In high school I was a bit of a troublemaker. It wasn’t out of the ordinary for me to be summoned to Mr. Reynolds’ office—the school’s vice principal—for some misdeed or other. After a few office visits, I quickly learned the value of a good story. If convincing enough, I could defray the accusations leveled against me. All I had to do was create plausible deniability.

Story Telling in the Evolutionary Paradigm

Storytelling isn’t just the purview of a mischievous kid facing the music in the principal’s office, it is part of the construct of science.

Recent work by a team of scientific investigators from the University of Florida (UF) highlights the central role that storytelling plays in evolutionary biology.¹ In fact, it is not uncommon for evolutionary biologists to weave grand narratives that offer plausible evolutionary stories for the emergence of biological or behavioral traits. And, though these accounts seem scientific, they are often unverifiable scientific explanations.

Inspired by Rudyard Kipling’s (1865–1936) book of children’s origin stories, the late evolutionary biologist Stephen Jay Gould (1941–2002) referred to these evolutionary tales as just-so stories. To be fair, others have been critical of Gould’s cynical view of evolutionary accounts, arguing that, in reality, just-so stories in evolutionary biology are actually hypotheses about evolutionary transformations. But still, more often than not, these “hypotheses” appear to be little more than convenient fictions.

An Evolutionary Just-So Story of Moths and Bats

The traditional evolutionary account of ultrasonic sound detection in nocturnal moths serves as a case in point. Moths (and butterflies) belong to one of the most important groups of insects: lepidoptera. This group consists of about 160,000 species, with nocturnal moths comprising over 75 percent of the group.

Moths play a key role in ecosystems. For example, they serve as one of the primary food sources for bats. Bats use echolocation to help them locate moths at night. Bats emit ultrasonic cries that bounce off the moths and reflect back to the bats, giving these predators the pinpoint location of the moths, even during flight.

Many nocturnal moth species have defenses that help them escape predation by bats. One defense is ears (located in different areas of their bodies) that detect ultrasonic sounds. This capability allows the moths to hear the bats coming and get out of their way.

For nearly a half century, evolutionary biologists explained moths’ ability to hear ultrasonic sounds as the outworking of an “evolutionary arms race” between echolocating bats and nocturnal moths. Presumably, bats evolved the ability to echolocate, allowing them to detect and prey upon moths at night by plucking them out of the air in mid-flight. In response, some groups of moths evolved ears that allowed them to detect the ultrasonic screeches emitted by bats, helping them to avoid detection.

Figure: Flying Pipistrelle bat. Image credit: Shutterstock

For 50 years, biologists have studied the relationship between echolocating bats and nocturnal moths with the assumption that this explanation is true. (I doubt Mr. Reynolds ever assumed my stories were true.) In fact, evolutionary accounts like this one provide evidence for the idea of coevolution. Advanced by Paul Ehrlich and Peter Raven in 1964, this evolutionary model maintains that ecosystems are shaped by species that affect one another’s evolution.

If the UF team’s work is to be believed, then it turns out that the story recounting the evolutionary arms race between nocturnal moths and echolocating bats is fictional. As team member Jesse Barber, a researcher who has studied bats and moths, complains, “Most of the introductions I’ve written in my papers [describing the coevolution of bats and moths] are wrong.”²

An Evolutionary Study on the Origin of Moths and Butterflies

To reach this conclusion, the UF team generated the most robust evolutionary tree (phylogeny) for lepidopterans to date. They also developed an understanding of the timing of events in lepidopteran natural history. They were motivated to take on this challenge because of the ecological importance of moths and butterflies. As noted, these insects play a central role in terrestrial ecosystems all over the world and coevolutionary models provide the chief explanations for their place in these ecosystems. But, as the UF researchers note, “These hypotheses have not been rigorously tested, because a robust lepidopteran phylogeny and timing of evolutionary novelties are lacking.”³

To remedy this problem, the researchers built a lepidopteran evolutionary tree from a data set of DNA sequences that collectively specified 2,100 protein-coding genes from 186 lepidopteran species. These species represented all the major divisions within this biological group. Then, they dated the evolutionary timing of key events in lepidopteran natural history from the fossil record.

