Where Science and Faith Converge
  • Competitive Endogenous RNA Hypothesis Supports the Case for Creation

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | May 15, 2019

    When Francis Crick, codiscoverer of the DNA double helix, first conceived of molecular biology’s organizing principle in 1958, he dubbed it the central dogma. He soon came to regret the term. In his autobiographical account, What Mad Pursuit, Crick writes:

    I called this idea the central dogma, for two reasons, I suspect. I had already used the obvious word hypothesis in the sequence hypothesis, and in addition I wanted to suggest that this new assumption was more central and more powerful….As it turned out, the use of the word dogma caused almost more trouble than it was worth. Many years later Jacques Monod pointed out to me that I did not appear to understand the correct use of the word dogma, which is a belief that cannot be doubted. I did apprehend this in a vague sort of way but since I thought that all religious beliefs were without foundation, I used the word the way I myself thought about it, not as most of the world does, and simply applied it to a grand hypothesis that, however plausible, had little direct experimental support.1

    Even though Crick rued labeling his idea as “dogma,” the term seems to fit, all the connotations aside, because of its singular importance to molecular biology.

    The Central Dogma of Molecular Biology

    The central dogma of molecular biology describes the directional flow of information in the cell, which moves from DNA to RNA to proteins. Information can flow from DNA to DNA during DNA replication, from DNA to RNA during transcription, and from RNA back to DNA during reverse transcription. However, biochemical information can’t flow from proteins to either RNA or DNA.

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    Figure 1: The Central Dogma of Molecular Biology. Image credit: Shutterstock

    Is There a New Dogma in Molecular Biology?

    In my opinion as a biochemist, if there is an idea that has the potential to rival the significance of the central dogma, it just might be the competitive endogenous RNA (ceRNA) hypothesis. This newer model provides a comprehensive description of the role messenger RNA (mRNA) molecules play in regulating gene expression, thereby influencing the flow of information from DNA to proteins.

    The ceRNA hypothesis also provides an elegant rationale for why the genomes of eukaryotic organisms contain pseudogenes (including unitary pseudogenes) and encode long noncoding RNA molecules. Additionally, it explains why duplicated pseudogenes resemble corresponding intact genes. In doing all this, the ceRNA hypothesis provides support for the RTB’s genomics model—which interprets the structure and activities associated with genomes from a creation or design standpoint. (An overview of the RTB genomics model can be found in the updated and expanded 2nd edition of Who Was Adam?)

    The Competitive Endogenous RNA Hypothesis

    I discuss the ceRNA hypothesis in a previous article. So, I’ll offer just a brief description here. According to the central dogma, the final step in the flow of biochemical information is the production of proteins at the ribosome, directed by the information housed in mRNA. Biochemists have discovered an elaborate mechanism that selectively degrades mRNA transcripts before they can reach this point. This degradation process controls gene expression by dictating the amount of protein produced.

    Molecules called microRNAs bind to the mRNA’s 3′ untranslated region, which flags the transcript for destruction by RNA-induced silencing complex (RISC). A number of distinct microRNA species exist in the cell. Each microRNA species bind to specific sites in the 3′ untranslated region of mRNA transcripts. (These binding locations are called microRNA response elements or MREs.)

    A network of genes shares the same set of MREs and, consequently, will bind to the same set of microRNAs. When one gene is transcribed, it will influence the expression of all the other genes in its network. And when one gene in the network becomes up-regulated (leading to increased transcription of that gene), the expression of all the genes in the network increases. Why? Because the increased level of that particular transcript exerts a “sponge effect” that consumes more of the microRNAs that would otherwise target other transcripts for degradation.

    The Competitive Endogenous RNA Hypothesis and the Role of Junk DNA

    The ceRNA hypothesis elegantly explains the functional utility of three classes of junk DNA: duplicated and unitary pseudogenes, plus long noncoding RNAs. As it turns out, the transcripts produced from these types of so-called junk DNA also harbor MREs. None of these transcripts codes for proteins yet they play an indispensable role in regulating gene expression. In fact, all three are much better suited for the role of molecular sponges precisely because they aren’t translated into proteins.

    Of particular utility are duplicated pseudogenes due to their close structural resemblance to the corresponding coding genes. Duplicated pseudogenes not only exert a sponge effect but also serve as decoys that allow the transcripts of the intact genes to escape degradation and to be translated into proteins.

    Is the Competitive Endogenous RNA Hypothesis Valid?

    This question has generated a minor scientific controversy. Some studies provide experimental support for this idea while others question the physiological relevance of ceRNAs. In light of this debate, a team of researchers headed by investigators from Columbia University sought to validate this hypothesis on a large-scale.2 They discovered that ceRNA interactions can disrupt the expression of thousands of genes. The team concluded that “ceRNA regulation is the norm not the exception…and that ceRNA interactions have genome-wide effects on gene expression.”3

    These researchers think that this insight sheds light on tumor biology because dysregulation of ceRNAs have been implicated in some cancers. Their work also has theological significance because it undermines one of the most significant challenges to design arguments and, in turn, can be marshaled in support of the RTB genomics model.

    The Competitive Endogenous Hypothesis and the Case for a Creator

    Evolutionary biologists have long maintained that identical (or nearly identical) junk DNA sequences (such as pseudogene sequences) found in corresponding locations in genomes of organisms that naturally cluster together (such as humans and the great apes) provide compelling evidence that these organisms must have evolved from a shared ancestor. This interpretation was compelling because junk DNA sequences seemed to be useless vestiges of evolutionary history.

    Creationists and intelligent design proponents had little to offer by way of evidence for the intentional design of genomes. But research in recent years has revealed that virtually every class of junk DNA has function. It seems, then, that shared junk DNA sequences can be understood as shared designs, which is what the RTB genomics model predicts.

    Additionally, the ceRNA hypothesis supports the RTB genomics even further. This hypothesis provides an elegant explanation for the widespread existence of pseudogenes in genomes and their structural similarity to intact genes.

    Could it be that the idea of religious dogma affirming a Creator’s role in life’s design and history has merit?

    Resources

    Endnotes
    1. Francis Crick, What Mad Pursuit (New York: Basic Books, 1988), 109.
    2. Hua-Sheng Chiu et al., “High-Throughput Validation of ceRNA Regulatory Networks,” BMC Genomics 18 (2017): 418, doi:10.1186/s12864-017-3790-7.
    3. Chiu et al., 418.
  • Pseudogene Discovery Pains Evolutionary Paradigm

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | May 08, 2019

    It was one of the most painful experiences I ever had. A few years ago, I had two back-to-back bouts of kidney stones. I remember it as if it were yesterday. Man, did it hurt when I passed the stones! All I wanted was for the emergency room nurse to keep the Demerol coming.

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    Figure 1: Schematic Depiction of Kidney Stones Moving through the Urinary Tract. Image Credit: Shutterstock

    When all that misery was going down, I wished I was one of those rare individuals who doesn’t experience pain. There are some people who, due to genetic mutations, live pain-free lives. This condition is called hypoalgesia. (Of course, there is a serious downside to hypoalgesia. Pain lets us know when our body is hurt or sick. Because hypoalgesics can’t experience pain, they are prone to serious injury, etc.)

    Biomedical researchers possess a keen interest in studying people with hypoalgesia. Identifying the mutations responsible for this genetic condition helps investigators understand the physiological processes that undergird the pain sensation. This insight then becomes indispensable to guiding efforts to develop new drugs and techniques to treat pain.

    By studying the genetic profile of a 66-year-old woman who lived a lifetime with pain-free injuries, a research team from the UK recently discovered a novel genetic mutation that causes hypoalgesia.1 The mutation responsible for this patient’s hypoalgesia occurred in a pseudogene, a region of the genome considered nonfunctional “junk DNA.”

    This discovery adds to the mounting evidence that shows junk DNA is functional. At this point, molecular geneticists have demonstrated that virtually every class of junk DNA has function. This notion undermines the best evidence for common descent and, hence, undermines an evolutionary interpretation of biology. More importantly, the discovery adds support for the competitive endogenous RNA hypothesis, which can be marshaled to support RTB’s genomics model. It is becoming more and more evident to me that genome structure and function reflect the handiwork of a Creator.

    The Role of a Pseudogene in Mediating Hypoalgesia

    To identify the genetic mutation responsible for the 66-year-old’s hypoalgesia, the research team scanned her DNA along with samples taken from her mother and two children. The team discovered two genetic changes: (1) mutations to the FAAH gene that reduced its expression, and (2) deletion of part of the FAAH pseudogene.

    The FAAH gene encodes for a protein called fatty acid amide hydrolase (FAAH). This protein breaks down fatty acid amides. Some of these compounds interact with cannabinoid receptors. These receptors are located in the membranes of cells found in tissues throughout the body. They mediate pain sensation, among other things. When fatty acid amide concentrations become elevated in the circulatory system, it produces an analgesic effect.

    Researchers found elevated fatty acid amide levels in the patient’s blood, consistent with reduced expression of the FAAH gene. It appears that both mutations are required for the complete hypoalgesia observed in the patient. The patient’s mother, daughter, and son all display only partial hypoalgesia. The mother and daughter have the same mutation in the FAAH gene but an intact FAAH pseudogene. The patient’s son is missing the FAAH pseudogene, but has a “normal” FAAH gene.

    Based on the data, it looks like proper expression levels of the FAAH gene require an intact FAAH pseudogene. This is not the first time that biomedical researchers have observed the same effect. There are a number of gene-pseudogene pairs in which both must be intact and transcribed for the gene to be expressed properly. In 2011, researchers from Harvard University proposed that the competitive endogenous RNA hypothesis explains why transcribed pseudogenes are so important for gene expression.2

    The Competitive Endogenous RNA Hypothesis

    Biochemists and molecular biologists have long believed that the primary mechanism for regulating gene expression centered around controlling the frequency and amount of mRNA produced during transcription. For housekeeping genes, mRNA is produced continually, while for genes that specify situational proteins, it is produced as needed. Greater amounts of mRNA are produced for genes expressed at high levels and limited amounts for genes expressed at low levels.

    Researchers long thought that once the mRNA was produced it would be translated into proteins, but recent discoveries indicate this is not the case. Instead, an elaborate mechanism exists that selectively degrades mRNA transcripts before they can be used to direct the protein production at the ribosome. This mechanism dictates the amount of protein produced by permitting or preventing mRNA from being translated. The selective degradation of mRNA also plays a role in gene expression, functioning in a complementary manner to the transcriptional control of gene expression.

    Another class of RNA molecules, called microRNAs, mediates the selective degradation of mRNA. In the early 2000s, biochemists recognized that by binding to mRNA (in the 3′ untranslated region of the transcript), microRNAs play a crucial role in gene regulation. Through binding, microRNAs flag the mRNA for destruction by RNA-induced silencing complex (RISC).

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    Figure 2: Schematic of the RNA-Induced Silencing Mechanism. Image Credit: Wikipedia

    Various distinct microRNA species in the cell bind to specific sites in the 3′ untranslated region of mRNA transcripts. (These binding locations are called microRNA response elements.) The selective binding by the population of microRNAs explains the role that duplicated pseudogenes play in regulating gene expression.

    The sequence similarity between the duplicated pseudogene and the corresponding “intact” gene means that the same microRNAs will bind to both mRNA transcripts. (It is interesting to note that most duplicated pseudogenes are transcribed.) When microRNAs bind to the transcript of the duplicated pseudogene, it allows the transcript of the “intact” gene to escape degradation. In other words, the transcript of the duplicated pseudogene is a decoy. The mRNA transcript can then be translated and, hence, the “intact” gene expressed.

    It is not just “intact” and duplicated pseudogenes that harbor the same microRNA response elements. Other genes share the same set of microRNA response elements in the 3′ untranslated region of the transcripts and, consequently, will bind the same set of microRNAs. These genes form a network that, when transcribed, will influence the expression of all genes in the network. This relationship means that all the mRNA transcripts in the network can function as decoys. This recognition accounts for the functional utility of unitary pseudogenes.

    One important consequence of this hypothesis is that mRNA has dual functions inside the cell. First, it encodes information needed to make proteins. Second, it helps regulate the expression of other transcripts that are part of its network.

    Junk DNA and the Case for Creation

    Evolutionary biologists have long maintained that identical (or nearly identical) pseudogene sequences found in corresponding locations in genomes of organisms that naturally group together (such as humans and the great apes) provide compelling evidence for shared ancestry. This interpretation was persuasive because molecular geneticists regarded pseudogenes as nonfunctional, junk DNA. Presumably, random biochemical events transformed functional DNA sequences (genes) into nonfunctional garbage.

    Creationists and intelligent design proponents had little to offer by way of evidence for the intentional design of genomes. But all this changed with the discovery that virtually every class of junk DNA has function, including all three types of pseudogenes (processed, duplicated, and unitary).

    If junk DNA is functional, then the sequences previously thought to show common descent could be understood as shared designs. The competitive endogenous RNA hypothesis supports this interpretation. This model provides an elegant rationale for the structural similarity between gene-pseudogene pairs and also makes sense of the widespread presence of unitary pseudogenes in genomes.

    Of course, this insight also supports the RTB genomics model. And that sure feels good to me.

    Resources

    Endnotes
    1. Abdella M. Habib et al., “Microdeletion in a FAAH Pseudogene Identified in a Patient with High Anandamide Concentrations and Pain Insensitivity,” British Journal of Anaesthesia, advanced access publication, doi:10.1016/j.bja.2019.02.019.
    2. Ana C. Marques, Jennifer Tan, and Chris P. Ponting, “Wrangling for microRNAs Provokes Much Crosstalk,” Genome Biology 12, no. 11 (November 2011): 132, doi:10.1186/gb-2011-12-11-132; Leonardo Salmena et al., “A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?”, Cell 146, no. 3 (August 5, 2011): 353–58, doi:10.1016/j.cell.2011.07.014.
  • Why Mitochondria Make My List of Best Biological Designs

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | May 01, 2019

    A few days ago, I ran across a BuzzFeed list that catalogs 24 of the most poorly designed things in our time. Some of the items that stood out from the list for me were:

    • serial-wired Christmas lights
    • economy airplane seats
    • clamshell packaging
    • juice cartons
    • motion sensor faucets
    • jewel CD packaging
    • umbrellas

    What were people thinking when they designed these things? It’s difficult to argue with BuzzFeed’s list, though I bet you might add a few things of your own to their list of poor designs.

    If biologists were to make a list of poorly designed things, many would probably include…everything in biology. Most life scientists are influenced by an evolutionary perspective. Thus, they view biological systems as inherently flawed vestiges cobbled together by a set of historically contingent mechanisms.

    Yet as our understanding of biological systems improves, evidence shows that many “poorly designed” systems are actually exquisitely assembled. It also becomes evident that many biological designs reflect an impeccable logic that explains why these systems are the way they are. In other words, advances in biology reveal that it makes better sense to attribute biological systems to the work of a Mind, not to unguided evolution.

    Based on recent insights by biochemist and origin-of-life researcher Nick Lane, I would add mitochondria to my list of well-designed biological systems. Lane argues that complex cells and, ultimately, multicellular organisms would be impossible if it weren’t for mitochondria.1 (These organelles generate most of the ATP molecules used to power the operations of eukaryotic cells.) Toward this end, Lane has demonstrated that mitochondria’s properties are just-right for making complex eukaryotic cells possible. Without mitochondria, life would be limited to prokaryotic cells (bacteria and archaea).

    To put it another way, Nick Lane has shown that prokaryotic cells could never evolve the complexity needed to form cells with complexity akin to the eukaryotic cells required for multicellular organisms. The reason has to do with bioenergetic constraints placed on prokaryotic cells. According to Lane, the advent of mitochondria allowed life to break free from these constraints, paving the way for complex life.

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    Figure 1: A Mitochondrion. Image credit: Shutterstock

    Through Lane’s discovery, mitochondria reveal exquisite design and logical architecture and operations. Yet this is not necessarily what I (or many others) would have expected if mitochondria were the result of evolution. Rather, we’d expect biological systems to appear haphazard and purposeless, just good enough for the organism to survive and nothing more.

    To understand why I (and many evolutionary biologists) would hold this view about mitochondria and eukaryotic cells (assuming that they were the product of evolutionary processes), it is necessary to review the current evolutionary explanation for their origins.

    The Endosymbiont Hypothesis

    Most biologists believe that the endosymbiont hypothesis is the best explanation for the origin of complex eukaryotic cells. This hypothesis states that complex cells originated when single-celled microbes formed symbiotic relationships. “Host” microbes (most likely archaea) engulfed other archaea and/or bacteria, which then existed inside the host as endosymbionts.

    The presumption, then, is that organelles, including mitochondria, were once endosymbionts. Evolutionary biologists believe that, once engulfed, the endosymbionts took up permanent residency within the host cell and even grew and divided inside the host. Over time, the endosymbionts and the host became mutually interdependent. For example, the endosymbionts provided a metabolic benefit for the host cell, such as serving as a source of ATP. In turn, the host cell provided nutrients to the endosymbionts. 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.

    Based on this scenario, there is no real rationale for the existence of mitochondria (and eukaryotic cells). They are the way they are because they just wound up that way.

    But Nick Lane’s insights suggest otherwise.

    Lane’s analysis identifies a deep-seated rationale that accounts for the features of mitochondria (and eukaryotic cells) related to their contribution to cellular bioenergetics. To understand why mitochondria and eukaryotic cells are the way they are, we first need to understand why prokaryotic cells can never evolve into large complex cells, a necessary step for the advent of complex multicellular organisms.

    Bioenergetics Constraints on Prokaryotic Cells

    Lane has discovered that bioenergetics constraints keep bacterial and archaeal cells trapped at their current size and complexity. Key to discovering this constraint is a metric Lane devised called Available Energy per Gene (AEG). It turns out that AEG in eukaryotic cells can be as much as 200,000 times larger than the AEG in prokaryotic cells. This extra energy allows eukaryotic cells to engage in a wide range of metabolic processes that support cellular complexity. Prokaryotic cells simply can’t afford such processes.

    An average eukaryotic cell has between 20,000 to 40,000 genes; a typical bacterial cell has about 5,000 genes. Each gene encodes the information the cell’s machinery needs to make a distinct protein. And proteins are the workhorse molecules of the cell. More genes mean a more diverse suite of proteins, which means greater biochemical complexity.

    So, what is so special about eukaryotic cells? Why don’t prokaryotic cells have the same AEG? Why do eukaryotic cells have an expanded repertoire of genes and prokaryotic cells don’t?

    In short, the answer is: mitochondria.

    On average, the volume of eukaryotic cells is about 15,000 times larger than that of prokaryotic cells. Eukaryotic cells’ larger size allows for their greater complexity. Lane estimates that for a prokaryotic cell to scale up to this volume, its radius would need to increase 25-fold and its surface area 625-fold.

    Because the plasma membrane of bacteria is the site for ATP synthesis, increases in the surface area would allow the hypothetically enlarged bacteria to produce 625 times more ATP. But this increased ATP production doesn’t increase the AEG. Why is that?

