Where Science and Faith Converge
  • Analysis of Genomes Converges on the Case for a Creator

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Nov 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.
  • Glue Production Is Not Evidence for Neanderthal Exceptionalism

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Nov 06, 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.”
  • Scientists Reverse the Aging Process: Exploring the Theological Implications

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Oct 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.
  • Origin and Design of the Genetic Code: A One-Two Punch for Creation

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Oct 23, 2019

    True confession: I am a sports talk junkie. It has gotten so bad that sometimes I would rather listen to people talk about the big game than actually watch it on TV.

    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.
  • New Insights into Genetic Code Optimization Signal Creator’s Handiwork

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Oct 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 codea 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.”
  • Is the Optimal Set of Protein Amino Acids Purposed by a Mind?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Oct 09, 2019

    As a graduate student and a postdoc, I spent countless hours in the lab doing research. Part of my work involved performing biochemical assays—laboratory procedures designed to measure the activities of biomolecules and biochemical systems.

    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.”
  • Can Dinosaurs Be Resurrected from Extinction?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Sep 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.
  • Primate Thanatology and the Case for Human Exceptionalism

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Sep 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.
  • Simple Biological Rules Affirm Creation

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Sep 04, 2019

    “Biology is the study of complicated things that give the appearance of having been designed for a purpose.”
    –Richard Dawkins

    To say that biological systems are complicated is an understatement.

    When I was in college, I had some friends who avoided taking courses in the life sciences because of the complexity of biological systems. On the other hand, I found the complexity alluring. It’s what drew me to biochemistry. I love to immerse myself in the seemingly never-ending intricacies of biomolecular systems and try to make sense of them.

    Perhaps nothing exemplifies the daunting complexity of biochemistry more than intermediary metabolism.

    Order in the Midst of Biochemical Complexity

    I remember a conversation I had years ago with a first-year graduate student who worked in the same lab as me when I was a postdoc at the University of Virginia. He was complaining about all the memorization he had to do for the course he was taking on intermediary metabolism. How else was he going to become conversant with all the different metabolic routes in the cell?

    I told him that he was approaching his classwork in the wrong way. Despite the complexity and chemical diversity of the metabolic pathways in the cell, a set of principles exists that dictates the architecture and operation of metabolic routes. I encouraged my lab mate to learn these principles because, once he did, he would be able to use them to write out all of the metabolic routes with minimal memorization.

    These principles make sense of the complexity of intermediary metabolism. Are there similar rules that make sense of biological diversity and complexity?

    Rules Govern Biological Systems

    As it turns out, the insight I offered my lab mate may well have been prescient.

    The idea that a simple set of principles—rules, if you will—accounts for the complexity and diversity of biological systems may be more widespread than life scientists fully appreciate. At least it appears this way based on work carried out recently by researchers from Duke University.1 These investigators discovered a simple rule that predicts the behavior of mutually beneficial symbiotic relationships (mutualism) in ecosystems. Mutualistic interactions play an important and dominant role in ecosystem stability.

    The Duke University scientists’ accomplishment represents a significant milestone. Lingchong You, one of the study’s authors, points out the difficulty of finding rules that govern all biological systems:

    “In a perfect world, you’d be able to follow a simple set of molecular rules to understand how every biological system operated. But, in reality, it’s difficult to establish rules that encompass the immense diversity and complexity of biological systems. Even when we do establish general rules, it’s still challenging to use them to explain and quantify various physical properties.”2

    Yet, You and his collaborators have done just that for mutualism. Their insight moves biology closer to physics and chemistry where simple rules can account for the physical world. Their work holds the potential to open up new vistas in the life sciences that can lead to a deeper, more fundamental understanding of biological systems.

    In fact, the researchers think that simple rules dictating the operation of biological systems may not be an unusual feature of mutualistic interactions but may apply more broadly. They write, “Beyond establishing another simple rule . . . we also demonstrated that one can purposefully seek an appropriate abstraction level where a simple unifying rule emerges over system diversity.”3

    If the Duke University scientists’ insight generally applies to biological systems, it has interesting theological implications. If biological systems do, indeed, conform to a simple set of rules, it becomes more reasonable to think that a Creator played a role in the origin, history, and design of life.

    I’ll explain how in a moment, but first let’s take a look at some details of the Duke University investigators’ work.

    Mutualism and Ecosystem Stability

    Biological organisms often form symbiotic relationships. When these relationships benefit all of the organisms involved, it is called mutualism. These mutualistic relationships are vital to ecosystems and they directly and indirectly benefit humanity. For example, coral reefs depend on mutualistic interactions between coral and algae. In turn, reefs provide habitats for a diverse ensemble of organisms that support human life and flourishing.

    Unfortunately, mutualistic systems can collapse when one or more of the partners experiences stress or disappears from the ecosystem. A disruption in a relationship can lead to the loss of other members of the ecosystem, thereby altering the ecosystem’s composition and opening up niches for invading organisms. Sadly, this type of collapse is happening in coral reefs around the world today.

    Mutualism Can Be Explained by a Simple Rule

    To gain insight into the rules that dictate ecosystem stability and predict collapse (due to a loss of mutualistic relationships), the Duke University researchers sought to develop a framework that would allow them to determine the outcome of mutualistic interactions. For the predictive framework, the scientists wrote 52 mathematical equations, each one specifically describing one of the various forms of mutualism. These equations were based on a simple biological logic; namely, mutualism consists of two or more populations of organisms that produce a benefit (B) for all the organisms that reduces the stress (S) they experience at a cost (C).

    Mathematical analysis of these equations allowed the researchers to discover a simple inequality that governs the transition from coexistence to collapse. As it turns out, mutualistic interactions remain stable when B > S, and they collapse when this inequality is not observed. Though intuitive, it is still remarkable that this simple relationship dictates the behavior of all types of mutualism.

    The researchers learned that determining the value of S is relatively straightforward. On the other hand, quantifying B proves to be a challenge due to the large number of variables such as temperature, nutrient availability, genetic variation, etc., that influence mutualistic interactions. To work around this problem, the researchers developed a machine-learning algorithm that could calculate B using the input of a large number of variables.

    This work has obvious importance for ecologists as ecosystems all over the planet face collapse. Beyond that, it has important theological implications when we recognize that a simple mathematical equation governs the behavior of mutualistic relationships among organisms.

    Let me explain.

    The Case for a Creator

    From my vantage point, one of the most intriguing aspects of our universe is its intelligibility and our capacity as human beings to make sense of the world around us—quite often, through the use of simple rules we have discovered. Along these lines, it is even more remarkable that the universe and its phenomena can be described using mathematical relationships, which reflects an underlying rationale to the universe itself.

    For most of the history of science, the discovery and exploration of the mathematical nature of the universe has been confined to physics and, to a lesser extent, chemistry. Because of the complexity and diversity of biological systems, many people working in the life sciences have questioned if simple mathematical rules exist in biology and could ever be discovered.

    But the discovery of a simple rule that predicts the behavior of mutualistic relationships in ecosystems suggests that mathematical relationships do describe and govern biological phenomena. And, as the researchers point out, their discovery may turn out to be the rule rather than the exception.

    From my perspective, a universe governed by mathematical relationships suggests that a deep, underlying rationale undergirds nature, which is precisely what I would expect if a Mind was behind the universe. To put it differently, if a Creator was responsible for the universe, as a Christian, I would expect that mathematical relationships would define the universe’s structure and function. In like manner, if the origin and design of living systems originated from a Creator, it would make sense that biological systems would possess an underlying mathematical structure as well—though it might be hard for us to discern these relationships because of the systems’ complexity.

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    Figure: The Mathematical Universe. Image credit: Shutterstock.

    The mathematical structure of the universe—and maybe even of biology—makes the world around us intelligible. And intelligibility is precisely what we would expect if the universe and everything in it were the products of a Creator—one who desired to make himself known to us through the creation (Romans 1:20). It is also what we would expect if human beings were made in God’s image (as Scripture describes), with the capacity to discern God’s handiwork in the world around us.

    A Case against Materialism

    But what if humans—including our minds—were cobbled together by evolutionary processes? Why would we expect human beings to be capable of making sense of the world around us? For that matter, why would we expect the universe—including the biological realm—to adhere to mathematical relationships?

    In other words, the mathematical undergirding of nature fits better in a theistic conception of reality than one rooted in materialism. And toward that end, the discovery by the Duke University investigators points to God’s role in the origin and design of life.

    Is There a Biological Anthropic Principle?

    As the Duke University scientists show, the discovery of a simple mathematical relationship describing the behavior of mutualistic interactions in ecosystems suggests that these types of relationships may be more commonplace than most life scientists thought or imagined. (See Biochemical Anthropic Principle in the Resources section.)

    This discovery also suggests that a cornerstone feature of ecosystems—mutualistic relationships—is not the haphazard product of evolutionary history. Instead, scientists observe a process fundamentally dictated and constrained by the laws of nature as revealed in the simple mathematical rule that describes the behavior of these systems. We can infer that mutualism within ecosystems may not be the outworking of chance events—the consequence of a historically contingent evolutionary process. Rather, these relationships appear to be fundamentally prescribed by the design of the universe. In other words, mutualism in ecosystems is inevitable in a universe like ours.

    For me, it is eerie to think that mutualism, which appears to be specified by the laws of nature, is precisely what is needed to maintain stable ecosystems. The universe appears to be structured in a just-right way so that stable ecosystems result. If the universe was any other way, then mutualism wouldn’t exist nor would ecosystems.

    One way to interpret this “coincidence” is to view it as evidence that our universe has been designed for a purpose. And purpose must come from a Mind—namely, God.

    Resources

    The Argument from Math and Beauty

    Designed for Discovery

    The Biochemical Anthropic Principle

    The Design of Intermediary Metabolism

    Endnotes
    1. Feilun Wu et al., “A Unifying Framework for Interpreting and Predicting Mutualistic Systems, Nature Communications 10 (2019): 242, doi:/10.1038/s41467-018-08188-5.
    2. Duke University, “Simple Rules Predict and Explain Biological Mutualism,” ScienceDaily (January 16, 2019), https://www.sciencedaily.com/releases/2019/01/190116110941.htm.
    3. Wu et al., “A Unifying Framework.”
  • ATP Transport Challenges the Evolutionary Origin of Mitochondria

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Aug 21, 2019

    In high school, I spent most Sunday mornings with my family gathered around the TV watching weekly reruns of the old Abbott and Costello movies.

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    Image: Bud Abbott and Lou Costello. Image credit: Wikipedia

    One of my favorite routines has the two comedians trying to help a woman get her parallel-parked car out of a tight parking spot. As Costello takes his place behind the wheel, Abbott tells him to “Go ahead and back up.” And of course, confusion and hilarity follow as Costello repeatedly tries to clarify if he is to “go ahead” or “back up,” finally yelling, “Will you please make up your mind!”

    As it turns out, biologists who are trying to account for the origin of mitochondria (through an evolutionary route) are just as confused about directions as Costello. Specifically, they are trying to determine which direction ATP transport occurred in the evolutionary precursors to mitochondria (referred to as pre-mitochondria).

    In an attempt to address this question, a research team from the University of Virginia (UVA) has added to the frustration, raising new challenges for evolutionary explanations for the origin of mitochondria. Their work threatens to drive the scientific community off the evolutionary route into the ditch when it comes to explaining the origin of eukaryotic cells.1

    To fully appreciate the problems this work creates for the endosymbiont hypothesis, a little background is in order. (For those familiar with the evidence for the endosymbiont hypothesis, you may want to skip ahead to The Role of Mitochondria.)

    The Endosymbiont Hypothesis

    Most biologists believe that the endosymbiont hypothesis serves as the best explanation for the origin of complex cells.

    According to this idea, complex cells originated when symbiotic relationships formed among single-celled microbes after free-living bacterial and/or archaeal cells were engulfed by a “host” microbe.

    The “poster children” of the endosymbiont hypothesis are mitochondria. Presumably, the mitochondria started its evolutionary journey as an endosymbiont. Evolutionary biologists believe that once engulfed by the host cell, this microbe took up permanent residency, growing and dividing inside the host. Over time, the endosymbiont and the host became mutually interdependent, with the endosymbiont providing a metabolic benefit for the host cell (such as providing a source of ATP). In turn, the host cell provided nutrients to the endosymbiont. Presumably, the endosymbiont gradually evolved into an organelle through a process referred to as genome reduction. This reduction resulted when genes from the endosymbiont’s genome were transferred into the genome of the host organism, generating the mitonuclear genome.

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    Image: Endosymbiont Hypothesis. Image credit: Wikipedia

    Evidence for the Endosymbiont Hypothesis

    Much of the evidence for the endosymbiotic origin of mitochondria centers around the similarity between mitochondria and bacteria. These organelles are about the same size and shape as typical bacteria and have a double membrane structure like gram-negative cells. These organelles also divide in a way that is reminiscent of bacterial cells.

    Biochemical evidence also exists for the endosymbiont hypothesis. Evolutionary biologists view the presence of the diminutive mitochondrial genome as a vestige of this organelle’s evolutionary history. They see the biochemical similarities between mitochondrial and bacterial genomes as further evidence for the evolutionary origin of these organelles.

