Pseudogenes: Argument for Evolution and Against Design?
Introduction
Pseudogenes are regions of non-coding DNA (DNA that does not code for functional protein) that has been apparently duplicated from functional genes. Genes, and even chromosomes and entire genomes can be duplicated through copying errors. If evolution were true, it would be expected that some of these duplicated genes would undergo mutation that could render them useless. These pseudogenes would be passed down from generation to generation and across species as one species evolved into another. Random mutations would be expected to be inserted into the sequence, since there would be no selection pressure to eliminate less fit sequences. An examination of these pseudogenes among families related through descent would be expected to reveal a simple inheritance of these pseudogenes and the mutations that they would have accumulated over time.
Non-coding DNA
Much has been made in the past of non-coding (does not code for messenger RNA or codes for defective mRNA, and therefore has no protein product) or "junk" DNA found in eukaryotes. To a large degree, these "non-useful" coding regions do not exist in the prokaryotes (bacteria). However, bacterial DNA is not enclosed in a nucleus, nor is it found in individual chromosomes (as in eukaryotes), but exists as just one long piece of DNA. At least nine classes of non-coding DNA are now recognized: introns, satellites, minisatellites, microsatellites, 3' untranslated regions, heterogeneous nuclear RNA, short interspersed elements, long interspersed elements, and pseudogenes. Pseudogenes are regions of DNA which resemble portions of coding genes from which they are hypothesized to have been derived. They themselves do not code for proteins, since they usually do not begin with a "start" coding sequence. The fact that pseudogenes are expressed to a high degree in mammals as opposed to other animals was the first hint that these sequences were not just non-functional relics of evolution.
Ways in which pseudogenes do not match the evolutionary paradigm
An article by Gary Gilbert published in the October, 1992 Spectrum magazine presented the beta globin pseudogene as compelling evidence for human's and ape's evolution from a common ancestor. Gilbert suggested pseudogenes, and other non-coding DNA, are molecular potsherds that can be used to reconstruct a species' evolutionary history, requiring that this DNA really have no function, but continues to be produced as a partial record of what once was an important adaptation.
A study by Minghetti and Dugaiczyk1 examined the enolase pseudogene, present in humans and four other primates, including the baboon, an Old World monkey. The accepted value of 5 x 10-9 nucleotide substitutions per site per year as the evolutionary rate for pseudogenes would lead one to conclude this pseudogene arose 14 million years ago. However, evolutionary theory states Old World monkeys diverged from the hominid lineage some 30 million years ago. It is difficult to explain how the sequence substitution rate would vary from one pseudogene to another, since they are non-coding, and, therefore, should not be subject to any form of natural selection.
What is common to all these pseudogene studies is that the pseudogenes from humans and apes are not identical. One would expect some similarity, since 98% of our genome is identical to that of chimpanzees. What is the purpose of this non-coding DNA? In humans, 97% of the genome is non-coding, suggesting that it must serve some purpose. Even evolution would not be expected to produce a species which has an efficiency of only 3%. Natural selection should have removed all this useless DNA. Much of the non-coding DNA that was once considered nonfunctional is actually highly functional. In fact, recent studies show that some of this non-coding DNA can control expression of other DNA, and other non-coding DNA probably serves to give structure to DNA and the chromosomes.
First proof for functionality in a pseudogene
The idea that pseudogenes are merely evolutionary relics has been so ingrained in the scientific community that few studies have actually attempted to find any kind of function for many of the thousands of mammalian pseudogenes. In fact, the first functional role for a pseudogene was found through a study that was not even designed to study pseudogenes.2 This study was looking at expression of a fruit fly gene that was being inserted into the genes of laboratory mice. The investigators produced several lines of mice by inserting the fruit fly gene randomly into the mouse DNA. However, just one line of the genetically-altered mice was found to have multi-organ failure in at least 80% of the individuals. Instead of discarding the aberrant line, the scientists probed to find out why the insertion was lethal. What they found is that the fruit fly gene had been inserted into the middle of a pseudogene sequence called Makorin1-p1. The scientists found that this pseudogene produced an mRNA product that regulated the expression of the functional Makorin1 gene. Not only was the pseudogene functional, but its destruction resulted in a lethal mutation in the mice. Scientists had found the first required pseudogene.