Based on their analysis, the research team concluded that the first lepidopteran appeared around 300 million years ago. This creature fed on nonvascular plants. Around 240 million years ago, lepidopterans with tubelike proboscises (long, sucking mouthpiece) appeared, allowing these insects to extract nectar from flowering plants.

These results cohere with the coevolutionary model that the first lepidopterans fed internally on plants and, later, externally, as they evolved the ability to access nectar from plants. Flowering plants appear around 260 million years ago, which is about the time that the tubelike proboscis appears in lepidopterans.

But perhaps the most important and stunning finding from their study stems from the appearance of hearing organs in moths. It looks as if these organs arose independently 9 separate times—around 80 to 90 million years ago—well before bats began to echolocate. (The earliest known bat from the fossil record with the capacity to echolocate is around 45 to 50 million years old.)

The UF investigators uncovered another surprising result related to the appearance of butterflies. They discovered that butterflies became diurnal (active in the daytime) around 98 million years ago. According to the traditional evolutionary story, butterflies (which are diurnal) evolved from nocturnal moths when they transitioned to daytime activities to escape predation of echolocating bats, which feed at night. But as with the origin of hearing organs in moths, the transition from nocturnal to diurnal behavior occurred well before the first appearance of echolocating bats and seems to have occurred independently at least two separate times.

It Just Isn’t So

The UF evolutionary biologists’ study demonstrates that the coevolutionary models for the origin of hearing organs in moths and diurnal behavior of butterflies—dominant for over a half century in evolutionary thought—are nothing more than just-so stories. They appear to make sense on the surface but are no closer to the truth than the tales I would weave in Mr. Reynolds’ office.

In light of this discovery, the research team posits two new evolutionary models for the origin of these two traits, respectively. Now scientists think that the evolutionary emergence of hearing organs in moths may have provided these insects the capacity for auditory surveillance of their environment. Their capacity to hear may have helped them detect the low-frequency sounds of flapping bird wings, for example, and avoid predation. Presumably, these same hearing organs later evolved to detect the high-frequency cries of bats. As for the evolutionary origin of diurnal behavior characteristic of butterflies, researchers now speculate that butterflies became diurnal to take advantage of flowers that bloom in the daytime.

Again, on the surface, these explanations seem plausible. But one has to wonder if these models, like their predecessors, are little more than just-so stories. In fact, this study raises a general concern: How much confidence can we place in any evolutionary account? Could it be that other evolutionary accounts are, in reality, good stories, but in the end will turn out to be just as fanciful as the stories written by Rudyard Kipling?

In and of itself, recognizing that many evolutionary models could just be stories doesn’t provide sufficient warrant for skepticism about the evolutionary paradigm. But it does give pause for thought. Plus, two insights from this study raise real concerns about the capacity of evolutionary processes to account for life’s history and diversity:

1. The discovery that ultrasonic hearing in moths arose independently nine separate times
2. The discovery that diurnal behavior in butterflies appeared independently in at least two separate instances

Convergence

Evolutionary biologists use the term convergence to refer to the independent origin of identical or nearly identical biological and behavioral traits in organisms that cluster into unrelated groups.

Convergence isn’t a rare phenomenon or limited to the independent origin of hearing organs in moths and diurnal behavior in butterflies. Instead, it is a widespread occurrence in biology, as evolutionary biologists Simon Conway Morris and George McGhee document in their respective books Life’s Solution and Convergent Evolution. It appears as if the evolutionary process routinely arrives at the same outcome, time and time again.⁴ In fact, biologists observe these repeated outcomes at the ecological, organismal, biochemical, and genetic levels.

From my perspective, the widespread occurrence of convergent evolution is a feature of biology that evolutionary theory can’t explain. I see the widespread occurrence of convergence as a failed scientific prediction of the evolutionary paradigm.

