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

Glue Production Is Not Evidence for Neanderthal Exceptionalism

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By Fazale Rana – November 6, 2019

Football players aren’t dumb jocks—though they often have that reputation. Football is a physically demanding sport that requires strength, toughness, agility, and speed. But it is also an intellectually demanding game.

Mastering a playbook, understanding which plays work best for the various in-game scenarios, recognizing defenses and offenses, and adjusting on the fly require hours of study and preparation. Football really is a thinking person’s game.

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Figure 1: Quarterback Calling an Audible at the Line of Scrimmage. Image Credit: Shutterstock

Some anthropologists view Neanderthals in the same way that many people view football players: as the “dumb jock” version of a hominin, a creature cognitively inferior to modern humans. Yet, other anthropologists dispute this characterization, arguing that it is undeserved. Instead, they claim that Neanderthals had cognitive capabilities on par with modern humans.

In support of their claim, these scientists point to finds in the archaeological record that seemingly suggest these hominins were exceptional, just like modern humans. As a case in point, archaeologists have unearthed evidence for tar production at a site in Italy that dates to around 200,000 years in age. They interpret this discovery as evidence that Neanderthals were using tar as glue for hafting (fixing) flint spearheads to wooden spear shafts.1 Archaeologists have also unearthed spearheads with tar residue from two sites in Germany, one dating to 120,000 years in age and the other between 40,000 to 80,000 years.2 Because these dates precede the arrival of modern humans into Europe, anthropologists assume the tar at these sites was deliberately produced and used by Neanderthals.

Adhesives as a Signature for Superior Cognition

Anthropologists consider the development of adhesives as a transformative technology. These materials would have provided the first humans the means to construct new types of complex devices and combine different types of materials (composites) into new technologies. Because of this new proficiency, anthropologists consider the production and use of adhesives to be diagnostic of advanced cognitive capabilities such as forward planning, abstraction, and understanding of materials.

Production of adhesives from natural sources, even by the earliest modern humans, appears to have been a complex operation that required precise temperature control and the use of earthen mounds, or ceramic or metal kilns. In addition, birch bark needed to be heated in the absence of oxygen. Because the first large-scale production of adhesives usually centered around the dry distillation of birch and pine barks to produce tar and pitch, researchers have assumed that this technique is the only way to generate tar.

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Figure 2: Tar Produced from Birch Bark. Image credit: Wikipedia

So, if Neanderthals were using tar as an adhesive, the reasoning goes, they must have been pretty impressive creatures.

In the summer of 2017 researchers from the University of Leiden published work that seemed to support this view.3 To address the question of how Neanderthals may have produced adhesives, these investigators conducted a series of experiments. They sought to learn how Neanderthals used the resources most reasonably available to them to obtain tar from birch bark through dry distillation.

By studying a variety of methods for dry distillation of tar from birch in a laboratory setting, the research team concluded that Neanderthals could have produced tar from birch bark if they had used methods that were simple enough that they wouldn’t require precise temperature control during the distillation. Still, these methods are complex enough that the researchers concluded that for Neanderthals to pull off this feat, they must have had advanced cognitive abilities similar to those of modern humans.

Is Adhesive Production and Use Evidence for Neanderthal Exceptionalism?

At the time this work was reported, I challenged this conclusion by noting that the simplicity of these production methods argued against advanced cognitive abilities in Neanderthals, not for them.

Recent work by researchers from Germany affirms my skepticism. Their research challenges the view that adhesive production and use constitutes evidence for human exceptionalism.4 The team wondered if a simpler way to produce tar—even simpler than the methods identified by the research team from the University of Leiden— exists. They also wondered if it was possible to produce tar in the presence of oxygen.

From their work, they discovered that burning birch bark (or branches from a birch tree with the bark still attached) adjacent to a rock with a vertical or subvertical surface is a way to collect tar, which naturally deposits on the rock surface as the bark burns. In other words, tar can be produced accidentally, instead of deliberately. And once produced, it can be scraped from the rock surface.

Using analytical techniques (gas chromatography coupled to mass spectrometry) to characterize the chemical makeup of the tar produced by this simple method, the research team showed that it is comparable to the chemical composition of tars produced by sophisticated dry distillation methods under anaerobic conditions. Because of the simplicity of this method, the research team thinks that collecting tar deposits from burning birch on rocks is the most likely way that Neanderthals produced tar, if they intentionally produced it at all.

According to the research team, “The identification of birch tar at archaeological sites can no longer be considered as a proxy for human (complex, cultural) behavior as previously assumed. In other words, our finding changes textbook thinking about what tar production is a smoking gun of.”5

One other point merits consideration: A growing body of evidence indicates that Neanderthals did not master fire, but rather used it opportunistically. In other words, these creatures could not create fire, but did harvest wildfires. Evidence demonstrates that there were vast periods of time during Neanderthals’ tenure in Europe when wildfires were rare because of cold climatic conditions. During these periods, Neanderthals didn’t use fire.

Because fire is central to the dry distillation methods, for a significant portion of their time on Earth Neanderthals would have been unable to extract tar and use it for hafting. Perhaps this factor explains why recovery of tar from Neanderthal sites is so rare. And could it be that Neanderthals were not intentionally producing tar? Instead, did tar just happen to collect on rock surfaces as a consequence of burning birch branches when these creatures were able to harvest fire?

What Difference Does It Make?

One of the most important ideas taught in Scripture is that human beings uniquely bear God’s image. As such, every human being has immeasurable worth and value. And because we bear God’s image, we can enter into a relationship with our Maker.

However, if Neanderthals possessed advanced cognitive ability just like that of modern humans, then it becomes difficult to maintain the view that modern humans are unique and exceptional. If human beings aren’t exceptional, then it becomes a challenge to defend the idea that human beings are made in God’s image.

Yet, claims that Neanderthals are cognitive equals to modern humans fail to withstand scientific scrutiny, time and time again, as this latest study demonstrates. It is unlikely that any of us will see a Neanderthal run onto the football field anytime soon.

Resources

Neanderthals Did Not Master Fire

Differences in Human and Neanderthal Brains

Endnotes
  1. Paul Peter Anthony Mazza et al., “A New Palaeolithic Discovery: Tar-Hafted Stone Tools in a European Mid-Pleistocene Bone-Bearing Bed,” Journal of Archaeological Science 33, no. 9 (September 2006): 1310–18, doi:10.1016/j.jas.2006.01.006.
  2. Johann Koller, Ursula Baumer, and Dietrich Mania, “High-Tech in the Middle Palaeolithic: Neandertal-Manufactured Pitch Identified,” European Journal of Archaeology 4, no. 3 (December 1, 2001): 385–97, doi:10.1179/eja.2001.4.3.385; Alfred F. Pawlik and Jürgen P. Thissen, “Hafted Armatures and Multi-Component Tool Design at the Micoquian Site of Inden-Altdorf, Germany,” Journal of Archaeological Science 38, no. 7 (July 2011): 1699–1708, doi:10.1016/j.jas.2011.03.001.
  3. P. R. B. Kozowyk et al., “Experimental Methods for the Palaeolithic Dry Distillation of Birch Bark: Implications for the Origin and Development of Neandertal Adhesive Technology,” Scientific Reports 7 (August 31, 2017): 8033, doi:10.1038/s41598-017-08106-7.
  4. Patrick Schmidt et al., “Birch Tar Production Does Not Prove Neanderthal Behavioral Complexity,” Proceedings of the National Academy of Sciences, USA 116, no. 36 (September 3, 2019): 17707–11, doi:10.1073/pnas.1911137116.
  5. Schmidt et al., “Birch Tar Production.”

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

Scientists Reverse the Aging Process: Exploring the Theological Implications

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By Fazale Rana – October 30, 2019

During those days people will seek death but will not find it; they will long to die, but death will elude them.

Revelation 9:6

I make dad noises now.

When I sit down, when I stand up, when I get out of bed, when I get into bed, when I bend over to pick up something from the ground, and when I straighten up again, I find myself involuntarily making noises—grunting sounds.

I guess it is all part of the aging process. My body isn’t quite what it used to be. If someone offered me an elixir that could turn back time and reverse the aging process, I would take it without hesitation. It’s no fun growing old.

