What would you say is the most readily recognizable scientific icon? Is it DNA, a telescope, or maybe a test tube?

Figure 1: Scientific Icons. Image credit: Shutterstock

Marketing experts recognize the power of icons. When used well, icons prompt consumers to instantly identify a brand or product. They can also communicate a powerful message with a single glance.

Though many skeptics question if it’s science at all, the intelligent design movement has identified a powerful icon that communicates its message. Today, when most people see an image the bacterial flagellum they immediately think: Intelligent Design.

This massive protein complex powerfully communicates sophisticated engineering that could only come from an Intelligent Agent. And along these lines, it serves as a powerful piece of evidence for a Creator’s handiwork. Careful study of its molecular architecture and operation provides detailed evidence that an Intelligent Agent must be responsible for biochemical systems and, hence, the origin of life. And, as it turns out, the more we learn about the bacterial flagellum, the more evident it becomes that a Creator must have played a role in the origin and design of life—at least at the biochemical level—as new research from Japan illustrates.¹

The Bacterial Flagellum

This massive protein complex looks like a whip extending from the bacterial cell surface. Some bacteria have only a single flagellum, others possess several flagella. Rotation of the flagellum(a) allows the bacterial cell to navigate its environment in response to various chemical signals.

Figure 2: Typical Bacteria with Flagella. Image credit: Shutterstock

An ensemble of 30 to 40 different proteins makes up the typical bacterial flagellum. These proteins function in concert as a literal rotary motor. The flagellum’s components include a rotor, stator, drive shaft, bushing, universal joint, and propeller. It is essentially a molecular-sized electrical motor directly analogous to human-produced rotary motors. The rotation is powered by positively charged hydrogen ions flowing through the motor proteins embedded in the inner membrane.

Figure 3: The Bacterial Flagellum. Image credit: Wikipedia

The Bacterial Flagellum and the Revitalized Watchmaker Argument

Typically, when intelligent design proponents/creationists use the bacterial flagellum to make the case for a Creator, they focus the argument on its irreducibly complex nature. I prefer a different tact. I like to emphasize the eerie similarity between rotary motors created by human designers and nature’ bacterial flagella.

The bacterial flagellum is just one of a large number of protein complexes with machine-like attributes. (I devote an entire chapter to biomolecular machines in my book The Cell’s Design.) Collectively, these biomolecular machines can be deployed to revitalize the Watchmaker argument.

Popularized by William Paley in the eighteenth century, this argument states that as a watch requires a watchmaker, so too, life requires a Creator. Following Paley’s line of reasoning, a machine is emblematic of systems produced by intelligent agents. Biomolecular machines display the same attributes as human-crafted machines. Therefore, if the work of intelligent agents is necessary to explain the genesis of machines, shouldn’t the same be true for biochemical systems?

Skeptics inspired by atheist philosopher David Hume have challenged this simple, yet powerful, analogy. They argue that the analogy would be compelling only if there is a high degree of similarity between the objects that form the analogy. Skeptics have long argued that biochemical systems and machines are too dissimilar to make the Watchmaker argument work.

However, the striking similarity between the machine parts of the bacterial flagellum and human-made machines cause this objection to evaporate. New work on flagella by Japanese investigators lends yet more support to the Watchmaker analogy.

New Insights into the Structure and Function of the Flagellum’s Universal Joint

The flagellum’s universal joint (sometimes referred to as the hook) transfers the torque generated by the motor to the propeller. The research team wanted to develop a deeper understanding of the relationship between the molecular structure of the hook and how the structural features influence its function as a universal joint.

Comprised of nearly 100 copies (monomers) of a protein called FlgE, the hook is a curved, tube-like structure with a hollow interior. FlgE monomers stack on top of each other to form a protofilament. Eleven protofilaments organize to form the hook’s tube, with the long axis of the protofilament aligning to form the long axis of the hook.

Each FlgE monomer consists of three domains, called D0, D1, and D2. The researchers discovered that when the FlgE monomers stack to form a protofilament, the D0, D1, and D2 domains of each of the monomers align along the length of the protofilament to form three distinct regions in the hook. These layers have been labeled the tube layer, the mesh layer, and the spring layer.

During the rotation of the flagellum, the protofilaments experience compression and extension. The movement of the domains, which changes their spatial arrangement relative to one another, mediates the compression and extension. These domain movements allow the hook to function as a universal joint that maintains a rigid tube shape against a twisting “force,” while concurrently transmitting torque from the motor to the flagellum’s filament as it bends along its axis.

Regardless of one’s worldview, it is hard not to marvel at the sophisticated and elegant design of the flagellum’s hook!

The Bacterial Flagellum and the Case for a Creator

If the Watchmaker argument holds validity, it seems reasonable to think that the more we learn about protein complexes, such as the bacterial flagellum, the more machine-like they should appear to be. This work by the Japanese biochemists bears out this assumption. The more we characterize biomolecular machines, the more reason we have to think that life stems from a Creator’s handiwork.