Convergence Should Be Rare, Not Widespread

In effect, chance governs biological and biochemical evolution at its most fundamental level. Evolutionary pathways consist of a historical sequence of chance genetic changes operated on by natural selection, which, too, consists of chance components. The consequences are profound. If evolutionary events could be repeated, the outcome would be dramatically different every time. The inability of evolutionary processes to retrace the same path makes it highly unlikely that the same biological and biochemical designs should appear repeatedly throughout nature.⁵

In support of this view, consider a 2002 landmark study carried out by two Canadian investigators who simulated macroevolutionary processes using autonomously replicating computer programs. In their study, the computer programs operated like digital organisms.⁶ The programs could be placed into different “ecosystems” and, because they replicate autonomously, they could evolve. By monitoring the long-term evolution of these digital organisms, the two researchers determined that evolutionary outcomes are historically contingent and unpredictable. Every time they placed the same digital organism in the same environment, it evolved along a unique trajectory.

In other words, given the historically contingent nature of the evolutionary mechanisms, we would expect convergence to be rare in the biological realm. Yet, biologists continue to uncover example after example of convergent features—some of which are quite astounding.

Bat Echolocation and Convergence

Biologists have discovered one such example of convergence in the origin of echolocating bats. Echolocation appears to have arisen two times independently: once in microbats and once in Rhinolophidae, a superfamily of megabats.⁷ Prior to this discovery, reported in 2000, biologists classified Rhinolophidae as a microbat based on their capability to echolocate. But DNA evidence indicates that this superfamily has greater affinity to megabats than to microbats. This result means that echolocation must have originated separately in the microbats and Rhinolophidae. Researchers have also shown that the same genetic and biochemical changes occurred in microbats and megabats to create their echolocating ability. These changes appear to have taken place in the gene prestin and in its protein-product, prestin.⁸

In other words, we observe two outcomes: (1) the traditional evolutionary accounts for coevolution among echolocating bats, nocturnal moths, and diurnal butterflies turned out to be just-so stories, and (2) the convergence observed in these three groups stands as independent and separate instances of failed predictions of the evolutionary paradigm.

Convergence and the Case for Creation

If the widespread occurrence of convergence can’t be explained through evolutionary theory, then how can it be explained?

It is not unusual for architects and engineers to redeploy the same design features, sometimes in objects, devices, or systems that are completely unrelated to one another. So, instead of viewing convergent features as having emerged through repeated evolutionary outcomes, we could understand them as reflecting the work of a divine mind. From this perspective, the repeated origins of biological features equate to the repeated creations by an intelligent Agent who employs a common set of solutions to address a common set of problems facing unrelated organisms.

Now that’s a story even Mr. Reynolds might believe.

Resources

• The Cell’s Design: How Chemistry Reveals the Creator’s Artistry by Fazale Rana (book)

Convergence of Echolocation

• “Echoes of Design: Independent Origins of Echolocation in Bats and Dolphins Challenge Biological Evolution” by Fazale Rana (article)
• “Convergence Drives Evolution Batty” by Fazale Rana (article)
• “Analysis of Genomes Converges on the Case for a Creator” by Fazale Rana (article)
• “Convergence: Evidence for a Single Creator” by Fazale Rana (article)

The Historical Contingency of the Evolutionary Process

• “Inability to Repeat Past Dooms Evolution” by Fazale Rana (article)
• “Historical Contingency and the Improbability of Protein Evolution, Part 1” by Fazale Rana (article)
• “Historical Contingency and the Improbability of Protein Evolution, Part 2” by Fazale Rana (article)
• “Long-Term Evolution Experiment: Evidence for the Evolutionary Paradigm? Part 1” by Fazale Rana (article)
• “Long-Term Evolution Experiment: Evidence for the Evolutionary Paradigm? Part 2” by Fazale Rana (article)

Few things in life get your attention like the subject of infectious disease. And this is especially true of pandemics (“all people” threatened by illness). It is, of course, natural to experience fear and concern during extraordinary times like this. There is great alarm about the illness and death caused by the coronavirus both in our country and worldwide. And there is also genuine anxiety about how society’s response to this health crisis (sheltering in or lockdown) will affect the world’s economy.

