Category: The Cell’s Design with Fazale Rana

Does Evolutionary Bias Create Unhealthy Stereotypes about Pseudogenes?

By Fazale Rana – March 18, 2020

Truth be told, we all hold to certain stereotypes whether we want to admit it or not. Though unfair, more often than not, these stereotypes cause little real damage.

Yet, there are instances when stereotypes can be harmful—even deadly. As a case in point, researchers have shown that stereotyping disrupts the healthcare received by members of so-called disadvantaged groups, such as African Americans, Latinos, and the poor.1

Healthcare providers are frequently guilty of bias towards underprivileged people. Often, the stereotyping is unconscious and unintentional. Still, this bias compromises the medical care received by people in these ethnic and socioeconomic groups.

Underprivileged patients are also guilty of stereotyping. It is not uncommon for these patients to perceive themselves as the victims of prejudice, even when their healthcare providers are genuinely unbiased. As a result, these patients don’t trust healthcare workers and, consequently, withhold information that is vital for a proper diagnosis.

Fortunately, psychologists have developed best practices that can reduce stereotyping by both healthcare practitioners and patients. Hopefully, by implementing these practices, the impact of stereotyping on the quality of healthcare can be minimized over time.

Recently, a research team from Australia identified another form of stereotyping that holds the potential to negatively impact healthcare outcomes.2 In this case, the impact of this stereotyping isn’t limited to disadvantaged people; it affects all of us.

A Bias Against Pseudogenes

These researchers have uncovered a bias in the way life scientists view the human genome (and the genomes of other organisms). Too often they regard the human genome as a repository of useless, nonfunctional DNA that arises as a vestige of evolutionary history. Because of this view, life scientists and the biomedical research community eschew studying regions of the human genome they deem to be junk DNA. This posture is not unreasonable. It doesn’t make sense to invest precious scientific resources to study nonfunctional DNA.

Many life scientists are unaware of their bias. Unfortunately, this stereotyping hinders scientific advance by delaying discoveries that could be translated into the clinical setting. Quite often, supposed junk DNA has turned out to serve a vital purpose. Failure to recognize this function not only compromises our understanding of genome biology, but also hinders biomedical researchers from identifying defects in these genomic regions that contribute to genetic diseases and disorders.

As psychologists will point out, acknowledging bias is the first step to solving the problems that stereotyping causes. This is precisely what these researchers have done by publishing an article in Nature Review Genetics.3 The team focused on DNA sequence elements called pseudogenes. Traditionally, life scientists have viewed pseudogenes as the remnants of once functional genes. Biologists have identified three categories of pseudogenes: (1) unitary, (2) duplicated, and (3) processed.

Researchers categorize DNA sequences as pseudogenes based on structural features. Such features indicate to the investigators that these sequence elements were functional genes at one time in evolutionary history, but eventually lost function due to mutations or other biochemical processes, such as reverse transcription and DNA insertion. Once a DNA sequence is labeled a pseudogene, bias sets in and researchers just assume that it lacks function—not because it has been experimentally demonstrated to be nonfunctional, but because of the stereotyping that arises out of the evolutionary paradigm.

The authors of the piece acknowledge that “the annotation of genomics regions as pseudogenes constitutes an etymological signifier that an element has no function and is not a gene. As a result, pseudogene-annotated regions are largely excluded from functional screen and genomic analyses.”4 In other words, the “pseudogene” moniker biases researchers to such a degree that they ignore these sequence elements as they study genome structure and function without ever doing the hard, experimental work to determine whether it is actually nonfunctional.

This approach is clearly misguided and detracts from scientific discovery. As the authors admit, “However, with a growing number of instances of pseudogene-annotated regions later found to exhibit biological function, there is an emerging risk that these regions of the genome are prematurely dismissed as pseudogenic and therefore regarded as void of function.”5

Discovering Function Despite Bias

The harmful effects of this bias become evident as biomedical researchers unexpectedly stumble upon function for pseudogenes, time and time, again, not because of the evolutionary paradigm, but despite it. These authors point out that many processed pseudogenes are transcribed and, of those, many are translated to produce proteins. Many unitary and duplicated pseudogenes are also transcribed. Some are also translated into proteins, but a majority are not. Instead they play a role in gene regulation as described by the competitive endogenous RNA hypothesis.

Still, there are some pseudogenes that aren’t transcribed and, thus, could rightly be deemed nonfunctional. However, the researchers point out that the current experimental approaches for identifying transcribed regions are less than ideal. Many of these methods may fail to detect pseudogene transcripts. However, as the researchers point out, even if a pseudogene isn’t transcribed it still may serve a functional role (e.g., contributing to chromosome three-dimensional structure and stability).