Well, I just might get my wish, thanks to the work of a research team from the US and Canada. These researchers demonstrated that they could disrupt the aging process and, in fact, reverse the biological clock in humans.1

This advance is nothing short of stunning. It opens up exciting—and disquieting—biomedical possibilities rife with ethical and theological ramifications. The work has other interesting implications, as well. It can be marshaled to demonstrate the scientific credibility of the Old Testament by making scientific sense of the long life spans of the patriarchs listed in the Genesis 5 and 11 genealogies.

Some Biological Consequences of Aging

Involuntary grunting is not the worse part of aging, by far. There are other more serious consequences, such as loss of immune function. Senescence (aging) of the immune system can contribute to the onset of cancer and increased susceptibility to pathogens. It can also lead to wide-scale inflammation. None of these are good.

As we age, our thymus decreases in size. And this size reduction hampers immune system function. Situated between the heart and sternum, the thymus plays a role in maturation of white blood cells, key components of the immune system. As the thymus shrinks with age, the immune system loses its capacity to generate sufficient levels of white blood cells, rendering older adults vulnerable to infections and cancers.

A Strategy to Improve Immune Function

Previous studies in laboratory animals have shown that administering growth hormone enlarges the thymus and, consequently, improves immune function. The research team reasoned that the same effect would be seen in human patients. But due to at least one of its negative side effects, the team couldn’t simply administer growth hormone without other considerations. Growth hormone lowers insulin levels and leads to a form of type 2 diabetes. To prevent this adverse effect, the researchers also administered two drugs commonly used to treat type 2 diabetes.

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Figure 1: The Structure of Human Growth Hormone. Image credit: Shutterstock

To test this idea, the researchers performed a small-scale clinical trial. The study began with ten men (finishing with nine) between the ages of 51 and 65. The volunteers self-administered the drug cocktail three to four times a week for a year. During the course of the study, the researchers monitored white blood cell levels and thymus size. They observed a rejuvenation of the immune system (based on the count of white blood cells in the blood). They also noticed changes in the thymus, with fatty deposits disappearing and thymus tissue returning.

Reversing the Aging Process

As an afterthought, the researchers decided to test the patient’s blood using an epigenetic clock that measures biological age. To their surprise, the researchers discovered that the drug cocktail reversed the biological age of the study participants by two years, compared to their chronological age. In other words, even though the patients gained one year in their chronological age during the course of the study, their bodies became younger, based on biological markers, by two years. This age reversal lasted for six months after the trial ended.

Thus, for the first time ever, researchers have been able to extend human life expectancy through an aging-intervention therapy. And while the increase in life expectancy was limited, this accomplishment serves as a harbinger of things to come, making the prospects of dramatically extending human life expectancy significantly closer to a reality.

This groundbreaking work carries significant biomedical, ethical, and theological implications, which I will address below. But the breakthrough is equally fascinating to me because it can be used to garner scientific support for Genesis 5 and 11.

Anti-Aging Technology and Biblical Long Life Spans

The mere assertion that humans could live for hundreds of years as described in the genealogies of Genesis 5 and 11 is, for many people, nothing short of absurd. Compounding this seeming absurdity is the claim in Genesis 6:3, which describes God intervening to shorten human life spans from about 900 to about 120 years. How can this dramatic change in human life spans be scientifically rational?

As I discuss in Who Was Adam?, advances in the biochemistry of aging provide a response to these challenging questions. Scientists have uncovered several distinct biochemical mechanisms that either cause, or are associated with, senescence. Even subtle changes in cellular chemistry can increase life expectancy by nearly 50 percent. These discoveries point to several possible ways that God could have allowed long life spans and then altered human life expectancy—simply by “tweaking” human biochemistry.

Thanks to these advances, biogerontologists have become confident that in the near future, they will be able to interrupt the aging process by direct intervention through altered diet, drug treatment, and gene manipulation. Some biogerontologists such as Aubrey de Grey don’t think it is out of the realm of possibility to extend human life expectancy to several hundred years—about the length of time the Bible claims that the patriarchs lived. The recent study by the US and Canadian investigators seems to validate de Grey’s view.

So, if biogerontologists can alter life spans—maybe someday on the order of hundreds of years—then the Genesis 5 and 11 genealogies no longer appear to be fantastical. And, if we can intervene in our own biology to alter life spans, how much easier must it be for God to do so?

Ethical Concerns

As mentioned, I would be tempted to take an anti-aging elixir if I knew it would work. And so would many others. What could possibly be wrong with wanting to live a longer, healthier, and more productive life? In fact, disrupting—and even reversing—the aging process would offer benefits to society by potentially reducing medical costs associated with age-related diseases such as dementia, cancer, heart disease, and stroke.

Yet, these biomedical advances in anti-aging therapies do hold the potential to change who we are as human beings. Even a brief moment of reflection makes it plain that wide-scale use of anti-aging treatments could bring about fundamental changes to economies, to society, and to families and put demands on limited planetary resources. In the end, anti-aging technologies may well be unsustainable, undesirable, and unwise. (For a more detailed discussion of the ethical issues surrounding anti-aging technology check out the book I cowrote with Kenneth Samples, Humans 2.0.)

Anti-Aging Therapies and Transhumanism

Many people rightly recognize the ethical concerns surrounding applications of anti-aging therapies, but a growing number see these technologies in a different light. They view them as paving the way to an exciting and hopeful future. The increasingly real prospects of extending human life expectancy by disrupting the aging process or even reversing the effects of aging are the types of advances (along with breakthroughs in CRISPR gene editing and computer-brain interfaces) that fuel an intellectual movement called transhumanism.

This idea has long been on the fringes of respected academic thought, but recently transhumanism has propelled its way into the scientific, philosophical, and cultural mainstreams. Advocates of the transhumanist vision maintain that humanity has an obligation to use advances in biotechnology and bioengineering to correct our biological flaws—to augment our physical, intellectual, and psychological capabilities beyond our natural limits. Perhaps there are no greater biological limitations that human beings experience than those caused by aging bodies and the diseases associated with the aging process.

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Figure 2: Transhumanism. Image credit: Shutterstock

Transhumanists see science and technology as the means to alleviate pain and suffering and to promote human flourishing. They note, in the case of aging, the pain, suffering, and loss associated with senescence in human beings. But the biotechnology we need to fulfill the transhumanist vision is now within grasp.

Anti-Aging as a Source of Hope and Salvation?

Using science and technology to mitigate pain and suffering and to drive human progress is nothing new. But transhumanists desire more. They advocate that we should use advances in biotechnology and bioengineering for the self-directed evolution of our species. They seek to fulfill the grand vision of creating new and improved versions of human beings and ushering in a posthuman future. In effect, transhumanists desire to create a utopia of our own design.

In fact, many transhumanists go one step further, arguing that advances in gene editing, computer-brain interfaces, and anti-aging technologies could extend our life expectancy, perhaps even indefinitely, and allow us to attain a practical immortality. In this way, transhumanism displays its religious element. Here science and technology serve as the means for salvation.

Transhumanism: a False Gospel?

But can transhumanism truly deliver on its promises of a utopian future and practical immortality?

In Humans 2.0, Kenneth Samples and I delineate a number of reasons why transhumanism is a false gospel, destined to disappoint, not fulfill, our desire for immortality and utopia. I won’t elaborate on those reasons here. But simply recognizing the many ethical concerns surrounding anti-aging technologies (and gene editing and computer-brain interfaces) highlights the real risks connected to pursuing a transhumanist future. If we don’t carefully consider these concerns, we might create a dystopian future, not a utopian world.

The mere risk of this type of unintended future should give us pause for thought about turning to science and technology for our salvation. As theologian Ronald Cole-Turner so aptly put it:

“We need to be aware that technology, precisely because of its beneficial power, can lead us to the erroneous notion that the only problems to which it is worth paying attention involve engineering. When we let this happen, we reduce human yearning for salvation to a mere desire for enhancement, a lesser salvation that we can control rather than the true salvation for which we must also wait.”2

Resources

Endnotes
  1. Gregory M. Fahy et al., “Reversal of Epigenetic Aging and Immunosenescent Trends in Humans,” Aging Cell (September 8, 2019): e13028, doi:10.1111/acel.13028.
  2. “Transhumanism and Christianity,” in Transhumanism and Transcendence: Christian Hope in an Age of Technological Enhancement, ed. Ronald Cole-Turner (Washington, D.C.: Georgetown University Press, 2011), 201.

