Endosymbiont Hypothesis and the Ironic Case for a Creator

endosymbionthypothesisandtheironic

BY FAZALE RANA – DECEMBER 12, 2018

i ·ro ·ny

The use of words to express something different from and often opposite to their literal meaning.
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.

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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.

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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.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/12/12/endosymbiont-hypothesis-and-the-ironic-case-for-a-creator

Spider Silk Inspires New Technology and the Case for a Creator

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BY FAZALE RANA – NOVEMBER 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.

 

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Figure 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

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BY FAZALE RANA – NOVEMBER 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?

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

The Optimal Design of the Genetic Code

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BY FAZALE RANA – OCTOBER 3, 2018

Were there no example in the world of contrivance except that of the eye, it would be alone sufficient to support the conclusion which we draw from it, as to the necessity of an intelligent Creator.

–William Paley, Natural Theology

In his classic work, Natural TheologyWilliam Paley surveyed a range of biological systems, highlighting their similarities to human-made designs. Paley noticed that human designs typically consist of various components that interact in a precise way to accomplish a purpose. According to Paley, human designs are contrivances—things produced with skill and cleverness—and they come about via the work of human agents. They come about by the work of intelligent designers. And because biological systems are contrivances, they, too, must come about via the work of a Creator.

For Paley, the pervasiveness of biological contrivances made the case for a Creator compelling. But he was especially struck by the vertebrate eye. For Paley, if the only example of a biological contrivance available to us was the eye, its sophisticated design and elegant complexity alone justify the “necessity of an intelligent creator” to explain its origin.

As a biochemist, I am impressed with the elegant designs of biochemical systems. The sophistication and ingenuity of these designs convinced me as a graduate student that life must stem from the work of a Mind. In my book The Cell’s Design, I follow in Paley’s footsteps by highlighting the eerie similarity between human designs and biochemical systems—a similarity I describe as an intelligent design pattern. Because biochemical systems conform to the intelligent design pattern, they must be the work of a Creator.

As with Paley, I view the pervasiveness of the intelligent design pattern in biochemical systems as critical to making the case for a Creator. Yet, in particular, I am struck by the design of a single biochemical system: namely, the genetic code. On the basis of the structure of the genetic code alone, I think one is justified to conclude that life stems from the work of a Divine Mind. The latest work by a team of German biochemists on the genetic code’s design convinces me all the more that the genetic code is the product of a Creator’s handiwork.1

To understand the significance of this study and the code’s elegant design, a short primer on molecular biology is in order. (For those who have a background in biology, just skip ahead to The Optimal Genetic Code.)

Proteins

The “workhorse” molecules of life, proteins take part in essentially every cellular and extracellular structure and activity. Proteins are chain-like molecules folded into precise three-dimensional structures. Often, the protein’s three-dimensional architecture determines the way it interacts with other proteins to form a functional complex.

Proteins form when the cellular machinery links together (in a head-to-tail fashion) smaller subunit molecules called amino acids. To a first approximation, the cell employs 20 different amino acids to make proteins. The amino acids that make up proteins possess a variety of chemical and physical properties.

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Figure 1: The Amino Acids. Image credit: Shutterstock

Each specific amino acid sequence imparts the protein with a unique chemical and physical profile along the length of its chain. The chemical and physical profile determines how the protein folds and, therefore, its function. Because structure determines the function of a protein, the amino acid sequence is key to dictating the type of work a protein performs for the cell.

DNA

The cell’s machinery uses the information harbored in the DNA molecule to make proteins. Like these biomolecules, DNA consists of chain-like structures known as polynucleotides. Two polynucleotide chains align in an antiparallel fashion to form a DNA molecule. (The two strands are arranged parallel to one another with the starting point of one strand located next to the ending point of the other strand, and vice versa.) The paired polynucleotide chains twist around each other to form the well-known DNA double helix. The cell’s machinery forms polynucleotide chains by linking together four different subunit molecules called nucleotides. The four nucleotides used to build DNA chains are adenosine, guanosine, cytidine, and thymidine, familiarly known as A, G, C, and T, respectively.

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Figure 2: The Structure of DNA. Image credit: Shutterstock

As noted, DNA stores the information necessary to make all the proteins used by the cell. The sequence of nucleotides in the DNA strands specifies the sequence of amino acids in protein chains. Scientists refer to the amino-acid-coding nucleotide sequence that is used to construct proteins along the DNA strand as a gene.

The Genetic Code

A one-to-one relationship cannot exist between the 4 different nucleotides of DNA and the 20 different amino acids used to assemble polypeptides. The cell addresses this mismatch by using a code comprised of groupings of three nucleotides to specify the 20 different amino acids.

The cell uses a set of rules to relate these nucleotide triplet sequences to the 20 amino acids making up proteins. Molecular biologists refer to this set of rules as the genetic code. The nucleotide triplets, or “codons” as they are called, represent the fundamental communication units of the genetic code, which is essentially universal among all living organisms.

Sixty-four codons make up the genetic code. Because the code only needs to encode 20 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.

Interestingly, some codons, called stop codons or nonsense codons, code no amino acids. (For example, the codon UGA is a stop codon.) These codons always occur at the end of the gene, informing the cell where the protein chain ends.

Some coding triplets, called start codons, play a dual role in the genetic code. These codons not only encode amino acids, but also “tell” the cell where a protein chain begins. For example, the codon GUG encodes the amino acid valine and also specifies the starting point of the proteins.