In light of this serious challenge that the world is now facing I offer two reflections that I hope will inspire and encourage you. Both of them are important lessons drawn from history.

1. Many Christians in church history faced similar health crises with courage and acts of selfless service.

Plagues in ancient Rome, the Middles Ages and Reformation, and in the modern world have caused similar health calamities. Yet often without the advantages of modern science and medicine many Christians acted bravely by loving their neighbor. They cared for the sick and dying even while jeopardizing their own health. Christians established makeshift hospitals, provided hospice care, and set up almshouses to help the sick and suffering. These selfless humanitarian efforts testified to the Christian faith’s deep ethical commitment to valuing human lives. At times it also led to the expansion of Christianity because people took notice of how these believers loved others unconditionally.

May these examples from church history motivate us today to acts of service for others. For example, without endangering anyone’s health we could consider donating blood, checking in (by calling) on the welfare of seniors, and volunteering to go shopping for people who need assistance. We can also seek to help those who are working on the frontlines of healthcare. This crisis can be an opportunity for us to serve others.

2. Good things can come out of times of sheltering in or being locked down because of disease.

The famous scientist Isaac Newton (1643-1727) faced the ominous “Black Death” during his lifetime. This forced him into strict quarantine. Yet he used his downtime prudently in his pursuit of scientific studies. Consider this quote about Newton from History.com:

“In 1665, following an outbreak of the bubonic plague in England, Cambridge University closed its doors, forcing Newton to return home to Woolsthorpe Manor. While sitting in the garden there one day, he saw an apple fall from a tree, providing him with the inspiration to eventually formulate his law of universal gravitation. Newton later relayed the apple story to William Stukeley, who included it in a book, ‘Memoir of Sir Isaac Newton’s Life,’ published in 1752.”

Sheltering in can be challenging and it is made more difficult with the uncertainties surrounding the dreaded coronavirus. But we can follow Newton’s example and seek to use our time prudently and keep our minds focused on things we can control. We can spend more time with family and trust that God will bring good things out of extremely trying times (Romans 8:28).

According to the Christian worldview, God is in sovereign control of what ultimately happens in the world. May this confidence in the Lord’s majesty motivate us in the pursuit of the theological virtues of faith, hope, and love.

May God grant you rest and peace in the midst of this pandemic storm.

Reflections: Your Turn What are your thoughts during this challenging time? Visit Reflections on WordPress to comment with your response.

Have you ever been embarrassed by burping in a public setting? I have. I remember a time I was speaking before an audience of a thousand-plus people and my message was also being live-streamed to the internet when I let out a loud burp into the microphone. My gaffe got the audience laughing and made them more comfortable listening to a science nerd talk about scientific evidences for the Christian faith.

Just like some good came out of my embarrassing burp, likewise a whole lot of good came from a massive burp that erupted from Earth’s interior billions of years ago. Without that burp there would be no civilization, no human race, and no advanced life of any kind.

To be sure, Earth’s interior has been releasing gas continuously throughout its history. Earth’s ongoing plate tectonic activity guarantees such a steady release of gas. A new set of measurements, however, reveals that a huge eruption of volatiles (gases) from Earth’s mantle led, in large part, to the transition from the Archaean Eon (4.56–2.45 billion years ago) to the Proterozoic Eon (2.45–0.543 billion years ago). This transition brought about the Great Oxidation Event, without which advanced life would never have been possible on Earth.

A team of four geochemists and geophysicists led by Bernard Marty at the Centre de Recherches Pétrographiques et Géochimiques (CRPG) in France published their analysis of flux measurements of volatiles from Earth’s mantle.¹ Marty’s team first established that mantle degassing increases the amount of the inert gas isotope, xenon-129. That is, there is a direct correlation between the amount of xenon-129 released into the atmosphere and the amounts of carbon dioxide, water, nitrogen, methane, and halogen gases that are simultaneously released into the atmosphere.