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

Origin and Design of the Genetic Code: A One-Two Punch for Creation

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By Fazale Rana – October 23, 2019

So, in the spirit of the endless debates that take place on sports talk radio, I ask: What duo is the greatest one-two punch in NBA history? Is it:

  • Kareem and Magic?
  • Kobe and Shaq?
  • Michael and Scottie?

Another confession: I am a science-faith junkie. I never tire when it comes to engaging in discussions about the interplay between science and the Christian faith. From my perspective, the most interesting facet of this conversation centers around the scientific evidence for God’s existence.

So, toward this end, I ask: What is the most compelling biochemical evidence for God’s existence? Is it:

  • The complexity of biochemical systems?
  • The eerie similarity between biomolecular motors and machines designed by human engineers?
  • The information found in DNA?

Without hesitation I would say it is actually another feature: the origin and design of the genetic code.

The genetic code is a biochemical code that consists of a set of rules defining the information stored in DNA. These rules specify the sequence of amino acids used by the cell’s machinery to synthesize proteins. The genetic code makes it possible for the biochemical apparatus in the cell to convert the information formatted as nucleotide sequences in DNA into information formatted as amino acid sequences in proteins.

 

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Figure: A Depiction of the Genetic Code. Image credit: Shutterstock

In previous articles (see the Resources section), I discussed the code’s most salient feature that I think points to a Creator’s handiwork: it’s multidimensional optimization. That optimization is so extensive that evolutionary biologists struggle to account for it’s origin, as illustrated by the work of biologist Steven Massey1.

Both the optimization of the genetic code and the failure of evolutionary processes to account for its design form a potent one-two punch, evincing the work of a Creator. Optimization is a marker of design, and if it can’t be accounted for through evolutionary processes, the design must be authentic—the product of a Mind.

Can Evolutionary Processes Generate the Genetic Code?

For biochemists working to understand the origin of the genetic code, its extreme optimization means that it is not the “frozen accident” that Francis Crick proposed in a classic paper titled “On the Origin of the Genetic Code.”2

Many investigators now think that natural selection shaped the genetic code, producing its optimal properties. However, I question if natural selection could evolve a genetic code with the degree of optimality displayed in nature. In the Cell’s Design (published in 2008), I cite the work of the late biophysicist Hubert Yockey in support of my claim.3 Yockey determined that natural selection would have to explore 1.40 x 1070 different genetic codes to discover the universal genetic code found in nature. Yockey estimated 6.3 x 1015 seconds (200 million years) is the maximum time available for the code to originate. Natural selection would have to evaluate roughly 1055 codes per second to find the universal genetic code. And even if the search time was extended for the entire duration of the universe’s existence, it still would require searching through 1052 codes per second to find nature’s genetic code. Put simply, natural selection lacks the time to find the universal genetic code.

Researchers from Germany raised the same difficulty for evolution recently. Because of the genetic code’s multidimensional optimality, they concluded that “the optimality of the SGC [standard genetic code] is a robust feature and cannot be explained by any simple evolutionary hypothesis proposed so far. . . . the probability of finding the standard genetic code by chance is very low. Selection is not an omnipotent force, so this raises the question of whether a selection process could have found the SGC in the case of extreme code optimalities.”4

Two More Evolutionary Mechanisms Considered

Life scientist Massey reached a similar conclusion through a detailed analysis of two possible evolutionary mechanisms, both based on natural selection.9

If the genetic code evolved, then alternate genetic codes would have to have been generated and evaluated until the optimal genetic code found in nature was discovered. This process would require that coding assignments change. Biochemists have identified two mechanisms that could contribute to coding reassignments: (1) codon capture and (2) an ambiguous intermediate mechanism. Massey tested both mechanisms.

Massey discovered that neither mechanism can evolve the optimal genetic code. When he ran computer simulations of the evolutionary process using codon capture as a mechanism, they all ended in failure, unable to find a highly optimized genetic code. When Massey ran simulations with the ambiguous intermediate mechanism, he could evolve an optimized genetic code. But he didn’t view this result as success. He learned that it takes between 20 to 30 codon reassignments to produce a genetic code with the same degree of optimization as the genetic code found in nature.

The problem with this evolutionary mechanism is that the number of coding reassignments observed in nature is scarce based on the few deviants of the genetic code thought to have evolved since the origin of the last common ancestor. On top of this problem, the structure of the optimized codes that evolved via the ambiguous intermediate mechanism is different from the structure of the genetic code found in nature. In short, the result obtained via the ambiguous intermediate mechanism is unrealistic.

As Massey points out, “The evolution of the SGC remains to be deciphered, and constitutes one of the greatest challenges in the field of molecular evolution.”10

Making Sense of Explanatory Models

In the face of these discouraging results for the evolutionary paradigm, Massey concludes that perhaps another evolutionary force apart from natural selection shaped the genetic code. One idea Massey thinks has merit is the Coevolution Theory proposed by J. T. Wong. Wong argued that the genetic code evolved in conjunction with the evolution of biosynthetic pathways that produce amino acids. Yet, Wong’s theory doesn’t account for the extreme optimization of the genetic code in nature. And, in fact, the relationships between coding assignments and amino acid biosynthesis appear to result from a statistical artifact, and nothing more.11 In other words, Wong’s ideas don’t work.

That brings us back to the question of how to account for the genetic code’s optimization and design.

As I see it, in the same way that two NBA superstars work together to help produce a championship-caliber team, the genetic code’s optimization and the failure of every evolutionary model to account for it form a potent one-two punch that makes a case for a Creator.

And that is worth talking about.

Resources

Endnotes
  1. Steven E. Massey, “Searching of Code Space for an Error-Minimized Genetic Code via Codon Capture Leads to Failure, or Requires at Least 20 Improving Codon Reassignments via the Ambiguous Intermediate Mechanism,” Journal of Molecular Evolution 70, no. 1 (January 2010): 106–15, doi:10.1007/s00239-009-9313-7.
  2. F. H. C. Crick, “The Origin of the Genetic Code,” Journal of Molecular Biology 38, no. 3 (December 28, 1968): 367–79, doi:10.1016/0022-2836(68)90392-6.
  3. Hubert P. Yockey, Information Theory and Molecular Biology (Cambridge, UK: Cambridge University Press, 1992), 180–83.
  4. Stefan Wichmann and Zachary Ardern, “Optimality of the Standard Genetic Code Is Robust with Respect to Comparison Code Sets,” Biosystems 185 (November 2019): 104023, doi:10.1016/j.biosystems.2019.104023.
  5. Massey, “Searching of Code Space.”
  6. Massey, “Searching of Code Space.”
  7. Ramin Amirnovin, “An Analysis of the Metabolic Theory of the Origin of the Genetic Code,” Journal of Molecular Evolution 44, no. 5 (May 1997): 473–76, doi:10.1007//PL00006170.

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

New Insights into Genetic Code Optimization Signal Creator’s Handiwork

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By Fazale Rana – October 16, 2019

I knew my career as a baseball player would be short-lived when, as a thirteen-year-old, I made the transition from Little League to the Babe Ruth League, which uses official Major League Baseball rules. Suddenly there were a whole lot more rules for me to follow than I ever had to think about in Little League.

Unlike in Little League, at the Babe Ruth level the hitter and base runners have to know what the other is going to do. Usually, the third-base coach is responsible for this communication. Before each pitch is thrown, the third-base coach uses a series of hand signs to relay instructions to the hitter and base runners.

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Credit: Shutterstock

My inability to pick up the signs from the third-base coach was a harbinger for my doomed baseball career. I did okay when I was on base, but I struggled to pick up his signs when I was at bat.

The issue wasn’t that there were too many signs for me to memorize. I struggled recognizing the indicator sign.

