Vestigial “Pseudogenes” Reconsidered

So-called “pseudogenes” are not so pseudo after all. Another Darwinian false lead delayed research for decades.

In his book Useless Organs, CEH contributing writer Dr Jerry Bergman documents how Darwinian beliefs retarded the progress of human physiology for over a century. The concept claimed that evolution left “vestigial organs” inside the human body (e.g., tonsils, the appendix, and more). All of those organs have now proven to be functional, if not essential. Darwin was wrong.

Now, a similar fake-science view is unraveling: the idea of pseudogenes (false genes). Darwinian geneticists said these were copies of genes that had mutated and degraded, and now are hanging around in the genome like freeloaders, doing nothing. Indications that this view was faulty have been building for years, but now, some scientists are saying it’s time to discard the conventional evolutionary wisdom about pseudogenes. In Nature Reviews Genetics, Cheetham, Faulkner and Dinger write about “Overcoming challenges and dogmas to understand the functions of pseudogenes.” Dogmas? Yes indeed:

Pseudogenes are defined as regions of the genome that contain defective copies of genes. They exist across almost all forms of life, and in mammalian genomes are annotated in similar numbers to recognized protein-coding genes. Although often presumed to lack function, growing numbers of pseudogenes are being found to play important biological roles. In consideration of their evolutionary origins and inherent limitations in genome annotation practices, we posit that pseudogenes have been classified on a scientifically unsubstantiated basis. We reflect that a broad misunderstanding of pseudogenes, perpetuated in part by the pejorative inference of the ‘pseudogene’ label, has led to their frequent dismissal from functional assessment and exclusion from genomic analyses. With the advent of technologies that simplify the study of pseudogenes, we propose that an objective reassessment of these genomic elements will reveal valuable insights into genome function and evolution.

Like pseudogenes, the label “vestigial organs” retarded scientific investigation for many years.

Good luck on insights into genome evolution, but Cheetham et al., in spite of being evolutionists, know dogma when they smell it. The whole concept of pseudogenes has been taught on a “scientifically unsubstantiated basis” for decades now, they say. Even the pejorative name “pseudogene” (fake gene) has retarded the search for finding uses for these sections of DNA code, just like the pejorative label “vestigial organs” did in the late 1800s throughout the 20th century. A reassessment is overdue.

Avoid the Pitfall into the Rut

Here’s a case where words have consequences. There are about 10,000 to 20,000 gene regions that have been labeled pseudogenic, the authors say. “As a result, pseudogene-annotated regions are largely excluded from functional screens and genomic analyses.” Geneticists have ignored these regions simply because of the “pseudogene” label.

We provide a critical analysis of the pitfalls of current approaches to annotating [labeling] pseudogenes and describe how methodological limitations and largely arbitrarily defined assumptions have inhibited research in pseudogene-annotated regions of the genome. Finally, we consider the scientific utility of the pseudogene concept in the context of evolutionary biology and the dogma established through virtue of the term itself. We propose that the availability of new technologies and approaches to study gene and genome function, together with the recalibration of how pseudogenes are perceived, will invigorate study into the biology of these regions of the genome.

Power of the Paradigm

The pseudogene label also shows how words and concepts can affect what questions scientists consider worth investigating. Pseudogenes have been considered part of the “junk DNA” category, a broader evolutionary concept that has impeded valuable research.

[T]he term pseudogene itself asserts a paradigm of non-functionality through its taxonomic construction. Pseudogenes are defined as defective and not genes. This point is highlighted because impartial language in science is known to inherently restrict the neutral investigation between conflicting paradigms. In the case of pseudogenes, the term itself is constructed to support the dominant paradigm and therefore limit, consciously or unconsciously, scientific objectivity in their investigation.

They add,

Although the pseudogene concept arose to describe an individual molecular phenomenon, the term was rapidly adopted to annotate tens of thousands of genomic regions that met only loosely defined criteria and was effectively axiomatized without being subject to any rigorous scientific debate. This lack of consensus-seeking process has left genome biology with a legacy concept that obscures objective investigation of genome function.

Treasures in the Junkpile

As with vestigial organs and junk DNA, the functional richness in pseudogenes has been slowly coming to light. The authors give several examples of functions among pseudogenes, including mutational sponges, regulation and decoys. If geneticists reverse the old paradigm and start looking more closely at these regions, they might discover valuable functions more rapidly. These could contribute to human health and well-being.

With renewed scientific objectivity, we anticipate that a wealth of discoveries to understand genome function, its role in disease and the development of new treatments is within reach.

The authors even advocate tossing the word “pseudogene” into the junk pile, and retrieving these genomic regions from the junk pile and taking them back into the lab. “Pseudogenes” need a better name. They are not genomic freeloaders.

Phillip Johnson, key motivator for the Intelligent Design movement, died Dec 2019.

What an anti-science belief system Darwinism has proved to be! Vestigial organs, junk DNA, and pseudogenes have been mislabeled, just like some people have been ignored with the label “heretic” or “maverick” or “extremist.” Lazy evolutionists have resorted to name-calling because of their worldview. They envision an evolving world that leaves junk in its wake. Intelligent design advocates would ask more fruitful questions when a mystery arises that defies understanding, like the late Philip Johnson advocated in his excellent book The Right Questions. Ask the right questions and you improve the odds of getting right answers.

Evolution News gave significant coverage of the paper by Cheetham et al. that is worth reading for those without access to the paper.