Evolutionary Story Tells the Tale of Creation

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By Fazale Rana – December 4, 2019

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.

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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

Convergence of Echolocation

The Historical Contingency of the Evolutionary Process

Endnotes
  1. Akito Y. Kawahara et al., “Phylogenomics Reveals the Evolutionary Timing and Pattern of Butterflies and Moths,” Proceedings of the National Academy of Sciences, USA 116, no. 45 (November 5, 2019): 22657–63, doi:10.1073/pnas.1907847116.
  2. Ed Yong, “A Textbook Evolutionary Story about Moths and Bats Is Wrong,” The Atlantic (October 21, 2019), https://www.theatlantic.com/science/archive/2019/10/textbook-evolutionary-story-wrong/600295/.
  3. Kawahara et al., “Phylogenomics.”
  4. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).
  5. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W. W. Norton & Company, 1990).
  6. Gabriel Yedid and Graham Bell, “Macroevolution Simulated with Autonomously Replicating Computer Programs,” Nature 420 (December 19, 2002): 810–12, doi:10.1038/nature01151.
  7. Emma C. Teeling et al., “Molecular Evidence Regarding the Origin of Echolocation and Flight in Bats,” Nature 403 (January 13, 2000): 188–92, doi:10.1038/35003188.
  8. Gang Li et al., “The Hearing Gene Prestin Reunites Echolocating Bats,” Proceedings of the National Academy of Sciences, USA 105, no. 37 (September 16, 2008): 13959–64, doi:10.1073/pnas.0802097105.

Reprinted with permission by the author

Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/11/21/vocal-signals-smile-on-the-case-for-human-exceptionalism

Evolution of Antibiotic Resistance Makes the Case for a Creator

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By Fazale Rana – November 27, 2019

It isn’t that hard to imagine, because antibiotics weren’t readily available for medical use until after World War II. And since that time, widespread availability of antibiotics has revolutionized medicine. However, the ability to practice modern medicine is being threatened because of the rise of antibiotic-resistant bacteria. Currently, there exists a pressing need to understand the evolution of antibiotic-resistant strains and to develop new types of antibiotics. Surprisingly, this worthy pursuit has unwittingly stumbled upon evidence for a Creator’s role in the design of biochemical systems.

Alexander Fleming (1881–1955) discovered the first antibiotic, penicillin, in 1928. But it wasn’t until Ernst Chain, Howard Florey, and Edward Abraham purified penicillin in 1942 and Norman Heatley developed a bulk extraction technique in 1945 that the compound became available for routine medical use.

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Figure 1: Alexander Fleming. Image Credit: Wikipedia

Prior to this time, people often died from bacterial infections. Complicating this vulnerability to microbial pathogens was the uncertain outcome of many medical procedures. For example, patients often died after surgery due to complications arising from infections.

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Figure 2: A generalized structure for penicillin antibiotics. Image credit: Shutterstock

Bacterial Resistance Necessitates New Antibiotics

Unfortunately, because of the growing threat of superbugs—antibiotic-resistant strains of bacteria—health experts around the world worry that we soon will enter into a post-antibiotic era in which modern medicine will largely revert to pre-World War II practices. According to Dr. David Livermore, laboratory director at Public Health England, which is responsible for monitoring antibiotic-resistant strains of bacteria, “A lot of modern medicine would become impossible if we lost our ability to treat infections.”1

Without antibiotics, people would routinely die of infections that we easily treat today. Abdominal surgeries would be incredibly risky. Organ transplants and chemotherapy would be out of the question. And the list continues.

The threat of entering into a post-antibiotic age highlights the desperate need to develop new types of antibiotics. It also highlights the need to develop a better understanding of evolutionary processes that lead to the emergence of antibiotic resistance in bacteria.

Recently, a research team from Michigan State University (MSU) published a report that offers insight into the latter concern. These researchers studied the evolution of antibiotic resistance in bacteria that had been serially cultured in the laboratory for multiple decades in media that was free from antibiotics.2 Through this effort, they learned that the genetic history of the bacterial strain plays a key role in its acquisition of resistance to antibiotics.

This work has important implications for public health, but it also carries theological implications. The decades-long experiment provides evidence that the elegant designs characteristic of biochemical and biological systems most likely stem from a Creator’s handiwork.

The Long-Term Evolution Experiment

To gain insight into the role that genetic history plays in the evolution of antibiotic resistance, the MSU researchers piggy-backed on the famous Long-Term Evolution Experiment (LTEE) at Michigan State University. Inaugurated in 1988, the LTEE is designed to monitor evolutionary changes in the bacterium E. coli, with the objective of developing an understanding of the evolutionary process.

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Figure 3: A depiction of E. coli. Image Credit: Shutterstock

The LTEE began with a single cell of E. coli that was used to generate twelve genetically identical lines of cells. The twelve clones of the parent E. coli cell were separately inoculated into a minimal growth medium containing low levels of glucose as the only carbon source. After growing overnight, an aliquot (equal fractional part) of each of the twelve cultures was transferred into fresh growth media. This process has been repeated every day for about thirty years. Throughout the experiment, aliquots of cells have been frozen every 500 generations. These frozen cells represent a “fossil record” of sorts that can be thawed out and compared to current and other past generations of cells.

Relaxed Selection and Decay of Antibiotic Resistance

In general, when a population of organisms no longer experiences natural selection for a particular set of traits (antibiotic resistance, in this case), the traits designed to handle that pressure may experience functional decay as a result of mutations and genetic drift. This process is called relaxed selection.

In the case of antibiotic resistance, when the threat of antibiotics is removed from the population (relaxed selection), it seems reasonable to think that antibiotic resistance would decline in the population because in most cases antibiotic resistance comes with a fitness cost. In other words, bacterial strains that acquire antibiotic resistance face a trade-off that makes them less fit in environments without the antibiotic.

