Where Science and Faith Converge
  • Does Development of Artificial Intelligence Undermine Human Exceptionalism?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jan 17, 2018

    In each case catalytic technologies, such as artificial wombs, the repair of brain injuries with prostheses and the enhancement of animal intelligence, will force us to choose between pre-modern human-racism and the cyborg citizenship implicit in the liberal democratic tradition.

    —James Hughes, Citizen Cyborg

    On one hand, it appeared to be nothing more than a harmless publicity stunt. On October 25, 2017, Saudi Arabia granted Sophia—a lifelike robot, powered by artificial intelligence software—citizenship. This took place at the FII conference, held in Riyahd, providing a prime opportunity for Hanson Robotics to showcase its most advanced robotics system to date. And, it also served as a chance for Saudi Arabia to establish itself as a world leader in AI technology.

    But, on the other hand, granting Sophia citizenship establishes a dangerous precedent, acting as a harbinger to a dystopian future where machines (and animals with enhanced intelligence) are afforded the same rights as human beings. Elevating machines to the same status as human beings threatens to undermine human dignity and worth and, along with it, the biblical conception of humanity.

    Still, the notion of granting citizenship to robots makes sense within a materialistic/naturalistic worldview. In this intellectual framework, human beings are largely regarded as biological machines and the human brain as an organic computer. If AI systems can be created with self-awareness and emotional capacity, what makes them any different from human beings? Is a silicon-based computer any different from one made up of organic matter?

    For many people, sentience or self-awareness is the key determinant of personhood. And persons are guaranteed rights, whether they are human beings, AI machines, or super-intelligent animals created by genetic engineering or implanting human brain organoids (grown in a lab) into the brains of animals.

    In other words, the way we regard AI technology has wide-ranging consequences for how we view and value human life. And while views of AI rooted in a materialistic/naturalistic worldview potentially threaten human dignity, a Christian worldview perspective of AI actually highlights human exceptionalism—in a way that aligns with the biblical concept of the image of God.

    Will AI Systems Ever Be Self-Aware?

    The linchpin for granting AI citizenship—and the same rights as human beings—is self-awareness.

    But are AI systems self-aware? And will they ever be?

    From my perspective, the answers to both questions are “no.” To be certain, AI systems are on a steep trajectory toward ever-increasing sophistication. But there is little prospect that they will ever truly be sentient. AI systems are becoming better and better at mimicking human cognitive abilities, emotions, and even self-awareness. But these systems do not inherently possess these capabilities—and I don’t think they ever will.

    Researchers are able to create AI systems with the capacity to mimic human qualities through the combination of natural-language processing and machine-learning algorithms. In effect, natural-language processing is pattern matching, in which the AI system employs prewritten scripts that are combined, spliced, and recombined to make the AI systems comments and responses to questions seem natural. For example, Sophia performs really well responding to scripted questions. But, when questions posed to her are off-script, she often provides nonsensical answers or responds with non-sequiturs. These failings reflect limitations of the natural-language processing algorithms. Undoubtedly, Sophia’s responses will improve thanks to machine-learning protocols. These algorithms incorporate new information into the software inputs to generate improved outcomes. In fact, through machine-learning algorithms, Sophia is “learning” how to emote, by controlling mechanical hardware to produce appropriate facial expressions in response to the comments made by “her” conversation partner. But, these improvements will just be a little bit more of the samediffering in degree, not kind. They will never propel Sophia, or any AI system, to genuine self-awareness.

    As the algorithms and hardware improve, Sophia (and other AI systems) are going to become better at mimicking human beings and, in doing so, seem to be more and more like us. But, even now, it is tempting to view Sophia as humanlike. But this tendency has little to do with AI technology. Instead, it has to do with our tendency to anthropomorphize animals and even inanimate objects. Often, we attribute human qualities to nonhuman, nonliving entities. And, undoubtedly, we will do the same for AI systems such as Sophia.

    Our tendency to anthropomorphize arises from our theory-of-mind capacity—unique to human beings. As human beings, we recognize that other people have minds just like ours. As a consequence of this capacity, we anticipate what others are thinking and feeling. But we can’t turn off our theory-of-mind abilities. And as a consequence, we attribute human qualities to animals and machines. To put it another way, AI systems seem to be self-aware, because we have an innate tendency to view them as such, even if they are not.

    Ironically, a quality unique to human beingsone that contributes to human exceptionalism and can be understood as a manifestation of the image of Godmakes us susceptible to seeing AI systems as sentient “beings.” And because of this tendency, and because of our empathy (which relates to our theory of mind capacity), we want to grant AI systems the same rights afforded to us. But when we think carefully about our tendency to anthropomorphize, it should become evident that our proclivity to regard AI systems as humanlike stems from the fact that we are made in God’s image.

    AI Systems and the Case for Human Exceptionalism

    There is another way that research in AI systems evinces human exceptionalism. It is provocative to think that human beings are the only species that has ever existed that has the capability to create machines that are like us—at least, in some sense. Clearly, this achievement is beyond the capabilities of the great apes, and no evidence exists to think that Neanderthals could have ever pulled off a feat such as creating AI systems. Neanderthals—who first appear in the fossil record around 250,000 to 200,000 years ago and disappear around 40,000 years ago—existed on Earth longer than modern humans have. Yet, our technology has progressed exponentially, while Neanderthal technology remained largely static.

    Our ability to create AI systems stems from the capacity for symbolism. As human beings, we effortlessly represent the world with discrete symbols. We denote abstract concepts with symbols. And our ability to represent the world symbolically has interesting consequences when coupled with our abilities to combine and recombine those symbols in a nearly infinite number of ways to create alternate possibilities.

    Our capacity for symbolism manifests in the form of language, art, music, and even body ornamentation. And we desire to communicate the scenarios we construct in our minds with other human beings. In a sense, symbolism and our open-ended capacity to generate alternative hypotheses are scientific descriptors of the image of God. No other creature, including the great apes or Neanderthals, possesses these two qualities. In short, we can create AI systems because we uniquely bear God’s image.

    AI Systems and the Case for Creation

    Our ability to create AI systems also provides evidence that we are the product of a Creator’s handiwork. The creation of AI systems requires the work of highly trained scientists and engineers who rely on several hundred years of scientific and technological advances. Creating AI systems requires designing and building highly advanced computer systems, engineering complex robotics systems, and writing sophisticated computer code. In other words, AI systems are intelligently designed. Or to put it another way, work in AI provides empirical evidence that a mind is required to create a mind—or, at least, a facsimile of a mind. And this conclusion means that the human mind must come from a Mind, as well. In light of this conclusion, is it reasonable to think that the human mind arose through unguided, undirected, historically contingent processes?

    Developments in AI will undoubtedly lead to important advances that will improve the quality of our lives. And while it is tempting to see AI systems in human terms, these devices are machines—and nothing more. No justification exists for AI systems to be granted the same rights as human beings. In fact, when we think carefully about the nature and origin of AI, these systems highlight our exceptional nature as human beings, evincing the biblical view of humanity.

    Only human beings deserve the rights of citizenship because these rights—justifiably called inalienable—are due us because we bear God’s image.

    Resources

  • Did Neanderthals Make Glue?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jan 10, 2018

    Fun fact: each year, people around the world purchase 50 billion dollars’ (US) worth of adhesives. But perhaps this statistic isn’t all that surprising—because almost everything we make includes some type of bonding agent.

    In the context of human prehistory, anthropologists consider adhesives to have been a transformative technology. They 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.

    Anthropologists also consider the production and use of adhesives to be a 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, requiring precise temperature control and the use of earthen mounds, or ceramic or metal kilns. The first large-scale production of adhesives usually centered around the dry distillation of birch and pine barks to produce tar and pitch.

    Even though modern humans perfected dry distillation methods for tar production, the archaeological record seemingly indicates that it wasn’t modern humans who first manufactured adhesives from tar, but, instead, Neanderthals. The oldest evidence for tar production and use dates to around 200,000 years ago, based on organic residues recovered from a site in Italy. It appears that Neanderthals were using the tar as glue for hafting flint spearheads to wooden spear shafts.1 Archaeologists have also unearthed spearheads with tar residue from two sites in Germany dating to 120,000 years in age and between 40,000 to 80,000 years in age, respectively.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.

    For some anthropologists, this evidence indicates that Neanderthals possessed advanced cognitive ability, just like modern humans. If this is the case, then modern humans are not unique and exceptional. And, if human beings aren’t exceptional, then it becomes a challenge to defend one of the central concepts in Scripture—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. (See Resources section below.) This, too, is the case when it comes to Neanderthal tar production.

    How Did Neanderthals Extract Tar from Birch Bark?

    Though it appears that Neanderthals were able to produce and use tar as an adhesive, anthropologists have no idea how they went about this task. Archaeologists have yet to unearth any evidence for ceramics at Neanderthal sites. To address this question, a team of researchers from the University of Leiden conducted a series of experiments, trying to learn how Neanderthals could dry distill tar from birch bark using the resources most reasonably available to them.

    The research team devised and evaluated three dry distillation methods:

    • The Ash Mound Method: This technique entails burying rolled up birch bark in hot ash and embers. The heat from the ash and embers distills the tar away from the birch bark, but because the bark is curled and buried, oxygen can’t easily get to the tar, preventing combustion.
    • The Pit Roll Method: This approach involves digging a cylindrical pit and then placing a burning piece of rolled-up birch bark in the pit, followed by covering it with earthen materials.
    • The Raised Structure Method: This method involves placing a vessel made out of birch bark in a pit, igniting it, and covering it with sticks, pebbles, and mud.

    Of the three methods, the researchers learned that the Pit Roll technique produced the most tar and was the most efficient method. Still, the amount of tar that was produced was not enough for large-scale use, but just enough to haft one or two spears at best. The tar produced by all three methods was too fluid to be used for hafting.

    Still, the research team concluded that Neanderthals could have dry distilled tar from birch bark, using methods that were simple and without the need to precisely control the distillation temperature. They also conclude that Neanderthals must have had advanced cognitive abilities—on par with modern humans—to pull off this feat.

    Did Neanderthals Have Similar Cognitive Capacity to Modern Humans?

    Does the ability of Neanderthals to dry distill tar (using crude methods) and use it to haft spears reflect sophisticated cognitive abilities? From my vantage point, no.

    The recognition that the methods Neanderthals most likely used to dry distill tar from birch bark didn’t require temperature control and were simple and crude argues against Neanderthal sophistication, not for it. To this point, it is worth noting that birch bark naturally curls, a factor critical to the success of the three dry distillation methods explored by the University of Leiden archaeologists. In other words, curling the birch bark was not something Neanderthals would have had to discover.

    It is also worth pointing out that recent work indicates that Neanderthals did not master fire, but instead made opportunistic use of fire. These creatures could not create fire, but, instead, harvested wildfires. There were vast periods of time during Neanderthals’ tenure in Europe when wildfires were rare because of cold climatic conditions, meaning Neanderthals didn’t have access to fire. Because fire is central to the dry distillation methods, Neanderthals would have been unable to extract tar and use it for hafting for a significant portion of their time on Earth. Perhaps this explains why recovery of tar from Neanderthal sites is a rare occurrence.

    Still, no matter how crude the method, dry distilling tar from birch bark seems to be pretty remarkable behavior—until we compare Neanderthal behavior to that of chimpanzees.

    Comparing Neanderthal Behavior to Chimpanzee Behavior

    In recent years, primatologists have observed chimpanzees in the wild engaging in some remarkable behaviors. For example, chimpanzees:

    • manufacture spears from tree branches, using a six-step process. In turn, these creatures use these spears to hunt bush babies
    • make stone tools that they use to break open nuts
    • collect branches from specific trees with appropriate mechanical characteristics and insect-repellent properties to build beds in trees
    • collect and consume plants with medicinal properties
    • understand and exploit the behavior of wildfires

    In light of these remarkable chimpanzee behaviors, the manufacture and use of tar by Neanderthals doesn’t seem that impressive. No one would equate a chimpanzee’s cognitive capacity with that of a modern human. And, likewise, no one should equate the cognitive capacity of Neanderthals with modern humans. In terms of sophistication, complexity, and efficiency, the tar production methods of modern humans are categorically different from those of Neanderthals, reflecting cognitive superiority of modern humans.

    Do Anthropologists Display a Bias against Modern Humans?

    Recently, in a New York Times article, science writer Jon Mooallem called attention to paleoanthropologists prejudices when it comes to Neanderthals. He pointed out that the limited data available to these scientists from the archaeological record forces them to rely on speculation. And this speculation is inevitably influenced by their preconceptions. Mooallem states,

    “All sciences operate by trying to fit new data into existing theories. And this particular science [archaeology], for which the “data” has always consisted of scant and somewhat inscrutable bits of rock and fossil, often has to lean on those metanarratives even more heavily. . . . Ultimately, a bottomless relativism can creep in: tenuous interpretations held up by webs of other interpretations, each strung from still more interpretations. Almost every archaeologist I interviewed complained that the field has become “overinterpreted”—that the ratio of physical evidence to speculation about that evidence is out of whack. Good stories can generate their own momentum.”3

    Mooallem’s critique applies to paleoanthropologists who are modern human supremacists and those with an anti-modern human bias that seeks to undermine the uniqueness and exceptionalism of modern humans. And, lately, reading the scientific literature in anthropology, I get the strong sense that there is a growing anti-modern human bias among anthropologists.

    In light of this anti-modern human bias, one could propose an alternate scenario for the association of tar with flint spearheads at a few Neanderthal sites that comport with the view that these creatures were cognitively inferior to modern humans. Perhaps Neanderthals threw birch or pine into a fire they harvested from a wildfire. And maybe a few pieces of bark or some pieces of branches near the edge of the fire naturally curled, leading to dry distillation” of small amounts of tar. Seeing the tar exude from the bark, perhaps a Neanderthal poked at it with his spear, coating the piece of flint with sticky tar.

    When we do our best to set aside our preconceptions, the collective body of evidence indicates that Neanderthals did not have the same cognitive capacity as modern humans.

    Resources

    Endnotes
    1. Paul Peter Anthony Mazza et al., “A New Palaeolithic Discovery: Tar-Hafted Stone Tool in a European Mid-Pleistocene Bone-Bearing Bed,” Journal of Archaeological Science 33 (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 (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 (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. Jon Mooallem, “Neanderthals Were People, Too,” New York Times Magazine, January 11, 2017, https://www.nytimes.com/2017/01/11/magazine/neanderthals-were-people-too.html.
  • New Research Douses Claim that Neanderthals Mastered Fire

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jan 03, 2018

    A few months ago, I posted a link on Twitter to a blog article I wrote challenging the claim that Neanderthals made jewelry and, therefore, possessed the capacity for symbolism.

    When I post articles about the cognitive abilities of Neanderthals, I expect them to generate a fair bit of discussion and opinions that differ from mine (and I expect this article about neanderthal’s use of fire to be no exception). But one response I received was unexpectedly jarring. It came from a Christian who accused me of being “out of touch,” wasting time discussing frivolous issues,” and “targeting the elite with a failed apologetic.” He admonished me to spend my time on real issues related to social justice concerns and chastised me for not focusing my efforts reaching out to the “marginalized.”

    As part of my reply to my new “friend,” I pointed out that the identity and capability of Neanderthals has a direct bearing on the gospel and, consequently, social injustices in our world, because it relates to the question of humanity’s origin and identity. And what we believe about where we come from really matters.

    Scripture teaches that human beings are uniquely made in God’s image. And, it is the image of God that renders human beings of infinite worth and value. Because we bear God’s image, Christ died to reconcile us to the Father. And, as Christians, the immeasurable value we place on all human life motivates us to battle against the injustices of the world—because the people who suffer these injustices are image bearers. According to Scripture, when we love and serve other human beings, it equates to loving and serving God.

    Yet, the biblical view of humanity has been supplanted in the scientific community by human evolution. According to this idea, human beings are not the product of a Creator’s handiwork—the crown of creation—but, like all life on Earth, we emerged through unguided, historically contingent processes. In the evolutionary paradigm, human beings hold no special status. Human beings possess no inherent worth. We possess no more value than any other creature that has ever existed throughout Earth’s history. Human beings lack any inherent worth or dignity in the evolutionary paradigm. And, within this framework, there can be no ultimate meaning or purpose to human life.

    Sadly, the evolutionary view of humanity is not confined to the halls of the academy. It permeates and influences cultures throughout the world. Once human life is rendered meaningless and stripped of its inherent value, there is no fundamental justification to stand against injustice. In fact, it becomes easier to excuse acts of injustice and becomes tolerable to look the other way when these acts occur. In the evolutionary framework, no genuine motivation exists to rescue the marginalized of our world. I would go one step further and argue that many of the social ills we face throughout the world have their etiology in the evolutionary view of humanity.

    I regard my work as a Christian apologist as an antidote to this toxic worldview. Towards this end, I strive to demonstrate the credibility of the biblical view of humanity—apart from biblical and theological appeals. In an increasingly secular world, we can’t simply adopt a theological stance, declaring that human beings bear God’s image, and leave it at that. Few nonbelievers will accept that approach. We must respond to the scientific challenge to the image of God with scientific evidence for human uniqueness and exceptionalism. This endeavor isn’t about challenging the elite with an obscure apologetic argument for the validity of Christianity. Ultimately, it is about establishing the foundation for the gospel and generating the impetus and justification to treat human beings as creatures with inherent worth and dignity. As Christian apologists when we “target the elite” with apologetic arguments for the Christian worldview, we are serving the marginalized in our world.

    As described in Who Was Adam? a scientific case can be marshaled for human exceptionalism in a way that aligns with the biblical view of the image of God. Remarkably, a growing minority of anthropologists and primatologists now believe that human beings really are exceptional. They contend that human beings do, indeed, differ in kind, not just degree, from other creatures. The scientists who argue for this updated perspective have developed evidence for human exceptionalism within the context of the evolutionary paradigm in their attempts to understand how the human mind evolved. Yet, ironically, these new insights marshal support for the biblical conception of humanity.

    However, one potential challenge to human exceptionalism relates to the cognitive capabilities of Neanderthals. Based on archeological and fossil finds some paleoanthropologists now argue that these hominids: (1) buried their dead; (2) made specialized tools; (3) used ochre; (4) produced jewelry; (5) created art; and (6) even had language capacities. These are behaviors one would naturally associate with the image bearers.

    Yet, as discussed in Who Was Adam? (and articles listed in the Resource section), careful examination of the archeological and fossil evidence reveals just how speculative the claims about Neanderthal “exceptionalism” are. Recent insights on Neanderthal fire use illustrate this point.

    Did Neanderthals Use Fire?

    While controversy abounds among paleoanthropologists about fire use by hominins such as Homo erectus, most scientists working in this field believe Neanderthals mastered fire. This view finds its basis in the discovery of primitive hearths, burned bones, heated lithics, and charcoal at Neanderthal archeological sites. Frankly, fire use by Neanderthals bothers me. If these creatures could create and use fire—in short, if they mastered fire (called pyrotechnology)it makes them much more like us—but uncomfortably so.

    Yet, recent work raises questions about Neanderthal fire usage.1 Careful assessment of archeological sites in southern France occupied by Neanderthals from about 100,000 to 40,000 years ago indicates that Neanderthals could not create fire. Instead, they made opportunistic use of natural fire when available to them.

    The French sites show clear evidence of fire use by Neanderthals. However, when researchers correlated the archeological layers harboring evidence for fire use with paleoclimate data, they found an unexpected pattern. Neanderthals used fire during warm climate conditions and failed to use fire during cold periods—the opposite of what would be predicted—if Neanderthals had mastery over fire.

