Evolution News and Views (ENV) provides original reporting and analysis about the debate over intelligent design and evolution, including breaking news about scientific research.

Evolution News and Views
Evolution NEWS
 

Paper Rebuffs Assumption that Pseudogenes Are Genetic "Junk," Claims Function Is "Widespread"

DNA through portal.jpg

Because evolutionary scientists have often operated under the presumption that our genomes are laden with functionless junk DNA, ENV's Jonathan M. recently found himself responding to ID-critic Paul McBride's skepticism of widespread functionality for pseudogenes. Jonathan M. cited a paper published earlier this year in the journal RNA Biology titled, "Pseudogenes are not pseudo any more." It's worth exploring this paper in more detail, since it offers a compelling review of many studies to conclude that functional pseudogenes are "widespread":

Pseudogenes were long considered as junk genomic DNA: present in the genome but non-coding and without function. However, discoveries in the ancient protist T. brucei, as well as in some metazoan, indicate that pseudogene regulation is widespread in eukaryotes. Accordingly, the moniker "pseudogene" has been challenged.

(Yan-Zi Wen, Ling-Ling Zheng, Liang-Hu Qu, Francisco J. Ayala and Zhao-Rong Lun, "Pseudogenes are not pseudo any more," RNA Biology, Vol. 9(1):27-32 (January, 2012).)

The authors write that there are some 8,000 processed pseudogenes in humans, plus many duplicates--but that does not mean they are largely junk. Huge percentages of these pseudogenes appear to be conserved across diverse species, suggesting function:
[C]omparative analysis of processed pseudogenes in the mouse and human genomes has surprisingly demonstrated that 60% of the processed pseudogenes are conserved in both mammalian species. The high abundance and conservation of the pseudogenes in a variety of species indicate that selective pressures preserve these genetic elements, and suggest that they may indeed perform important biological functions.
The authors further note that "pseudogenes in mouse have been confirmed to produce stable transcripts" and observe that many pseudogenes are known to be transcribed in humans. In fact, pseudogenes make up a heavy proportion of the human transcriptome:
Surprisingly, the proportion of transcribed human pseudogenes in the transcriptome has been confirmed to be up to 20% on the basis of systematic series of specific RACE analysis, tiling microarray, and high through-put sequencing.
They then ask the obvious question: "if pseudogenes are dysfunctional, why are they so highly expressed?" They suggest two possible explanations. One possibility is that pseudogenes aren't functional, but are accidentally transcribed as the result of other cellular processes. This, of course, would be a huge waste of cellular resources. The second possibility is that they are transcribed because they are functional. They prefer the second option:
An alternative explanation, which we are more inclined to accept, is that the pseudogene transcripts are in fact functional but not random products. More and more accumulating examples support this alternative explanation.
They then discuss an impressive list of discovered functions for pseudogenes, including:
  • They may function as "intracellular inhibitors in cell development" where pseudogenes can "suppress the translation of the functional counterparts."
  • They may regulate gene expression through RNA interference (RNAi), where small interfering RNAs (siRNAs) can be generated by pseudogenes that play roles in RNAi pathways.
  • They may produce transcripts which serve as "endogenous competitive RNAs to their cognate genes," also helping to regulate gene expression.
  • They may yield transcripts which produce functional proteins. One example given is the nanog pseudogene which is known to yield proteins in cancer cell lines.
Changing the Starting Assumptions

After widespread function is discovered for a type of "junk" DNA, we've often seen evolutionists respond by trying to rewrite history to suggest no one never had ever maintained that that type of DNA was junk. Lest anyone forget the history of pseudogenes, this paper not only argues for "widespread" function in pseudogenes, but it also makes it clear they have been assumed to be "junk" or "garbage" DNA:

We discuss the regulatory mechanisms of pseudogenes at the post-transcriptional level and advance new ideas towards understanding the evolution of these sometimes, called "garbage genes" or "junk DNA," seeking to stimulate the interest of scientist and additional research on the subject.
One reason why evolutionists have been so slow to abandon the assumption that pseudogenes are junk may be because their functions are difficult to detect. As the authors observe, "almost all pseudogenes that exhibit significant biological activity are expressed in specific tissue or cell lines." Thus, it's not the case that every functional pseudogene will be expressed in every single cell--only specific tissues or cell lines may use the pseudogene for some function.

Additionally, it's difficult to detect function for pseudogenes because for years we lacked the research tools to understand how they influenced gene expression. Many evolutionary scientists assumed they were "junk" based upon their DNA sequences, but improvements in research techniques should dramatically improve our ability to detect their functions:

Altogether, these results indicate that the discovery of pseudogene functions depends on the skills and methodologies used. Many expressed pseudogenes remain to be annotated. We believe that more and more functional pseudogenes will be discovered as novel biological technologies are developed in the future.
They conclude "The study of functional pseudogenes is just at the beginning." It seems that ID proponents have been correct to urge a "wait and see" approach to pseudogenes.

The implication is that materialists who wish to view the genome as junk-filled can no longer justify the starting assumption that pseudogenes are functionless junk. We're just beginning to understand their functions, and we're just beginning to develop the technology to understand what they do. As technology improves, more and more functional pseudogenes will be discovered in the future. In essence, the message of this paper is that the working assumption that pseudogenes are functionless junk is no longer supported by the evidence.