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Figure 3: The Genetic Code. Image credit: Shutterstock

The Optimal Genetic Code

Based on visual inspection of the genetic code, biochemists had long suspected that the coding assignments weren’t haphazard—a frozen accident. Instead it looked to them like a rationale undergirds the genetic code’s architecture. This intuition was confirmed in the early 1990s. As I describe in The Cell’s Design, at that time, scientists from the University of Bath (UK) and from Princeton University quantified the error-minimization capacity of the genetic code. Their initial work indicated that the naturally occurring genetic code withstands the potentially harmful effects of substitution mutations better than all but 0.02 percent (1 out of 5,000) of randomly generated genetic codes with codon assignments different from the universal genetic code.2

Subsequent analysis performed later that decade incorporated additional factors. For example, some types of substitution mutations (called transitions) occur more frequently in nature than others (called transversions). As a case in point, an A-to-G substitution occurs more frequently than does either an A-to-C or an A-to-T mutation. When researchers included this factor into their analysis, they discovered that the naturally occurring genetic code performed better than one million randomly generated genetic codes. In a separate study, they also found that the genetic code in nature resides near the global optimum for all possible genetic codes with respect to its error-minimization capacity.3

It could be argued that the genetic code’s error-minimization properties are more dramatic than these results indicate. When researchers calculated the error-minimization capacity of one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution where the naturally occurring genetic code’s capacity occurred outside the distribution. Researchers estimate the existence of 1018 (a quintillion) possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. Nearly all of these codes fall within the error-minimization distribution. This finding means that of 1018 possible genetic codes, only a few have an error-minimization capacity that approaches the code found universally in nature.

Frameshift Mutations

Recently, researchers from Germany wondered if this same type of optimization applies to frameshift mutations. Biochemists have discovered that these mutations are much more devastating than substitution mutations. Frameshift mutations result when nucleotides are inserted into or deleted from the DNA sequence of the gene. If the number of inserted/deleted nucleotides is not divisible by three, the added or deleted nucleotides cause a shift in the gene’s reading frame—altering the codon groupings. Frameshift mutations change all the original codons to new codons at the site of the insertion/deletion and onward to the end of the gene.

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Figure 4: Types of Mutations. Image credit: Shutterstock

The Genetic Code Is Optimized to Withstand Frameshift Mutations

Like the researchers from the University of Bath, the German team generated 1 million random genetic codes with the same type and degree of redundancy as the genetic code found in nature. They discovered that the code found in nature is better optimized to withstand errors that result from frameshift mutations (involving either the insertion or deletion of 1 or 2 nucleotides) than most of the random genetic codes they tested.

The Genetic Code Is Optimized to Harbor Multiple Overlapping Codes

The optimization doesn’t end there. In addition to the genetic code, genes harbor other overlapping codes that independently direct the binding of histone proteins and transcription factors to DNA and dictate processes like messenger RNA folding and splicing. In 2007, researchers from Israel discovered that the genetic code is also optimized to harbor overlapping codes.4

The Genetic Code and the Case for a Creator

In The Cell’s Design, I point out that common experience teaches us that codes come from minds. By analogy, the mere existence of the genetic code suggests that biochemical systems come from a Mind. This conclusion gains considerable support based on the exquisite optimization of the genetic code to withstand errors that arise from both substitution and frameshift mutations, along with its optimal capacity to harbor multiple overlapping codes.

The triple optimization of the genetic code arises from its redundancy and the specific codon assignments. Over 1018 possible genetic codes exist and any one of them could have been “selected” for the code in nature. Yet, the “chosen” code displays extreme optimization—a hallmark feature of designed systems. As the evidence continues to mount, it becomes more and more evident that the genetic code displays an eerie perfection.5

An elegant contrivance such as the genetic code—which resides at the heart of biochemical systems and defines the information content in the cell—is truly one in a million when it comes to reasons to believe.

Resources

Endnotes

  1. Regine Geyer and Amir Madany Mamlouk, “On the Efficiency of the Genetic Code after Frameshift Mutations,” PeerJ 6 (2018): e4825, doi:10.7717/peerj.4825.
  2. David Haig and Laurence D. Hurst, “A Quantitative Measure of Error Minimization in the Genetic Code,” Journal of Molecular Evolution33 (1991): 412–17, doi:1007/BF02103132.
  3. Gretchen Vogel, “Tracking the History of the Genetic Code,” Science281 (1998): 329–31, doi:1126/science.281.5375.329; Stephen J. Freeland and Laurence D. Hurst, “The Genetic Code Is One in a Million,” Journal of Molecular Evolution 47 (1998): 238–48, doi:10.1007/PL00006381.; Stephen J. Freeland et al., “Early Fixation of an Optimal Genetic Code,” Molecular Biology and Evolution 17 (2000): 511–18, doi:10.1093/oxfordjournals.molbev.a026331.
  4. Shalev Itzkovitz and Uri Alon, “The Genetic Code Is Nearly Optimal for Allowing Additional Information within Protein-Coding Sequences,” Genome Research(2007): advanced online, doi:10.1101/gr.5987307.
  5. In The Cell’s Design, I explain why the genetic code cannot emerge through evolutionary processes, reinforcing the conclusion that the cell’s information systems—and hence, life—must stem from the handiwork of a Creator.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/10/03/the-optimal-design-of-the-genetic-code

The Multiplexed Design of Neurons

multiplexeddesignneurons

BY FAZALE RANA – AUGUST 22, 2018

In 1910, Major General George Owen Squier developed a technique to increase the efficiency of data transmission along telephone lines that is still used today in telecommunications and computer networks. This technique, called multiplexing, allows multiple signals to be combined and transmitted along a single cable, making it possible to share a scarce resource (available phone lines, in Squier’s day).