Measurements by Marty’s team showed that during the Archaean Eon, xenon-129 in Earth’s atmosphere was depleted relative to the modern atmospheric composition. In the words of Marty’s team, this depletion “would require the degassing rate of Earth at the end of the Archaean to be at least one order of magnitude [at least a factor of ten times] higher than today.”²

Source of the High Degassing Rates
Marty’s team demonstrated that the intense degassing at the end of the Archaean Eon cannot be explained by any conceivable plate tectonic activity. Rather, the degassing must have arisen from a relatively brief burst of intense mantle convection activity that generated several extensive “mush ocean events.”

Mush oceans refer to liquid crystal mushes (magma suspended in a liquid phase) that existed within certain regions of the oceanic crust. Previously, researchers had shown that during long periods of sluggish plate tectonics, such as what typified the Archaean Eon, mush ocean events can occur.³

Marty’s team explained how these melt inclusions in oceanic crust occur. Mantle convection would need to melt the mantle just below Earth’s crust. A buildup of heat in the mantle generated by the radioactive decay of the superabundance of uranium and thorium that existed at that time in Earth’s core would explain the needed mantle convection.

Mush ocean events would have increased the overturn rate of cooled material in the crust and the asthenosphere (the thin layer just below the crust where the crust begins to melt into the mantle). This overturning caused the much-enhanced degassing. The increased overturning, however, also resulted in high rates of heat loss and, thus, rapid cooling of the upper mantle and crust. Hence, the mush oceans, increased overturning, and much-enhanced degassing were sustained for, at most, only 300 million years.

The high degassing rate of xenon-129 that Marty’s team determined to occur at the end of the Archaean Eon would have been accompanied by equally high degassing rates of water, carbon dioxide, nitrogen, and sulfur dioxide. The degassing flux of carbon dioxide and sulfur dioxide, for example, would have been 17–170 times higher than the present rates.⁴

Source of Sulfur Dioxide Emission
The high flux of sulfur dioxide into the atmosphere came from the mush ocean events that gave rise to an explosive growth of continental landmasses. I wrote about the isotope evidence for this explosive growth of continents in a previous blog.⁵ The same isotope evidence revealed that the explosive growth occurred between 2.45 and 2.33 billion years ago—a key time in Earth’s history, as we’ll see below.

Part of this continental growth included the Matachewan Large Igneous Province (LIP), a large continental flood basalt formation. Remains of the Matachewan LIP cover nearly all of Ontario, Manitoba, continental Nunavut, Wyoming, and North Dakota and large fractions of Quebec, Montana, Minnesota, Finland, Sweden, and northwestern Russia.

The Matachewan LIP was a region of intense volcanic eruptions. Unlike volcanoes that erupt below the ocean surface, volcanic eruptions on continents emit enormous quantities of sulfur dioxide. Dating measurements on the Matachewan LIP flood basalts yield the date for the start of the intense volcanic eruptions of 2,452.5±6.2 million years ago.⁶ This date is indistinguishable from the date of 2,450±10 million years ago for the start of the Great Oxidation Event.⁷

High Degassing Rates Outcomes
During this period of volcanic eruptions, the release of huge quantities of sulfur dioxide (SO₂) into the atmosphere would have reacted with water vapor (H₂O) to produce large amounts of sulfuric acid (H₂SO₄):

4SO₂ + 4H₂O → H₂S + 3H₂SO₄

Dissolution of this sulfuric acid into the oceans beginning 2,450 million years ago would have been metabolized by sulfate-reducing bacteria to produce pyrite (FeS₂). Here is the relevant chemical reaction:

6Fe₂O₃ + 48Ca²⁺ + 48HCO₃^– + 24SO₄^2- → 12FeS₂ + 48CaCO₃ + 24H₂O + 45O₂

Therefore, for every 32 moles of sulfur dioxide released into the atmosphere by continental volcanic eruptions up to 45 moles of molecular oxygen may be produced by sulfate-reducing bacteria in the oceans. (One mole = 6.02214076 x 10²³, the number of atoms in 12 grams of carbon.)