Genetic History and the Re-Evolution of Antibiotic Resistance

In light of this expectation, the MSU researchers wondered how readily bacteria that have experienced relaxed selection can overcome loss of antibiotic resistance when the antibiotic is reintroduced to the population.

To explore this question, the researchers examined the evolution of antibiotic resistance in the LTEE ancestor by exposing it to a set of different antibiotics and compared its propensity to acquire antibiotic resistance with four strains of E. coli derived from the LTEE ancestor (that underwent 50,000 generations of daily growth and transfer into fresh media in the absence of exposure to antibiotics).

As expected, the MSU team discovered that 50,000 generations of relaxed selection rendered the four strains more susceptible to four different antibiotics (ampicillin, ceftriaxone, ciprofloxacin, and tetracycline) compared to the LTEE ancestor. When they exposed these strains to the different antibiotics, the researchers discovered that acquisition of antibiotic resistance was idiosyncratic: some strains more readily evolved antibiotic resistance than the LTEE ancestor and others were less evolvable.

Investigators explained this difference by arguing that during the period of relaxed selection some of the strains experienced mutations that constrained the evolution of antibiotic resistance, whereas others experienced mutations that potentiated (activated) the evolution of antibiotic resistance. That is, historical contingency has played a key role in the acquisition of antibiotic resistance. Different bacterial lineages accumulated genetic differences that influence their capacity to evolve and adapt in new directions.

Historical Contingency

This study follows on the heels of previous studies that demonstrate the historical contingency of the evolutionary process.3 In other words, chance governs biological and biochemical evolution at its most fundamental level. As the MSU researchers observed, evolutionary pathways consist of a historical sequence of chance genetic changes operated on by natural selection (or that experience relaxed selection), which, too, consists of chance components.

Because of the historically contingent nature of the evolutionary process, it is highly unlikely that the same biological and biochemical designs should appear repeatedly throughout nature. In his book Wonderful Life, Stephen Jay Gould used the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time.4

The “Problem” of Convergence

And yet, we observe the opposite pattern in biology. From an evolutionary perspective, it appears as if the evolutionary process independently and repeatedly arrived at the same outcome, time and time again (convergence). As evolutionary biologists Simon Conway Morris and George McGhee point out in their respective books Life’s Solution and Convergent Evolution, identical evolutionary outcomes are a widespread feature of the biological realm.5

Scientists see these repeated outcomes at ecological, organismal, biochemical, and genetic levels. To illustrate the pervasiveness of convergence at the biochemical level, I describe 100 examples of convergence in my book The Cell’s Design.6

From my perspective, the widespread occurrence of convergent evolution is a feature of biology that evolutionary theory can’t genuinely explain. In fact, given the clear-cut demonstration that the evolutionary process is historically contingent, I see the widespread occurrence of convergence as a failed scientific prediction for the evolutionary paradigm.

 

Evolution in Bacteria Doesn’t Equate to Large-Scale Evolution

The evolution of E. coli in the LTEE doesn’t necessarily validate the evolutionary paradigm. Just because such change is observed in a microbe doesn’t mean that evolutionary processes can adequately account for life’s origin and history, and the full range of biodiversity.

 

Convergence and the Case for Creation

Instead of viewing convergent features as having emerged through repeated evolutionary outcomes, we could understand them as reflecting the work of a divine Mind. In this scheme, 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.

Sadly, many in the scientific community are hesitant to embrace this perspective because they are resistant to the idea that design and purpose may play a role in biology. But, one can hope that someday the scientific community will be willing to move into a post-evolution future as the evidence for a Creator’s role in biology mounts.

Resources

The Historical Contingency of the Evolutionary Process

Microbial Evolution and the Validity of the Evolutionary Paradigm

Endnotes
  1. Sarah Bosley, “Are You Ready for a World without Antibiotics?” The Guardian, August 12, 2010, https://www.theguardian.com/society/2010/aug/12/the-end-of-antibiotics-health-infections.
  2. Kyle J. Card et al., “Historical Contingency in the Evolution of Antibiotic Resistance after Decades of Relaxed Selection,” PLoS Biology 17, no. 10 (October 23, 2019): e3000397, doi:10.1371/journal.pbio.3000397.
  3. Zachary D. Blount et al., “Historical Contingency and the Evolution of a Key Innovation in an Experimental Population of Escherichia coli,” Proceedings of the National Academy of Sciences USA 105, no. 23 (June 10, 2008): 7899-7906, doi:10.1073/pnas.0803151105.
  4. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W.W. Norton & Company, 1990).
  5. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).
  6. Fazale Rana, The Cell’s Design: How Chemistry Reveal the Creator’s Artistry (Grand Rapids, MI: Baker, 2008).

Reprinted with permission by the author

Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/11/21/vocal-signals-smile-on-the-case-for-human-exceptionalism

Analysis of Genomes Converges on the Case for a Creator

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By Fazale Rana – November 13, 2019

Are you a Marvel or a DC fan?

Do you like the Marvel superheroes better than those who occupy the DC universe? Or is it the other way around for you?