    The presence of the unique lipid, cardiolipin, in the mitochondrial inner membrane also serves as evidence for the endosymbiont hypothesis. This important lipid component of bacterial inner membranes is absent in the membranes of eukaryotic cells—except for the inner membranes of mitochondria. In fact, biochemists consider cardiolipin a signature lipid for mitochondria and a vestige of the organelle’s evolutionary history.

    The Role of Mitochondria

    Mitochondria serve cells in a number of ways, including:

    • Calcium storage
    • Calcium signaling
    • Signaling with reactive oxygen species
    • Regulation of cellular metabolism
    • Heat production
    • Apoptosis

    Arguably one of the most important functions of mitochondria relates to their role in energy conversion. This organelle generates ATP molecules by processing the breakdown products of glycolysis through the tricarboxylic acid cycle and the electron transport chain.

    Biochemists refer to ATP as a high-energy compound—it serves as an energy currency for the cell, and most cellular processes are powered by ATP. One way that ATP provides energy is through its conversion to ADP and an inorganic phosphate molecule. This breakdown reaction liberates energy that can be coupled to cellular activities that require energy.

     

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    Image: The ATP/ADP Reaction Cycle. Image credit: Shutterstock

    ATP Production and Transport

    The enzyme complex ATP synthase, located in the mitochondrial inner membrane, generates ATP from ADP and inorganic phosphate, using a proton gradient generated by the flow of electrons through the electron transport chain. As ATP synthase generates ATP, it deposits this molecule in the innermost region of the mitochondria (called the matrix or the lumen).

    In order for ATP to become available to power cellular processes, it has to be transported out of the lumen and across the mitochondrial inner membrane into the cytoplasm. Unfortunately, the inner mitochondrial membrane is impermeable to ATP (and ADP). In order to overcome this barrier, a protein embedded in the inner membrane called ATP/ADP translocase performs the transport operation. Conveniently, for every molecule of ATP transported out of the lumen, a molecule of ADP is transported from the cytoplasm into the lumen. In turn, this ADP is converted into ATP by ATP synthase.

    Because of the importance of this process, copies of ATP/ADP translocase comprises 10% of the proteins in the inner membrane.

    If this enzyme doesn’t function properly, it will result in mitochondrial myopathies.

    The Problem ATP Transport Causes for The Endosymbiont Hypothesis

    Two intertwined questions confronting the endosymbiont hypothesis relate to the evolutionary driving force behind symbiogenesis and the nature of pre-mitochondria.

    Traditionally, evolutionary biologists have posited that the host cell was an anaerobe, while the endosymbiont was an aerobic microbe, producing ATP from lactic acid generated by the host cell. (Lactic acid is the breakdown product of glucose in the absence of oxygen).

    But, as cell biologist Franklin Harold points out, this scenario has an inherent flaw. Namely, if the endosymbiont is producing ATP necessary for its survival from host cell nutrients, why would it relinquish some—or even all—of the ATP it produces to the host cell?

    According to Harold, “The trouble is that unless the invaders share their bounty with the host, they will quickly outgrow him; they would be pathogens, not symbionts.”2

    And, the only way they could share their bounty with the host cell is to transport ATP from the engulfed cell’s interior to the host cell’s cytoplasm. While mitochondria accomplish this task with the ATP/ADP translocase, there is no good reason to think that the engulfed cell would do this. Given the role ATP plays as the energy currency in the cell and the energy that is expended to make this molecule, there is no advantage for the engulfed cell to pump ATP from its interior to the exterior environment.

    Harold sums up the problem this way: “Such a carrier would not have been present in the free-living symbiont but must have been acquired in the course of its enslavement; it cannot be called upon to explain the initial benefits of the association.”3

    In other words, currently, there is no evolutionary explanation for why the ATP/ADP translocase in the mitochondrial inner membrane—a protein central to the role of mitochondria in eukaryotic cells—pumps ATP from the lumen to the cytoplasm.

    Two Alternative Models

    This problem has led evolutionary biologists to propose two alternative models to account for the evolutionary driving force behind symbiogenesis: 1) the hydrogen hypothesis; and 2) the oxygen scavenger hypothesis.

    The hydrogen hypothesis argues that the host cell was a methanogenic member of archaea that consumed hydrogen gas and the symbiont was a hydrogen-generating alpha proteobacteria.

    The oxygen-scavenging model suggests that the engulfed cell was aerobic, and because it used oxygen, it reduced the amount of oxygen in the cytoplasm of the host cell, thought to be an anaerobe.

    Today, most evolutionary biologists prefer the hydrogen hypothesis—in part because the oxygen scavenger model, too, has a fatal flaw. As Harold points out, “This [oxygen scavenger model], too, is dubious, because respiration generates free radicals that are known to be a major source of damage to cellular membranes and genes.”4

    Moving Forward, Or Moving Backward?

    To help make headway, two researchers from UVA attempted to reconstruct the evolutionary precursor to mitochondria, dubbed pre-mitochondria.

    Operating within the evolutionary framework, these two investigators reconstructed the putative genome of pre-mitochondria using genes in the mitochondrial genome and genes from the nuclear genomes of organisms they believe were transferred to the nucleus during the process of symbiogenesis. (Genes that clustered with alphaproteobacterial genes were deemed to be of mitochondrial origin.)

    Based on their reconstruction, they conclude that the original engulfed cell actually used its ATP/ADP translocase to import ATP from the host cell cytoplasm into its interior, exchanging the ATP for an ADP. This is the type of ATP/ADP translocase found in obligate intracellular parasites alive today.

    According to the authors, this means that:

    “Pre-mitochondrion [was] an ‘energy scavenger’ and suggests an energy parasitism between the endosymbiont and its host at the origin of the mitochondria. . . . This is in sharp contrast with the current role of mitochondria as the cell’s energy producer and contradicts the traditional endosymbiotic theory that the symbiosis was driven by the symbiont supplying the host ATP.5

    The authors speculate that at some point during symbiogenesis the ATP/ADP translocase went ahead and backed up, reversing direction. But, this explanation is little more than a just-so story with no evidential support. Confounding their conjecture is their discovery that the ATP/ADP translocase found in mitochondria is evolutionarily unrelated to the ATP/ADP translocases found in obligate intracellular parasites.

    The fact that the engulfed cell was an obligate intracellular parasite not only brings a halt to the traditional version of the endosymbiont hypothesis, it flattens the tires of both the oxygen scavenger model and hydrogen hypothesis. According to Wang and Wu (the UVA investigators):

    “Our results suggest that mitochondria most likely originated from an obligate intracellular parasite and not from a free-living bacterium. This has important implications for our understanding of the origin of mitochondria. It implies that at the beginning of the endosymbiosis, the bacterial symbiont provided no benefits whatsoever to the host. Therefore we argue that the benefits proposed by various hypotheses (e.g, oxygen scavenger and hydrogen hypotheses) are irrelevant in explaining the establishment of the initial symbiosis.”6

    If the results of the analysis by the UVA researchers stand, it leaves evolutionary biologists with no clear direction when it comes to determining the evolutionary driving force behind the early stages of symbiogenesis or the evolutionary route to mitochondria.

    It seems that the more evolutionary biologists probe the question of mitochondrial origins, the more confusion and uncertainty results. In fact, there is not a coherent compelling evolutionary explanation for the origin of eukaryotic cells—one of the key events in life’s history. The study by the UVA investigators (along with other studies) casts aspersions on the most prominent evolutionary explanations for the origin of eukaryotes, justifying skepticism about the grand claim of the evolutionary paradigm: namely, that the origin, design, and history of life can be explained exclusively through evolutionary processes.

    In light of this uncertainty, can the origin of mitochondria, and hence eukaryotic cells, be better explained by a creation model? I think so, but for many scientists this is a road less traveled.

    Resources

    Challenges to the Endosymbiont Hypothesis:

    In Support of a Creation Model for the Origin of Eukaryotic Cells:

    ATP Production and the Case for a Creator:

    Endnotes
    1. Zhang Wang and Martin Wu, “Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite,” PLOS One 9, no. 10 (October 15, 2014): e110685, doi:10.1371/journal.pone.0110685.
    2. Franklin M. Harold, In Search of Cell History: The Evolution of Life’s Building Blocks (Chicago, IL: The University of Chicago Press, 2014), 131.
    3. Harold, In Search of Cell History, 131.
    4. Harold, In Search of Cell History, 132.
    5. Wang and Wu, “Phylogenomic Reconstruction.
    6. Wang and Wu, “Phylogenomic Reconstruction.
  • Does Information Come from a Mind?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Aug 14, 2019

    Imagine youre flying over the desert, and you notice a pile of rocks down below. Most likely, you would think little of it. But suppose the rocks were arranged to spell out a message. I bet you would conclude that someone had arranged those rocks to communicate something to you and others who might happen to fly over the desert.

    You reach that conclusion because experience has taught you that messages come from persons/people—or, rather, that information comes from a mind. And, toward that end, information serves as a marker for the work of intelligent agency.

    blog__inline--does-information-come-from-a-mind

    Image credit: Shutterstock

    Recently, a skeptic challenged me on this point, arguing that we can identify numerous examples of natural systems that harbor information, but that the information in these systems arose through natural processes—not a mind.

    So, does information truly come from a mind? And can this claim be used to make a case for a Creator’s existence and role in life’s origin and design?

    I think it can. And my reasons are outlined below.

    Information and the Case for a Creator

    In light of the (presumed) relationship between information and minds, I find it provocative that biochemical systems are information systems.

    Two of the most important classes of information-harboring molecules are nucleic acids (DNA and RNA) and proteins. In both cases, the information content of these molecules arises from the nucleotide and amino acid sequences, respectively, that make up these two types of biomolecules.

    The information harbored in nucleotide sequences of nucleic acids and amino acid sequences of proteins is digital information. Digital information is represented by a succession of discrete units, just like the ones and zeroes that encode the information manipulated by electronic devices. In this respect, sequences of nucleotides and amino acids for discrete informational units that encode the information in DNA and RNA and proteins, respectively.

    But the information in nucleic acids and proteins also has analog characteristics. Analog information varies in an uninterrupted continuous manner, like radio waves used for broadcasting purposes. Analog information in nucleic acids and proteins are expressed through the three-dimensional structures adopted by both classes of biomolecules. (For more on the nature of biochemical information, see Resources.)

    If our experience teaches us that information comes from minds, then the fact that key classes of biomolecules are comprised of both digital and analog information makes it reasonable to conclude that life itself stems from the work of a Mind.

    Is Biochemical Information Really Information?

    Skeptics, such as philosopher Massimo Pigliucci, often dismiss this particular design argument, maintaining that biochemical information is not genuine information. Instead, they maintain that when scientists refer to biomolecules as harboring information, they are employing an illustrative analogy—a scientific metaphor—and nothing more. They accuse creationists and intelligent design proponents of misconstruing scientists use of analogical language to make the case for a Creator.1

    In light of this criticism, it is worth noting that the case for a Creator doesn’t merely rest on the presence of digital and analog information in biomolecules, but gains added support from work in information theory and bioinformatics.

    For example, information theorist Bernd-Olaf Küppers points out in his classic work Information and the Origin of Life that the structure of the information housed in nucleic acids and proteins closely resembles the hierarchical organization of human language.2 This is what Küppers writes:

    The analogy between human language and the molecular genetic language is quite strict. . . . Thus, central problems of the origin of biological information can adequately be illustrated by examples from human language without the sacrifice of exactitude.3

    Added to this insight is the work by a team from NIH who discovered that the information content of proteins bears the same mathematical structure as human language. To this end, they discovered that a universal grammar exists that defines the structure of the biochemical information in proteins. (For more details on the NIH teams work, see Resources.)

    In other words, the discovery that the biochemical information shares the same features as human language deepens the analogy between biochemical information and the type of information we create as human designers. And, in doing so, it strengthens the case for a Creator.

    Further Studies that Strengthen the Case for a Creator

    So, too, does other work, such as studies in DNA barcoding. Biologists have been able to identify, catalog, and monitor animal and plant species using relatively short, standardized segments of DNA within genomes. They refer to these sequences as DNA barcodes that are analogous to the barcodes merchants use to price products and monitor inventory.

    Typically, barcodes harbor information in the form of parallel dark lines on a white background, creating areas of high and low reflectance that can be read by a scanner and interpreted as binary numbers. Barcoding with DNA is possible because this biomolecule, at its essence, is an information-based system. To put it another way, this work demonstrates that the information in DNA is not metaphorical, but is in fact informational. (For more details on DNA barcoding, see DNA Barcodes Used to Inventory Plant Biodiversity in Resources.)

    Work in nanotechnology also strengthens the analogy between biochemical information and the information we create as human designers. For example, a number of researchers are exploring DNA as a data storage medium. Again, this work demonstrates that biochemical information is information. (For details on DNA as a data storage medium, see Resources.)

