Junk DNA

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.

Oklahoma Evolution Workshop, Part Three

The workshop sponsored by Oklahomans for Excellence in Science Education has brought together high school teachers and college faculty from Oklahoma and Texas. It began Friday night, October 5, and continues this morning. A few minutes ago, I blogged about the first two presentations, both of which addressed the scientific way of knowing about the world.

Now, Dr. Richard Broughton, a zoologist at the University of Oklahoma, is discussing how to interpret phylogenetic trees and how the phylogenetic way of thinking has changed our view of life. A millennium ago, scholars all believed that everything from the simplest animals to humans formed a scale of being from lower to higher. After Darwin, most scientists accepted that all organisms were part of a tree of life, rooted in a common ancestor--but they still accepted humans as the top of the tree, as if this is what the tree was meant to produce. But, when you think about real trees, you would never think that the top twig (if you can even identify it) is what the tree is all about. Modern evolutionary thinking identifies all species as being equally "evolved," all of them (us) being twigs on the tree.

Phylogenetic thinking has gotten scientists to think in terms of evolutionary branch points. Mammals, for example, all share a common ancestor (phylogenetic branch point), while all birds share a common (dinosaur) ancestor. Further back in time, birds and mammals shared a common vertebrate ancestor. This ancestor had the same limb bone pattern found in birds and humans, therefore this pattern is homologous. But this ancestor did not fly; bat and bird wings are, therefore, analogous--they evolved separately, despite their similar appearance. Phylogenetic trees can be based on physical characteristics (bones, wings, etc.) or on DNA data.
Rich had the participants figure out a phylogenetic tree based on a set of xerox copies; the ones that have the same shared derived characters (smudges made in copying) have a more recent common ancestor than the other. Therefore phylogenetic analysis can be used to figure out the pedigree of, for example, ancient Biblical manuscripts.

One of the best pieces of genetic evidence for a shared ancestry of chimps and humans is human chromosome 2. The genes of human chromosome 2 line up with those of two chimp chromosomes, but one of them is reversed. Human chromosome 2 has nonfunctional telomeres in the middle, and a nonfunctional centromere--which exactly fits what you would expect if two ancestral chromosomes fused together end to end in the human lineage, but not in chimps. But, as Rich emphasized, there are a lot of other pieces of genetic evidence, including shared noncoding DNA inherited from a shared ancestor. You can construct a phylogenetic tree of primates based on nothing but ERV (endogenous retroviruses; dead viruses that got stuck in the chromosomes) and it matches the phylogenetic trees constructed on the basis of completely different sets of data. The recent availability of whole-genome sequencing has allowed many new examples to be found. A group discussion revealed that no coherent explanations have been offered for these genetic patterns by creationists, who reject shared ancestry.

Even something as easy to understand as vitamin C provides evidence of evolutionary ancestry. The bodies of most mammals can make vitamin C, but primates cannot. Primates must get vitamin C from their food. By chance, the ancestors of mammals lost the ability to produce vitamin C, but it didn't matter, because they ate lots of fruit. We still have the gene for making vitamin C, but it sits unused in our chromosomes.

Scientists study species such as fruit flies--why? Some politicians think this is ridiculous, and boldly say so. But we share a lot of genes with fruit flies, and we can learn a lot about these genes by studying fruit flies. It is evolution that makes sense of this pattern. It confirms what Darwin said, even though he could not have imagined any of these molecular patterns.

DNA, Intelligent Design, and Theodicy, Part Two

In the previous entry I presented one of the main points that John C. Avise made in his recent book Inside the Human Genome: A Case for Non-Intelligent Design. If God designed the world, why are there so many, and such horrific, mutations in the human genome? Not only is there a huge number of different genetic diseases, but each one of these diseases can be caused by numerous different mutations. Mutations happen so often that the same diseases keep evolving over and over and over. This presents a major challenge to theodicy, which is the attempt to justify God in a world of suffering—in this case, genetically-based suffering. Thus one of Avise’s points is that, if God designed DNA, he could have made more efficient repair mechanisms to counteract the (perhaps inevitable) mutations.

Avise goes on to make another, very important challenge to theodicy: the very structure of the genome itself is inconsistent with the idea that the genome, or the human body, or the world was designed by God. Not just the mutations in the genome, but its very structure.