Two British geochemists, Jake Ciborowski and Andrew Kerr, calculated that, at a minimum, the Matachewan LIP by itself pumped 2.47 quadrillion kilograms of oxygen into the atmosphere.⁸ This amount of oxygen was sufficient to raise the atmospheric oxygen level from 0.0001 percent previous to 2.45 billion years ago to greater than 0.23 percent after 2.45 billion years ago.

The Matachewan LIP is the first massive igneous event that occurs after the emergence of continents. This event brought about a major shift in volcanic gas chemistry. The resultant atmospheric oxygen stopped the mass-independent fractionation of sulfur and initiated the oxygenation of Earth’s atmosphere. These results led to Earth’s transition from being able to support only the most primitive of microbes to being able to support a wide diversity of advanced life-forms.

The release of huge quantities of carbon dioxide into the atmosphere also played a crucial role. The dramatic rise in atmospheric oxygen brought methanogenesis to a near halt. Methanogens (methane-producing bacteria) can barely survive even trace levels of oxygen. Consequently, the atmospheric oxygen rise caused a sharp drop in atmospheric methane, a powerful greenhouse gas. The high degassing rate of carbon dioxide, another greenhouse gas, that occurred at the end of the Archaean Eon largely compensated for the loss of atmospheric methane.

As it was, the abrupt rise of atmospheric oxygen brought about by the Matachewan LIP event led to several long glaciation events. Thanks to the input of extra carbon dioxide into the atmosphere, these glaciation events never caused Earth to become a permanent snowball (completely covered with a thick layer of ice and snow) that snuffed out life. Thanks to the extra carbon dioxide not being overwhelmingly abundant, the glaciation events were sufficiently severe to lay down some of Earth’s richest metal ore deposits⁹—deposits that proved crucial in the launch of human global civilization.

Earth’s big burp not only occurred at a just-right location but also at a just-right time. The Sun’s luminosity is not constant. As its nuclear furnace continues to fuse hydrogen into helium, the Sun becomes progressively brighter. The figure below shows how the Sun brightens throughout the history of life on Earth.

Figure: Sun’s Luminosity throughout Its History
Image credit: Hugh Ross

If Earth’s big burp had occurred any earlier, the resultant cooling would have led to a permanent snowball and the end of all life. If Earth’s big burp had occurred any later, there would not have been adequate time between the burp and the moment when the Sun would be too bright for advanced life to exist. This precise timing was needed for biodeposits (such as fossil fuels) to be built up and for the necessary chemical transformations of Earth’s surface environment to occur in order to support global human civilization.

Earth’s series of just-right events accompanying the big burp provides yet more evidence for the supernatural, super-intelligent handiwork of God for the specific benefit of life, of human beings, and human civilization.

Featured image: Banded iron rock formations like this one in Karijini National Park, Western Australia, will form under the oxygen-poor conditions that characterized the time just before and after the Great Oxidation Event.
Image credit: Graeme Churchard, Creative Commons Attribution

Time to confess. I now consider myself an evolutionary creationist. I have no choice. The evidence for biological evolution is so overwhelming…

…Just kidding! April Fool’s!

I am still an old-earth creationist. Even though the evolutionary paradigm is the prevailing framework in biology, I am skeptical about facets of it. I am more convinced than ever that a creation model approach is the best way to view life’s origin, design, and history. It’s not to say that there isn’t evidence for common descent; there is. Still, even with this evidence, I prefer old-earth creationism for three reasons.

• First, a creation model approach can readily accommodate the evidence for common descent within a design framework.
• Second, the evolutionary paradigm struggles to adequately explain many of the key transitions in life’s history.
• Third, the impression of design in biology is overwhelming—and it’s becoming more so every day.

And that is no joke.

Take the human genome as an example. When it comes to understanding its structure and function, we are in our infancy. As we grow in our knowledge and insight, it becomes increasingly apparent that the structural and functional features of the human genome (and the genomes of other organisms) display more elegance and sophistication than most life scientists could have ever imagined—at least, those operating within the evolutionary framework. On the other hand, the elegance and sophistication of genomes is expected for creationists and intelligent design advocates. To put it simply, the more we learn about the human genome, the more it appears to be the product of a Mind.