Today, there are a number of ways to carry out multiplexing. One of them is called time-division multiplexing. While other forms of multiplexing can be used for analog data, this technique can only be applied to digital data. Data is transmitted as a collection of bits along a single channel separated by a time interval that allows the data groups to be directed to the appropriate receiver.

Researchers from Duke University have discovered that neurons employ time-division multiplexing to transmit multiple electrical signals along a single axon.1 The remarkable similarity between data transmission techniques used by neurons and telecommunication systems and computer networks is provocative. It can also be marshaled to add support to the revitalized Watchmaker argument for God’s existence and role in the origin and design of life.

A brief primer on neurons will help us better appreciate the work of the Duke research team.

Neurons

The primary component of the nervous system (the brain, spinal cord, and the peripheral system of nerves), neurons are electrically excitable cells that rely on electrochemical processes to receive and send electrical signals. By connecting to each other through specialized structures called synapses, neurons form pathways that transmit information throughout the nervous system.

Neurons consist of the soma or cell body, along with several outward extending projections called dendrites and axons.

multiplexed-design-of-neuronsImage credit: Wikipedia

Dendrites are “tree-like” projections that extend from the soma into the synaptic space. Receptors on the surface of dendrites bind neurotransmitters deposited by adjacent neurons in the synapse. These binding events trigger an electrical signal that travels along the length of the dendrites to the soma. However, axons conduct electrical impulses away from the soma toward the synapse, where this signal triggers the release of neurotransmitters into the extracellular medium, initiating electrical activity in the dendrites of adjacent neurons.

Sensory Neurons

In the world around us, many things happen at the same time. And we need to be aware of all of these events. Sensory neurons react to stimuli, communicating information about the environment to our brains. Many different types of sensory neurons exist, making possible our sense of sight, smell, taste, hearing, touch, and temperature. These sensory neurons have to be broadly tuned and may have to respond to more than one environmental stimulus at the same time. An example of this scenario would be carrying on a conversation with a friend at an outdoor café while the sounds of the city surround us.

The Duke University researchers wanted to understand the mechanism neurons employ when they transmit information about two or more environmental stimuli at the same time. To accomplish this, the scientists trained two macaques (monkeys) to look in the direction of two distinct sounds produced at two different locations in the room. After achieving this step, the researchers planted electrodes into the inferior colliculus of the monkeys’ brains and used these electrodes to record the activity of single neurons as the monkeys responded to auditory stimuli. The researchers discovered that each sound produced a unique firing rate along single neurons and that when the two sounds were presented at the same time, the neuron transmitting the electrical signals alternated back and forth between the two firing rates. In other words, the neurons employed time-division multiplexing to transmit the two signals.

Neuron Multiplexing and the Case for Creation

The capacity of neurons to multiplex signals generated by environmental stimuli exemplifies the elegance and sophistication of biological designs. And it is discoveries such as these that compel me to believe that life must stem from the work of a Creator.

But the case for a Creator extends beyond the intuition of design. Discoveries like this one breathe new life into the Watchmaker argument.

British natural theologian William Paley (1743–1805) advanced this argument by pointing out that the characteristics of a watch—with the complex interaction of its precision parts for the purpose of telling time—implied the work of an intelligent designer. Paley asserted by analogy that just as a watch requires a watchmaker, so too, does life require a Creator, since organisms display a wide range of features characterized by the precise interplay of complex parts for specific purposes.

Over the centuries, skeptics have maligned this argument by claiming that biological systems only bear a superficial similarity to human designs. That is, the analogy between human designs and biological systems is weak and, therefore, undermines the conclusion that a Divine Watchmaker exits. But, as I discuss in The Cell’s Design, the discovery of molecular motors, biochemical watches, and DNA computers—biochemical complexes with machine-like characteristics—energizes the argument. These systems are identical to the highly sophisticated machines and devices we build as human designers. In fact, these biochemical systems have been directly incorporated into nanotechnologies. And, we recognize that motors and computers, not to mention watches, come from minds. So, why wouldn’t we conclude that these biochemical systems come from a mind, as well?

Analogies between human machines and biological systems are not confined to biochemical systems. We see them at the biological level as well, as the latest work by the research team from Duke University illustrates.

It is fascinating to me that as we learn more about living systems, whether at the molecular scale, the cellular level, or the systems stage, we discover more and more instances in which biological systems bear eerie similarities to human designs. This learning strengthens the Watchmaker argument and the case for a Creator.

Resources

Endnotes

  1. Valeria C. Caruso et al., “Single Neurons May Encode Simultaneous Stimuli by Switching between Activity Patterns,” Nature Communications 9 (2018): 2715, doi:10.1038/s41467-018-05121-8.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/08/22/the-multiplexed-design-of-neurons

Design Principles Explain Neuron Anatomy

designprinciples

BY FAZALE RANA – AUGUST 15, 2018

It’s one of the classic episodes of I Love Lucy. Originally aired on September 15, 1952, the episode entitled “Job Switching” finds Lucy and Ethel working at a candy factory. They have been assigned to an assembly line, where they are supposed to pick up pieces of candy from a moving conveyor belt, wrap them, and place the candy back on the assembly line. But the conveyor belt moves too fast for Lucy and Ethel to keep up. Eventually, they both start stuffing pieces of candy into their mouths, under their hats, and in their blouses, as fast as they can as pieces of candy on the assembly line quickly move beyond their reach—a scene of comedic brilliance.