Even though you might prefer DC over Marvel (or Marvel over DC), over the years these two comic book rivals have often created superheroes with nearly identical powers. In fact, a number of Marvel and DC superheroes are so strikingly similar that their likeness to one another is obviously intentional.1

Here are just a few of the superheroes Marvel and DC have ripped off each other:

  • Superman (DC, created in 1938) and Hyperion (Marvel, created in 1969)
  • Batman (DC, created in 1939) and Moon Knight (Marvel, created in 1975)
  • Green Lantern (DC, created in 1940) and Nova (Marvel, created in 1976)
  • Catwoman (DC, created in 1940) and Black Cat (Marvel, created in 1979)
  • Atom (DC, created in 1961) and Ant-Man (Marvel, created in 1962)
  • Aquaman (DC, created in 1941) and Namor (Marvel, created in 1939)
  • Green Arrow (DC, created in 1941) and Hawkeye (Marvel, created in 1964)
  • Swamp Thing (DC, created in 1971) and Man Thing (Marvel, created in 1971)
  • Deathstroke (DC, created in 1980) and Deadpool (Marvel, created in 1991)

This same type of striking similarity is also found in biology. Life scientists have discovered countless examples of biological designs that are virtually exact replicas of one another. Yet, these identical (or nearly identical) designs occur in organisms that belong to distinct, unrelated groups (such as the camera eyes of vertebrates and octopi). Therefore, they must have an independent origin.

 

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Figure 1: The Camera Eyes of Vertebrates (left) and Cephalopods (right); 1: Retina; 2: Nerve Fibers; 3: Optic Nerve; 4: Blind Spot. Image credit: Wikipedia

From an evolutionary perspective, it appears as if the evolutionary process independently and repeatedly arrived at the same outcome, time and time again. As evolutionary biologists Simon Conway Morris and George McGhee point out in their respective books, Life’s Solution and Convergent Evolution, identical evolutionary outcomes are a widespread feature of the biological realm.2 Scientists observe these repeated outcomes (known as convergence) 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 genuinely explain. In fact, I see pervasive convergence as a failed scientific prediction—for the evolutionary paradigm. Recent work by a research team from Stanford University demonstrates my point.3

These researchers discovered that identical genetic changes occurred when: (1) bats and whales “evolved” echolocation, (2) killer whales and manatees “evolved” specialized skin in support of their aquatic lifestyles, and (3) pikas and alpacas “evolved” increased lung capacity required to live in high-altitude environments.

Why do I think this discovery is so problematic for the evolutionary paradigm? To understand my concern, we first need to consider the nature of the evolutionary process.

Biological Evolution Is Historically Contingent

Essentially, 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.

The concept of historical contingency embodies this idea and is the theme of Stephen Jay Gould’s book Wonderful Life.4 To help illustrate the concept, Gould uses the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time.

Are Evolutionary Processes Historically Contingent?

Gould based the concept of historical contingency on his understanding of the evolutionary process. In the decades since Gould’s original description of historical contingency, several studies have affirmed his view.

For example, in a landmark study in 2002, two Canadian investigators simulated macroevolutionary processes using autonomously replicating computer programs, with the programs operating like digital organisms.5 These programs were placed into different “ecosystems” and, because they replicated autonomously, could evolve. By monitoring the long-term evolution of the 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.

The Origin of Echolocation

One of the most remarkable examples of convergence is the independent origin of echolocation (sound waves emitted from an organism to an object and then back to the organism) in bats (chiropterans) and cetaceans (toothed whales). Research indicates that echolocation arose independently in two different groups of bats and also in the toothed whales.

 

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Figure 2: Echolocation in Bats. Image credit: Shutterstock

One reason why this example of convergence is so remarkable has to do with the way some evolutionary biologists account for the widespread occurrences of convergence in biological systems. Undaunted by the myriad examples of convergence, these scientists assert that independent evolutionary outcomes result when unrelated organisms encounter nearly identical selection forces (e.g., environmental, competitive, and predatory pressures). According to this idea, natural selection channels unrelated organisms down similar pathways toward the same endpoint.

But this explanation is unsatisfactory because bats and whales live in different types of habitats (terrestrial and aquatic). Consequently, the genetic changes responsible for the independent emergence of echolocation in the chiropterans and cetaceans should be distinct. Presumably, the evolutionary pathways that converged on a complex biological system such as echolocation would have taken different routes that would be reflected in the genomes. In other words, even though the physical traits appear to be identical (or nearly identical), the genetic makeup of the organisms should reflect an independent evolutionary history.

But this expectation isn’t borne out by the data.

Genetic Convergence Parallels Trait Convergence

In recent years, evolutionary biologists have developed interest in understanding the genetic basis for convergence. Specifically, these scientists want to understand the genetic changes that lead to convergent anatomical and physiological features (how genotype leads to phenotype).

Toward this end, a Stanford research team developed an algorithm that allowed them to search through entire genome sequences of animals to identify similar genetic features that contribute to particular biological traits.6 In turn, they applied this method to three test cases related to the convergence of:

  • echolocation in bats and whales
  • scaly skin in killer whales
  • lung structure and capacity in pikas and alpacas

The investigators discovered that for echolocating animals, the same 25 convergent genetic changes took place in their genomes and were distributed among the same 18 genes. As it turns out, these genes play a role in the development of the cochlear ganglion, thought to be involved in echolocation. They also discovered that for aquatic mammals, there were 27 identical convergent genetic changes that occurred in same 15 genes that play a role in skin development. And finally, for high-altitude animals, they learned that the same 25 convergent genetic changes occurred in the same 16 genes that play a role in lung development.

In response to this finding, study author Gill Bejerano remarked, “These genes often control multiple functions in different tissues throughout the body, so it seems it would be very difficult to introduce even minor changes. But here we’ve found that not only do these very different species share specific genetic changes, but also that these changes occur in coding genes.”7

In other words, these results are not expected from an evolutionary standpoint. It is nothing short of amazing that genetic convergence would parallel phenotypic convergence.

On the other hand, these results make perfect sense from a creation model vantage point.

Convergence and the Case for Creation

Instead of viewing convergent features as having emerged through repeated evolutionary outcomes, we could understand them as reflecting the work of a Divine Mind. In this scheme, 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.