    Finally, researchers have learned that the protein machines that operate on DNA during processes such as transcription, replication, and repair literally operate like a computer system. In fact, the similarity is so strong that this insight has spawned a new area of nanotechnology called DNA computing. In other words, the cell’s machinery manipulates information in the same way human designers manipulate digital information. For more details, take a look at the article “Biochemical Turing Machines ‘Reboot’ the Watchmaker Argument” in Resources.)

    The bottom line is this: The more we learn about the architecture and manipulation of biochemical information, the stronger the analogy becomes.

    Does Information Come from a Mind?

    Other skeptics challenge this argument in a different way. They assert that information can originate without a mind. For example, a skeptic recently challenged me this way:

    “A volcano can generate information in the rocks it produces. From [the] information we observe, we can work out what it means. Namely, in this example, that the rock came from the volcano. There was no Mind in information generation, but rather minds at work, generating meaning.

    Likewise, a growing tree can generate information through its rings. Humans can also generate information by producing sound waves.

    However, I dont think that volcanoes have minds, nor do trees—at least not the way we have minds.”

    –Roland W. via Facebook

    I find this to be an interesting point. But, I don’t think this objection undermines the case for a Creator. Ironically, I think it makes the case stronger. Before I explain why, though, I need to bring up an important clarification.

    In Roland’s examples, he conflates two different types of information. When I refer to the analogy between human languages and biochemical information, I am specifically referring to semantic information, which consists of combinations of symbols that communicate meaning. In fact, Roland’s point about humans generating information with sound waves is an example of semantic information, with the sounds serving as combinations of ephemeral symbols.

    The type of information found in volcanic rocks and tree rings is different from the semantic information found in human languages. It is actually algorithmic information, meaning that it consists of a set of instructions. And technically, the rocks and tree rings dont contain this information—they result from it.

    The reason why we can extract meaning and insight from rocks and tree rings is because of the laws of nature, which correspond to algorithmic information. We can think of these laws as instructions that determine the way the world works. Because we have discovered these laws, and because we have also discovered nature’s algorithms, we can extract insight and meaning from studying rocks and tree rings.

    In fact, Küppers points out that biochemical systems also consist of sets of instructions instantiated within the biomolecules themselves. These instructions direct activities of the biomolecular systems and, hence, the cell’s operations. To put it another way, biochemical information is also algorithmic information.

    From an algorithmic standpoint, the information content relates to the complexity of the instructions. The more complex the instructions, the greater the information content. To illustrate, consider a DNA sequence that consists of alternating nucleotides, AGAGAGAG . . . and so on. The instructions needed to generate this sequence are:

    1. Add an A
    2. Add a G
    3. Repeat steps 1 and 2, x number of times, where x corresponds to the length of the DNA sequence divided by 2

    But what about a DNA sequence that corresponds to a typical gene? In effect, because there is no pattern to that sequence, the set of instructions needed to create that sequence is the sequence itself. In other words, a much greater amount of algorithmic information resides in a gene than in a repetitive DNA sequence.

    And, of course, our common experience teaches us that information—whether it’s found in a gene, a rock pile, or a tree ring—comes from a Mind.

    Resources

    Endnotes
    1. For example, see Massimo Pigliucci and Maarten Boudry, “Why Machine-Information Metaphors Are Bad for Science and Science Education,” Science and Education 20, no. 5–6 (May 2011): 453–71; doi:10.1007/s11191-010-9267-6.
    2. Bernd-Olaf Küppers, Information and the Origin of Life (Boston, MA: MIT Press, 1990), 24–25.
    3. Küppers, Information, 23.
  • New Insights into Endothermy Heat Up the Case for a Creator

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Aug 07, 2019

    I feel cold all the time.

    When I was younger, I was always hot. I needed to be in air conditioning everywhere I went. I could never get the temperature cold enough. But now that I am older, I feel like a frail person who is always chilled, needing to drape myself with a blanket to keep warm.

    Nevertheless, like all human beings, I am still warm-blooded. I am an endotherm, as are all mammals and birds.

    For many biologists, endothermy represents a bit of an enigma. Maintaining a constant body temperature requires an elevated basal metabolic rate. But the energy needed to preserve a constant body temperature doesn’t come cheap. In fact, warm-blooded animals demand 30 times the energy per unit time compared to cold-blooded (ectothermic) creatures.

    Though biologists have tried to account for endothermy, no model has adequately explained why birds and mammals are warm-blooded. The advantages of being warm-blooded over being cold-blooded have not seemed to adequately outweigh costs—until now.

    Recently, a biologist from the University of Nevada, Reno, Michael L. Logan, published a model that helps make sense of this enigma.1 His work evokes the optimal design and elegant rationale for endothermy in birds and mammals—and ectothermy in amphibians and reptiles.

    An Explanation for Endothermy

    For endothermy to exist, it must confer some significant advantage for animals constant, elevated body temperatures.

    Logan argues that endothermy maintains mammalian and bird body temperatures close to the thermal optimum for immune system functionality. The operations of the immune system are temperature-dependent. If the temperature is too low or too high, the immune system responds poorly to infectious agents. But an elevated and stable body temperature primes mammalian and bird immune systems to rapidly and effectively respond to pathogens. When birds and mammals acquire a pathogen, their bodies mount a fever response. This slight elevation in temperature places their body temperature at the thermal optimum.

    In other words, the fever response plays a critical role when animals battle infectious agents. And warm-blooded animals have the advantage of possessing body temperatures close to ideal.

    Temperature and Immune System Function

    A body of evidence indicates that the immune systems components display temperature-dependent changes in activity. As it turns out, fever optimizes immune system function by:

    1. Increasing the flow of blood through the bloodstream because of the vasodilation (blood vessel expansion) associated with fever. This increased blood flow accelerates the movement of immune cells throughout the body, giving them more timely access to pathogens.
    2. Increasing binding of immune system proteins to immune cells, assisting their trafficking to lymph tissue.
    3. Increasing cellular activity, such as proliferation and differentiation of immune cells and phagocytosis.

    blog__inline--new-insights-into-endothermy

    Figure: The Human Immune System. Image credit: Shutterstock

    Other studies indicate that some pathogens, such as fungi, lose virulence at higher temperatures, further accounting for elevated body temperatures and the importance of the fever response. Of course, if body temperature becomes too high, it will compromise immune system function, moving it away from the temperature optimum and leading to other complications. So, the fever response must be carefully regulated.

    Heres the key point: the metabolic costs of endothermy are justified because warm-bloodedness allows the immune systems of birds and mammals to be near enough to the temperature optimum that infectious agents can be quickly cleared from their bodies.

    Fever Response in Ectotherms

    Cold-blooded animals (ectotherms) also mount a fever response to infectious agents for the same reason as endotherms. However, the body temperature of ectotherms is set by their surroundings. This limitation means that ectotherms need to regulate their body temperature and mount the fever response through their behavior by moving into spaces with elevated temperatures. Doing so places them at the mercy of environmental changes. This condition means that cold-blooded creatures experience a significant time lag between the onset of infection and the fever response. It also means that, in some cases, ectotherms can’t elevate their body temperature to the immune system optimum if, for example, it is night or overcast.

    Finally, in an attempt to elevate their body temperatures, ectotherms need to be out from under cover, making themselves vulnerable to predators. So, according to Logan’s model, endothermy offers some tangible advantages compared to ectothermy.

    But endothermy comes at a cost. As mentioned, the metabolic cost of endothermy is extensive compared to ectothermy. Pathogen virulence marks another disadvantage. Logan points out that pathogens that infect cold-blooded animals are much less virulent than pathogens that infect warm-blooded creatures.

    Endothermy and Ectothermy Trade-Offs

    So, when it comes to regulation of animal body temperature, a set of trade-offs exists that include:

    • Metabolic costs
    • Immune system responsiveness and effectiveness
    • Pathogen virulence
    • Vulnerability to predators

    These trade-offs can be managed by two viable strategies: endothermy and ectothermy. Each has advantages and disadvantages. And each is optimized in its own right.

    Regulation of Body Temperature and the Case for a Creator

    Logan seeks to account for the evolutionary origins of endothermy by appealing to the advantages it offers organisms battling pathogens. But, examining Logans scenario leaves one feeling as if the explanation is little more than an evolutionary just-so story.

    When endothermy presented an enigma for biologists, it would have been hard to argue that it reflected the handiwork of a Creator, particularly in light of its large metabolic cost. But now that scientists understand the trade-offs in play and the optimization associated with the endothermic lifestyle, we can also interpret the optimization of endothermy and ectothermy as evidence for design.

    From my vantage point, optimization signifies the handiwork of a Creator. As I discuss in The Cell’s Design, saying something is optimized is equivalent to saying it is well-designed. The optimization of an engineered system doesn’t just happen. Rather, such systems require forethought, planning, and careful attention to detail. In the same way, the optimized designs of biological systems like endothermy and ectothermy reasonably point to the work of a Creator.

    And I am chill with that.

    Resources

    Endnotes
    1. Michael L. Logan, “Did Pathogens Facilitate the Rise of Endothermy?” Ideas in Ecology and Evolution 12 (June 4, 2019): 1–8, https://ojs.library.queensu.ca/index.php/IEE/article/view/13342.
  • Is SETI an Intelligent Design Research Program?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jul 24, 2019

    When I was a little kid, my father was chair of the physics department at West Virginia Institute of Technology (WVIT). We lived in faculty housing on the outskirts of the WVIT campus and, as a result, the college grounds became my playground.

    I have always felt at home on college and university campuses. Perhaps this is one reason I enjoy speaking at university venues. I also love any chance I get to interact with college students. They have inquisitive minds and they won’t hesitate to challenge ideas.

    Skeptical Challenge

    A few years ago I was invited to present a case for a Creator, using evidence from biochemistry, at Cal Poly San Luis Obispo. During the Q&A session, a skeptical student challenged my claims, insisting that intelligent design/creationism isn’t science. In leveling this charge, he was advocating scientism—the view that science is the only way to discover truth; in fact, science equates to truth. Thus, if something isn’t scientific, then it can’t be true. On this basis he rejected my claims.

    You might be surprised by my response. I agreed with my questioner.

    My case for a Creator based on the design of biochemical systems is not science. It is a philosophical and theological argument informed by scientific discovery. In other words, scientific discoveries have metaphysical implications. And, by identifying and articulating those implications, I built a case for God’s existence and role in the origin and design of life.

    Having said this, I do think that design detection is legitimately part of the fabric of science. We can use scientific methodologies to detect the work of intelligent agency. That is, we can develop rigorous scientific evidence for intelligent design. I also think we can ascribe attributes to the intelligent designer from scientific evidence at hand.

    In defense of this view, I (and others who are part of the Intelligent Design Movement, or IDM) have pointed out that there are branches of science that function as intelligent design programs, such as research in archaeology and the Search for Extraterrestrial Intelligence (SETI). We stand to learn much from these disciplines about the science of design detection. (For a detailed discussion, see the Resources section.)

    SETI and Intelligent Design

    Recently, I raised this point in a conversation with another skeptic. He challenged me on that point, noting that Seth Shostak, an astronomer from the SETI Institute, wrote a piece for Space.com repudiating the connection between intelligent design (ID) and SETI, arguing that they don’t equate.

     

    blog__inline--is-seti-an-intelligent-design-research-program
    SONY DSC

    Figure: Seth Shostak. Image credit: Wikipedia

    According to Shostak,

    “They [intelligent design proponents] point to SETI and say, ‘upon receiving a complex radio signal from space, SETI researchers will claim it as proof that intelligent life resides in the neighborhood of a distant star. Thus, isn’t their search completely analogous to our own line of reasoning—a clear case of complexity implying intelligence and deliberate design? And SETI, they would note, enjoys widespread scientific acceptance.”1

    Shostak goes on to say, “If we as SETI researchers admit this is so, it sounds as if were guilty of promoting a logical double standard. If the ID folks arent allowed to claim intelligent design when pointing to DNA, how can we hope to claim intelligent design on the basis of a complex radio signal?”2

    In an attempt to distinguish the SETI Institute from the IDM, Shostak asserts that ID proponents make their case for intelligent design based on the complexity of biological and biochemical systems. But this is not what the SETI Institute does. According to Shostak, “The signals actually sought by today’s SETI searches are not complex, as the ID advocates assume. We’re not looking for intricately coded messages, mathematical series, or even the aliens’ version of ‘I Love Lucy.’”

    Instead of employing complexity as an indicator of intelligent agency, SETI looks for signals that display the property of artificiality. What they mean by artificiality is that specifically, SETI is looking for a simple signal of narrow-band electromagnetic radiation that forms an endless sinusoidal pattern. According to SETI investigators, this type of signal does not occur naturally. Shostak also points out that the context of the signal is important. If the signal comes from a location in space that couldn’t conceivably harbor life, then SETI researchers would be less likely to conclude that it comes from an intelligent civilization. On the other hand, if the signal comes from a planetary system that appears life-friendly, this signal would be heralded as a successful detection event.