    Instead, this unusual correlation indicates that Neanderthals made opportunistic use of fire. Lightning strikes that would generate natural fires are much more likely to occur during warm periods. Instead of creating fire, Neanderthals most likely collected natural fire and cultivated it as long as they could before it extinguished.

    Such evidence shows that human beings are unique and exceptional in our capacity to create and curate fire, distinguishing us from Neanderthals.

    Chimpanzees Exploit Natural Fire

    Still, the capacity to make opportunistic use of fire seems pretty impressive. At least until Neanderthal behavior is compared to that of chimpanzees. Recent work by Jill Pruetz indicates that these great apes understand the behavior of natural fires and even exploit them.2 Pruetz and her collaborator observed the response of the Fongoli community of chimpanzees to two wildfires in the spring of 2006. The members of the community calmly monitored the fires at close range and then changed their behavior in anticipation of the fires’ movement. To put it another way, the chimpanzees’ behavior was predictive, not responsive. This capacity is impressive, because the behavior of natural fires is complex, depending on wind speed and direction and the amount and type of fuel sources.

    So, as impressive as Neanderthal behavior may seem, their opportunistic use of fire seems more closely in line with chimpanzee behavior than that of human beings, who create and control fire at will. In fact, Pruetz believes one reason chimpanzees don’t harvest natural fire relates to their lack of manual dexterity.

    How Did Neanderthals Survive Cold Climates without Fire?

    If Neanderthals were opportunistic exploiters of fire and it was only available to them when the climate was warm, how did they survive the cold? One possibility is that they simply migrated from cold climes to warmer ones.

    Another possibility is that the hominins made clothing. At least, this is the common narrative about Neanderthals. Yet, recent work indicates that this popular depiction is incorrect. These creatures did not make clothing from animal skins, but instead made use of animal hides as capes.3

    A team of paleoanthropologists reached this conclusion by studying the faunal remains at Neanderthal and modern human archeological sites and comparing them to a database of animals used to make cold weather clothing. While both modern humans and Neanderthals used deer, bison, and bear hides for body coverings, the remains of these creatures were found more frequently at modern human archeological sites. Additionally, the remains of smaller creatures, such as weasels, wolverines, and dogs were found at modern human sites but were absent from sites occupied by Neanderthals. These smaller animals have no food value. Instead, modern humans used the animal hides to trim clothing.

    This data indicates that modern humans made much more frequent use of animal hides for clothing than did Neanderthals. And when modern humans made clothing, it was more elaborate and well-fitted than the coverings made by Neanderthals. This conclusion finds added support from the discovery of bone needles at modern human archeological sites (and the absence of these artifacts at Neanderthal sites), and reflects cognitive differences between human beings and Neanderthals.

    Even though Neanderthals made poorly crafted body coverings and most likely made little use of fire during cold periods, they were aided in their survival of frigid conditions by the design of their bodies. Anthropologists describe Neanderthals as having a hyper-polar body design that made them well-adapted to live under frozen conditions. Neanderthal bodies were stout and compact, comprised of barrel-shaped torsos and shorter limbs, which helped them retain body heat. Their noses were long and sinus cavities extensive, which helped them warm the cold air they breathed before it reached their lungs. Neanderthals most likely survived the cold because of their body design, not because of their cognitive abilities.

    Even though many paleoanthropologists assert that Neanderthals possessed cognitive abilities on par with modern humans, careful evaluation finds these claims wanting, time and time again, as the latest insights about fire use by these hominins attest.

    Compared to the hominins, including Neanderthals, human beings do, indeed, appear to be exceptional in a way that aligns with the image of God. These are far from “frivolous issues.” The implications are profound.

    What we think about Neanderthals really matters.

    Resources

    Endnotes
    1. Dennis M. Sandgathe et al., “Timing of the Appearance of Habitual Fire Use,” Proceedings of the National Academy of Sciences, USA 108 (July 19, 2011), E298, doi:10.1073/pnas.1106759108; Paul Goldberg et al., “New Evidence on Neandertal Use of Fire: Examples from Roc de Marsal and Pech de l’Azé IV,” Quaternary International 247 (2012), 325–40, doi:10.1016/j.quaint.2010.11.015; Dennis M. Sandgathe et al., “On the Role of Fire in Neanderthal Adaptations in Western Europe: Evidence from Pech de l’Azé IV and Roc de Marsal, France,” PaleoAnthropology (2011), 216–42, doi:10.4207/PA.2011.ART54.
    2. Jill D. Pruetz and Thomas C. LaDuke, “Brief Communication: Reaction to Fire by Savanna Chimpanzees (Pan troglodytes verus) at Fongoli, Senegal: Conceptualization of “Fire Behavior” and the Case for a Chimpanzee Model,” American Journal of Physical Anthropology 141 (April 2010) 646–50, doi:10.1002/ajpa.21245.
    3. Mark Collard et al., “Faunal Evidence for a Difference in Clothing Use between Neanderthals and Early Modern Humans in Europe,” Journal of Anthropological Archaeology 44 B (December 2016), 235–46, doi:org/10.1016/j.jaa.2016.07.010.
  • Does the Recovery of Oils from a Fossilized Bird Evince a Young Earth?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Dec 20, 2017

    Now the Berean Jews were of more noble character than those in Thessalonica, for they received the message with great eagerness and examined the Scriptures every day to see if what Paul said was true.

    –Acts 17:11

    Is there scientific evidence that the earth is only 6,000 years old?

    In spite of the valiant efforts of young-earth creationists (YECs), I have yet to come across any compelling scientific arguments that the earth is only a few thousand years old. At least not until I learned about the numerous discoveries of soft-tissue remnants associated with fossils that date to several hundred million years in age, in some instances. (For a detailed survey of the soft tissues recovered from the fossil record, check out my book, Dinosaur Blood and the Age of the Earth.) These discoveries give me some pause for thought about the age-of-the-earth measurements.

    These types of discoveries generate a lot of excitement among paleontologists. Having access to soft-tissue materials provides the scientific community with inspiring new insights into the biology of these ancient creatures.

    They also create a lot of excitement for YECs, because the findings suggest to them that the geologists’ dating methods are unreliable. Before these discoveries, very few scientists would have ever thought that soft-tissue materials could survive in the geological layers for thousands—let alone hundreds of millions—of years because of unrelenting decomposition processes. And yet, the number of soft-tissue fossil discoveries continues to mount. For example, investigators from the UK, the US, and Germany recently reported on the recovery of endogenous oils from the fossilized uropygial gland of a bird specimen that dates to 48 million years in age.1 I will take a closer look at what they found after a bit of explanation to show why it is critical to understand such a discovery.

    For YECs, the isolation of soft-tissue materials from fossils indicates that the fossils cannot be millions of years old but, at best, only a few thousand years old—and most likely deposited by a catastrophic worldwide flood. They reason that if the fossils are only a few thousand years old, then the methods used to age-date the fossils must be faulty. That being the case, then the same methods used to date the earth, too, must be flawed.

    As an old-earth creationist, I must admit the discovery of soft-tissue materials associated with fossils represents one of the most interesting arguments for a young earth I’ve encountered. On the surface, the argument seems reasonable. Perhaps it isn’t surprising that many YEC organizations (such as Answers in Genesis, Creation Ministries International, and the Institute for Creation Research) have elevated the existence of soft tissue materials in the fossil record to one of their central arguments for a young earth. I observe many well-meaning Christians following suit, using this same argument in their efforts to convince seekers and skeptics about the scientific reliability of the Genesis 1 creation account. Unfortunately, most people who are scientifically minded fail to find this argument persuasive because of the overwhelming amount of scientific evidence for the reliability of radiometric dating. And as a result, skeptics are often driven further away from the Christian faith.

    When using scientific discoveries to demonstrate God’s existence and to defend the reliability of the biblical creation accounts, it is critical to adopt a posture like that of the Bereans. It is incumbent on all of us to investigate or “examine” on our own to ensure the arguments we use are sound.

    That’s why I wrote Dinosaur Blood and the Age of the Earth. In this book, I make every effort to take the soft-tissue argument seriously. But, following the Bereans’ example, I thoroughly examine each premise of their argument to see if it holds up to scrutiny, including their central claim: soft-tissue materials cannot persist in fossils that are millions of years old.

    Though admittedly counterintuitive, after thorough investigation into this claim, I have come to believe that soft-tissue remnants can survive in the fossil record. To illustrate how this survival is possible, let’s use the recently discovered 48-million-year preening oil isolated, fossilized uropygial gland as a case study.

    Discovery of Preening Oil in a 48-Million-Year-Old Fossilized Gland

    The 48-million-year-old fossil bird specimen that possessed uropygial gland oils was recovered from the Messel Pit. Located in Darmstadt, Germany, this UNESCO World Heritage site has yielded a number of important vertebrate fossils throughout its history and still serves as a source of exciting new fossil discoveries today.

    While carefully examining this bird specimen (which still remains unclassified), the paleontologists noted the outline of the uropygial gland at the base of the tail region. To confirm this interpretation, the researchers attempted to extract remnants of preening oil from this putative gland. Motivated by previous soft-tissue finds and the discovery of lipids (a class of biomolecules that include oils) in other ancient geological deposits, the research team removed milligram amounts of the fossilized uropygial gland from the specimen and extracted material from the sample. Afterward, they subjected the extracts to chemical analysis, relying on a technique known as pyrolysis-gas chromatography-mass spectrometry. Analysis with this technique begins with a heating step that decomposes the analytes into small molecular fragments that, in turn, are separated by gas chromatography and then analyzed by mass spectrometry. This technique produces profiles of molecular fragments that serve as a fingerprint, helping scientists determine the identity of compounds in the sample.

    The research team detected C-8 to C-30 n-alkanes, n-alkenes, and alkylbenzenes in the uropygial gland extracted—as expected if the fossil contained remnants for preening oil. The profiles of the fossilized uropygial gland extracts differed from the profiles of extracts taken from shales that make up the geological layer that originally housed the fossil specimen. This result indicates that the uropygial gland extracts are not due to contamination from the surrounding geological layers. When the researchers compared the extracts of the fossilized glands to extracts of uropygial glands of extant birds (such as the common blackbird, the ringed teal, and the middle spotted woodpecker), they noted a difference in the profiles. This difference most likely reflects chemical alteration of the original preening oil during the fossilization process.

    How the Preening Oil Was Preserved

    So how can soft tissue material, such as preening oil, persist in fossils for millions and millions of years?

    In Dinosaur Blood and the Age of the Earth, I point out that paleontologists believe that soft-tissue preservation reflects a race between two competing processes: decomposition and mineral entombment. If mineral entombment wins, then whatever soft tissue that has avoided decomposition remains behind—for millions and millions of years. Once encased in mineral deposits, soft-tissue materials become isolated and protected from the environment, arresting the decomposition processes that would otherwise destroy them.

    Anything that slows down the rate of decomposition will help soft-tissue materials to hang around long enough for mineral entombment to take place. One factor contributing to soft-tissue survival is the structural durability of the molecules that make up the soft tissues. In most instances, the soft tissues that survive are made up of highly durable materials. Toward this end, some of the components of preening oil (such as long chain alkanes) are chemically inert, making them resistant to chemical decomposition.

    Though usually destructive, in some instances chemical reactivity can contribute to soft-tissue survival. This reactivity likely contributed to the survival of the preening oil. The team of paleontologists believes that the alkene components of the preening oils reacted to form high-molecular-weight polymers that, in turn, became resistant to chemical decomposition.

    While not subject to chemical decomposition, long chain hydrocarbons would serve as an ideal food source for microbes in the environment. This process would work against preservation. But, microbial decomposition of preening oil is unlikely, because some of the components of the uropygial gland secretions possess antimicrobial activities.

    Also, the shale that harbored the fossil bird is oxygen-depleted. The absence of oxygen in this geological setting most likely contributed to soft-tissue survival, preventing oxidative decomposition of the preening oil.

    In other words, there are several collective mechanisms in play that would stave off the decomposition of the original preening oil, though it does look as if the original material did become chemically altered. The bottom line: There is no reason to think that soft-tissue materials derived from the original preening oil in the uropygial glands could not persist for 48 million years or longer in the fossil record.

    At first glance, the soft-tissue argument for a young earth seems so compelling. Yet, when carefully evaluated (“examined”), it simply doesn’t hold up.

    Becoming Bereans

    As Christians, we should expect that there will be scientific discoveries that affirm our faith by revealing God’s fingerprints in nature and by supporting the creation accounts found in Scripture. Key biblical passages (such as Psalm 19 and Romans 1:20) teach this much. Yet, we must also recognize that as human beings interpreting nature (through science) and interpreting Scripture can be complex undertakings. As such, we can make mistakes. We are fallen creatures, we have limited knowledge, insight, and understanding, and we have preconceived notions . . . all of which influence our interpretations. And, it is for these reasons that we must all operate like the Bereans. We should respond to scientific arguments for the Christian faith with eagerness, but before we use them, we must rigorously evaluate them to ensure their validity and, if valid, to understand the arguments’ limitations. Sincere, well-meaning Christians can be wrong and can unintentionally mislead other Christians. But, when that happens it is our fault, not theirs, if we are mislead because we have failed to take the “noble,” Berean-like approach and do our homework.

    Resources to Dig Deeper

    Endnotes
    1. Shane O’Reilly et al., “Preservation of Uropygial Gland Lipids in a 48-Million-Year-Old Bird,” Proceedings of the Royal Society B 284 (October 18, 2017): doi:10.1098/rspb.2017.1050.
  • Brain Synchronization Study Evinces the Image of God

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Dec 13, 2017

    As I sit down at my computer to compose this post, the new Justice League movie has just hit the theaters. Even though it has received mixed reviews, I can’t wait to see this latest superhero flick. With several superheroes fighting side-by-side, it begs the question: “Who is the most powerful superhero in the DC universe?”

    I’m not sure how you would respond, but in my opinion, it’s not Superman or Wonder Woman. Instead, it’s a superhero that didn’t appear in the Justice League movie (but he is a longtime member of the Justice League in the comic books): the Martian Manhunter.

    Originally from Mars, J’onn J’onzz possesses superhuman strength and endurance, just like Superman. He can fly and shoot energy beams out of his eyes. But, he also has shapeshifting abilities and is a powerful telepath. It would be fun to see Superman and the Martian Manhunter tangle. My money would be on J’onn J’onzz because of his powerful telepathic abilities. As a telepath, he can read minds, control people’s thoughts and memories, create realistic illusions, and link minds together.

    blog__inline--brain-synchronization-study

    Image credit: Fazale Rana

    Even though it is fun (and somewhat silly) to daydream about superhuman strength and telepathic abilities, recent work by Spanish neuroscientists from the Basque Center on Cognition, Brain, and Language indicates that mere mortals do indeed have an unusual ability that seems a bit like telepathy. When we engage in conversations with one another—even with strangers—the electrical activities of our brains synchronize.1 In part, this newfound ability may provide the neurological basis for the theory of mind and our capacity to form complex, hierarchical social relationships, properties uniquely displayed by human beings. In other words, this discovery provides more reasons to think that human beings are exceptional in a way that aligns with the biblical concept of the image of God.

    Brain Synchronization

    Most brain activity studies focus on individual subjects and their responses to single stimuli. For example, single-person studies have shown that oscillations in electrical activity in the brain couple with speech rhythms when the test subject is either listening or speaking. The Spanish neuroscientists wanted to go one step further. They wanted to learn what happens to brain activities when two people engage one another in a conversation.

    To find out, they assembled 15 dyads (14 men and 16 women) consisting of strangers who were 20–30 years in age. They asked the members of each dyad to exchange opinions on sports, movies, music, and travel. While the strangers conversed, the researchers monitored electrical activities in the brains using EEG technology. As expected, they detected coupling of brain electrical activities with the speech rhythms in both speakers and listeners. But, to their surprise, they also detected pure brain entrainment in the electrical activities of the test subject, independent of the physical properties of the sound waves associated with speaking and listening. To put it another way, the brain activities of the two people in the conversation became synchronized, establishing a deep connection between their minds.

    Brain Synchronization and the Image of God

    The notion that human beings differ in degree, not kind, from other creatures has been a mainstay concept in anthropology and primatology for over 150 years. And it has been the primary reason why so many people have abandoned the belief that human beings bear God’s image. Yet, this stalwart view in anthropology is losing its mooring, with the concept of human exceptionalism taking its place. A growing minority of anthropologists and primatologists now believe that human beings really are exceptional. They contend that human beings do, indeed, differ in kind, not merely degree, from other creatures, including Neanderthals. Ironically, the scientists who argue for this updated perspective have developed evidence for human exceptionalism in their attempts to understand how the human mind evolved. But, instead of buttressing human evolution, these new insights marshal support for the biblical conception of humanity.

    Anthropologists identify at least four interrelated qualities that make us exceptional: (1) symbolism, (2) open-ended generative capacity, (3) theory of mind, and (4) our capacity to form complex social networks.

    As human beings, we effortlessly represent the world with discrete symbols. We denote abstract concepts with symbols. And our ability to represent the world symbolically has interesting consequences when coupled with our abilities to combine and recombine those symbols in a countless number of ways to create alternate possibilities. Our capacity for symbolism manifests in the form of language, art, music, and even body ornamentation. And we desire to communicate the scenarios we construct in our minds with other human beings.

    But there is more to our interactions with other human beings than a desire to communicate. We want to link our minds together. And we can do this because we possess a theory of mind. In other words, we recognize that other people have minds just like ours, allowing us to understand what others are thinking and feeling. We also have the brain capacity to organize people we meet and know into hierarchical categories, allowing us to form and engage in complex social networks.

    In effect, these qualities could be viewed as scientific descriptors of the image of God.

    It is noteworthy that all four of these qualities are on full display in the Spanish neuroscientists study. The capacity to offer opinions on a wide range of topics and to communicate our ideas with language reflects our symbolism and our open-ended generative capacity. I find it intriguing that the oscillations of our brain’s electrical activity couples with the rhythmic patterns created by speech—suggesting our brains are hard-wired to support our desire to communicate with one another symbolically. I also find it intriguing that our brains become coupled at an even deeper level when we converse, consistent with our theory of mind and our capacity to enter into complex social relationships.

    Even though many people in the scientific community promote a view of humanity that denigrates the image of God, common-day experience continually supports the notion that we are unique and exceptional as human beings. But, for me, I find it even more gratifying to learn that scientific investigations into our cognitive and behavioral capacities continue to affirm human exceptionalism and, with it, the image of God. Indeed, we are the crown of creation.

    Resources to Dig Deeper

    Endnotes
    1. Alejandro Pérez et al., “Brain-to-Brain Entrainment: EEG Interbrain Synchronization While Speaking and Listening,” Scientific Reports 7 (June 23, 2017): 4190, doi:10.1038/s41598-017-04464-4.
  • Molecular Scale Robotics Build Case for Design

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Dec 06, 2017

    Sometimes bigger is better, and other times, not so much—particularly for scientists working in the field of nanotechnology.

    Scientists and engineers working in this area are obsessed with miniaturization. And because of this obsession, they have developed techniques to manipulate matter at the molecular scale. Thanks to these advances, they can now produce novel materials (that could never be produced with macro-scale methods) with a host of applications. They also use these techniques to fabricate molecular-level devices—nanometer-sized machines—made up of complex arrangements of atoms and molecules. They hope that these machines will perform sophisticated tasks, giving researchers full control of the molecular domain.