    The bacteria would have to produce 625 times more proteins to support the increased ATP production. Because the cell’s machinery must access the bacteria’s DNA to make these proteins, a single copy of the genome is insufficient to support all of the activity centered around the synthesis of that many proteins. In fact, Lane estimates that for bacteria to increase its ATP production 625-fold, it would require 625 copies of its genome. In other words, even though the bacteria increased in size, in effect, the AEG remains unchanged.

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    Figure 2: ATP Production at the Cell Membrane Surface. Image credit: Shutterstock

    Things become more complicated when factoring in cell volume. When the surface area (and concomitant ATP production) increase by a factor of 625, the volume of the cell expands 15,000 times. To satisfy the demands of a larger cell, even more copies of the genome would be required, perhaps as many as 15,000. But energy production tops off at a 625-fold increase. This mismatch means that the AEG drops by 25 percent per gene. For a genome consisting of 5,000 genes, this drop means that a bacterium the size of a eukaryotic cell would have about 125,000 times less AEG than a typical eukaryotic cell and 200,000 times less AEG when compared to eukaryotes with genome sizes approaching 40,000 genes.

    Bioenergetic Freedom for Eukaryotic Cells

    Thanks to mitochondria, eukaryotic cells are free from the bioenergetic constraints that ensnare prokaryotic cells. Mitochondria generate the same amount of ATP as a bacterial cell. However, their genome consists of only 13 proteins, thus the organelle’s ATP demand is low. The net effect is that the mitochondria’s AEG skyrockets. Furthermore, mitochondrial membranes come equipped with an ATP transport protein that can pump the vast excess of ATP from the organelle interior into the cytoplasm for the eukaryotic cell to use.

    To summarize, mitochondria’s small genome plus its prodigious ATP output are the keys to eukaryotic cells’ large AEG.

    Of course, this raises a question: Why do mitochondria have genomes at all? Well, as it turns out, mitochondria need genomes for several reasons (which I’ve detailed in previous articles).

    Other features of mitochondria are also essential for ATP production. For example, cardiolipin in the organelle’s inner membrane plays a role in stabilizing and organizing specific proteins needed for cellular energy production.

    From a creation perspective it seems that if a Creator was going to design a eukaryotic cell from scratch, he would have to create an organelle just like a mitochondrion to provide the energy needed to sustain the cell’s complexity with a high AEG. Far from being an evolutionary “kludge job,” mitochondria appear to be an elegantly designed feature of eukaryotic cells with a just-right set of properties that allow for the cellular complexity needed to sustain complex multicellular life. It is eerie to think that unguided evolutionary events just happened to traverse the just-right evolutionary path to yield such an organelle.

    As a Christian, I see the rationale that undergirds the design of mitochondria as the signature of the Creator’s handiwork in biology. I also view the anthropic coincidence associated with the origin of eukaryotic cells as reason to believe that life’s history has purpose and meaning, pointing toward the advent of complex life and humanity.

    So, now you know why mitochondria make my list.

    Resources

    Endnotes
    1. Nick Lane, “Bioenergetic Constraints on the Evolution of Complex Life,” Cold Spring Harbor Perspectives in Biology 6, no. 5 (May 2014): a015982, doi:10.1101/cshperspect.a015982.
  • Self-Assembly of Protein Machines: Evidence for Evolution or Creation?

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

    I finally upgraded my iPhone a few weeks ago from a 5s to an 8 Plus. I had little choice. The battery on my cell phone would no longer hold a charge.

    I’d put off getting a new one for as long as possible. It just didn’t make sense to spend money chasing the latest and greatest technology when current cell phone technology worked perfectly fine for me. Apart from the battery life and a less-than-ideal camera, I was happy with my iPhone 5s. Now I am really glad I made the switch.

    Then, the other day I caught myself wistfully eyeing the iPhone X. And, today, I learned that Apple is preparing the release of the iPhone 11 (or XI or XT). Where will Apple’s technology upgrades take us next? I can’t wait to find out.

    Have I become a technology junkie?

    It is remarkable how quickly cell phone technology advances. It is also remarkable how alluring new technology can be. The next thing you know, Apple will release an iPhone that will assemble itself when it comes out of the box. . . . Probably not.

    But, if the work of engineers at MIT ever reaches fruition, it is possible that smartphone manufacturers one day just might rely on a self-assembly process to produce cell phones.

    A Self-Assembling Cell Phone

    The Self-Assembly Lab at MIT has developed a pilot process to manufacture cell phones by self-assembly.

    To do this, they designed their cell phone to consist of six parts that fit together in a lock-in-key manner. By placing the cell phone pieces into a tumbler that turns at the just-right speed, the pieces automatically combine with one another, bit by bit, until the cell phone is assembled.

    Few errors occur during the assembly process. Only pieces designed to fit together combine with one another because of the lock-in-key fabrication.

    Self-Assembly and the Case for a Creator

    It is quite likely that the work of MIT’s Self-Assembly Lab (and other labs like it) will one day revolutionize manufacturing—not just for iPhones, but for other types of products as well.

    As alluring as this new technology might be, I am more intrigued by its implications for the creation-evolution controversy. What do self-assembly processes have to do with the creation-evolution debate? More than we might realize.

    I believe self-assembly processes strengthen the watchmaker argument for God’s existence (and role in the origin of life). Namely, this cutting-edge technology makes it possible to respond to a common objection leveled against this design argument.

    To understand why this engineering breakthrough is so important for the Watchmaker argument, a little background is necessary.

    The Watchmaker Argument

    Anglican natural theologian William Paley (1743–1805) posited the Watchmaker argument in the eighteenth century. It went on to become one of the best-known arguments for God’s existence. The argument hinges on the comparison Paley made between a watch and a rock. He argued that a rock’s existence can be explained by the outworking of natural processes—not so for a watch.

    The characteristics of a watch—specifically the complex interaction of its precision parts for the purpose of telling time—implied the work of an intelligent designer. Employing an analogy, Paley asserted that just as a watch requires a watchmaker, so too, life requires a Creator. Paley noted that biological systems display a wide range of features characterized by the precise interplay of complex parts designed to interact for specific purposes. In other words, biological systems have much more in common with a watch than a rock. This similarity being the case, it logically follows that life must stem from the work of a Divine Watchmaker.

    Biochemistry and the Watchmaker Argument

    As I discuss in my book The Cell’s Design, advances in biochemistry have reinvigorated the Watchmaker argument. The hallmark features of biochemical systems are precisely the same properties displayed in objects, devices, and systems designed and crafted by humans.

    Cells contain protein complexes that are structured to operate as biomolecular motors and machines. Some molecular-level biomachines are strict analogs to machinery produced by human designers. In fact, in many instances, a one-to-one relationship exists between the parts of manufactured machines and the molecular components of biomachines. (A few examples of these biomolecular machines are discussed in the articles listed in the Resources section.)

    We know that machines originate in human minds that comprehend and then implement designs. So, when scientists discover example after example of biomolecular machines inside the cell with an eerie and startling similarity to the machines we produce, it makes sense to conclude that these machines and, hence, life, must also have originated in a Mind.

    A Skeptic’s Challenge

    As you might imagine, skeptics have leveled objections against the Watchmaker argument since its introduction in the 1700s. Today, when skeptics criticize the latest version of the Watchmaker argument (based on biochemical designs), the influence of Scottish skeptic David Hume (1711–1776) can be seen and felt.

    In his 1779 work Dialogues Concerning Natural Religion, Hume presented several criticisms of design arguments. The foremost centered on the nature of analogical reasoning. Hume argued that the conclusions resulting from analogical reasoning are only sound when the things compared are highly similar to each other. The more similar, the stronger the conclusion. The less similar, the weaker the conclusion.

    Hume dismissed the original version of the Watchmaker argument by maintaining that organisms and watches are nothing alike. They are too dissimilar for a good analogy. In other words, what is true for a watch is not necessarily true for an organism and, therefore, it doesn’t follow that organisms require a Divine Watchmaker, just because a watch does.

    In effect, this is one of the chief reasons why some skeptics today dismiss the biochemical Watchmaker argument. For example, philosopher Massimo Pigliucci has insisted that Paley’s analogy is purely metaphorical and does not reflect a true analogical relationship. He maintains that any similarity between biomolecular machines and human designs reflects merely illustrative analogies that life scientists use to communicate the structure and function of these protein complexes via familiar concepts and language. In other words, it is illegitimate to use the “analogies” between biomolecular machines and manufactured machines to make a case for a Creator.1

    A Response Based on Insights from Nanotechnology

    I have responded to this objection by pointing out that nanotechnologists have isolated biomolecular machines from the cell and incorporated these protein complexes into nanodevices and nanosystems for the explicit purpose of taking advantage of their machine-like properties. These transplanted biomachines power motion and movements in the devices, which otherwise would be impossible with current technology. In other words, nanotechnologists view these biomolecular systems as actual machines and utilize them as such. Their work demonstrates that biomolecular machines are literal, not metaphorical, machines. (See the Resources section for articles describing this work.)

    Is Self-Assembly Evidence of Evolution or Design?

    Another criticism—inspired by Hume—is that machines designed by humans don’t self-assemble, but biochemical machines do. Skeptics say this undermines the Watchmaker analogy. I have heard this criticism in the past, but it came up recently in a dialogue I had with a skeptic in a Facebook group.

    I wrote that “What we discover when we work out the structure and function of protein complexes are features that are akin to an automobile engine, not an outcropping of rocks.”

    A skeptic named Maurice responded: “Your analogy is false. Cars do not spontaneously self-assemble—in that case there is a prohibitive energy barrier. But hexagonal lava rocks can and do—there is no energy barrier to prohibit that from happening.”

    Maurice argues that my analogy is a poor one because protein complexes in the cell self-assemble, whereas automobile engines can’t. For Maurice (and other skeptics), this distinction serves to make manufactured machines qualitatively different from biomolecular machines. On the other hand, hexagonal patterns in lava rocks give the appearance of design but are actually formed spontaneously. For skeptics like Maurice, this feature indicates that the design displayed by protein complexes in the cell is apparent, not true, design.

    Maurice added: “Given that nature can make hexagonal lava blocks look ‘designed,’ it can certainly make other objects look ‘designed.’ Design is not a scientific term.”

    Self-Assembly and the Watchmaker Argument

    This is where the MIT engineers’ fascinating work comes into play.

    Engineers continue to make significant progress toward developing self-assembly processes for manufacturing purposes. It very well could be that in the future a number of machines and devices will be designed to self-assemble. Based on the researchers’ work, it becomes evident that part of the strategy for designing machines that self-assemble centers on creating components that not only contribute to the machine’s function, but also precisely interact with the other components so that the machine assembles on its own.

    The operative word here is designed. For machines to self-assemble they must be designed to self-assemble.

    This requirement holds true for biochemical machines, too. The protein subunits that interact to form the biomolecular machines appear to be designed for self-assembly. Protein-protein binding sites on the surface of the subunits mediate this self-assembly process. These binding sites require high-precision interactions to ensure that the binding between subunits takes place with a high degree of accuracy—in the same way that the MIT engineers designed the cell phone pieces to precisely combine through lock-in-key interactions.

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    Figure: ATP Synthase is a biomolecular motor that is literally an electrically powered rotary motor. This biomachine is assembled from protein subunits. Credit: Shutterstock

    The level of design required to ensure that protein subunits interact precisely to form machine-like protein complexes is only beginning to come into full view.2 Biochemists who work in the area of protein design still don’t fully understand the biophysical mechanisms that dictate the assembly of protein subunits. And, while they can design proteins that will self-assemble, they struggle to replicate the complexity of the self-assembly process that routinely takes place inside the cell.

    Thanks to advances in technology, biomolecular machines’ ability to self-assemble should no longer count against the Watchmaker argument. Instead, self-assembly becomes one more feature that strengthens Paley’s point.

    The Watchmaker Prediction

    Advances in self-assembly also satisfy the Watchmaker prediction, further strengthening the case for a Creator. 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.

    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, though previously unrecognized, will become evident in the operation of the cell’s molecular systems. In other words, if the Watchmaker argument truly serves as evidence for a Creator’s existence, then it is reasonable to expect that life’s biochemical machinery anticipates human technological advances.

    In effect, the developments in self-assembly technology and its prospective use in future manufacturing operations fulfill the Watchmaker prediction. Along these lines, it’s even more provocative to think that cellular self-assembly processes are providing insight to engineers who are working to develop similar technology.

    Maybe I am a technology junkie, after all. I find it remarkable that as we develop new technologies we discover that they already exist in the cell, and because they do the Watchmaker argument becomes more and more compelling.

    Can you hear me now?

    Resources

    The Biochemical Watchmaker Argument

    Challenges to the Biochemical Watchmaker Argument

    Endnotes
    1. Massimo Pigliucci and Maarten Boudry, “Why Machine-Information Metaphors are Bad for Science and Science Education,” Science and Education 20, no. 5–6 (May 2011): 453–71; doi:10.1007/s11191-010-9267-6.
    2. For example, see Christoffer H. Norn and Ingemar André, “Computational Design of Protein Self-Assembly,” Current Opinion in Structural Biology 39 (August 2016): 39–45, doi:10.1016/j.sbi.2016.04.002.
  • Does Transhumanism Refute Human Exceptionalism? A Response to Peter Clarke

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Apr 03, 2019

    I just finished binge-watching Altered Carbon. Based on the 2002 science fiction novel written by Richard K. Morgan, this Netflix original series is provocative, to say the least.

    Altered Carbon takes place in the future, where humans can store their personalities as digital files in devices called stacks. These disc-like devices are implanted at the top of the spinal column. When people die, their stacks can be removed from their body (called sleeves) and stored indefinitely until they are re-sleeved—if and when another body becomes available to them.

    In this world, people who possess extreme wealth can live indefinitely, without ever having to spend any time in storage. Referred to as Meths (after the biblical figure Methuselah, who lived 969 years), the wealthy have the financial resources to secure a continual supply of replacement bodies through cloning. Their wealth also affords them the means to back up their stacks once a day, storing the data in a remote location in case their stacks are destroyed. In effect, Meths use technology to attain a form of immortality.

    Forthcoming Posthuman Reality?

    The world of Altered Carbon is becoming a reality right before our eyes. Thanks to recent advances in biotechnology and bioengineering, the idea of using technology to help people live indefinitely no longer falls under the purview of science fiction. Emerging technologies such as CRISPR-Cas9 gene editing and brain-computer interfaces offer hope to people suffering from debilitating diseases and injuries. They can also be used for human enhancements—extending our physical, intellectual, and psychological capabilities beyond natural biological limits.

    These futuristic possibilities give fuel to a movement known as transhumanism. Residing on the fringe of the academy and culture for several decades, the movement has gone mainstream in the ivory towers of the academy and on the street. Sociologist James Hughes describes the transhumanist vision this way in his book Citizen Cyborg:

    “In the twenty-first century the convergence of artificial intelligence, nanotechnology and genetic engineering will allow human beings to achieve things previously imagined only in science fiction. Lifespans will extend well beyond a century. Our senses and cognition will be enhanced. We will gain control over our emotions and memory. We will merge with machines, and machines will become more like humans. These technologies will allow us to evolve into varieties of “posthumans” and usher us into a “transhuman” era and society. . . . Transhuman technologies, technologies that push the boundaries of humanism, can radically improve our quality of life, and . . . we have a fundamental right to use them to control our bodies and minds. But to ensure these benefits we need to democratically regulate these technologies and make them equally available in free societies.”1

    blog__inline--does-transhumanism-refute-human-exceptionalism

    Figure 1: The transhumanism symbol. Image credit: Wikimedia Commons

    In short, transhumanists want us to take control of our own evolution, transforming human beings into posthumans and in the process creating a utopian future that carves out a path to immortality.

    Depending on one’s philosophical or religious perspective, transhumanists’ vision and the prospects of a posthuman reality can bring excitement or concern or a little bit of both. Should we pursue the use of technology to enhance ourselves, transcending the constraints of our biology? What role should these emerging biotechnologies play in shaping our future? What are the boundaries for developing and using these technologies? Should there be any boundaries?2

    All of these questions revolve around a central question: Who are we as human beings?

    Are Humans Exceptional?

    Prior to the rising influence of transhumanism, the answer to this question followed along one of two lines. For people who hold to a Judeo-Christian worldview, human beings are exceptional, standing apart from all other creatures on the planet. Accordingly, our exceptional nature results from the image of God. As image bearers, human beings have infinite worth and value.

    On the other hand, those influenced by the evolutionary paradigm maintain that human beings are nothing more than animals—differing in degree, not kind, from other creatures. In fact, many who hold this view of humanity find the notion of human exceptionalism repugnant. In their view, to elevate the value of human beings above that of other creatures constitutes speciesism and reflects an unjustifiable arrogance.

    And now transhumanism enters into the fray. People on both sides of the controversy about human nature and identity argue that transhumanism brings an end to any notion about human exceptionalism, once and for all.

    One is Peter Clarke. In an article published on the Areo website entitled “Transhumanism and the Death of Human Exceptionalism,” Clarke says:

    “As a philosophical movement, transhumanism advocates for improving humanity through genetic modifications and technological augmentations, based upon the position that there is nothing particularly sacred about the human condition. It acknowledges up front that our bodies and minds are riddled with flaws that not only can but should be fixed. Even more radically, as the name implies, transhumanism embraces the potential of one day moving beyond the human condition, transitioning our sentience into more advanced forms of life, including genetically modified humans, superhuman cyborgs, and immortal digital intelligences.”3

    On the other side of the aisle is Wesley J. Smith of the Discovery Institute. In his article “Transhumanist Bill of Wrongs,” Smith writes:

    “Transhumanism would shatter human exceptionalism. The moral philosophy of the West holds that each human being is possessed of natural rights that adhere solely and merely because we are human. But transhumanists yearn to remake humanity in their own image—including as cyborgs, group personalities residing in the Internet Cloud, or AI-controlled machines. That requires denigrating natural man as unexceptional to justify our substantial deconstruction and redesign.”4

    In other words, transhumanism highlights the notion that our bodies, minds, and personalities are inherently flawed and we have a moral imperative, proponents say, to correct these flaws. But this view denigrates humanity, opponents say, and with it the notion of human exceptionalism. For Clarke, this nonexceptional perspective is something to be celebrated. For Smith, transhumanism is of utmost concern and must be opposed.

    Evidence of Exceptionalism

    While I am sympathetic to Smith’s concern, I would take a differing perspective. I find that transhumanism provides one of the most powerful pieces of evidence for human exceptionalism—and along with it the image of God.

    In my forthcoming book (coauthored with Ken Samples), Humans 2.0, I write:

    “Ironically, progress in human enhancement technology and the prospects of a posthuman future serve as one of the most powerful arguments for human exceptionalism and, consequently, the image of God. Human beings are the only species that exists—or that has ever existed—that can create technologies to enhance our capabilities beyond our biological limits. We alone work toward effecting our own immortality, take control of evolution, and look to usher in a posthuman world. These possibilities stem from our unique and exceptional capacity to investigate and develop an understanding of nature (including human biology) through science and then turn that insight into technology.”5

    Our ability to carry out the scientific enterprise and develop technology stems from four qualities that a growing number of anthropologists and primatologists think are unique to humans, including:

    • symbolism
    • open-ended generative capacity
    • theory of mind
    • our capacity to form complex social networks

    From my perspective as a Christian, these qualities stand as scientific descriptors of the image of God.