    Artificiality and Intelligent Design

    I agree with Shostak. Artificiality, not complexity, is the best indicator of intelligent design. And, it is also important to rule out natural process explanations. I can’t speak for all creationists and ID proponents, but the methodology I use to detect design in biological systems is precisely the same one the SETI Institute employs.

    In my book The Cell’s Design, I propose the use of an ID pattern to detect design. Toward this end, I point out that objects, devices, and systems designed by human beings—intelligent designers—are characterized by certain properties that are distinct from objects and systems generated by natural processes. To put it in Shostak’s terms, human designs display artificiality. And we can use the ID pattern as a way to define what artificiality should look like.

    Here are three ways I adopt this approach:

    1. In The Cell’s Design, I follow after natural theologian William Paley’s work. Paley described designs created by human beings as contrivances in which the concept of artificiality was embedded. I explain examples of such artificiality in biochemical systems.
    2. In Origins of Life (a work I coauthored with astronomer Hugh Ross) and Creating Life in the Lab, I point out that natural processes don’t seem to be able to account for the origin of life and, hence, the origin of biochemical systems.
    3. Finally, in Creating Life in the Lab, I show that attempts to create protocells starting with simple molecules and attempts to recapitulate the different stages in the origin-of-life pathway depend upon intelligent agency. This dependence further reinforces the artificiality displayed by biochemical systems.

    Collectively, all three books present a comprehensive case for a Creator’s role in the origin and fundamental design of life, with each component of the overall case for design resting on the artificiality of biochemical systems. So, even though the SETI Institute may want to distance themselves from the IDM, SETI is an intelligent design program. And intelligent design is, indeed, part of the construct of science.

    In other words, scientists from a creation model perspective can make a rigorous scientific case for the role of intelligent agency in the origin and design of biochemical systems, and even assign attributes to the designer. At that point, we can then draw metaphysical conclusions about who that designer might be.

    Resources

    Endnotes
    1. Seth Shostak, “SETI and Intelligent Design,” Space.com (December 1, 2005), https://www.space.com/1826-seti-intelligent-design.html.
    2. Shostak, “SETI and Intelligent Design.”
  • Does Old-Earth Creationism Make God Deceptive?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jul 17, 2019

    “Are [vestigial structures] unequivocal evidence of evolution?

    No. Are they reasonable evidence of evolution? Yes.

    Ditto gene sequences.

    Appearance of evolution is no more a valid deflection [for the overwhelming evidence for evolution] than the appearance of age is a valid dodge of the overwhelming confluence of evidence of antiquity.

    Both are sinking ships. I got off before going under with you on this one.”

    —Hill R. (a former old-earth creationist who now espouses theistic evolution/evolutionary creationism)

    Most people who follow my work at Reasons to Believe know I question the grand claim of the evolutionary paradigm; namely, that evolutionary processes provide the exclusive explanation for the origin, design, and history of life. In light of my skepticism, friends and foes alike often ask me how I deal with (what many people perceive to be) the compelling evidence for the evolutionary history of life, such as vestigial structures and shared genetic features in genomes.

    As part of my response, I point out that this type of evidence for evolution can be accommodated by a creation model, with the shared features reflecting common design, not common descent—particularly now that we know that there is a biological rationale for many vestigial structures and shared genetic features. This response prompted my friend Hill R. to level his objection. In effect, Hill says I am committing the “appearance of evolution” fallacy, which he believes is analogous to the “appearance of age” fallacy committed by young-earth creationists (YECs).

    Hill is not alone in his criticism. Other people who embrace theistic evolution/evolutionary creation (such as my friends at BioLogos) level a similar charge. According to these critics, both appearance of age and appearance of evolution fallacies make God deceptive.

    If biological systems are designed, but God made them appear as if they evolved, then the conclusions we draw when we investigate nature are inherently untrustworthy. This is a problem because, according to Scripture, God reveals himself to us through the record of nature. But if we are misled by natures features and, consequently, draw the wrong conclusion, then it makes God deceptive. However, God cannot lie or deceive. It is contrary to his nature.

    So, how do I respond to this theological objection to RTB’s creation model?

    Before I reply, I want to offer a little more background information to make sure that anyone who is unfamiliar with this concern can better appreciate the seriousness of the charge against our creation model. If you don’t need the background explanation, then feel free to skip ahead to A Response to the Appearance of Evolution Challenge.

    Evidence for Evolution: Vestigial Structures

    Evolutionary biologists often point to vestigial structures—such as the pelvis and hind limbs of whales and dolphins (cetaceans)—as compelling evidence for biological evolution. Evolutionary biologists view vestigial structures this way because they are also homologous (structurally similar) structures. Vestigial structures are rudimentary body parts that are smaller and simpler than the corresponding features possessed by the other members of a biological group. As a case in point, the whale pelvis and hind limbs are homologous to the pelvis and hind limbs of all other mammals.

    blog__inline--does-old-earth-creationism-make-god-deceptive-1

    Figure 1: Whale Pelvis. Image credit: Shutterstock

    Evolutionary biologists believe that vestigial structures were fully functional at one time but degenerated over the course of many generations because the organisms no longer needed them to survive in an ever-changing environment—for example, when the whale ancestor transitioned from land to water. From an evolutionary standpoint, fully functional versions of these structures existed in the ancestral species. The structures’ form and function may be retained (possibly modified) in some of the evolutionary lineages derived from the ancestral species, but if no longer required, the structures become diminished (and even lost) in other lineages.

    Evidence for Evolution: Shared Genetic Features

    Evolutionary biologists also consider shared genetic features found in organisms that naturally group together as compelling evidence for common descent. One feature of particular interest is the identical (or nearly identical) DNA sequence patterns found in genomes. According to this line of reasoning, the shared patterns arose as a result of a series of substitution mutations that occurred in the common ancestor’s genome. Presumably, as the varying evolutionary lineages diverged from the nexus point, they carried with them the altered sequences created by the primordial mutations.

    Synonymous mutations play a significant role in this particular argument for common descent. Because synonymous mutations don’t alter the amino acid sequence of proteins, their effects are considered to be inconsequential. (In a sense, they are analogous to vestigial anatomical features.) So, when the same (or nearly the same) patterns of synonymous mutations are observed in genomes of organisms that cluster together into the same group, most life scientists interpret them as compelling evidence of the organisms’ common evolutionary history.

    A Response to the Evidence for Evolution

    As a rejoinder to this evidence, I point out that we continue to uncover evidence that vestigial structures display function (see Vestigial Structures are Functional in the Resources section.) Likewise, evidence is beginning to accumulate that synonymous mutations have functional consequences. (see Shared Genetic Features Reflect Design in the Resources section.) Again, if these features have functional utility, then they can reasonably be interpreted as the Creator’s handiwork.

    But, even though these biological features bear function, many critics of the RTB model think that the shared features of these biological systems still bear the hallmarks of an evolutionary history. Therefore, they argue that these features look as if they evolved. And if so, we are guilty of the “appearance of evolution fallacy.

    Appearance of Age and the Appearance of Evolution

    In 1857, Philip Gosse, a biologist and preacher from England, sought to reconcile the emerging evidence for Earth’s antiquity with Scripture. Gosse was convinced that the earth was old. He was also convinced that Scripture taught that the earth was young. In an attempt to harmonize these disparate stances, he proposed the appearance of age argument in a book titled Omphalos. In this work, Gosse argued that God created Earth in six days, but made it with the appearance of age.

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    Figure 2: Philip Henry Gosse, 1855. Image credit: Wikipedia

    This idea persists today, finding its way into responses modern-day YECs make to the scientific evidence for Earth’s and life’s antiquity. For many people (including me), the appearance of age argument is fraught with theological problems, the chief one being that it makes God deceptive. If Earth appears to be old, and it measures to be old, yet it is young, then we can’t trust anything we learn when we study nature. This problem is not merely epistemological; it is theological because nature is one way that God has chosen to make himself known to us. But if our investigation of nature is unreliable, then it means that God is untrustworthy.

    In other words, on the surface, both the appearance of age and the appearance of evolution arguments made by YECs and old-earth creationists (OECs), respectively, seem to be equally problematic.

    But does the RTB position actually commit the appearance of evolution fallacy? Does it suffer from the same theological problems as the argument first presented by Gosse in Omphalos? Are we being hypocritical when we criticize the appearance of age fallacy, only to commit the appearance of evolution fallacy?

    A Response to the Appearance of Evolution Challenge

    This charge against the RTB creation model neglects to fully represent the reasons I question the evolutionary paradigm.

    First, my skepticism is not theologically motivated but scientifically informed. For example, I point out in an article I recently wrote for Sapientia that a survey of the scientific literature makes it clear that evolutionary theory as currently formulated cannot account for the key transitions in life’s history, including:

    • the origin of life
    • the origin of eukaryotic cells
    • the origin of body plans
    • the origin of human exceptionalism

    Additionally, some predictions that flow out of the evolutionary paradigm have failed (such as the widespread prevalence of convergence), further justifying my skepticism. (See Scientific Challenges to the Evolutionary Paradigm in the Resources section.)

    In other words, when we interpret shared features as a manifestation of common design (including vestigial structures and shared genetic patterns), it is in the context of scientifically demonstrable limitations of the evolutionary framework to fully account for life’s origin, history, and design. To put it differently, because of the shortcomings of evolutionary theory, we don’t see biological systems as having evolved. Rather, we think they’ve been designed.

    Appearance of Design Fallacy

    Even biologists who are outspoken atheists readily admit that biological and biochemical systems appear to be designed. Why else would Nobel Laureate Francis Crick offer this word of caution to scientists studying biochemical systems: “Biologists must keep in mind that what they see was not designed, but rather evolved.”1 What other reason would evolutionary biologist Richard Dawkins offer for defining biology as “the study of complicated things that give the appearance of having been designed for a purpose”?2

    Biologists can’t escape the use of design language when they describe the architecture and operation of biological systems. In and of itself, this practice highlights the fact that biological systems appear to be designed, not evolved.

    To sidestep the inexorable theological implications that arise when biologists use design language, biologist Colin Pittendrigh coined the term teleonomy in 1958 to describe systems that appear to be purposeful and goal-directed, but aren’t. In contrast with teleology—which interprets purposefulness and goal-directedness as emanating from a Mind— teleonomy views design as the outworking of evolutionary processes. In other words, teleonomy allows biologists to utilize design language— when they describe biological systems—without even a tinge of guilt.

    In fact, the teleonomic interpretation of biological design resides at the heart of the Darwinian revolution. Charles Darwin claimed that natural selection could account for the design of biological systems. In doing so, he supplanted Mind with mechanism. He replaced teleology with teleonomy.

    Prior to Darwin, biology found its grounding in teleology. In fact, Sir Richard Owen—one of England’s premier biologists in the early 1800s—produced a sophisticated theoretical framework to account for shared biological features found in organisms that naturally cluster together (homologous structures). For Owen (and many biologists of his time) homologous structures were physical manifestations of an archetypal design that existed in the Creator’s mind.

    Thus, shared biological features—whether anatomical, physiological, biochemical, or genetic—can be properly viewed as evidence for common design, not common descent. In fact, when Darwin proposed his theory of evolution, he appropriated Owen’s concept of the archetype but then replaced it with a hypothetical common ancestor.

    Interestingly, Owen (and other like-minded biologists) found an explanation for vestigial structures like the pelvis and hind limb bones (found in whales and snakes) in the concept of the archetype. They regarded these structures as necessary to the architectural design of the organism. In short, a model that interprets shared biological characteristics from a design/creation model framework has historical precedence and is based on the obvious design displayed by biological systems.

    Given the historical precedence for interpreting the appearance of design in biology as bona fide design and the inescapable use of design language by biologists, it seems to me that RTBs critics commit the appearance of design fallacy when they (along with other biologists) claim that things in biology look designed, but they actually evolved.

    Theories Are Underdetermined by Data

    A final point. One of the frustrating aspects of scientific discovery relates to whats called the underdetermination thesis.3 Namely, two competing theories can explain the same set of data. According to this idea, theories are underdetermined by data. This limitation means that two or more theories—that may be radically different from one another—can equally account for the same data. Or, to put it another way, the methodology of science never leads to one unique theory. Because of this shortcoming, other factors—nonscientific ones—influence the acceptance or rejection of a scientific theory, such as a commitment to mechanistic explanations to explain all of biology.

    As a consequence of the underdetermination theory, evolutionary models don’t have the market cornered when it comes to offering an interpretation of biological data. Creation models, such as the RTB model—which relies on the concept of common design—also makes sense of the biological data. And given the inability of current evolutionary theory to explain key transitions in life’s history, maybe a creation model approach is the better alternative.

    In other words, when we interpret vestigial structures and shared genetic features from a creation model perspective, we are not committing an appearance of age type of fallacy, nor are we making God deceptive. Instead, we are offering a common sense and scientifically robust interpretation of the elegant designs so prevalent throughout the living realm.

    Far from a sinking ship one should abandon, a creation model offers a lifeline to scientific and biblical integrity.