To prevent the opposing team from stealing the signs, it is common for the third-base coach to use an indicator sign. Each time he relays instructions, the coach randomly runs through a series of signs. At some point in the sequence, the coach gives the indicator sign. When he does that, it means that the next signal is the actual sign.

All of this activity was simply too much for me to process. When I was at the plate, I couldn’t consistently keep up with the third-base coach. It got so bad that a couple of times the third-base coach had to call time-out and have me walk up the third-base line, so he could whisper to me what I was to do when I was at the plate. It was a bit humiliating.

Codes Come from Intelligent Agents

The signs relayed by a third-base coach to the hitter and base runners are a type of code—a set of rules used to convert and convey information across formats.

Experience teaches us that it takes intelligent agents, such as baseball coaches, to devise codes, even those that are rather basic in their design. The more sophisticated a code, the greater the level of ingenuity required to develop it.

Perhaps the most sophisticated codes of all are those that can detect errors during data transmission.

I sure could have used a code like that when I played baseball. It would have helped me if the hand signals used by the third-base coach were designed in such a way that I could always understand what he wanted, even if I failed to properly pick up the indicator signal.

The Genetic Code

As it turns out, just such a code exists in nature. It is one of the most sophisticated codes known to us—far more sophisticated than the best codes designed by the brightest computer engineers in the world. In fact, this code resides at the heart of biochemical systems. It is the genetic code.

This biochemical code consists of a set of rules that define the information stored in DNA. These rules specify the sequence of amino acids that the cell’s machinery uses to build proteins. In this process, information formatted as nucleotide sequences in DNA is converted into information formatted as amino acid sequences in proteins.

Moreover, the genetic code is universal, meaning that all life on Earth uses it.1

Biochemists marvel at the design of the genetic code, in part because its structure displays exquisite optimization. This optimization includes the capacity to dramatically curtail errors that result from mutations.

Recently, a team from Germany identified another facet of the genetic code that is highly optimized, further highlighting its remarkable qualities.2

The Optimal Genetic Code

As I describe in The Cell’s Design, scientists from Princeton University and the University of Bath (UK) quantified the error-minimization capacity of the genetic code during the 1990s. Their work indicated that the universal genetic code is optimized to withstand the potentially harmful effects of substitution mutations better than virtually any other conceivable genetic code.3

In 2018, another team of researchers from Germany demonstrated that the universal genetic code is also optimized to withstand the harmful effects of frameshift mutations—again, better than other conceivable codes.4

In 2007, researchers from Israel showed that the genetic code is also optimized to harbor overlapping codes.5 This is important because, in addition to the genetic code, regions of DNA harbor other overlapping codes that direct the binding of histone proteins, transcription factors, and the machinery that splices genes after they have been transcribed.

The Robust Optimality of the Genetic Code

With these previous studies serving as a backdrop, the German research team wanted to probe more deeply into the genetic code’s optimality. These researchers focused on potential optimality of three properties of the genetic code: (1) resistance to harmful effects of substitution mutations, (2) resistance to harmful effects of frameshift mutations, and (3) capacity to support overlapping genes.

As with earlier studies, the team assessed the optimality of the naturally occurring genetic code by comparing its performance with sets of random codes that are conceivable alternatives. For all three property comparisons, they discovered that the natural (or standard) genetic code (SGC) displays a high degree of optimality. The researchers write, “We find that the SGC’s optimality is very robust, as no code set with no optimised properties is found. We therefore conclude that the optimality of the SGC is a robust feature across all evolutionary hypotheses.”6

On top of this insight, the research team adds one other dimension to multidimensional optimality of the genetic code: its capacity to support overlapping genes.

Interestingly, the researchers also note that the results of their work raise significant challenges to evolutionary explanations for the genetic code, pointing to the code’s multidimensional optimality that is extreme in all dimensions. They write:

We conclude that the optimality of the SGC is a robust feature and cannot be explained by any simple evolutionary hypothesis proposed so far. . . . the probability of finding the standard genetic code by chance is very low. Selection is not an omnipotent force, so this raises the question of whether a selection process could have found the SGC in the case of extreme code optimalities.7

While natural selection isn’t omnipotent, a transcendent Creator would be, and could account for the genetic code’s extreme optimality.

The Genetic Code and the Case for a Creator

In The Cell’s Design, I point out that our common experience teaches us that codes come from minds. It’s true on the baseball diamond and true in the computer lab. By analogy, the mere existence of the genetic code suggests that biochemical systems come from a Mind—a conclusion that gains additional support when we consider the code’s sophistication and exquisite optimization.

The genetic code’s ability to withstand errors that arise from substitution and frameshift mutations, along with its optimal capacity to harbor multiple overlapping codes and overlapping genes, seems to defy naturalistic explanation.

As a neophyte playing baseball, I could barely manage the simple code the third-base coach used. How mind-boggling it is for me when I think of the vastly superior ingenuity and sophistication of the universal genetic code.

And, just like the hitter and base runner work together to produce runs in baseball, the elegant design of the genetic code and the inability of evolutionary processes to account for its extreme multidimensional optimization combine to make the case that a Creator played a role in the origin and design of biochemical systems.

With respect to the case for a Creator, the insight from the German research team hits it out of the park.

Resources:

Endnotes
  1. Some organisms have a genetic code that deviates from the universal code in one or two of the coding assignments. Presumably, these deviant codes originate when the universal genetic code evolves, altering coding assignments.
  2. Stefan Wichmann and Zachery Ardern, “Optimality of the Standard Genetic Code Is Robust with Respect to Comparison Code Sets,” Biosystems 185 (November 2019): 104023, doi:10.1016/j.biosystems.2019.104023.
  3. David Haig and Laurence D. Hurst, “A Quantitative Measure of Error Minimization in the Genetic Code,” Journal of Molecular Evolution 33, no. 5 (November 1991): 412–17, doi:1007/BF02103132; Gretchen Vogel, “Tracking the History of the Genetic Code,” Science 281, no. 5375 (July 17, 1998): 329–31, doi:1126/science.281.5375.329; Stephen J. Freeland and Laurence D. Hurst, “The Genetic Code Is One in a Million,” Journal of Molecular Evolution 47, no. 3 (September 1998): 238–48, doi:10.1007/PL00006381; Stephen J. Freeland et al., “Early Fixation of an Optimal Genetic Code,” Molecular Biology and Evolution 17, no. 4 (April 2000): 511–18, 10.1093/oxfordjournals.molbev.a026331.
  4. Regine Geyer and Amir Madany Mamlouk, “On the Efficiency of the Genetic Code after Frameshift Mutations,” PeerJ 6 (May 21, 2018): e4825, doi:10.7717/peerj.4825.
  5. Shalev Itzkovitz and Uri Alon, “The Genetic Code Is Nearly Optimal for Allowing Additional Information within Protein-Coding Sequences,” Genome Research 17, no. 4 (April 2007): 405–12, doi:10.1101/gr.5987307.
  6. Wichmann and Ardern, “Optimality.”
  7. Wichmann and Ardern, “Optimality.”

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

Is the Optimal Set of Protein Amino Acids Purposed by a Mind?

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By Fazale Rana – October 9, 2019

To get our assays to work properly, we had to carefully design and optimize each test before executing it with exacting precision in the laboratory. Optimizing these assays was no easy feat. It could take weeks of painstaking effort to get the protocols just right.

My experiences working in the lab taught me some important lessons that I carry with me today as a Christian apologist. One of these lessons has to do with optimization. Optimized systems don’t just happen, whether they are laboratory procedures, manufacturing operations, or well-designed objects or devices. Instead, optimization results from the insights and efforts of intelligent agents, and therefore serves as a sure indicator of intelligent design.

As it turns out, nearly every biochemical system appears to be highly optimized. For me, this fact indicates that life stems from a Mind. And as life scientists continue to characterize biochemical systems, they keep discovering more and more examples of biochemical optimization, as recent work by a large team of collaborators working at the Earth-Life Science Institute (ELSI) in Tokyo, Japan, illustrates.1

These researchers uncovered more evidence that the twenty amino acids encoded by the genetic code possess the optimal set of physicochemical properties. If not for these properties, it would not be possible for the cell to build proteins that could support the wide range of activities required to sustain living systems. This insight gives us important perspective into the structure-function relationships of proteins. It also has theological significance, adding to the biochemical case for a Creator.