    Recently, scientists from the University of Manchester in the UK achieved a milestone in nanotechnology when they designed the first-ever molecular robot that can be deployed to build molecules in the same way that robotic arms on assembly lines manufacture automobiles.1 These molecular robots can be used to improve the efficiency of chemical reactions and make it possible for organic chemists to design synthetic routes that, up to this point, were inconceivable.

    Undoubtedly, this advance will pave the way for more cost-effective, greener chemical reactions at the bench and plant scales. It will also grant organic chemists greater control over chemical reactions, paving the way for the synthesis of new types of compounds including drugs and other pharmaceutical agents.

    As exciting as these prospects are, perhaps the greater significance of this research lies in the intriguing theological implications. For example, comparison of the molecular robots to the biomolecular machines in the cell—machines that carry out similar assembly-line operations—highlights the elegant designs of biochemical systems, evincing a Creator’s handiwork. This research is theologically provocative in another way. It demonstrates human exceptionalism and, by doing so, supports the biblical claim that human beings are made in the image of God.

    Molecular Robotics

    University of Manchester chemists built molecular robots that consist of about 150 atoms of carbon, nitrogen, oxygen, and hydrogen. Though these robots consist of a relatively small number of atoms, the arrangement of these atoms makes the molecular robots structurally complex.

    The robots’ architecture is organized around a molecular-scale platform. Located in the middle of the platform is a molecular arm that extends upward and then bends at a 90-degree angle. This molecular prosthesis binds molecules at the end of the arm and then can be made to swivel between the two ends of the platform as researchers add different chemicals to the reaction. The swiveling action brings the bound molecule in juxtaposition to the chemical groups at the tip ends of the platform. When reactants are added to the solution, these compounds will react with the bound molecule differently depending on the placement of the arm, whether it is oriented toward one end of the platform or the other. In this way, the bound molecule—call it A—can react through two cycles of arm placement to form one of four possible compounds—B, C, D, and E. In this scheme, unwanted side reactions are kept to a minimum, because the bound molecule is precisely positioned next to either of the two ends of the molecular platform. This specificity improves the reaction efficiency, while at the same time making it possible for chemists to generate compounds that would be impossible to synthesize without the specificity granted by the molecular robots.

    Molecular Robots Make the Case for Design

    Many researchers working in nanotechnology did not think that the University of Manchester scientists—or any scientists, for that matter—could design and build a molecular robot that could carry out high precision molecular assembly. In the abstract of their paper, the Manchester team writes, “It has been convincingly argued that molecular machines that manipulate individual atoms, or highly reactive clusters of atoms, with Ångstrom precision are unlikely to be realized.”2

    Yet, the researchers were motivated to try to achieve this goal because molecular machines with this capacity exist inside the cell. They continue, “However, biological molecular machines routinely position rather less reactive substrates in order to direct chemical reaction sequences.”3 To put it another way, the Manchester chemists derived insight and inspiration from the biomolecular machines inside the cell to design and build their molecular robot.

    As I have written about before, the use of designs in biochemistry to inspire advances in nanotechnology make possible a new design argument, one I call the converse watchmaker argument. Namely, if biological designs are the work of a Creator, these systems should be so well-designed that they can serve as engineering models and otherwise inspire the development of new technologies.

    Comparison of the molecular robots designed by the University of Manchester team with a typical biomolecular machine found in the cell illustrates this point. The newly synthesized molecular robot consists of around 150 atoms, yet it took an enormous amount of ingenuity and effort to design and make. Still, this molecular machine is far less efficient than the biomolecular machines found in the cell. The cell’s biomolecular machines consist of thousands of atoms and are much more elegant and sophisticated than the man-made molecular robots. Considering these differences, is it reasonable to think that the biomolecular machines in the cell resulted from unguided, undirected, contingent processes when they are so much more advanced than the molecular robots built by scientists—some of them among the best chemists in the world?

    The only reasonable explanation is that the biomolecular machines in the cell stem from the work of a mind—a divine mind with unlimited creative capacity.

    Molecular Robots Make the Case for Human Exceptionalism

    Though unimpressive when compared to the elegant biomolecular machines in the cell, molecular robots still stand as a noteworthy scientific accomplishment—one might even say they represent science at its very best. And this accomplishment stresses the fact that human beings are the only species that has ever existed that can create technologies as advanced as the molecular robots invented by the University of Manchester chemists. Our capacity to investigate and understand nature through science and then turn that insight into technologies is unique to human beings. No other creature that exists today or that has ever existed, possesses this capability.

    Thomas Suddendorf puts it this way:

    “We reflect on and argue about our present situation, our history, and our destiny. We envision wonderful harmonious worlds as easily as we do dreadful tyrannies. Our powers are used for good as they are for bad, and we incessantly debate which is which. Our minds have spawned civilizations and technologies that have changed the face of the Earth, while our closest living animal relatives sit unobtrusively in their remaining forests. There appears to be a tremendous gap between human and animal minds.”4

    Anthropologists believe that symbolism accounts for the gap between humans and the great apes. As human beings, we effortlessly represent the world with discrete symbols. We denote abstract concepts with symbols. And our ability to represent the world symbolically has interesting consequences when coupled with our abilities to combine and recombine those symbols in a nearly infinite number of ways to create alternate possibilities.

    Our capacity for symbolism manifests in the form of language, art, music, and even body ornamentation. And we desire to communicate the scenarios we construct in our minds with other human beings. In a sense, symbolism and our open-ended capacity to generate alternative hypotheses are scientific descriptors of the image of God.

    There also appears to be a gap between human minds and the minds of the hominins, such as Neanderthals, who preceded us in the fossil record. It is true: claims abound about Neanderthals possessing the capacity for symbolism. Yet, as I discuss in Who Was Adam, those claims do not withstand scientific scrutiny. Recently, paleoanthropologist Ian Tattersall and linguist Noam Chomsky (along with other collaborators) argued that Neanderthals could not have possessed language and, hence, symbolism, because their crude “technology” remained stagnant for the duration of their time on Earth. Neanderthals—who first appear in the fossil record around 250,000 to 200,000 years ago and disappear around 40,000 years ago—existed on Earth longer than modern humans have. Yet, our technology has progressed exponentially, while Neanderthal technology remained largely static. According to Tattersall, Chomsky, and their coauthors:

    “Our species was born in a technologically archaic context, and significantly, the tempo of change only began picking up after the point at which symbolic objects appeared. Evidently, a new potential for symbolic thought was born with our anatomically distinctive species, but it was only expressed after a necessary cultural stimulus had exerted itself. This stimulus was most plausibly the appearance of language. . . . Then, within a remarkably short space of time, art was invented, cities were born, and people had reached the moon.”5

    In effect, these researchers echo Suddendorf’s point. The gap between human beings and the great apes and hominins becomes most apparent when we consider the remarkable technological advances we have made during our tenure as a species. And this mind-boggling growth in technology points to our exceptionalism as a species, affirming the biblical view that, as human beings, we uniquely bear God’s image.

    Resources to Dig Deeper

    Endnotes
    1. Salma Kassem et al., “Stereodivergent Synthesis with a Programmable Molecular Machine,” Nature 549 (September 21, 2017): 374–8, doi:10.1038/nature23677.
    2. Kassem et al., “Stereodivergent Synthesis,” 374.
    3. Kassem et al., “Stereodivergent Synthesis,” 374.
    4. Thomas Suddendorf, The Gap: The Science of What Separates Us from Other Animals (New York: Basic Books, 2013), 2.
    5. Johan J. Bolhuis et al., “How Could Language Have Evolved?” PLoS Biology 12 (August 26, 2014): e1001934, doi:10.1371/journal.pbio.1001934.
  • Fatty Acids Are Beautiful

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Nov 22, 2017

    Who says that fictions onely and false hair
    Become a verse? Is there in truth no beauty?
    Is all good structure in a winding stair?
    May no lines passe, except they do their dutie
    Not to a true, but painted chair?

    ­–George Herbert, “Jordan (I)”

    I doubt the typical person would ever think fatty acids are a thing of beauty. In fact, most people try to do everything they can to avoid them—at least in their diets. But, as a biochemist who specializes in lipids (a class of biomolecules that includes fatty acids) and cell membranes, I am fascinated by these molecules—and by the biochemical and cellular structures they form.

    I know, I know—Im a science geek. But for me, the chemical structures and the physicochemical properties of lipids are as beautiful as an evening sunset. As an expert, I thought I knew most of what there is to know about fatty acids, so I was surprised to learn that researchers from Germany recently uncovered an elegant mathematical relationship that explains the structural makeup of fatty acids.1 From my vantage point, this newly revealed mathematical structure boggles my mind, providing new evidence for a Creator’s role in bringing life into existence.

    Fatty Acids

    To first approximation, fatty acids are relatively simple compounds, consisting of a carboxylic acid head group and a long-chain hydrocarbon tail.

    blog__inline--fatty-acids-are-beautiful-1

    Structure of two typical fatty acids
    Image credit: Edgar181/Wikimedia Commons

    Despite their structural simplicity, a bewildering number of fatty acid species exist. For example, the hydrocarbon chain of fatty acids can vary in length from 1 carbon atom to over 30. One or more double bonds can occur at varying positions along the chain, and the double bonds can be either cis or trans in geometry. The hydrocarbon tails can be branched and can be modified by carbonyl groups and by hydroxyl substituents at varying points along the chain. As the hydrocarbon chains become longer, the number of possible structural variants increases dramatically.

    How Many Fatty Acids Exist in Nature?

    This question takes on an urgency today because advances in analytical techniques now make it possible for researchers to identify and quantify the vast number of lipid species found in biological systems, birthing the discipline of lipidomics. Investigators are interested in understanding how lipid compositions vary spatially and temporally in biological systems and how these compositions change in response to altered physiological conditions and pathologies.

    To process and make sense of the vast amount of data generated in lipidomics studies, biochemists need to have some understanding of the number of lipid species that are theoretically possible. Recently, researchers from Friedrich Schiller University in Germany took on this challenge—at least, in part—by attempting to calculate the number of chemical species that exist for fatty acids varying in size from 1 to 30 atoms.

    Fatty Acids and Fibonacci Numbers

    To accomplish this objective, the German researchers developed mathematical equations that relate the number of carbon atoms in fatty acids to the number of structural variants (isomers). They discovered that this relationship conforms to the Fibonacci series, with the number of possible fatty acid species increasing by a factor of 1.618—the golden mean—for each carbon atom added to the fatty acid. Though not immediately evident when first examining the wide array of fatty acids found in nature, deeper analysis reveals that a beautiful yet simple mathematical structure underlies the seemingly incomprehensible structural diversity of these biomolecules.

    This discovery indicates it is unlikely that the fatty acid compositions found in nature reflect the haphazard outcome of an undirected, historically contingent evolutionary history, as many biochemists are prone to think. Instead, the fatty acids found throughout the biological realm appear to be fundamentally dictated by the tenets of nature. It is provocative to me that the fatty acid diversity produced by the laws of nature is precisely the isomers needed to for life to be possiblea fitness to purpose, if you will.

    Understanding this mathematical relationship and knowing the theoretical number of fatty acid species will certainly aid biochemists working in lipidomics. But for me, the real significance of these results lies in the philosophical and theological arenas.

    The Mathematical Beauty of Fatty Acids

    The golden mean occurs throughout nature, describing the spiral patterns found in snail shells and the flowers and leaves of plants, as examples, highlighting the pervasiveness of mathematical structures and patterns that describe many aspects of the world in which we live.

    But there is more. As it turns out, we perceive the golden mean to be a thing of beauty. In fact, architects and artists often make use of the golden mean in their work because of its deeply aesthetic qualities.

    Everywhere we look in nature—whether the spiral arms of galaxies, the shell of a snail, or the petals of a flower—we see a grandeur so great that we are often moved to our very core. This grandeur is not confined to the elements of nature we perceive with our senses; it also exists in the underlying mathematical structure of nature, such the widespread occurrence of the Fibonacci sequence and the golden mean. And it is remarkable that this beautiful mathematical structure even extends to the relationship between the number of carbon atoms in a fatty acid and the number of isomers.

    As a Christian, nature’s beauty—including the elegance exemplified by the mathematically dictated composition of fatty acids—prompts me to worship the Creator. But this beauty also points to the reality of God’s existence and supports the biblical view of humanity. If God created the universe, then it is reasonable to expect it to be a beautiful universe. Yet, if the universe came into existence through mechanism alone, there is no 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 aesthetic sense. But 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.

    Resources to Dig Deeper

    Endnotes
    1. Stefan Schuster, Maximilian Fichtner, and Severin Sasso, “Use of Fibonacci Numbers in Lipidomics—Enumerating Various Classes of Fatty Acids,” Scientific Reports 7 (January 2017): 39821, doi:10.1038/srep39821.
  • Ribosomes: Manufactured by Design, Part 2

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Nov 08, 2017

    “I hope there are no creationists in the audience, but it would be a miracle if a strand of RNA ever appeared on the primitive Earth.”1

    Hugh Ross and I witnessed the late origin-of-life researcher, Leslie Orgel, make this shocking proclamation at the end of a lecture he presented at the 13th International Conference on the Origin of Life (ISSOL 2002).

    Orgel was one of the originators of the RNA world hypothesis. And because of his prominence in the origin-of-life research community, the conference organizers granted Orgel the honor of opening ISSOL 2002 with a plenary lecture on the status of the RNA world hypothesis. During his presentation, Orgel described problem after problem with the leading origin-of-life explanation, reaching the tongue-in-cheek conclusion that it would require a miracle for this evolutionary scenario to yield RNA, let alone the first life-forms. (For a detailed discussion of the problems with the RNA world hypothesis, see my book Creating Life in the Lab.)

    Despite these problems, many origin-of-life researchers—including Leslie Orgel (while he was alive)—remain convinced that the RNA world scenario must be the explanation for the emergence of life via chemical evolution. Why? For one key reason: the intermediary role RNA plays in protein synthesis.

    The RNA World Hypothesis

    The RNA world hypothesis posits that biochemistry was initially organized exclusively around RNA and only later did evolutionary processes transform the RNA world into the familiar DNA-protein world of contemporary organisms. If this model is correct, then the DNA-protein world represents the historically contingent outworking of evolutionary history. To put it another way, contemporary biochemistry has been cobbled together by unguided evolutionary forces and the role RNA plays in protein synthesis is an accidental outcome.

    The discovery of ribozymes in the 1980s provided initial support for the RNA world scenario. These RNA molecules possess functional capabilities, behaving just like enzymes. In other words, RNA not only harbors information like DNA, it also carries out cellular functions like proteins. Origin-of-life researchers take RNA’s dual capacities as evidence that life could have been organized around RNA biochemistry. These same researchers presume that evolutionary processes later apportioned RNA’s twofold capabilities between DNA (information storage) and proteins (function). Origin-of-life researchers often point to RNA’s intermediary role in protein synthesis as evidence for the RNA world hypothesis. Again, RNA’s reduced role in contemporary biochemical systems stands as a vestige of evolutionary history, with RNA viewed as a sort of molecular fossil.

    Ribosomes serve as a prime illustration of RNA’s role as a go-between in protein synthesis. As subcellular particles, ribosomes catalyze (assist) the chemical reactions that form the bonds between the amino acid subunits of the proteins. Two subunits of different sizes (comprised of proteins and RNA molecules) combine to form a functional ribosome. In organisms like bacteria, the large subunit (LSU) contains 2 ribosomal RNA (rRNA) molecules and about 30 different protein molecules. The small subunit (SSU) consists of a single rRNA molecule and about 20 proteins. In more complex organisms, the LSU is formed by 3 rRNA molecules that combine with around 50 distinct proteins, and the SSU consists of a single rRNA molecule and over 30 different proteins.

    The rRNA molecules function as scaffolding, organizing the myriad ribosomal proteins. They also catalyze the chain-forming reactions between amino acids. In other words, the ribosome is a ribozyme. At the ISSOL 2002 meeting, I heard Orgel adamantly insist that the RNA world hypothesis must be valid because rRNA catalyzes protein bond formation.

    Orgel’s perspective gains support considering the inefficiency of ribozymes as catalysts. Protein enzymes are much more efficient than ribozymes. In other words, it seemingly would be better and more efficient to design ribosomes so that proteins catalyzed bond formation between amino acids, not rRNA. This reason convinces origin-of-life researchers that the role rRNAs play in protein synthesis is a haphazard consequence of life’s historically contingent evolutionary history.

    But recent work by scientists from Harvard and Uppsala Universities paints a different picture of the compositional makeup of ribosomes, and in doing so, undermines what many origin-of-life researchers believe to be the most compelling evidence for the RNA world hypothesis. These researchers demonstrate that the compositional makeup of ribosomes does not appear to be the accidental outworking of an unguided, contingent process. Instead, an exquisite molecular logic accounts for the composition and structural properties of the protein and rRNA components of ribosomes.2

    Is There a Rationale for Ribosome Structure?

    As part of their research efforts, the Harvard and Uppsala University investigators were specifically trying to answer several questions related to the composition of ribosomes, including:

    1. Why are ribosomes made up of so many proteins?
    2. Why are ribosomal proteins nearly the same size?
    3. Why are ribosomal proteins smaller than typical proteins?
    4. Why are ribosomes made up of so few rRNA molecules?
    5. Why are rRNA molecules so large?
    6. Why do ribosomes employ rRNA as the catalyst to form bonds between amino acids, instead of proteins which are much more efficient as enzymes?

    Ribosomes Make Ribosomes

    Before a cell can replicate, ribosomes must manufacture the proteins needed to form more ribosomes—in fact, ribosomes need to manufacture enough proteins to form a full complement of these subcellular complexes. This ensures that both daughter cells have the sufficient number of protein-manufacturing machines to thrive once the cell division process is completed. Because of this constraint, cell replication cannot proceed until a duplicate population of ribosomes is produced.

    Ribosome Composition is Optimal for Efficient Production of Ribosomes

    As discussed in an earlier blog post, the Harvard and Uppsala University investigators discovered that if ribosomal proteins were large, or if these biomolecules were variable in size, ribosome production would be slow and inefficient. Building ribosomes with smaller, uniform-size proteins represents the faster way to duplicate the ribosome population, permitting the cell replication to proceed in a timely manner. They also determined that the optimal number of ribosomal proteins is between 50 to 80—the number of ribosomal proteins found in nature. In short, the composition of these sub cellular complexes appears to be undergirded by an elegant molecular rationale.

    As part of their mathematical modeling study, these researchers also provided an explanation for why ribosomes are made up of large RNA molecules. Because the number of steps involved in rRNA production is fewer than the steps required for protein manufacture, rRNA molecules can be made more rapidly than proteins. This being the case, ribosome production is more efficient when these organelles are built using fewer and larger rRNA molecules as opposed to smaller, more numerous ones.

    The research team learned that ribosomes containing more rRNA can be built faster than ribosomes made up of more proteins. This fact helps explain why rRNA operates as the catalytic portion of ribosomes (linking amino acids together to construct proteins), though less efficient as a catalyst than proteins.

    These insights also explain the compositional differences among ribosomes found in bacteria, eukaryotic cells, and mitochondria. Bacteria, which typically replicate faster than eukaryotic cells, possess ribosomes that contain proportionally more rRNA and fewer proteins than ribosomes found in eukaryotic cells. Mitochondria—organelles found in eukaryotic cells—possess ribosomes with a much greater ratio of proteins to rRNA than eukaryotic cells. This observation makes sense because ribosomes in mitochondria don’t produce themselves.