    Resources

    Vestigial Structures Are Functional

    Shared Genetic Features Reflect Design

    Scientific Challenges for the Evolutionary Paradigm

    Archetype Biology

    Endnotes
    1. Francis Crick, What Mad Pursuit: A Personal View of Scientific Discovery (New York: Basic Books, 1988), 138.
    2. Richard Dawkins, The Blind Watchmaker: Why the Evidence for Evolution Reveals a Universe without Design (New York: W. W. Norton, 1996), 4.
    3. Val Dusek, Philosophy of Technology: An Introduction (Malden, MA: Blackwell Publishing, 2006), 12.
  • Membrane Biochemistry Challenges Route to Evolutionary Origin of Complex Cells

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jul 10, 2019

    If you find yourself in need of directions when traveling through New England and you ask a local for help, he or she just might reply, “You can’t get there from here.” As you can imagine, these aren’t welcome words, particularly when all you want to do is make your way to your destination.

    Unfortunately, the same thing could be said to biologists trying to discover the evolutionary route that led to the emergence of complex, eukaryotic cells. No matter the starting point, it seems as if you just can’t get there from here.

    This frustration becomes most evident as evolutionary biologists try to account for the biochemical makeup of the membranes found in eukaryotic cells. In my opinion, this struggle is not just an inconvenient detour. As the following paragraphs show, obstacles line the roadway, ultimately leading to a dead end that exposes the shortcomings of the endosymbiont hypothesis—a cornerstone idea in evolutionary biology.

    Endosymbiont Hypothesis

    Most biologists believe that the endosymbiont hypothesis stands as the best explanation for the origin of complex cells. According to this hypothesis, complex cells originated when symbiotic relationships formed among single-celled microbes after free-living bacterial and/or archaeal cells were engulfed by a “host” microbe.

    The mitochondrion represents the “poster child” of the endosymbiont hypothesis. Presumably, this organelle started as an endosymbiont. Evolutionary biologists believe that once engulfed by the host cell, the microbe took up permanent residency, growing and dividing inside the host. Over time, the endosymbiont and host became mutually interdependent, with the endosymbiont providing a metabolic benefit—such as a source of ATP—for the host cell. In turn, the host cell provided nutrients to the endosymbiont. Presumably, the endosymbiont gradually evolved into an organelle through a process referred to as genome reduction. This reduction resulted when genes from the endosymbiont’s genome were transferred into the genome of the host organism.

    Evidence for the Endosymbiont Hypothesis
    1. Most of the evidence for the endosymbiont hypothesis centers around mitochondria and their similarity to bacteria. Mitochondria are about the same size and shape as a typical bacterium and have a double membrane structure like gram-negative cells. These organelles also divide in a way that is reminiscent of bacterial cells.

    2. Biochemical evidence also exists for the endosymbiont hypothesis. Evolutionary biologists view the presence of the diminutive mitochondrial genome as a vestige of this organelle’s evolutionary history. They see the biochemical similarities between mitochondrial and bacterial genomes as further evidence for the evolutionary origin of these organelles.

    3. The presence of the unique lipid, cardiolipin, in the mitochondrial inner membrane also serves as evidence for the endosymbiont hypothesis. This important lipid component of bacterial inner membranes is not found in the membranes of eukaryotic cells—except for the inner membranes of mitochondria. In fact, biochemists consider it a signature lipid for mitochondria and a vestige of the organelle’s evolutionary history. So far, the evolutionary route looks well-paved and clear.

    Discovery of Lokiarchaeota

    Evolutionary biologists have also developed other lines of evidence in support of the endosymbiont hypothesis. For example, biochemists have discovered that the genetic core (DNA replication and the transcription and translation of genetic information) of eukaryotic cells resembles that of the archaea. This similarity suggests to many biologists that a microbe belonging to the archaeal domain served as the host cell that gave rise to eukaryotic cells.

    Life scientists think they may have determined the identity of that archaeal host. In 2015, a large international team of collaborators reported the discovery of Lokiarchaeota, a new phylum belonging to the archaea. This phylum clusters with eukaryotes on the evolutionary tree. Analysis of the genomes of Lokiarchaeota identifies a number of genes involved in membrane-related activities, suggesting that this microbe may well have possessed the ability to engulf other microbes.1 At this point, it looks like you can get there from here.

    Challenges to the Endosymbiont Hypothesis

    Despite this seemingly compelling evidence, the evolutionary route to the first eukaryotic cells is littered with potholes. I have written several articles detailing some of the obstacles. (See Challenges to the Endosymbiont Hypothesis in the Resources section.) Also, a divide on the evolutionary roadway called the lipid divide compounds the problem for the endosymbiont hypothesis.

    Lipid Divide

    The lipid divide refers to the difference in the chemical composition of the cell membranes found in bacteria and archaea. Phospholipids comprise the cell membranes of both sorts of microbes. But the similarity ends there. The chemical makeup of the phospholipids is distinct in bacteria and archaea.

    Bacterial phospholipids are built around a d-glycerol backbone, which has a phosphate moiety bound to the glycerol in the sn-3 position. Two fatty acids are bound to the d-glycerol backbone at the sn-1 and sn-2 positions. In water, these phospholipids assemble into bilayer structures.

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    Figure: Difference between archaeal (top) and bacterial (middle and bottom) phospholipids. Features include 1: isoprene chains, 2: ether linkage, 3: l-glycerol, 4 and 8: phosphate group, 5: fatty acid chains, 6: ester linkages, 7: d-glycerol, 9: lipid bilayer of bacterial membranes, 10: lipid monolayer found in some archaea. Image credit: Wikipedia

    Archaeal phospholipids are constructed around an l-glycerol backbone (which produces membrane lipids with different stereochemistry than bacterial phospholipids). The phosphate moiety is attached to the sn-1 position of glycerol. Two isoprene chains are bound to the sn-2 and sn-3 positions of l-glycerol via ether linkages. Some archaeal membranes are formed from phospholipid bilayers, while others are formed from phospholipid monolayers.

    Presumably, the structural features of the archaeal phospholipids serve as an adaptation that renders them ideally suited to form stable membranes in the physically and chemically harsh environments in which many archaea find themselves.

    Lipid Divide Frustrates the Origin of Eukaryotic Cell Membranes

    In light of the lipid divide and the evidence that seemingly indicates that the endosymbiotic host cell likely belonged to Lokiarchaeota, it logically follows that the membrane composition of eukaryotic cells should be archaeal-like. But, this expectation is not met and the evolutionary route encounters another pothole. Instead, the cell membranes of eukaryotic cells closely resemble bacterial membranes.

    One way to repair the roadway is to posit that during the evolutionary process that led to the emergence of eukaryotic cells, a transition from archaeal-like membranes to bacterial-like membranes took place. In fact, supporting evidence comes from laboratory studies demonstrating that stable bilayers can form from a mixture of bacterial and archaeal phospholipids, even though the lipids from the two sources have opposite stereochemistry.

    Evolutionary biologists Purificación López-García and David Moreira question if evidence can be marshaled in support of this scenario for two reasons.2 First, mixing of phospholipids in the lab is a poor model for cell membranes that function as a “dynamic cell-environment interface.”3

    Second, they question if this transition is feasible given how exquisitely optimized membrane proteins must be to fit into cell membranes. The nature of protein optimization is radically different for bacterial and archaeal membranes. Because cell membrane systems are optimized, the researchers question if an adequate driving force for this transition exists.

    In other words, these two scientists express serious doubts about the biochemical viability of a transitional stage between archaeal membranes. In light of these obstacles, López-García and Moreira write, “The archaea-to-bacteria membrane shift remains the Achilles’ heel for these models [that propose an archaeal host for endosymbionts].”4

    In other words, you can’t get there from here.

    Can Lokiarchaeota Traverse the Lipid Divide?

    In the midst of this uncertain evolutionary route, a recent study by investigators from the Netherlands seems to point the way toward the evolutionary origin of eukaryotic membranes.5 Researchers screened the Lokiarchaeota genome for enzymes that would take part in phospholipid synthesis with the hope of finding clues about how this transition may have occurred. They conclude that this group of microbes could not make l-glycerol-1-phosphate (a key metabolic intermediate in the production of archaeal phospholipids) because it lacked the enzyme glycerol-1-phosphate dehydrogenase (G1PDH). They also discovered evidence that suggests that this group of microbes could make fatty acids and chemically attach them to sugars. The researchers argue that Lokiarchaeota could make some type of hybrid phospholipid with features of both archaeal and bacterial phospholipids.

    The team’s approach to understanding how evolutionary processes could bridge the lipid divide and account for the origin of eukaryotic membranes is clever and inventive, to be sure. But it is far from convincing for at least four reasons.

    1. Absence of evidence is not evidence of absence, as the old saying goes. Just because the research team didn’t find the gene for G1PDH in the Lokiarchaeota genetic material doesn’t mean this microbe didn’t have the capacity to make archaeal-type phospholipids. Toward this end, it is important to note that researchers have not cultured any microbe that belongs to this group organisms. The groups existence is inferred from metagenomic analysis, which involves isolating small fragments of DNA from the environment (in this case a hydrothermal vent system in the Atlantic Ocean, called Loki’s Castle) and stitching them together into a genome. The Lokiarchaeota “genome” is low quality (1.4-fold coverage) and incomplete (8 percent of the genome is missing). Around one-third (32 percent) of the genome codes for proteins with unknown function. Could it be that an enzyme capable of generating l-glycerol-1-phosphate exists in the mysterious third of the genome? Or in the missing 8 percent?

    2. While the researchers discovered that genes could conceivably work together to make d-glycerol-3-phosphate (though the enzymes encoded by these genes perform different metabolic functions), they found no direct evidence that Lokiarchaeota produces d-glycerol-3-phosphate. Nor did they find evidence for glycerol-3-phosphate dehydrogenase (G3PDH) in the Lokiarchaeota genetic material. This enzyme plays a key role in the synthesis of phospholipids in bacteria.

    3. Though the researchers found evidence that Lokiarchaeota had the capacity to make fatty acids, some of the genes required for the process seem to have been acquired by these microbes via horizontal gene transfer with genetic material from bacteria. (It should be noted that 29 percent of the Lokiarchaeota genome comes from the bacteria.) It is not clear when Lokiarchaeota acquired these genes and, therefore, if this metabolic capability has any bearing on the origin of eukaryotes.

    4. The researchers present no evidence that Lokiarchaeota possessed the protein machinery that would chemically attach isoprenoid lipids to d-glycerol-3-phosphate via ether linkages.

    Thus, the only way to establish Lokiarchaeota membranes as a transitional evolutionary pathway between those found in Archaea and Bacteria is to perform chemical analysis of its membranes. At this juncture, such analysis is impossible to perform because no one has been able to culture Lokiarchaeota. In fact, other evidence suggests that this group of microbes possessed archaeal-type membranes. Researchers have recovered archaeal lipids in the sediments surrounding Loki’s Castle, but they have not recovered bacterial-like lipids.

    More Lipid Divide Frustration

    Given these problems, could it be that the host microbe for the endosymbiont was a member of Bacteria, not Archaea? While this model would solve the problem of the lipid divide, it leaves unexplained the similarity between the genetic core of eukaryotes and the Archaea. Nor does it account for the grouping of eukaryotes with the Archaea.

    It doesn’t look like you can get there from here, either.

    Evolutionary biologists Jonathan Lombard, Purificación López-García and David Moreira sum things up when they write, “The origin of eukaryotic membranes is a problem that is rarely addressed by the different hypotheses that have been proposed to explain the emergence of eukaryotes.”6 Yet, until this problem is adequately addressed, the evolutionary route to eukaryotes will remain obscure and the endosymbiont hypothesis noncompelling.

    In light of this challenge and others, maybe a better way to make sense of the origin of eukaryotic cells is to view them as the Creator’s handiwork. For many scientists, it is a road less traveled, but it accounts for all of the data. You can get there from here.

    Resources

    Challenges to the Endosymbiont Hypothesis

    Support for a Creation Model for the Origin of Eukaryotic Cells

    Endnotes
    1. Anja Spang et al., “Complex Archaea that Bridge the Gap between Prokaryotes and Eukaryotes,” Nature 521 (May 14, 2015): 173–79, doi:10.1038/nature14447; Katarzyna Zaremba-Niedzwiedzka et al., “Asgard Archaea Illuminate the Origin of Eukaryotic Cellular Complexity,” Nature 541 (January 19, 2017): 353–58, doi:10.1038/nature21031.
    2. Purificación López-García and David Moreira, “Open Questions on the Origin of Eukaryotes,” Trends in Ecology and Evolution 30, no. 11 (November 2015): 697–708, doi:10.1016/j.tree.2015.09.005.
    3. López-García and Moreira, “Open Questions.”
    4. López-García and Moreira, “Open Questions.”
    5. Laura Villanueva, Stefan Schouten, and Jaap S. Sinninghe Damsté, “Phylogenomic Analysis of Lipid Biosynthetic Genes of Archaea Shed Light on the ‘Lipid Divide,’” Environmental Microbiology 19, no. 1 (January 2017): 54–69, doi:10.1111/1462-2920.13361.
    6. Jonathan Lombard, Purificación López-García, and David Moreira, “The Early Evolution of Lipid Membranes and the Three Domains of Life,” Nature Reviews Microbiology 10 (June 11, 2012): 507–15, doi:10.1038/nrmicro2815.
  • Ancient Mouse Fur Discovery with Mighty Implications

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jun 26, 2019

    “What a mouse! . . . WHAT A MOUSE!”

