Monday, September 13, 2021

Recommended reading for the remaining fans of Richard Dawkins


Pseudogenes Aren’t Nonfunctional Relics that Refute Intelligent Design

Casey Luskin

September 9, 2021, 6:36 AM

[[If you need an example of the tone and accuracy of the debate about evolution, here is a good example. I highly recommend Dr. Luskin’s work in general.]]

Photo by Ann Kathrin Bopp via Unsplash.

We’ve been discussing a video in which Richard Dawkins claims that the evidence for common ancestry refutes intelligent design (see here, here, and here). We first saw that contrary to Dawkins, the genetic data does not yield “a perfect hierarchy” or “perfect family tree.” Then we saw that a treelike data structure does not necessarily refute intelligent design. But Dawkins isn’t done. At the end of his answer in the video, Dawkins raises the issue of “pseudogenes,” which he claims “don’t do anything but are vestigial relicts of genes that once did something.” Dawkins says elsewhere that pseudogenes “are never transcribed or translated. They might as well not exist, as far as the animal’s welfare is concerned.” These claims represent a classic but false “junk DNA” argument against intelligent design. 

Functions of Pseudogenes 

Pseudogenes can yield functional RNA transcripts, functional proteins, or perform a function without producing any transcript. A 2012 paper in Science Signaling noted that although “pseudogenes have long been dismissed as junk DNA,” recent advances have established that “the DNA of a pseudogene, the RNA transcribed from a pseudogene, or the protein translated from a pseudogene can have multiple, diverse functions and that these functions can affect not only their parental genes but also unrelated genes.” The paper concludes that “pseudogenes have emerged as a previously unappreciated class of sophisticated modulators of gene expression.” 

A 2011 paper in the journal RNA concurs:

Pseudogenes have long been labeled as ‘junk’ DNA, failed copies of genes that arise during the evolution of genomes. However, recent results are challenging this moniker; indeed, some pseudogenes appear to harbor the potential to regulate their protein-coding cousins. 

Likewise, a 2012 paper in RNA Biology states that “pseudogenes were long considered as junk genomic DNA” but “pseudogene regulation is widespread in eukaryotes.” Because pseudogenes may only function in specific tissues and/or only during particular stages of development, their true functions may be difficult to detect. The RNA Biology paper concludes that “the study of functional pseudogenes is just at the beginning” and predicts “more and more functional pseudogenes will be discovered as novel biological technologies are developed in the future.” 

When we do carefully study pseudogenes, we often find function. One paper in Annual Review of Genetics observed: “pseudogenes that have been suitably investigated often exhibit functional roles.” A 2020 paper in Nature Reviews Genetics cautioned that pseudogene function is “Prematurely Dismissed” due to “dogma.” The paper cautions that there are many instances where DNA that was dismissed as pseudogene junk was later found to be functional: “with a growing number of instances of pseudogene-annotated regions later found to exhibit biological function, there is an emerging risk that these regions of the genome are prematurely dismissed as pseudogenic and therefore regarded as void of function.” Indeed, the literature is full of papers reporting function in what have been wrongly labeled “pseudogenes.” 

Fingers in Ears?

At the end of the video, Dawkins says: “I find it extremely hard to imagine how any creationist who actually bothered to listen to that could possibly doubt the fact of evolution. But they don’t listen…they simply stick their fingers in their ear and say la la la.” It’s safe to say that Dawkins was wrong about many things in this video, but I’m not here to make any accusations about fingers and ears. I will say that the best resolution to these kinds of questions is to listen to the data, keep an open mind, and to think critically. When we’re wiling to do this, a lot of exciting new scientific possibilities open up — ones that don’t necessarily include traditional neo-Darwinian views of common ancestry or a “perfect hierarchy” in the tree of life, and ones that readily point toward intelligent design.