    It Would Be a Miracle if a Strand of RNA Appeared on the Primitive Earth

    An exquisite molecular rationale undergirds the number and size of rRNA molecules in ribosomes and accounts for why the ribosome is a ribozyme. The work of the Harvard and Uppsala University scientists undermines the view that ribosomes were cobbled together as a result of the evolutionary transition from the RNA world to the DNA/protein world. If the presence and role of RNA molecules in ribosomes were simply vestiges of life’s origin out of an RNA world, then there should not be an elegant molecular logic that accounts for ribosome compositions in bacteria and eukaryotic organisms. In other words, it doesn’t appear as if ribosomes are the unintended outcome of an unguided evolutionary process.

    This conclusion gains support from earlier work by life scientist Ian S. Dunn. As I wrote about in a previous blog post, Dunn has uncovered a molecular rationale for the intermediary role messenger RNA (mRNA) plays in protein synthesis. Again, it indicates that the intermediary role of RNA molecules in protein synthesis is a necessary design of a DNA/protein world, not a molecular vestige of life’s evolutionary origin that proceeds through an RNA world.

    Given these new insights and the intractable problems with the RNA world scenario, I must agree with Leslie Orgel. It would be a miracle if a strand of RNA appeared on the primitive Earth—unless a Creator intervened.

    Resources to Dig Deeper

    Endnotes
    1. Fazale Rana, Creating Life in the Lab: How New Discoveries in Synthetic Biology Make a Case for the Creator (Grand Rapids, MI: Baker Books, 2011), 161.
    2. Shlomi Reuveni, Måns Ehrenberg, and Johan Paulsson, “Ribosomes Are Optimized for Autocatalytic Production,” Nature 547 (July 20, 2017): 293–7, doi:10.1038/nature22998.
  • Ribosomes: Manufactured by Design, Part 1

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Nov 01, 2017

    Before joining Reasons to Believe in 1999, I spent seven years working in R&D at a Fortune 500 company, which meant that I spent most of my time in a chemistry laboratory alongside my colleagues trying to develop new technologies with the hope that one day our ideas would become a reality, making their way onto store shelves.

    From time to time, my work would be interrupted by an urgent call from one of our manufacturing plants. Inevitably, there was some crisis requiring my expertise as a chemist to troubleshoot. Often, I could solve the plant’s problem over the phone, or by analyzing a few samples sent to my lab. But, occasionally, the crisis necessitated a trip to the plant. These trips weren’t much fun. They were high pressure, stressful situations, because the longer the plant was offline, the more money it cost the company.

    But, once the crisis abated, we could breathe easier. And that usually afforded us an opportunity to tour the plant.

    It was a thrill to see working assembly lines manufacturing our products. These manufacturing operations were engineering marvels to behold, efficiently producing high-quality products at unimaginable speeds.

    The Cell as a Factory

    Inside each cell, an ensemble of manufacturing operations exists, more remarkable than any assembly line designed by human engineers. Perhaps one of the most astounding is the biochemical process that produces proteins—the workhorse molecules of life. These large complex molecules work collaboratively to carry out every cellular operation and contribute to the formation of all the structures within the cell.

    Subcellular particles called ribosomes produce proteins through an assembly-line-like operation, replete with sophisticated quality control checkpoints. (As discussed in The Cell’s Design, the similarity between the assembly-line production of proteins and human manufacturing operations bolsters the Watchmaker argument for God’s existence.)

    Ribosomes

    About 23 nanometers in diameter, ribosomes play a central role in protein synthesis by catalyzing (assisting) the chemical reactions that form the bonds between the amino acid subunits of proteins. A human cell may contain up to half a million ribosomes. A typical bacterium possesses about 20,000 of these subcellular structures, comprising one-fourth the total bacterial mass.

    Two subunits of different sizes (comprised of proteins and RNA molecules) combine to form a functional ribosome. In organisms like bacteria, the large subunit (LSU) contains 2 ribosomal RNA (rRNA) molecules and about 30 different protein molecules. The small subunit (SSU) consists of a single rRNA molecule and about 20 proteins. In more complex organisms, the LSU is formed by 3 rRNA molecules that combine with around 50 distinct proteins and the SSU consists of a single rRNA molecule and over 30 different proteins. The rRNAs act as scaffolding that organizes the myriad ribosomal proteins. They also catalyze the chain-forming reactions between amino acids.

    Ribosomes Make Ribosomes

    Before a cell can replicate, ribosomes must manufacture the proteins needed to form more ribosomes—in fact, the cell’s machinery needs to manufacture enough ribosomes to form a full complement of these subcellular complexes. This ensures that both daughter cells have the sufficient number of protein-manufacturing machines to thrive once the cell division process is completed. Because of this constraint, cell replication cannot proceed until a duplicate population of ribosomes is produced.

    Is There a Rationale for Ribosome Structure?

    Clearly, ribosomes are complex subcellular particles. But, is there any rhyme or reason for their structure? Or are ribosomes the product of a historically contingent evolutionary history?

    New work by researchers from Harvard University and Uppsala University in Sweden provides key insight into the compositional make up of ribosomes, and, in doing so, help answer these questions.1

    As part of their research efforts, the Harvard and Uppsala University investigators were specifically trying to answer several questions related to the composition of ribosomes, including:

    1. Why are ribosomes made up of so many proteins?
    2. Why are ribosomal proteins nearly the same size?
    3. Why are ribosomal proteins smaller than typical proteins?
    4. Why are ribosomes made up of so few rRNA molecules?
    5. Why are rRNA molecules are so large?
    6. Why do ribosomes employ rRNA as the catalyst to form bonds between amino acids, instead of proteins which are much more efficient as enzymes?

    Ribosome Composition Is Optimal for Efficient Production of Ribosomes

    Using mathematical modeling, the Harvard and Uppsala University investigators discovered that if ribosomal proteins were larger, or if these biomolecules were variable in size, ribosome production would be slow and inefficient. Building ribosomes with smaller, uniform-size proteins represents the faster way to duplicate the ribosome population, permitting the cell replication to proceed in a timely manner.

    These researchers also learned that if the ribosomal proteins were any shorter, inefficient ribosome production also results. This inefficiency stems from biochemical events needed to initiate protein production. If proteins are too short, then the initiation events take longer than the elongation processes that build the protein chains.

    The bottom line: The mathematical modeling work by the Harvard and Uppsala University research team indicates that the sizes of ribosomal proteins are optimal to ensure the most rapid and efficient production of ribosomes. The mathematical modeling also determined that the optimal number of ribosomal proteins is between 50 to 80—the number of ribosomal proteins found in nature.

    Ribosome Composition Is Optimal to Produce a Varied Population of Ribosomes

    The insights of this work have bearing on the recent discovery that within cells a heterogeneous population of ribosomes exists, not a homogeneous one as biochemists have long thought.2 Instead of every ribosome in the cell being identical, capable of producing each and every protein the cell needs, a diverse ensemble of distinct ribosomes exists in the cell. Each type of ribosome manufactures characteristically distinct types of proteins. Typically, ribosomes produce proteins that work in conjunction to carry out related cellular functions. The heterogeneous makeup of ribosomes contributes to the overall efficiency of protein production, and also provides an important means to regulate protein synthesis. It wouldn’t make sense to use an assembly line to make both consumer products, such as antiperspirant sticks, and automobiles. In the same manner, it doesn’t make sense to use the same ribosomes to make the myriad proteins, performing different functions for the cell.

    Because ribosomes consist of a large number of small proteins, the cell can efficiently produce heterogeneous populations of ribosomes by assembling a ribosomal core and then including and excluding specific ribosomal proteins to generate a diverse population of ribosomes.3 In other words, the protein composition of ribosomes is optimized to efficiently replicate a diverse population of these subcellular particles.

    The Case for Creation

    The ingenuity of biochemical systems was one of the features of the cell’s chemistry that most impressed me as a graduate student (and moved me toward the recognition that there was a Creator). And the latest work by researchers on ribosome composition from Harvard and Uppsala Universities provides another illustration of the clever way that biochemical systems are constructed. The composition of these subcellular structures doesn’t appear to be haphazard—a frozen accident of a historically contingent evolutionary process—but instead is undergirded by an elegant molecular rationale, consistent with the work of a mind.

    The case for intelligent design gains reinforcement from the optimal composition of ribosomal proteins. Quite often, designs produced by human beings have been optimized, making this property a telltale signature for intelligent design. In fact, optimality is most often associated with superior designs.

    As I pointed out in The Cell’s Design, ribosomes are chicken-and-egg systems. Because ribosomes are composed of proteins, proteins are needed to make proteins. As with ingenuity and optimality, this property also evinces for the work of intelligent agency. Building a system that displays this unusual type of interdependency requires, and hence, reflects the work of a mind.

    On the other hand, the chicken-and-egg nature of ribosome biosynthesis serves as a potent challenge to evolutionary explanations for the origin of life.

    The Challenge to Evolution

    Because ribosomes are needed to make the proteins needed to make ribosomes, it becomes difficult to envision how this type of chicken-and-egg system could emerge via evolutionary processes. Protein synthesis would have to function optimally at the onset. If it did not, it would lead to a cycle of auto-destruction for the cell.

    Ribosomes couldn’t begin as crudely operating protein-manufacturing machines that gradually increased in efficiency—evolving step-by-step—toward the optimal systems, characteristic of contemporary biochemistry. If error-prone, ribosomes will produce defective proteins—including ribosomal proteins. In turn, defective ribosomal proteins will form ribosomes even more prone to error, setting up the auto-destruct cycle. And in any evolutionary scheme, the first ribosomes would have been error-prone.

    The compositional requirement that ribosomal proteins be of the just-right size and uniform in length only exacerbates this chicken-and-egg problem. Even if ribosomes form functional, intact proteins, if these proteins arent the correct number, size, or uniformity then ribosomes couldnt be replicated fast enough to support cellular reproduction.

    In short, the latest insights in the protein composition of ribosomes provides compelling reasons to think that life must stem from a Creator’s handiwork.

    So does the compositional makeup of ribosomal RNA molecules, which will be the topic of my next blog post.

    Resources

    Endnotes
    1. Shlomi Reuveni et al., “Ribosomes Are Optimized for Autocatalytic Production,” Nature 547 (July 20, 2017): 293–97, doi:10.1038/nature22998.
    2. Zhen Shi et al., “Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-Wide,” Molecular Cell 67 (July 6, 2017): 71–83, doi:10.1016/j.molcel.2017.05.021.
    3. Jeffrey A. Hussmann et al., “Ribosomal Architecture: Constraints Imposed by the Need for Self-Production,” Current Biology 27 (August 21, 2017): R798–R800, doi:10.1016/j.cub.2017.06.080.
  • Evolutionary Paradigm Lacks Explanation for Origin of Mitochondria and Eukaryotic Cells

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Oct 03, 2017

    You carried the cross
    Of my shame
    Oh my shame
    You know I believe it
    But I still haven’t found
    What I’m looking for

    —Adam Clayton, Dave Evans, Larry Mullen, Paul David Hewson, Victor Reina

    One of my favorite U2 songs is “I Still Haven’t Found What I’m Looking For.” For me, it’s a reminder that because of Christ, my life has meaning, purpose, and a sense of destiny. Still, I will never discover ultimate fulfillment in this world no matter how hard I search, but in the world to come—the new heaven and new earth.

    Though their pursuit is scientific and not religious, many scientists have also failed to find what they have been looking for. Physicists are on a quest to find the Theory of Everything—a Grand Unified Theory (GUT) that can account for everything in physics. However, a GUT eludes them.

    On the other hand, life scientists appear to have found it. They claim to have discovered biology’s GUT: the theory of evolution. Many biologists assert that evolutionary mechanisms can fully account for the origin, history, and design of life. And they are happy to sing about their discovery any chance they get.

    Yet, despite this claim, the evolutionary paradigm seems to come up short time and time again when it comes to explaining key events in life’s history. And this failure serves as the basis for my skepticism regarding the evolutionary paradigm.

    Currently, evolutionary biologists lack explanations for the key transitions in life’s history, including thes

    • origin of life,
    • origin of eukaryotic cells,
    • origin of sexual reproduction,
    • origin of body plans,
    • origin of consciousness,
    • and the origin of human exceptionalism.

    To be certain, evolutionary biologists have proposed models to explain each of these transitions, but the models consistently fail to deliver, as a recent review article published by two prominent evolutionary biologists from the Hungarian Academy of Sciences illustrates.In this article, these researchers point out the insufficiency of the endosymbiont hypothesis—the leading evolutionary model for the origin of eukaryotic cells—to account for the origin of mitochondria and, hence, eukaryogenesis.

    The Endosymbiont Hypothesis

    Lynn Margulis (1938–2011) advanced the endosymbiont hypothesis for the origin of eukaryotic cells in the 1960s, building on the ideas of Russian botanist, Konstantin Mereschkowski. Taught in introductory high school and college biology courses, Margulis’s work has become a cornerstone idea of the evolutionary paradigm. This classroom exposure explains why students often ask me about the endosymbiont hypothesis when I speak on university campuses. Many first-year biology students and professional life scientists alike find the evidence for this idea compelling and, consequently, view it as providing broad support for an evolutionary explanation for the history and design of life.

    According to the 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. (Ingested cells that take up permanent residence within other cells are referred to as endosymbionts.)

    Presumably, organelles such as mitochondria were once endosymbionts. Once engulfed, the endosymbionts took up permanent residency within the host, with the endosymbiont growing and dividing inside the host. Over time, the endosymbionts and the host became mutually interdependent, with the endosymbionts providing a metabolic benefit for the host cell. The endosymbionts gradually evolved into organelles through a process referred to as genome reduction. This reduction resulted when genes from the endosymbionts’ genomes were transferred into the genome of the host organism. Eventually, the host cell evolved the machinery to produce the proteins needed by the former endosymbiont and processes to transport those proteins into the organelle’s interior.

    Evidence for the Endosymbiont Hypothesis

    The similarity between organelles and bacteria serve as the main line of evidence for the endosymbiont hypothesis. For example, mitochondria—which are believed to be descended from a group of alpha-proteobacteria—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.

    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 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 this organelle’s evolutionary history.2

    Does the Endosymbiont Hypothesis Successfully Account for the Origin of Mitochondria?

    Despite the seemingly compelling evidence for the endosymbiont hypothesis, evolutionary biologists lack a genuine explanation for the origin of mitochondria, and, in a broader context, the origin of eukaryotic cells. In their recently published critical review, Zachar and Szathmary point out that evolutionary biologists have proposed over twenty different evolutionary scenarios for the mitochondrial origins that umbrella underneath the endosymbiont hypothesis. Of these, they identify eight that are reasonable, casting the others aside. Still, these eight hypotheses fail to fully account for the origin of mitochondria. The Hungarian biologists delineate twelve questions that any successful endosymbiogenesis model must answer. In turn, they demonstrate that none of these models answers all the questions. In doing so, the two researchers call for a new theory.

    In the article’s abstract, the authors state, “The origin of mitochondria is a unique and hard evolutionary problem, embedded within the origin of eukaryotes. . . . Contending theories widely disagree on ancestral partners, initial conditions and unfolding events. There are many open questions but there is no comparative examination of hypotheses. We have specified twelve questions about the observable facts and hidden processes leading to the establishment of the endosymbiont that a valid hypothesis must address. There is no single theory capable of answering all questions.”3

    Space doesn’t permit me to discuss each of the questions posed by the pair of biologists. Still, I would like to call attention to a few problems confronting the endosymbiont hypothesis, highlighted in their critical review.

    Lack of Transitional Intermediates. Biologists have yet to discover any single-celled organisms that represent transitional intermediates between prokaryotes and eukaryotic cells. (There are some eukaryotes that lack mitochondria, but they appear to have lost these organelles.) All complex cells display the eukaryotic hallmark features. In other words, it looks as if eukaryotic cells emerged in a short period of time, without any transitional forms. In fact, some biologists dub the transition the eukaryotic big bang.

    Chimeric Nature of Eukaryotic Cells. Eukaryotic cells possess an unusual combination of features. Their information-processing systems resemble those of archaea, but their membranes and energy metabolism are bacteria-like. There is no plausible evolutionary scenario to explain this blend of features. It would require the archaeon host to replace its membranes while retaining all its information-processing genes. Evolutionary biologists know of no instance in which this type of transition took place, nor do they know how it could have occurred.

    Absence of Membrane Bioenergetics in the Host. All prokaryotic organisms rely on their plasma membrane to produce energy. If eukaryotic cells emerged via endosymbiogenesis, then the plasma membranes of eukaryotic cells should possess vestiges of that past function. Yet, the plasma membranes of eukaryotic cells show no traces of this essential biochemical feature.

    Mechanism of Inclusion. The most plausible way for the endosymbiont to be taken up by the host cell is through a process called phagocytosis. But why wouldn’t the engulfed cell be digested by the host? How did the endosymbiont escape destruction? And, if it somehow survived, why doesn’t the mitochondria possess a triple membrane system, with the outermost membrane derived from the phagosome?

    Early Selective Advantage. Once inside the host, why didn’t the endosymbiont simply reproduce, overrunning the host cell? What benefit would it be for the host cell to initially harbor the endosymbiont? Currently, evolutionary biologists don’t have answers to troubling questions such as these.

    The challenges delineated by the Hungarian biologists aren’t the only ones faced by evolutionary models for endosymbiogenesis. As I discuss in a previous article, mitochondrial protein biogenesis poses another difficult problem for the endosymbiont hypothesis.

    The authors of the critical review sum it up this way: “The integration of mitochondria was a major transition, and a hard one. It poses puzzles so complicated that new theories are still generated 100 years since endosymbiogenesis was first proposed by Konstantin Mereschkowsky and 50 years since Lynn Margulis cemented the endosymbiotic origin of mitochondria into evolutionary biology. . . . One would expect that by this time, there is a consensus about the transition, but far from that even the most fundamental points are still debated.”4

    Though evolutionary biologists claim to have life’s history all figured out, in reality they are like most of us—they still haven’t found what they are looking for.

    Resources

    Endnotes

    1. Istvan Zachar and Eors Szathmary, “Breath-Giving Cooperation: Critical Review of Origin of Mitochondria Hypotheses,” Biology Direct 12 (August 14, 2017): 19, doi:10.1186/s13062-017-0190-5.
    2. In previous posts (here, here, and here), I explain the rationale for mitochondrial DNA and the presence of cardiolipin in the inner mitochondrial membrane from a creation model/intelligent design vantage point and, in doing so, demonstrate that the two biochemical features aren’t uniquely explained by the endosymbiont hypothesis.
    3. Zachar and Szathmary, “Breath-Giving Cooperation.”
    4. Zachar and Szathmary, “Breath-Giving Cooperation.”
  • Whale Vocal Displays Make Beautiful Case for a Creator

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Sep 26, 2017

    There is the sea, vast and spacious,
    teeming with creatures beyond number—
    living things both large and small.
    There the ships go to and fro,
    and Leviathan, which you formed to frolic there.

    —Psalm 104:25–26

    A few weeks ago, I did something I always wanted to do. I listened to the uncut, live version of the Allman Brothers’ Mountain Jam from beginning to end. Thirty-four minutes in length, this song appears on The Allman Brothers’ live At Fillmore East album. Though The Allman Brothers are among my favorite groups, I have never had the time and motivation to listen to this song in its entirety. I like listening to jam bands, but a thirty-four-minute song . . . in any case, a cross-country flight finally afforded me the opportunity to give my undivided attention to this jam band masterpiece. What an incredible display of musicianship!