This chaotic (albeit hilarious) scene is a good analogy for how neurons would transmit electrical signals throughout the nervous system if not for the clever design of the axons that project from the nerve cell’s soma, or cell body.

The principles that undergird the design of axons were recently discovered by a team of bioengineers at the University of California, San Diego (UCSD).1 Insights such as this highlight the elegant designs that characterize biological systems—designs worthy to be called the Creator’s handiwork—no joke.

Neurons

The primary component of the nervous system (the brain, spinal cord, and the peripheral system of nerves), neurons are electrically excitable cells, thanks to electrochemical processes that take place across their cell membranes. These electrochemical activities allow the cells to receive and send electrical signals. By connecting to each other through specialized structures called synapses, neurons form pathways that transmit information throughout the nervous system. Neurologists refer to these pathways as neural circuits.

The heart of a neuron is the soma or cell body. This portion of the cell harbors the nucleus. Two sets of projections emanate from the soma: dendrites and axons. Dendrites are “tree-like” projections that extend from the soma into the synaptic space. Receptors on the surface of dendrites bind neurotransmitters deposited by adjacent neurons in the synapse. These binding events trigger an electrical signal that travels along the length of the dendrites to the soma. On the other hand, axons conduct electrical impulses away from the soma toward the synapse where this signal triggers the release of neurotransmitters into the extracellular medium, initiating electrical activity in the dendrites of adjacent neurons. Many dendrites feed the soma, but the soma gives rise to only a single axon, though the axon can branch extensively for some types of nerve cells. Axons vary significantly in terms of their diameter and length. Their diameter ranges from 1 to 20 microns. Axons can be quite long, up to a meter in length.

design-principles-explain-neuron-anatomy

Image: A Neuron. Image source: Wikipedia

The electrical excitability of neurons stems from the charge separation across its cell or plasma membrane that arises due to concentration differences in positively charged sodium, potassium, and calcium ions between the cell’s interior and exterior surroundings. This charge difference sets up a voltage across the membrane that is maintained by the activity of proteins embedded within the membranes called ion pumps. This voltage is called the resting potential. When the neuron binds neurotransmitters, this event triggers membrane-bound proteins called ion channels to open up, allowing ions to flow across the membrane. This causes a localized change in the membrane voltage that propagates along the length of the dendrite or axon. This propagating voltage change is called an action potential. When the action potential reaches the end of the axon, it triggers the release of neurotransmitters into the synaptic space.

Why Are Neurons the Way They Are?

The UCSD researchers wanted to understand the principles that undergird the neuron design, specifically why the length and diameter of the axons varies so much. Previous studies indicate that axons aren’t structured to minimize the use of cellular material—otherwise they wouldn’t be so long and convoluted. Nor are they structured for speed because axons don’t propagate electrical signals as fast as they could, theoretically speaking.

Even though the UCSD bioengineers adhere to the evolutionary paradigm, they were convinced that design principles must exist that explain the anatomy and physiology of neurons. From my perspective, their conviction is uncharacteristic of many life scientists because of the nature of evolutionary mechanisms (unguided, historically contingent processes that co-opt and cobble together existing designs to create new biological systems). Based on these mechanisms, there need not be any rationale for why things are the way they are. In fact, many evolutionary biologists view most biological systems as flawed, imperfect systems that are little more than kludge jobs.

But their conviction paid off. They discovered an elegant rationale that explains the variation in axon lengths.

Refraction Ratio

The UCSD investigators reasoned that the cellular architecture of axons may reflect a trade-off between (1) the speed of signal transduction along the axon, and (2) the time it takes the axon to reset the resting potential after the action potential propagates along the length of the axon and to ready the cell for the next round of neurotransmitter release.

To test this idea, the research team defined a quantity they dubbed the refraction ratio. This is the ratio of the refractory period of a neuron and the time it takes the electrical signal to transmit along the length of the axon. These researchers calculated the refraction ratio for 12,000 axon branches of rat basket cells. (These are a special type of neuron with heavily branched axons.) They found the information they needed for these calculations in the NeuroMorpho database. They determined that the average value for the refraction ratio was 0.92. The ideal value for the refraction ratio is 1.0. A value of 1.0 for the refraction ratio reflects optimal efficiency. In other words, the refraction ratio appears to be nearly optimal.

If not for this optimization, then signal transmission along axons would suffer the same fate as the pieces of candy on the assembly line manned by Lucy and Ethel. Things would become a jumbled mess along the length of the axons and at the synaptic terminus. And, if this happened, the information transmitted by the neurons would be lost.

The researchers concluded that the axon diameter—and, more importantly, its length—are varied to ensure that the refraction ratio remains as close to 1.0 as possible. This design principle explains why the shape, length, and width of axons varies so much. The reset time (refractory period) cannot be substantially altered. But the axon geometry can be altered, and this variation controls the transmission time of the electrical signal along the axon. To put it another way, axon geometry is analogous to slowing down or speeding up the conveyor belt to ensure that the candy factory workers can wrap as many pieces of candy as possible, without having to eat any or tuck them under their hats.