In fact, the advances in genomics over the last decade have forced life scientists to radically alter their views of genome biology. When the human genome was first sequenced in 2000, biologists considered most of the sequence elements to be nonfunctional, useless DNA. Now biologists recognize that virtually every class of these so-called junk DNA sequences serve key functional roles.

If most of the DNA sequence elements in the human genome were truly junk, then I’d agree that it makes sense to view them as evolutionary leftovers, especially because these junk DNA sequences appear in corresponding locations of the human and primate genomes. It is for these reasons that biologists have traditionally interpreted these shared sequences as the most convincing evidence for common descent.

However, now that we have learned that these sequences are functional, I think it is reasonable to regard them as the handiwork of a Creator, intentionally designed to contribute to the genome’s biology. In this framework, the shared DNA sequences in the human and primate genomes reflect common design, not common descent.

Still, many biologists reject the common design interpretation, while continuing to express confidence in the evolutionary model. Their certainty reflects a commitment to methodological naturalism, but there is another reason for their confidence. They argue that the human genome (and the genomes of other organisms) display other architectural and operational features that the evolutionary framework explains best—and, in their view, these features tip the scales toward the evolutionary interpretation.

Yet, researchers continue to make discoveries about junk DNA that counterbalance the evidence for common descent, including these structural and functional features. Recent insights into pseudogene biology nicely illustrate this trend.

Pseudogenes

Most life scientists view pseudogenes as the remnants of once-functional genes. Along these lines, biologists have identified three categories of pseudogenes (unitary, duplicated, and processed) and proposed three distinct mechanisms to explain the origin of each class. These mechanisms produce distinguishing features that allow investigators to identify certain DNA sequences as pseudogenes. However, a pre-commitment to the evolutionary paradigm can influence many biologists to declare too quickly that pseudogenes are nonfunctional based on their sequence characteristics.¹

As the old adage goes: theories guide, experiments decide. There is an accumulation of experimental data which indicates that pseudogenes from all three classes have utility.

A number of research teams have demonstrated that the cell’s machinery transcribes processed pseudogenes and, in turn, these transcripts are translated into proteins. Both duplicated and unitary pseudogenes are also transcribed. However, except for a few rare cases, these transcripts are not translated into proteins. Most of duplicated and unitary pseudogene transcripts serve a regulatory role, described by the competitive endogenous RNA hypothesis.

In other words, the experimental support for pseudogene function seemingly hinges on the transcription of these sequences. That leads to the question: What about pseudogene sequences located in genomes that aren’t transcribed? A number of pseudogenic sequences in genomes seemingly sit dormant. They aren’t transcribed and, presumably, have no utility whatsoever.

For many life scientists, this supports the evolutionary account for pseudogene origins, making it the preferred explanation over any model that posits the intentional design of pseudogene sequences. After all, why would a Creator introduce mutationally damaged genes that serve no function? Isn’t it better to explain the presence of functional processed pseudogenes as the result of neofunctionalization, whereby evolutionary mechanisms co-opt processed pseudogenes and use them as the raw material to evolve DNA sequence elements into new genes?

Or, perhaps, is it better to view the transcripts of regulatory unitary and duplicated pseudogenes as the functional remnants of the original genes whose transcripts played a role in regulatory networks with other RNA transcripts? Even though these pseudogenes no longer direct protein production, they can still take part in the regulatory networks comprised of RNA transcripts.

Are Untranscribed Pseudogenes Really Untranscribed?

Again, remember that support for the evolutionary interpretation of pseudogenes rests on the belief that some pseudogenes are not transcribed. What happens to this support if these DNA sequences are transcribed, meaning we simply haven’t detected or identified their transcripts experimentally?

As a case in point, in a piece for Nature Reviews, a team of collaborators from Australia argue that failure to detect pseudogene transcripts experimentally does not confirm the absence of a transcription.² For example, the transcripts for a pseudogene transcribed at a low level may fall below the experimental detection limit. This particular pseudogene would appear inactive to researchers when, in fact, the opposite is the case. Additionally, pseudogene expression may be tissue-specific or may take place at certain points in the growth and development process. If the assay doesn’t take these possibilities into account, then failure to detect pseudogene transcripts could just mean that the experimental protocol is flawed.