    Humpback Whale Acoustical Displays

    Rockers aren’t the only ones who can get a bit carried away when performing a song. Humpback whales are notorious for their jam-band-like acoustical displays. These creatures produce elaborate patterns of sounds that researchers dub songs. The whale songs can last for up to 30 minutes, and some whales will repeatedly perform the same song for up to 24 hours.

    Humpback whale songs display a complex hierarchical organization. The most basic element of the song consists of a single sound, called a unit. These creatures combine units together to form phrases. In turn, they combine phrases to form themes. Finally, they combine themes to form a song, with each theme connected by transitional phrasing.

    Researchers aren’t certain why humpback whales engage in these complex acoustical displays. Only the males sing. Perhaps their singing establishes dominance within the group. Most researchers think that the males sing to attract females. (Even for whales, the musicians get the girls.)

    Humpback whales in the same area perform the same song. But, their songs continually evolve. Researchers refer to the complete transformation of one whale song into another as a revolution. As the songs evolve, each member of the group learns the new variant. When one group of humpback whales encounters another group, the two groups exchange songs. This exchange accelerates the song revolution. As a result of this encounter, members of both groups develop and learn a new song.

    How Do Humpback Whales Learn Songs?

    Researchers from the UK and Australia wanted to understand how humpback whales learn new songs.1 Their query is part of a bigger question: How do animals transmit culture—learned information and behaviors—to other members of the group and to the next generation?

    To answer this question, the research team recorded 9,300 acoustical displays over the course of two complete song revolutions for the humpback whales of the South Pacific. Among these recordings, they discovered hybrid songs—vocal displays comprised of bits and pieces of both the old and the new songs. They concluded that these hybrids songs captured the transition from one song to the next.

    These song hybrids consisted of phrases and themes from the old and new songs spliced together. The structure of hybrid songs indicated to the research team that humpback whales must learn songs in the same way that humans learn languages, by learning bits and piecing them together.

    Rock on!

    The Creator’s Artistry

    Sometimes, as Christian apologists, we tend to think of God solely as an Engineer who creates with only one specific purpose or function in mind. But, the insights researchers have gained into the vocal displays of the humpback whales reminds me that the God I worship is also a Divine Artist—a God who creates for his enjoyment.

    Scripture supports this idea. Psalm 104:25 states that God formed the leviathan (which in this passage seems to refer to whales) on day five to frolic in the vast, spacious seas. In other words, God created the great sea mammals for no other purpose than to play!

    Artistry and engineering are not mutually exclusive. Engineers often design cars and buildings to be both functionally efficient and aesthetically pleasing. But sometimes, as humans, we create for no other reason than for our pleasure and for others to enjoy and be moved by our work.

    Nature’s Beauty and God’s Existence

    The humpback whale exemplifies the remarkable beauty of the natural world. Everywhere we look in nature—whether the night sky, the oceans, the rain forests, the deserts, even the microscopic world—we see a grandeur so great that we are often moved to our very core.

    Watching a humpback whale breach or hearing a recording of its vocal displays is more than sufficient to produce in us that sense of awe and wonder. And yet, our wonder and amazement only grow as we study these creatures using sophisticated scientific techniques.

    For Christians, nature’s beauty prompts us to worship the Creator. But it also points to the reality of God’s existence and supports the biblical view of humanity.

    As philosopher Richard Swinburne argues, “If God creates a universe, as a good workman, he will create a beautiful universe. On the other hand, if the universe came into existence without being created by God, there is no reason to suppose that it would be a beautiful universe.”2 In other words, the beauty in the world around us signifies the Divine.

    But, as human beings, why do we perceive beauty in the world? In response to this question, Swinburne asserts, “There is certainly no particular reason why, if the universe originated uncaused, psycho-physical laws…would bring about aesthetic sensibilities in humans.”3 But, 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.

    In short, the humpback whales’ acoustical displaysa jam band masterpiecesing of the Creator’s existence and his artistry.

    Resources

    Endnotes

    1. Ellen C. Garland et al., “Song Hybridization Events during Revolutionary Song Change Provide Insights into Cultural Transmission in Humpback Whales,” Proceedings of the National Academy of Sciences USA 114 (July 25, 2017): 7822–29, doi:10.1073/pnas.1621072114.
    2. Richard Swinburne, The Existence of God, 2nd ed. (New York: Oxford University Press, 2004), 190–91.
    3. Swinburne, Existence of God, 190–91.
  • The Human Genome: Copied by Design

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Sep 19, 2017

    The time my wife Amy and I spent in graduate school studying biochemistry were some of the best days of our lives. But it wasn’t all fun and games. For the most part, we spent long days and nights working in the lab.

    But we weren’t alone. Most of the graduate students in the chemistry department at Ohio University kept the same hours we did, with all-nighters broken up around midnight by “Dew n’ Donut” runs to the local 7-Eleven. Even though everybody worked hard, some people were just more productive than others. I soon came to realize that activity and productivity were two entirely different things. Some of the busiest people I knew in graduate school rarely accomplished anything.

    This same dichotomy lies at the heart of an important scientific debate taking place about the meaning of the ENCODE project results. This controversy centers around the question: Is the biochemical activity measured for the human genome merely biochemical noise or is it productive for the cell? Or to phrase the question the way a biochemist would: Is biochemical activity associated with the human genome the same thing as biochemical function?

    The answer to this question doesn’t just have scientific implications. It impacts questions surrounding humanity’s origin. Did we arise through evolutionary processes or are we the product of a Creator’s handiwork?

    The ENCODE Project

    The ENCODE project—a program carried out by a consortium of scientists with the goal of identifying the functional DNA sequence elements in the human genome—reported phase II results in the fall of 2012. To the surprise of many, the ENCODE project reported that around 80% of the human genome displays biochemical activity, and hence function, with the expectation that this percentage should increase with phase III of the project.

    If valid, the ENCODE results force a radical revision of the way scientists view the human genome. Instead of a wasteland littered with junk DNA sequences (as the evolutionary paradigm predicts), the human genome (and the genomes of other organisms) is packed with functional elements (as expected if a Creator brought human beings into existence).

    Within hours of the publication of the phase II results, evolutionary biologists condemned the ENCODE results, citing technical issues with the way the study was designed and the way the results were interpreted. (For a response to these complaints go here, here, and here.)

    Is Biochemical Activity the Same Thing As Function?

    One of the technical complaints relates to how the ENCODE consortium determined biochemical function. Critics argue that ENCODE scientists conflated biochemical activity with function. For example, the ENCODE Project determined that about 60% of the human genome is transcribed to produceRNA. ENCODE skeptics argue that most of these transcripts lack function. Evolutionary biologist Dan Graur has asserted that “some studies even indicate that 90% of transcripts generated by RNA polymerase II may represent transcriptional noise.”In other words, the biochemical activity measured by the ENCODE project can be likened to busy but nonproductive graduate students who hustle and bustle about the lab but fail to get anything done.

    When I first learned how many evolutionary biologists interpreted the ENCODE results I was skeptical. As a biochemist, I am well aware that living systems could not tolerate such high levels of transcriptional noise.

    Transcription is an energy- and resource-intensive process. Therefore, it would be untenable to believe that most transcripts are mere biochemical noise. Such a view ignores cellular energetics. Transcribing 60% of the genome when most of the transcripts serve no useful function would routinely waste a significant amount of the organism’s energy and material stores. If such an inefficient practice existed, surely natural selection would eliminate it and streamline transcription to produce transcripts that contribute to the organism’s fitness.

    Most RNA Transcripts Are Functional

    Recent work supports my intuition as a biochemist. Genomics scientists are quickly realizing that most of the RNA molecule transcribed from the human genome serve critical functional roles.

    For example, a recently published report from the Second Aegean International Conference on the Long and the Short of Non-Coding RNAs (held in Greece between June 9–14, 2017) highlights this growing consensus. Based on the papers presented at the conference, the authors of the report conclude, “Non-coding RNAs . . . are not simply transcriptional by-products, or splicing artefacts, but comprise a diverse population of actively synthesized and regulated RNA transcripts. These transcripts can—and do—function within the contexts of cellular homeostasis and human pathogenesis.”2

    Shortly before this conference was held, a consortium of scientists from the RIKEN Center for Life Science Technologies in Japan published an atlas of long non-coding RNAs transcribed from the human genome. (Long non-coding RNAs are a subset of RNA transcripts produced from the human genome.) They identified nearly 28,000 distinct long non-coding RNA transcripts and determined that nearly 19,200 of these play some functional role, with the possibility that this number may increase as they and other scientific teams continue to study long non-coding RNAs.3 One of the researchers involved in this project acknowledges that “There is strong debate in the scientific community on whether the thousands of long non-coding RNAs generated from our genomes are functional or simply byproducts of a noisy transcriptional machinery . . . we find compelling evidence that the majority of these long non-coding RNAs appear to be functional.”4

    Copied by Design

    Based on these results, it becomes increasingly difficult for ENCODE skeptics to dismiss the findings of the ENCODE project. Independent studies affirm the findings of the ENCODE consortium—namely, that a vast proportion of the human genome is functional.

    We have come a long way from the early days of the human genome project. When completed in 2003, many scientists at that time estimated that around 95% of the human genome consisted of junk DNA. And in doing so, they seemingly provided compelling evidence that humans must be the product of an evolutionary history.

    But, here we are, nearly 15 years later. And the more we learn about the structure and function of genomes, the more elegant and sophisticated they appear to be. And the more reasons we have to think that the human genome is the handiwork of our Creator.

    Resources

    Endnotes

    1. Dan Graur et al., “On the Immortality of Television Sets: ‘Function’ in the Human Genome According to the Evolution-Free Gospel of ENCODE,” Genome Biology and Evolution5 (March 1, 2013): 578–90, doi:10.1093/gbe/evt028.
    2. Jun-An Chen and Simon Conn, “Canonical mRNA is the Exception, Rather than the Rule,” Genome Biology 18 (July 7, 2017): 133, doi:10.1186/s13059-017-1268-1.
    3. Chung-Chau Hon et al., “An Atlas of Human Long Non-Coding RNAs with Accurate 5′ Ends,” Nature 543 (March 9, 2017): 199–204, doi:10.1038/nature21374.
    4. RIKEN, “Improved Gene Expression Atlas Shows that Many Human Long Non-Coding RNAs May Actually Be Functional,” ScienceDaily, March 1, 2017, www.sciencedaily.com/releases/2017/03/170301132018.htm.
  • Dollo’s Law at Home with a Creation Model, Reprised*

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Sep 12, 2017

    *This article is an expanded and updated version of an article published in 2011 on reasons.org.

    Published posthumously, Thomas Wolfe’s 1940 novel, You Can’t Go Home Againconsidered by many to be his most significant work—explores how brutally unfair the passage of time can be. In the finale, George Webber (the story’s protagonist) concedes, “You can’t go back home” to family, childhood, familiar places, dreams, and old ways of life.

    In other words, there’s an irreversible quality to life. Call it the arrow of time.

    Like Wolfe, most evolutionary biologists believe there is an irreversibility to life’s history and the evolutionary process. In fact, this idea is codified in Dollo’s Law, which states that an organism cannot return, even partially, to a previous evolutionary stage occupied by one of its ancestors. Yet, several recent studies have uncovered what appears to be violations of Dollo’s Law. These violations call into question the sufficiency of the evolutionary paradigm to fully account for life’s history. On the other hand, the return to ‘ancestral states’ finds an explanation in an intelligent design/creation model approach to life’s history.

    Dollo’s Law

    French paleontologist Louis Dollo formulated the law that bears his name in 1893 before the advent of modern-day genetics, basing it on patterns he unearthed from the fossil record. Today, his idea finds undergirding in contemporary understanding of genetics and developmental biology.

    Evolutionary biologist Richard Dawkins explains the modern-day conception of Dollo’s Law this way:

    “Dollo’s Law is really just a statement about the statistical improbability of following exactly the same evolutionary trajectory twice . . . in either direction. A single mutational step can easily be reversed. But for larger numbers of mutational steps . . . mathematical space of all possible trajectories is so vast that the chance of two trajectories ever arriving at the same point becomes vanishingly small.”1

    If a biological trait is lost during the evolutionary process, then the genes and developmental pathways responsible for that feature will eventually degrade, because they are no longer under selective pressure. In 1994, using mathematical modeling, researchers from Indiana University determined that once a biological trait is lost, the corresponding genes can be “reactivated” with reasonable probability over time scales of five hundred thousand to six million years. But once a time span of ten million years has transpired, unexpressed genes and dormant developmental pathways become permanently lost.2

    In 2000, a scientific team from the University of Oregon offered a complementary perspective on the timescale for evolutionary reversals when they calculated how long it takes for a duplicated gene to lose function.3 (Duplicated genes serve as a proxy for dormant genes rendered useless because the trait they encode has been lost.) According to the evolutionary paradigm, once a gene becomes duplicated, it is no longer under the influence of natural selection. That is, it undergoes neutral evolution, and eventually becomes silenced as mutations accrue. As it turns out, the half-life for this process is approximately four million years. To put it another way, sixteen to twenty-four million years after the duplication event, the duplicated gene will have completely lost its function. Presumably, this result applies to dormant, unexpressed genes rendered unnecessary because the trait they specify is lost.

    Both scenarios assume neutral evolution and the accumulation of mutations in a clockwise manner. But what if the loss of gene function is advantageous? Collaborative work by researchers from Harvard University and NYU in 2007 demonstrated that loss of gene function can take place on the order of about one million years if natural selection influences gene loss.4 This research team studied the loss of eyes in the cave fish, the Mexican tetra. Because they live in a dark cave environment, eyes serve no benefit for these creatures. The team discovered that eye reduction offers an advantage for these fish, because of the high metabolic cost associated with maintaining eyes. The reduced metabolic cost associated with eye loss accelerates the loss of gene function through the operation of natural selection.

    Based on these three studies, it is reasonable to conclude that once a trait has been lost, the time limit for evolutionary reversals is on the order of about 20 million years.

    The very nature of evolutionary mechanisms and the constraints of genetic mutations make it extremely improbable that evolutionary processes would allow an organism to revert to an ancestral state or to recover a lost biological trait. You can’t go home again.

    Violations of Dollo’s Law

    Despite this expectation, over the course of the last several years, researchers have uncovered several instances in which Dollo’s Law has been violated. A brief description of a handful of these occurrences follows:

    The re-evolution of mandibular teeth in the frog genus Gastrotheca. This group is the only one that includes living frogs with true teeth on the lower jaw. When examined from an evolutionary framework, mandibular teeth were present in ancient frogs and then lost in the ancestor of all living frogs. It also looks as if teeth have been absent in frogs for 225 million years before they reappeared in Gastrotheca.5

    The re-evolution of oviparity in sand boas. When viewed from an evolutionary perspective, it appears as if live-birth (viviparity) evolved from egg-laying (oviparity) behaviors in reptiles several times. For example, estimates indicate that this evolutionary transition has occurred in snakes at least thirty times. As a case in point, there are 41 species of boas in the Old and New Worlds that give live births. Yet, two recently described sand boas, the Arabian sand boas (Eryx jayakari) and the Saharan sand boa (Eryx muelleri) lay eggs. Phylogenetic analysis carried out by researchers from Yale University indicates that the egg-laying in these two species of sand boas re-evolved 60 million years after the transition to viviparity took place.6

    The re-evolution of rotating sex combs in Drosophila. Sex combs are modified bristles unique to male fruit flies, used for courtship and mating. Compared to transverse sex combs, rotating sex combs result when several rows of bristles undergo a rotation of ninety degrees. In the ananassae fruit fly group most of the twenty or so species have simple transverse sex combs, with Drosophila bipectinata and Drosophila parabipectinata the two exceptions. These fruit fly species possess rotating sex combs. Phylogenetic analysis conducted by investigators from the University of California, Davis indicates that the rotating sex combs in these two species re-evolved, twelve million years after being lost.7

    The re-evolution of sexuality in mites belonging to the taxa, Crotoniidae. Mites exhibit a wide range of reproductive modes, including parthenogenesis. In fact, this means of reproduction is prominent in the group Oribatida, clustering into two subgroups that display parthenogenesis, almost exclusively. However, residing within one of these clusters is the taxa Crotoniidae, which displays sexual reproduction. Based on an evolutionary analysis, a team of German researchers conclude this group re-evolved the capacity for sexual reproduction.8

    The re-evolution of shell coiling in limpets. From an evolutionary perspective, the coiled shell has been lost in gastropod lineages numerous times, producing a limpet shape, consisting of a cap-shaped shell and a large foot. Evolutionary biologists have long thought that the loss of the coiled shell represents an evolutionary dead end. However, researchers from Venezuela have shown that coiled shell morphology re-evolved, at least one time, in calyptraeids, 20 to 100 million years after its loss.9

    This short list gives just a few recently discovered examples of Dollo’s Law violations. Surveying the scientific literature, evolutionary biologist J. J. Wiens identified an additional eight examples in which Dollo’s Law was violated and determined that in all cases the lost trait reappeared after at least 20 million years had passed and in some instances after 120 million years had transpired.10

    Violation of Dollo’s Law and the Theory of Evolution

    Given that the evolutionary paradigm predicts that re-evolution of traits should not occur after the trait has been lost for twenty million years, the numerous discoveries of Dollo’s Law violations provide a basis for skepticism about the capacity of the evolutionary paradigm to fully account for life’s history. The problem is likely worse than it initially appears. J. J. Wiens points out that Dollo’s Law violations may be more widespread than imagined, but difficult to detect for methodological reasons.11

    In response to this serious problem, evolutionary biologists have offered two ways to account for Dollo’s Law violations.12 The first is to question the validity of the evolutionary analysis that exposes the violations. To put it another way, these scientists claim that the recently identified Dollo’s Law violations are artifacts of the evolutionary analysis, and not real. However, this work-around is unconvincing. The evolutionary biologists who discovered the different examples of Dollo’s Law violations were aware of this complication and took painstaking efforts to ensure the validity of the evolutionary analysis they performed.

    Other evolutionary biologists argue that some genes and developmental modules serve more than one function. So, even though the trait specified by a gene or a developmental module is lost, the gene or the module remains intact because they serve other roles. This retention makes it possible for traits to re-evolve, even after a hundred million years. Though reasonable, this explanation still must be viewed as speculative. Evolutionary biologists have yet to apply the same mathematical rigor to this explanation as they have when estimating the timescale for loss of function in dormant genes. These calculations are critical given the expansive timescales involved in some of the Dollo’s Law violations.

    Considering the nature of evolutionary processes, this response neglects the fact that genes and developmental pathways will continue to evolve under the auspices of natural selection, once a trait is lost. Free from the constraints of the lost function, the genes and developmental modules experience new evolutionary possibilities, previously unavailable to them. The more functional roles a gene or developmental module assumes, the less likely it is that these systems can evolve. Shedding one of their roles increases the likelihood that these genes and developmental pathways will become modified as the evolutionary process explores new space now available to it. In this scenario, it is reasonable to think that natural selection could modify the genes and developmental modules to such an extent that the lost trait would be just as unlikely to re-evolve as it would if gene loss was a consequence of neutral evolution. In fact, the study of eye loss in the Mexican tetra suggests that the modification of these genes and developmental modules could occur at a faster rate if governed by natural selection rather than neutral evolution.