    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.

    Human 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.

    For anthropologists and primatologists who think that human beings differ in kind—not degree—from other animals, these qualities demarcate us from the great apes and Neanderthals. The separation becomes most apparent when we consider the remarkable technological advances we have made during our tenure as a species. Primatologist 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.”6

    Moreover, no convincing evidence exists that leads us to think that Neanderthals shared the qualities that make us exceptional. 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 paleoanthropologist Ian Tattersall and linguist Noam 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.”7

    In other words, the evolution of human technology signifies that there is something special—exceptional—about us as human beings. In this sense, transhumanism highlights our exceptional nature precisely because the prospects for controlling our own evolution stem from our ability to advance technology.

    To be clear, transhumanism possesses an existential risk for humanity. Unquestioningly, it has the potential to strip human beings of dignity and worth. But, ironically, transhumanism is possible only because we are exceptional as human beings.

    Responsibility as the Crown of Creation

    Ultimately, our exceptional nature demands that we thoughtfully deliberate on how to use emerging biotechnologies to promote human flourishing, while ensuring that no human being is exploited or marginalized by these technologies. It also means that we must preserve our identity as human beings at all costs.

    It is one thing to enjoy contemplating a posthuman future by binge-watching a sci-fi TV series. But, it is another thing altogether to live it out. May we be guided by ethical wisdom to live well.

    Resources

    Endnotes
    1. James Hughes, Citizen Cyborg: Why Democratic Societies Must Respond to the Redesigned Humans of the Future (Cambridge, MA: Westview Press, 2004), xii.
    2. Ken Samples and I take on these questions and more in our book Humans 2.0, due to be published in July of 2019.
    3. Peter Clarke, Transhumanism and the Death of Human Exceptionalism, Areo (March 6, 2019), https://areomagazine.com/2019/03/06/transhumanism-and-the-death-of-human-exceptionalism/.
    4. Wesley J. Smith,Transhumanist Bill of Wrongs, Discovery Institute (October 23, 2018), https://www.discovery.org/a/transhumanist-bill-of-wrongs/.
    5. Fazale Rana with Kenneth Samples, Humans 2.0: Scientific, Philosophical, and Theological Perspectives on Transhumanism (Covina, CA: RTB Press, 2019) in press.
    6. Thomas Suddendorf, The Gap: The Science of What Separates Us from Other Animals (New York: Basic Books, 2013), 2.
    7. Johan J. Bolhuis et al., “How Could Language Have Evolved?” PLoS Biology 12, no.8 (August 26, 2014): e1001934, doi:10.1371/journal.pbio.1001934.
  • Timing of Neanderthals’ Disappearance Makes Art Claims Unlikely

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Mar 27, 2019

    In Latin it literally means, “somewhere else.”

    Legal experts consider an alibi to be one of the most effective legal defenses available in a court of law because it has the potential to prove a defendant’s innocence. It goes without saying: if a defendant has an alibi, it means that he or she was somewhere else when the crime was committed.

    As it turns out, paleoanthropologists have discovered that Neanderthals have an alibi, of sorts. Evidence indicates that they weren’t the ones to scratch up the floor of Gorham’s Cave.

    Based on recent radiocarbon dates measured for samples from Bajondillo Cave (located on the southern part of the Iberian Peninsula—southwest corner of Europe), a research team from the Japan Agency for Marine-Earth Science and Technology and several Spanish institutions determined that modern humans made their way to the southernmost tip of Iberia around 43,000 years ago, displacing Neanderthals.1

    Because Neanderthals disappeared from Iberia at that time, it becomes unlikely that they were responsible for hatch marks (dated to be 39,000 years in age) made on the floor of Gorham’s Cave on the island of Gibraltar. These scratches have been interpreted by some paleoanthropologists as evidence that Neanderthals possessed symbolic capabilities.

    But how could Neanderthals have made the hatch marks if they weren’t there? Ladies and gentlemen of the jury: the perfect alibi. Instead, it looks as if modern humans were the culprits who marked up the cave floor.

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    Figure 1: Gorham’s Cave. Image credit: Wikipedia

    The Case for Neanderthal Exceptionalism

    Two of the biggest questions in anthropology today relate to Neanderthals:

    • When did these creatures disappear from Europe?
    • Did they possess symbolic capacity like modern humans, thus putting their cognitive abilities on par with ours as a species?

    For paleoanthropologists, these two questions have become inseparable. With regard to the second question, some paleoanthropologists are convinced that Neanderthals displayed symbolic capabilities.

    It is important to note that the case for Neanderthal symbolism is largely based on correlations between the archaeological and fossil records. Toward this end, some anthropologists have concluded that Neanderthals possessed symbolism because researchers have recovered artifacts (presumably reflecting symbolic capabilities) from the same layers that harbored Neanderthal fossils. Unfortunately, this approach is complicated by other studies that show that the cave layers have been mixed by either cave occupants (either hominid or modern human) or animals living in the caves. This mixing leads to the accidental association of fossil and archaeological remains. In other words, the mixing of layers raises questions about who the manufacturers of these artifacts were.

    Because we know modern humans possess the capacity for symbolism, it is much more likely that modern humans, not Neanderthals, made the symbolic artifacts, in these instances. Then, only through an upheaval of the cave layers did the artifacts mix with Neanderthal remains. (See the Resources section for articles that elaborate this point.)

    More often than not, archaeological remains are unearthed by themselves with no corresponding fossil specimens. This is the reason why understanding the timing of Neanderthals disappearance and modern humans arrival in different regions of Europe becomes so important (and why the two questions interrelate). Paleoanthropologists believe that if they can show that Neanderthals lived in a locale at the time symbolic artifacts were produced, then it becomes conceivable that these creatures made the symbolic items. This interpretation increases in plausiblity if no modern humans were around at the time.

    Some researchers have argued along these lines regarding the hatch marks found on the floor of Gorham’s Cave.2 The markings were made in the bedrock of the cave floor. The layers above the bedrock date to between 30,000 and 39,000 years in age. Some paleoanthropologists argue that Neanderthals must have made the markings. Why? Because, even though modern humans were already in Europe by that time, these paleoanthropologists think that modern humans had not yet made their way to the southern part of the Iberian Peninsula. These same researchers also think that Neanderthals survived in Iberia until about 32,000 years ago, even though their counterparts in other parts of Europe had already disappeared. So, on this basis, paleoanthropologists conclude that Neanderthals produced the hatch marks and, thus, displayed symbolic capabilities.

    blog__inline--timing-of-neanderthals-disappearance-2

    Figure 2: Hatch marks on the floor of Gorham’s Cave. Image credit: Wikipedia

    When Did Neanderthals Disappear from Iberia?

    But recent work challenges this conclusion. The Spanish and Japanese team took 17 new radiocarbon measurements from layers of the Bajondillo Cave (located in southern Iberia, near Gorham’s Cave) with the hopes of precisely documenting the change in technology from Mousterian (made by Neanderthals) to Aurignacian (made by modern humans). This transition corresponds to the replacement of Neanderthals by modern humans elsewhere in Europe.

    The researchers combined the data from their samples with previous measurements made at the site to pinpoint this transition at around 43,000 years ago—not 32,000 years ago. In other words, modern humans occupied Iberia at the same time they occupied other places in Europe. This result also means that Neanderthals had disappeared from Iberia well before the hatch marks in Gorham’s Cave were made.

    Were Neanderthals Exceptional Like Modern Humans?

    Though claims of Neanderthal exceptionalism abound in the scientific literature and in popular science articles, the claims universally fail to withstand ongoing scientific scrutiny, as this latest discovery attests. Simply put, based on the archaeological record, there are no good reasons to think that Neanderthals displayed symbolism.

    From my perspective, the case for Neanderthal symbolism seems to be driven more by ideology than actual scientific evidence.

    It is also worth noting that comparative studies on Neanderthal and modern human brain structures also lead to the conclusion that humans displayed symbolism and Neanderthals did not. (See the Resources section for articles that describe this work in more detail.)

    Why Does It Matter?

    Questions about Neanderthal symbolic capacity and, hence, exceptionalism have bearing on how we understand human beings. Are human beings unique in our capacity for symbolism or is this quality displayed by other hominins? If humans are not alone in our capacity for symbolism, then we aren’t exceptional. And, if we aren’t exceptional then it becomes untenable to embrace the biblical concept of human beings as God’s image bearers. (As a Christian, I see symbolism as a manifestation of the image of God.)

    But, based on the latest scientific evidence, the verdict is in: modern humans are the only species to display the capacity for symbolism. In this way, scientific advance affirms that humans are exceptional in a way that aligns with the biblical concept of the image of God.

    The Neanderthals alibi holds up. They werent there, but humans were. Case closed.

    Resources

    Endnotes
    1. Miguel Cortés-Sánchez et al., “An Early Aurignacian Arrival in Southwestern Europe,” Nature Ecology and Evolution 3 (January 21, 2019): 207–12, doi:10.1038/s41559-018-0753-6.
    2. Joaquín Rodríguez-Vidal et al., “A Rock Engraving Made by Neanderthals in Gibraltar,” Proceedings of the National Academy of Sciences USA 111, no. 37 (September 16, 2014): 13301–6, doi:10.1073/pnas.1411529111.
  • Origins of Monogamy Cause Evolutionary Paradigm Breakup

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Mar 20, 2019

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

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

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

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

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

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

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

    Historical Contingency

    To appreciate why I believe this discovery is problematic for the evolutionary paradigm, it is necessary to consider the nature of evolutionary mechanisms. According to the evolutionary biologist Stephen Jay Gould (1941–2002), evolutionary transformations occur in a historically contingent manner.4 This means that the evolutionary process consists of an extended sequence of unpredictable, chance events. If any of these events were altered, it would send evolution down a different trajectory.

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

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

    A Failed Prediction of the Evolutionary Paradigm

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

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

    Convergent Origins of Monogamy

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

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

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

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

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

    So, is there another way to explain convergence?

    Convergence and the Case for a Creator

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

    In light of this historical precedence, I interpret convergent features (analogies) as the handiwork of a Divine mind. The repeated origins of biological features equate to the repeated creations by an intelligent Agent who employs a common set of solutions to address a common set of problems facing unrelated organisms.

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

    Resources

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

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Mar 13, 2019

    Sometimes I just can’t help myself. I know it’s clickbait but I click on the link anyway.

    A few days ago, as a result of momentary weakness, I found myself reading an article from the ScoopWhoop website, “16 Things Most of Us Think Are the Same but Actually Aren’t.”

    OK. OK. Now that you saw the title you want to click on the link, too.

    To save you from wasting five minutes of your life, here is the ScoopWhoop list:

    • Weather and Climate
    • Turtle and Tortoise
    • Jam and Jelly
    • Eraser and Rubber
    • Great Britain and the UK
    • Pill and Tablet
    • Shrimp and Prawn
    • Butter and Margarine
    • Orange and Tangerine
    • Biscuits and Cookies
    • Cupcakes and Muffins
    • Mushrooms and Toadstools
    • Tofu and Paneer
    • Rabbits and Hares
    • Alligators and Crocodiles
    • Rats and Mice

    And there you have it. Not a very impressive list, really.

    If I were putting together a biochemist’s version of this list, I would start with synonymous mutations. Even though many life scientists think they are the same, studies indicate that they “actually aren’t.”

    If you have no idea what I am talking about or what this insight has to do with the creation/evolution debate, let me explain by starting with some background information, beginning with the central dogma of molecular biology and the genetic code.

    Central Dogma of Molecular Biology

    According to this tenet of molecular biology, the information stored in DNA is functionally expressed through the activities of proteins. When it is time for the cell’s machinery to produce a particular protein, it copies the appropriate information from the DNA molecule through a process called transcription and produces a molecule called messenger RNA (mRNA). Once assembled, mRNA migrates to the ribosome, where it directs the synthesis of proteins through a process known as translation.

    blog__inline--biochemical-synonyms-restate-1

    Figure 1: The central dogma of molecular biology. Image credit: Shutterstock

    The Genetic Code

    At first glance, there appears to be a mismatch between the stored information in DNA and the information expressed in proteins. A one-to-one relationship cannot exist between the four different nucleotides that make up DNA and the twenty different amino acids used to assemble proteins. The cell handles this mismatch by using a code comprised of groupings of three nucleotides, called codons, to specify the twenty different amino acids.

     

    blog__inline--biochemical-synonyms-restate-2

    Figure 2: Codons. Image credit: Wikipedia

    The cell uses a set of rules to relate these nucleotide triplet sequences to the twenty amino acids that comprise proteins. Molecular biologists refer to this set of rules as the genetic code. The nucleotide triplets represent the fundamental units of the genetic code. The code uses each combination of nucleotide triplets to signify an amino acid. This code is essentially universal among all living organisms.

    Sixty-four codons make up the genetic code. Because the code only needs to encode twenty amino acids, some of the codons are redundant. That is, different codons code for the same amino acid. In fact, up to six different codons specify some amino acids. Others are specified by only one codon.1

    blog__inline--biochemical-synonyms-restate-3

    Figure 3: The genetic code. Image credit: Shutterstock

    A little more background information about mutations will help fill out the picture.

    Mutations

    A mutation refers to any change that takes place in the DNA nucleotide sequence. DNA can experience several different types of mutations. Substitution mutations are one common type. When a substitution mutation occurs, one (or more) of the nucleotides in the DNA strand is replaced by another nucleotide. For example, an A may be replaced by a G, or a C may be replaced by a T. This substitution changes the codon. Interestingly, the genetic code is structured in such a way that when substitution mutations take place, the resulting codon often specifies the same amino acid (due to redundancy) or an amino acid that has similar chemical and physical properties to the amino acid originally encoded.

    Synonymous and Nonsynonymous Mutations

    When substitution mutations generate a new codon that specifies the same amino acid as initially encoded, it’s referred to as a synonymous mutation. However, when a substitution produces a codon that specifies a different amino acid, it’s called a nonsynonymous mutation.

    Nonsynonymous mutations can be deleterious if they affect a critical amino acid or if they significantly alter the chemical and physical profile along the protein chain. If the substituted amino acid possesses dramatically different physicochemical properties from the native amino acid, it may cause the protein to fold improperly. Improper folding impacts the protein’s structure, yielding a biomolecule with reduced or even lost function.

    On the other hand, biochemists have long thought that synonymous mutations have no effect on protein structure and function because these types of mutations don’t change the amino acid sequences of proteins. Even though biochemists think that synonymous mutations are silent—having no functional consequences—evolutionary biologists find ways to use them, including using patterns of synonymous mutations to establish evolutionary relationships.

    Patterns of Synonymous Mutations and the Case for Biological Evolution

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

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

    It is conceivable that nonsynonymous mutations, which alter the protein amino acid sequences, may impart some type of benefit and, therefore, shared patterns of nonsynonymous changes could be understood as evidence for shared design. (See the last section of this article.) But this is not the case when it comes to synonymous mutations, which raises the question: Why would a Creator intentionally introduce new codons that code for the same amino acid into genes when these changes have no functional utility?

    Apart from invoking a Creator, the shared patterns of synonymous mutations make perfect sense if genomes have been shaped by evolutionary processes and an evolutionary history. However, this argument for biological evolution (shared ancestry) and challenge to a creation model interpretation (shared design) hinges on the underlying assumption that synonymous mutations have no functional consequence.

    But what if this assumption no longer holds?

    Synonymous Mutations Are Not Interchangeable

    Biochemists used to think that synonymous mutations had no impact whatsoever on protein structure and, hence, function, but this view is changing thanks to studies such as the one carried out by researchers at University of Colorado, Boulder.2

    These researchers discovered synonymous mutations that increase the translational efficiency of a gene (found in the genome of Salmonella enterica). This gene codes for an enzyme that plays a role in the biosynthetic pathway for the amino acid arginine. (This enzyme also plays a role in the biosynthesis of proline.) They believe that these mutations alter the three-dimensional structure of the DNA sequence near the beginning of the coding portion of the gene. They also think that the synonymous mutations improve the stability of the messenger RNA molecule. Both effects would lead to greater translational efficiency at the ribosome.

    As radical (and unexpected) as this finding may seem to be, it follows on the heels of other recent discoveries that also recognize the functional importance of synonymous mutations.3 Generally speaking, biochemists have discovered that synonymous mutations function to influence not only the rate and efficiency of translation (as the scientists from the University of Colorado, Bolder learned) and the folding of the proteins after they are produced at the ribosome.

    Even though synonymous mutations leave the amino acid sequence of the protein unchanged, they can exert influence by altering the:

    • regulatory regions of the gene that influence the transcription rate
    • secondary and tertiary structure of messenger RNA that influences the rate of translation
    • stability of messenger RNA that influences the amount of protein produced
    • translation rate that influences the folding of the protein as it exits the ribosome

    Biochemists are just beginning to come to terms with the significance of these discoveries, but it is already clear that synonymous mutations have biomedical consequences.4 They also impact models for molecular evolution. But for now, I want to focus on the impact these discoveries has on the creation/evolution debate.

    Patterns of Synonymous Mutations and the Case for Creation

    As noted, many people consider the most compelling evidence for common descent to be the shared genetic features displayed by organisms that naturally cluster together. But if life is the product of a Creator’s handiwork, the shared genetic features could be understood as shared designs deployed by a Creator. In fact, a historical precedent exists for the common design interpretation. Prior to Darwin, biologists viewed shared biological features as manifestations of archetypical designs that existed in the Creator’s mind.

    But the common design interpretation requires that the shared features be functional. (Or, that they arise independently in a nonrandom manner.) For those who view life from the framework of the evolutionary paradigm, the shared patterns of synonymous mutations invalidate the common design explanation—because these mutations are considered to be functionally insignificant.

    But in the face of mounting evidence for the functional importance of synonymous mutations, this objection to common design has begun to erode. Though many life scientists are quick to dismiss the common design interpretation of biology, advances in molecular biology continue to strengthen this explanation and, with it, the case for a Creator.

    Resources

    Endnotes
    1. As I discuss in The Cell’s Design, the rules of the genetic code and the nature of the redundancy appear to be designed to minimize errors in translating information from DNA into proteins that would occur due to substitution mutations. This optimization stands as evidence for the work of an intelligent Agent.
    2. JohnCarlo Kristofich et al., “Synonymous Mutations Make Dramatic Contributions to Fitness When Growth Is Limited by Weak-Link Enzyme,” PLoS Genetics 14, no. 8 (August 27, 2018): e1007615, doi:10.1371/journal.pgen.1007615.
    3. Here are a few representative studies that ascribe functional significance to synonymous mutations: Anton A. Komar, Thierry Lesnik, and Claude Reiss, “Synonymous Codon Substitutions Affect Ribosome Traffic and Protein Folding during in vitro Translation,” FEBS Letters 462, no. 3 (November 30, 1999): 387–91, doi:10.1016/S0014-5793(99)01566-5; Chung-Jung Tsai et al., “Synonymous Mutations and Ribosome Stalling Can Lead to Altered Folding Pathways and Distinct Minima,” Journal of Molecular Biology 383, no. 2 (November 7, 2008): 281–91, doi:10.1016/j.jmb.2008.08.012; Florian Buhr et al., “Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations,” Molecular Cell Biology 61, no. 3 (February 4, 2016): 341–51, doi:10.1016/j.molcel.2016.01.008; Chien-Hung Yu et al., “Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding,” Molecular Cell Biology 59, no. 5 (September 3, 2015): 744–55, doi:10.1016/j.molcel.2015.07.018.
    4. Zubin E. Sauna and Chava Kimchi-Sarfaty,” Understanding the Contribution of Synonymous Mutations to Human Disease,” Nature Reviews Genetics 12 (August 31, 2011): 683–91, doi:10.1038/nrg3051.
  • Discovery of Intron Function Interrupts Evolutionary Paradigm

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Mar 06, 2019

    Nobody likes to be interrupted when they are talking. It feels disrespectful and can be frustrating. Interruptions derail the flow of a conversation.