The abstract from a commentary in issue of Nature in which the study was published indicated:
"'Pseudogenes' are produced from functional genes during evolution, and are thought to be simply molecular fossils. The unexpected discovery of a biological function for one pseudogene challenges that popular belief."3
Since this first study, many other studies have found that pseudogenes exhibit functional activity, including gene expression, gene regulation, and generation of genetic diversity.4 Recent work shows that up to 50% of pseudogenes in some genomes appear to be transcriptionally active.5 A large study (over 350 investigators), comprehensively examining 1% of the human genome, estimated that at least 19% of all pseudogenes are transcribed.6
Pseudogenes and siRNA
Another study has found that numerous pseudogene transcripts interact with protein-coding mRNAs to form dsRNAs, which are processed into endo-siRNAs, through the action of a ribonuclease enzyme called Dicer.7 Dicer cleaves double-stranded RNA (dsRNA) into short double-stranded RNA fragments called small interfering RNA (siRNA), which are about 20-25 nucleotides long. In the study, cells that were Dicer knockouts (the Dicer gene was deleted) expressed more transcripts of several genes, indicating that these pseudogene-derived endo-siRNAs were active in gene regulation through RNA interference pathways. As time goes on, more and more functions are being found for pseudogenes.
Evolutionists' assumptions about God
Does the presence of pseudogenes eliminate the possibility that God created life? To come to this conclusion, there are some assumptions that are implicit in the evolutionists' argument. The first assumption is that God would only create new creatures by producing an entirely new copy of DNA. In other words, DNA would be expected to be completely redesigned from any previously existing organism. Is this the way God works? We know from science that the Sun is a second generation star - formed from the remains of a supernova. For this reason, the Solar System is highly metal enriched, which is required for the existence of life on earth.8 Therefore, God does reuse material when designing "new" structures. When Jesus made wine at the marriage feast in Cana of Galilee (John 2:1-11), He did not begin with nothing or air, but began with water. Part of the water was changed into alcohol, but greater than 80% of the original water was unchanged. When God brings a person to salvation, He does not change the genetics or physical makeup of the individual. The person remains in the same body - often a body that has been ravaged by the effects of a lifetime of sinful behavior.
A good analogy in the design of a genetic code is the design of computer programs. I do a significant amount of computer programming as part of my job. When I write programs, I always reuse sections of code in the new programs. I do not begin by writing an entire program from scratch. This would be silly, and highly inefficient. The computer program consists of the GUI (graphical user interface) and the code that performs the actual computations. This is analogous to biological organisms. The GUI is the phenotype (the way the organism looks) and the code that performs the computations is the biochemical pathways. If one Designer created all biological organisms, we would expect to see similar genetic code for both phenotype and biochemical pathways. This is a good argument in favor of monotheism as opposed to polytheism.
A creationary model for genetic similarity
The Bible says that God created humans from the dust of the earth.9 This statement suggests that humans were designed from preexisting material. I propose that part of this "dust" consists of the genetic code of previously existing organisms. If you were going to create a new species of primate, you would begin with primate DNA. This DNA would be altered to form the unique characteristics of the new species. I believe that this is the method that God used to create new species of life on earth. How does this differ from evolution driven through natural selection and how can you distinguish the two methods? Naturalistic evolution could, in theory, produce some of the changes in structures that would account for some of the phenotypic differences observed between the old and new species. However, evolution is unable to account for the design of new structures. Even more of a problem are the ravages of mutation on the genomes of organisms.10 Mutation, the mechanism by which evolutionary change is proposed to occur, most often has no effect upon the fitness of an organism. In humans, these "neutral" mutations occur at a rate of 2.6 mutations per person per generation. However, deleterious mutations occur at a rate of 1.6 mutations per person per generation. Although these deleterious mutations are usually recessive (not expressed unless there are two copies), they will accumulate in the gene pool over time. Decreases in population size leads to the expression of these deleterious mutations through inbreeding, which seriously affects the fitness of the species. In fact, this is the mechanism by which species go extinct. Because of the small amount of genetic variation among humans, evolutionists have proposed that the human species went through a population bottleneck in the recent past. However, such a bottleneck would lead to expression of deleterious mutations, which would further drive down the population numbers, leading to extinction. I believe that God created humans by editing primate DNA - adding new features and removing the deleterious mutations of this DNA template. If evolution were the mechanism by which species arose, deleterious mutations would continue to accumulate as new species evolved. This mechanism would lead to ever increasingly defective DNA through the biological history of the earth. How does this creationary model relate to pseudogenes? Since pseudogenes are not deleterious, I believe that God left them in the genome as part of the filler DNA required to maintain chromosome structure and function.