The similarity of the DNA sequences of pseudogenes and their corresponding “sister” genes causes another complication. It can be hard to experimentally distinguish between a pseudogene and its “intact” sister gene. This limitation means that, in some instances, pseudogene transcripts may be misidentified as the transcripts of the “intact” gene. Again, this can lead researchers to conclude mistakenly that the pseudogene isn’t transcribed.

Are Untranscribed Pseudogenes Really Nonfunctional?

These very real experimental challenges notwithstanding, there are pseudogenes that indeed are not transcribed, but it would be wrong to conclude that they have no role in gene regulation. For example, a large team of international collaborators demonstrated that a pseudogene sequence contributes to the specific three-dimensional architecture of chromosomes. By doing so, this sequence exerts influence over gene expression, albeit indirectly.³

Another research team determined that a different pseudogene plays a role in maintaining chromosomal stability. In laboratory experiments, they discovered that deleting the DNA region that harbors this pseudogene increases chromosomal recombination events that result in the deletion of pieces of DNA. This deletion is catastrophic and leads to DiGeorge/velocardiofacial syndrome.⁴

To be clear, these two studies focused on single pseudogenes. We need to be careful about extrapolating the results to all untranscribed pseudogenes. Nevertheless, at minimum, these findings open up the possibility that other untranscribed pseudogene sequences function in the same way. If past history is anything to go by when it comes to junk DNA, these two discoveries are most likely harbingers of what is to come. Simply put, we continue to uncover unexpected function for pseudogenes (and other classes of junk DNA).

Common Design or Common Descent?

Not that long ago, shared nonfunctional, junk DNA sequences in the human and primate genomes were taken as prima facia evidence for our shared evolutionary history with the great apes. There was no way to genuinely respond to the challenge junk DNA posed to creation models, other than to express the belief that we would one day discover function for junk DNA sequences.

Subsequently, discoveries have fulfilled a key scientific prediction made by creationists and intelligent design proponents alike. These initial discoveries involved single, isolated pseudogenes. Later studies demonstrated that pseudogene function is pervasive, leading to new scientific ideas such as the competitive endogenous RNA hypothesis, that connect the sequence similarity of pseudogenes and “intact” genes to pseudogene function. Researchers are beginning to identify functional roles for untranscribed pseudogenes. I predict that it is only a matter of time before biologists concede that the utility of untranscribed pseudogenes is pervasive and commonplace.

The creation model interpretation of shared junk DNA sequences becomes stronger and stronger with each step forward, which leads me to ask, When are life scientists going to stop fooling around and give a creation model approach a seat at the biology table?

Resources

• Who Was Adam? A Creation Model Approach to the Origin of Humanity, 2nd exp. ed., by Fazale Rana with Hugh Ross (book)
• The Cell’s Design: How Chemistry Reveals the Creator’s Artistry by Fazale Rana (book)
• “Pseudogene Decoy Reveal Hidden Evidence for Design” by Fazale Rana (article)
• “Functional Pseudogenes Are Everywhere!” by Fazale Rana (article)
• “High Levels of Pseudogene Expression Help Silence the Case for Common Descent” by Fazale Rana (article)
• “Scientific Upset: More Functions for Pseudogenes” by Fazale Rana (article)
• “Pseudogene Discovery Pains Evolutionary Paradigm” by Fazale Rana (article)
• “Unitary Pseudogenes Have Function!, Part 1” by Fazale Rana (article)
• “Unitary Pseudogenes Have Function!, Part 2” by Fazale Rana (article)
• “Competitive Endogenous RNA Hypothesis Supports the Case for Creation” by Fazale Rana (article)
• “Does the Evolutionary Paradigm Stymie Scientific Advance?” by Fazale Rana (article)
• “Evolution’s Flawed Approach to Science” by Fazale Rana (article)