    Violation of Dollo’s Law and the Case for Creation

    While Dollo’s Law violations are problematic for the evolutionary paradigm, the re-evolution—or perhaps, more appropriately, the reappearance—of the same biological traits after their disappearance makes sense from a creation model/intelligent design perspective. The reappearance of biological systems could be understood as the work of the Creator. It is not unusual for engineers to reuse the same design or to revisit a previously used design feature in a new prototype. While there is an irreversibility to the evolutionary process, designers are not constrained in that way and can freely return to old designs.

    Dollo’s Law violations are at home in a creation model, highlighting the value of this approach to understanding life’s history.

    Endnotes

    1. Richard Dawkins, The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe without Design (New York: W.W. Norton, 2015), 94.
    2. Charles R. Marshall, Elizabeth C. Raff, and Rudolf A. Raff, “Dollo’s Law and the Death and Resurrection of Genes,” Proceedings of the National Academy of Sciences USA 91 (December 6, 1994): 12283–87.
    3. Michael Lynch and John S. Conery, “The Evolutionary Fate and Consequences of Duplicate Genes, Science 290 (November 10, 2000): 1151–54, doi:10.1126/science.290.5494.1151.
    4. Meredith Protas et al., “Regressive Evolution in the Mexican Cave Tetra, Astyanax mexicanus, Current Biology 17 (March 6, 2007): 452–54, doi:10.1016/j.cub.2007.01.051.
    5. John J. Wiens, “Re-evolution of Lost Mandibular Teeth in Frogs after More than 200 Million Years, and Re-evaluating Dollo’s Law,” Evolution 65 (May 2011): 1283–96, doi:10.1111/j.1558-5646.2011.01221.x.
    6. Vincent J. Lynch and Günter P. Wagner, “Did Egg-Laying Boas Break Dollo’s Law? Phylogenetic Evidence for Reversal to Oviparity in Sand Boas (Eryx: Boidae),” Evolution 64 (January 2010): 207–16, doi:10.1111/j.1558-5646.2009.00790.x.
    7. Thaddeus D. Seher et al., “Genetic Basis of a Violation of Dollo’s Law: Re-Evolution of Rotating Sex Combs in Drosophila bipectinata,” Genetics 192 (December 1, 2012): 1465–75, doi:10.1534/genetics.112.145524.
    8. Katja Domes et al., “Reevolution of Sexuality Breaks Dollo’s Law,” Proceedings of the National Academy of Sciences USA 104 (April 24, 2007): 7139–44, doi:10.1073/pnas.0700034104.
    9. Rachel Collin and Roberto Cipriani, “Dollo’s Law and the Re-Evolution of Shell Coiling,” Proceedings of the Royal Society B 270 (December 22, 2003): 2551–55, doi:10.1098/rspb.2003.2517.
    10. Wiens, “Re-evolution of Lost Mandibular Teeth in Frogs.”
    11. Wiens, “Re-evolution of Lost Mandibular Teeth in Frogs.
    12. Rachel Collin and Maria Pia Miglietta, “Reversing Opinions on Dollo’s Law,” Trends in Ecology and Evolution 23 (November 2008): 602–9, doi:10.1016/j.tree.2008.06.013.
  • Is 75% of the Human Genome Junk DNA?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Aug 29, 2017

    By the rude bridge that arched the flood,
    Their flag to April’s breeze unfurled,
    Here once the embattled farmers stood,
    And fired the shot heard round the world.

    –Ralph Waldo Emerson, Concord Hymn

    Emerson referred to the Battles of Lexington and Concord, the first skirmishes of the Revolutionary War, as the “shot heard round the world.”

    While not as loud as the gunfire that triggered the Revolutionary War, a recent article published in Genome Biology and Evolution by evolutionary biologist Dan Graur has garnered a lot of attention,1 serving as the latest salvo in the junk DNA wars—a conflict between genomics scientists and evolutionary biologists about the amount of functional DNA sequences in the human genome.

    Clearly, this conflict has important scientific ramifications, as researchers strive to understand the human genome and seek to identify the genetic basis for diseases. The functional content of the human genome also has significant implications for creation-evolution skirmishes. If most of the human genome turns out to be junk after all, then the case for a Creator potentially suffers collateral damage.

    According to Graur, no more than 25% of the human genome is functional—a much lower percentage than reported by the ENCODE Consortium. Released in September 2012, phase II results of the ENCODE project indicated that 80% of the human genome is functional, with the expectation that the percentage of functional DNA in the genome would rise toward 100% when phase III of the project reached completion.

    If true, Graur’s claim would represent a serious blow to the validity of the ENCODE project conclusions and devastate the RTB human origins creation model. Intelligent design proponents and creationists (like me) have heralded the results of the ENCODE project as critical in our response to the junk DNA challenge.

    Junk DNA and the Creation vs. Evolution Battle

    Evolutionary biologists have long considered the presence of junk DNA in genomes as one of the most potent pieces of evidence for biological evolution. Skeptics ask, “Why would a Creator purposely introduce identical nonfunctional DNA sequences at the same locations in the genomes of different, though seemingly related, organisms?”

    When the draft sequence was first published in 2000, researchers thought only around 2–5% of the human genome consisted of functional sequences, with the rest being junk. Numerous skeptics and evolutionary biologists claim that such a vast amount of junk DNA in the human genome is compelling evidence for evolution and the most potent challenge against intelligent design/creationism.

    But these arguments evaporate in the wake of the ENCODE project. If valid, the ENCODE results would radically alter our view of the human genome. No longer could the human genome be regarded as a wasteland of junk; rather, the human genome would have to be recognized as an elegantly designed system that displays sophistication far beyond what most evolutionary biologists ever imagined.

    ENCODE Skeptics

    The findings of the ENCODE project have been criticized by some evolutionary biologists who have cited several technical problems with the study design and the interpretation of the results. (See articles listed under “Resources to Go Deeper” for a detailed description of these complaints and my responses.) But ultimately, their criticisms appear to be motivated by an overarching concern: if the ENCODE results stand, then it means key features of the evolutionary paradigm can’t be correct.

    Calculating the Percentage of Functional DNA in the Human Genome

    Graur (perhaps the foremost critic of the ENCODE project) has tried to discredit the ENCODE findings by demonstrating that they are incompatible with evolutionary theory. Toward this end, he has developed a mathematical model to calculate the percentage of functional DNA in the human genome based on mutational load—the amount of deleterious mutations harbored by the human genome.

    Graur argues that junk DNA functions as a sponge absorbing deleterious mutations, thereby protecting functional regions of the genome. Considering this buffering effect, Graur wanted to know how much junk DNA must exist in the human genome to buffer against the loss of fitness—which would result from deleterious mutations in functional DNA—so that a constant population size can be maintained.

    Historically, the replacement level fertility rates for human beings have been two to three children per couple. Based on Graur’s modeling, this fertility rate requires 85–90% of the human genome to be composed of junk DNA in order to absorb deleterious mutations—ensuring a constant population size, with the upper limit of functional DNA capped at 25%.

    Graur also calculated a fertility rate of 15 children per couple, at minimum, to maintain a constant population size, assuming 80% of the human genome is functional. According to Graur’s calculations, if 100% of the human genome displayed function, the minimum replacement level fertility rate would have to be 24 children per couple.

    He argues that both conclusions are unreasonable. On this basis, therefore, he concludes that the ENCODE results cannot be correct.

    Response to Graur

    So, has Graur’s work invalidated the ENCODE project results? Hardly. Here are four reasons why I’m skeptical. 

    1. Graur’s estimate of the functional content of the human genome is based on mathematical modeling, not experimental results.

    An adage I heard repeatedly in graduate school applies: “Theories guide, experiments decide.” Though the ENCODE project results theoretically don’t make sense in light of the evolutionary paradigm, that is not a reason to consider them invalid. A growing number of studies provide independent experimental validation of the ENCODE conclusions. (Go here and here for two recent examples.)

    To question experimental results because they don’t align with a theory’s predictions is a Bizarro World” approach to science. Experimental results and observations determine a theory’s validity, not the other way around. Yet when it comes to the ENCODE project, its conclusions seem to be weighed based on their conformity to evolutionary theory. Simply put, ENCODE skeptics are doing science backwards.

    While Graur and other evolutionary biologists argue that the ENCODE results don’t make sense from an evolutionary standpoint, I would argue as a biochemist that the high percentage of functional regions in the human genome makes perfect sense. The ENCODE project determined that a significant fraction of the human genome is transcribed. They also measured high levels of protein binding.

    ENCODE skeptics argue that this biochemical activity is merely biochemical noise. But this assertion does not make sense because (1) biochemical noise costs energy and (2) random interactions between proteins and the genome would be harmful to the organism.

    Transcription is an energy- and resource-intensive process. To believe that most transcripts are merely biochemical noise would be untenable. Such a view ignores cellular energetics. Transcribing a large percentage of the genome when most of the transcripts serve no useful function would routinely waste a significant amount of the organism’s energy and material stores. If such an inefficient practice existed, surely natural selection would eliminate it and streamline transcription to produce transcripts that contribute to the organism’s fitness.

    Apart from energetics considerations, this argument ignores the fact that random protein binding would make a dire mess of genome operations. Without minimizing these disruptive interactions, biochemical processes in the cell would grind to a halt. It is reasonable to think that the same considerations would apply to transcription factor binding with DNA.

    2. Graur’s model employs some questionable assumptions.

    Graur uses an unrealistically high rate for deleterious mutations in his calculations.

    Graur determined the deleterious mutation rate using protein-coding genes. These DNA sequences are highly sensitive to mutations. In contrast, other regions of the genome that display function—such as those that (1) dictate the three-dimensional structure of chromosomes, (2) serve as transcription factors, and (3) aid as histone binding sites—are much more tolerant to mutations. Ignoring these sequences in the modeling work artificially increases the amount of required junk DNA to maintain a constant population size.

    3. The way Graur determines if DNA sequence elements are functional is questionable. 

    Graur uses the selected-effect definition of function. According to this definition, a DNA sequence is only functional if it is undergoing negative selection. In other words, sequences in genomes can be deemed functional only if they evolved under evolutionary processes to perform a particular function. Once evolved, these sequences, if they are functional, will resist evolutionary change (due to natural selection) because any alteration would compromise the function of the sequence and endanger the organism. If deleterious, the sequence variations would be eliminated from the population due to the reduced survivability and reproductive success of organisms possessing those variants. Hence, functional sequences are those under the effects of selection.

    In contrast, the ENCODE project employed a causal definition of function. Accordingly, function is ascribed to sequences that play some observationally or experimentally determined role in genome structure and/or function.

    The ENCODE project focused on experimentally determining which sequences in the human genome displayed biochemical activity using assays that measured

    • transcription,
    • binding of transcription factors to DNA,
    • histone binding to DNA,
    • DNA binding by modified histones,
    • DNA methylation, and
    • three-dimensional interactions between enhancer sequences and genes.

    In other words, if a sequence is involved in any of these processes—all of which play well-established roles in gene regulation—then the sequences must have functional utility. That is, if sequenceQperforms functionG, then sequenceQis functional.

    So why does Graur insist on a selected-effect definition of function? For no other reason than a causal definition ignores the evolutionary framework when determining function. He insists that function be defined exclusively within the context of the evolutionary paradigm. In other words, his preference for defining function has more to do with philosophical concerns than scientific ones—and with a deep-seated commitment to the evolutionary paradigm.

    As a biochemist, I am troubled by the selected-effect definition of function because it is theory-dependent. In science, cause-and-effect relationships (which include biological and biochemical function) need to be established experimentally and observationally, independent of any particular theory. Once these relationships are determined, they can then be used to evaluate the theories at hand. Do the theories predict (or at least accommodate) the established cause-and-effect relationships, or not?

    Using a theory-dependent approach poses the very real danger that experimentally determined cause-and-effect relationships (or, in this case, biological functions) will be discarded if they don’t fit the theory. And, again, it should be the other way around. A theory should be discarded, or at least reevaluated, if its predictions don’t match these relationships.

    What difference does it make which definition of function Graur uses in his model? A big difference. The selected-effect definition is more restrictive than the causal-role definition. This restrictiveness translates into overlooked function and increases the replacement level fertility rate.

    4. Buffering against deleterious mutations is a function.

    As part of his model, Graur argues that junk DNA is necessary in the human genome to buffer against deleterious mutations. By adopting this view, Graur has inadvertently identified function for junk DNA. In fact, he is not the first to argue along these lines. Biologist Claudiu Bandea has posited that high levels of junk DNA can make genomes resistant to the deleterious effects of transposon insertion events in the genome. If insertion events are random, then the offending DNA is much more likely to insert itself into “junk DNA” regions instead of coding and regulatory sequences, thus protecting information-harboring regions of the genome.

    If the last decade of work in genomics has taught us anything, it is this: we are in our infancy when it comes to understanding the human genome. The more we learn about this amazingly complex biochemical system, the more elegant and sophisticated it becomes. Through this process of discovery, we continue to identify functional regions of the genome—DNA sequences long thought to be junk.

    In short, the criticisms of the ENCODE project reflect a deep-seated commitment to the evolutionary paradigm and, bluntly, are at war with the experimental facts.

    Bottom line: if the ENCODE results stand, it means that key aspects of the evolutionary paradigm can’t be correct.

    Resources to Go Deeper

    Endnotes

    1. Dan Graur, “An Upper Limit on the Functional Fraction of the Human Genome,” Genome Biology and Evolution 9 (July 2017): 1880–85, doi:10.1093/gbe/evx121.
  • DNA Replication Winds Up the Case for Intelligent Design

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Aug 08, 2017

    One of my classmates and friends in high school was a kid we nicknamed “Radar.” He was a cool kid who had special needs. He was mentally challenged. He was also funny and as good-hearted as they come, never causing any real problems—other than playing hooky from school, for days on end. Radar hated going to school.

    When he eventually showed up, he would be sent to the principal’s office to explain his unexcused absences to Mr. Reynolds. And each time, Radar would offer the same excuse: his grandmother died. But Mr. Reynolds didn’t buy it—for obvious reasons. It didn’t require much investigation on the principal’s part to know that Radar was lying.

    Skeptics have something in common with my friend Radar. They use the same tired excuse when presented with compelling evidence for design from biochemistry. Inevitably, they dismiss the case for a Creator by pointing out all the “flawed” designs in biochemical systems. But this excuse never sticks. Upon further investigation, claimed instances of bad designs turn out to be elegant, in virtually every instance, as recent work by scientists from UC Davis illustrates.

    These researchers accomplished an important scientific milestone by using single molecule techniques to observe the replication of a single molecule of DNA.1 Their unexpected insights have bearing on how we understand this key biochemical operation. The work also has important implications for the case for biochemical design.

    For those familiar with DNA’s structure and replication process, you can skip the next two sections. But for those of you who are not, a little background information is necessary to appreciate the research team’s findings and their relevance to the creation-evolution debate.

    DNA’s Structure

    DNA consists of two molecular chains (called “polynucleotides”) aligned in an antiparallel fashion. (The two strands are arranged parallel to one another with the starting point of one strand of the polynucleotide duplex located next to the ending point of the other strand and vice versa.) The paired molecular chains twist around each other forming the well-known DNA double helix. The cell’s machinery generates the polynucleotide chains using four different nucleotides: adenosineguanosinecytidine, and thymidine, abbreviated as A, G, C, and T, respectively.

    A special relationship exists between the nucleotide sequences of the two DNA strands. Biochemists say the DNA sequences of the two strands are complementary. When the DNA strands align, the adenine (A) side chains of one strand always pair with thymine (T) side chains from the other strand. Likewise, the guanine (G) side chains from one DNA strand always pair with cytosine (C) side chains from the other strand. Biochemists refer to these relationships as “base-pairing rules.” Consequently, if biochemists know the sequence of one DNA strand, they can readily determine the sequence of the other strand. Base-pairing plays a critical role in DNA replication.

    Image 1: DNA’s Structure

    DNA Replication

    Biochemists refer to DNA replication as a “template-directed, semiconservative process.” By “template-directed,” biochemists mean that the nucleotide sequences of the “parent” DNA molecule function as a template, directing the assembly of the DNA strands of the two “daughter” molecules using the base-pairing rules. By “semiconservative,” biochemists mean that after replication, each daughter DNA molecule contains one newly formed DNA strand and one strand from the parent molecule.

    Image 2: Semiconservative DNA Replication

    Conceptually, template-directed, semiconservative DNA replication entails the separation of the parent DNA double helix into two single strands. By using the base-pairing rules, each strand serves as a template for the cell’s machinery to use when it forms a new DNA strand with a nucleotide sequence complementary to the parent strand. Because each strand of the parent DNA molecule directs the production of a new DNA strand, two daughter molecules result. Each one possesses an original strand from the parent molecule and a newly formed DNA strand produced by a template-directed synthetic process.

    DNA replication begins at specific sites along the DNA double helix, called “replication origins.” Typically, prokaryotic cells have only a single origin of replication. More complex eukaryotic cells have multiple origins of replication.

    The DNA double helix unwinds locally at the origin of replication to produce what biochemists call a “replication bubble.” During the course of replication, the bubble expands in both directions from the origin. Once the individual strands of the DNA double helix unwind and are exposed within the replication bubble, they are available to direct the production of the daughter strand. The site where the DNA double helix continuously unwinds is called the “replication fork.” Because DNA replication proceeds in both directions away from the origin, there are two replication forks within each bubble.

    Image 3: DNA Replication Bubble

    DNA replication can only proceed in a single direction, from the top of the DNA strand to the bottom. Because the strands that form the DNA double helix align in an antiparallel fashion with the top of one strand juxtaposed with the bottom of the other strand, only one strand at each replication fork has the proper orientation (bottom-to-top) to direct the assembly of a new strand, in the top-to-bottom direction. For this strand—referred to as the “leading strand”—DNA replication proceeds rapidly and continuously in the direction of the advancing replication fork.

    DNA replication cannot proceed along the strand with the top-to-bottom orientation until the replication bubble has expanded enough to expose a sizable stretch of DNA. When this happens, DNA replication moves away from the advancing replication fork. DNA replication can only proceed a short distance for the top-to-bottom-oriented strand before the replication process has to stop and wait for more of the parent DNA strand to be exposed. When a sufficient length of the parent DNA template is exposed a second time, DNA replication can proceed again, but only briefly before it has to stop again and wait for more DNA to be exposed. The process of discontinuous DNA replication takes place repeatedly until the entire strand is replicated. Each time DNA replication starts and stops, a small fragment of DNA is produced.

    Biochemists refer to these pieces of DNA (that will eventually compose the daughter strand) as “Okazaki fragments”—after the biochemist who discovered them. Biochemists call the strand produced discontinuously the “lagging strand” because DNA replication for this strand lags behind the more rapidly produced leading strand. One additional point: the leading strand at one replication fork is the lagging strand at the other replication fork since the replication forks at the two ends of the replication bubble advance in opposite directions.

    An ensemble of proteins is needed to carry out DNA replication. Once the origin recognition complex (which consists of several different proteins) identifies the replication origin, a protein called “helicase” unwinds the DNA double helix to form the replication fork.

    Image 4: DNA Replication Proteins

    Once the replication fork is established and stabilized, DNA replication can begin. Before the newly formed daughter strands can be produced, a small RNA primer must be produced. The protein that synthesizes new DNA by reading the parent DNA template strand—DNA polymerase—can’t start production from scratch. It must be primed. A massive protein complex, called the “primosome,” which consists of over 15 different proteins, produces the RNA primer needed by DNA polymerase.