    The editors tell me that I need to interrupt this lead to provide a “tease” for what is to come. So, here goes: Interruptions happen in biochemical systems, too. Life scientists long thought that these interruptions disrupted the flow of biochemical information. But, it turns out these interruptions serve an important function, offering a rejoinder a common argument against intelligent design.

    Now back to the lead.

    Perhaps it is no surprise that some psychologists study interruptions1 with the hope of discovering answers to questions such as:

    • Why do people interrupt?
    • Who is most likely to interrupt?
    • Do we all perceive interruptions in the same way?

    While there is still much to learn about the science of interruptions, psychologists have discovered that men interrupt more often than women. Ironically, men often view women who interrupt as ruder and less intelligent than men who interrupt during conversations.

    Researchers have also found that a person’s cultural background influences the likelihood that he or she will interrupt during a discourse. Personality also plays a role. Some people are more sensitive to pauses in conversation and, therefore, find themselves interrupting more often than those who are less uncomfortable with periods of silence.

    Psychologists have learned that not all interruptions are the same. Some people interrupt because they want the “floor.” These people are called intrusive interrupters. Cooperative interrupters help move the conversation along by agreeing with the speaker and finishing the speaker’s thoughts.

    Interruptions are not confined to conversations. They are a part of life, including the biochemical operations that take place inside the cell.

    In fact, biochemists have discovered that the information harbored in genes, which contains the instructions to build proteins—the workhorse molecules of the cell—experience interruptions in their coding sequences. These intrusive interruptions would disrupt the flow of information in the cell during the process of protein synthesis if the interrupting sequences weren’t removed by the cell’s machinery.

    Molecular biologists have long viewed these genetic “interruptions” (called introns) as serving no useful purpose for the cell, with introns comprising a portion of the junk DNA found in the genomes of eukaryotic organisms. But it turns out that introns—like cooperative interruptions during a conversation—serve a useful purpose, according to the recent work of two independent teams of molecular biologists.

    Introns Are Abundant

    Noncoding regions within genes, introns consist of DNA sequences that interrupt the coding regions (called exons) of a gene. Introns are pervasive in genomes of eukaryotic organisms. For example, 90 percent of genes in mammals consists of introns, with an average of 8 per gene.

    After the information stored in a gene is copied into messenger RNA, the intron sequences are excised, and the exons spliced together by a protein-RNA complex known as a spliceosome.

    blog__inline--discovery-of-intron-function-1

    Figure 1: Drawing of pre-mRNA to mRNA. Image credit: Wikipedia

    Molecular biologists have long wondered why eukaryotic genes would be riddled with introns. Introns seemingly make the structure and expression of eukaryotic genes unnecessarily complicated. What possible purpose could introns serve? Researchers also thought that once the introns were spliced out of the messenger RNA sequences, they were discarded as genetic debris.

    Introns Serve a Functional Purpose

    But recent work by two independent research teams from Sherbrooke University in Quebec, Canada, and MIT, respectively, indicates that molecular biologists have been wrong about introns. They have learned that once spliced from messenger RNA, these fragments play a role in helping cells respond to stress.

    Both research teams studied baker’s yeast. One advantage of using yeast as a model organism relates to the relatively small number of introns (295) in its genome.

    blog__inline--discovery-of-intron-function-2

    Figure 2: A depiction of baker’s yeast. Image credit: Shutterstock

    Taking advantage of the limited number of introns in baker’s yeast, the team from Sherbrooke University created hundreds of yeast strains—each one missing just one of its introns. When grown under normal conditions with a ready supply of available nutrients, the strains missing a single intron grew normally—suggesting that introns aren’t of much importance. But when the researchers grew the yeast cells under conditions of food scarcity, the yeast with the deleted introns frequently died.2

    The MIT team observed something similar. They noticed that during the stationary phase of growth (when nutrients become depleted, slowing down growth), introns spliced from RNA accumulated in the growth medium. The researchers deleted the specific introns that they found in the growth medium from the baker’s yeast genome and discovered that the resulting yeast strains struggled to survive under nutrient-poor conditions.3

    At this point, it isn’t clear how introns help cells respond to stress caused by a lack of nutrients, but they have some clues. The Sherbrooke University team thinks that the spliced-out introns play a role in repressing the production of proteins that help form ribosomes. These biochemical machines manufacture proteins. Because protein synthesis requires building block materials and energy, during periods when nutrients are scarce, protein production slows down in cells. Ratcheting down protein synthesis impedes cell growth but affords them a better chance to survive a lack of nutrients. One way cells can achieve this objective is to stop making ribosomes.

    The MIT team thinks that some spliced-out introns interact with spliceosomes, preventing them from splicing out other introns. When this disruption happens, it slows down protein synthesis.

    Both research groups believe that in times when nutrients are abundant, the spliced-out introns are broken down by the cell’s machinery. But when nutrients are scarce, that condition triggers intron accumulation.

    At this juncture, it isn’t clear if the two research teams have uncovered distinct mechanisms that work collaboratively to slow down protein production, or if they are observing facets of the same mechanism. Regardless, it is evident that introns display functional utility. It’s a surprising insight that has important ramifications for our understanding of the structure and function of genomes. This insight has potential biomedical utility and theological implications, as well.

    Intron Function and the Case for Creation

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

    Yet, a growing body of data indicates that virtually every category of so-called junk DNA displays function. We can now add introns—cooperative interrupters—to the list. And based on the data on hand, we can make a strong case that most of the sequence elements in genomes possess functional utility.

    Could it be that scientists really don’t understand the biology of genomes? Or maybe we have the wrong paradigm?

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

    But what if the genome is viewed from a creation model framework?

    The elegance and sophistication of genomes are features that are increasingly coming into scientific view. And this is precisely what I would expect if genomes were the product of a Mind—the handiwork of a Creator.

    Now that is a discovery worth talking about.

    Resources

    Endnotes
    1. Teal Burrell, “The Science behind Interrupting: Gender, Nationality and Power, and the Roles They Play,” Post Magazine (March 14, 2018), https://www.scmp.com/magazines/post-magazine/long-reads/article/2137023/science-behind-interrupting-gender-nationality; Alex Shashkevich, “Why Do People Interrupt? It Depends on Whom You’re Talking To,” The Guardian (May 18, 2018), https://www.theguardian.com/lifeandstyle/2018/may/18/why-do-people-interrupt-it-depends-on-whom-youre-talking-to.
    2. Julie Parenteau et al., “Introns Are Mediators of Cell Response to Starvation,” Nature 565 (January 16, 2019): 612–17, doi:10.1038/s41586-018-0859-7.
    3. Jeffrey T. Morgan, Gerald R. Fink, and David P. Bartel, “Excised Linear Introns Regulate Growth in Yeast,” Nature 565 (January 16, 2019): 606–11, doi:10.1038/s41586-018-0828-1.
  • Molecular Logic of the Electron Transport Chain Supports Creation

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Feb 27, 2019

    “It was said that some scientists attended the oxidative phosphorylation sessions of the Federation meetings because they knew a good punch up was on the cards.”

    —John Prebble, Department of Biological Sciences, University of London

    It has been described as one of the most “heated and acrimonious debates in biochemistry during the twentieth century,”1 and its resolution carries implications for a different ideological conflict—that of the origin of life.

    This battle royale (dubbed the Ox Phos Wars) took place in the 1960s and early 1970s. At that time, biochemists were trying to decipher the mechanism used by mitochondria to produce the high-energy compound called ATP (adenosine triphosphate) through a process called oxidative phosphorylation (Ox Phos for short). Many components of the cell’s machinery use ATP to power their operations.

    blog__inline--molecular-logic-of-the-electron-transport-chain-1

    Figure 1: A schematic of the synthesis and breakdown cycle of ATP and ADP. Image credit: Shutterstock

    So acrimonious was the debate that scientists involved in this controversy often came close to blows when publicly debating the mechanism of oxidative phosphorylation. Much of the controversy centered around an idea known as the chemiosmotic theory, proposed by biochemist Peter Mitchell. He argued that the electron transport chain generates a proton gradient across the mitochondrial inner membrane and, in turn, exploits that gradient through a coupling process to drive the synthesis of ATP from ADP (adenosine diphosphate) and inorganic phosphate. (see figures 1 and 2). (The reverse reaction liberates chemical energy that drives many biochemical processes.)

    blog__inline--molecular-logic-of-the-electron-transport-chain-2

    Figure 2: A schematic of the chemiosmotic theory. Image credit: Shutterstock

    At the time, this idea was met with a large measure of skepticism by biochemists. It didn’t fit with the orthodoxy, characteristic of classical biochemistry. Biochemists found Mitchell’s ideas hard to understand and his personality abrasive, both of which led to the acrimony.

    Origin-of-life researcher Leslie Orgel referred to the chemiosmotic theory as one of the most counterintuitive ideas to ever come out of biology, comparing it to the ideas that formed the foundations of quantum mechanics and relativity.2

    Many biochemists preferred the chemical theory of oxidative phosphorylation over Mitchell’s chemiosmotic theory. Researchers thought that the phosphate group added to ADP was transferred from one of the components of the electron transport chain. In an attempt to support this idea, many biochemists frantically searched for a chemical intermediate with a high-energy phosphate moiety that could power the synthesis of ATP.

    The chemical theory was based on a process called substrate-level phosphorylation, exemplified by two reactions that form ATP during glycolysis. In one reaction, 1,3-diphosphoglycerate transfers one of its phosphate groups to ADP to form ATP. (In this case, 3-diphosphoglycerate serves as the intermediate with a high-energy phosphate moiety.) In the second reaction, phosphoenolpyruvate transfers a phosphate group to ADP to make ATP, with phosphoenolpyruvate functioning as the intermediate bearing a high-energy phosphate residue. (See figure 3.)

    As it turns out, the elusive intermediate was never found, forcing adherents of the chemical theory to abandon their model. Peter Mitchell’s idea won the day. In fact, Mitchell was awarded the Nobel Prize in Chemistry in 1978 for his contribution to understanding the mechanism of oxidative phosphorylation.

    Today, biochemists readily recognize the importance of proton gradients and the chemiosmotic process. Proton gradients are pervasive in living systems. Mitochondria are not alone. Chloroplasts rely on proton gradients during the process of photosynthesis. Bacteria and archaea also use proton gradients across their plasma membranes to harvest energy. Cells use proton gradients to transport material across cell membranes. And proton gradients even power the bacterial flagellum.

    Now that oxidative phosphorylation is understood, some evolutionary biologists and origin-of-life researchers have turned their attention to two questions: (1) How did chemiosmosis originate? and (2) Why are proton gradients so central to biochemical operations?

    Oxidative Phosphorylation and the Evolutionary Paradigm

    For many evolutionary biologists, understanding the origin of oxidative phosphorylation (and the use of proton gradients, in general) assumes a position of unique prominence because of the central role this process plays in harvesting energy in both prokaryotic and eukaryotic organisms. In other words, understanding the origin of oxidative phosphorylation (and use of proton gradients) is central to understanding the origin of life and the fundamental design of biochemical systems.

    Because the use of proton gradients in living systems is odd and counterintuitive, it becomes tempting for many origin-of-life researchers and evolutionary biologists to conclude that chemiosmosis reflects the outworking of a historically contingent evolutionary process that relied on existing systems and designs that were co-opted and, in turn, modified. This notion becomes reinforced by the work of origin-of-life researcher Nick Lane.

    Lane and his collaborators conclude that proton gradients must have been integral to the biochemistry of LUCA (the last universal common ancestor) because proton gradients are a near-universal feature of living systems. If so, then the use of proton gradients must have emerged during the origin-of-life process before LUCA originated. Lane and his team go so far as to propose that the first proto-cells emerged near hydrothermal vents and made use of naturally occurring proton gradients found in these environments as their energy source.3

    Once this system was in place, the strategy was retained in the cell lines that diverged from these early proto-cellular entities as the electron transport chain evolved from a simple, naturally occurring vent process to the complex process found in both prokaryotic and eukaryotic organisms. In other words, it would seem that the odd, counterintuitive nature of proton gradients reflects the happenstance outworking of chemical evolution that began when the naturally occurring proton gradients were co-opted in the early stages of chemical evolution.

    But Lane’s recent insight indicates that, though counterintuitive, the use of proton gradients to harvest the energy required to make ATP makes sense, displaying an exquisite molecular rationale.4 And if so, it forces a rethink of the explanation for the origin of chemiosmosis. To appreciate this shift in perspective, it is helpful to understand the process of oxidative phosphorylation, beginning with glycolysis and the Kreb’s cycle.

    Glycolysis and the Kreb’s Cycle

    The glycolytic pathway converts the fuel molecule glucose (a 6-carbon sugar) into two pyruvate molecules (3-carbon). This process proceeds through eleven chemical intermediates and nets 2 molecules of ATP (generated through substrate-level phosphorylation) and two molecules of NADH (nicotinamide adenine dinucleotide). NADH harbors high-energy electrons generated from the energy liberated from the breakdown and oxidation of glucose. As it turns out, the NADH molecules play a central role in generating most of the ATP produced when a sugar molecule breaks down.

    blog__inline--molecular-logic-of-the-electron-transport-chain-3

    Figure 3: Glycolysis. Image credit: Shutterstock

    The pyruvate generated by glycolysis is transported across the mitochondrial inner membrane into the matrix of the organelle. Here pyruvate is transformed into a molecule of carbon dioxide and a 2-carbon intermediate called acetyl CoA. This process generates 2 additional molecules of NADH.

    In turn, the Kreb’s cycle converts each acetyl CoA molecule into two molecules of carbon dioxide. (The net reaction: a 6-carbon glucose molecule breaks down into 6 carbon dioxide molecules.) During the process, the breakdown of each acetyl CoA molecule generates 1 ATP molecule (via substrate-level phosphorylation) and 3 molecules of NADH. Additionally, 1 molecule of FADH2 is formed. Like NADH, this molecule possesses high-energy electrons. (See figure 4.)

    blog__inline--molecular-logic-of-the-electron-transport-chain-4

    Figure 4: Kreb’s cycle. Image credit: Shutterstock

    The Electron Transport Chain and Oxidative Phosphorylation

    The high-energy electrons of NADH and FADH2 are transferred to the electron transport chain, which is embedded in the inner membrane.

    Four protein complexes (dubbed I, II, III, and IV) make up the electron transport chain. The high-energy electrons from NADH and FADH2 are shuffled from one protein complex to the next, with each transfer releasing energy that is used to transport protons from the mitochondrial matrix across the inner membrane, establishing the proton gradient. (See figure 5.) Oxygen is the final electron acceptor in the electron transport chain. The electrons transferred to oxygen lead to the formation of a water molecule.

    Because protons are positively charged, the exterior region outside the inner membrane is positively charged and the interior region is negatively charged. The charge differential created by the proton gradient is analogous to a battery and the inner membrane is like a capacitor.

    blog__inline--molecular-logic-of-the-electron-transport-chain-5

    Figure 5: Electron Transport Chain. Image credit: Shutterstock

    The coupling of the proton gradient to ATP synthesis occurs as a result of the flow of positively charged protons through the F0 component of a protein complex called F1-F0ATPase (also embedded in the mitochondrial inner membrane). F1-F0ATPase uses this flux to convert electrochemical energy into mechanical energy that, in turn, is used to drive the formation of ATP from ADP and inorganic phosphate.

    The Molecular Logic of Proton Gradients

    So, why are chemiosmosis and proton gradients universal features of living systems? Are they an outworking of a historically contingent evolutionary process? Or is there something more at work?

    Even though proton gradients seem counterintuitive at first glance, the use of proton gradients to power the production of ATP and other cellular processes reflects an underlying ingenuity and exquisite molecular logic. Research shows that proton gradients allow the cell to efficiently extract as much energy as possible from the breakdown of glucose (and other biochemical foodstuffs).5 On the other hand, if ATP was produced exclusively by substrate-level phosphorylation, using a high-energy chemical intermediate, much of the energy liberated from the breakdown of glucose would be lost as heat.

    To understand why this is so, consider this analogy. Suppose people in a particular community receive their daily allotment of water in a 10-gallon bucket. The water they receive each day is retrieved from a reservoir with a 12-gallon bucket and then transferred to their bucket. In the process, two gallons of water is lost. Now, suppose the water from the reservoir is retrieved with a 12-gallon bucket but dumped into a secondary reservoir that has a tap. The tap allows each 10-gallon bucket to be filled without losing two gallons. Though the procedure is indirect and more complicated, using the secondary reservoir to distribute water is more efficient in the long run. In the first scenario, it takes 60 gallons of water (transferred from the reservoir in five 12-gallon buckets) to fill up five 10-gallon buckets. In the second scenario, the same amount of water transferred from the reservoir can fill six 10-gallon buckets. With each transfer, the additional two gallons accumulate in the reservoir until there is enough water to fill another 10-gallon bucket.

    With substrate-level phosphorylation, when the phosphate group is transferred from the high-energy intermediate to ADP to form ATP, excess energy released during the transfer is lost as heat. It takes 7 kcal/mole of energy to add a phosphate group to ADP to form ATP. Let’s say that the hypothetical chemical intermediate releases 10 kcal/mole when its high-energy phosphate bond is broken. Three kcal/mole of energy is lost.

    On the other hand, using the electron transport chain to build up a proton gradient is like the reservoir in our analogy. It allows that extra three kcal/mole to be stored in the proton gradient. We can think of the F1-F0ATPase as analogous to the tap. It uses 7 kcal/mole of energy released when protons flow through its channels to drive the formation of ATP from ADP and inorganic phosphate. The unused energy from the proton gradient continues to accumulate until enough energy is available to form another ATP molecule. So, in our hypothetical scenario, if the cell used substrate-level phosphorylation to make ATP, 70 molecules of the high-energy intermediate would yield 70 molecules of ATP with 210 kcal/mole of energy released as heat. But, using the electron transport chain to generate proton gradients yields 100 ATP molecules with no energy lost as heat.

    Chemiosmotic Theory and the Case for Creation

    The elegant molecular rationale that undergirds the use of proton gradients to harvest energy and to power certain cellular processes makes it unlikely that this biochemical feature reflects the outcome of a historically contingent process that just happened upon proton gradients. Instead, it points to a set of principles that underlie the structure and function of biochemical systems—principles that appear to have been set in place from the beginning of the universe.

