has function, we just don’t know what it is.

ID proponent Stephen Meyer, for example, said:

“For example, we predicted very early on that the junk DNA was not junk. We did that on the basis of an ID perspective. “

There have been two basic approaches to the question of junk DNA. The first can be characterized as an argument from exclusion. If we don’t know what part of the genome does, we conclude that it probably has no function. But we recognize that these parts of the genome have no known function, and therefore as new discoveries are made some of these parts may flip from unknown to known. Therefore the percentage of the genome that is junk is likely to shrink over time. This doesn’t mean, of course, that it will necessarily shrink to zero.

The second strategy is to look for evidence from which we can reasonably infer that a part of the genome is functional or not. For example, some stretches of DNA appear to be viral DNA that was inserted into the genome, and then became nonfunction through mutations. It is hard to imagine what purpose these viral inclusions serve. Other sections of DNA appear to be copies of known genes that also have mutated and become noncoding, so-called “pseudogenes.” There are also stretches of DNA that are monotonous repeats.

You can further look at DNA to see how often it mutates. Mutations in function DNA has a chance of causing problems, and therefore such mutations are selected against. The more critical the exact structure of a protein is, then the fewer mutations it will accrue over time. Such proteins are said to be highly conserved. This is because any mutation is likely to be fatal. Other proteins can tolerate some mutations.

We also know what the average background mutation rate is. Therefore, if a section of DNA were truly junk, and the sequence of base pairs was of no functional importance, then that region of the DNA should experience the full background mutation rate without any negative selective pressure. Functional parts of the DNA will have less than the full background mutation rate, to whatever extent they are conserved. Using this kind of analysis it seems that at most 20% of our genome is functional – or at least has a function which depends on the genetic sequence.

There is also the ENCODE project which looked at a different piece of information. They analyzed which parts of the human genome are ever transcribed or have regulatory segments bind to them. In other words, they looked for evidence of any activity on the genome. They concluded from their analysis that 80% of the genome is functional. Creationists interestingly celebrated, even though this still left 20% of the genome as junk.

But the conclusions of the ENCODE authors have been soundly criticized. The kinds of activity they found could easily be incidental, and not functional. So they did not demonstrate that 80% of the genome is actually functional.

Currently the consensus is that between 10 and 20% of the human genome is functional, and the rest is junk. Junk does not mean completely inactive. It also does not mean that evolution will not by chance use some of it as raw material. It just means we could live without it, and it is not currently serving any real function.

There is yet another way to approach the question of how much of our genome is junk, called “genetic load.”  Essentially you can calculate how many functional mutations there should be in an individual (developmental load) and over evolutionary time (phylogenetic load).

Evolutionary biologist Dan Graur just published a recent estimate of developmental load, the number of mutations that could be tolerated with each child born, given the known rate of background mutations. He did this in a new way – calculating what the birth rate would have to be in order to maintain population size given the death rate from deleterious mutations. That death rate is determined by the mutation rate and the size of the vulnerable genome. He compared this to historical birth rates and population growth.

From that he calculates that the size of the functional genome is between 10-15% with an upper limit of 25%. This depends on what you accept as the mutation rate, but he considered the range of estimates in his calculation. For example:

“For 80 percent of the human genome to be functional, each couple in the world would have to beget on average 15 children and all but two would have to die or fail to reproduce,” he wrote. “If we use the upper bound for the deleterious mutation rate (2 × 10⁻⁸ mutations per nucleotide per generation), then … the number of children that each couple would have to have to maintain a constant population size would exceed the number of stars in the visible universe by ten orders of magnitude.”

This is an interesting line of evidence, and certainly needs to be accounted for, but there are a lot of assumptions and therefore potential for adjustments based on unknown factors. I do think he has convincingly argued that the percentage of the genome that is junk is high, and is almost certainly not zero.

The implications of this, and pretty much all of genetics, is clear – life evolved. The fingerprints of evolutionary history are clearly left behind in all genomes. The molecular evidence for common descent is, in my opinion, an undeniable slam dunk. That does not prevent creationists from denying it, however, with clearly forced intellectual squirming.