Reasons to Believe

High Levels of Pseudogene Expression Help Silence the Case for Common Descent

Based on a study of cells derived from 13 different tissue types, researchers have demonstrated that pseudogenes are expressed at high levels. These high levels of expression indicate the central importance of pseudogenes in cell differentiation and the progression of cancers. As researchers continue to uncover function for pseudogenes, their interpretation as molecular fossils in the genomes becomes less tenable.

Pop psychologists identify four personality types: driver, analytical, friendly, and expressive. The latter group includes outgoing individuals who talk a lot. They are energetic and often quite charismatic, drawing people to themselves. While people with an expressive personality can make those they interact with feel valued, their talkative nature can be overwhelming.

Psychologists aren’t the only ones who study levels of expression. Biochemists do so, also—but instead of focusing their attention on people, they are interested in genes. Just like people, genes differ in their level of expression.

The cell’s machinery uses processes, known collectively as gene expression, to convert information stored in DNA into functional products like proteins and RNA molecules. Similar to human personalities, some genes are highly expressed and others are barely expressed at all.  

Gene expression is one of the most important processes in biology. The patterns of gene expression define an organism by converting the genetic information stored in the genome into biological traits. For example, humans and chimpanzees have highly similar genomes (and in effect the same gene set), but have different gene expression patterns. These differences in gene expression account for the biological and behavioral uniqueness of these two primates.

It turns out that gene expression level also plays an important role in the common descent debate taking place among evangelical Christians. Of specific interest is the expression level of pseudogenes in the human genome. Scientists and Christians who favor the proposal that God used the evolutionary process to create (evolutionary creationism) maintain that shared pseudogenes in the genomes of humans and the great apes provide incontrovertible evidence for common descent.

I have written extensively about pseudogenes in the past. Specifically addressing what they are, the different types, and why evolutionary biologists view these shared sequence elements as evidence for common descent. I also articulate why I think that pseudogenes can be interpreted as evidence for a Creator’s handiwork. For background information on pseudogenes, I invite you to check out any of the articles linked below.

Evolutionary biologists consider pseudogenes to be the dead, useless remains of once functional genes. According to this view, extensive mutations destroyed the capacity of the cell’s machinery to “read” and process the information contained in these genes. Still, pseudogenes possess the tell-tale signatures that allow molecular biologists to recognize them as genes, albeit nonfunctional ones.

For evolutionary biologists, shared nonfunctional DNA sequences (or so-called junk DNA) clearly indicate that these organisms shared a common ancestor. According to their interpretation, the junk DNA segments arose prior to the time the organisms diverged from their mutual evolutionary ancestor.

When evolutionary biologists interpret shared genetic features as evidence for common descent, they make a number of assumptions. One of the most important is that shared features lack function. It makes no sense for a Creator to introduce identical (or nearly identical) features—at corresponding locations—into the genomes of two or more organisms. Yet, if these organisms share an evolutionary history, then shared nonfunctional genetic features find a ready explanation.

However, over the course of the last decade or so, researchers have uncovered evidence that the three classes of pseudogenes all display function. The links below will take you to articles I’ve written that progressively document discoveries of pseudogene function and its central role in regulating gene expression.

As it turns out, the pseudogene RNA transcripts (which are produced by the cell’s machinery from the DNA sequences of pseudogenes) take part in an elaborate network of RNA molecules. The relative levels of the RNA transcripts within the network influence the amount of protein products generated at the ribosomes, thereby impacting gene expression. Researchers have proposed the competitive endogenous RNA (ceRNA) hypothesis to describe and account for these interactions and their role in gene regulation.

In other words, biochemists and molecular biologists have discovered a key functional role for pseudogenes that depends in part on their sequence similarity to the corresponding “intact” genes. That being the case, the shared presence of pseudogenes in genomes could just as easily reflect the work of a Creator—common design, if you will—instead of common descent.

When I’ve shared the implications of the ceRNA hypothesis privately and publically with scientists who are friendly to the evolutionary paradigm, their response is to acknowledge function for pseudogenes, but they rightly point out that this idea is only relevant for pseudogenes that are expressed. What about the pseudogenes in the human genome that aren’t expressed? In other words, the ceRNA hypothesis only supports common design if most of the pseudogenes in the genome are expressed.

Work published in the summer of 2012 addresses this concern.1 A large team of collaborators from America and India systematically measured the expression of pseudogenes in cells taken from 248 cancerous and 45 benign cell lines representing 13 tissue types. They noted that pseudogene expression was “surprisingly prevelant.”2 Pseudogene expression fell into two categories: ubiquitous (expressed in all cell lines, at all times) and lineage-specific (expressed only in certain cell lines at certain points in the life cycle, and throughout the course of development).

The researchers concluded that: “transcribed pseudogenes are a significant contributor to the transcriptional landscape of cells and are positioned to play significant roles in cellular differentiation and cancer progression.”3

Subjects: Junk DNA

Dr. Fazale Rana

In 1999, I left my position in R&D at a Fortune 500 company to join Reasons to Believe because I felt the most important thing I could do as a scientist is to communicate to skeptics and believers alike the powerful scientific evidence—evidence that is being uncovered day after day—for God’s existence and the reliability of Scripture. Read more about Dr. Fazale Rana

References:

  1. Shanker Kalyana-Sundaram et al., “Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers,” Cell 149 (June 22, 2012): 1622–34.
  2. Ibid.,1622.
  3. Ibid.