Definitions
“Pseudogenes are dysfunctional relatives of genes that have lost their protein-coding ability or are otherwise no longer expressed in the cell. Pseudogenes often result from the accumulation of multiple mutations within a gene whose product is not required for the survival of the organism.” (1)
“They are different from normal genes due to a lack of protein-coding ability resulting from a variety of disabling mutations.” (1)
“Because pseudogenes are generally thought of as the last stop for genomic material that is to be removed from the genome, they are often labeled as junk DNA.” (1)
“Pseudogenes are genomic DNA sequences similar to normal genes but non-functional; they are regarded as defunct relatives of functional genes.” (2)
“A gene that doesn’t function is called a pseudogene.” –Jerry Coyne, Why Evolution is True
There are three types of pseudogenes:
- Processed: “When a portion of the mRNA transcript of a gene is spontaneously reverse transcribed back into DNA and inserted into chromosomal DNA.” (1)
- Non-processed: Copied genes that acquire mutations.
- Disabled: When the original gene is mutated. An example of a fixed-disabled gene is GLO.
How are Pseudogenes Identified?
- “We can define a pseudogene operationally as a fragment of nucleotide sequence that resembles a known protein’s domains but with stop codons or frameshifts mid-domain.”
- There are believed to be between 12,600 and 19,700 pseudogenes. (5)
- “How pervasive are ‘functional’ pseudogenes? Many pseudogenes have been identified in all sorts of organisms on the grounds that they are duplicated genes that exhibit stop codons or other disabling mutations in their DNA sequences, so that they cannot have the full function of the original genes from which derived. In many of these cases, however, it remains unknown, because it has not been investigated, whether the pseudogenes, described only on the basis of DNA sequences, may have acquired regulatory or other functions, or play a role in generating genetic variability.” –Balakirev and Ayala, “Pseudogenes: are they ‘junk’ or functional DNA?” in the Annual Review of Genetics 37:137-138, 2003
- “There seems to be the case that some functionality has been discovered in all cases, or nearly all, whenever this possibility has been pursued with suitable investigations. One may well conclude that most pseudogenes retain or acquire some functionality and, thus, that it may not be appropriate to define pseudogenes as non-functional sequences of genomic DNA originally derived from functional genes, or as ‘genes that are no longer expressed but bear sequence similarity to active genes.’” IBID, pg. 114
How Do Pseudogenes ‘Prove’ Evolution?
- “In any study of molecular evolution, it is necessary to compare and contrast genes from a variety of organisms to gauge how the organisms have adapted to ensure their survival. Pseudogenes are vitally important since they provide a record of how the genomic DNA has been changed without such evolutionary pressure and can be used as a model for determining the underlying rates of nucleotide substitution, insertion and deletion in the greater genome.” (2)
- Pseudogenes are here called adaptations that have survival value, but if pseudogenes result from mutations (which are random, see below), how can they be called adaptations?
- “Pseudogenes contain fascinating biological and evolutionary histories within their sequences. This is due to a pseudogene’s shared ancestry with a functional gene: in the same way that Darwin thought of two species as possibly having a shared common ancestry followed by millions of years of evolutionary divergence, a pseudogene and its associated functional gene also share a common ancestor and have diverged as separated genetic entities over millions of years.” (1)
- “Shared sequences of apparently non-functional DNA are a major line of evidence of common descent…pseudogenes can serve as raw material for evolution…” (6)
Pseudogenes Are Functional
- “Although not protein-coding, the DNA of pseudogenes may be functional, similar to other kinds of non-coding DNA which can have a regulatory role.” (1)
- “By definition, pseudogenes lack a functioning gene product. However, the classification of pseudogenes generally relies on computational analysis of genomic sequences using complex algorithms. This has led to the incorrect identification of pseudogenes.” (1)
- Examples given at (1): Drosophila, MKRN1, Phosphoglycerate mutase 3, siRNAs, PTENP1, KRAS1P.
Examples of Pseudogenes
- The OR (olfactory receptor) genes in humans.
- Humans have a diminished sense of smell compared to most primates and a large number of OR pseudogenes. It is believed that as our sense of smell became less necessary over time, OR pseudogenes become more common.
- A recent study published in Gene 304:87-96, 2003 by A. Whinnett and N.I. Mundy, it is noted: “It has generally been assumed that OR pseudogene formation has a close relationship to olfactory function. However, it is likely that there is a background rate of OR gene turnover (duplications and pseudogene formation) in all lineages, and that for many of these events the functional consequences are minimal.”
- There is no linear, phylogenic OR pseudogene emergence, but rather all lineages show OR pseudogenes. So there has been a decrease in olfactory function across the board.
- GLO, or GULO and Vitamin C Biosynthesis
- Humans are one of many species (apes, monkeys, guinea pigs) that are unable to produce their own vitamin C. We require dietary sources of the vitamin. In other species, an enzyme known as Gulono Lactone Oxidase (GLO/GULO) converts gulono lactone into absorbic acid.
- It is believed that regions in the human genome correspond to parts of the functional GLO gene found in other mammals and that lesions found in common between GLO pseudogenes in simian primates (shared mistakes) argue strongly for common ancestry.