    The most obvious and direct way for the first protocells to harvest energy would seemingly involve some type of mechanism that resembled substrate-level phosphorylation, not an indirect and more complicated mechanism that relies on proton gradients. If the origin of chemiosmosis and the use of proton gradients was, indeed, a historically contingent outcome—predicated on the fact that the first protocells just happened to employ a natural proton gradient—it seems almost eerie to think that evolutionary processes blindly stumbled upon what would later become such an elegant and efficient energy-harvesting process. And a process necessary for advanced life to be possible on Earth.

    If not for chemiosmosis, it is unlikely that eukaryotic cells and, hence, complex life such as animals, plants, and fungi, could have ever existed. Substrate-level phosphorylation just isn’t efficient enough to support the energy demands of eukaryotic organisms.

    It is also difficult to imagine how the natural proton gradients exploited by the first protocells could have been co-opted and then evolved so quickly into the complex components of the electron transport chain and F1-F0ATPase coupling mechanism found in cells that preceded LUCA. Not only are the components of the electron transport chain complex, but they have to work together in an integrated manner to establish the proton gradient across mitochondrial membranes (and the plasma membranes of bacteria and archaea). Without the existence of the F1-F0ATPase (or some other mechanism) to couple proton gradients to the synthesis of ATP, the generation of proton gradients would be for naught. The origin of the electron transport chain and F1-F0ATPase have to coincide.

    On the other hand, the ingenious use of proton gradients and the elegant molecular logic that accounts for their universal use by living systems are exactly the features I would expect if life stems from the work of a Mind. Moreover, the architecture and operation of complex I and F1-F0ATPase add to the case for creation. These two complexes are molecular motors that bear an startling similarity to man-made machines, revitalizing the Watchmaker argument for God’s existence.

    As noted, the use of proton gradients points to a set of deep, underlying principles that arise from the very nature of the universe itself and dictate how life must be. The molecular rationale that undergirds the use of proton gradients and their near-universal occurrence in living organisms suggests that proton gradients are an indispensable feature of living organisms. In other words, without the use of proton gradients to harvest energy and drive cellular processes, advanced life would not be possible. Or another way to say it: if life was discovered elsewhere in the universe, it would have to employ proton gradients to harvest energy.

    It is remarkable to think that proton gradients, which are a manifestation of the laws of nature, are, at the same time, precisely the type of system advanced life needs to exist. One way to interpret this “coincidence” is that it serves as evidence that our universe has been designed for a purpose.

    And as a Christian, I find that notion to resonate powerfully with the idea that life manifests from an intelligent Agent—namely, God.

    Resources

    Endnotes
    1. John Prebble, “Peter Mitchell and the Ox Phos Wars,” Trends in Biochemical Sciences 27 (April 1, 2002): 209–12, doi:10.1016/S0968-0004(02)02059-5.
    2. Leslie E. Orgel, “Are You Serious, Dr. Mitchell?” Nature 402 (November 4, 1999): 17, doi:10.1038/46903.
    3. Nick Lane, John F. Allen, and William Martin, “How Did LUCA Make a Living? Chemiosmosis in the Origin of Life,” Bioessays 32 (2010): 271–80, doi:10.1002/bires.200900131.
    4. Nick Lane, “Why Are Cells Powered by Proton Gradients?” Nature Education 3 (2010): 18.
    5. Nick Lane, “Bioenergetic Constraints on the Evolution of Complex Life,” Cold Spring Harbor Perspectives in Biology 6 (2014): a015982, doi:10.1101/cshperspect.a015982.
  • Electron Transport Chain Protein Complexes Rev Up the Case for a Creator

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Feb 06, 2019

    As a little kid, I spent many a Saturday afternoon “helping” my dad work on our family car. What a clunker.

    We didn’t have a garage, so we parked our car on the street in front of the house. Our home was built into a hillside and the only way to get to our house was to climb a long flight of stairs from the street.

    I wasn’t very old at the time—maybe 6 or 7—so my job was to serve as my dad’s gofer. Instead of asking me to carry his toolbox up and down the flight of stairs, he would send me back and forth when he needed a particular tool. It usually went like this: “Fuz, go get me a screwdriver.” Up and down the stairs I would go. And, when I returned: “That’s the wrong screwdriver. Get me the one with the flat head.” Again, after I returned from another roundtrip on the stairs: “No, the one with the flat head and the blue handle.” Up and down the stairs I went, but again: “Why did you bring all of the screwdrivers? Take the rest of them back up the stairs and put them in the toolbox.” By the time he finished working on our car I was frustrated and exhausted.

    Even though I didn’t have a lot of fun helping my dad, I did enjoy peering under the hood of our car. I was fascinated by the engine. From my vantage point as a little kid, the car’s engine seemed to be bewilderingly complex. And somehow my dad knew what to do to make the car run. Clearly, he understood how it was designed and assembled.

    As a graduate student, when I began studying biochemistry in earnest, I was taken aback by the bewildering complexity of the cell’s chemical systems. Like an automobile engine, the cell’s complexity isn’t haphazard, but instead displays a remarkable degree of order and organization. There is an underlying ingenuity to the way biochemical systems are put together and the way they operate. And, for the most part, biochemists have acquired a good understanding of how these systems are designed.

    Along these lines, one of the most remarkable and provocative insights into biochemical systems has been the discovery of protein complexes that serve the cell as molecular-scale machines and motors—many of which bear an eerie similarity to man-made machines. Two recent studies illustrate this stunning similarity by revealing new information about the structure and function of two protein complexes that are part of the electron transport chain: the F1-F0 ATPase and respiratory complex I. These ubiquitous protein complexes are two of the most important enzymes in biology because of the central role they play in energy-harvesting reactions.

    F1-F0 ATPase

    This well-studied protein complex plays a key role in harvesting energy for the cell to use. F1-F0 ATPase is a molecular-scale rotary motor (see figure 1). The F1 portion of the complex is mushroom-shaped and extends above the membrane’s surface. The “button of the mushroom” literally corresponds to an engine turbine. The F1-F0 ATPase turbine interacts with the part of the complex that looks like a “mushroom stalk.” This stalk-like component functions as a rotor.

     

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    Figure 1: A cartoon of the F1-F0 ATPase rotary motor. Image credit: Reasons to Believe

    Located in the inner membrane of mitochondria, F1-F0 ATPase makes use of a proton gradient across the inner membrane to drive the production of ATP (adenosine triphosphate), a high-energy compound used by the cell to power many of its operations. Because protons are positively charged, the exterior region outside the inner membrane is positively charged and the interior region is negatively charged. The charge differential created by the proton gradient is analogous to a battery and the inner membrane is like a capacitor.

    The flow of positively charged hydrogen ions through the F0 component, embedded in the cell membrane, drives the rotation of the rotor. A rod-shaped protein structure that also extends above the membrane surface serves as a stator. This protein rod interacts with the turbine, holding it stationary as the rotor rotates.

    The electrical current that flows through the channels of the F0 complex is transformed into mechanical energy, which then drives the rotor’s movement. A cam that extends at a right angle from the rotor’s surface causes displacements of the turbine. These back-and-forth motions are used to produce ATP.

    Even though biochemists have learned a lot about this protein complex, they still don’t understand some things. Recently, a team of collaborators from the US determined the path that protons take as they move through the F0 component embedded in the inner membrane.1

    To accomplish this feat, the research team trapped the enzyme complex into a single conformation by fusing the stator to the rotor. This procedure exposed the channels in the F0 complex and revealed the precise path taken by the protons as they move across the inner membrane. As protons shuttle through these channels, they trigger conformational changes that drive the rotation of the rotor by one full turn for each proton as it moves through the channel.

    Respiratory Complex I

    Respiratory complex I serves as the first enzyme complex of the electron transport chain. This complex transfers high-energy electrons from a compound called nicotinamide adenine dinucleotide (NADH) to a small molecule associated with the inner membrane of mitochondria called coenzyme Q. The high-energy electrons of NADH are captured during glycolysis and the Kreb’s cycle, two metabolic pathways involved in the breakdown of the sugar, glucose.

    During the electron-transfer process, respiratory complex I also transports four protons from the mitochondria’s interior across the inner membrane to the exterior space (figure 2). In other words, respiratory complex I helps to generate the proton gradient F1-F0 ATPase uses to generate ATP. By some estimates, respiratory complex I is responsible for establishing about 40 percent of the proton gradient across the inner membrane.

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    Figure 2: A cartoon of the electron transport chain. Image credit: Shutterstock

    Massive in size, 45 individual protein subunits comprise respiratory complex I. The subunits interact to form two arms, one embedded in the inner membrane and one extending into the mitochondrial matrix. The two arms are arranged to form an L-shaped geometry.

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    Figure 3: A cartoon of respiratory complex I. Image credit: Wikipedia

    The electron transfer process occurs in the peripheral arm that extends into the mitochondrial matrix (upward in figure 3). Conversely, the proton transport mechanism takes place in the membrane-embedded arm (to the right).

    The mechanism of proton translocation across the inner membrane served as the focus of a study conducted by a research team from Oxford University in the UK.2 These researchers discovered that proton transport across the inner membrane is driven by the machine-like behavior of respiratory complex I. The process of transferring electrons through the peripheral arm results in conformational changes (changes in shape) in this part of the complex. This conformational change drives the motion of an alpha-helix cylinder like a piston in the membrane arm of the complex. The pumping motion of the alpha-helix causes three other cylinders to tilt and, in doing so, opens up channels for protons to move through the membrane arm of the complex.

    Revitalized Watchmaker Argument

    Biochemists discovery of enzymes with machine-like domains, as exemplified by F1-F0 ATPase and respiratory complex I, revitalize the Watchmaker argument. Popularized by William Paley in the eighteenth century, this argument states that as a watch requires a watchmaker, so, too, does life require a Creator.

    This simple yet powerful analogy has been challenged by skeptics like David Hume, who assert that the necessary conclusion of a Creator, based on analogical reasoning, is only compelling if there is a high degree of similarity between the objects that form the analogy. Skeptics have long argued that nature and a watch are sufficiently dissimilar so that the conclusion drawn from the Watchmaker argument is unsound.

    But due to the striking similarity between the machine parts of these enzymes and man-made devices, the discovery of enzymes with domains that are direct analogs to man-made devices addresses this concern. Toward this end, it is provocative that the more we learn about enzyme complexes such as F1-F0 ATPase, the more its machine-like character becomes apparent. It is also thought-provoking that as biochemists study the structure and function of protein complexes, new examples of analogs to man-made machines emerge. In both cases, the Watchmaker argument receives new vitality.

    As a little kid, peering under the hood of our family car and watching my father work on the engine convinced me that some really smart people who knew what they were doing designed and built that machine. In like manner, the remarkable machine-like properties displayed by many protein complexes in the cell make it rational to conclude that life comes from the work of a Mind.

    Resources

    Endnotes
    1. Anurag P. Srivastava et al., “High-Resolution Cryo-EM Analysis of the Yeast ATP Synthase in a Lipid Membrane,” Science 360, no. 6389 (May 11, 2018), doi:10.1126/science.aas9699.
    2. Rouslan G. Efremov et al., “The Architecture of Respiratory Complex I,” Nature 465 (May 27, 2010): 441–45, doi:10.1038/nature09066.
  • Early Cave Art Supports the Image of God

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jan 30, 2019

    The J. Paul Getty Museum in Los Angeles houses one of my favorite paintings: Édouard Manet’s The Rue Mosnier with Flags.

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    Figure 1: The Getty Center. Image credit: Shutterstock

    This masterpiece depicts the Rue Mosnier (an urban street) as seen from the window of Manet’s art studio on June 30, 1878, a national holiday in France. Flags line both sides of the Rue Mosnier, decorations that are part of the day’s celebration.

    Photos of this piece of art simply don’t do it justice. When viewing the original in person, the bright colors of the flags—the whites, blues, and reds—leap off the canvas. And yet, there is an element of darkness to the painting. Meant to be viewed from left to right, the first thing the viewer sees in the corner of the painting is a disabled veteran struggling to make his way up the street. The flags on the left side of the street—though brilliantly colored—hang limp. Yet, as the viewer’s gaze moves down and across the street, the flags are depicted as flapping in the breeze. The focal point of the painting is found near the center of the piece, where two women in brilliantly white dresses disembark from a carriage.

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    Figure 2: The Rue Mosnier with Flags by Édouard Manet. Image credit: WikiArt

    Some scholars believe that through The Rue Mosnier with Flags, Manet was portraying the inequities of French society in his day. Others see the painting as communicating a sense of optimism and hope for the future as France recovered from the Franco-Prussian War (1870–71).

    Art and Symbolic Capacity

    For many people, our ability to create and contemplate art serves as a defining feature of humanity—a quality that reflects our capacity for sophisticated cognitive processes. Art is a manifestation of symbolism. Through art (as well as music and language), we express and communicate complex ideas and emotions. We accomplish this feat by representing the world—and even ideas—with symbols. And, we can manipulate symbols, embedding one within the other to create alternate possibilities.

    Because artwork reflects the capacity for symbolism and open-ended generative capacity, it has become the focal point of some very big questions in anthropology. The earliest humans produced impressive artistic displays on the cave walls of Europe that date to around 40,000 years in age—the time when humans first made their way to this part of the world.

    But when did art first appear? Did it arise after humans made their way into Europe? Did it arise in Africa before humanity began to migrate around the world? Did art emerge suddenly? Did it appear gradually? Is artistic expression unique to human beings, or did other hominins, such as Neanderthals, produce art? The answers to these questions have important implications for how we understand humanity’s origin and place in the cosmos.

    As a Christian, I view these questions as vitally important for establishing the credibility of the biblical accounts of human origins and the biblical perspective on human beings. I believe that our capacity to make art is a manifestation of the image of God. As such, the appearance of art (as well as other artifacts that reflect our capacity for symbolism) serve as a diagnostic in the archaeological record for the image of God. The archaeological record provides the means to characterize the mode and tempo of the appearance of behavior that reflects the image of God. If the biblical account of human origins is true, then I would expect that artistic expression should be unique to modern humans and should appear at the same time that we made our first appearance as a species.

    So, is artistic expression unique to modern humans? This question has generated quite a bit of controversy. Some scientific evidence indicates that Neanderthals displayed the capacity for artistic expression (and hence, the capacity for symbolism). On the other hand, a number of studies question Neanderthal capacity for art (and, consequently, symbolism). In fact, when taken as a whole, the evidence indicates that Neanderthals were cognitively inferior to modern humans. (For more details, check out the articles listed in the Resources section.)

    When did artistic expression in humans appear? Some evidence indicates that artistic expression appeared well after anatomically modern humans first appeared. To put it another way: there is evidence that anatomically modern humans appeared before behaviorally modern humans.

    On the other hand, the most recent evidence indicates that the capacity for symbolism and advanced cognition appeared much earlier than many anthropologists thought. And that time of origin is close to the time that anatomically modern humans made their first appearance, as three recent discoveries attest.

    Oldest Animal Drawings in Asia

    Cave art in Europe has been well-known and carefully investigated by archaeologists and anthropologists for nearly a century. This work gives the impression that artistic capacity appeared only after anatomically modern humans made their way into Europe—about 100,000 years after anatomically modern humans appeared on Earth. To say it another way, anatomically modern humans appeared before our advanced cognitive abilities.

    Yet, in recent years archaeologists have gained access to a growing archaeological record in Asia—and characterizing these archaeological sites changes everything. In 2014, a large team of collaborators from Australia dated hand stencils discovered on the walls of a cave in Sulawesi, Indonesia, to be between 35,000 to 40,000 years in age.1 Originally discovered in the 1950s, this artwork was initially dated to be about 10,000 years old. The team redated the art using a newly developed technique that measures the age of calcite deposits—left behind by water flowing down the cave walls—overlaying the art. (Trace amounts of radioactive uranium and thorium isotopes associated with the calcite can be used to date the mineral deposits and, thus, provide a minimum age for the artwork.)2

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    Figure 3: A modern-day re-creation of hand stencils found in the caves of Europe and Asia. Image credit: Shutterstock

    Recently, this same team applied the same technique to animal drawings in the caves of Borneo, dating one drawing to be a minimum age of 40,000 years old. They also dated hand stencils from this cave to be between 37,000 and 52,000 years in age.3

    The hand stencils and art reflect the same quality and character as the cave art found in Europe. And it is older. This discovery means that modern humans most likely had the capacity to make art before beginning their migrations around the world from out of Africa.

    Oldest Abstract Drawings in Africa

    A recent discovery by a team of anthropologists and archaeologists from the University of Witwatersrand in South Africa also supports the notion that artistic expression emerged prior to the migration of humans around the world.4 These researchers recovered a silcrete flake from a layer in the Blombos Cave that dates to about 73,000 years in age. (The Blombos Cave is located in the coastal area of South Africa, around 150 miles east of Cape Town.)

    This silcrete flake looks as if it was broken off from a grindstone used to turn ochre into a powder. The silcrete flake has a crosshatch pattern on it that appears to have been intentionally drawn using an ochre crayon. Because the crosshatch markings end abruptly, it looks like they were part of a large, abstract drawing made on the grindstone. When the researchers tried to reproduce the pattern in the lab, it required a steady hand and a determined effort.

    The Blombos Cave has previously yielded other artifacts that evince the capacity for symbolism. Additionally, the crosshatch symbol has been found etched into ochre and ostrich eggshells from other sites in South Africa. But this recent find represents the first and oldest example of the symbol having been drawn on an artifact’s surface.

    Additional Evidence for Advanced Cognition

    In addition to art, anthropologists believe that another diagnostic of cognitive complexity in humans is the manufacture and use of specialized bone tools. In 2012, researchers unearthed a bone in a cave near the Atlantic coastline of Morocco. To manufacture this knife, modern humans had to remove the rib from a herbivore and then cut it in half, lengthwise. The tool manufacturers had to then scrape and chip away the bone to give it a knife-like shape. Anthropologists believe that the manufacture of bone tools, such as this rib knife, reflects the capacity for strategic planning for future survival.

    Recently, an international team of researchers provided a detailed characterization of this tool and dated it to be around 90,000 years in age.5 This insight indicates that the capacity for advanced cognition existed (at least minimally) around 90,000 years ago.

    A Convergence of Evidence

    These recent findings signify that advanced cognitive ability, including the capacity to make art, originated close to the same time that anatomically modern humans first appear in the fossil record. In fact, (as I have written about earlier) linguist Shigeru Miyagawa believes that artistic expression emerged in Africa earlier than 125,000 years ago. Archaeologists have discovered rock art produced by the San people that dates to 72,000 years ago. This art shares certain elements with the cave art found in Europe. Because the San diverged from the modern human lineage around 125,000 years ago, the ancestral people groups that gave rise to both lines must have possessed the capacity for artistic expression before that time.

    It is also significant that the globular brain shape of modern humans first appears in the archaeological record around 130,000 years ago. As I have written previously, globular brain shape allows for the expansion of the parietal lobe, which is responsible for these capacities:

    • Perception of stimuli
    • Sensorimotor transformation (which plays a role in planning)
    • Visuospatial integration (which provides hand-eye coordination needed for throwing spears and making art)
    • Imagery
    • Self-awareness
    • Working and long-term memory

    In other words, the archaeological and fossil records increasingly indicate that anatomically and behaviorally modern humans emerged at the same time, as predicted by the biblical creation accounts.