The Importance of Axon Geometry

The researchers from UCSD think that the design principles they have uncovered may be helpful in understanding some neurological disorders. They reason that if a disease leads to changes in neuronal anatomy, the axon geometry may no longer be optimized (causing the refraction ratio to deviate from its ideal value). This deviation will lead to loss of information when nerve cells transmit electrical signals through neural circuits, potentially contributing to the etiology of neurological diseases.

This research team also thinks that their insights might have use in computer technology. Understanding the importance of refraction ratio should benefit the design of machine-learning systems based on brain-like neural networks. At this time, the design of machine-learning systems doesn’t account for the time it takes for signals to reach neural network nodes. By incorporating this temporal parameter into the design, the researchers believe that they can dramatically improve the power of neural networks. In fact, this research team is now building new types of machine-learning architectures based on these new insights.2

Axon Geometry and the Case for Creation

The elegant, optimized, sophisticated, and ingenious design displayed by axon geometry is the type of evidence that convinced me, as an agnostic graduate student studying biochemistry, that life must stem from the work of a Creator. The designs we observe in biology (and biochemistry) are precisely the types of designs that we would expect to see if a Creator was responsible for life’s origin, history, and design.

On the other hand, evolutionary mechanisms (based on unguided, directionless processes that rely on co-opting and modifying existing designs to create biological innovation) are expected to yield biological designs that are inherently limited and flawed. For many life scientists, the varying length and meandering, convoluted paths taken by axons serve as a reminder that evolution produces imperfect designs, just good enough for survival, but nothing more.

And, in spite of this impoverished view of biology, the UCSD bioengineers were convinced that there must be a design principle that explained the variable length of axons. And herein lies the dilemma faced by many life scientists. The paradigm they embrace demands that they view biological systems as flawed and imperfect. Yet, biological systems appear to be designed for a purpose. And, hence, biologists can’t stop from using design language when they describe the structure and function of these systems. Nor can they keep themselves from seeking design principles when they study the architecture and operation of these systems. In other words, many life scientists operate as if life was the product of a Creator’s handiwork, though they might vehemently deny God’s influence in shaping biology—and even go as far as denying God’s existence. In this particular case, the commitment these researchers had to a de facto design paradigm paid off handsomely for them—and scientific advance.

The Converse Watchmaker Argument

Along these lines, it is provocative that the insights the researchers gleaned regarding axon geometry and the refraction ratio may well translate into improved designs for neural networks and machine-learning systems. The idea that biological designs can inspire engineering and technology advances makes possible a new argument for God’s existence—one I have named the converse Watchmaker argument.

The argument goes something 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 and otherwise inspire the development of new technologies.

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

It is even more astounding to think that engineers would turn to biological designs to inspire their work if biological systems were truly generated by an unguided, historically contingent process, as evolutionary biologists claim.

Using biological designs to guide engineering efforts seems to be fundamentally incompatible with an evolutionary explanation for life’s origin and history. To think otherwise is only possible after taking a few swigs of “Vitameatavegamin” mix.

Resources

Endnotes

  1. Francesca Puppo, Vivek George, and Gabriel A. Silva, “An Optimized Structure-Function Design Principle Underlies Efficient Signaling Dynamics in Neurons,” Scientific Reports 8 (2018): 10460, doi:10.1038/s41598-018-28527-2.
  2. Katherine Connor, “Why Are Neuron Axons Long and Spindly? Study Shows They’re Optimizing Signaling Efficiency,” UC San Diego News Center, July 11, 2018, https://ucsdnews.ucsd.edu/pressrelease/why_are_neuron_axons_long_and_spindly.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/08/15/design-principles-explain-neuron-anatomy

Evolution’s Flawed Approach to Science

evolutionsflawedapproach

BY FAZALE RANA – AUGUST 8, 2018

One of the things I find most troubling about the evolutionary paradigm is the view it fosters about the nature of biological systems—including human beings.

Evolution’s mechanisms, it is said, generate biological innovations by co-opting existing designs and cobbling them together to create new ones. As a result, many people in the scientific community regard biological systems as fundamentally flawed.

As biologist Ken Miller explains in an article for Technology Review:

“Evolution . . . does not produce perfection. The fact that every intermediate stage in the development of an organ must confer a selective advantage means that the simplest and most elegant design for an organ cannot always be produced by evolution. In fact, the hallmark of evolution is the modification of pre-existing structures. An evolved organism, in short, should show the tell-tale signs of this modification.1″

So, instead of regarding humans as “fearfully and wonderfully made” (as Scripture teaches), the evolutionary paradigm denigrates human beings, as a logical entailment of its mechanisms. It renders human beings as nothing more than creatures that have been cobbled together by evolutionary mechanisms.

Adding to this concern is the impact that the evolutionary paradigm has on scientific advance. Because many in the scientific community view biological systems as fundamentally flawed, they are predisposed to conclude—oftentimes, prematurely—that biological systems lack function or purpose when initial investigations into these systems fail to uncover any obvious rationale for why these systems are the way they are. And, once these investigators conclude that a biological system is flawed, the motivation to continue studying the system dissipates. Why try to understand a flawed design? Why focus attention on biological systems that lack function? Why invest research dollars studying systems that serve no purpose?

I would contend that viewing biological systems as the Creator’s handiwork provides a superior framework for promoting scientific advance, particularly when the rationale for the structure and function of a particular biological system is not apparent. If biological systems have been created, then there must be good reasons why these systems are structured and function the way they do. And this expectation drives further study of seemingly nonfunctional, purposeless systems with the full anticipation that their functional roles will eventually be uncovered.