Like the superhero rip-offs in the Marvel and DC comics, the convergent features in biology appear to be intentional, reflecting a teleology that appears to be endemic in living systems.

Resources

Convergence of Echolocation

The Historical Contingency of the Evolutionary Process

Endnotes
  1. Jamie Gerber, “15 DC and Marvel Superheroes Who Are Strikingly Similar,” ScreenRant (November 12, 2016), screenrant.com/marvel-dc-superheroes-copies-rip-offs/.
  2. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).
  3. Amir Marcovitz et al., “A Functional Enrichment Test for Molecular Convergent Evolution Finds a Clear Protein-Coding Signal in Echolocating Bats and Whales,” Proceedings of the National Academy of Sciences, USA 116, no. 42 (October 15, 2019), 21094–21103, doi:10.1073/pnas.1818532116.
  4. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W. W. Norton & Company, 1990).
  5. Gabriel Yedid and Graham Bell, “Macroevolution Simulated with Autonomously Replicating Computer Programs,” Nature 420 (December 19, 2002): 810–12, doi:10.1038/nature01151.
  6. Marcovitz et al., “A Functional Enrichment Test.”
  7. Stanford Medicine, “Scientists Uncover Genetic Similarities among Species That Use Sound to Navigate,” ScienceDaily, October 4, 2019, sciencedaily.com/releases/2019/10/191004105643.htm.

Reprinted with permission by the author

Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2019/11/13/analysis-of-genomes-converges-on-the-case-for-a-creator

Origins of Monogamy Cause Evolutionary Paradigm Breakup

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BY FAZALE RANA – MARCH 20, 2019

Gregg Allman fronted the Allman Brothers Band for over 40 years until his death in 2017 at the age of 69. Writer Mark Binelli described Allman’s voice as “a beautifully scarred blues howl, old beyond its years.”1

A rock legend who helped pioneer southern rock, Allman was as well known for his chaotic, dysfunctional personal life as for his accomplishments as a musician. Allman struggled with drug abuse and addiction. He was also married six times, with each marriage ending in divorce and, at times, in a public spectacle.

In a 2009 interview with Binelli for Rolling Stone, Allman reflected on his failed marriages: “To tell you the truth, it’s my sixth marriage—I’m starting to think it’s me.”2

Allman isn’t the only one to have trouble with marriage. As it turns out, so do evolutionary biologists—but for different reasons than Greg Allman.

To be more exact, evolutionary biologists have made an unexpected discovery about the evolutionary origin of monogamy (a single mate for at least a season) in animals—an insight that raises questions about the evolutionary explanation. Based on recent work headed by a large research team of investigators from the University of Texas (UT), Austin, it looks like monogamy arose independently, multiple times, in animals. And these origin events were driven, in each instance, by the same genetic changes.3

In my view, this remarkable example of evolutionary convergence highlights one of the many limitations of evolutionary theory. It also contributes to my skepticism (and that of other intelligent design proponents/creationists) about the central claim of the evolutionary paradigm; namely, the origin, design, history, and diversity of life can be fully explained by evolutionary mechanisms.

At the same time, the independent origins of monogamy—driven by the same genetic changes—(as well as other examples of convergence) find a ready explanation within a creation model framework.

Historical Contingency

To appreciate why I believe this discovery is problematic for the evolutionary paradigm, it is necessary to consider the nature of evolutionary mechanisms. According to the evolutionary biologist Stephen Jay Gould (1941–2002), evolutionary transformations occur in a historically contingent manner.This means that the evolutionary process consists of an extended sequence of unpredictable, chance events. If any of these events were altered, it would send evolution down a different trajectory.

To help clarify this concept, Gould used the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time. In other words, the evolutionary process should not repeat itself. And rarely should it arrive at the same end point.

Gould based the concept of historical contingency on his understanding of the mechanisms that drive evolutionary change. Since the time of Gould’s original description of historical contingency, several studies have affirmed his view. (For descriptions of some representative studies, see the articles listed in the Resources section.) In other words, researchers have experimentally shown that the evolutionary process is, indeed, historically contingent.

A Failed Prediction of the Evolutionary Paradigm

Given historical contingency, it seems unlikely that distinct evolutionary pathways would lead to identical or nearly identical outcomes. Yet, when viewed from an evolutionary standpoint, it appears as if repeated evolutionary outcomes are a common occurrence throughout life’s history. This phenomenon—referred to as convergence—is widespread. Evolutionary biologists Simon Conway Morris and George McGhee point out in their respective books, Life’s Solution and Convergent Evolution, that identical evolutionary outcomes are a characteristic feature of the biological realm.5 Scientists see these repeated outcomes at the ecological, organismal, biochemical, and genetic levels. In fact, in my book The Cell’s Design, I describe 100 examples of convergence at the biochemical level.

In other words, biologists have made two contradictory observations within the evolutionary framework: (1) evolutionary processes are historically contingent and (2) evolutionary convergence is widespread. Since the publication of The Cell’s Design, many new examples of convergence have been unearthed, including the recent origin of monogamy discovery.

Convergent Origins of Monogamy

Working within the framework of the evolutionary paradigm, the UT research team sought to understand the evolutionary transition to monogamy. To achieve this insight, they compared the gene expression profiles in the neural tissues of reproductive males for closely related pairs of species, with one species displaying monogamous behavior and the other nonmonogamous reproduction.

The species pairs spanned the major vertebrate groups and included mice, voles, songbirds, frogs, and cichlids. From an evolutionary perspective, these organisms would have shared a common ancestor 450 million years ago.