    And, while these first humans didn’t have the luxury of spending an afternoon in an art museum contemplating artistic masterpieces, they displayed the image of God by producing art that, for them, apparently had profound meaning.

    Resources

    Endnotes
    1. M. Aubert et al., “Pleistocene Cave Art from Sulawesi, Indonesia,” Nature 514 (October 9, 2014): 223–27, doi:10.1038/nature13422.
    2. It should be noted that the dating method used by these researchers has been criticized by a number of different research teams as potentially yielding artificially high ages. Knowing this concern, the team deliberately took steps to ensure that the sampling of the art and application of the dating method took into account the dating technique’s limitations.-
    3. M. Aubert et al., “Palaeolithic Cave Art in Borneo,” Nature 564 (November 7, 2018): 254–57, doi:10.1038/s41586-018-0679-9.
    4. Christopher S. Henshilwood et al., “An Abstract Drawing from the 73,000-Year-Old Levels at Blombos Cave, South Africa,” Nature 562 (2018): 115–18, doi:10.1038/s41586-018-0514-3.
    5. Abdeljalil Bouzouggar et al., “90,000 Year-Old Specialised Bone Technology in the Aterian Middle Stone Age of North Africa,” PLoS ONE 13 (October 3, 2018):e0202021, doi:10.1371/journal.pone.0202021.
  • Does Animal Planning Undermine the Image of God?

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

    A few years ago, we had an all-white English Bulldog named Archie. He would lumber toward even complete strangers, eager to befriend them and earn their affections. And people happily obliged this playful pup.

    Archie wasn’t just an adorable dog. He was also well trained. We taught him to ring a bell hanging from a sliding glass door in our kitchen so he could let us know when he wanted to go out. He rarely would ring the bell. Instead, he would just sit by the door and wait . . . unless the neighbor’s cat was in the backyard. Then, Archie would repeatedly bang on the bell with great urgency. He had to get the cat at all costs. Clearly, he understood the bell’s purpose. He just chose to use it for his own devices.

    Anyone who has owned a cat or dog knows that these animals do remarkable things. Animals truly are intelligent creatures.

    But there are some people who go so far as to argue that animal intelligence is much more like human intelligence than we might initially believe. They base this claim, in part, on a handful of high-profile studies that indicate that some animals such as great apes and ravens can problem-solve and even plan for the future—behaviors that make them like us in some important ways.

    Great Apes Plan for the Future

    In 2006, two German anthropologists conducted a set of experiments on bonobos and orangutans in captivity that seemingly demonstrated that these creatures can plan for the future. Specifically, the test subjects selected, transported, and saved tools for use 1 hour and 14 hours later, respectively.1

    To begin the study, the researchers trained both bonobos and orangutans to use a tool to get a reward from an apparatus. In the first experiment, the researchers blocked access to the apparatus. They laid out eight tools for the apes to select—two were suitable for the task and six were unsuitable. After selecting the tools, the apes were ushered into another room where they were kept for 1 hour. The apes were then allowed back into the room and granted access to the apparatus. To gain the reward, the apes had to select the correct tool and transport it to and from the waiting area. The anthropologists observed that the apes successfully obtained the reward in 70 percent of the trials by selecting and hanging on to the correct tool as they moved from room to room.

    In the second experiment, the delay between tool selection and access to the apparatus was extended to 14 hours. This experiment focused on a single female individual. Instead of taking the test subject to the waiting room, the researchers took her to a sleeping room one floor above the waiting room before returning her to the room with the apparatus. She selected and held on to to the tool for 14 hours while she moved from room to room in 11 of the 12 trials—each time successfully obtaining the reward.

    On the basis of this study, the researchers concluded that great apes have the ability to plan for the future. They also argued that this ability emerged in the common ancestor of humans and great apes around 14 million years ago. So, even though we like to think of planning for the future as one of the “most formidable human cognitive achievements,”2 it doesn’t appear to be unique to human beings.

    Ravens Plan for the Future

    In 2017, two researchers from Lund University in Sweden demonstrated that ravens are capable of flexible planning just like the great apes.3 These cognitive scientists conducted a series of experiments with ravens, demonstrating that the large black birds can plan for future events and exert self-control for up to 17 hours prior to using a tool or bartering with humans for a reward. (Self-control is crucial for successfully planning for the future.)

    The researchers taught ravens to use a tool to gain a reward from an apparatus. As part of the training phase, the test subjects also learned that other objects wouldn’t work on the apparatus.

    In the first experiment, the ravens were exposed to the apparatus without access to tools. As such, they couldn’t gain the reward. Then the researchers removed the apparatus. One hour later, the ravens were taken to a different location and offered tools. Then, the researchers presented them with the apparatus 15 minutes later. On average, the raven test subjects selected and used tools to gain the reward in approximately 80 percent of the trials.

    In the next experiment, the ravens were trained to barter by exchanging a token for a food reward. After the training, the ravens were taken to a different location and presented with a tray containing the token and three distractor objects by a researcher who had no history of bartering with the ravens. As with the results of the tool selection experiment, the ravens selected and used the token to successfully barter for food in approximately 80 percent of the trials.

    When the scientists modified the experimental design to increase the time delay from 15 minutes to 17 hours between tool or token selection and access to the reward, the ravens successfully completed the task in nearly 90 percent of the trials.

    Next, the researchers wanted to determine if the ravens could exercise self-control as part of their planning for the future. First, they presented the ravens with trays that contained a small food reward. Of course, all of the ravens took the reward. Next, the researchers offered the ravens trays that had the food reward and either tokens or tools and distractor items. By selecting the token or the tools, the ravens were ensured a larger food reward in the future. The researchers observed that the ravens selected the tool in 75 percent of the trials and the token in about 70 percent, instead of taking the small morsel of food. After selecting the tool or token, the ravens were given the opportunity to receive the reward about 15 minutes later.

    The researchers concluded that, like the great apes, ravens can plan for the future. Moreover, these researchers argue that this insight opens up greater possibilities for animal cognition because, from an evolutionary perspective, ravens are regarded as avian dinosaurs. And mammals (including the great apes) are thought to have shared an evolutionary ancestor with dinosaurs 320 million years ago.

    Are Humans Exceptional?

    In light of these studies (and others like them), it becomes difficult to maintain that human beings are exceptional. Self-control and the ability to flexibly plan for future events is considered by many to be the cornerstone of human cognition. Planning for the future requires mental representation of temporally distant events, the ability to set aside current sensory inputs for unobservable future events, and an understanding of what current actions result in achieving a future goal.

    For many Christians, such as me, the loss of human exceptionalism is concerning because if this idea is untenable, so, too, is the biblical view of human nature. According to Scripture, human beings stand apart from all other creatures because we bear God’s image. And, because every human being possesses the image of God, every human being has intrinsic worth and value. But if, in essence, human beings are no different from animals, it is challenging to maintain that we are the crown of creation, as Scripture teaches.

    Yet recent work by biologist Johan Lind from Stockholm University (Sweden) indicates that the results of these two studies and others like them may be misleading. In effect, when properly interpreted, these studies pose no threat to human exceptionalism in any way. According to Lind, animals can engage in behavior that resembles flexible planning through a different behavior: associative learning.4 If so, this insight preserves the case for human exceptionalism and the image of God, because it means that only humans engage in genuine flexible planning for the future through higher-order cognitive processes.

    Associative Learning and Planning for the Future

    Lind points out that researchers working in artificial intelligence (AI) have long known that associative learning can produce complex behaviors in AI systems that give the appearance of having the capacity for planning. (Associative learning is the process that animals [and AI systems] use to establish an association between two stimuli or events, usually by the use of punishments or rewards.)

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    Figure 1: An illustration of associative learning in dogs. Image credit: Shutterstock

    Lind wonders why researchers studying animal cognition ignore the work in AI. Applying the insights from the work on AI systems, Lind developed mathematical models based on associative learning that he used to simulate results of the studies on the great apes and ravens. He discovered that associative learning produced the same behaviors as observed by the two research teams for the great apes and ravens. In other words, planning-like behavior can actually emerge through associative learning. That is, the same processes that give AI systems the capacity to beat humans in chess can, through associative learning, account for the planning-like behavior of animals.

    The results of Lind’s simulations mean that it is most likely that animals “plan” for the future in ways that are entirely different from humans. In effect, the planning-like behavior of animals is an outworking of associative learning. On the other hand, humans uniquely engage in bona fide flexible planning through advanced cognitive processes such as mental time travel, among others.

    Humans Are Exceptional

    Even though the idea of human exceptionalism is continually under assault, it remains intact, as the latest work by Johan Lind illustrates. When the entire body of evidence is carefully weighed, there really is only one reasonable conclusion: Human beings uniquely possess advanced cognitive abilities that make possible our capacity for symbolism, open-ended generative capacity, theory of mind, and complex social interactions—scientific descriptors of the image of God.

    Resources

    Endnotes
    1. Nicholas J. Mulcahy and Josep Call, “Apes Save Tools for Future Use,” Science 312 (May 19, 2006): 1038–40, doi:10.1126/science.1125456.
    2. Mulcahy and Call, “Apes Save Tools for Future Use.”
    3. Can Kabadayi and Mathias Osvath, “Ravens Parallel Great Apes in Flexible Planning for Tool-Use and Bartering,” Science 357 (July 14, 2017): 202–4, doi:10.1126/science.aam8138.
    4. Johan Lind, “What Can Associative Learning Do for Planning?” Royal Society Open Science 5 (November 28, 2018): 180778, doi:10.1098/rsos.180778.
  • Prebiotic Chemistry and the Hand of God

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Jan 16, 2019

    “Many of the experiments designed to explain one or other step in the origin of life are either of tenuous relevance to any believable prebiotic setting or involve an experimental rig in which the hand of the researcher becomes for all intents and purposes the hand of God.”

    Simon Conway Morris, Life’s Solution

    If you could time travel, would you? Would you travel to the past or the future?

    If asked this question, I bet many origin-of-life researchers would want to travel to the time in Earth’s history when life originated. Given the many scientifically impenetrable mysteries surrounding life’s genesis, I am certain many of the scientists working on these problems would love to see firsthand how life got its start.

    It is true, origin-of-life researchers have some access to the origin-of-life process through the fossil and geochemical records of the oldest rock formations on Earth—yet this evidence only affords them a glimpse through the glass, dimly.

    Because of these limitations, origin-of-life researchers have to carry out most of their work in laboratory settings, where they try to replicate the myriad steps they think contributed to the origin-of-life process. Pioneered by the late Stanley Miller in the early 1950s, this approach—dubbed prebiotic chemistry—has become a scientific subdiscipline in its own right.

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    Figure 1: Chemist Stanley Miller, circa 1980. Image credit: Wikipedia

    Prebiotic Chemistry

    In effect, the goals of prebiotic chemistry are threefold.

    • Proof of principle. The objective of these types of experiments is to determine—in principle—if a chemical or physical process that could potentially contribute to one or more steps in the origin-of-life pathway even exists.
    • Mechanism studies. Once processes have been identified that could contribute to the emergence of life, researchers study them in detail to get at the mechanisms undergirding these physicochemical transformations.
    • Geochemical relevance. Perhaps the most important goal of prebiotic studies is to establish the geochemical relevance of the physicochemical processes believed to have played a role in life’s start. In other words, how well do the chemical and physical processes identified and studied in the laboratory translate to early Earth’s conditions?

    Without question, over the last 6 to 7 decades, origin-of-life researchers have been wildly successful with respect to the first two objectives. It is safe to say that origin-of-life investigators have demonstrated that—in principle—the chemical and physical processes needed to generate life through chemical evolutionary pathways exist.

    But when it comes to the third objective, origin-of-life researchers have experienced frustration—and, arguably, failure.

    Researcher Intervention and Prebiotic Chemistry

    In an ideal world, humans would not intervene at all in any prebiotic study. But this ideal isn’t possible. Researchers involve themselves in the experimental design out of necessity, but also to ensure that the results of the study are reproducible and interpretable. If researchers don’t set up the experimental apparatus, adjust the starting conditions, add the appropriate reactants, and analyze the product, then by definition the experiment would never happen. Utilizing carefully controlled conditions and chemically pure reagents is necessary for reproducibility and to make sense of the results. In fact, this level of control is essential for proof-of-principle and mechanistic prebiotic studies—and perfectly acceptable.

    However, when it comes to prebiotic chemistry’s third goal, geochemical relevance, the highly controlled conditions of the laboratory become a liability. Here researcher intervention becomes potentially unwarranted. It goes without saying that the conditions of early Earth were uncontrolled and chemically and physically complex. Chemically pristine and physically controlled conditions didn’t exist. And, of course, origin-of-life researchers weren’t present to oversee the processes and guide them to their desired end. Yet, it is rare for prebiotic simulation studies to fully take the actual conditions of early Earth into account in the experimental design. It is rarer for origin-of-life investigators to acknowledge this limitation.

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    Figure 2: Laboratory technician. Image credit: Shutterstock

    This complication means that many prebiotic studies designed to simulate processes on early Earth seldom accomplish anything of the sort due to excessive researcher intervention. Yet, it isn’t always clear when examining an experimental design if researcher involvement is legitimate or unwarranted.

    As I point out in my book Creating Life in the Lab (Baker, 2011), one main reason for the lack of progress relates to the researcher’s role in the experimental design—a role not often recognized when experimental results are reported. Origin-of-life investigator Clemens Richert from the University of Stuttgart in Germany now acknowledges this very concern in a recent comment piece published by Nature Communications.1

    As Richert points out, the role of researcher intervention and a clear assessment of geochemical relevance is rarely acknowledged or properly explored in prebiotic simulation studies. To remedy this problem, Richert calls for origin-of-life investigators to do three things when they report the results of prebiotic studies.

    • State explicitly the number of instances in which researchers engaged in manual intervention.
    • Describe precisely the prebiotic scenario a particular prebiotic simulation study seeks to model.
    • Reduce the number of steps involving manual intervention in whatever way possible.

    Still, as Richert points out, it is not possible to provide a quantitative measure (a score) of geochemical relevance. And, hence, there will always be legitimate disagreement about the geochemical relevance of any prebiotic experiment.

    Yet, Richert’s commentary represents an important first step toward encouraging more realistic prebiotic simulation studies and a more cautious approach to interpreting the results of these studies. Hopefully, it will also lead to a more circumspect assessment on the importance of these types of studies for accounting for the various steps in the origin-of-life process.

    Researcher Intervention and the Hand of God

    One concern not addressed by Richert in his commentary piece is the fastidiousness of many of the physicochemical transformations origin-of-life researchers deem central to chemical evolution. As I discuss in Creating Life in the Lab, mechanistic studies indicate that these processes are often dependent upon exacting conditions in the laboratory. To put it another way, these processes only take place—even under the most ideal laboratory conditions—because of human intervention. As a corollary, these processes would be unproductive on early Earth. They often require chemically pristine conditions, unrealistically high concentrations of reactants, carefully controlled order of additions, carefully regulated temperature, pH, salinity levels, etc.

    As Richert states, “It’s not easy to see what replaced the flasks, pipettes, and stir bars of a chemistry lab during prebiotic evolution, let alone the hands of the chemist who performed the manipulations. (And yes, most of us are not comfortable with the idea of divine intervention.)”2

    Sadly, since I made the point about researcher intervention nearly a decade ago, it has often been ignored, dismissed, and even ridiculed by many in the scientific community—simply because I have the temerity to think that a Creator brought life into existence.

    Even though Richert and his many colleagues in the origin-of-life research community do whatever they can to eschew a Creator’s role in the origin-of-life, could it be that abiogenesis (life from nonlife) required the hand of God—divine intervention?

    I would argue that this conclusion follows from nearly seven decades of work in prebiotic chemistry and the consistent demonstration of the central role that origin-of-life researchers play in the success of prebiotic simulation studies. It is becoming increasingly evident for whoever will “see” that the hand of the researcher serves as the analog for the hand of God.

    Resources

    Endnotes
    1. Clemens Richert, “Prebiotic Chemistry and Human Intervention,” Nature Communications 9 (December 12, 2018): 5177, doi:10.1038/s41467-018-07219-5.
    2. Richert, “Prebiotic Chemistry.
  • Long Noncoding RNAs Extend the Case for Creation

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

    I don’t like to think of myself as technology-challenged, but I am beginning to wonder if I just might be. As a case in point, I have no clue about all the things my iPhone can do. It isn’t uncommon for someone (usually much younger than me) to point out features of my iPhone that I didn’t even know existed. (And, of course, there is the TV remote—but that will have to serve as material for another lead.)

    The human genome is a lot like my iPhone. The more the scientific community learns about it, the more complex it becomes and the more functionality it displays—functionality about which no one in the scientific community had a clue. It has become commonplace for scientists to discover that features of the human genome—long thought to be useless vestiges of an evolutionary history—actually serve a critical role in the structure and function of the genome.

    Long noncoding RNAs (lncRNAs) illustrate this point nicely. This broad category of RNA molecules consists of transcripts (where genetic information is transferred from DNA to messenger RNA) that are over 200 nucleotides in length but are not translated into proteins.

    Though numbers vary from source to source, estimates indicate that somewhere between 60 to 90 percent of the human genome is transcribed. Yet only 2 percent of the genome consists of transcripts that are directly used to produce proteins. Of the transcripts that are untranslated, researchers estimate that somewhere between 60,000 to 120,000 of the transcripts are noncoding RNAs. Researchers categorize these transcripts as microRNAs (miRNAs), piwi-interacting RNAs (piwiRNAs), small interfering RNAs (siRNAs) and lncRNAs. The first three types of RNAs are relatively small in size and play a role in regulating gene expression.

    blog__inline--long-noncoding-rnas-1

    Figure 1: Transcription and Translation. Image credit: Shutterstock

    Initially, researchers thought for the most part that lncRNAs were transcriptional noise—junk. But this view has changed in recent years. Evidence continues to accrue demonstrating that lncRNAs play a wide range of roles in the cell.1 And as evidence for the utility of lncRNAs mounts, the case for the design of the human genome expands.

    The Functional Utility of Long Noncoding RNAs

    As it turns out, lncRNAs are extremely versatile molecules that can interact with: (1) other RNA molecules, (2) DNA, (3) proteins, and (4) cell membranes. This versatility opens up the possibility that these molecules play a diverse role in cellular metabolism.

    Recently, Harry Krause, a molecular geneticist from the University of Toronto, published two review articles summarizing the latest insights into lncRNA function. These insights, including the four to follow, demonstrate the functional pervasiveness of the transcripts.

    lncRNAs regulate gene expression. lncRNAs influence gene expression by a variety of mechanisms. One is through interactions with other transcripts forming RNA-RNA duplexes that typically interfere with translation of protein-coding messenger RNAs.

