Special Explanations - From Biologos, Christians explaining pseudogene evidence for macroevolution.
Signature in the Pseudogenes - Part 1
Signature in the Pseudogenes - Part 2
The RTB Model and Pseudogenes
1. Junk DNA - some functions and effects have been found for the 98% of DNA that does not code for proteins; the term should be discarded. A: True. The term was first used nearly 50 years ago and is now archaic. It is understandable how it came to be used as deleting large sections of non coding areas had no visible effect on the organism and no products were known from nearly 98% of the genome.
2. Why aren’t pseudogenes, which are damaged, eliminated by selection forces? A: They are neutral. A duplicated pseudogene still has a functioning parental gene nearby. If the defective gene has no effect on the organism it will generally continue to age and accumulate mutations. Or, as in vitamin C, there is enough C in the diet so the gene knock-out was not expressed as a disease until we traveled away from the food source, such as British “limeys” on their ships.
3. Pseudogenes shared between organisms are often not identical. A: Yes, that’s the whole point. They accumulate different mutations in different organisms and that is how we can trace back origins and shared ancestry from the formation of new species.
4. Mutations are not random. For example, there appear to be ‘hot spots’ that have higher mutation rates. A: Within these hot spots, or general areas, the mutations are still random.
5. Insertions are not random. A: Same principle. Some areas may be more likely to have insertions, but within those general areas the insertions are generally random.
6. Much of the non coding regions of the genome are transcribed into RNA. A: True, but just because it undergoes transcription does not mean that this equals function.
7. The Lord inserted them for a reason we do not understand, perhaps to test our faith. A: This is the same argument in a different form that is used repeatedly when an observation dose not fit a particular theology. Past versions include that supposedly fossils were put in place to test us and light was made in transit just to give the appearance of age. So God is the great deceiver? Is this an intellectually satisfying answer?
8. Some pseudogenes have been found to have functions. A: True, but like vestigial structures discussed elsewhere on this site, vestigial structures or genes by definition do not have the function that they originally possessed. They are still false genes compared to the original unaltered gene, and so can be used to test common ancestry, whether they have a new function or not. If even a few functions are found, the hundreds of thousands of remaining examples would continue to support the concepts of pseudogenes and common ancestry.
9. Just because scientists do not currently know the function of a portion of DNA does not mean that they do not have functions. A: the evidence is that pseudogenes match original functional genes but they have been rendered non functional for their original function due to deleterious mutations and copying errors. They may be found later to have other influences, but their original function has been lost. As Max states: “Imagine a defendant at a murder trial defending himself - against overwhelming incriminating evidence - with the parallel argument: that since some convicted criminals have later been exonerated, he (the current defendant) should therefore be acquitted now, because someday in the future, evidence might be found to clear him.”
10. One gene, Mkrn1-pl has been found in yeast to have a well described function. A: It’s in mice, not yeast. Hirotsune’s 2003 paper has since been refuted by a subsequent paper by Gray et al. in a 2006 PNAS paper and there is no known evidence of function.
11. The genes were inactivated at “The Fall”. A: Many pseudogenes are shared by apes and humans, at the same location and share the same defect. It is a more logical conclusion that they were inherited from a common ancestry. There are now tens of thousands of pseudogenes known. Did God knock out all the shared genes across species lines in multiple species at the same position with some of the same mutations just to fool us into seeing a false pattern? And what about the accumulated mutations afterward that demonstrate deep time and interspecies relatedness?
12. Pseudogenes can provide a backup copy that could be repaired later in case the functional gene becomes corrupted (gene conversion). A: Although this may rarely occur, actually the opposite is well known whereby a pseudogene induces damaging mutations in a nearby functional gene. Diseases that have resulted include Gaucher’s disease, pseudoxanthoma elasticum, polycystic kidney disease (autosomal dominant), a type of hereditary cataract, and von Willebrand’s disease.
All these objections and probably more are really peripheral issues. One has to question what the real motive is behind all the various objections, when under careful analysis the challenges to pseudogene observations leading to evidence of common ancestry and macroevolution fail. Certainly, other believers who actually do work in closely related fields of molecular genomics accept the conclusions of common ancestry (Collins, Miller, Biologos web site, etc.) in contrast to others who are just reading the literature and looking for any publications that could support their views.
The central observations are that pseudogenes exist, and that they are deactivated former functional genes due to mutations, duplications and insertions. There are hundreds of thousands known and more are identified each year. Many have identical errors in them and occur at the same chromosomal position when compared across species. These similar pseudogenes also have other mutations present and the accumulation of these mutations can be used to trace speciation and evolution, giving us a DNA history book to read that confirms the fossil record overall and enriches our shared heritage of life on our planet. Unfortunately, when one encounters dueling Ph.D.s it is important to go to the original sources that are used to check for quotes out of context, agendas and assumptions, and poor scholarship which can give insights into who really knows what they are writing about.
Addendum - In the June 24, 2010 Nature issue researchers report another possible function for pseudogenes. The pseudogene PTENP1 appears to act as a decoy for its functional gene. As the SN article points out, it is too soon to tell how much of this function will translate across to thousands of other pseudogenes. And of course, finding a function does not neutralize the concept of derived genes that hark back to origins of original functional genes and thus point to shared ancestry, as has been repeatedly mentioned in this section. Source: Science News.
The Real Life of Pseudogenes (Gerstein and Zheng) **. Link
Wikipedia: Non coding DNA. Link
Wikipedia: Human genome. Link
Wikipedia: Pseudogene. Link
Pseudogenes: Are They “Junk” or Functional DNA?”. Link
Comparative analysis of processed ribosomal protein pseudogenes. Link
Michael Behe’s Amazon Blog. Link
Identification and analysis of unitary pseudogenes... **. Link
Pseudogenes in the ENCODE regions:... Link.
Origins of New Genes and Pseudogenes **. Link
Pseudogenes (Gerstein Lab Publications). **. Link
Molecular Evidence 4: Redundant Pseudogenes. Link
Plagiarized Errors and Molecular Genetics. (Max) **. Link
(nearly 10 years old but still a good review - also see recent comments in the sidebar)
Response to AFDave (Max) **. Link
Facts of Evolution: Retroviruses and Pseudogenes. (8 min. YouTube) Link
Human Genomics: Vesiges of Eden or Skeletons in the Closet (Dennis Venema) Link
(Great overall reveiw of many of of genomic evidences for macroevolution)
A Tale of Three Creationists, Part 3 (Venema) Link (GULO and Guinea Pigs)
Pseudogenes (Indiana University Lesson B) Link
References - Objections
Potentially decisive evidence against pseudogenes. Link
Pseudogenes. (Pitman) Link
Molecular History Research Center. Link
Adam and Eve, Vitamin C, and Pseudogenes. (ICR) Link.
Shared Errors in the DNA of Humans and Apes (Plaisted) Link
Guinea Pigs & Humans Link
** - These articles are especially good, and much material was used from them to produce this section. Little of the material in this section is original.