Monogamous behavior is remarkably complex. It involves the formation of bonds between males and females, care of offspring by both parents, and increased territorial defense. Yet, the researchers discovered that in each instance of monogamy the gene expression profiles in the neural tissues of the monogamous species were identical and distinct from the gene expression patterns for their nonmonogamous counterparts. Specifically, they observed the same differences in gene expression for the same 24 genes. Interestingly, genes that played a role in neural development, cell-cell signaling, synaptic activity, learning and memory, and cognitive function displayed enhanced gene expression. Genes involved in gene transcription and AMPA receptor regulation were down-regulated.

So, how do the researchers account for this spectacular example of convergence? They conclude that a “universal transcriptomic mechanism” exists for monogamy and speculate that the gene modules needed for monogamous behavior already existed in the last common ancestor of vertebrates. When needed, these modules were independently recruited at different times in evolutionary history to yield monogamous species.

Yet, given the number of genes involved and the specific changes in gene expression needed to produce the complex behavior associated with monogamous reproduction, it seems unlikely that this transformation would happen a single time, let alone multiple times, in the exact same way. In fact, Rebecca Young, the lead author of the journal article detailing the UT research team’s work, notes that “Most people wouldn’t expect that across 450 million years, transitions to such complex behaviors would happen the same way every time.”6

So, is there another way to explain convergence?

Convergence and the Case for a Creator

Prior to Darwin (1809–1882), biologists referred to shared biological features found in organisms that cluster into disparate biological groups as analogies. (In an evolutionary framework, analogies are referred to as evolutionary convergences.) They viewed analogous systems as designs conceived by the Creator that were then physically manifested in the biological realm and distributed among unrelated organisms.

In light of this historical precedence, I interpret convergent features (analogies) as the handiwork of a Divine mind. 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.

Thus, the idea of monogamous convergence seems to divorce itself from the evolutionary framework, but it makes for a solid marriage in a creation model framework.

Resources

Endnotes
  1. Mark Binelli, “Gregg Allman: The Lost Brother,” Rolling Stone, no. 1082/1083 (July 9–23, 2009), https://www.rollingstone.com/music/music-features/gregg-allman-the-lost-brother-108623/.
  2. Binelli, “Gregg Allman: The Lost Brother.”
  3. Rebecca L. Young et al., “Conserved Transcriptomic Profiles underpin Monogamy across Vertebrates,” Proceedings of the National Academy of Sciences, USA 116, no. 4 (January 22, 2019): 1331–36, doi:10.1073/pnas.1813775116.
  4. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W. W. Norton & Company, 1990).
  5. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).
  6. University of Texas at Austin, “Evolution Used Same Genetic Formula to Turn Animals Monogamous,” ScienceDaily (January 7, 2019), www.sciencedaily.com/releases/2019/01/1901071507.htm.

Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2019/03/20/origins-of-monogamy-cause-evolutionary-paradigm-breakup

Believing Impossible Things: Convergent Origins of Functional Junk DNA Sequences

believingimpossiblethings

BY FAZALE RANA – MARCH 14, 2018

In a classic scene from Alice in Wonderland, the story’s heroine informs the White Queen, “One can’t believe impossible things,” to which, the White Queen—scolding Alice—replies, “I daresay you haven’t had much practice. When I was your age, I always did it for half-an-hour a day. Why, sometimes I’ve believed as many as six impossible things before breakfast.”

If recent work by researchers from UC Santa Cruz and the University of Rochester (New York) is to be taken as true, it would require evolutionary biologists to believe two impossible things—before, during, and after breakfast. These scientific investigators have discovered something that is hard to believe about the role SINE DNA plays in gene regulation, raising questions about the validity of the evolutionary explanation for the architecture of the human genome.1 In fact, considering the implications of this work, it would be easier to believe that the human genome was shaped by a Creator’s handiwork than by evolutionary forces.

SINE DNA

One of the many classes of noncoding or junk DNA, short interspersed elements, or SINE DNA sequences, range in size from 100 to 300 base pairs (genetic letters). In primates, the most common SINEs are the Alu sequences. There are about 1.1 million Alu copies in the human genome (roughly 12 percent of the genome).

SINE DNA sequences (including Alu sequences) contain a DNA segment used by the cell’s machinery to produce an RNA message. This feature allows SINEs to be transcribed. Because of this feature, molecular biologists also categorize SINE DNA as a retroposon. Molecular biologists believe that SINE sequences can multiply in number within an organism’s genome through the activity of the enzyme, reverse transcriptase. Presumably, once SINE DNA becomes transcribed, reverse transcriptase converts SINE RNA back into DNA. The reconverted DNA sequence then randomly reintegrates back into the genome. It’s through this duplication and reintegration mechanism that SINE sequences proliferate as they move around, or retrotranspose, throughout the genome. To say it differently, molecular biologists believe that over time, transcription of SINE DNA and reverse transcription of SINE RNA increases the copy number of SINE sequences and randomly disperses them throughout an organism’s genome.

Molecular biologists have discovered numerous instances in which nearly identical SINE segments occur at corresponding locations in the genomes of humans, chimpanzees, and other primates. Because the duplication and movement of SINE DNA appear to be random, evolutionary biologists think it unlikely that SINE sequences would independently appear in the same locations in the genomes of humans and chimpanzees (and other primates). And given their supposed nonfunctional nature, shared SINE DNA in humans and chimpanzees seemingly reflects their common evolutionary ancestry. In fact, evolutionary biologists have gone one step further, using SINE Alu sequences to construct primate evolutionary trees.