    Researchers have recently learned that lncRNAs can also influence gene expression by interacting with DNA. These interactions result in either: (1) a triple helix, made up of two DNA strands intertwined with one RNA strand, or (2) a double helix with the lncRNA intertwined with one of the DNA strands, leaving the other exposed as a single strand. When these duplexes form, the lncRNA forms a hairpin loop that can either indiscriminately or selectively attract transcription factors.

    blog__inline--long-noncoding-rnas-2

    Figure 2: A Hairpin Loop. Image credit: Wikipedia

    Though researchers are still learning about the role lncRNAs play in gene regulation, these varied interactions with DNA and proteins suggest that lncRNAs may influence gene expression through a variety of mechanisms.

    lncRNAs form microbodies within the nucleus and cytoplasm. A second function recognizes that lncRNAs interact with proteins to form hydrogel-like structures in the nucleus and cytoplasm. These structures are dense and heavily cross-linked subcellular structures that serve as functionally specific regions without a surrounding membrane. (In a sense, the microbodies could be viewed as somewhat analogous to ribosomes, the protein-RNA complexes that synthesize proteins.) In the nucleus, microbodies play a role in transcriptional processing, storage, and stress response. In the cytoplasm, microbodies play a role in storage, processing, and trafficking.

    lncRNAs interact with cell membranes. A third role stems from laboratory studies where lncRNAs have been shown to interact with model cell membranes. Such interactions suggest that lncRNAs may play a role in mediating biochemical processes that take place at cell membranes. Toward this end, researchers have recently observed certain lncRNA species interacting with phosphatidylinositol 3,4,5-triphosphate. This cell membrane component plays a central role in signal transduction inside cells.

    lncRNAs are associated with exosomes. Finally, lncRNAs have been found inside membrane-bound vesicles that are secreted by cells (called exosomes). These vesicles mediate cell-cell communication.

    In short, the eyes of the scientific community have been opened. And they now see the functional importance and functional diversity of lncRNAs. Given the trend line, it seems reasonable to think that the functional range of lncRNAs will only expand as researchers continue to study the human genome (and genomes of other organisms).

    The growing recognition of the functional versatility of lncRNAs aligns with studies demonstrating that other regions of the genome—long thought to be nonfunctional—do, in fact, play key roles in gene expression and other facets of cellular metabolism. Most significantly, toward this end, the functional versatility of lncRNAs supports the conclusions of the ENCODE Project—conclusions that have been challenged by some people in the scientific community.

    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, the ENCODE Project, reported phase II results in the fall of 2012. (Currently, ENCODE is in phase IV.) To the surprise of many, the ENCODE Project reported that around 80 percent of the human genome displays biochemical activity—hence, function—with the expectation that this percentage should increase as results from phases III and IV of the project are reported.

    The ENCODE results have generated quite a bit of controversy. One of the most prominent complaints about the ENCODE conclusions relates to the way the consortium determined biochemical function. Critics argue that ENCODE scientists conflated biochemical activity with function. As a case in point, the critics argue that most of the transcripts produced by the human genome (which include lncRNAs) must be biochemical noise. This challenge flows out of predictions of the evolutionary paradigm. Yet, it is clear that the transcripts produced by the human genome are functional, as numerous studies on the functional significance of lncRNAs attest. In other words, the biochemical activity detected by ENCODE equates to biochemical function—at least with respect to transcription.

    A New View of Genomes

    These types of insights are radically changing scientists view of the human genome. Rather than a wasteland of junk DNA sequences stemming from the vestiges of an evolutionary history, genomes appear to be incredibly complex, sophisticated biochemical systems, with most of the genome serving useful and necessary functions.

    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 percent of the human genome consists of junk DNA. That acknowledgment seemingly provided compelling evidence that humans must be the product of an evolutionary history.

    Nearly 15 years later the evidence suggests that the more we learn about the structure and function of genomes, the more elegant and sophisticated they appear to be. It is quite possible that most of the human genome is functional.

    For creationists and intelligent design proponents, this changing view of the human genome—similar to discovering exciting new features of an iPhone—provides reasons to think that it is the handiwork of our Creator. A skeptic might ask, Why would a Creator make genomes littered with so much junk? But if a vast proportion of genomes consists of functional sequences, this challenge no longer carries weight and it becomes more and more reasonable to interpret genomes from within a creation model/intelligent design framework.

    Resources

    Endnotes
    1. Allison Jandura and Henry M. Krause, “The New RNA World: Growing Evidence for Long Noncoding RNA Functionality,” Trends in Genetics 33 (October 1, 2017): 665– 76, doi:10.1016/j.tig.2017.08.002; Henry M. Krause, “New and Prospective Roles for lncRNAs in Organelle Formation and Function,” Trends in Genetics 34 (October 1, 2018): 736–45, doi:10.1016/j.tig.2018.06.005.
  • Soft Tissue Preservation Mechanism Stabilizes the Case for Earth’s Antiquity

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Dec 19, 2018

    One of the highlights of the year at Reasons to Believe (well, it’s a highlight for some of us, anyway) is the white elephant gift exchange at our staff Christmas party. It is great fun to laugh together as a staff as we take turns unwrapping gifts—some cheesy, some useless, and others highly prized—and then “stealing” from one another those two or three gifts that everyone seems to want.

    Over the years, I have learned a few lessons about choosing a white elephant gift to unwrap. Avoid large gifts. If the gift is a dud, large items are more difficult to find a use for than small ones. Also, more often than not, the most beautifully wrapped gifts turn out to be the biggest letdowns of all.

    Giving and receiving gifts isn’t just limited to Christmas. People exchange all types of gifts with one another for all sorts of reasons.

    Gifting is even part of the scientific enterprise—with the gifts taking on the form of scientific discoveries and advances. Many times, discoveries lead to new beneficial insights and technologies—gifts for humanity. Other times, these breakthroughs are gifts for scientists, signaling a new way to approach a scientific problem or opening up new vistas of investigation.

    Soft Tissue Remnants Preserved in Fossils

    One such gift was given to the scientific community over a decade ago by Mary Schweitzer, a paleontologist at North Carolina State University. Schweitzer and her team of collaborators recovered flexible, hollow, and transparent blood vessels from the remains of a T. rex specimen after removing the mineral component of the fossil.1 These blood vessels harbored microstructures with a cell-like morphology (form and structure) that she and her collaborators interpreted to be the remnants of red blood cells. This work showed conclusively that soft tissue materials could be preserved in fossil remains.

    Though unexpected, the discovery was a landmark achievement for paleontology. Since Schweitzer’s discovery, paleontologists have unearthed the remnants of all sorts of soft tissue materials from fossils representing a wide range of organisms. (For a catalog of some of these finds, see my book Dinosaur Blood and the Age of the Earth.)

    With access to soft tissue materials in fossils, paleontologists have a new window into the biology of Earth’s ancient life.

    The Scientific Case for a Young Earth

    Some Christians also saw Schweitzer’s discovery as a gift. But for them the value of this scientific present wasn’t the insight it provides about past life on Earth. Instead, they viewed this discovery (and others like it) as evidence that the earth must be no more than a few thousand years old. From a young-earth creationist (YEC) perspective, the survival of soft tissue materials in fossils indicates that these remains can’t be millions of years old. As a case in point, at the time Schweitzer reported her findings, John Morris, a young-earth proponent from the Institute for Creation Research, wrote:

    Indeed, it is hard to imagine how soft tissue could have lasted even 5,000 years or so since the Flood of Noah’s day when creationists propose the dinosaur was buried. Such a thing could hardly happen today, for soft tissue decays rather quickly under any condition.2

    In other words, from a YEC perspective, it is impossible for fossils to contain soft tissue remnants and be millions of years old. Soft tissues shouldn’t survive that long; they should readily degrade in a few thousand years. From a YEC view, soft tissue discoveries challenge the reliability of radiometric dating methods used to determine the fossils’ ages and, consequently, Earth’s antiquity. Furthermore, these breakthrough discoveries provide compelling scientific evidence for a young earth and support the idea that the fossil record results from a recent global (worldwide) flood.

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

    Preservation of Soft Tissues in Fossil Remains

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

    In Dinosaur Blood and the Age of the Earth, I describe several mechanisms that likely promote soft tissue survival. Since the book’s publication (2016), researchers have deepened their understanding of the processes that make it possible for soft tissues to survive. The recent work of an international team of collaborators headed by researchers from Yale University provides an example of this growing insight.3

    These researchers discovered that the deposition environment during the fossilization process plays a significant role in soft tissue preservation, and they have identified the chemical reactions that contribute to this preservation. The team examined 24 specimens of biomineralized vertebrate tissues ranging in age from modern to the Late Jurassic (approximately 163–145 million years ago) time frame. These specimens were taken from both chemically oxidative and reductive environments.

    After demineralizing the samples, the researchers discovered that all modern specimens yielded soft tissues. However, demineralization only yielded soft tissues for fossils formed under oxidative conditions. Fossils formed under reductive conditions failed to yield any soft tissue material, whatsoever. The soft tissues from the oxidative settings (which included extracellular matrices, cell remnants, blood vessel remnants, and nerve materials) were stained brown. Researchers noted that the brown color of the soft tissue materials increased in intensity as a function of the fossil’s age, with older specimens displaying greater browning than younger specimens.

    The team was able to reproduce this brown color in soft tissues taken from modern-day specimens by heating the samples and exposing them to air. This process converted the soft tissues from translucent white to brown in appearance.

    Using Raman spectroscopy, the researchers detected spectral signatures for proteins and N-heterocycle pyridine rings in the soft tissue materials. They believe that the N-heterocycle pyridine rings arise from the formation of advanced glycoxidation end-products (AGEs) and advanced lipoxidation end-products (ALEs). AGEs and ALEs are the by-products of the reactions that take place between proteins and sugars (AGEs) and proteins and lipids or fats (ALEs). (As an aside, AGEs and ALEs form when foods are cooked, and they occur at high levels when food is burnt, giving overly cooked foods their brownish color.) The researchers noted that spectral features for N-heterocycle pyridine rings become more prominent for soft tissues isolated from older fossil specimens, with the spectral features for the proteins becoming less pronounced.

    AGEs and ALEs are heavily cross-linked compounds. This chemical property makes them extremely difficult to break down once they form. In other words, the formation of AGEs and ALEs in soft tissue remnants delays their decomposition long enough for mineral entombment to take place.

    Iron from the environment or released from red blood cells promotes the formation of AGEs and ALEs. So do alkaline conditions.

    In addition to stabilizing soft tissues from degradation because of the cross-links, AGEs and ALEs protect adjacent proteins from breakdown because of their hydrophobic (water repellent) nature. Water promotes soft tissue breakdown through a chemical process called hydrolysis. But because AGEs and ALEs are hydrophobic, they inhibit the hydrolytic reactions that would otherwise break down proteins that escape glycoxidation and lipoxidation reactions.

    Finally, AGEs and ALEs are also resistant to microbial attack, further adding to the stability of the soft tissue materials. In other words, soft tissue materials recovered from fossil specimens are not the original, intact material, because they have undergone extensive chemical alteration. As it turns out, this alteration stabilized the soft tissue remnants long enough for mineral entombment to occur.

    In short, this research team has made significant strides toward understanding the process by which soft tissue materials become preserved in fossil remains. The recovery of soft tissue materials from the ancient fossil remains makes perfect sense within an old-earth framework. These insights also undermine what many people believe to be one of the most compelling scientific arguments for a young earth.

    Why Does It Matter?

    In my experience, many skeptics and seekers alike reject Christian truth claims because of the misperception that Genesis 1 teaches that the earth is only 6,000 years old. This misperception becomes reinforced by vocal (and well-meaning) YECs who not only claim the only valid interpretation of Genesis 1 is the calendar-day view, but also maintain that ample scientific evidence—such as the recovery of soft tissue remnants in fossils—exists for a young earth.

    Yet, as the latest work headed by scientists from Yale University demonstrates, soft tissue remnants associated with fossils find a ready explanation from an old-earth standpoint. It has been a gift to science that advances understanding of a sophisticated process.

    Unfortunately, for YECs the fossil-associated soft tissues have turned out to be little more than a bad white elephant gift.

    Resources:

    Endnotes
    1. Mary H. Schweitzer et al., “Soft-Tissue Vessels and Cellular Preservation in Tyrannosaurus rex,” Science 307 (March 25, 2005): 1952–55, doi:10.1126/science.1108397.
    2. John D. Morris, “Dinosaur Soft Parts,” Acts & Facts (June 1, 2005), icr.org/article/2032/.
    3. Jasmina Wiemann et al., “Fossilization Transforms Vertebrate Hard Tissue Proteins into N-Heterocyclic Polymers,” Nature Communications 9 (November 9, 2018): 4741, doi:10.1038/s41467-018-07013-3.
  • Endosymbiont Hypothesis and the Ironic Case for a Creator

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Dec 12, 2018

    i ·ro ·ny

    1. The use of words to express something different from and often opposite to their literal meaning.
    2. Incongruity between what might be expected and what actually occurs.

    —The Free Dictionary

    People often use irony in humor, rhetoric, and literature, but few would think it has a place in science. But wryly, this has become the case. Recent work in synthetic biology has created a real sense of irony among the scientific community—particularly for those who view life’s origin and design from an evolutionary framework.

    Increasingly, life scientists are turning to synthetic biology to help them understand how life could have originated and evolved. But, they have achieved the opposite of what they intended. Instead of developing insights into key evolutionary transitions in life’s history, they have, ironically, demonstrated the central role intelligent agency must play in any scientific explanation for the origin, design, and history of life.

    This paradoxical situation is nicely illustrated by recent work undertaken by researchers from Scripps Research (La Jolla, CA). Through genetic engineering, the scientific investigators created a non-natural version of the bacterium E. coli. This microbe is designed to take up permanent residence in yeast cells. (Cells that take up permanent residence within other cells are referred to as endosymbionts.) They hope that by studying these genetically engineered endosymbionts, they can gain a better understanding of how the first eukaryotic cells evolved. Along the way, they hope to find added support for the endosymbiont hypothesis.1

    The Endosymbiont Hypothesis

    Most biologists believe that the endosymbiont hypothesis (symbiogenesis) best explains one of the key transitions in life’s history; namely, the origin of complex cells from bacteria and archaea. Building on the ideas of Russian botanist Konstantin Mereschkowski, Lynn Margulis (1938–2011) advanced the endosymbiont hypothesis in the 1960s to explain the origin of eukaryotic cells.

    Margulis’s work has become an integral part of the evolutionary paradigm. Many life scientists 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 this hypothesis, complex cells originated when symbiotic relationships formed among single-celled microbes after free-living bacterial and/or archaeal cells were engulfed by a “host” microbe. Presumably, organelles such as mitochondria were once endosymbionts. Evolutionary biologists believe that once engulfed by the host cell, the endosymbionts took up permanent residency, with the endosymbiont growing and dividing inside the host.

    Over time, the endosymbionts and the host became mutually interdependent. Endosymbionts provided a metabolic benefit for the host cell—such as an added source of ATP—while the host cell provided nutrients to the endosymbionts. Presumably, 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.

    blog__inline--endosymbiont-hypothesis-and-the-ironic-case-for-a-creator-1

    Figure 1: Endosymbiont hypothesis. Image credit: Wikipedia.

    Life scientists point to a number of similarities between mitochondria and alphaproteobacteria as evidence for the endosymbiont hypothesis. (For a description of the evidence, see the articles listed in the Resources section.) Nevertheless, they don’t understand how symbiogenesis actually occurred. To gain this insight, scientists from Scripps Research sought to experimentally replicate the earliest stages of mitochondrial evolution by engineering E. coli and brewer’s yeast (S. cerevisiae) to yield an endosymbiotic relationship.

    Engineering Endosymbiosis

    First, the research team generated a strain of E. coli that no longer has the capacity to produce the essential cofactor thiamin. They achieved this by disabling one of the genes involved in the biosynthesis of the compound. Without this metabolic capacity, this strain becomes dependent on an exogenous source of thiamin in order to survive. (Because the E. coli genome encodes for a transporter protein that can pump thiamin into the cell from the exterior environment, it can grow if an external supply of thiamin is available.) When incorporated into yeast cells, the thiamin in the yeast cytoplasm becomes the source of the exogenous thiamin, rendering E. coli dependent on the yeast cell’s metabolic processes.

    Next, they transferred the gene that encodes a protein called ADP/ATP translocase into the E. coli strain. This gene was harbored on a plasmid (which is a small circular piece of DNA). Normally, the gene is found in the genome of an endosymbiotic bacterium that infects amoeba. This protein pumps ATP from the interior of the bacterial cell to the exterior environment.2

    The team then exposed yeast cells (that were deficient in ATP production) to polyethylene glycol, which creates a passageway for E. coli cells to make their way into the yeast cells. In doing so, E. coli becomes established as endosymbionts within the yeast cells’ interior, with the E. coli providing ATP to the yeast cell and the yeast cell providing thiamin to the bacterial cell.

    Researchers discovered that once taken up by the yeast cells, the E. coli did not persist inside the cell’s interior. They reasoned that the bacterial cells were being destroyed by the lysosomal degradation pathway. To prevent their destruction, the research team had to introduce three additional genes into the E. coli from three separate endosymbiotic bacteria. Each of these genes encodes proteins—called SNARE-like proteins—that interfere with the lysosomal destruction pathway.

    Finally, to establish a mutualistic relationship between the genetically-engineered strain of E. coli and the yeast cell, the researchers used a yeast strain with defective mitochondria. This defect prevented the yeast cells from producing an adequate supply of ATP. Because of this limitation, the yeast cells grow slowly and would benefit from the E. coli endosymbionts, with the engineered capacity to transport ATP from their cellular interior to the exterior environment (the yeast cytoplasm.)

    The researchers observed that the yeast cells with E. coli endosymbionts appeared to be stable for 40 rounds of cell doublings. To demonstrate the potential utility of this system to study symbiogenesis, the research team then began the process of genome reduction for the E. coli endosymbionts. They successively eliminated the capacity of the bacterial endosymbiont to make the key metabolic intermediate NAD and the amino acid serine. These triply-deficient E. coli strains survived in the yeast cells by taking up these nutrients from the yeast cytoplasm.

    Evolution or Intentional Design?

    The Scripps Research scientific team’s work is impressive, exemplifying science at its very best. They hope that their landmark accomplishment will lead to a better understanding of how eukaryotic cells appeared on Earth by providing the research community with a model system that allows them to probe the process of symbiogenesis. It will also allow them to test the various facets of the endosymbiont hypothesis.

    In fact, I would argue that this study already has made important strides in explaining the genesis of eukaryotic cells. But ironically, instead of proffering support for an evolutionary origin of eukaryotic cells (even though the investigators operated within the confines of the evolutionary paradigm), their work points to the necessary role intelligent agency must have played in one of the most important events in life’s history.

    This research was executed by some of the best minds in the world, who relied on a detailed and comprehensive understanding of biochemical and cellular systems. Such knowledge took a couple of centuries to accumulate. Furthermore, establishing mutualistic interactions between the two organisms required a significant amount of ingenuity—genius that is reflected in the experimental strategy and design of their study. And even at that point, execution of their experimental protocols necessitated the use of sophisticated laboratory techniques carried out under highly controlled, carefully orchestrated conditions. To sum it up: intelligent agency was required to establish the endosymbiotic relationship between the two microbes.

    blog__inline--endosymbiont-hypothesis-and-the-ironic-case-for-a-creator-2

    Figure 2: Lab researcher. Image credit: Shutterstock.