Recent history validates the creation model approach. During the course of the last couple of decades, the scientific community has made discovery after discovery demonstrating (1) function for biological systems long thought to be useless evolutionary vestiges, or (2) an ingenious rationale for the architecture and operation of systems long regarded as flawed designs. (For examples, see the articles listed in the Resources section.)

These discoveries were made not because of the evolutionary paradigm but in spite of it.

So often, creationists and intelligent design proponents are accused of standing in the way of scientific advance. Skeptics of creation claim that if we conclude that God created biological systems, then science grinds to a halt. If God made it, then why continue to investigate the system in question?

But, I would assert that the opposite is true. The evolutionary paradigm stultifies science by viewing biological systems as flawed and vestigial. Yet, for the biological systems discussed in the articles listed in the Resources section, the view spawned by the evolutionary paradigm delayed important advances that could have been leveraged for biomedical purposes sooner, alleviating a lot of pain and suffering.

Because a creation model perspective regards designs in nature as part of God’s handiwork, it provides the motivation to keep pressing forward, seeking a rationale for systems that seemingly lack purpose. In the handful of instances in which the scientific community has adopted this mindset, it has been rewarded, paving the way for new scientific insight that leads to biomedical breakthroughs.

Resources

Endnotes

  1. Kenneth R. Miller, “Life’s Grand Design,” Technology Review 97 (February/March 1994): 24–32.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/08/08/evolution-s-flawed-approach-to-science

Mitochondria’s Deviant Genetic Code: Evolution or Creation?

mitochondriasdeviantgeneticcode

BY FAZALE RANA – APRIL 18, 2018

When I was in high school, I had the well-deserved reputation of being a wise guy—though the people who knew me then might have preferred to call me a wise—, instead. Either way, for being a wise guy, I sure didn’t display much wisdom during my teenage years.

I would like to think that I am wiser today. But, the little wisdom I do possess didn’t come easy. To quote singer and songwriter, Helen Reddy, “It’s wisdom born of pain.”

Life’s hardships sure have a way of teaching you lessons. But, I also learned that there is a shortcut to gaining wisdom—if you are wise enough to recognize it. (See what I did there?) It is better to solicit the advice of wise people than to gain wisdom through life’s bitter experiences. And, perhaps there was no wiser person ever than Solomon. Thankfully, Solomon’s wisdom was captured in the book of Proverbs. Many of life’s difficulties can be sidestepped if we are willing to heed Solomon’s advice.

Solomon gained his wisdom through observation and careful reflection. But, his wisdom also came through divine inspiration, and according to Solomon, it was through wisdom that God created the world in which we live (Proverbs 8:22–31). And, it is out of this wisdom that the Holy Spirit inspired Solomon to offer the insights found in the Proverbs.

In Psalm 104, the Psalmist (presumably David) echoes the same idea as Solomon: God created our world through wisdom. The Psalmist writes:

How many are your works, Lord!

In wisdom you made them all;

Based on Proverbs 8 and Psalm 104, I would expect God’s wisdom to be manifested in the created order. The Creator’s fingerprints—so evident in nature—should not only reflect the work of intelligent agency but also display undeniable wisdom. In my view, that wisdom should be reflected in the elegance, cleverness, and ingenuity of the designs seen throughout nature. Designs that reflect an underlying purpose. And these features are exactly what we observe when we study the biological realm—as demonstrated by recent work on aquatic mammal body size conducted by investigators from Stanford University.1

Body Sizes of Aquatic Mammals

Though the majority of the world’s mammals live in terrestrial habitats, the most massive members of this group reside in Earth’s oceans. For evolutionary biologists, common wisdom has it that the larger size of aquatic mammals reflects fewer evolutionary constraints on their body size because they live in the ocean. After all, the ocean habitat is more expansive than those found on land, and aquatic animals don’t need to support their weight because they are buoyed by the ocean.

As it turns out, common wisdom is wrong in this case. Through the use of mathematical modeling (employing body mass data from about 3,800 living species of aquatic mammals and around 3,000 fossil species), the research team from Stanford learned that living in an aquatic setting imposes tight constraints on body size, much more so than when animals live on land. In fact, they discovered (all things being equal) that the optimal body mass for aquatic mammals is around 1,000 pounds. Interestingly, the body mass distributions for members of the order Sirenia (dugongs and manatees), and the clades Cetacea (whales and dolphins), and Pinnipeds (sea lions and seals) cluster near 1,000 pounds.

Scientists have learned that the optimal body mass of aquatic mammals displays an underlying biological rationale and logic. It reflects a trade-off between two opposing demands: heat retention and caloric intake. Because the water temperatures of the oceans are below mammals’ body temperatures, heat retention becomes a real problem. Mammals with smaller bodies can’t consume enough food to compensate for heat loss to the oceans, and they don’t have the mass to retain body heat. The way around this problem is to increase their body mass. Larger bodies do a much better job at retaining heat than do smaller bodies. But, the increase in body mass can’t go unchecked. Maintaining a large body requires calories. At some point, metabolic demands outpace the capacity for aquatic mammals to feed, so body mass has to be capped (near 1,000 pounds).

The researchers noted a few exceptions to this newly discovered “rule.” Baleen whales have a body mass that is much greater than 1,000 pounds. But, as the researchers noted, these creatures employ a unique feeding mechanism that allows them to consume calories needed to support their massive body sizes. Filter feeding is a more efficient way to consume calories than hunting prey. The other exception is creatures such as otters. The researchers believe that their small size reflects a lifestyle that exploits both aquatic and terrestrial habitats.