Dynamic properties of the hook assembly add to the Watchmaker argument (when applied to the bacterial flagellum). This structure is much more sophisticated and ingenious than the design of a typical universal joint crafted by human designers. This elegance and ingenuity of the hook are exactly the attributes I would expect if a Creator played a role in the origin and design of life.

Message received, loud and clear.

Resources

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

The Bacterial Flagellum and the Case for a Creator

• “The Provocative Case for Intelligent Design: New Discovery Highlights Machine-Like Character of the Bacterial Flagellum” by Fazale Rana (article)
• “Bacterial Flagellum Structure Stacks the Case for Intelligent Design” by Fazale Rana (article)
• “Manufacturing the Case for Intelligent Design” by Fazale Rana (article)
• “Increasing the Torque on Intelligent Design” by Fazale Rana (article)
• “Changing Gears” by David Rogstad (article)

Can Intelligent Design Be Part of the Scientific Construct?

• “Is SETI an Intelligent Design Program?” by Fazale Rana (article)
• “Can Science Detect the Creator’s Fingerprints in Nature?” by Fazale Rana (article)
• “Can Intelligent Design Be Part of the Construct of Science?” by Fazale Rana (article)

RTB is committed to the goal of showing exemplary character when Christians disagree with one another. We aim to do so respectfully and humbly as we pursue and help others pursue truth. Such respect and humility become especially important when we disagree on topics of importance such as how to reconcile scientific data and biblical accounts of human origins.

You may wonder how people who are committed to seeking the truth can often interpret the data so differently. The reality is that disagreement is not just an issue in science and theology but in all areas of human reasoning and worldview formation. It’s known as the underdetermination of a theory.¹ People who readily acknowledge this underdetermination often qualify their acknowledgment by adding that although this is true, science (or observational or empirical data of any kind) can rule out certain theories as inconsistent with the data. Obviously this addendum is also true.

Yet, the underdetermination of theories also means that there are (and always will be) theories in obvious conflict that are, nevertheless, empirical equivalents. This means that they account for the empirical data equally but differently. Still some theories may require more ad hoc (unevidenced) assumptions or additions to fit the same data into one or more possible theories.

Applying Respectful Dialogue in Light of the Underdetermination of Theories

I recently appeared on The Language of God (LoG), a podcast produced by BioLogos and hosted by philosopher James (Jim) Stump.² Stump interviewed several people about the topic of Adam and Eve and the scientific data supporting or challenging their existence, their relationship to our current human populations, and the dating of any possible historical progenitor pair.³ Stump did an excellent job of asking pertinent scientific and theological questions.

In an episode entitled “Adam and Eve” Stump and Deborah (Deb) Haarsma, president of BioLogos, discuss complex topics touching on science and Scripture and what each is telling us about Adam and Eve and human origins. Interspersed in their discussion are comments from the guests Stump interviewed earlier.

Together, Stump and Haarsma highlight the biggest theological issues that arise from perceived and real tensions at the interface of mainstream science and traditional biblical views. These issues include biblical authority itself, as well as accounting for the universality of human sinfulness and the image of God in humanity.

Stump acknowledges a range of perspectives on issues of how best to understand Adam and Eve in the biblical account of creation found in Genesis. He promises not to provide a definitive answer to such complex questions, but rather ways to think about the issues that help maintain a commitment to the truthfulness of God’s revelations in Scripture and in the natural world (via science). I commend him on his approach and success in clearly articulating various views.

As Stump introduces the possible ways to reconcile the biblical data with the scientific data, he offers three varying views of Adam and Eve. These are the three most prominent among possible views for considering who Adam and Eve were, and they serve as topics in the 3-chapter podcast.

• Chapter 1: Sole progenitor pair
• Chapter 2: Representative pair
• Chapter 3: Nonhistorical figures (some would say archetypical or literary)

I was pleased to participate and share my views with Stump for production of this LoG podcast. Although my views are rightly reflected, I was a bit disappointed when I listened to the podcast. Let me share why.

Sole Progenitor Pair at an Intermediate Date

In the LoG episode, three distinct ideas are conflated: (1) the sole-progenitor model of human origins, (2) “traditional” understanding of human origins, and (3) a young-earth creationist (YEC) model of human origins. This conflation obscures the fact that RTB has a tenable model of human origins which affirms traditional commitments, such as sole-progenitorship.

For brevity’s sake, I will refer to three ways to describe the dating of the sole progenitor pair: recent (less than 10-12 kya [thousand years ago]), intermediate (50-200 kya), and ancient (>450 kya). Stump and Haarsma acknowledge that the sole progenitor pair has some alternate possible datings (not just a couple constrained to YEC recent interpretations). But it is unfortunate that RTB’s sole progenitor model—with an intermediate dating for Adam and Eve—is not presented well, especially when three of the five guests might find an intermediate dating for the sole progenitor pair model much more tenable than the impression the podcast leaves.