Before describing the ELSI team’s work and its theological implications, a little background might be helpful for some readers. For those who are familiar with basic biochemistry, just skip ahead to Why These Twenty Amino Acids?

Background: Protein Structure

Proteins are large, complex molecules that play a key role in virtually all of the cell’s operations. Biochemists have long known that the three-dimensional structure of a protein dictates its function. Because proteins are such large, complex molecules, biochemists categorize protein structure into four different levels: primary, secondary, tertiary, and quaternary structures.

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Figure 1: The Four Levels of Protein Structure. Image credit: Shutterstock

  • A protein’s primary structure is the linear sequence of amino acids that make up each of its polypeptide chains.
  • The secondary structure refers to short-range three-dimensional arrangements of the polypeptide chain’s backbone arising from the interactions between chemical groups that make up its backbone. Three of the most common secondary structures are the random coil, alpha (α) helix, and beta (β) pleated sheet.
  • Tertiary structure describes the overall shape of the entire polypeptide chain and the location of each of its atoms in three-dimensional space. The structure and spatial orientation of the chemical groups that extend from the protein backbone are also part of the tertiary structure.
  • Quaternary structure arises when several individual polypeptide chains interact to form a functional protein complex.

Background: Amino Acids

The building blocks of proteins are amino acids. These compounds are characterized by having both an amino group and a carboxylic acid bound to a central carbon atom. Also bound to this carbon are a hydrogen atom and a substituent that biochemists call an R group.

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Figure 2: The Structure of a Typical Amino Acid. Image credit: Shutterstock

The R group determines the amino acid’s identity. For example, if the R group is hydrogen, the amino acid is called glycine. If the R group is a methyl group, the amino acid is called alanine.

Close to 150 amino acids are found in proteins. But only 19 amino acids (plus 1 imino acid, called proline) are specified by the genetic code. Biochemists refer to these 20 as the canonical set.

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Figure 3: The Protein-Forming Amino Acids. Image credit: Shutterstock

A protein’s primary structure forms when amino acids react with each other to form a linear chain, with the amino group of one amino acid combining with the carboxylic acid of another to form an amide linkage. (Sometimes biochemists call the linkage a peptide bond.)

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Figure 4: The Chemical Linkage between Amino Acids. Image credit: Shutterstock

The repeating amide linkages along the amino acid chain form the protein’s backbone. The amino acids’ R groups extend from the backbone, creating a distinct physicochemical profile along the protein chain for each unique amino acid sequence. To first approximation, this unique physicochemical profile dictates the protein’s higher-order structures and, hence, the protein’s function.

Why These Twenty Amino Acids?

Research has revealed that the set of amino acids used to build proteins is universal. In other words, the proteins found in every organism on Earth are made up of the same canonical set.

Biochemists have long wondered: Why these 20 amino acids?

In the early 1980s biochemists discovered that an exquisite molecular rationale undergirds the amino acid set used to make proteins.2 Every aspect of amino acid structure has to be precisely the way it is for life to be possible. On top of that, biochemists concluded that the set of 20 amino acids possesses the “just-right” physical and chemical properties that evenly and uniformly vary across a broad range of size, charge, and hydrophobicity (water resistance). In fact, it appears as if the amino acids selected for proteins seem to form a uniquely optimal set of 20 amino acids compared to random sets of amino acids.3

With these previous studies as a backdrop, the ELSI investigators wanted to develop a better understanding of the optimal nature of the universal set of amino acids used to build proteins. They also wanted to gain insight into the origin of the canonical set.

To do this they used a library of 1,913 amino acids (including the 20 amino acids that make up the canonical set) to construct random sets of amino acids. The researchers varied the set sizes from 3 to 20 amino acids and evaluated the performance of the random sets in terms of their capacity to support: (1) the folding of protein chains into three-dimensional structures; (2) protein catalytic activity; and (3) protein solubility.

They discovered that if a random set of amino acids included even a single amino acid from the canonical set, it dramatically out-performed random sets of the same size without any of the canonical amino acids. Based on these results, the researchers concluded that each of the 20 amino acids used to build proteins stands out, possessing highly unusual properties that make them ideally suited for their biochemical role, confirming the results of previous studies.

An Evolutionary Origin for the Canonical Set?

The ELSI researchers believe that—from an evolutionary standpoint—these results also shed light as to how the canonical set of amino acids emerged. Because of the unique adaptive properties of the canonical amino acids, the researchers speculate that “each time a CAA [canonical amino acid] was discovered and embedded during evolution, it provided an adaptive value unusual among many alternatives, and each selective step may have helped bootstrap the developing set to include still more CAAs.”4

In other words, the researchers offer the conjecture that whenever the evolutionary process stumbled upon one of the amino acids in the canonical set and incorporated it into nascent biochemical systems, the addition offered such a significant evolutionary advantage that it became instantiated into the biochemistry of the emerging cellular systems. Presumably, as this selection process occurred repeatedly over time, members of the canonical set would be added, one by one, to the evolving amino acid set, eventually culminating in the full canonical set.

Scientists find further support for this scenario in the following observation: some of the canonical amino acids seemingly play a more important role in optimizing smaller sets of amino acids, some play a more important role in optimizing intermediate size sets of amino acids, and others play a more prominent role in optimizing larger sets. They argue that this difference may reflect the sequence by which amino acids were added to the evolving set of amino acids as life emerged.

On the surface, this evolutionary explanation is not unreasonable. But more careful consideration of the idea raises concerns. For example, just because a canonical amino acid becomes incorporated into a set of amino acids and improves its adaptive value doesn’t mean that the resulting set of amino acids could produce the range of proteins with the solubility, foldability, and catalytic range needed to support life processes. Intuitively, it seems to me as a biochemist, that there must be a threshold for the number of canonical amino acids in any set of amino acids for it to have the range of physicochemical properties needed to build all the proteins needed to support minimal life.

I also question this evolutionary scenario because some of the amino acids that optimize smaller sets would not have been the ones present initially on the early Earth because they cannot be made by prebiotic reactions. Instead, many of the amino acids that optimize smaller sets can only be generated through biosynthetic routes that must have emerged much later in any evolutionary scenario for the origin of life.5 This limitation also means that the only way for some of the canonical amino acids to become incorporated into the canonical set is that multi-step biosynthetic routes for those amino acids evolved first. But if the full canonical set isn’t available, then it is questionable if the proteins needed to catalyze the biosynthesis of these amino acid would exist, resulting in a chicken-and-egg dilemma.

In light of these concerns, is there a better explanation for the highly optimized canonical set of amino acids?

A Creator’s Role?

Optimality of the universal set of protein amino acids finds explanation if life stems from a Creator’s handiwork. As noted, optimization is an indicator of intelligent design, achieved through foresight and preplanning. Optimization requires inordinate attention to detail and careful craftsmanship. By analogy, the optimized biochemistry epitomized by the amino acid set that makes up proteins rationally points to the work of a Creator.

Is There a Biochemical Anthropic Principle?

This discovery also leads to another philosophical implication: It lends support to the existence of a biochemical anthropic principle.

The ELSI researchers speculate that no matter the starting point in the evolutionary process, the pathways will all converge at the canonical set of amino acids because of the acids’ unusual adaptive properties. In other words, the amino acids that make up the universal set of protein-coding amino acids are not the outworking of an historically contingent evolutionary process, but instead seem to be fundamentally prescribed by the laws of nature. To put it differently, it appears as if the canonical set of amino acids has been preordained in some way.6 One of the study’s authors, Rudrarup Bose, suggests that “Life may not be just a set of accidental events. Rather, there may be some universal laws governing the evolution of life.”7

Though I prefer to see the origin of life as a creation event, it is important to recognize that even if one were to adopt an evolutionary perspective on life’s origin, it looks as if a Mind is responsible for jimmy-rigging the process to a predetermined endpoint. It looks as if a Mind purposed for life to be present in the universe and structured the laws of nature so that, in this case, the uniquely optimal canonical set of amino acids would inevitably emerge.