SINE DNA Is Functional

Even though many people view shared junk DNA sequences as the most compelling evidence for biological evolution, the growing recognition that virtually every class of junk DNA has function undermines this conclusion. For if these shared sequences are functional, then one could argue that they reflect the Creator’s common design, not shared evolutionary ancestry and common descent. As a case in point, in recent years, molecular biologists have learned that SINE DNA plays a vital role in gene regulation through a variety of distinct mechanisms.2

Staufen-Mediated mRNA Decay

One way SINE sequences regulate gene expression is through a pathway called Staufen-mediated messenger RNA (mRNA) decay (SMD). Critical to an organism’s development, SMD plays a key role in cellular differentiation. SMD is characterized by a complex mechanism centered around the destruction of mRNA. When this degradation takes place, it down-regulates gene expression. The SMD pathway involves binding of a protein called Staufen-1 to one of the ends of the mRNA molecule (dubbed the 3´untranslated region). Staufen-1 binds specifically to double-stranded structures in the 3´untranslated region. This double strand structure forms when Alu sequences in the 3´untranslated region bind to long noncoding RNA molecules containing Alu sequences. This binding event triggers a cascade of additional events that leads to the breakdown of messenger RNA.

Common Descent or Common Design?

As an old-earth creationist, I see the functional role played by noncoding DNA sequences as a reflection of God’s handiwork, defending the case for design from a significant evolutionary challenge. To state it differently: these findings mean that it is just as reasonable to conclude that the shared SINE sequences in the genomes of humans and the great apes reflect common design, not a shared evolutionary ancestry.

In fact, I would maintain that it is more reasonable to think that functional SINE DNA sequences reflect common design, rather than common descent, given the pervasive role these sequence elements play in gene regulation. Because Alu sequences are only found in primates, they must have originated fairly recently (when viewed from an evolutionary framework). Yet, they play an integral and far-reaching role in gene regulation.

And herein lies the first impossible thing evolutionary biologists must believe: Somehow Alusequences arose and then quickly assumed a central place in gene regulation. According to Carl Schmid, a researcher who uncovered some of the first evidence for the functional role played by SINE DNA, “Sine Alus have appeared only recently within the primate lineage, this proposal [of SINE DNA function] provokes the challenging question of how Alu RNA could have possibly assumed a significant role in cell physiology.”3

How Does Junk DNA Acquire Function?

Still, those who subscribe to the evolutionary framework do not view functional junk DNA as incompatible with common descent. They argue that junk DNA acquired function through a process called neofunctionalization. In the case of SMD mediated by Alu sequences in the human genome, evolutionary biologists maintain that occasionally these DNA elements will become incorporated into the 3´untranslated regions of genes and regions of the human genome that produce long noncoding RNAs, and, occasionally, by chance, some of the Alusequences in long noncoding RNAs will have the capacity to pair with the 3´untranslated region of specific mRNAs. When this happens, these Alu sequences trigger SMD-mediated gene regulation. And if this gene regulation has any advantage, it will persist so that over time, some Alu sequences will eventually evolve to assume a role in SMD-mediated gene regulation.

Is Neofunctionalization the Best Explanation for SINE Function?

At some level, this evolutionary scenario seems reasonable (the concerns expressed by Carl Schmid notwithstanding). Still, neofunctionalization events should be relatively rare. And because of the chance nature of neofunctionalization, it would be rational to think that the central role SINE sequences play in SMD gene regulation would be unique to humans.

Why would I make this claim? Based on the nature of evolutionary mechanisms, chance should govern biological and biochemical evolution at its most fundamental level (assuming it occurs). Evolutionary pathways consist of a historical sequence of chance genetic changes operated on by natural selection, which also 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.

The concept of historical contingency embodies this idea and is the theme of Stephen Jay Gould’s book Wonderful Life. According to Gould,

“No finale can be specified at the start, none would ever occur a second time in the same way, because any pathway proceeds through thousands of improbable stages. Alter any early event, ever so slightly, and without apparent importance at the time, and evolution cascades into a radically different channel.”4

To help clarify the concept of historical contingency, Gould used the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and let the tape run again, the results would be completely different each time. The very essence of the evolutionary process renders evolutionary outcomes nonrepeatable.

Gould’s perspective of the evolutionary process has been affirmed by other researchers who have produced data, indicating that if evolutionary processes explain the origin of biochemical systems, they must be historically contingent.

Did SMD Evolve Twice?

Yet, collaborators from UC Santa Cruz and the University of Rochester discovered that SINE-mediated SMD appears to have evolved independently—two separate times—in humans and mice, the second impossible thing evolutionary biologists have to believe.

Though rodents don’t possess Alu sequences, they do possess several other SINE elements, labeled B1, B2, B4, and ID. Remarkably, these B/ID sequences occur in regions of the mouse genome corresponding to regions of the human-harboring Alu sequences. And, when the B/ID sequences are associated with the 3´untranslated regions of genes, the mRNA produced from these genes is down-regulated, suggesting that these genes are under the influence of the SMD-mediated pathway—an unexpected result.

But, this finding is not nearly as astonishing as something else the research team discovered. By comparing about 1,200 human-mouse gene pairs in myoblasts, the researchers discovered 24 genes in this cell type that were identical in the human and mouse genomes. These identical genes performed the same physiological role and possessed SINE elements (Alu and B/ID, respectively) and were regulated by the SMD mechanism.

Evolutionary biologists believe that Alu and B/ID SINE sequences emerged independently in the rodent and human lineages. If so, this means that the evolutionary processes must have independently produced the identical outcome—SINE-mediated SMD gene regulation—24 separate times for each of the 24 identical genes. As the researchers point out, chance alone cannot explain their findings. Yet, evolutionary mechanisms are historically contingent and should not yield identical outcomes. This impossible scenario causes me to question if neofunctionalization is the explanation for functional SINE DNA.

And yet, this is not the first time that life scientists have discovered the independent emergence of identical function for junk DNA sequences.

So, which is the better explanation for functional junk DNA sequences: neofunctionalization through historically contingent evolutionary processes or the work of a Mind?