Conclusion 
Until 2003, evolutionists claimed that pseudogenes were the best evidence that macroevolution was purely an undirected function of mutation. However, recent studies have shown that some pseudogenes are actually required an organism's survival. A survey of the human genome has shown that 19% of pseudogenes are transcribed, implying that they are functional. Subsequently, it was shown that transcripts of pseudogenes are involved in gene regulation through RNA interference pathways. However, it is also possible that non-transcribed pseudogenes might perform regulatory functions in nearby genes. So, I would not be surprised that a thorough examination of our genome will reveal function in at least half of all pseudogenes, with the remainder playing some role in chromosomal stability and structure. We will continue to report new studies and findings as they become available.
Related Pages 
- When Junk DNA Isn't Junk
- Bad Designs in Biology? - Why the "Best" Examples Are Bad
- Intentional Deception by Evolutionists
Related Resources 
PSEUDOGENES AND ORIGINS L. J. Gibson, Geoscience Research Institute (from Origins 21(2):91-108, 1994)
Fazale Rana (Ph.D.
in chemistry), vice president of research and apologetics at
Reasons To Believe, has written a
new book,
The Cell's Design: How Chemistry Reveals the Creator's Artistry, that
attempts to show that cellular biochemistry points to the existence of the
Creator who designed it. Whereas most intelligent design books attempt to show
the existence of design by demonstrating the existence of irreducible
complexity, Dr. Rana examines the cell's biochemistry with broad strokes of how
everything works together with such marvelous fidelity. So, even if a single
piece or line of evidence might be dismissed as a statistical outlier, the
weight of evidence makes a powerful case for design by a Creator.
Darwin's
God: Evolution and the Problem of Evil by Cornelius G. Hunter. Biophysicist
Cornelius Hunter examines the evolutionary argument common among atheists
"God would not have done it that way." Hunter points out that
this argument is nothing less than theology under the guise of
"biology."
Reasons
To Believe's third in a series of books proposing a testable creation model
takes on the origin and design of the universe. Previous books,
Origins of Life: Biblical and Evolutionary Models Face Off
and Who
Was Adam?: A Creation Model Approach to the Origin of Man, examined the
origin of life on earth and the origin of mankind, respectively.
Creation As Science develops a biblical creation model and compares
the predictions of this model compared to a naturalistic model, young earth
creationism, and theistic evolution. This biblical creation model is divided
into four main areas, the origin of the universe, the origin of the Solar
System, the history of life on earth, and the origin and history of mankind.
The Edge of Evolution: The Search for the Limits of Darwinism by Michael Behe
Darwin's Black Box author Michael Behe takes on the limits of evolution through an examination of specific genetic examples. Behe finds that mutation and natural selection is capable of generating trivial examples of evolutionary change. Although he concludes that descent with modification has occurred throughout biological history, the molecular devices found throughout nature cannot be accounted for through natural selection and mutation. Behe's book claims to develop a framework for testing intelligent design by defining the principles by which Darwinian evolution can be distinguished from design.
References 
- Minghetti PP. and Dugaiczyk A. 1993. The emergence of new DNA repeats and the divergence of primates. Proceedings of the National Academy of Sciences of the United States of America 90(5):1872-1876.
- Hirotsune, S., Yoshida, N., Chen, A., Garrett, L., Sugiyama, F., Takahashi, S., Yagami, K., Wynshaw-Boris, A., and Yoshiki, A. 2003. An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423: 91-96.
- Lee, J. T. 2003. Molecular biology: Complicity of gene and pseudogene [News and Views] Nature 423: 26-28.
- Balakirev, E. S. and F. J. Ayala. 2003. PSEUDOGENES: Are They "Junk" or Functional DNA? Ann. Rev. Genetics 37: 123-151.
- Zheng, D. and M. B. Gerstein. 2007. The Ambiguous Boundary between Genes and Pseudogenes: The Dead Rise Up, or Do They? Trends in Genetics 23: 219-24.
- The ENCODE Project Consortium. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
- Oliver H. Tam, O. H. et al. 2008. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453: 534-538.
- Leslie Mullen. 2001. In Search of the Milky Way's Habitable Zone
- Then the LORD God formed man of dust from the ground, and breathed into his nostrils the breath of life; and man became a living being. (Genesis 2:7)
- Crow, J.F. 1999. The odds of losing at genetic roulette. Nature
397: 293-294.
Eyre-Walker, A. & Keightley, P. D. 1999. High genomic deleterious mutation rates in hominids. Nature 397, 344-347.
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