- Humans and guinea pigs share 36% identical lesions in GLO pseudogenes. Does this prove that humans are closely related to guinea pigs?
- “Occam’s razor dictates that ‘shared mistakes’ be approached in terms of parallel mutations rather than common evolutionary ancestry.” –John Woodmorappe (7)
- It is sometimes argued that humans have a deactivated tail gene:
- The gene that appears to be connected to tail formation is the Wnt-3a gene.
- Regarding “Wnt gene expression during mouse gastrulation” it was learned in a 1994 study that “Only Wnt-3a, Wnt-5a, and Wnt-5b are expressed in the primitive streak and tailbud.” (8)
- The Wnt gene family is also exhibited in the human genome, but it doesn’t appear to be a deactivated tail gene or related to tails in any direct way:
- From Gene Cards, the Human Gene Compendium: “The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis [formation of tumors] and in several developmental processes…It encodes a protein which shows 96% amino acid identity to mouse Wnt3A protein, and 84% to human WNT 3 protein.” (9)
- “Diseases associated with WNT3A include osteoporosis, early-onset autosomal dominant [juvenile osteoporosis], and hypotrichosis simplex [juvenile hair loss].” (9)
- While the human WNT3A gene may be similar to the WNT3A gene in mice, it doesn’t mean that the human WNT3A gene is somehow a deactivated tail gene or indicative of phylogeny. They may be similar because they have other similar functions.
- Functional Protein Redundancy:
- TalkOrigins argues that there are ubiquitous genes (genes that all living organisms share) that have large numbers of “different functionally equivalent forms.” (10) Because there are so many aa combinations of the same protein, if two organisms share the same aa combination of that protein, the only explanation is common descent.
- The example given is that of ‘cytochrome c,’ which is a key enzyme in oxidation reactions.
- James S. Allan with CMI explains, “It consists of a chain of 112 aa, 19 of which occur in exactly the same sequential order positions in all organisms tested. Differences in the identity and positions of the remaining 93 amino acids are considered to be the result of mutational substitution during the course of evolution.” (11)
- There are a minimum of 2.3 x 1093 possible functional cytochrome c protein sequences (10).
- “There is no a priori reason for two different species to have the same, or even mildly similar, cytochrome c protein sequences.” (10)
- Humans and chimps have the same cytochrome c protein sequence.
- From TalkOrigins: “The clincher is that the two DNA sequences that code forcytochrome c in humans and chimps differ by only four nucleotides (a 1.2% difference), even though there are 1049 different sequences that could code for this protein.” (10)
- The Creation explanation:
- As Dr. Allen explains, there are thousands of other genetic differences between chimps and humans…so how could the cytochrome c protein sequence have remained intact for so long? A good question.
- A creationist will argue that homologies such as this only prove common design.
Other Points To Consider
- “Pseudogenes are sometimes difficult to identify and characterize in genomes, because the two requirements of homology and nonfunctionality are usually implied through sequence alignments rather than biologically proven.” (1)
- Homology is implied by sequence identity between the DNA sequences of the pseudogene and parent gene. After aligning the two sequences, the percentage of identical base pairs is computed. A high sequence identity (usually between 40% and 100%) means that it is highly likely that these two sequences diverged from a common ancestral sequence (are homologous), and highly unlikely that these two sequences have evolved independently.” (1)
- In evolutionary terms, pseudogenes equate a loss of function. After all, these were once protein-coding genes that have lost their protein-coding ability, even though they may still perform regulatory roles. So pseudogenes cannot serve as evidence of a gain in information or ability, or of onward, upward evolution.
- Pseudogenes can arise due to duplication. These are “modifications (mutations, insertions, deletions, frame shifts) to the DNA sequence of a gene [that can] occur during duplication. These disablements can result in loss of gene function at the transcription or translation level (or both) since the sequence no longer results in the productions of a protein. Copies of genes that are disabled in such a manner are termed non-processed or duplicated pseudogenes.”
- What this means is that pseudogenes can arise due to random chance and can have nothing to do with the alleged evolution or devolution between species.
- Who is to say that this is proof of phylogeny and not of genetic breakdown (loss of information and function) from optimal design?
- The creation worldview not only allows for such, but predicts such!
Sources:
(1) http://en.wikipedia.org/wiki/Pseudogene#cite_note-pmid3909943-1
(2) http://www.pseudogene.org/background.php
(3) http://en.wikipedia.org/wiki/Homology_(biology)
(4) http://homepage.usask.ca/~ctl271/857/def_homolog.shtml
(5) http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004351
(6) http://en.wikipedia.org/wiki/Noncoding_DNA#Noncoding_DNA_and_evolution
(7) http://creation.com/potentially-decisive-evidence-against-pseudogene-shared-mistakes
(8) S Takada, K.L. Stark, M.J. Shea, Wnt-3a regulates somite and tailbud formation in the mouse embryo, Genes & Development, 1994 8:174-189
(9) http://www.genecards.org/cgi-bin/carddisp.pl?gene=WNT3A
m3rcy Triumphs 