As Alice emphatically complained, “One can’t believe impossible things.”

Resources

Endnotes

  1. Brownyn A. Lucas et al., “Evidence for Convergent Evolution of SINE-Directed Staufen-Mediated mRNA Decay,” Proceedings of the National Academy of Sciences, USA Early Edition (January 2018): doi:10.1073/pnas.1715531115.
  2. Reyad A. Elbarbary et al., “Retrotransposons as Regulators of Gene Function,” Science 351 (February 12, 2016): doi:10.1126/science.aac7247.
  3. Carl W. Schmid, “Does SINE Evolution Preclude Alu Function?” Nucleic Acid Research 26 (October 1998): 4541–50, doi:10.1093/nar/26.20.4541.
  4. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W. W. Norton & Company, 1989), 51.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/03/14/believing-impossible-things-convergent-origins-of-functional-junk-dna-sequences

Like a Fish Out of Water: Why I’m Skeptical of the Evolutionary Paradigm

likeafishoutofwater

BY FAZALE RANA – JULY 27, 2016

I am skeptical that evolutionary processes can fully account for life’s origin, history, and design—and that often makes me feel like a fish out of water.

“Mainstream” scientists view biological evolution as the organizing principle in biology. In fact, Russian geneticist Theodosius Dobzhansky famously wrote, “Nothing in biology makes sense except in the light of evolution.”1 So, when I question evolutionary explanations, I become an outsider. I am outside the fish bowl, looking in. Because I’m a biochemist, my critics accuse me of being either dishonest or incompetent. Why else would I question the “fact” of evolution in the face of the overwhelming evidence for common descent? They claim that theological—not scientific motivations fuel my skepticism.

I would partially agree with that assessment. I find it hard to square certain features of the evolutionary framework with some of Christianity’s most important biblical and theological ideas. But, I also think that there are some very real scientific problems associated with the evolutionary paradigm. The deficiencies are best exposed by failed predictions.

From my perspective, the unpredicted pervasiveness of convergence justifies skepticism about evolution’s capacity to fully account for the history and diversity of life on Earth. Convergence stands as a failed prediction.

Convergence

One of evolution’s failed predictions relates to the phenomenon known as convergence. This concept describes instances in which unrelated organisms possess nearly identical anatomical and physiological characteristics. Presumably, evolutionary pathways independently produced these identical (or near identical) features. Yet convergence doesn’t make much sense from an evolutionary perspective. Indeed, if evolution is responsible for the diversity of life, one would expect convergence to be extremely rare. As a I wrote in a previous blog post, the mechanism that drives the evolutionary process consists of an extended sequence of unpredictable, chance events. Given this mechanism, it seems improbable that disparate evolutionary pathways would ever lead to the same biological feature. To put it another way, examples of convergence should be rare.

The concept of historical contingency embodies the notion that evolution should be nonrepeatable, and is the theme of Stephen Jay Gould’s book Wonderful Life.2 To help clarify the concept of historical contingency, Gould used the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time.

Yet, biological convergence is widespread.3 Recently, researchers from the University of New South Wales (in Australia) added to the examples of convergence at an organismal level. From an evolutionary perspective, they showed that amphibious behavior in fish evolved 33 separate times among extant groups! In fact, in one family, fish adopted a terrestrial life style between 3 to 7 times.

This result was unexpected. One of the researchers involved with the study stated, “Because of the challenges fish face in being able to breathe and move and reproduce on land, it had been thought this was a rare occurrence.”4

Recently, another team of investigators from the University of Kansas identified another example of biochemical convergence. They showed that venom evolved, separately and independently, 18 times in fish that live in freshwater and marine environments. This result is all the more surprising because—as William Leo Smith, one of the study’s authors points out— “fish venoms are often super complicated, big molecules.”5

Does the Widespread Occurrence of Convergence Falsify Evolution?

From my perspective, the unpredicted pervasiveness of convergence justifies skepticism about evolution’s capacity to fully account for the history and diversity of life on Earth. It stands as a failed prediction. Yet many evolutionary biologists don’t see it that way. For example, the scientists from the University of New South Wales responded to their unexpected find this way: “Now we have shown this initial transition to land is quite common, it seems these challenges can be readily overcome.”6 However, their interpretation entails circular reasoning. Biologists thought that fish moving to land would be difficult given the immense challenges associated with this transition. But, when it was found to be a frequent occurrence, then they conclude it must be easy. But they have no reason to think it must be easy other than the widespread occurrence of this transition. I would contend that this circular reasoning reflects a deep-seated, a priori commitment to the evolutionary paradigm, in which evolution is accepted as fact, and no evidence can ever count against it.

Convergence and the Case for Intelligent Design

Though the idea of convergence fits awkwardly within the evolutionary framework, it makes perfect sense if a Creator is responsible for life. Instead of convergent features emerging through repeated evolutionary outcomes, they could be understood as reflecting the work of a Divine mind. 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.

Resources
The Cell’s Design (book)

Endnotes
  1. Theodosius Dobzhansky, “Nothing in Biology Makes Sense Except in the Light of Evolution,” American Biology Teacher 35 (March 1971): 125–29.
  2. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W.W. Norton & Company, 1990).
  3. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).
  4. University of New South Wales, “Fish Out of Water Are More Common Than Thought,” ScienceDaily, June 22, 2016, https://www.sciencedaily.com/releases/2016/06/160622102129.htm.
  5. University of Kansas, “Researchers Tally Huge Number of Venomous Fishes, Tout Potential for Medical Therapies,” ScienceDaily, July 5, 2016, https://www.sciencedaily.com/releases/2016/07/160705160206.htm.
  6. “Fish Out of Water,” ScienceDaily.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/07/27/like-a-fish-out-of-water-why-i’m-skeptical-of-the-evolutionary-paradigm

Historical Contingency and the Improbability of Protein Evolution, Part 2 (of 2)

historicalcontingencyandtheimprobability

BY FAZALE RANA – JULY 20, 2016

A few weeks ago, Kathy Emmons of WORD FM in Pittsburg interviewed me about the connection between human evolution and human trafficking. During the interview, she asked me if theological or scientific concerns drove my skepticism about human evolution. My answer is both.

