Jay Wile
[Originally published in 2012 as The ENCODE Data and Pseudogenes]
As I mentioned in two previous posts (here and here), the coordinated release of scientific papers from the ENCODE project has produced an enormous amount of amazing data when it comes to the human genome and how cells in the body use the information stored there.
While the majority of commentary regarding these data has focused on the fact that human cells use more than 80% of the DNA found in them, I think some of the most interesting scientific results have gotten very little attention. They are contained in a paper that was published in a journal named Genome Biology, and they relate to the pseudogenes found in human DNA.
For those who are not aware, a pseudogene is a DNA sequence that looks a lot like a gene, but because of some details in the sequence, it cannot be used to make a protein.
Remember, a gene’s job is to provide a “recipe” for the cell so that it can make a protein. Well, a pseudogene looks a lot like a recipe for a protein, but it cannot be used that way. Think of your favorite recipe in a cookbook. If you use it a lot, it probably has stains on it because it has been open while you are cooking. Imagine what would happen if the recipe got so stained that certain important instructions were rendered unreadable.
For someone who has never looked at the recipe before, he might recognize that it is a recipe, but because certain important instructions are unreadable, he will never be able to use the recipe to make the dish. That’s what a pseudogene is like. It looks like a recipe for a protein, but certain important parts have been damaged so that they cannot be used properly anymore. As a result, the recipe cannot be used by the cell to make a protein.
Pseudogenes have been promoted by evolutionists as completely functionless and as evidence against the idea that the human genome is the result of design. Here is how Dr. Kenneth R. Miller put it back in 1994:1
From a design point of view, pseudogenes are indeed mistakes. So why are they there? Intelligent design cannot explain the presence of a nonfunctional pseudogene, unless it is willing to allow that the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. Evolution, however, can explain them easily. Pseudogenes are nothing more than chance experiments in gene duplication that have failed, and they persist in the genome as evolutionary remnants…
Obviously, Dr. Miller didn’t understand intelligent design or creationism when he wrote that, as they can both explain nonfunctional pseudogenes. Before I discuss that, however, I need to point out that since 1994, functions have been found for certain pseudogenes.
As far as I can tell, the first definitive evidence for function in a pseudogene came in 2003, when Shinji Hirotsune and colleagues found that a specific pseudogene was involved in regulating the functional gene that it resembles.2 Since then, functions for several other pseudogenes have been found. In fact, a recent paper in RNA Biology suggests that the use of pseudogenes as regulatory agents is “widespread.”3
Even though functions have been found for many pseudogenes, the question remains: Are most pseudogenes functional, or are most of them non-functional? Well, based on the ENCODE results, we might have the answer. While the ENCODE results indicate that the vast majority of the genome is functional, they also indicate that the vast majority of pseudogenes are, in fact, non-functional.
While this result might sound counter-intuitive, it seems to be borne out by the data. First, let’s look at the numbers. The researchers found more than 12,000 sequences in human DNA that might be reasonably called pseudogenes. Based on several lines of analysis, they suggest that there might be as many as 14,112 pseudogenes in the human genome. However, identification of pseudogenes can be complicated, so in the end, they say that they are only confident in the identification of 11,216 actual pseudogenes. They call this group their “survey set.”
As I discussed previously, the ENCODE team assumes that any sequence of DNA that is transcribed by the cell is functional. After all, the process of transcription consumes a lot of resources and energy, and it is hard to believe that the cell would waste it all on DNA sequences that aren’t used.
So this part of the ENCODE team specifically wanted to see how many of the pseudogenes they identified were actually transcribed. The answer is only 876 of them. Out of all 11,216 pseudogenes that they confidently identified, less than 8% are actually transcribed. Based on their definition of functional, then, less than 8% of pseudogenes in the human genome are functional.4
Now the authors are quick to point out that their identification of transcribed pseudogenes is conservative, so there may be many more. Also, as I pointed out, the ENCODE team has not studied all cell types in the human body, so there might be some cell types that have not been studied that use some pseudogenes the ENCODE results indicate are non-functional.
However, based on these results, it is hard to believe that we will ever see the percentage of functional pseudogenes increase to anywhere near 51%. As a result, I think that based on the ENCODE data, it seems that most pseudogenes are, indeed, non-functional.
So let’s now revisit Dr. Miller’s statement. He claims that intelligent design can’t explain non-functional pseudogenes. Of course, that’s just not true. In fact, intelligent design would predict the existence of pseudogenes. After all, we know that mutations occur in the genome and often, those mutations result in the destruction of genetic information. Thus, it is not surprising that some genes have been “broken” as a result of mutation.
Creationism would also expect pseudogenes, since creationism says that after God created the world and the life in it, there was a terrible event called the Fall, and creation groans as a result (Romans 8:22). Thus, it is not surprising that over time, the Fall has resulted in the destruction of some genes.
What both intelligent design and creationism predict is that the vast majority of the genome is functional, because if too much damage is done to an intricately-designed system, it simply won’t work anymore. So if the vast majority of the genome is non-functional, that would be difficult (if not impossible) for intelligent design or creationism to explain. Of course, the ENCODE results indicate that this is not an issue, since they find evidence that human cells use more than 80% of the genome.
In the end, then, the ENCODE data tell us that while the majority of the human genome is probably functional, the majority of pseudogenes are probably not. This tells me something important. Most likely, some DNA sequences that have been identified as pseudogenes are probably not broken versions of functional genes. Most likely, they are regulatory elements that were designed into the genome. At the same time, however, most of what have been identified as pseudogenes are, indeed, broken genes, and they do appear to be useless. Obviously, this conclusion is subject to change based on new information, but it does seem to be what the ENCODE data are telling us.
[For a more recent discussion of this subject, see Pseudo-pseudogenes: Revealing further complexity in the genome on Creation.com]
References
- Kenneth R. Miller, “Life’s Grand Design,” Technology Review 97(2):24-32, 1994.
- Shinji Hirotsune, et. al., “An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene,” Nature 423:91-96, 2003.
- Yan-Zi Wen, Ling-Ling Zheng, Liang-Hu Qu, Francisco J. Ayala and Zhao-Rong Lun, “Pseudogenes are not pseudo any more,” RNA Biology 9(1):27-32, 2012.
- Baikang Pei, et. al., “The GENCODE pseudogene resource,” Genome Biology 13:R51, 2012.