    The narrator’s exclamation became the signature cry each time the superhero Mighty Mouse carried out the most impossible of feats.

    A parody of Superman, Mighty Mouse was the 1942 creation of Paul Terry of Terrytoons Studio for 20th Century Fox. Since then, Mighty Mouse has appeared in theatrical shorts and films, Saturday morning cartoons, and comic books.

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    Figure 1: Mighty Mouse. Image credit: Wikipedia

    Throughout each episode, the characters sing faux arias—mocking opera—with Mighty Mouse belting out, “Here I am to save the day!” each time he flies into action. As you would expect, many of the villains Mighty Mouse battles are cats, with his archnemesis being a feline named Oil Can Harry.

    Mouse Fur Discovery

    Recently, a team of researchers headed by scientists from the University of Manchester in the UK went to heroic measures to detect pigments in a 3-million-year-old mouse fossil, nicknamed—you guessed it—“mighty mouse.”1 To detect the pigments, the researchers developed a new method that employs Synchrotron Rapid Scanning X-Ray Fluorescence Imaging to map metal distributions in the fossil, which, in turn, correlate with the types of pigments found in the animal’s fur when it was alive.

    This work paves the way for paleontologists to develop a better understanding of past life on Earth, with fur pigmentation being unusually important. The color of an animal’s fur has physiological and behavioral importance and can change relatively quickly over the course of geological timescales through microevolutionary mechanisms.

    This discovery also carries importance for the science-faith conversation. Some Christians believe that the recovery of soft tissue remnants, such as the pigments that make up fur, call into question the scientific methods used to determine the age of geological formations and the fossil record. This uncertainty opens up the possibility that our planet (and life on Earth) may be only 6,000 years old.

    Is the young-earth interpretation of this advance valid? Is it possible for soft tissue materials to survive for millions of years? If so, how?

    Detection of 3-Million-Year-Old Pigment

    University of Manchester researchers applied their methodology to an exceptionally well-preserved 3-million-year-old fossil specimen (Apodemus atavus) recovered from the Willershausen conservation site in Germany. The specimen was compressed laterally during the fossilization process and is so well-preserved that imprints of its fur are readily visible.

    The research team indirectly identified the pigments that at one time colored the fur by mapping the distribution of metals in the fossil specimen. These metals are known to associate with the pigments eumelanin and pheomelanin, the two main forms of melanin. (Eumelanin produces black and brown hues. Pheomelanin imparts fur, skin, and feathers with a light reddish-brown color.) As it turns out, copper ions chemically interact with eumelanin and pheomelanin. On the other hand, zinc (Zn) ions interact exclusively with pheomelanin by binding to sulfur (S) atoms that are part of this pigment’s molecular structure. Zinc doesn’t interact with eumelanin because sulfur is not part of its chemical composition.

    The research team mapped the Zn and S distributions of the mighty mouse fossil and concluded that much of the fur was colored with pheomelanin and, therefore, must have been reddish brown. They failed to detect any pigment in the fur coating the animal’s underbelly and feet, leading them to speculate that the mouse had white fur coating its stomach and feet.

    What a piece of science! . . . WHAT A PIECE OF SCIENCE!

    Soft Tissues and the Scientific Case for a Young Earth

    Paleontologists see far-reaching implications for this work. Roy Wogelius, one of the scientists leading the study, hopes that “these results will mean that we can become more confident in reconstructing extinct animals and thereby add another dimension to the study of evolution.”2

    Young-earth creationists (YECs) also see far-reaching implications for this study. Many argue that advances such as this one provide compelling evidence that the earth is young and that the fossil record was laid down as a consequence of a recent global flood.

    The crux of the YEC argument centers around the survivability of soft tissue materials. According to common wisdom, soft tissue materials should rapidly degrade once the organism dies. If this is the case, then there is no way soft tissue remnants should hang around for thousands of years, let alone millions. The fact that these materials can be recovered from fossil specimens indicates that the preserved organisms must be only a few thousand years old. And if thats the case, then the methods used to date the fossils cannot be valid.

    At first glance, the argument carries some weight. Most people find it hard to envision how soft tissue materials could survive for vast periods of time, given the wide range of mechanisms that drive the degradation of biological materials.

    Preservation Mechanisms for Soft Tissues in Fossils

    Despite this initial impression, over the last decade or so paleontologists have identified a number of mechanisms that can delay the degradation of soft tissues long enough for them to become entombed within a mineral shell. When this entombment occurs, the degradation process dramatically slows down. In other words, it is a race against time. Can mineral entombment take place before the soft tissue materials fully decompose? If so, then soft tissue remnants can survive for hundreds of millions of years. And any chemical or physical process that can delay the degradation will contribute to soft tissue survival by giving the entombment process time to take place.

    In Dinosaur Blood and the Age of the Earth, I describe several mechanisms that likely promote soft tissue survival. I also discuss the molecular features that contribute to soft tissue preservation in fossils. Not all molecules are made equally. Some are fragile and some robust. Two molecular properties that make molecules unusually durable are cross-linking and aromaticity. As it turns out, eumelanin and pheomelanin possess both.

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    Figure 2: Chemical Structure of Eumelanin. Image credit: Wikipedia

    blog__inline--ancient-mouse-fur-discovery-3

    Figure 3: Chemical Structure of Pheomelanin. Image credit: Wikipedia

    When considering the chemical structures of eumelanin and pheomelanin, it isn’t surprising that these materials persist in the fossil record for millions of years. In fact, researchers have isolated eumelanin from a fossilized cephalopod ink sac that dates to around 160 million years ago.3

    It is also worth noting that the mouse specimen was well-preserved, making it even more likely that durable soft-tissue materials would persist in the fossil. And, keep in mind that the research team detected trace amounts of pigments using sophisticated, state-of-the-art chemical instrumentation.

    In short, the recovery of trace levels of soft-tissue materials from fossil remains is not surprising. Soft-tissue materials associated with the mighty mouse specimen—and other fossils, for that matter— can’t save the day for the young-earth paradigm, but they find a ready explanation in an old-earth framework.

    Resources

    Endnotes
    1. Phillip L. Manning et al., “Pheomelanin Pigment Remnants Mapped in Fossils of an Extinct Mammal,” Nature Communications 10, (May 21, 2019): 2250, doi:10.1038/s41467-019-10087-2.
    2. DOE/SLAC National Accelerator Laboratory, “In a First, Researchers Identify Reddish Coloring in an Ancient Fossil,” Science Daily, May 21, 2019, https://www.sciencedaily.com/releases/2019/05/190521075110.htm
    3. Keely Glass et al., “Direct Chemical Evidence for Eumelanin Pigment from the Jurassic Period,” Proceedings of the National Academy of Sciences USA 109, no. 26 (June 26, 2012): 10218–23, doi:10.1073/pnas.1118448109.
  • Satellite DNA: Critical Constituent of Chromosomes

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jun 19, 2019

    There is a lot that evolutionary biologists can learn about the purpose of junk DNA from my wife.

    Let me explain.

    Recently, I wound up with a disassembled cabinet in the trunk of my car. Neither my wife Amy nor I could figure out where to put the cabinet in our home and we didn’t want to store it in the garage. The cabinet had all its pieces and was practically new. So, I offered it to a few people, but there were no takers. It seemed that nobody wanted to assemble the cabinet.

    Getting Rid of the Junk

    After driving around with the cabinet pieces in my trunk for a few days, I channeled my inner Marie Kondo. This cabinet wasn’t giving me any joy by taking up valuable space in the trunk. So, I made a quick detour on my way home from the office and donated the cabinet to a charity.

    When I told Amy what I had done, she expressed surprise and a little disappointment. If she had known I was going to donate the cabinet, she would have kept it for its glass doors. In other words, if I hadn’t donated the cabinet, it would have eventually wound up in our garage because it has nice glass doors that Amy thinks she could have repurposed.

    There is a point to this story: The cabinet was designed for a purpose and, at one time, it served a useful function. But once it was disassembled and put in the trunk of my car, nobody seemed to want it. Disassembling the cabinet transformed it into junk. And since my wife loves to repurpose things, she saw a use for it. She didn’t perceive the cabinet as junk at all.

    The moral of my little story also applies to the genomes of eukaryotic organisms. Specifically, is it time that evolutionary scientists view some kinds of DNA not as junk, but rather as purposeful genetic elements?

    Junk in the Genome

    Many biologists hold the view that a vast proportion of the genomes of other eukaryotic organisms is junk, just like the disassembled cabinet I temporarily stored in my car. They believe that, like the unwanted cabinet, many of the different types of “junk” DNA in genomes originated from DNA sequences that at one time performed useful functions. But these functional DNA sequences became transformed (like the disassembled cabinet) into nonfunctional elements.

    Evolutionary biologists consider the existence of “junk” DNA as one of the most potent pieces of evidence for biological evolution. According to this view, junk DNA results when undirected biochemical processes and random chemical and physical events transform a functional DNA segment into a useless molecular artifact. Junk pieces of DNA remain part of an organisms genome, persisting from generation to generation as a vestige of evolutionary history.

    Evolutionary biologists highlight the fact that, in many instances, identical (or nearly identical) segments of junk DNA appear in a wide range of related organisms. Frequently, the identical junk DNA segments reside in corresponding locations in these genomes—and for many biologists, this feature clearly indicates that these organisms shared a common ancestor. Accordingly, the junk DNA segment arose prior to the time that the organisms diverged from their shared evolutionary ancestor and then persisted in the divergent evolutionary lines.

    One challenging question these scientists ask is, Why would a Creator purposely introduce nonfunctional, junk DNA at the exact location in the genomes of different, but seemingly related, organisms?

    Satellite DNA

    Satellite DNA, which consists of nucleotide sequences that repeat over and over again, is one class of junk DNA. This highly repetitive DNA occurs within the centromeres of chromosomes and also in the chromosomal regions adjacent to centromeres (referred to as pericentromeric regions).

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    Figure: Chromosome Structure. Image credit: Shutterstock

    Biologists have long regarded satellite DNA as junk because it doesn’t encode any useful information. Satellite DNA sequences vary extensively from organism to organism. For evolutionary biologists, this variability is a sure sign that these DNA sequences cant be functional. Because if they were, natural selection would have prevented the DNA sequences from changing. On top of that, molecular biologists think that satellite DNAs highly repetitive nature leads to chromosomal instability, which can result in genetic disorders.

    A second challenging question is, Why would a Creator intentionally introduce satellite DNA into the genomes of eukaryotic organisms?

    What Was Thought to Be Junk Turns Out to Have Purpose

    Recently, a team of biologists from the University of Michigan (UM) adopted a different stance regarding the satellite DNA found in pericentromeric regions of chromosomes. In the same way that my wife Amy saw a use for the cabinet doors, the researchers saw potential use for satellite DNA. According to Yukiko Yamashita, the UM research head, “We were not quite convinced by the idea that this is just genomic junk. If we don’t actively need it, and if not having it would give us an advantage, then evolution probably would have gotten rid of it. But that hasn’t happened.”1

    With this mindset—refreshingly atypical for most biologists who view satellite DNA as junk—the UM research team designed a series of experiments to determine the function of pericentromeric satellite DNA.2 Typically, when molecular biologists seek to understand the functional role of a region of DNA, they either alter it or splice it out of the genome. But, because the pericentromeric DNA occupies such a large proportion of chromosomes, neither option was available to the research team. Instead, they made use of a protein found in the fruit fly Drosophila melanogaster, called D1. Previous studies demonstrated that this protein binds to satellite DNA.

    The researchers disabled the gene that encodes D1 and discovered that fruit fly germ cells died. They observed that without the D1 protein, the germ cells formed micronuclei. These structures reflect chromosomal instability and they form when a chromosome or a chromosomal fragment becomes dislodged from the nucleus.

    The team repeated the study, but this time they used a mouse model system. The mouse genome encodes a protein called HMGA1 that is homologous to the D1 protein in fruit flies. When they damaged the gene encoding HMGA1, the mouse cells also died, forming micronuclei.

    As it turns out, both D1 and HMGA1 play a crucial role, ensuring that chromosomes remain bundled in the nucleus. These proteins accomplish this feat by binding to the pericentromeric satellite DNA. Both proteins have multiple binding sites and, therefore, can simultaneously bind to several chromosomes at once. The multiple binding interactions collect chromosomes into a bundle to form an association site called a chromocenter.

    The researchers aren’t quite sure how chromocenter formation prevents micronuclei formation, but they speculate that these structures must somehow stabilize the nucleus and the chromosomes housed in its interior. They believe that this functional role is universal among eukaryotic organisms because they observed the same effects in fruit flies and mice.