Along these lines, it is remarkable to think that the canonical set of amino acids has the precise properties needed for life to exist. This “coincidence” is eerie, to say the least. As a biochemist, I interpret this coincidence as evidence that our universe has been designed for a purpose. It is provocative to think that regardless of one’s perspective on the origin of life, the evidence converges toward a single conclusion: namely that life manifests from an intelligent agent—God.

Resources

The Optimality of Biochemical Systems

The Biochemical Anthropic Principle

Endnotes
  1. Melissa Ilardo et al., “Adaptive Properties of the Genetically Encoded Amino Acid Alphabet Are Inherited from Its Subset,” Scientific Reports 9, no. 12468 (August 28, 2019), doi:10.1038/s41598-019-47574-x.
  2. Arthur L. Weber and Stanley L. Miller, “Reasons for the Occurrence of the Twenty Coded Protein Amino Acids,” Journal of Molecular Evolution 17, no. 5 (September 1981): 273–84, doi:10.1007/BF01795749; H. James Cleaves II, “The Origin of the Biologically Coded Amino Acids,” Journal of Theoretical Biology 263, no. 4 (April 2010): 490–98, doi:10.1016/j.jtbi.2009.12.014.
  3. Gayle K. Philip and Stephen J. Freeland, “Did Evolution Select a Nonrandom ‘Alphabet’ of Amino Acids?” Astrobiology 11, no. 3 (April 2011), 235–40, doi:10.1089/ast.2010.0567; Matthias Granhold et al., “Modern Diversification of the Amino Acid Repertoire Driven by Oxygen,” Proceedings of the National Academy of Sciences, USA 115, no. 1 (January 2, 2018): 41–46, doi:10.1073/pnas.1717100115.
  4. Ilardo et al., “Adaptive Properties.”
  5. J. Tze-Fei Wong and Patricia M. Bronskill, “Inadequacy of Prebiotic Synthesis as Origin of Proteinous Amino Acids,” Journal of Molecular Evolution 13, no. 2 (June 1979): 115–25, doi:10.1007/BF01732867.
  6. Tokyo Institute of Technology, “Scientists Find Biology’s Optimal ‘Molecular Alphabet’ May Be Preordained,” ScienceDaily, September 10, 2019, http://www.sciencedaily.com/releases/2019/09/190910080017.htm.
  7. Tokyo Institute, “Scientists Find.”

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

Can Dinosaurs Be Resurrected from Extinction?

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By Fazale Rana – September 25, 2019

If you could visit a theme park that offered you a chance to view and even interact with real-life dinosaurs, would you go? I think I might. Who wants to swim with dolphins when you can hang out with dinosaurs? Maybe even ride one?

Well, if legendary paleontologist Jack Horner has his way, we just might get our wish—and, it could be much sooner than any of us realize. Horner is a champion of the scientific proposal to resurrect dinosaurs from extinction. And it looks like this idea might have a real chance at success.

Horner’s not taking the “Jurassic Park/World” approach of trying to clone dinosaurs from ancient DNA (which won’t work for myriad technical reasons). He wants to transform birds into dinosaur-like creatures by experimentally manipulating their developmental processes in a laboratory setting.

The Evolutionary Connection between Birds and Dinosaurs

The basis for Horner’s idea rises out of the evolutionary paradigm. Most paleontologists think that birds and dinosaurs share an evolutionary history. These scientists argue that shared anatomical features (a key phrase we’ll return to) between birds and certain dinosaur taxa demonstrate their evolutionary connection. Currently, paleontologists place dinosaurs into two major groups: avian and nonavian dinosaurs. Accordingly, paleontologists think that birds are the evolutionary descendants of dinosaurs.

So, if Horner and others are successful, what does this mean for creation? For evolution?

Reverse Evolution

In effect, Horner and other interested scientists seek to reverse what they view as the evolutionary process, converting birds into an evolutionarily ancestral state. Dubbed reverse evolution, this approach will likely become an important facet of paleontology in the future. Evolutionary biologists believe that they can gain understanding of how biological transformations took place during life’s history by experimentally reverting organisms to their ancestral state. Reverse evolution experiments fuse insights from paleontology with those from developmental biology, molecular biology, comparative embryology, and genomics. Many life scientists are excited, because, for the first time, researchers can address questions in evolutionary biology using an experimental strategy.

Proof-of-Principle Studies

The first bird that researchers hope to reverse-evolve into a dinosaur-like creature is the chicken (Gallus gallus). This makes sense. We know a whole lot about chicken biology, and life scientists can leverage this understanding to precisely manipulate the embryonic progression of chicks so that they develop into dinosaur-like creatures.

As I described previously (see Resources for Further Exploration), in 2015 researchers from Harvard and Yale Universities moved the scientific community one step closer to creating a “chickenosaurus” by manipulating chickens in ovo to develop snout-like structures, instead of beaks, just like dinosaurs.1

Now, two additional proof-of-principle studies demonstrate the feasibility of creating a chickenosaurus. Both studies were carried out by a research team from the Universidad de Chile.

In one study, the research team coaxed chicken embryos to develop a dinosaur-like foot structure, instead of the foot structure characteristic of birds.2 A bird’s foot has a perching digit that points in the backward direction, in opposition to the other toes. The perching digit allows birds to grasp. In contrast, the corresponding toe in dinosaurs is nonopposable, pointing forward.

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Figure 1: Dinosaur Foot Structure. Image credit: Shutterstock

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Figure 2: Bird Foot Structure. Image credit: Shutterstock

The researchers took advantage of the fact that vertebrate skeletons are plastic, meaning that their structure can be altered by muscle activity. These types of skeletal alterations most commonly occur during embryonic and juvenile stages of growth and development.

Investigators discovered that muscle activity causes the perching toe of birds to reorient during embryonic development from originally pointing forward to adopting an opposable orientation. Specifically, the activity of three muscles (flexor hallucis longus, flexor hallucis brevis, and musculus extensor hallucis longus) creates torsion that twists the first metatarsal, forcing the perching digit into the opposable position.

The team demonstrated that by injecting the compound decamethonium bromide into a small opening in the eggshell just before the torsional twisting of the first metatarsal takes place, they could prevent this foot bone from twisting. The compound causes muscle paralysis, which limits the activity of the muscles that cause the torsional stress on the first metatarsal. The net result: the chick developed a dinosaur-like foot structure.

In a second study, this same research team was able to manipulate embryonic development of chicken embryos to form a dinosaur-like leg structure.3 The lower legs of vertebrates consist of two bones: the tibia and the fibula. In most vertebrates, the fibula is shaped like a tube, extending all the way to the ankle. In birds, the fibula is shorter than the tibia and has a spine-like morphology (think chicken drumsticks).

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Figure 3: The Lower Leg of a Chicken. Image credit: Shutterstock

Universidad de Chile researchers discovered that the gene encoding the Indian Hedgehog protein becomes active at the distal end of the fibula during embryonic development of the lower leg in chicks, causing the growth of the fibula to cease. They also learned that the event triggering the increased activity of the Indian Hedgehog gene likely relates to the depletion of the Parathyroid Hormone-Related Protein near the distal end of the fibula. This protein plays a role in stimulating bone growth.

The researchers leveraged this insight to experimentally create a chick with dinosaur-like lower legs. Specifically, they injected the amniotic region of the chicken embryo with cyclopamine. This compound inhibits the activity of Indian Hedgehog. They discovered that this injection altered fibula development so that it was the same length as the tibia, contacting the ankle, just like in dinosaurs.

These two recent experiments on foot structure along with the previous one on snout structure represent science at its best. While the experiments reside at the proof-of-principle stage, they still give scientists like Jack Horner reason to think that we just might be able to resurrect dinosaurs from extinction one day. These experiments also raise scientific and theological questions.

Do Studies in Reverse Evolution Support the Evolutionary Paradigm?

On the surface, these studies seemingly make an open-and-shut case for the evolutionary origin of birds. It is impressive that researchers can rewind the tape of life and convert chickens into dinosaur-like creatures.