The hosts seem to reject correlation of the data with dates (for a sole progenitor pair) younger than about 10 kya and older than about 300 kya based on general observations related to:

• Recent dating of widespread agricultural signs in the archeological record leads to rejection of dating in line with an intermediate or ancient view.
• Multiple allele frequency or allele frequency spectrum data (a measurement of population diversity based on comparing similar sites within human chromosomes)⁴ indicates that dates younger than 500 kya should be rejected. And according to BioLogos participant Dennis Venema, biologist at Trinity Western University, scientific analysis can’t tell us anything reliable about human origins at or beyond that 500 ky point.
• Fossil records of anatomically modern human remains, dating back 200–300 kya, indicate that more recent dating should be rejected (<10 ky).
• Claims that modern human behaviors such as use of fire date back to very early dates (circa 500 kya) lead to rejection of an early or intermediate dating.

Stump admits the complexity of the discussion, and I readily acknowledge that the BioLogos hosts cannot address all the details.

Nevertheless, the RTB model can account for all the points raised above, perhaps with some modifications to underlying assumptions. Yet the hosts do not consider the RTB model in their analysis. They present the data in support of an evolutionary interpretation of human origins, calling for a very ancient sole progenitor pair or a very recent (perhaps non-historical) Adam and Eve—neglecting and/or rejecting RTB’s model with an intermediate dating (50–200 kya) for a sole progenitor pair. We are in the process of addressing points of tension between the RTB model and mainstream science. Yet the RTB sole progenitor pair model successfully fits the scientific data and the biblical data within this intermediate range, and acknowledging this would have brought clarity to the general listener.

Interpreting Human Population Genetics

Venema addresses the genetic data, which Haarsma seems to indicate is what persuaded her not to hold an intermediate date for Adam and Eve. Unfortunately, I think the data and interpretation presented to listeners are filled with inaccuracies. Through multiple conversations over the past two years with computational biologist and founder of Peaceful Science, S. Joshua Swamidass, it has become clear to me that the perspective shared in this podcast is scientifically unsubstantiated.

Recently, in a lecture presented to the RTB scholar community, Swamidass, a Christian who affirms evolutionary science, graciously explained how the evidence against RTB’s position has been overstated. In his presentation, Swamidass explains how some of the arguments against RTB’s model have included misrepresentations of population genetics that cannot be found in the peer-review literature. For example, it was often reported that population genetics estimates of ancestral population size are the minimum population size, rather than the average population size.

However, by modeling population diversity and dynamics (with many evolutionary, mainstream scientific assumptions considered), it is possibly consistent with the evidence that our ancestral population dipped to as low as 10–20 individuals at 200 kya, and possibly to a single couple near 500 kya (or even more recently if other data is incorporated into the modeling, such as interbreeding with other hominids).

The podcast hosts don’t address these caveats and, along with Venema, repeat the unsubstantiated claim that the human population never dipped below thousands in the previous 500 ky. They agree a bottleneck less than thousands can be definitely ruled out. I think they brush aside the intermediate dating of a sole progenitor pair too quickly and without a fair representation of the data.

Disappointed but Looking Forward to Further Dialogue

To summarize, I think the hosts dismissed RTB’s intermediate sole progenitor pair position without adequate representation of the data or our model. Of course, the time constraints would not permit detailed analysis of RTB’s model nor was this the focus of the podcast. We acknowledge that some assessments of genetic data and their significance to the RTB model are works in progress. We are always ready to acknowledge when our model needs revision, and we expect some adjustments may be necessary in light of accumulating genetic data and subsequent computational analyses. We are working with Peaceful Science to examine these possibilities and refine our model as needed.

As an RTB scholar I was looking for an acknowledgement that we have an empirically equivalent model that dates a sole progenitor pair to an intermediate date, and that correlates much of the scientific and biblical data within this range. It would have given the listener a clearer understanding of options in this category. I hope the hosts will take a closer look at Who Was Adam?, the genetic data, and Swamidass’s presentation, and revise their future commentaries.

Yet despite my disappointment, I was treated with graciousness and respect on this podcast and have always been throughout my history with RTB in interactions with our colleagues at BioLogos. Certainly, none of us knows the details of God’s creation perfectly. I hope I always remember to treat others’ positions fairly and to give people the benefit of the doubt, especially when we find ourselves honestly interpreting the same data differently.

Like those at BioLogos and Peaceful Science, we at RTB are committed to continuing the conversation with respect and humility, as we engage in the intellectual exchange of possible interpretations and pursuit of the truth. As iron sharpens iron so one person sharpens another. We are looking forward to continuing the dialogue at an upcoming workshop at RTB (January 2020). And I’m looking forward to writing future blogs that share these dialogues and aspects of the RTB human origins model as they continue to develop.

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)