This page in it's entirety is copied here from the web-site of Truth in Science with kind permission. Truth in Science state on their web-site in 2012 that "We believe that a critical examination of Darwinism and the controversy that surrounds it will enable students to become better scientists. Nevertheless, many schools are reluctant to teach the controversy".
Pseudogenes are DNA sequences that resemble protein-coding genes but they are not transcribed to a messenger RNA (mRNA) in a way that could then be translated into some functional protein. Many have suggested that pseudogenes are simply molecular fossils that illustrate and provide evidence for evolutionary history. Implicit in this argument is that pseudogenes are genetic relics that have lost their original protein-coding function which had been possessed by some ancestral creature. In support of this argument, evolutionary scientists point to the fact that pseudogenes are scattered throughout the genomes of all higher species (animals and plants) and, in particular, there are many similar pseudogenes found in all primates.
For example, identical beta-globin pseudogenes have been found in both humans and chimpanzees and this fact has been used as an argument by Professor Kenneth Miller in his book "Only a Theory" for the common ancestry of the two species . In his own words:-
"Hemoglobin is the oxygen-carrying protein that makes blood red. A single molecule of hemoglobin consists of two copies of a molecule called alpha-globin and two of another called beta-globin. The genes for beta-globin, of which there are five functional copies, are found on human chromosome 16. Right in the middle of this hardworking group of genes, however, is a broken one, which geneticists call a pseudogene. Its DNA base sequence is nearly identical to that of its neighbors, so it's easy to recognize it as beta-globin, but it contains a series of errors in its sequence that keeps it from working. One of them prevents the gene from ever being copied into RNA (an essential step for a gene to work), one would prevent any RNA that did get made from directing the synthesis of a protein, and the remaining four would completely disrupt any protein that somehow managed to get produced anyway … Our genome was originally designed with six working copies of the beta-globin genes, and therefore the loss of one of them from such molecular errors is no big deal. Therefore all humans alive today are descended from individuals in which those mistakes first cropped up. Fair enough. But guess what: We're not the only organisms with a set of beta-globin genes, and we’re not the only ones with a pseudogene right in the middle of the set … Gorillas and chimpanzees have them too and they are arranged in exactly the same way … [with] exactly the same set of molecular errors.” [Only a Theory pages 101-102].
Biologists have identified two distinct types of pseudogene which are often described as "processed" and "unprocessed". As a general rule, processed pseudogenes are located on different chromosomes from their corresponding functional protein-coding gene. Most biologists believe that they were created by the retro-transposition of the mRNA transcripts from the functional parent gene. The evidence for this is the fact that processed pseudogenes lack introns. Introns are sequences that are scattered throughout the DNA of a protein-coding gene and which are transcribed into the original mRNA. Introns (unlike exons), however, are edited out of mRNA by specific enzymes before protein translation begins. The function of introns remains unclear although there is increasing evidence that they contain vital information and are involved in parent gene regulation. Remarkably but very appropriately, this has been shown to be the case for the beta-globin gene .
Processed pseudogenes also lack regulatory sequences that control the expression of protein-coding genes and these include promoters and specific sequences which bind to enhancers and inhibitors. These regulator sequences are usually found “upstream” of the protein-coding gene (before the start sequence). Processed pseudogenes also have poly-adenine tails which are characteristic of the terminal end of a messenger RNA. In addition, the pseudogenes are usually flanked by repeat sequences of DNA which is characteristic of mobile genomic elements.
All of this evidence is very suggestive of the processed pseudogene being derived from an mRNA which has been re-located and reverse transcribed back into DNA. This mechanism is somewhat similar to the incorporation of a viral RNA into the host genome at specific sites also characterised by regions of repetitive DNA. The retrovirus (e.g. HIV) may possess its own reverse transcriptase enzyme to override the host’s own genetic machinery.
Processed pseudogenes may be complete or incomplete copies (i.e. fragments). Unprocessed pseudogenes, however, are usually found in close proximity to their corresponding protein-coding gene usually on the same chromosome. As a general rule, and unlike processed pseudogenes, they possess introns and other associated upstream regulatory sequences. Nevertheless, it is believed that the expression of these “genes” is prevented by mutations, deletions and/or insertions of “correct” nucleotides. These genetic changes may lead to premature termination or may introduce “frameshifts” that render the message apparently meaningless.
It is suggested that unprocessed pseudogenes might arise by gene duplication. Inevitably, the duplicated gene would be in close proximity to the parent but would then be free to accumulate random mutations without actually harming the organism, as it would still possess the original functional copy. For example, the beta-globin pseudogene mentioned by Miller could be an example of an unprocessed pseudogene as it has been suggested that the pseudogene was initially produced by the duplication of the gamma-A-globin gene because of the high degree of homology (sequence similarity) between the two genetic sequences . In primates, the beta-globin pseudogene has no start codon (AUG) as well as several stop codons. Thus there can be no mRNA transcribed and no protein made. This scenario, however, may not be the complete picture. For example, the goat embryo apparently retains a beta-globin pseudogene which has been shown to functional in-vitro .
Are some pseudogenes functional?
Conservation of similar genetic sequences between species may indicate that pseudogenes (or any other non-protein coding sequence) might possess important biological function even though we might not know what that function might be. For example, Miller is very keen to point out the similarity between the beta-globin pseudogene in primates when he says:
"Gorillas and chimpanzees have them too and they are arranged in exactly the same way … [with] exactly the same set of molecular errors." [Only a Theory, pages 101-102 with emphasis added].