But deeper reflection points in a different direction.

All three studies highlight the amount of knowledge and insight about the developmental process required to carry out the reverse evolution experiments. The ingenious strategy the researchers employed to alter the developmental trajectory is equally impressive. They had to precisely time the addition of chemical agents at the just-right levels in order to influence muscle activity in the embryo’s foot or gene activity in the chick’s developing lower legs. Recognizing the knowledge, ingenuity, and skill required to alter embryological development in a coherent way that results in a new type of creature forces the question: Is it really reasonable to think that unguided, historically contingent processes could carry out such transformations when small changes in development can have profound effects on an organism’s anatomy?

It seems that the best the evolutionary process could achieve would be the generation of “monsters” with little hope of survival. Why? Because evolutionary mechanisms can only change gene expression patterns in a random, haphazard manner. I would contend that the coherent, precisely coordinated genetic changes needed to generate one biological system from another signals a Creator’s handiwork, not undirected evolutionary mechanisms, as the explanation for life’s history.

Can a Creation Model Approach Explain the Embryological Similarities?

Though the work in reverse evolution seems to fit seamlessly within an evolutionary framework, observations from these studies can be explained from a creation model perspective.

Key to this explanation is the work of Sir Richard Owen, a preeminent biologist who preceded Charles Darwin. In contemporary biology, scientists view shared features possessed by related organisms as evidence of common ancestry. Birds and theropod dinosaurs would be a case in point. But for Owen, shared anatomical features reflected an archetypal design that originated in the Mind of the First Cause. Toward this end, the anatomical features shared by birds and theropods can be understood as reflecting common design, not common descent.

Though few biologists embrace Owen’s ideas today, it is important to note that his ideas were not tried and found wanting. They simply were abandoned in favor of Darwin’s theory, which many biologists preferred because it provided a mechanistic explanation for life’s history and the origin of biological systems. In fact, Darwin owes a debt of gratitude to Owen’s thinking. Darwin coopted the idea of the archetype, but then replaced the canonical blueprint that existed in the Creator’s Mind (per Owen) with a hypothetical common ancestor.

This archetypal approach to biology can account for the results of reverse-evolution studies. Accordingly, the researchers have discovered differences in the developmental program that affect variations in the archetype, yielding differences in modern birds and long-extinct dinosaurs.

The idea of the archetype can extend to embryonic growth and development. One could argue that the Creator appears to have developed a core (or archetypal) developmental algorithm that can be modified to yield disparate body plans. From a creation model standpoint, then, the researchers from Harvard and Yale Universities and the Universidad de Chile didn’t reverse the evolutionary process. They unwittingly reverse-engineered a dinosaur-like developmental algorithm from a bird-like developmental program.

Why Would God Create Using the Same Design Templates?

There may well be several reasons why a Creator would design living systems around a common set of templates. In my estimation, the most significant reason is discoverability.

Shared anatomical and physiological features, as well as shared features of embryological development make it possible to apply what we learn by studying one organism to others. This shared developmental program makes it possible to use our understanding of embryological growth and development to reengineer a bird into a dinosaur-like creature. Discoverability makes it easier to appreciate God’s glory and grandeur, as evinced in biochemical systems by their elegance, sophistication, and ingenuity.

Discoverability also reflects God’s providence and care for humanity. If not for the shared features, it would be nearly impossible for us to learn enough about the living realm for our benefit. Where would biomedical science be without the ability to learn fundamental aspects about our biology by studying model organisms such as chickens? And where would our efforts to re-create dinosaurs be if not for the biological designs they share with birds?

Resources for Further Exploration

Reverse Evolution

Shared Biological Designs and the Creation Model

Endnotes
  1. Bhart-Anjan S. Bhullar et al., “A Molecular Mechanism for the Origin of a Key Evolutionary Innovation, the Bird Beak and Palate, Revealed by an Integrative Approach to Major Transitions in Vertebrate History,” Evolution 69, no. 7 (2015): 1665–77, doi:10.1111/evo.12684.
  2. João Francisco Botelho et al., “Skeletal Plasticity in Response to Embryonic Muscular Activity Underlies the Development and Evolution of the Perching Digit of Birds,” Scientific Reports 5 (May 14, 2015): 9840, doi:10.1038/srep09840.
  3. João Francisco Botelho et al., “Molecular Developments of Fibular Reduction in Birds and Its Evolution from Dinosaurs,” Evolution 70, no. 3 (March, 2016): 543–54, doi:10.1111/evo.12882.

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

Primate Thanatology and the Case for Human Exceptionalism

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By Fazale Rana – September 18, 2019

I will deliver this people from the power of the grave;
I will redeem them from death.
Where, O death, are your plagues?
Where, O grave, is your destruction?

Hosea 13:14

It was the first time someone I knew died. I was in seventh grade. My classmate’s younger brother and two younger sisters perished in a fire that burned his family’s home to the ground. We lived in a small rural town in West Virginia at the time. Everyone knew each other and the impact of that tragedy reverberated throughout the community.

I was asked to be a pallbearer at the funeral. To this day, I remember watching my friend’s father with a cast on one arm and another on one of his legs, hobble up to each of the little caskets to touch them one last time as he sobbed uncontrollably right before we lifted and carried the caskets to the waiting hearses.

Death is part of life and our reaction to death is part of what makes us human. But, are humans unique in this regard?

Funerary Practices

Human responses to death include funerary practices—ceremonies that play an integral role in the final disposition of the body of the deceased.

Anthropologists who study human cultures see funerals as providing important scientific insight into human nature. These scientists define funerals as cultural rituals designed to honor, remember, and celebrate the life of those who have died. Funerals provide an opportunity for people to express grief, mourn loss, offer sympathy, and support the bereaved. Also, funerals often serve a religious purpose that includes (depending on the faith tradition) praying for the person who has died, helping his or her soul transition to the afterlife (or reincarnate).

Funerary Practices and Human Exceptionalism

For many anthropologists, human funerary practices are an expression of our capacities for:

  • symbolism
  • open-ended generative manipulation of symbols
  • theory of mind
  • complex, hierarchical social interactions

Though the idea of human exceptionalism is controversial within anthropology today, a growing minority of anthropologists argue that the combination of these qualities sets us apart from other creatures. They make us unique and exceptional.

As a Christian, I view this set of qualities as scientific descriptors of the image of God. That being the case, then, from my vantage point, human funerary practices (along with language, music, and art) are part of the body of evidence that we can marshal to make the case that human beings uniquely bear God’s image.

What about Neanderthals?

But are human beings really unique and exceptional?

Didn’t Neanderthals bury their dead? Didn’t these hominins engage in funerary practices just like modern humans do?

If the answer to these questions is yes, then for some people it undermines the case for human uniqueness and exceptionalism and, along with it, the scientific case for the image of God. If Neanderthal funerary practices flow out of the capacity for symbolism, open-ended generative capacity, etc., then it means that Neanderthals must have been like us. They must have been exceptional, too, and humans don’t stand apart from all other creatures on Earth, as the Scriptures teach.

Did Neanderthals Bury Their Dead?

But, could these notions about Neanderthal exceptionalism be premature? Although there is widespread belief that Neanderthals buried their dead in a ritualistic manner and even though this claim can be attested in the scientific literature, a growing body of archeological evidence challenges this view.

Many anthropologists question if Neanderthal burials were in fact ritualistic. (If they weren’t, then it most likely indicates that these hominins didn’t have a concept of the afterlife—a concept that requires symbolism and open-ended generative capacities.) Others go so far as to question if Neanderthals buried their dead at all. (For an in-depth discussion of the scientific challenges to Neanderthal burials, see the Resources section below.)

Were Neanderthal Burials an Evolutionary Precursor to Human Funerary Practices?

It is not unreasonable to think that these hominins may well have disposed of corpses and displayed some type of response when members of their group died. Over the centuries, keen observers (including primatologists, most recently) have documented nonhuman primates inspecting, protecting, retrieving, carrying, and dragging the dead bodies of members of their groups.1 In light of these observations, it makes sense to think that Neanderthals may have done something similar.

