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This assertion was made at times before we knew very much about the genome or pseudogenes. Such premature assertions are generally naive and such has proved to be the case with respect to pseudogenes.

Pseudogenes are regions of DNA that look very much like protein-coding elements (genes, sensu stricto), but which either are missing the introns present in the requisite functional genes or have stop codons in all three reading frames (i.e., have no open reading frame). For many years these regions were considered to be inactive remnants of previously functional genes that were perhaps evolving new functions (but see answer to previous question for another take on this idea).

It has been claimed that the similar placement of the genes and pseudogenes in the beta hemoglobin gene family of chimp and human and the similar modifications of the beta hemoglobin pseudogenes in both species could only be explained if the two species shared a common ancestor. This presumptuous assertion could be challenged on several grounds, but such challenges are no longer necessary.

This bubble was burst by the surrendipitous discovery that the disruption of a pseudogene in mice (Makorin 1-p1) by an inserted sequence of DNA resulted in the failure of another gene related to the pseudogene (Makorin1), even though the normal gene was located on another chromosome1. The authors state: "Our findings demonstrate a specific regulatory role of an expressed pseudogene, and point to the functional significance of non-coding RNAs." Clearly the "pseudogenes" were functional and had an apparent regulatory role in the expression of the normal gene. Although we do not yet know the rest of the story, we can no longer talk about pseudogenes as "Junk DNA." Instead, as some of us have long suspected, they do have regulatory function, and may be involved in regulating the genes they are related to structurally.That this is not an isolated discovery is becoming more apparent with every experiment2

In a recent article the authors go even farther, suggesting a classification system is necessary for "pseudogenes":

"Pseudogenes have long been considered to be ‘dead’, nonfunctional by-products of genome evolution. However, several lines of evidence now show that some pseudogenes are transcriptionally ‘alive’, and a few might even have biochemical roles. Therefore, the boundary between genes (often considered to be ‘living’) and pseudogenes (often considered to be ‘dead’) might be ambiguous and difficult to define. [In this paper], we examine the evidence for and against pseudogene functionality, and we argue that the time is ripe for revising the definition of a pseudogene. Furthermore, we suggest a classification system to accommodate pseudogenes with various levels of functionality.3

 Incidentally, this is just another example of how the sterility of modern evolutionary theory prevents advances in science. One who saw a purpose and designer in nature would be more likely to ascribe a function to such misunderstood phenomena as pseudogenes and "Junk DNA" than would one who chose to see no evidence of a design or designer in nature. And as in this case, one would be justly rewarded for such insights.

1. Shinji Hirotsune, Noriyuki Yoshida, Amy Chen, Lisa Garrett, Fumihiro Sugiyama, Satoru Takahashi, Ken-Ichi Yagami, Anthony Wynshaw-Boris & Atsushi Yoshiki.An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423, 91 - 96 (01 May 2003);

2. Evgeniy S. Balakirev and Francisco J. Ayala. Pseudogenes: Are They "Junk" or Functional DNA? Annual Review of Genetics Dec 2003, Vol. 37, pp. 123-151

3. Deyou Zheng, and Mark B. Gerstein. The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they? Trends in Genetics, articles in press (April, 2007) ______________________________________________________

Ó 2007 Arthur V. Chadwick, Ph.D.