Argument for God’s Existence from Wisdom

The discovery that the body mass of aquatic mammals has been optimized is one more example of the many elegant designs found in biological systems—designs worthy to be called the Creator’s handiwork. However, from my perspective, this optimization also reflects the Creator’s sagacity as he designed mammals for the purpose of living in the earth’s oceans.

But, instead of relying on intuition alone to make a case for a Creator, I want to present a formal argument for God’s existence based on the wisdom of biology’s designs. To make this argument, I follow after philosopher Richard Swinburne’s case for God’s existence based on beauty. Swinburne argues, “If God creates a universe, as a good workman he will create a beautiful universe. On the other hand, if the universe came into existence without being created by God, there is no reason to suppose that it would be a beautiful universe.”2 In other words, the beauty in the world around us signifies the Divine.

In like manner, if God created the universe, including the biological realm, we should expect to see wisdom permeating the designs in nature. On the other hand, if the universe came into being without God’s involvement, then there is no reason to think that the designs in nature would display a cleverness and ingenuity that affords a purpose—a sagacity, if you will. In fact, evolutionary biologists are quick to assert that most biological designs are flawed in some way. They argue that there is no purpose that undergirds biological systems. Why? Because evolutionary processes do not produce biological systems from scratch, but from preexisting systems that are co-opted through a process dubbed exaptation (by the late evolutionary biologist Stephen Jay Gould), and then modified by natural selection to produce new designs.3 According to biologist Ken Miller:

“Evolution . . . does not produce perfection. The fact that every intermediate stage in the development of an organ must confer a selective advantage means that the simplest and most elegant design for an organ cannot always be produced by evolution. In fact, the hallmark of evolution is the modification of pre-existing structures. An evolved organism, in short, should show the tell-tale signs of this modification.”4

And yet we see designs in biology that are not just optimized, but characterized by elegance, cleverness, and ingenuity—wisdom.

Truly, God is a wise guy.

Resources

Endnotes

  1. William Gearty, Craig R. McClain, and Jonathan L. Payne, “Energetic Tradeoffs Control the Size Distribution of Aquatic Mammals,” Proceedings of the National Academy of Sciences USA (March 2018): doi:10.1073/pnas.1712629115.
  2. Richard Swinburne, The Existence of God, 2nd ed. (New York: Oxford University Press, 2004), 190–91.
  3. Stephen Jay Gould and Elizabeth S. Vrba, “Exaptation: A Missing Term in the Science of Form,” Paleobiology8 (January 1, 1982): 4–15, doi:10.1017/S0094837300004310.
  4. Kenneth R. Miller, “Life’s Grand Design,” Technology Review 97 (February/March 1994): 24–32.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/04/11/mitochondria-s-deviant-genetic-code-evolution-or-creation

Why Are Whales So Big? In Wisdom God Made Them That Way

whyarewhalessobig

BY FAZALE RANA – APRIL 18, 2018

When I was in high school, I had the well-deserved reputation of being a wise guy—though the people who knew me then might have preferred to call me a wise—, instead. Either way, for being a wise guy, I sure didn’t display much wisdom during my teenage years.

I would like to think that I am wiser today. But, the little wisdom I do possess didn’t come easy. To quote singer and songwriter, Helen Reddy, “It’s wisdom born of pain.”

Life’s hardships sure have a way of teaching you lessons. But, I also learned that there is a shortcut to gaining wisdom—if you are wise enough to recognize it. (See what I did there?) It is better to solicit the advice of wise people than to gain wisdom through life’s bitter experiences. And, perhaps there was no wiser person ever than Solomon. Thankfully, Solomon’s wisdom was captured in the book of Proverbs. Many of life’s difficulties can be sidestepped if we are willing to heed Solomon’s advice.

Solomon gained his wisdom through observation and careful reflection. But, his wisdom also came through divine inspiration, and according to Solomon, it was through wisdom that God created the world in which we live (Proverbs 8:22–31). And, it is out of this wisdom that the Holy Spirit inspired Solomon to offer the insights found in the Proverbs.

In Psalm 104, the Psalmist (presumably David) echoes the same idea as Solomon: God created our world through wisdom. The Psalmist writes:

How many are your works, Lord!

In wisdom you made them all;

Based on Proverbs 8 and Psalm 104, I would expect God’s wisdom to be manifested in the created order. The Creator’s fingerprints—so evident in nature—should not only reflect the work of intelligent agency but also display undeniable wisdom. In my view, that wisdom should be reflected in the elegance, cleverness, and ingenuity of the designs seen throughout nature. Designs that reflect an underlying purpose. And these features are exactly what we observe when we study the biological realm—as demonstrated by recent work on aquatic mammal body size conducted by investigators from Stanford University.1

Body Sizes of Aquatic Mammals

Though the majority of the world’s mammals live in terrestrial habitats, the most massive members of this group reside in Earth’s oceans. For evolutionary biologists, common wisdom has it that the larger size of aquatic mammals reflects fewer evolutionary constraints on their body size because they live in the ocean. After all, the ocean habitat is more expansive than those found on land, and aquatic animals don’t need to support their weight because they are buoyed by the ocean.