I find it difficult to reconcile the idea of human evolution with passages in the Old and New Testaments that address human origins. But, I also think that there are significant scientific problems confronting the evolutionary paradigm. A recent study by scientists from the Universities of Oregon and Chicago highlights one of those scientific challenges.1

As described in a previous post, these researchers wanted to develop a better understanding of the role that chance historical events play in evolutionary processes. To do this, they reconstructed what they believe to be the evolutionary pathway that led to the emergence of the cortisol-specific glucocorticoid receptor protein, a key component of the vertebrate endocrine system. Based on their reconstruction, it appears that seven amino acid changes transformed the ancestral receptor protein into one that exclusively binds cortisol. They determined that two of the changes were permissive. That is, these changes do not contribute to the binding specificity of the glucocorticoid receptor, but must occur before any of the functional changes took place. Based on their analysis, it appears that the permissive changes were highly improbable, leading the researchers to conclude that historical contingency plays a central role in evolutionary transformations.

According to the researchers:

“If evolutionary history could be replayed from the ancestral starting point, the same kind of permissive substitutions would be unlikely to occur. The transition to GR’s [glucocorticoid receptor’s] present form and function would likely be inaccessible, and different outcomes would almost certainly ensue. Cortisol-specific signaling might evolve by a different mechanism in the GR . . . or the vertebrate endocrine system more generally—would be substantially different.”2

Historical Contingency

The concept of historical contingency is the theme of the late Stephen Jay Gould’s book Wonderful Life.3 According to this idea, the evolutionary process consists of an extended sequence of unpredictable, chance events. To help clarify this concept, Gould used the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time.

Gould envisioned historical contingency as primarily resulting from external events (such as climate change or asteroid impacts). But this latest work indicates that the intrinsic complexity of proteins also contributes to historical contingency, because of the necessity and low probability of of permissive amino acid substitutions that support functional changes.

How Widespread Is Historical Contingency?

The question then becomes: How widely applicable is this result? The research team from the Universities of Oregon and Chicago expressed uncertainty regarding this point, but other studies indicate that historical contingency must play a prominent role in molecular evolution.

For example, the long-term evolution experiment conducted by Richard Lenski’s group at Michigan State University demonstrated that the emergence of citrate metabolism in E. coliunder aerobic conditions was historically contingent, predicated on a sequence of chance molecular events. (For more information, see the articles listed under “Resources.”)

Using simulations to monitor the evolution of a protein dubbed argT, researchers from the University of Pennsylvania showed that genetic mutations selected by the evolutionary process are dependent on previous mutations, and over time it becomes increasingly difficult to reverse mutational transformations.4 In other words, an amino acid substitution that occurs in a protein today and is accepted by the evolutionary process would most likely be deleterious if it occurred in the past (because of the central role permissive substitutions play in evolutionary history). Consequently, this mutational change would be selected against by the evolutionary process. One of the researchers involved in this study, Joshua Plotkin, stated,

“There is intrinsically a huge amount of contingency in evolution. Whatever mutations happen to come first set the stage for what other later mutations are permissible. Indeed, history channels evolution down a certain path. Gould’s famous tape of life would be very different if replayed, even more different than Gould might have imagined.”5

A Failed Prediction of the Evolutionary Paradigm

Because the evolutionary process is historically contingent, it seems unlikely that evolutionary processes would lead to identical or nearly identical outcomes. Yet, when viewed from an evolutionary standpoint, it appears as if repeated evolutionary outcomes have been a common occurrence throughout life’s history. This phenomenon—referred to as convergence—is widespread. Evolutionary biologists Simon Conway Morris and George McGhee point out in their respective books Life’s Solution and Convergent Evolution, that identical evolutionary outcomes are a characteristic feature of the biological realm.6 Scientists see these repeated outcomes at the ecological, organismal, biochemical, and genetic levels. In fact, in my book The Cell’s Design, I describe 100 examples of convergence at the biochemical level.

I regard the widespread occurrence of convergence to one of evolution’s failed predictions, and, as I told Kathy Emmons, a justifiable reason to be skeptical of the claim that evolutionary processes can fully explain the history, diversity, and design of life.

In an upcoming blog post, I will further explore the challenge convergence poses for the evolutionary paradigm.

Stay tuned… (or set your tape player to “record.”)

 

Resources

Endnotes

  1. Michael Harms and Joseph Thornton, “Historical Contingency and Its Biophysical Basis in Glucocorticoid Receptor Evolution,” Nature 512 (August 2014): 203–07, doi:10.1038/nature13410.
  2. Ibid., 207.
  3. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W.W. Norton & Company, 1990).
  4. Premal Shah, David McCandlish, and Joshua Plotkin, “Contingency and Entrenchment in Protein Evolution under Purifying Selection,” Proceedings of the National Academy of Sciences, USA 112 (June 2015): E3226–E3235, doi: 10.1073/pnas.1412933112.
  5. University of Pennsylvania, “Evolution Is Unpredictable and Irreversible, Biologists Show,” ScienceDaily,June 8, 2015, sciencedaily.com/releases/2015/06/150608213032.htm.
  6. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2016/07/20/historical-contingency-and-the-improbability-of-protein-evolution-part-2-(of-2)