This Nature article raises a number of questions and concerns for me as a biochemist:

  • How widespread is this bias?
  • If this type of stereotyping exists toward pseudogenes, does it exist for other classes of junk DNA?
  • How well do we really understand genome structure and function?
  • Do we have the wrong perspective on the genome, one that stultifies scientific advance?
  • Does this bias delay the understanding and alleviation of human health concerns?

Is the Evolutionary Paradigm the Wrong Framework to Study Genomes?

Based on this article, I think it is safe to conclude that we really don’t understand the molecular biology of genomes. We are living in the midst of a scientific revolution that is radically changing our view of genome structure and function. The architecture and operations of genomes appear to be far more elegant and sophisticated than anyone ever imagined—at least within the confines of the evolutionary paradigm.

This insight also leads me to question if the evolutionary paradigm is the proper framework for thinking about genome structure and function. From my perspective, treating biological systems as the Creator’s handiwork provides a superior approach to understanding the genome. A creation model approach promotes scientific advance, particularly when the rationale for the structure and function of a particular biological system is not apparent. This expectation forces researchers to keep an open mind and drives further study of seemingly nonfunctional, purposeless systems with the full anticipation that their functional roles will eventually be uncovered.

Over the last several years, I have raised concerns about the bias life scientists have harbored as they have worked to characterize the human genome (and genomes of other organisms). It is gratifying to me to see that there are life scientists who, though committed to the evolutionary paradigm, are beginning to recognize this bias as well.

The first step to addressing the problem of stereotyping—in any sector of society—is to acknowledge that it exists. Often, this step is the hardest one to take. The next step is to put in place structures to help overcome its harmful influence. Could it be that part of the solution to this instance of scientific stereotyping is to grant a creation model approach access to the scientific table?

Resources

Pseudogene Function

The Evolutionary Paradigm Hinders Scientific Advance

Endnotes
  1. For example, see Joshua Aronson et al., “Unhealthy Interactions: The Role of Stereotype Threat in Health Disparities,” American Journal of Public Health 103 (January 1, 2013): 50–56, doi:10.2105/AJPH.2012.300828.
  2. Seth W. Cheetham, Geoffrey J. Faulkner, and Marcel E. Dinger, “Overcoming Challenges and Dogmas to Understand the Functions of Pseudogenes,” Nature Reviews Genetics 21 (March 2020): 191–201, doi:10.1038/s41576-019-0196-1.
  3. Cheetham, Faulkner, and Dinger, 191–201.
  4. Cheetham, Faulkner, and Dinger, 191–201.
  5. Cheetham, Faulkner, and Dinger, 191–201.

Reprinted with permission by the author

Original article at:

https://reasons.org/explore/blogs/the-cells-design

New Genetic Evidence Affirms Human Uniqueness

By Fazale Rana – March 4, 2020

It’s a remarkable discovery—and a bit gruesome, too.

It is worth learning a bit about some of its unseemly details because this find may have far-reaching implications that shed light on our origins as a species.

In 2018, a group of locals discovered the remains of a two-year-old male puppy in the frozen mud (permafrost) in the eastern part of Siberia. The remains date to 18,000 years in age. Remarkably, the skeleton, teeth, head, fur, lashes, and whiskers of the specimen are still intact.

Of Dogs and People

The Russian scientists studying this find (affectionately dubbed Dogor) are excited by the discovery. They think Dogor can shed light on the domestication of wolves into dogs. Biologists believe that this transition occurred around 15,000 years ago. Is Dogor a wolf? A dog? Or a transitional form? To answer these questions, the researchers have isolated DNA from one of Dogor’s ribs, which they think will provide them with genetic clues about Dogor’s identity—and clues concerning the domestication process.

Biologists study the domestication of animals because this process played a role in helping to establish human civilization. But biologists are also interested in animal domestication for another reason. They think this insight will tell us something about our identity as human beings.

In fact, in a separate study, a team of researchers from the University of Milan in Italy used insights about the genetic changes associated with the domestication of dogs, cats, sheep, and cattle to identify genetic features that make human beings (modern humans) stand apart from Neanderthals and Denisovans.1 They conclude that modern humans share some of the same genetic characteristics as domesticated animals, accounting for our unique and distinct facial features (compared to other hominins). They also conclude that our high level of cooperativeness and lack of aggression can be explained by these same genetic factors.

This work in comparative genomics demonstrates that significant anatomical and behavioral differences exist between humans and hominins, supporting the concept of human exceptionalism. Though the University of Milan researchers carried out their work from an evolutionary perspective, I believe their insights can be recast as scientific evidence for the biblical conception of human nature; namely, creatures uniquely made in God’s image.