While it doesn’t appear that Neanderthals responded to death in the same way we do, it is tempting (within the context of the evolutionary paradigm) to view Neanderthal behavior as an evolutionary stepping-stone to the funerary practices of modern humans.

But, is this transitional view the best explanation for Neanderthal burials—assuming that these hominins did, indeed, dispose of group members’ corpses? Research in thanatology (the study of dying and death) among nonhuman primates holds the potential to shed light on this question.

The Nonhuman Primate Response to Death

Behavioral evolution researchers André Gonçalves and Susana Caravalho recently reviewed studies in primate thanatology—categorizing and interpreting the way these creatures respond to death. In the process, they sought to explain the role the death response plays among various primate groups.

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Figure 1: Monkey Sitting over the Body of a Deceased Relative. Image credit: Shutterstock

When characterizing the death response of nonhuman primates, Gonçalves and Caravalho group the behaviors of these creatures into two categories: (1) responses to infant deaths and (2) responses to adult deaths.

In most primate taxa (classified groups), when an infant dies the mother will carry the dead baby for days before abandoning it, often grooming the corpse and swatting away flies. Eventually, she will abandon it. Depending on the taxon, in some instances young females will carry the infant’s remains for a few days after the mother abandons it. Most other members in the group ignore the corpse. At times, they will actively avoid both mother and corpse when the stench becomes overwhelming.

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Figure 2: Baboon Mother with a Child. Image credit: Shutterstock

The death of an adult member of the group tends to elicit a much more pervasive response than does the death of an infant. The specific nature of the response depends upon the taxon and also on other factors such as: (1) the bond between individual members of the group and the deceased; (2) the social status of the deceased; and (3) the group structure of the particular taxon. Typically, the closer the bond between the deceased and the group member the longer the duration of the death response. The same is true if the deceased is a high-ranking member of the group.

Often the death response includes vocalizations that connote alarm and distress. Depending on the taxon, survivors may hit and pull at the corpse, as if trying to rouse it. Other times, it appears that survivors hit the corpse out of frustration. Sometimes groups members will sniff at the corpse or peer at it. In some taxa, survivors will groom the corpse or stroke it gently, while swatting away flies. In other taxa, survivors will stand vigil over the corpse, guarding it from scavengers.

In some instances, survivors return to the corpse and visit it for days. After the corpse is disposed, group members may continue to visit the site for quite some time. In other taxa, group members may avoid the death site. Both behaviors indicate that group members understand that an event of great importance to the group took place at the site where a member died.

Are Humans and Nonhuman Primates Different in Degree? Or Kind?

It is clear that nonhuman primates have an awareness of death and, for some primate taxa, it seems as if members of the group experience grief. Some anthropologists and primatologists see this behavior as humanlike. It’s easy to see why. We are moved by the anguish and confusion these creatures seem to experience when one of their group members dies.

For the most part, these scientists would agree that the human response to death is more complex and sophisticated. Yet, they see human behavior as differing only in degree rather than kind when compared to other primates. Accordingly, they interpret primate death awareness as an evolutionary antecedent to the sophisticated funerary practices of modern humans, with Neanderthal behavior part of the trajectory. And for this reason, they maintain that human beings really aren’t unique or exceptional.

The Trouble with Anthropomorphism

One problem with this conclusion (even within an evolutionary framework) is that it fails to account for the human tendency toward anthropomorphism. As part of our human nature, we possess theory of mind. We recognize that other human beings have minds like ours. And because of this capability, we know what other people are thinking and feeling. But, we don’t know how to turn this feature on and off. As a result, we also apply theory of mind to animals and inanimate objects, attributing humanlike behaviors and motivations to them, though they don’t actually possess these qualities.

British ethnologist Marian Stamp Dawkins argues in her book Why Animals Matter that scientists studying animal behavior fall victim to the tendency to anthropomorphize just as easily as the rest of us. Too often, researchers interpret experimental results from animal behavioral studies and from observations of animal behavior in captivity and the wild in terms of human behavior. When they do, these researchers ascribe human mental experiences—thoughts and feelings—to animals. Dawkins points out that when investigators operate this way, it leads to untestable hypotheses because we can never truly know what occurs in animal minds. Moreover, Dawkins argues that we tend to prefer anthropomorphic interpretations to other explanations. She states, “Anthropomorphism tends to make people go for the most human-like explanation and ignore the other less exciting ones.”2

A lack of awareness of our tendency toward anthropomorphism raises questions about the all-too-common view that the death response of nonhuman primates—and Neanderthals—is humanlike and an evolutionary antecedent to modern human funerary practices. This is especially true in light of the explanation offered by Gonçalves and Caravalho for the death response in primates.

The two investigators argue that the response of mothers to the death of their infants is actually maladaptive (from an evolutionary perspective). Carrying around dead infants and caring for them is energetically costly and hinders their locomotion. Both consequences render them vulnerable to predators. The pair explain this behavior by arguing that the mother’s response to the death of her infant falls on the continuum of care-taking behavior and can be seen as a trade-off. In other words, nonhuman primate mothers who have a strong instinct to care for their offspring will ensure the survival of their infant. But if the infant dies, the instinct is so strong that they will continue to care for it after its death.

Gonçalves and Caravalho also point out that the death response toward adult members of the group plays a role in reestablishing new group dynamics. Depending on the primate taxon, the death of members shifts the group’s hierarchical structure. This being the case, it seems reasonable to think that the death response helps group members adjust to the new group structure as survivors take on new positions in the hierarchy.

Finally, as Dawkins argues, we can’t know what takes place in the minds of animals. Therefore, we can’t legitimately attribute human mental experiences to animals. So, while it may seem to us as if some nonhuman primates experience grief as part of the death response, how do we know that this is actually the case? Evidence for grief often consists of loss of appetite and increased vocalizations. However, though these changes occur in response to the death of a group member, there may be other explanations for these behaviors that have nothing to do with grief at all.

Death Response in Nonhuman Primates and Neanderthals

Study of primate thanatology also helps us to put Neanderthal burial practices (assuming that these hominins buried dead group members) into context. Often, when anthropologists interpret Neanderthal burials (from an evolutionary perspective), they are comparing these practices to human funerary practices. This comparison makes it seem like Neanderthal burials are part of an evolutionary trajectory toward modern human behavior and capabilities.

But what if the death response of nonhuman primates is factored into the comparison? When we add a second endpoint, we find that the Neanderthal response to death clusters more closely to the responses displayed by nonhuman primates than to modern humans. And as remarkable as the death response of nonhuman primates may be, it is categorically different from modern human funerary practices. To put it another way, modern human funerary practices reflect our capacity for symbolism, open-ended manipulation of symbols, theory of mind, etc. In contrast, the death response of nonhuman primates and hominins, such as Neanderthals, seems to serve utilitarian purposes. So, it isn’t the presence or absence of the death response that determines our exceptional nature. Instead, it is a death response shaped by our capacity for symbolism and open-ended generative capacity that highlights our exceptional uniqueness.

Modern humans really do seem to stand apart compared to all other creatures in a way that aligns with the biblical claim that human beings uniquely possess and express the image of God.

RTB’s biblical creation model for human origins, described in Who Was Adam?, views hominins such as Neanderthals as creatures created by God’s divine fiat that possess intelligence and emotional capacity. These animals were able to employ crude tools and even adopt some level of “culture,” much like baboons, gorillas, and chimpanzees. But they were not spiritual beings made in God’s image. That position—and all of the intellectual, relational, and symbolic capabilities that come with it—remains reserved for modern humans alone.

Resources for Further Exploration

Did Neanderthals Bury Their Dead?

Nonhuman Primate Behavior

Problem-Solving in Animals and Human Exceptionalism

Endnotes
  1. André Gonçalves and Susana Caravalho, “Death among Primates: A Critical Review of Nonhuman Primate Interactions towards Their Dead and Dying,” Biological Reviews 94, no. 4 (April 4, 2019), doi:10.1111/brv.12512.
  2. Marian Stamp Dawkins, Why Animals Matter: Animal Consciousness, Animal Welfare, and Human Well-Being (New York, Oxford University Press, 2012), 30.

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