    This study teaches us two additional lessons. One, so-called junk DNA may serve a structural role in the cell. Most molecular biologists are quick to overlook this possibility because they are hyper-focused on the informational role (encoding the instructions to make proteins) DNA plays.

    Two, just because regions of the genome readily mutate without consequences doesn’t mean these sequences aren’t serving some kind of functional role. In the case of pericentromeric satellite DNA, the sequences vary from organism to organism. Most molecular biologists assume that because the sequences vary, they must not be functionally important. For if they were, natural selection would have prevented them from changing. But this study demonstrates that DNA sequences can vary—particularly if DNA is playing a structural role—as long as they dont compromise DNA’s structural utility. In the case of pericentromeric DNA, apparently the nucleotide sequence can vary quite a bit without compromising its capacity to bind chromocenter-forming proteins (such as D1 and HMGA1).

    Is the Evolutionary Paradigm the Wrong Framework to Study Genomes?

    Scientists who view biology through the lens of the evolutionary paradigm are often quick to conclude that the genomes of organisms reflect the outworking of evolutionary history. Their perspective causes them to see the features of genomes, such as satellite DNA, as little more than the remnants of an unguided evolutionary process. Within this framework, there is no reason to think that any particular DNA sequence element harbors function. In fact, many life scientists regard these “evolutionary vestiges” as junk DNA. This clearly was the case for satellite DNA.

    Yet, a growing body of data indicates that virtually every category of so-called junk DNA displays function. In fact, based on the available data, a strong case can be made that most sequence elements in genomes possess functional utility. Based on these insights, and the fact that pericentromeric satellite DNA persists in eukaryotic genomes, the team of researchers assumed that it must be functional. Its a clear departure from the way most biologists think about genomes.

    Based on this study (and others like it), I think it is safe to conclude that we really don’t understand the molecular biology of genomes.

    It seems to me that we live in the midst of a revolution in our understanding of genome structure and function. Instead of being a wasteland of evolutionary debris, the architecture and operations of genomes appear to be far more elegant and sophisticated than anyone ever imagined—at least within the confines of the evolutionary paradigm.

    This insight also leads me to wonder if we have been using the wrong paradigm all along to think about genome structure and function. I contend that viewing biological systems as the Creator’s handiwork provides a superior framework for promoting scientific advance, particularly when the rationale for the structure and function of a particular biological system is not apparent. Also, in addressing the two challenging questions, if biological systems have been created, then there must be good reasons why these systems are structured and function the way they do. And this expectation drives further study of seemingly nonfunctional, purposeless systems with the full anticipation that their functional roles will eventually be uncovered.

    Though committed to an evolutionary interpretation of biology, the UM researchers were rewarded with success when they broke ranks with most evolutionary biologists and assumed junk regions of the genome were functional. Their stance illustrates the power of a creation model approach to biology.

    Sadly, most evolutionary biologists are like me when it comes to old furniture. We lack vision and are quick to see it as junk, when in fact a treasure lies in front of us. And, if we let it, this treasure will bring us joy.

    Resources

    Endnotes
    1. University of Michigan, “Scientists Discover a Role for ‘Junk’ DNA,” ScienceDaily (April 11, 2018), www.sciencedaily.com/releases/2018/04/180411131659.htm.
    2. Madhav Jagannathan, Ryan Cummings, and Yukiko M. Yamashita, “A Conserved Function for Pericentromeric Satellite DNA,” eLife 7 (March 26, 2018): e34122, doi:10.7554/eLife.34122.
  • Frog Choruses Sing Out a Song of Creation

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jun 12, 2019

    My last name, Rana, is Sanskrit in origin, referring to someone who descends from the Thar Ghar aristocracy. Living in Southern California means I don’t often meet Urdu-speaking people who would appreciate the regal heritage connected to my family name. But I do meet a lot of Spanish speakers. And when I introduce myself, I often see raised eyebrows and smiles.

    In Spanish, Rana means frog.

    My family has learned to embrace our family’s namesake. In fact, when our kids were little, my wife affectionately referred to our five children as ranitas—little frogs.

     

     

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    Image: Five Ranitas. Image credit: Shutterstock

    Our feelings about these cute and colorful amphibians aside, frogs are remarkable creatures. They engage in some fascinating behaviors. Take courtship, as an example. In many frog species, the males croak to attract the attention of females, with each frog species displaying its own distinct call.

    Male frogs croak by filling their vocal sacs with air. This allows them to amplify their croaks for up to a mile away. Oftentimes, male frogs in the same vicinity will all croak together, forming a chorus.

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    Image: Male Frog Croaking to Attract a Female. Image credit: Shutterstock

    As it turns out, female frogs aren’t the only ones who respond to frog croaks.

    A research team from Japan has spent a lot of time listening to and analyzing frog choruses with the hopes of understanding the mathematical structure of the sounds that frogs collectively make when they call out to females. Once they had the mathematical model in hand, the researchers discovered that they could use it to improve the efficiency of wireless data transfer systems.1

    This work serves as one more example of scientists and engineers applying insights from biology to drive technology advances and breakthroughs. This approach to technology development (called biomimetics and bioinspiration)—exemplified by the impressive work of the Japanese researchers—has significance that extends beyond engineering. It can be used to make the case that a Creator must have played a role in the design and history of life by marshaling support for two distinct arguments for God’s existence:

    Frog Choruses: A Cacophony or a Symphony?

    Anyone who has spent time near a pond at night certainly knows the ruckus that an army of male frogs can make when each of them is vying for the attention of females.

    All the male frogs living near the pond want to attract females to the same breeding site, but, in doing so, each individual also wants to attract females to his specific territory. Field observations indicate that, instead of engaging in a croaking free-for-all (with neighboring frogs trying to outperform one another), the army of frogs engages in a carefully orchestrated acoustical presentation. As a result, male frogs avoid call overlap with neighboring males on a short timescale, while synchronizing their croaks with the other frogs to produce a chorus on a longer timescale.

    The frogs avoid call overlap by alternating between silence and croaking, coordinating with neighboring frogs so that when one frog rests, another croaks. This alternating back-and-forth makes it possible for each individual frog to be heard amid the chorus, and it also results in a symphonic chorus of frog croaks.

    The Mathematical Structure of Frog Choruses

    To dissect the mathematical structure of frog choruses, the research team placed three male Japanese tree frogs into individual mesh cages that were set along a straight line, with a two-foot separation between each cage. The researchers recorded the frog’s croaks using microphones placed by each cage.

    They observed that all three frogs alternated their calls, forming a triphasic synchronization. One frog croaked continuously for a brief period of time and then would rest, while the other two frogs took their turn croaking and resting. The researchers determined that the rest breaks for the frogs were important because of the amount of energy it takes the frogs to produce a call.

    All three frogs would synchronize the start and stop of their calls to produce a chorus followed by a period of silence. They discovered that the time between choruses varied quite a bit, without rhyme or reason, and was typically much longer than the chorus time. On the other hand, the croaking of each individual lasted for a predictable time duration that was followed immediately by the croaking of a neighboring frog.

    By analyzing the acoustical data, the researchers developed a mathematical model to describe the croaking of individual frogs and the collective behavior of the frogs when they belted out a chorus of calls. Their model consisted of both deterministic and stochastic components.

    Use of Frog Choruses for Managing Data Traffic

    The researchers realized that the mathematical model they developed could be applied to control wireless sensor networks, such as those that make up the internet of things. These networks entail an array of sensor nodes that transmit data packets, delivering them to a gateway node by multi-hop communication, with data packets transmitted from sensor to sensor until it reaches the gate. During transmission, it is critical for the system to avoid the collision of data packets. It is also critical to regulate the overall energy consumption of the system, to avoid wasting valuable energy resources.

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    Image: The Internet of Things Made Up of Wireless Sensors. Image credit: Shutterstock

    Through simulation studies, the Japanese team demonstrated that the mathematical model inspired by frog choruses averted the collision of data packets in a wireless sensor array, maximized network connectivity, and enhanced efficiency of the array by minimizing power consumption. The researchers conclude, “This study highlights the unique dynamics of frog choruses over multiple time scales and also provides a novel bio-inspired technology.”2

    As important as this work may be for inspiring new technologies, as a Christian, I find its real significance in the theological arena.

    Frog Choruses and the Argument from Beauty

    The grandeur of nature touches the very core of who we are—if we take the time to let it. But, as the work by the Japanese researchers demonstrates, the grandeur we see all around us in nature isn’t confined to what we perceive with our immediate senses. It exists in the underlying mathematical structure of nature. It is nothing short of amazing to think that such exquisite organization and orchestration characterizes frog choruses, so much so that it can inspire sophisticated data management techniques.

    From my vantage point, the beauty and mathematical elegance of nature points to the reality of a Creator.

    If God created the universe, then it is reasonable to expect it to be a beautiful universe, one that displays an even deeper underlying beauty in the mathematical structure that defines the universe itself and phenomena within the universe. Yet if the universe came into existence through mechanism alone, there isn’t any real reason to think it would display beauty. In other words, the beauty in the world around us signifies the divine.

    Furthermore, if the universe originated through uncaused physical mechanisms, there is no reason to think that humans would possess an appreciation for beauty.

    A quick survey of the scientific and popular literature highlights the challenge that the origin of our aesthetic sense creates for the evolutionary paradigm.3 Plainly put: evolutionary biologists have no real explanation for the origin of our aesthetic sense. To be clear, evolutionary biologists have posited explanations to account for the genesis of our capacity to appreciate beauty. But after examining these ideas, we walk away with the strong sense that they are not much more than “just-so stories,” lacking any real evidential support.

    On the other hand, if human beings are made in God’s image, as Scripture teaches, we should be able to discern and appreciate the universe’s beauty, made by our Creator to reveal his glory and majesty.

    Frog Choruses and the Converse Watchmaker Argument

    The idea that biological designs—such as the courting behavior of male frogs—can inspire engineering and technology advances is also highly provocative for other reasons. First, it highlights just how remarkable and elegant the designs found throughout the living realm actually are.

    I think that the elegance of these designs points to a Creator’s handiwork. It also makes possible a new argument for God’s existence—one I have named the converse Watchmaker argument. (For a detailed discussion, see my essay titled “The Inspirational Design of DNA” in the book Building Bridges.)

    The argument can be stated like this:

    • If biological designs are the work of a Creator, then these systems should be so well-designed that they can serve as engineering models for inspiring the development of new technologies.
    • Indeed, this scenario plays out in the engineering discipline of biomimetics.
    • Therefore, it becomes reasonable to think that biological designs are the work of a Creator.

    In fact, I will go one step further. Biomimetics and bioinspiration logically arise out of a creation model approach to biology. That designs in nature can be used to inspire engineering makes sense only if these designs arose from an intelligent Mind. The mathematical structure of frog choruses is yet another example of such bioinspiration.

    Frogs really are amazing—and regal—creatures. Listening to a frog chorus can connect us to the beauty of the world around us. And it will one day help all of our electronic devices to connect together. And that’s certainly something to sing about.

    Resources

    Endnotes
    1. Ikkyu Aihara et al., “Mathematical Modelling and Application of Frog Choruses As an Autonomous Distributed Communication System, Royal Society Open Science 6, no. 1 (January 2, 2019): 181117, doi:10.1098/rsos.181117.
    2. Aihara et al., “Mathematical Modelling and Application.
    3. For example, see Ferris Jabr, “How Beauty is Making Scientists Rethink Evolution,” The New York Times Magazine, January 9, 2019, https://www.nytimes.com/2019/01/09/magazine/beauty-evolution-animal.html.
  • Why Would God Create a World with Parasites?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jun 05, 2019

    A being so powerful and so full of knowledge as a God who could create the universe, is to our finite minds omnipotent and omniscient, and it revolts our understanding to suppose that his benevolence is not unbounded, for what advantage can there be in the sufferings of millions of lower animals throughout almost endless time? This very old argument from the existence of suffering against the existence of an intelligent first cause seems to me a strong one; whereas, as just remarked, the presence of much suffering agrees well with the view that all organic beings have been developed through variation and natural selection.1

    —Charles Darwin, The Autobiography of Charles Darwin

    If God exists and if he is all-powerful, all-knowing, and all-good, why is there so much pain and suffering in the world? This conundrum keeps many skeptics and seekers from the Christian faith and even troubles some Christians.

    Perhaps nothing epitomizes the problem of pain and suffering more than the cruelty observed in nature. Indeed, what advantage can there be in the suffering of millions of animals?

    Often, the pain and suffering animals experience is accompanied by unimaginable and seemingly unnecessary cruelty.

    Take nematodes (roundworms) as an example. There are over 10,000 species of nematodes. Some are free-living. Others are parasitic. Nematode parasites infect humans, animals, plants, and insects, causing untold pain and suffering. But their typical life cycle in insects seems especially cruel.

    Nematodes that parasitize insects usually are free-living in their adult form but infest their host in the juvenile stage. The infection begins when the juvenile form of the parasite enters into the insect host, usually through a body opening, such as the mouth or anus. Sometimes the juveniles drill through the insect’s cuticle.