As it turns out, common wisdom is wrong in this case. Through the use of mathematical modeling (employing body mass data from about 3,800 living species of aquatic mammals and around 3,000 fossil species), the research team from Stanford learned that living in an aquatic setting imposes tight constraints on body size, much more so than when animals live on land. In fact, they discovered (all things being equal) that the optimal body mass for aquatic mammals is around 1,000 pounds. Interestingly, the body mass distributions for members of the order Sirenia (dugongs and manatees), and the clades Cetacea (whales and dolphins), and Pinnipeds (sea lions and seals) cluster near 1,000 pounds.

Scientists have learned that the optimal body mass of aquatic mammals displays an underlying biological rationale and logic. It reflects a trade-off between two opposing demands: heat retention and caloric intake. Because the water temperatures of the oceans are below mammals’ body temperatures, heat retention becomes a real problem. Mammals with smaller bodies can’t consume enough food to compensate for heat loss to the oceans, and they don’t have the mass to retain body heat. The way around this problem is to increase their body mass. Larger bodies do a much better job at retaining heat than do smaller bodies. But, the increase in body mass can’t go unchecked. Maintaining a large body requires calories. At some point, metabolic demands outpace the capacity for aquatic mammals to feed, so body mass has to be capped (near 1,000 pounds).

The researchers noted a few exceptions to this newly discovered “rule.” Baleen whales have a body mass that is much greater than 1,000 pounds. But, as the researchers noted, these creatures employ a unique feeding mechanism that allows them to consume calories needed to support their massive body sizes. Filter feeding is a more efficient way to consume calories than hunting prey. The other exception is creatures such as otters. The researchers believe that their small size reflects a lifestyle that exploits both aquatic and terrestrial habitats.

Argument for God’s Existence from Wisdom

The discovery that the body mass of aquatic mammals has been optimized is one more example of the many elegant designs found in biological systems—designs worthy to be called the Creator’s handiwork. However, from my perspective, this optimization also reflects the Creator’s sagacity as he designed mammals for the purpose of living in the earth’s oceans.

But, instead of relying on intuition alone to make a case for a Creator, I want to present a formal argument for God’s existence based on the wisdom of biology’s designs. To make this argument, I follow after philosopher Richard Swinburne’s case for God’s existence based on beauty. Swinburne argues, “If God creates a universe, as a good workman he will create a beautiful universe. On the other hand, if the universe came into existence without being created by God, there is no reason to suppose that it would be a beautiful universe.”2 In other words, the beauty in the world around us signifies the Divine.

In like manner, if God created the universe, including the biological realm, we should expect to see wisdom permeating the designs in nature. On the other hand, if the universe came into being without God’s involvement, then there is no reason to think that the designs in nature would display a cleverness and ingenuity that affords a purpose—a sagacity, if you will. In fact, evolutionary biologists are quick to assert that most biological designs are flawed in some way. They argue that there is no purpose that undergirds biological systems. Why? Because evolutionary processes do not produce biological systems from scratch, but from preexisting systems that are co-opted through a process dubbed exaptation (by the late evolutionary biologist Stephen Jay Gould), and then modified by natural selection to produce new designs.3 According to biologist Ken Miller:

“Evolution . . . does not produce perfection. The fact that every intermediate stage in the development of an organ must confer a selective advantage means that the simplest and most elegant design for an organ cannot always be produced by evolution. In fact, the hallmark of evolution is the modification of pre-existing structures. An evolved organism, in short, should show the tell-tale signs of this modification.”4

And yet we see designs in biology that are not just optimized, but characterized by elegance, cleverness, and ingenuity—wisdom.

Truly, God is a wise guy.

Resources

Endnotes

  1. William Gearty, Craig R. McClain, and Jonathan L. Payne, “Energetic Tradeoffs Control the Size Distribution of Aquatic Mammals,” Proceedings of the National Academy of Sciences USA (March 2018): doi:10.1073/pnas.1712629115.
  2. Richard Swinburne, The Existence of God, 2nd ed. (New York: Oxford University Press, 2004), 190–91.
  3. Stephen Jay Gould and Elizabeth S. Vrba, “Exaptation: A Missing Term in the Science of Form,” Paleobiology8 (January 1, 1982): 4–15, doi:10.1017/S0094837300004310.
  4. Kenneth R. Miller, “Life’s Grand Design,” Technology Review 97 (February/March 1994): 24–32.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/04/18/why-are-whales-so-big-in-wisdom-god-made-them-that-way

Molecular Scale Robotics Build Case for Design

molecularscalerobotics

BY FAZALE RANA – DECEMBER 6, 2017

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

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

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

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

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

Molecular Robotics

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

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

Molecular Robots Make the Case for Design

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

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

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

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

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

Molecular Robots Make the Case for Human Exceptionalism

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

Thomas Suddendorf puts it this way:

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

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

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

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

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

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

Resources to Dig Deeper

Endnotes

  1. Salma Kassem et al., “Stereodivergent Synthesis with a Programmable Molecular Machine,” Nature 549 (September 21, 2017): 374–8, doi:10.1038/nature23677.
  2. Kassem et al., “Stereodivergent Synthesis,” 374.
  3. Kassem et al., “Stereodivergent Synthesis,” 374.
  4. Thomas Suddendorf, The Gap: The Science of What Separates Us from Other Animals (New York: Basic Books, 2013), 2.
  5. Johan J. Bolhuis et al., “How Could Language Have Evolved?” PLoS Biology 12 (August 26, 2014): e1001934, doi:10.1371/journal.pbio.1001934.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2017/12/06/molecular-scale-robotics-build-case-for-design