    Once primed, DNA polymerase will continuously produce DNA along the leading strand. However, for the lagging strand, DNA polymerase can only generate DNA in spurts to produce Okazaki fragments. Each time DNA polymerase generates an Okazaki fragment, the primosome complex must produce a new RNA primer.

    Once DNA replication is completed, the RNA primers are removed from the continuous DNA of the leading strand and from the Okazaki fragments that make up the lagging strand. A protein called a “3’-5’ exonuclease” removes the RNA primers. A different DNA polymerase fills in the gaps created by the removal of the RNA primers. Finally, a protein called a “ligase” connects all the Okazaki fragments together to form a continuous piece of DNA out of the lagging strand.

    Are Leading and Lagging Strand Polymerases Coordinated?

    Biochemists had long assumed that the activities of the leading and lagging strand DNA polymerase enzymes were coordinated. If not, then DNA replication of one strand would get too far ahead of the other, increasing the likelihood of mutations.

    As it turns out, the research team from UC Davis discovered that the activities of the two polymerases are not coordinated. Instead, the leading and lagging strand DNA polymerase enzymes replicate DNA autonomously. To the researchers’ surprise, they learned that the leading strand DNA polymerase replicated DNA in bursts, suddenly stopping and starting. And when it did replicate DNA, the rate of production varied by a factor of ten. On the other hand, the researchers discovered that the rate of DNA replication on the lagging strand depended on the rate of RNA primer formation.

    The researchers point out that if not for single molecule techniques—in which replication is characterized for individual DNA molecules—the autonomous behavior of leading and lagging strand DNA polymerases would not have been detected. Up to this point, biochemists have studied the replication process using a relatively large number of DNA molecules. These samples yield average replication rates for leading and lagging strand replication, giving the sense that replication of both strands is coordinated.

    According to the researchers, this discovery is a “real paradigm shift, and undermines a great deal of what’s in the textbooks.”Because the DNA polymerase activity is not coordinated but autonomous, they conclude that the DNA replication process is a flawed design, driven by stochastic (random) events. Also, the lack of coordination between the leading and lagging strands means that leading strand replication can get ahead of the lagging strand, yielding long stretches of vulnerable single-stranded DNA.

    Diminished Design or Displaced Design?

    Even though this latest insight appears to undermine the elegance of the DNA replication process, other observations made by the UC Davis research team indicate that the evidence for design isn’t diminished, just displaced.

    These investigators discovered that the activity of helicase—the enzyme that unwinds the double helix at the replication fork—somehow senses the activity of the DNA polymerase on the leading strand. When the DNA polymerase stalls, the activity of the helicase slows down by a factor of five until the DNA polymerase catches up. The researchers believe that another protein (called the “tau protein”) mediates the interaction between the helicase and DNA polymerase molecules. In other words, the interaction between DNA polymerase and the helicase compensates for the stochastic behavior of the leading strand polymerase, pointing to a well-designed process.

    As already noted, the research team also learned that the rate of lagging strand replication depends on primer production. They determined that the rate of primer production exceeds the rate of DNA replication on the leading strand. This fortuitous coincidence ensures that as soon as enough of the bubble opens for lagging strand replication to continue, the primase can immediately lay down the RNA primer, restarting the process. It turns out that the rate of primer production is controlled by the primosome concentration in the cell, with primer production increasing as the number of primosome copies increase. The primosome concentration appears to be fine-tuned. If the concentration of this protein complex is too large, the replication process becomes “gummed up”; if too small, the disparity between leading and lagging strand replication becomes too great, exposing single-stranded DNA. Again, the fine-tuning of primosome concentration highlights the design of this cellular operation.

    It is remarkable how two people can see things so differently. For scientists influenced by the evolutionary paradigm, the tendency is to dismiss evidence for design and, instead of seeing elegance, become conditioned to see flaws. Though DNA replication takes place in a haphazard manner, other features of the replication process appear to be engineered to compensate for the stochastic behavior of the DNA polymerases and, in the process, elevate the evidence for design.

    And, that’s no lie.

    Resources

    Endnotes

    1. James E. Graham et al., “Independent and Stochastic Action of DNA Polymerases in the Replisome,” Cell 169 (June 2017): 1201–13, doi:10.1016/j.cell.2017.05.041.
    2. Bec Crew, “DNA Replication Has Been Filmed for the First Time, and It’s Not What We Expected,” ScienceAlert, June 19, 2017, https://sciencealert.com/dna-replication-has-been-filmed-for-the-first-time-and-it-s-stranger-than-we-thought.
  • How Are Sea Slugs a Failed Prediction of the Evolutionary Paradigm?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jul 18, 2017

    Test them all; hold on to what is good.

    –1 Thessalonians 5:21

    What is your definition of success?

    The answer to this question most likely depends on the person you ask. People view success differently.

    However, subjectivity is not the case when it comes to scientific theories. Success in science is based on a singular criterion: how well does the theory perform at predicting future scientific outcomes?

    Scientific predictions arise as the logical entailments of the theory at hand. In turn, scientists use these predictions to assess the theory’s validity. If experimental results and observations fulfill the theory’s predictions, then scientists consider it sound. If observations and results don’t match the predictions, then scientists are forced to revise and even discard, the theory under evaluation. In short, successful scientific theories have explanatory and predictive power.

    It is for this reason many biologists view the theory of evolution as a valid paradigm for interpreting the origin, history, and design of life. And it is for this reason many biologists regard the theory of evolution as biology’s grand unifying theory.

    However, the evolutionary paradigm has yet to adequately explain key events in life’s history, such as (1) the origin of life, (2) the origin of body plans, (3) the origin of sexual reproduction, (4) the trigger for the sociocultural big bang and human exceptionalism, and (5) the origin of consciousness. The evolutionary paradigm also suffers from failed predictions, as recent work by a team of neuroscientists from Georgia State University attests.1

    Swimming Sea Slugs

    The Georgia State University researchers characterized the neural circuits involved in the swimming behavior of a group of sea slugs called the nudibranchs. These creatures serve as an ideal model system to study neural circuits because relatively large neurons make up their neural systems. The sea slugs’ neural circuits are simple and straightforward to map. On top of that, the sea slugs’ neural circuits regulate simple behaviors. These properties make it easy to characterize and, then, manipulate the neural circuitry of these creatures.

    Biologists have identified about 2,000 species of nudibranchs. Of this number, about 50 swim with a characteristic left-right motion.

    The Georgia State scientists investigated the neural mechanism associated with the left-right swimming behavior of two sea slug species: the giant nudibranch and the hooded nudibranch. From an evolutionary perspective, these two sea slugs share an evolutionary ancestor. In fact, all 50 left-right swimming sea slugs belong to the same branch of the evolutionary tree. (In technical terms, they are monophyletic.)

    Predictions of the Evolutionary Model

    Given that the left-right swimming nudibranchs are monophyletic, the evolutionary model predicts that the morphology, genetics, and behavior originated in the common ancestor of this group. And, given that the swimming behavior of this group is shared among all members (homologous), the expectation is that the neurons and neural circuitry that control this behavior should also be shared among all members.

    The Georgia State scientists say, “. . . Behavioral morphology is often assumed to involve similarity in underlying neuronal mechanisms. . . . Behaviors that are homologous and similar in form would naturally be assumed to be produced by similar neural mechanisms.”2

    Sea Slug Neural Circuitry

    Consistent with the predictions of the evolutionary paradigm, the researchers discovered that the neurons of the giant and hooded nudibranchs were homologous. But, to their surprise, they discovered that the underlying neural mechanisms that controlled the swimming behavior of the two sea slugs were distinct.

    In fact, using a technique called dynamic clamping, the Georgia State scientists could modify the neural circuitry of one sea slug to be the same as the other, all the while inducing the same swimming behavior.

    Masking the Failure of the Evolutionary Paradigm

    The unexpected discovery of distinct neural circuitry in the giant and hooded nudibranchs stands as a failed prediction of the evolutionary paradigm. So how do the Georgia State scientists respond to this discovery?

    First, they point out that their findings support the notion of neural plasticity, with the same neurons supporting multiple neural circuits and varying neural circuits producing the same behavior. But, neural plasticity doesn’t fully account for this finding. If the two sea slugs weren’t part of the same branch on the evolutionary tree, one could argue that the difference in neural circuits represents an example of convergence.

    The researchers suggest that perhaps the divergence of the neural circuitry from the neural mechanism displayed by the shared ancestor of the nudibranch is due to a phenomenon they dub neural drift. This doesn’t seem plausible given the importance of the swimming behavior for sea slug survival. Altering the neural circuitry would alter this behavior, compromising the sea slug’s fitness.

    In fact, there is no independent evidence whatsoever for neural drift. It is a made-up, ad hoc phenomenon that creates a diversion, masking the fact that the results from this study represent a failed prediction of the evolutionary paradigm.

    While this failed prediction is not sufficient to overthrow the evolutionary paradigm, it does justify skepticism about the capacity of evolutionary theory—as currently conceived—to fully explain life’s design and diversity.

    Resources

    Endnotes

    1. Akira Sakurai and Paul S. Katz, “Artificial Synaptic Rewiring Demonstrates that Distinct Neural Circuit Configuration Underlie Homologous Behaviors,” Current Biology 27 (June 19, 2017): 1–14, doi:10.1016/j.cub.2017.05.016.
    2. Ibid.
  • Why Did God Create the Thai Liver Fluke?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jul 11, 2017

    The Thai liver fluke causes quite a bit of human misery. This parasite infects fish living in the rivers of Southeast Asia, which, in turn, infects people who eat the fish.

    Raw and fermented fish make up a big part of the diet of people in Southeast Asia. For example, in Thailand, a popular culinary item is called sour fish. This “delicacy” is prepared by mixing raw fish with garlic, salt, seasoning, and rice. After rolling the mixture into a ball, it is placed in a plastic bag and left to ferment in the hot sun for several days.

    The fermentation process isn’t sufficient to kill the cysts of the Thai liver fluke embedded in the muscles of the infected fish. So, when people eat sour fish (or raw fish), they risk ingesting the parasite.

    The Thai Liver Fluke Life Cycle

    After ingestion, the cysts open in the digestive track of the human host, releasing the fluke. This parasite travels through the bile duct, making its way into the liver, where it takes up residence.

    Once in the liver, the fluke lays eggs that are carried into the host’s digestive track by bile secreted by the liver. In turn, the eggs are released into the environment with human excrement. After being ingested by snails, the eggs hatch, producing larvae that escape from the snail. The free-living larvae infect fish, forming cysts in their skin, fins, and muscle.

    Image: Life cycle of Opisthorchis viverrini. Image source: Wikipedia

    The Thai liver fluke is a master of disguise, evading the immune system of the human host and living for decades in the liver. Unless the infestation is extreme, people infected with the fluke are completely unaware that they harbor this parasite.

    Estimates indicate that 10% of the Thai population is infected with the Thai liver fluke. But in the villages of northern Thailand, where the consumption of raw and fermented fish is higher than in other areas of the country, 45% of the people carry the parasite.

    The Thai Liver Fluke and Cancer

    The Thai liver fluke can live for several decades in the host’s liver without much consequence. But eventually, the burden of the infection catches up with the human host, leading to an aggressive and deadly form of liver cancer that claims about 26,000 Thai lives each year. Once the cancer is detected, most patients die within a year.

    Biomedical researchers think the liver cancer is triggered by the Thai liver fluke, which munches on the host’s liver. Interestingly, the fluke’s saliva contains a protein (called granulin-like protein) that stimulates cell growth and division. These processes help the liver to repair itself after being damaged by the fluke. In effect, the parasite eats part of the liver, supercharges the liver to repair itself, and then eats the new tissue, repeating the cycle for decades. The repeated wounding and repairing of the liver tissue accompanied by rapid cell division eventually leads to the onset of cancer.

    The Thai Liver Fluke and God’s Goodness

    The problems caused by the Thai liver fluke are not limited to the biomedical arena. This parasite causes theological issues, as well. Why would a good God create the Thai liver fluke? Questions like this one fall under the problem of evil.

    Philosophers and theologians recognize two kinds of evil: moral and natural.Moral evil stems from human action (or inaction in some cases). Natural evil proceeds from nature itself—earthquakes, tornadoes, floods, diseases, and the like.

    Natural evil seems to present a greater theological challenge than moral evil does. Skeptics could agree that God can be excused for the free-will actions of human beings who violate his standard of goodness, but they reason that natural disasters and disease don’t result from human activity. Therefore, this type of “evil” must be attributed solely to God.

    Are Some Forms of Natural Evil Actually Moral Evil?

    As I have previously argued, many times natural evil is moral evil in disguise. (See the Resources section below.) In other words, the suffering humans experience stems from human moral failing and poor judgment, not the actual natural phenomenon.

    This most certainly seems to be the case when it comes to the Thai liver fluke. Liver cancer caused by parasite infestations would plummet if people stopped eating raw fish and developed better public sanitation systems and practices.

    So, is it God’s fault that humans become infected with the Thai liver fluke? Or is it because the people of northern Thailand suffer from poverty and a lack of sanitation—ultimately, conditions caused by human moral failing? Is it God’s fault that people of Southeast Asia develop liver cancer from fluke infestations, when they eat raw and fermented fish instead of properly cooking the meat, knowing the adverse health effects?

    Parasites Play a Critical Role in Ecological Systems

    Still, the question remains: Why would God create parasites at all?

    As it turns out, parasites play an indispensable role in ecosystem health.1 Though these creatures make minor contributions to the biomass of ecosystems, they have a significant effect on several ecosystem parameters, including biodiversity. In fact, some ecologists believe that an ecosystem becomes more robust and functions better as parasite diversity increases.

    Considering this insight, a rationale exists as to why God would create the Thai liver fluke to be a member of the ecosystems of the rivers in Southeast Asia. This parasite infects any carnivore (dogs, cats, rats, and pigs) that eats fish from these rivers, not just humans. Undoubtedly infecting these carnivores influences a variety of ecosystem processes, such as species competition, and energy flow through the ecosystem. The harm this parasite causes humans is an unintended consequence of imprudent human activities—not the inherent design of nature.

    Parasites and God’s Providence

    Remarkably, recent work by scientists from the Australian Institute of Tropical Health and Medicine (AITHM) indicates that the suffering caused by the Thai liver fluke may fulfill a higher purposea greater good.

    These researchers believe that the Thai liver fluke may hold the key to effectively treat slow- and non-healing wounds caused by diabetes.2

    High blood glucose levels associated with diabetes compromise the circulatory and immune systems. This compromised condition inhibits wound repair due to restricted blood flow to the site of the injury. It also makes the wound much more prone to infection.

    The AITHM researchers realized that the granulin-like protein produced by the Thai liver fluke could be used to promote healing of chronic wounds because it promotes rapid cell proliferation in the liver. If incorporated into a cream, this protein could be topically applied to the wounds, stimulating wound repair. This treatment would dramatically reduce the cost of treating chronic wounds and significantly improve the treatment outcomes.

    Ironically, the properties of the granulin-like protein that make this biomolecule so insidious are exactly the properties that make it useful to treat diabetics’ wounds. To put it another way, the Thai liver fluke is beneficial to humanity.

    The idea that God designed nature to be useful for humanity is a facet of divine providence. In Christian theology, this idea refers to God’s continual role in: (1) preserving his creation; (2) ensuring that everything happens; and (3) guiding the universe. The concept of divine providence also posits that when God created the world he built into the creation everything humans (and other living organisms) would need. Accordingly, every good thing that people possess has been provided and preserved by God, either directly or indirectly.

    On this basis, as counterintuitive as this may initially seem, it could be argued that as part of his providence, God created the Thai liver fluke for humanity’s use and benefit.

    And we know that in all things God works for the good of those who love him, who have been called according to his purpose.

    –Romans 8:28

    Resources

    Endnotes

    1. Peter J. Hudson, Andrew P. Dobson, and Kevin D. Lafferty, “Is a Healthy Ecosystem One that Is Rich in Parasites?” Trends in Ecology and Evolution 21 (July 2006): 381–85, doi:10.1016/j.tree.2006.04.007.
    2. Paramjit S. Bansal et al., “Development of a Potent Wound Healing Agent Based on the Liver Fluke Granulin Structural Fold,” Journal of Medicinal Chemistry 60 (April 20, 2017): 4258–66, doi:10.1021/acs.jmedchem.7b00047.
  • Can Intelligent Design Be Part of the Construct of Science?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jun 27, 2017

    “If this result stands up to scrutiny, it does indeed change everything we thought we knew about the earliest human occupation of the Americas.”1

    This was the response of Christopher Stringer—a highly-regarded paleoanthropologist at the Natural History Museum in London—to the recent scientific claim that Neanderthals made their way to the Americas 100,000 years before the first modern humans.2

    At this point, many anthropologists have expressed skepticism about this claim, because it requires them to abandon long-held ideas about the way the Americas were populated by modern humans. As Stringer cautions, “Many of us will want to see supporting evidence of this ancient occupation from other sites before we abandon the conventional model.”3

    Yet, the archaeologists making the claim have amassed an impressive cache of evidence that points to Neanderthal occupation of North America.

    As Stringer points out, this work has radical implications for anthropology. But, in my view, the importance of the work extends beyond questions relating to human migrations around the world. It demonstrates that intelligent design/creation models have a legitimate place in science.

    The Case for Neanderthal Occupation of North America

    In the early 1990s, road construction crews working near San Diego, CA, uncovered the remains of a single mastodon. Though the site was excavated from 1992 to 1993, scientists were unable to date the remains. Both radiocarbon and luminescence dating techniques failed.

    Recently, researchers turned failure into success, age-dating the site to be about 130,000 years old, using uranium-series disequilibrium methods. This result shocked them because analysis at the site indicated that the mastodon remainswere deliberately processed by hominids, most likely Neanderthals.

    The researchers discovered that the mastodon bones displayed spiral fracture patterns that looked as if a creature, such as a Neanderthal, struck the bone with a rock—most likely to extract nutrient-rich marrow from the bones. The team also found rocks (called cobble) with the mastodon bones that bear markings consistent with having been used to strike bones and other rocks.

    To confirm this scenario, the archaeologists took elephant and cow bones and broke them open with a hammerstone. In doing so, they produced the same type of spiral fracture patterns in the bones and the same type of markings on the hammerstone as those found at the archaeological site. The researchers also ruled out other possible explanations, such as wild animals creating the fracture patterns on the bones while scavenging the mastodon carcass.

    Despite this compelling evidence, some anthropologists remain skeptical that Neanderthals—or any other hominid—modified the mastodon remains. Why? Not only does this claim fly in the face of the conventional explanation for the populating of the Americas by humans, but the sophistication of the tool kit does not match that produced by Neanderthals 130,000 years ago based on archaeological sites in Europe and Asia.

    So, did Neanderthals make their way to the Americas 100,000 years before modern humans? An interesting debate will most certainly ensue in the years to come.

    But, this work does make one thing clear: intelligent design/creation is a legitimate part of the construct of science.

    A Common Skeptical Response to the Case for a Creator

    Based on my experience, when confronted with scientific evidence for a Creator, skeptics will often summarily dismiss the argument by asserting that intelligent design/creation isn’t science and, therefore, it is not legitimate to draw the conclusion that a Creator exists from scientific advances.

    Undergirding this objection is the conviction that science is the best, and perhaps the only, way to discover truth. By dismissing the evidence for God’s existence—insisting that it is nonscientific—they hope to undermine the argument, thereby sidestepping the case for a Creator.

