One of the strongest evidences of our evolutionary ancestry is that we carry around, inside of our very chromosomes, DNA that is left over from our evolutionary ancestors. Most of it is DNA that functioned as genes in our evolutionary ancestors, but today are inactivated (pseudogenes). One example among many is our olfactory proteins. We have about 350 of them, which means that we can distinguish about 350 primary odors (and a very large number of odor combinations). Other mammals such as dogs and mice have about 1000. They can distinguish many more odors than we can. Dogs and mice depend on scent information to survive, while primates such as humans depend more on vision, which is why we can get by with fewer of them. But here is the evolutionary part. We have about 650 olfactory pseudogenes. That is, we have the genetic material for all 1000 scent genes, but 650 of them are sitting in our chromosomes unused. We also have vestigial centromeres and telomeres in our chromosome 2, left over from the time when two ape chromosomes merged together into one.
This noncoding DNA was, in the past, called “junk DNA.” This term is now seldom used, however, because it turns out that, although pseudogenes and other noncoding DNA are no longer used for their original function, they often have a regulatory role. That is, they don’t do what they originally did, but they do something. A big group of scientists, Project ENCODE, recently published their results that indicate that at least 80 percent of noncoding DNA has some function.
So it turns out that much of the noncoding DNA is not junk after all. Creationists jumped up and down with joy at this announcement. They claimed that the newest genetic evidence shows that God created all the DNA to be useful.
But not so fast. What, exactly, is that use? As I noted above, many pseudogenes now have a regulatory function. For example, the olfactory pseudogenes no longer produce olfactory proteins, but they do something. As one creationist article said, “Over 80 percent of the human genome is actively involved in at least one or more biochemical reactions associated with gene regulation in at least one type of cell. Nearly all of the genome lies within close proximity to some sort of regulatory event and, therefore, very little of the genome can be considered extraneous to its full function.” However, these pseudogenes are still recognizably similar to the olfactory genes of other mammals. Their structure is mostly suited for the production of scent detection proteins, a function they no longer have. Their regulatory function is largely unrelated to their structure; the regulatory function is incidental to their structure. That is, the genes became pseudogenes and then later took on a regulatory function. They are still pseudogenes and are still evidence of evolutionary ancestry.
Let me draw a parallel that will make this clearer. Like many of you, we have a ski machine. We used to use it when we lived in Minnesota, where the year was divided into ice vs. mosquitoes. In order to get walking exercise, we needed the machine. We brought it with us to Oklahoma, but today it stands in the bathroom where its major function is for drying towels and washcloths. We can actually take walks outside most of the year, and no longer need this piece of exercise equipment. Now, a drying rack does not need belts and wheels and foot rails and a digital distance monitor. It is not junk—it is a perfectly serviceable drying rack—but its ski-machine structure is vestigial. It is a pseudogene of a ski machine, so to speak.
And this is why the creationist use of Project ENCODE results as supposed proof of intelligent design is invalid. Noncoding DNA is not junk but neither was it designed in detail for its current function. It is not junk but it is vestigial. In this sense it is no different from other vestigial characteristics. Staminodes in female flowers used to be stamens. They no longer produce pollen, and are therefore vestigial, but they still function in attracting pollinators. They are now just sticks, their original function gone, but they are pretty sticks that attract bees. They are not junk, but they are vestigial.