    Or, to put it differently, the endosymbiotic relationship between these two organisms was intelligently designed. (All this work was necessary to recapitulate only the presumed first step in the process of symbiogenesis.) This conclusion gains added support given some of the significant problems confronting the endosymbiotic hypothesis. (For more details, see the Resources section.) By analogy, it seems reasonable to conclude that eukaryotic cells, too, must reflect the handiwork of a Divine Mind—a Creator.

    Resources

    Endnotes
    1. Angad P. Mehta et al., “Engineering Yeast Endosymbionts as a Step toward the Evolution of Mitochondria,” Proceedings of the National Academy of Sciences, USA 115 (November 13, 2018): doi:10.1073/pnas.1813143115.
    2. ATP is a biochemical that stores energy used to power the cell’s operation. Produced by mitochondria, ATP is one of the end products of energy harvesting pathways in the cell. The ATP produced in mitochondria is pumped into the cell’s cytoplasm from within the interior of this organelle by an ADP/ATP transporter.
  • Did Neanderthals Start Fires?

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Dec 05, 2018

    It is one of the most iconic Christmas songs of all time.

    Written by Bob Wells and Mel Torme in the summer of 1945, “The Christmas Song (subtitled “Chestnuts Roasting on an Open Fire”) was crafted in less than an hour. As the story goes, Wells and Torme were trying to stay cool during the blistering summer heat by thinking cool thoughts and then jotting them down on paper. And, in the process, “The Christmas Song” was born.

    Many of the song’s lyrics evoke images of winter, particularly around Christmastime. But none has come to exemplify the quiet peace of a Christmas evening more than the song’s first line, “Chestnuts roasting on an open fire . . . ”

    Gathering around the fire to stay warm, to cook food, and to share in a community has been an integral part of the human experience throughout history—including human prehistory. Most certainly our ability to master fire played a role in our survival as a species and in our ability as human beings to occupy and thrive in some of the world’s coldest, harshest climates.

    But fire use is not limited only to modern humans. There is strong evidence that Neanderthals made use of fire. But, did these creatures have control over fire in the same way we do? In other words, did Neanderthals master fire? Or, did they merely make opportunistic use of natural fires? These questions are hotly debated by anthropologists today and they contribute to a broader discussion about the cognitive capacity of Neanderthals. Part of that discussion includes whether these creatures were cognitively inferior to us or whether they were our intellectual equals.

    In an attempt to answer these questions, a team of researchers from the Netherlands and France characterized the microwear patterns on bifacial (having opposite sides that have been worked on to form an edge) tools made from flint recovered from Neanderthal sites, and concluded that the wear patterns suggest that these hominins used pyrite to repeatedly strike the flint. This process generates sparks that can be used to start fires.1 To put it another way, the researchers concluded that Neanderthals had mastery over fire because they knew how to start fires.

    blog__inline--did-neanderthals-start-fires-1

    Figure 1: Biface tools for cutting or scraping. Image credit: Shutterstock

    However, a closer examination of the evidence along with results of other studies, including recent insight into the cause of Neanderthal extinction, raises significant doubts about this conclusion.

    What Do the Microwear Patterns on Flint Say?

    The investigators focused on the microwear patterns of flint bifaces recovered from Neanderthal sites as a marker for fire mastery because of the well-known practice among hunter-gatherers and pastoralists of striking flint with pyrite (an iron disulfide mineral) to generate sparks to start fires. Presumably, the first modern humans also used this technique to start fires.

    blog__inline--did-neanderthals-start-fires-2

    Figure 2: Starting a fire with pyrite and flint. Image credit: Shutterstock

    The research team reasoned that if Neanderthals started fires, they would use a similar tactic. Careful examination of the microwear patterns on the bifaces led the research team to conclude that these tools were repeatedly struck by hard materials, with the strikes all occurring in the same direction along the bifaces’ long axis.

    The researchers then tried to experimentally recreate the microwear pattern in a laboratory setting. To do so, they struck biface replicas with a number of different types of materials, including pyrites, and concluded that the patterns produced by the pyrite strikes most closely matched the patterns on the bifaces recovered from Neanderthal sites. On this basis, the researchers claim that they have found evidence that Neanderthals deliberately started fires.

    Did Neanderthals Master Fire?

    While this conclusion is possible, at best this study provides circumstantial, not direct, evidence for Neanderthal mastery of fire. In fact, other evidence counts against this conclusion. For example, bifaces with the same type of microwear patterns have been found at other Neanderthal sites, locales that show no evidence of fire use. These bifaces would have had a range of usages, including butchery of the remains of dead animals. So, it is possible that these tools were never used to start fires—even at sites with evidence for fire usage.

    Another challenge to the conclusion comes from the failure to detect any pyrite on the bifaces recovered from the Neanderthal sites. Flint recovered from modern human sites shows visible evidence of pyrite. And yet the research team failed to detect even trace amounts of pyrite on the Neanderthal bifaces during the course of their microanalysis.

    This observation raises further doubt about whether the flint from the Neanderthal sites was used as a fire starter tool. Rather, it points to the possibility that Neanderthals struck the bifaces with materials other than pyrite for reasons not yet understood.

    The conclusion that Neanderthals mastered fire also does not square with results from other studies. For example, a careful assessment of archaeological sites in southern France occupied by Neanderthals from about 100,000 to 40,000 years ago indicates that Neanderthals could not create fire. Instead, these hominins made opportunistic use of natural fire when it was available to them.2

    These French sites do show clear evidence of Neanderthal fire use, but when researchers correlated the archaeological layers displaying evidence for fire use with the 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 mastered fire.

    Lightning strikes that would generate natural fires are much more likely to occur during warm periods. Instead of creating fire, Neanderthals most likely harnessed natural fire and cultivated it as long as they could before it extinguished.

    Another study also raises questions about the ability of Neanderthals to start fires.3 This research indicates that cold climates triggered Neanderthal extinctions. By studying the chemical composition of stalagmites in two Romanian caves, an international research team concluded that there were two prolonged and extremely cold periods between 44,000 and 40,000 years ago. (The chemical composition of stalagmites varies with temperature.)

    The researchers also noted that during these cold periods, the archaeological record for Neanderthals disappears. They interpret this disappearance to reflect a dramatic reduction in Neanderthal population numbers. Researchers speculate that when this population downturn took place during the first cold period, modern humans made their way into Europe. Being better suited for survival in the cold climate, modern human numbers increased. When the cold climate mitigated, Neanderthals were unable to recover their numbers because of the growing populations of modern humans in Europe. Presumably, after the second cold period, Neanderthal numbers dropped to the point that they couldn’t recover, and hence, became extinct.

    But why would modern humans be more capable than Neanderthals of surviving under extremely cold conditions? It seems as if it should be the other way around. Neanderthals had a hyper-polar body design that made them ideally suited to withstand cold 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. But, despite this advantage, Neanderthals died out and modern humans thrived.

    Some anthropologists believe that the survival discrepancy could be due to dietary differences. Some data indicates that modern humans had a more varied diet than Neanderthals. Presumably, these creatures primarily consumed large herbivores—animals that disappeared when the climatic conditions turned cold, thereby threatening Neanderthal survival. On the other hand, modern humans were able to adjust to the cold conditions by shifting their diets.

    But could there be a different explanation? Could it be that with their mastery of fire, modern humans were able to survive cold conditions? And did Neanderthals die out because they could not start fires?

    Taken in its entirety, the data seems to indicate that Neanderthals lacked mastery of fire but could use it opportunistically. And, in a broader context, the data indicates that Neanderthals were cognitively inferior to humans.

    What Difference Does It Make?

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

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

    Yet, claims that Neanderthals are cognitive equals to modern humans fail to withstand scientific scrutiny, time and time, again. Now it’s time to light a fire in my fireplace and enjoy a few contemplative moments thinking about the real meaning of Christmas.

    Resources

    Endnotes
    1. A. C. Sorensen, E. Claud, and M. Soressi, “Neanderthal Fire-Making Technology Inferred from Microwear Analysis,” Scientific Reports 8 (July 19, 2018): 10065, doi:10.1038/s41598-018-28342-9.
    2. 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 Neandertal 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.
    3. Michael Staubwasser et al., “Impact of Climate Change on the Transition of Neanderthals to Modern Humans in Europe,” Proceedings of the National Academy of Sciences, USA 115 (September 11, 2018): 9116–21, doi:10.1073/pnas.1808647115.
  • Spider Silk Inspires New Technology and the Case for a Creator

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Nov 28, 2018

    Mark your calendars!

    On December 14th (2018), Columbia Pictures—in collaboration with Sony Pictures Animation—will release a full-length animated feature: Spider-Man: Into the Spider-Verse. The story features Miles Morales, an Afro-Latino teenager, as Spider-Man.

    Morales accidentally becomes transported from his universe to ours, where Peter Parker is Spider-Man. Parker meets Morales and teaches him how to be Spider-Man. Along the way, they encounter different versions of Spider-Man from alternate dimensions. All of them team up to save the multiverse and to find a way to return back to their own versions of reality.

    What could be better than that?

    In 1962, Spider-Man’s creators, Stan Lee and Steve Ditko, drew inspiration for their superhero in the amazing abilities of spiders. And today, engineers find similar inspiration, particularly, when it comes to spider silk. The remarkable properties of spider’s silk is leading to the creation of new technologies.

    Synthetic Spider Silk

    Engineers are fascinated by spider silk because this material displays astonishingly high tensile strength and ductility (pliability), properties that allow it to absorb huge amounts of energy before breaking. Only one-sixth the density of steel, spider silk can be up to four times stronger, on a per weight basis.

    By studying this remarkable substance, engineers hope that they can gain insight and inspiration to engineer next-generation materials. According to Northwestern University researcher Nathan C. Gianneschi, who is attempting to produce synthetic versions of spider silk, “One cannot overstate the potential impact on materials and engineering if we can synthetically replicate the natural process to produce artificial fibers at scale. Simply put, it would be transformative.”1

    Gregory P. Holland of San Diego State University, one of Gianneschi’s collaborators, states, “The practical applications for materials like this are essentially limitless.”2 As a case in point, synthetic versions of spider silk could be used to make textiles for military personnel and first responders and to make construction materials such as cables. They would also have biomedical utility and could be used to produce environmentally friendly plastics.

    The Quest to Create Synthetic Spider Silk

    But things aren’t that simple. Even though life scientists and engineers understand the chemical structure of spider’s silk and how its structural features influence its mechanical properties, they have not been able to create synthetic versions of it with the same set of desired properties.

    blog__inline--spider-silk-inspires-new-technologyFigure 1: The Molecular Architecture of Spider Silk. Fibers of spider silk consist of proteins that contain crystalline regions separated by amorphous regions. The crystals form from regions of the protein chain that fold into structures called beta-sheets. These beta-sheets stack together to give the spider silk its tensile strength. The amorphous regions give the silk fibers ductility. Image credit: Chen-Pan Liao.

    Researchers working to create synthetic spider silk speculate that the process by which the spider spins the silk may play a critical role in establishing the biomaterial’s tensile strength and ductility. Before it is extruded, silk exists in a precursor form in the silk gland. Researchers think that the key to generating synthetic spider silk with the same properties as naturally formed spider silk may be found by mimicking the structure of the silk proteins in precursor form.

    Previous work suggests that the proteins that make up spider silk exist as simple micelles in the silk gland and that when spun from this form, fibers with greater-than-steel strength are formed. But researchers’ attempts to apply this insight in a laboratory setting failed to yield synthetic silk with the desired properties.

    The Structure of Spider Silk Precursors

    Hoping to help unravel this problem, a team of American collaborators led by Gianneschi and Holland recently provided a detailed characterization of the structure of the silk protein precursors in spider glands.3 They discovered that the silk proteins form micelles, but the micelles aren’t simple. Instead, they assemble into a complex structure comprised of a hierarchy of subdomains. Researchers also learned that when they sheared these nanoassemblies of precursor proteins, fibers formed. If they can replicate these hierarchical nanostructures in the lab, researchers believe they may be able to construct synthetic spider silk with the long-sought-after tensile strength and ductility.

    Biomimetics and Bioinspiration

    Attempts to find inspiration for new technology is n0t limited to spider silk. It has become rather commonplace for engineers to employ insights from arthropod biology (which includes spiders and insects) to solve engineering problems and to inspire the invention of new technologies—even technologies unlike anything found in nature. In fact, I discuss this practice in an essay I contributed for the book God and the World of Insects.

    This activity falls under the domain of two relatively new and exciting areas of engineering known as biomimetics and bioinspiration. As the names imply, biomimetics involves direct mimicry of designs from biology, whereas bioinspiration relies on insights from biology to guide the engineering enterprise.

    The Converse Watchmaker Argument for God’s Existence

    The idea that biological designs can inspire engineering and technology advances is highly provocative. It highlights the elegant designs found throughout the living realm. In the case of spider silk, design elegance is not limited to the structure of spider silk but extends to its manufacturing process as well—one that still can’t be duplicated by engineers.

    The elegance of these designs makes possible a new argument for God’s existence—one I have named the converse Watchmaker argument. (For a detailed discussion see the essay I contributed to the book Building Bridges, entitled, “The Inspirational Design of DNA.”)

    The argument can be stated like this: if biological designs are the work of a Creator, then these systems should be so well-designed that they can serve as engineering models for inspiring the development of new technologies. Indeed, this scenario is what scientists observe in nature. Therefore, it becomes reasonable to think that biological designs are the work of a Creator.

    Biomimetics and the Challenge to the Evolutionary Paradigm

    From my perspective, the use of biological designs to guide engineering efforts seems fundamentally at odds with evolutionary theory. Generally speaking, evolutionary biologists view biological systems as the products of an unguided, historically contingent process that co-opts preexisting systems to cobble together new ones. Evolutionary mechanisms can optimize these systems, but even then they are, in essence, still kludges.

    Given the unguided nature of evolutionary mechanisms, does it make sense for engineers to rely on biological systems to solve problems and inspire new technologies? Is it in alignment with evolutionary beliefs to build an entire subdiscipline of engineering upon mimicking biological designs? I would argue that these engineering subdisciplines do not fit with the evolutionary paradigm.

    On the other hand, biomimetics and bioinspiration naturally flow out of a creation model approach to biology. Using designs in nature to inspire engineering only makes sense if these designs arose from an intelligent Mind, whether in this universe or in any of the dimensions of the Spider-Verse.

    Resources

    Endnotes
    1. Northwestern University, “Mystery of How Black Widow Spiders Create Steel-Strength Silk Webs further Unravelled,” Phys.org, Science X, October 22, 2018, https://phys.org/news/2018-10-mystery-black-widow-spiders-steel-strength.html.
    2. Northwestern University, “Mystery of How Black Widow Spiders Create.”
    3. Lucas R. Parent et al., “Hierarchical Spidroin Micellar Nanoparticles as the Fundamental Precursors of Spider Silks,” Proceedings of the National Academy of Sciences USA (October 2018), doi:10.1073/pnas.1810203115.
  • Vocal Signals Smile on the Case for Human Exceptionalism

    by Telerik.Sitefinity.DynamicTypes.Model.Authors.Author | Nov 21, 2018

    Before Thanksgiving each year, those of us who work at Reasons to Believe (RTB) headquarters take part in an annual custom. We put our work on pause and use that time to call donors, thanking them for supporting RTB’s mission. (It’s a tradition we have all come to love, by the way.)

    Before we start making our calls, our ministry advancement team leads a staff meeting to organize our efforts. And each year at these meetings, they remind us to smile when we talk to donors. I always found this to be an odd piece of advice, but they insist that when we talk to people, our smiles come across over the phone.

    Well, it turns out that the helpful advice of our ministry advancement team has scientific merit, based on a recent study from a team of neuroscientists and psychologists from France and the UK.1 This research highlights the importance of vocal signaling for communicating emotions between people. And from my perspective, the work also supports the notion of human exceptionalism and the biblical concept of the image of God.

    We Can Hear Smiles

    The research team was motivated to perform this study in order to learn the role vocal signaling plays in social cognition. They chose to focus on auditory “smiles,” because, as these researchers point out, smiles are among the most powerful facial expressions and one of the earliest to develop in children. As I am sure we all know, smiles express positive feelings and are contagious.

    When we smile, our zygomaticus major muscle contracts bilaterally and causes our lips to stretch. This stretching alters the sounds of our voices. So, the question becomes: Can we hear other people when they smile?

    blog__inline--vocal-signals-smile-on-the-case-for-human-exceptionalism

    Figure 1: Zygomaticus major. Image credit: Wikipedia

    To determine if people can “hear” smiles, the researchers recorded actors who spoke a range of French phonemes, with and without smiling. Then, they modeled the changes in the spectral patterns that occurred in the actors’ voices when they smiled while they spoke.

    The researchers used this model to manipulate recordings of spoken sentences so that they would sound like they were spoken by someone who was smiling (while keeping other features such as pitch, content, speed, gender, etc., unchanged). Then, they asked volunteers to rate the “smiley-ness” of voices before and after manipulation of the recordings. They found that the volunteers could distinguish the transformed phonemes from those that weren’t altered.

    Next, they asked the volunteers to mimic the sounds of the “smiley” phonemes. The researchers noted that for the volunteers to do so, they had to smile.

    Following these preliminary experiments, the researchers asked volunteers to describe their emotions when listening to transformed phonemes compared to those that weren’t transformed. They found that when volunteers heard the altered phonemes, they expressed a heightened sense of joy and irony.

    Lastly, the researchers used electromyography to monitor the volunteers’ facial muscles so that they could detect smiling and frowning as the volunteers listened to a set of 60 sentences—some manipulated (to sound as if they were spoken by someone who was smiling) and some unaltered. They found that when the volunteers judged speech to be “smiley,” they were more likely to smile and less likely to frown.

    In other words, people can detect auditory smiles and respond by mimicking them with smiles of their own.

    Auditory Signaling and Human Exceptionalism

    This research demonstrates that both the visual and auditory clues we receive from other people help us to understand their emotional state and to become influenced by it. Our ability to see and hear smiles helps us develop empathy toward others. Undoubtedly, this trait plays an important role in our ability to link our minds together and to form complex social structures—two characteristics that some anthropologists believe contribute to human exceptionalism.

    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. And, yet, these new insights can be used to 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.

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

    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 so 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 possess the brain capacity to organize people we meet and know into hierarchical categories, allowing us to form and engage in complex social networks.

    Thus, I would contend that our ability to hear people’s smiles plays a role in theory of mind and our sophisticated social capacities. It contributes to human exceptionalism.

    In effect, these four qualities could be viewed as scientific descriptors of the image of God. In other words, evidence for human exceptionalism is evidence that human beings bear God’s image.

    So, even though many people in the scientific community promote a view of humanity that denigrates the image of God, scientific evidence and common-day experience continually support the notion that we are unique and exceptional as human beings. It makes me grin from ear to ear to know 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. And that makes me thankful!

    Resources

    Endnotes
    1. Pablo Arias, Pascal Belin, and Jean-Julien Aucouturier, “Auditory Smiles Trigger Unconscious Facial Imitation,” Current Biology 28 (July 23, 2018): PR782–R783, doi:10.1016/j.cub.2018.05.084.

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