    There are several ways to respond to this objection. One way is to highlight the fact that intelligent design is part of the construct of science. This response is not motivated by a desire to reform science, but by a desire to move the scientific evidence into a category that forces skeptics to interact with it properly.

    The Case for a Creator’s Role in the Origin of Life

    It is interesting to me that the line of reasoning the archaeologists use to establish the presence of Neanderthals in North America equates to the line of reasoning I use to make the case that the origin of life reflects the product of a Creator’s handiwork, as presented in my three books: The Cell’s Design, Origins of Life, and Creating Life in the Lab. There are three facets to this line of reasoning.

    The Appearance of Design

    The archaeologists argued that: (1) the arrangement of the bones and the cobble and (2) the markings on the cobble and the fracture patterns on the bones appear to result from the intentional activity of a hominid. To put it another way, the archaeological site shows the appearance of design.

    In The Cell’s Design I argue that the analogies between biochemical systems and human designs evince the work of a Mind, serving to revitalize Paley’s Watchmaker argument for God’s existence. In other words, biochemical systems display the appearance of design.

    Failure to Explain the Evidence through Natural Processes

    The archaeologists explored and rejected alternative explanations—such as scavenging by wild animals—for the arrangement, fracture patterns, and markings of the bones and stones.

    In Origins of Life, Hugh Ross (my coauthor) and I explore and demonstrate the deficiency of natural process, mechanistic explanations (such as replicator-first, metabolism-first, and membrane-first scenarios) for the origin of life and, hence, biological systems.

    Reproduction of the Design Patterns

    The archaeologists confirmed—by striking elephant and cow bones with a rock—that the markings on the cobble and the fracture patterns on the bone were made by a hominid. That is, through experimental work in the laboratory, they demonstrated that the design features were, indeed, produced by intelligent agency.

    In Creating Life in the Lab, I describe how work in synthetic biology and prebiotic chemistry empirically demonstrate the necessary role intelligent agency plays in transforming chemicals into living cells. In other words, when scientists go into the lab and create protocells, they are demonstrating that the design of biochemical systems is intelligent design.

    So, is it legitimate for skeptics to reject the scientific case for a Creator, by dismissing it as non-scientific?

    Work in archaeology illustrates that intelligent design is an integral part of science, and it highlights the fact that the same scientific reasoning used to interpret the mastodon remains discovered near San Diego, likewise, undergirds the case for a Creator.

    Resources

    Endnotes

    1. Colin Barras, “First Americans May Have Been Neanderthals 130,000 Years Ago,” New Scientist, April 26, 2017, https://www.newscientist.com/article/2129042-first-americans-may-have-been-neanderthals-130000-years-ago/.
    2. Steven R. Holen et al., “A 130,000-Year-Old Archaeological Site in Southern California, USA,” Nature 544 (April 27, 2017): 479–83, doi:10.1038/nature22065.
    3. Barras, “First Americans.”
  • DNA Wired for Design

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jun 20, 2017

    Though this be madness, yet there is method
    int.

    Hamlet (Act II, scene II)

    Was Hamlet crazy? Or was he feigning madness so he could investigate the murder of his father without raising suspicion?

    In my senior year of high school, Mrs. Hodges assigned our class these questions as the topic for the first essay we wrote for honors English. I made the case that Hamlet was perfectly sane. Indeed, there was method to his madness.

    I wound up with a B- on the assignment. Mrs. Hodges wasn’t impressed with my reasoning, writing on my paper in red ink, “You aren’t qualified to comment on Hamlet’s sanity. You are not a psychologist!” When she returned my paper, I muttered, “Of course, I’m not a psychologist. I’m a high school student. You were the one who asked me to speculate on his sanity. And then when I do . . .”

    I was reminded of this high school memory a few days ago while contemplating the structure and function of DNA. This biomolecule’s design is “crazy.” Yet every detail of DNA’s structure is crucial for the role it plays as an information storage system in the cell. You might say there is biochemical method to DNA’s madness when it comes to its properties. One of DNA’s “insane” features is its capacity to conduct electrical current through the interior of the double helix.

    DNA Wires

    Caltech chemist Jacqueline Barton discovered this phenomenon in the early 1990s. Barton and her collaborators attached different chemical groups to the two ends of the DNA double helix. Both compounds possessed redox centers (metal atoms that can give off and take up electrons). When they blasted one of the redox centers with a pulse of light, it ejected an electron that was taken up by the redox center attached to the opposite end of the DNA molecule, causing the compound to emit a flash of light. The researchers concluded that the ejected electron must have travelled through the interior of the double helix from one redox center to the other.

    Shortly after this discovery, Barton and her team learned that electrical charges  move through DNA only when the double helix is intact. Electrical current won’t flow through single-stranded DNA, nor will it flow if the DNA double helix is distorted, due to damage or misincorporation of DNA subunits during replication.

    These (and other) observations indicate that the conductance of electrical charge through the DNA molecule stems from π-π stacking interactions of the nucleobases in the double helix interior. These interactions produce a molecular orbital that spans the length of the double helix. In effect, the molecular orbital functions like a wire running through DNA’s interior.

    DNA Wires and Nanoelectronics

    Charge conductance through the DNA double helix occurs more rapidly than it does through “standard” molecular wires made from inorganic materials. These “insane” transport speeds have inspired researchers to explore the possibility of using DNA as molecular scale wiring in nanoelectronic devices. In fact, some researchers think that DNA wires might become an integral feature for the next generation of medical diagnostic equipment.

    Does DNA Function as a Wire in the Cell?

    While the charge conductance through the DNA double helix is an interesting and potentially useful property, biochemists have long wondered if DNA functions as a nanowire in the cell.

    In 2009, Barton and her team discovered the answer to this question. DNA’s capacity to transmit electrical charges along the length of the double helix plays a key role in the DNA repair process, and recently Barton’s collaborators have demonstrated that DNA’s wire property plays an important role in the initiation of DNA replication. Both processes are important for DNA to function as an information storage system. Repairing damage to DNA insures the integrity of the information it houses. And DNA replication makes it possible to pass this information on to the next generation. There is a purpose to every aspect of DNA’s properties—a method to the madness.

    Detecting Damage to DNA

    Damage to DNA distorts the double helix. In a process called base excision repair, the cell’s machinery recognizes and removes the damaged portion of the DNA molecule, replacing it with the correct DNA subunits.

    For some time, biochemists puzzled over how the DNA repair enzymes located the damaged regions. In the bacteria E. coli, two repair enzymes, dubbed EndoIII and MutY, occur at low levels. (E. coli is a model organism often used by biochemists to study cellular processes.) Biochemists estimate that less than 500 copies of EndoIII exist in the cell and around 30 copies of MutY. These are low numbers considering the task at hand. These repair enzymes bear the responsibility of surveying the E. coli genome for damage—a genome that consists of over 4.6 million base pairs (genetic letters).

    Barton and her team discovered that the two repair enzymes possess a redox center consisting of an iron-sulfur cluster (4Fe4S) that has no enzymatic activity.1 They speculated and then demonstrated that the 4Fe4S cluster functions just like the compounds they attached to the DNA double helix in their original experiment in the 1990s.

    It turns out Barton and her team were right. These repair proteins bind to DNA. Once bound, they send an electron from the 4Fe4S redox center through the interior of the double helix, which establishes a current through the DNA molecule. Once the repair protein loses an electron, it cannot dissociate from the DNA double helix. Other repair proteins bound to the DNA pick up the electrons from the DNA’s interior at their iron-sulfur redox center. When they do, they dissociate from the DNA and resume their migration along the double helix. Eventually, the migrating repair protein will bind to the DNA again, sending an electron through the DNA’s interior.

    This process is repeated, over and over again. However, if the DNA becomes damaged and the double helix distorted, then the DNA wire breaks, interrupting the flow of electrons. When this happens, the repair proteins remain attached to the DNA close to the location of the damage—thus, initiating the repair process.

    Initiating DNA Replication

    Recently, Barton and her team discovered that charge conductance through DNA also plays a critical role in the early stages of DNA replication.DNA replication—the process of generating two daughter molecules identical to the parent molecule—serves an essential life function.

    DNA replication begins at specific sites along the double helix, called replication origins. Typically, prokaryotic cells, such as E. coli, have only a single origin of replication.

    The replication machinery locally unwinds the DNA double helix at the origin of replication to produce a replication bubble. Once the individual strands of the DNA double helix unwind and are exposed within the replication bubble, they are available to direct the production of the daughter strand.

    Before the newly formed daughter strands can be produced, a small RNA primer must be produced. DNA polymerase—the protein that synthesizes new DNA by reading the parent template strand—can’t start production from scratch. It must be primed. The primosome, a massive protein complex that consists of over 15 different proteins (including the enzyme primase), produces the RNA primer. From there, DNA polymerase takes over and begins synthesizing the daughter DNA strand.

    Barton and her team discovered that the handoff between primase and DNA polymerase relies on DNA’s wire property. Both primase and DNA polymerase possess 4Fe4S redox clusters. When primase’s 4Fe4S redox center loses an electron, this protein binds to DNA to produce the RNA primer. When primase’s 4Fe4S redox center picks up an electron, the protein detaches from the DNA to end the production of the RNA primer.

    When DNA polymerase binds to the DNA to begin the process of daughter strand synthesis, it sends an electron from its 4Fe4S redox center along the double helix formed by the parent DNA-RNA primer. When the electron reaches the 4Fe4S redox center of primase, it brings the production of the RNA primer to a halt.

    DNA Wires and the Case for a Creator

    The work by Barton and her colleagues highlights the elegant and sophisticated design of biochemical systems. DNAs wire property is so remarkable that it serves as inspiration for the design of the next generation of electronic devices—at the nanoscale. The use of biological designs to drive technological advance is one of the most exciting areas in engineering. This area of study—called biomimetics and bioinspiration—presents us with new reasons to believe that life stems from a Creator. It paves the way for a new type of design argument I dub the converse Watchmaker argument: If biological designs are the work of a Creator, then these systems should be so well-designed that they can serve as engineering models and, otherwise, inspire the development of new technologies.

    The converse Watchmaker argument complements William Paley’s classical Watchmaker argument for God’s existence. In my book The Cell’s Design, I describe how recent advances in biochemistry revitalize this classical argument. Over the last few decades, one of the most astounding insights from biochemistry is the recognition that many biochemical systems display the same properties as human designs. This similarity can be used to argue that life must come from the work of a Mind.

    The Watchmaker Prediction

    In conjunction with my presentation of the revitalized Watchmaker argument in The Cell’s Design, I proposed the Watchmaker prediction. I contend that many of the cell’s molecular systems currently go unrecognized as analogs to human designs because the corresponding technology has yet to be developed. That is, the Watchmaker argument may well become stronger in the future, and its conclusion more certain, as human technology advances.

    The possibility that advances in human technology will ultimately mirror the molecular technology that already exists as an integral part of biochemical systems leads to the Watchmaker prediction: As human designers develop new technologies, examples of these technologies, which previously went unrecognized, will become evident in the operation of the cell’s molecular systems. In other words, if the Watchmaker analogy truly serves as evidence for the Creator’s existence, then it is reasonable to expect that life’s biochemical machinery anticipates human technological advances.

    The Watchmaker Prediction, Satisfied

    The discovery that DNA’s wire properties are critical for DNA repair and the initiation of DNA replication fulfills the Watchmaker prediction. Barton and her team recognized the physiological importance of DNA charge conductance a year after The Cell’s Design was published.

    Nanoscientists have been working to develop molecular-scale nanowires for the last couple of decades. The discovery of DNA’s wire properties occurred in this context. In other words, as new technology emerged—in this case, nanoelectronics—we have discovered its existence inside the cell.

    Considering the wire properties of DNA, it is not madness to think that a Creator exists and played a role in life’s genesis.

    Resources

    Endnotes

    1. Amie K. Boal et al., “Redox Signaling between DNA Repair Proteins for Efficient Lesion Detection,” Proceedings of the National Academy of Sciences, USA 106 (September 8, 2009): 15237–42, doi:10.1073/pnas.0908059106Pamel A. Sontz et al., “DNA Charge Transport as a First Step in Coordinating the Detection of Lesions by Repair Proteins,” Proceedings of the National Academy of Sciences, USA 109 (February 7, 2012): 1856–61, doi:10.1073/pnas.1120063109; Michael A. Grodick, Natalie B. Muren, and Jacqueline K. Barton, “DNA Charge Transport within the Cell,” Biochemistry 54 (February 3, 2015): 962–73, doi:10.1021/bi501520w.
    2. Elizabeth O’Brien et al., “The [4Fe4S] Cluster of Human DNA Primase Functions as a Redox Switch Using DNA Charge Transport,” Science 355 (February 24, 2017): doi:10.1126/science.aag1789.
  • DNA: Digitally Designed

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | May 24, 2017

    We live in uncertain and frightening times.

    There seems to be no end to the serious risks confronting humanity. In fact, in 2014, USA Today published an article identifying the 10 greatest threats facing our world:

    • Fiscal crises in key economies
    • Structurally high unemployment/underemployment
    • Water crises
    • Severe income disparity
    • Failure to climate change mitigation and adaptation
    • Greater incidence of extreme weather events (e.g., floods, storms, fires)
    • Global governance failure
    • Food crises
    • Failure of a major financial mechanism/institution
    • Profound political and social instability

    If this list isn’t bad enough, another crisis looms in our near future: a data storage crisis.

    Thanks to the huge volume of scientific data generated by disciplines such as genomics and the explosion of YouTube videos, 44 trillion gigabytes of digital data currently exist in the world. To put this in context, each person in a worldwide population of 10 billion people would have to store over 6,000 CDs to house this data. Estimates are that if we keep generating data at this pace, we will run out of high-quality silicon needed to make data storage devices by 2040.1

    Compounding this problem are the limitations of current data storage technology. Because of degradative processes, hard disks have a lifetime of about 3 years and magnetic tapes about 10 years. These storage systems must be kept in controlled environments—which makes data storage an expensive proposition.

    Digital Data Storage in DNA

    Because of DNA’s role as a biochemical data storage system (in which the data is digitized), researchers are exploring the use of this biomolecule as the next-generation digital data storage technology. As proof of principle, a team of researchers from Harvard University headed up by George Church coded the entire contents of a 54,000-word book (including 11 JPEG images) into DNA fragments.

    The researchers chose to encode the book’s contents into small DNA fragments—devoting roughly two-thirds of the sequence for data and the remainder for information that can be used to locate the content within the entire data block. In this sense, their approach is analogous to using page numbers to order and locate the contents of a book.

    Since then, researchers have encoded computer programs, operating systems, and even movies into DNA.

    Because DNA is so highly optimized to store information, it is an ideal data storage medium. (For details regarding the optimal nature of DNA’s structure, see The Cell’s Design.) Researchers think that DNA has the capacity to store data near the theoretical maximum. About one-half pound of DNA can store all the data that exists in the world today.

    Limitations of DNA Data Storage

    Despite its promises, there are some significant technical hurdles to overcome before DNA can serve as a data storage system. Cost and time are two limitations. It is expensive and time-consuming to produce and read the synthetic DNA used to store information. As technology advances, the cost and time requirements associated with DNA data storage will likely improve. Still, because of these limitations, most technologists think that the best use of DNA will be for archival storage of data.

    Another concern is the long-term stability of DNA. Over time, DNA degrades. Researchers believe that redundancy may be one way around this problem. By encoding the same data in multiple pieces of DNA, data lost because of DNA degradation can be recovered.

    The processes of making and reading synthetic DNA also suffer from error. Current technology has an error rate of 1 in 100. Recently, researchers from Columbia University achieved a breakthrough that allows them to elegantly address loss of information from DNA due to degradation or miscoding that takes place when DNA is made and read. These researchers successfully applied techniques used for “noisy communication” operations to DNA data storage.2

    With these types of advances, the prospects of using DNA to store digital data may soon become a reality. And unlike other data storage technologies, DNA will never become obsolete.

    Biomimetics and Bioinspiration

    The use of biological designs to drive technological advance is one of the most exciting areas in engineering. This area of study—called biomimetics and bioinspiration—presents us with new reasons to believe that life stems from a Creator. As the names imply, biomimetics involves direct copying (or mimicry) of designs from biology, whereas bioinspiration relies on insights from biology to guide the engineering enterprise. DNA’s capacity to inspire engineering efforts to develop new data storage technology highlights this biomolecules elegant, sophisticated design and, at the same time, raises a troubling question for the evolutionary paradigm.

    The Converse Watchmaker Argument

    Biomimetics and bioinspiration pave the way for a new type of design argument I dub the converse Watchmaker argument: If biological designs are the work of a Creator, then these systems should be so well-designed that they can serve as engineering models and otherwise inspire the development of new technologies.

    At some level, I find the converse Watchmaker argument more compelling than the classical Watchmaker analogy. It is remarkable to me that biological designs can inspire engineering efforts.

    It is even more astounding to think that biomimetics and bioinspiration programs could be so successful if biological systems were truly generated by an unguided, historically contingent process, as evolutionary biologists claim.

    Biomimetics and Bioinspiration: The Challenge to the Evolutionary Paradigm

    To appreciate why work in biomimetics and bioinspiration challenge the evolutionary paradigm, we need to discuss the nature of the evolutionary process.

    Evolutionary biologists view biological systems as the outworking of unguided, historically contingent processes that co-opt preexisting designs to cobble together new systems. Once these designs are in place, evolutionary mechanisms can optimize them, but still, these systems remain—in essence—kludges.

    Most evolutionary biologists are quick to emphasize that evolutionary processes and pathways seldom yield perfect designs. Instead, most biological designs are flawed in some way. To be certain, most biologists would concede that natural selection has produced biological designs that are well-adapted, but they would maintain that biological systems are not well-designed. Why? Because evolutionary processes do not produce biological systems from scratch, but from preexisting systems that are co-opted through a process dubbed exaptation and then modified by natural selection to produce new designs. Once formed, these new structures can be fine-tuned and optimized through natural selection to produce well-adapted designs, but not well-designed systems.

    If biological systems are, in effect, kludged together, why would engineers and technologists turn to them for inspiration? If produced by evolutionary processes—even if these processes operated over the course of millions of years—biological systems should make unreliable muses for technology development. Does it make sense for engineers to rely on biological systems—historically contingent and exapted in their origin—to solve problems and inspire new technologies, much less build an entire subdiscipline of engineering around mimicking biological designs?

    Using biological designs to guide engineering efforts seems to be fundamentally incompatible with an evolutionary explanation for life’s origin and history. On the other hand, biomimetics and bioinspiration naturally flow out of an intelligent design/creation model approach to biology. Using biological systems to inspire engineering makes better sense if the designs in nature arise from a Mind.

    Resources

    The Cell’s Design: How Chemistry Reveals the Creator’s Artistry by Fazale Rana (book)
    iDNA: The Next Generation of iPods?” by Fazale Rana (article)
    Harvard Scientists Write the Book on Intelligent Design—in DNA” by Fazale Rana (article)
    Digital and Analog Information Housed in DNA by Fazale Rana (article)
    Engineer’s Muse: The Design of Biochemical Systemsby Fazale Rana (article)

    Endnotes
    1. Andy Extance, “How DNA Could Store All the Worlds Data, Nature 537 (September 2, 2016): 22–24, doi:10.1038/537022a.
    2. Yaniv Erlich and Dina Zielinski, “DNA Fountain Enables a Robust and Efficient Storage Architecture,” Science 355 (March 3, 2017): 950–54, doi:10.1126/science.aaj2038.

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