    Once inside the host, the juveniles release bacteria that infect and kill the host, liquefying its internal tissues. As long as the supply of host tissue holds out, the juveniles will live within the insect’s body, even reproducing. When the food supply runs out, the nematodes exit the insect and seek out another host.

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    Figure 1: An Entomopathogenic Nematode Juvenile. Image credit: Shutterstock

    Why would God create a world with parasitism? Could God really be responsible for a world like the one we inhabit? Many skeptics would answer “no” and conclude that God must not exist.

    A Christian Response to the Problem of Evil

    One way to defend God’s existence and goodness in the face of animal pain and suffering is to posit that there just might be good reasons for God to create the world the way it is. Perhaps what we are quick to label as evil may actually serve a necessary function.

    This perspective gains support based on some recent insights into the benefits that insect parasites impart to ecosystems. A research team from the University of Georgia (UGA) recently unearthed one example of the important role played by these parasites.2 These researchers demonstrated that nematode-infected horned passalus beetles (bess beetles) are more effective at breaking down dead logs in the forest than their parasite-free counterparts—and this difference benefits the ecosystem. Here’s how.

    The Benefit Parasites Provide to the Ecosystem

    The horned passalus lives in decaying logs. The beetles consume wood through a multistep process. After ingesting the wood, these insects excrete it in a partially digested form. The wood excrement becomes colonized by bacteria and fungi and then is later re-consumed by the beetle.

    These insects can become infected by a nematode parasite (Chondronema passali). The parasite inhabits the abdominal cavity of the beetle (though not its gastrointestinal tract). When infected, the horned passalus can harbor thousands of individual nematodes.

    To study the effect of this parasite on the horned passalus and the forest ecosystem inhabited by the insect, researchers collected 113 individuals from the woods near the UGA campus. They also collected pieces of wood from the logs bearing the beetles.

    In the laboratory, they placed each of the beetles in separate containers that also contained pieces of wood. After three months, they discovered that the beetles infected with the nematode parasite processed 15 percent more wood than beetles that were parasite-free. Apparently, the beetles compensate for the nematode infection by consuming more food. One possible reason for the increased wood consumption may be due to the fact that the parasites draw away essential nutrients from the beetle host, requiring the insect to consume more food.

    While it isn’t clear if the parasite infestation harms the beetle (infected beetles have reduced mobility and loss of motor function), it is clear that the infestation benefits the ecosystem. These beetles play a key role in breaking down dead logs and returning nutrients to the forest soil. By increasing the beetles wood consumption, the nematodes accelerate this process, benefiting the ecosystem’s overall health.

    Cody Prouty, one of the projects researchers, points out “that although the beetle and the nematode have a parasitic relationship, the ecosystem benefits from not only the beetle performing its function, but the parasite increasing the efficiency of the beetle. Over the course of a few years, the parasitized beetles could process many more logs than unparasitized beetles, and lead to an increase of organic matter in soils.”3

    This study is not the first to discover benefits parasites impart to ecosystems. Parasites play a role in shaping ecosystem biodiversity and they intertwine with the food web. The researchers close their article this way: “Countering long-standing unpopular views of parasites is certainly challenging, but perhaps evidence like that presented here will be of use in this effort.”4

    Such evidence does not revolt our understanding, as Darwin might suggest, but instead enhances our insights into the creation and helps counter the challenge of the problem of evil. Even creatures as gruesome as parasites can serve a beneficial purpose in creation and maybe could rightfully be understood as good.

    Resources

    Endnotes
    1. Charles Darwin, The Autobiography of Charles Darwin: 1809–1882 (New York: W. W. Norton, 1969), 90.
    2. Andrew K. Davis and Cody Prouty, “The Sicker the Better: Nematode-Infected Passalus Beetles Provide Enhanced Ecosystem Services, Biology Letters 15, no. 5 (2019): 20180842, doi:10.1098/rsbl.2018.0842.
    3. University of Georgia, “Parasites Help Beetle Hosts Function More Effectively,” ScienceDaily (May 1, 2019), https://www.sciencedaily.com/releases/2019/05/190501131435.htm.
    4. Davis and Prouty,“The Sicker the Better,” 3.
  • Biochemical Grammar Communicates the Case for Creation

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | May 29, 2019

    As I get older, I find myself forgetting things—a lot. But, thanks to smartphone technology, I have learned how to manage my forgetfulness by using the “Notes” app on my iPhone.

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    Figure 1: The Apple Notes app icon. Image credit: Wikipedia

    This app makes it easy for me to:

    • Jot down ideas that suddenly come to me
    • List books I want to read and websites I want to visit
    • Make note of musical artists I want to check out
    • Record “to do” and grocery lists
    • Write down details I need to have at my fingertips when I travel
    • List new scientific discoveries with implications for the RTB creation model that I want to blog about, such as the recent discovery of a protein grammar calling attention to the elegant design of biochemical systems

    And the list goes on. I will never forget, again!

    On top of that, I can use the Notes app to categorize and organize all my notes and house them in a single location. Thus, I don’t have to manage scraps of paper that invariably wind up getting scattered all over the place—and often lost.

    And, as a bonus, the Notes app anticipates the next word I am going to use even before I type it. I find myself relying on this feature more and more. It is much easier to select a word than type it out. In fact, the more I use this feature, the better the app becomes at anticipating the next word I want to type.

    Recently, a team of bioinformaticists from the University of Alabama, Birmingham (UAB) and the National Institutes of Health (NIH) used the same algorithm the Notes app uses to anticipate word usage to study protein architectures.1 Their analysis reveals new insight into the structural features of proteins and also highlights the analogy between the information housed in these biomolecules and human language. This analogy contributes to the revitalized Watchmaker argument presented in my book The Cell’s Design.

    N-Gram Language Modeling

    The algorithm used by the Notes app to anticipate the next word the user will likely type is called n-gram language modeling. This algorithm determines the probability of a word being used based on the previous word (or words) typed. (If the probability is based on a single word, it is called a unigram probability. If the calculation is based on the previous two words, it is called a bigram probability, and so on.) This algorithm “trains” the Notes app so that the more I use it, the more reliable the calculated probabilities—and, hence, the better the word recommendations.

    N-Gram Language Modeling and the Case for a Creator

    To understand why the work of research team from UAB and NIH provides evidence for a Creator’s role in the origin and design of life, a brief review of protein structure is in order.

    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. 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.

     

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    Figure 2: The four levels of protein structure. Image credit: Shutterstock

    Protein Domains

    Within the tertiary structure of proteins, biochemists have discovered compact, self-contained regions that fold independently. These three-dimensional regions of the protein’s structure are called domains. Some proteins consist of a single compact domain, but many proteins possess several domains. In effect, domains can be thought to be the fundamental units of a protein’s tertiary structure. Each domain possesses a unique biochemical function. Biochemists refer to the spatial arrangement of domains as a protein’s domain architecture.

    Researchers have discovered several thousand distinct protein domains. Many of these domains recur in different proteins, with each protein’s tertiary structure comprised of a mix-and-match combination of protein domains. Biochemists have also learned that a relationship exists between the complexity of an organism and the number of unique domains found in its set of proteins and the number of multi-domain proteins encoded by its genome.

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    Figure 3: Pyruvate kinase, an example of a protein with three domains. Image credit: Wikipedia

    The Key Question in Protein Chemistry

    As much progress as biochemists have made characterizing protein structure over the last several decades, they still lack a fundamental understanding of the relationship between primary structure (the amino acid sequence) and tertiary structure and, hence, protein function. In order to develop this insight, they need to determine the “rules” that dictate the way proteins fold. Treating proteins as information systems can help determine some of these rules.

    Protein as Information Systems

    Proteins are not only large, complex molecules but also information-harboring systems. The amino acid sequence that defines a protein’s primary structure is a type of information—biochemical information—with the individual amino acids analogous to the letters that make up an alphabet.

    N-Gram Analysis of Proteins

    To gain insight into the relationship between a protein’s primary structure and its tertiary structures, the researchers from UAB and NIH carried out an n-gram analysis on the 23 million protein domains found in the protein sets of 4,800 species found across all three domains of life.

    These researchers point out that an individual amino acid in a protein’s primary structure doesn’t contain information just as an individual letter in an alphabet doesn’t harbor any meaning. In human language, the most basic unit that conveys meaning is a word. And, in proteins, the most basic unit that conveys biochemical meaning is a domain.

    To decipher the “grammar” used by proteins, the researchers treated adjacent pairs of protein domains in the tertiary structure of each protein in the sample set as a bigram (similar to two words together). Surveying the proteins found in their data set of 4,800 species, they discovered that 95% of all the possible domain combinations don’t exist!

    This finding is key. It indicates that there are, indeed, rules that dictate the way domains interact. In other words, just like certain word combinations never occur in human languages because of the rules of grammar, there appears to be a protein “grammar” that constrains the domain combinations in proteins. This insight implies that physicochemical constraints (which define protein grammar) dictate a protein’s tertiary structure, preventing 95% of conceivable domain-domain interactions.

    Entropy of Protein Grammar

    In thermodynamics, entropy is often used as a measure of the disorder of a system. Information theorists borrow the concept of entropy and use it to measure the information content of a system. For information theorists, the entropy of a system is indirectly proportional to the amount of information contained in a sequence of symbols. As the information content increases, the entropy of the sequence decreases, and vice versa. Using this concept, the UAB and NIH researchers calculated the entropy of the protein domain combinations.

    In human language, the entropy increases as the vocabulary increases. This makes sense because, as the number of words increases in a language, the likelihood that random word combinations would harbor meaning decreases. In like manner, the research team discovered that the entropy of the protein grammar increases as the number of domains increases. (This increase in entropy likely reflects the physicochemical constraints—the protein grammar, if you will—on domain interactions.)

    Human languages all carry the same amount of information. That is to say, they all display the same entropy content. Information theorists interpret this observation as an indication that a universal grammar undergirds all human languages. It is intriguing that the researchers discovered that the protein “languages” across prokaryotes and eukaryotes all display the same level of entropy and, consequently, the same information content. This relationship holds despite the diversity and differences in complexity of the organism in their data set. By analogy, this finding indicates that a universal grammar exists for proteins. Or to put it another way, the same set of physicochemical constraints dictate the way protein domains interact for all organisms.

    At this point, the researchers don’t know what the grammatical rules are for proteins, but knowing that they exist paves the way for future studies. It also generates hope that one day biochemists might understand them and, in turn, use them to predict protein structure from amino acid sequences.

    This study also illustrates how fruitful it can be to treat biochemical systems as information systems. The researchers conclude that “The similarities between natural languages and genomes are apparent when domains are treated as functional analogs of words in natural languages.”2

    In my view, it is this relationship that points to a Creator’s role in the origin and design of life.

    Protein Grammar and the Case for a Creator

    As discussed in The Cell’s Design, the recognition that biochemical systems are information-based systems has interesting philosophical ramifications. Common, everyday experience teaches that information derives solely from the activity of human beings. So, by analogy, biochemical information systems, too, should come from a divine Mind. Or at least it is rational to hold that view.

    But the case for a Creator strengthens when we recognize that it’s not merely the presence of information in biomolecules that contributes to this version of a revitalized Watchmaker analogy. Added vigor comes from the UAB and NIH researchers’ discovery that the mathematical structure of human languages and biochemical languages is identical.

    Skeptics often dismiss the updated Watchmaker argument by arguing that biochemical information is not genuine information. Instead, they maintain that when scientists refer to biomolecules as harboring information, they are employing an illustrative analogy—a scientific metaphor—and nothing more. They accuse creationists and intelligent design proponents of misconstruing their use of analogical language to make the case for design.3

    But the UAB and NIH scientists’ work questions the validity of this objection. Biochemical information has all of the properties of human language. It really is information, just like the information we conceive and use to communicate.

    Is There a Biochemical Anthropic Principle?

    This discovery also yields another interesting philosophical implication. It lends support to the existence of a biochemical anthropic principle. Discovery of a protein grammar means that there are physicochemical constraints on protein structure. It is remarkable to think that protein tertiary structures may be fundamentally dictated by the laws of nature, instead of being the outworking of an historically contingent evolutionary history. To put it differently, the discovery of a protein grammar reveals that the structure of biological systems may reflect some deep, underlying principles that arise from the very nature of the universe itself. And yet these structures are precisely the types of structures life needs to exist.

    I interpret this “coincidence” as evidence that our universe has been designed for a purpose. And as a Christian, I find that notion to resonate powerfully with the idea that life manifests from an intelligent Agent—namely, God.

    Resources to Dig Deeper

    Endnotes
    1. Lijia Yu et al., “Grammar of Protein Domain Architectures,” Proceedings of the National Academy of Sciences, USA 116, no. 9 (February 26, 2019): 3636–45, doi:10.1073/pnas.1814684116.
    2. Yu et al., 3636–45.
    3. For example, see Massimo Pigliucci and Maarten Boudry, “Why Machine-Information Metaphors Are Bad for Science and Science Education,” Science and Education 20, no. 5–6 (May 2011): 453–71; doi:10.1007/s11191-010-9267-6.

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