The human genome is full of stuff that interferes with the use of genetic information to produce healthy and functional enzymes and bodies. First, consider the fact that only about 1 percent of human DNA codes for those enzymes. About 68 percent of the DNA consists of non-coding DNA that is between the genes, and about 31 percent of the DNA consists of non-coding DNA that is inside of the genes. This is, at best, a clumsy system, because whenever a cell divides, all of this DNA is copied, not just the DNA that the cell will use. In addition, since each gene is broken into little “exon” fragments by a large amount of internal “intron” DNA, the genetic information must be spliced together in order to be put to use. That is, to get a functional enzyme, the genetic information from lots of exon fragments has to be cobbled together. If it works, there is no problem, but the whole system is so cumbersomely complex that it often fails. Not only are many genetic diseases caused by mutations in the genes themselves, but many genetic diseases are caused by (or also caused by) failures of the cell to deal properly with the non-coding DNA and the splicing.

Much of the non-coding DNA bears the clear mark of evolutionary origin. For example, there are a lot of pseudogenes, which are old genes that are not used anymore. Some of them are extra, duplicated copies of genes, complete with their introns (unprocessed pseudogenes); others are DNA copies of RNA transcripts, from which the introns have been removed (processed pseudogenes). There are also lots of mobile genetic elements, which either have or had the ability to move around among the chromosomes. Some of them are transposons, which can “cut and paste,” to use Avise’s metaphor, moving from one place to another. Some of them are retrotransposons, which can “copy and paste,” with one copy being left behind and the other going to a new place in the genome. Many of these retrotransposons are old dead viruses. We know this because they still have major chunks of the reverse transcriptase enzyme, an enzyme used only by certain kinds of viruses! Retrotransposons cannot actually become viruses anymore, because they have lost the genes that allow them to make protein capsules. Another evolutionary pattern is that species that have the most similar genetic DNA also have the most similar non-coding DNA, which makes no sense if they do not share a common evolutionary ancestry. You see, we know where much of this non-coding DNA came from, and it is not part of a system designed by a God.

There are even examples of some genes fighting against other genes. Some mutations cause a gene to over-represent itself in the next generation (“selfish genes”), which is harmful to the organism that carries it; and there are other mutations that suppress those selfish genes. So not only does the genome contain a clumsy load of non-coding DNA, but even DNA that fights against itself.

We know that such complexity of non-coding DNA is not necessary for the function of a genetic system, because bacteria do not have any of this: no introns, no pseudogenes, no transposons. They get by just fine without them.

The more we learn about DNA, the more we see that there is really no place for a Creator or Designer to fit in. It looks like, in Avise’s words, the Creator’s “primary role was to set into operation natural evolutionary forces.” Yes, you can believe that God designed evolution, and then let evolution do everything. But this would be like saying that angels push the planets around the sun by means of the laws of gravity and momentum. To slip God into an invisible realm behind the operation of natural laws, including genetic processes, seems more and more like fantasy.

And it sets God up for culpability for an immense amount of human suffering. Mutations of genes (previous essay) and malfunctions of genetic operation (this essay) cause human misery and death, in addition to killing perhaps one-third of fertilized egg cells. If God is behind the processes of human genetics, says Avise, then God is the “world’s leading abortionist and mass murderer.” Does this offend you? Then you need to reconsider what you believe about the role that God might play in the universe.

Creationists often claim that all of these mutations and flaws have occurred just since the Fall of Man. There is no Biblical basis for this belief. Genesis says, cursed is the ground, not cursed is the chromosome. Some creationists insist that the pre-Flood world had few if any mutations, which is why people lived to be over nine hundred years old. Either way, this entire burden of bad genes would have accumulated just in the last few thousand years. Mutations are not accumulating that rapidly today. Some creationists believe that Satan designed all the bad things in the genome. This is, needless to say, also without any scriptural basis. In no part of the Bible is Satan depicted as being smart enough to have redesigned the entire architecture of the human genome.

Don’t miss my new book, Life of Earth: Portrait of a Beautiful, Middle-Aged, Stressed-Out World, just published by Prometheus Books.