Biological Changes that Led to Animal Domestication

Biologists believe that during the domestication process, many of the same biological changes took place in dogs, cats, sheep, and cattle. For example, they think that during domestication, mild deficits in neural crest cells resulted. In other words, once animals are domesticated, they produce fewer, less active neural crest cells. These stem cells play a role in neural development; thus, neural crest cell defects tend to make animals friendlier and less aggressive. This deficit also impacts physical features, yielding smaller skulls and teeth, floppy ears, and shorter, curlier tails.

Life scientists studying the domestication process have identified several genes of interest. One of these is BAZ1B. This gene plays a role in the maintenance of neural crest cells and controls their migration during embryological development. Presumably, changes in the expression of BAZ1B played a role in the domestication process.

Neural Crest Deficits and Williams Syndrome

As it turns out, there are two genetic disorders in modern humans that involve neural crest cells: Williams-Beuren syndrome (also called Williams syndrome) and Williams-Beuren region duplication syndrome. These genetic disorders involve the deletion or duplication, respectively, of a region of chromosome 7 (7q11.23). This chromosomal region harbors 28 genes. Craniofacial defects and altered cognitive and behavioral traits characterize these disorders. Specifically, people with these syndromes have cognitive limitations, smaller skulls, and elf-like faces, and they display excessive friendliness.

Among the 28 genes impacted by the two disorders is the human version of BAZ1B. This gene codes for a type of protein called a transcription factor. (Transcription factors play a role in regulating gene expression.)

The Role of BAZ1B in Neural Crest Cell Biology

To gain insight into the role BAZ1B plays in neural crest cell biology, the European research team developed induced pluripotent stem cell lines from (1) four patients with Williams syndrome, (2) three patients with Williams-Beuren region duplication syndrome, and (3) four people without either disorder. Then, they coaxed these cells in the laboratory to develop into neural crest cells.

Using a technique called RNA interference, they down-regulated BAZ1B in all three types of neural crest cells. By doing this, the researchers learned that changes in the expression of this gene altered the migration rates of the neural crest cells. Specifically, they discovered that neural crest cells developed from patients with Williams-Beuren region duplication syndrome migrated more slowly than control cells (generated from test subjects without either syndrome) and neural crest cells derived from patients with Williams syndrome migrated more rapidly than control cells.

The discovery that the BAZ1B gene influences neural crest cell migration is significant because these cells have to migrate to precise locations in the developing embryo to give rise to distinct cell types and tissues, including those that form craniofacial features.

Because BAZ1B encodes for a transcription factor, when its expression is altered, it alters the expression of genes under its control. The team discovered that 448 genes were impacted by down-regulating BAZ1B. They learned that many of these impacted genes play a role in craniofacial development. By querying databases of genes that correlate with genetic disorders, researchers also learned that, when defective, some of the impacted genes are known to cause disorders that involve altered facial development and intellectual disabilities.

Lastly, the researchers determined that the BAZ1B protein (again, a transcription factor) targets genes that influence dendrite and axon development (which are structures found in neurons that play a role in transmissions between nerve cells).

BAZ1B Gene Expression in Modern and Archaic Humans

With these findings in place, the researchers wondered if differences in BAZ1B gene expression could account for anatomical and cognitive differences between modern humans and archaic humans—hominins such as Neanderthals and Denisovans. To carry out this query, the researchers compared the genomes of modern humans to Neanderthals and Denisovans, paying close attention to DNA sequence differences in genes under the influence of BAZ1B.

This comparison uncovered differences in the regulatory region of genes targeted by the BAZ1B transcription factor, including genes that control neural crest cell activities and craniofacial anatomy. In other words, the researchers discovered significant genetic differences in gene expression among modern humans and Neanderthals and Denisovans. And these differences strongly suggest that anatomical and cognitive differences existed between modern humans and Neanderthals and Denisovans.

Did Humans Domesticate Themselves?

The researchers interpret their findings as evidence for the self-domestication hypothesis—the idea that we domesticated ourselves after the evolutionary lineage that led to modern humans split from the Neanderthal/Denisovan line (around 600,000 years ago). In other words, just as modern humans domesticated dogs, cats, cattle, and sheep, we domesticated ourselves, leading to changes in our anatomical features that parallel changes (such as friendlier faces) in the features of animals we domesticated. Along with these anatomical changes, our self-domestication led to the high levels of cooperativeness characteristic of modern humans.

On one hand, this is an interesting account that does seem to have some experimental support. But on the other, it is hard to escape the feeling that the idea of self-domestication as the explanation for the origin of modern humans is little more than an evolutionary just-so story.

It is worth noting that some evolutionary biologists find this account unconvincing. One is William Tecumseh Fitch III—an evolutionary biologist at the University of Vienna. He is skeptical of the precise parallels between animal domestication and human self-domestication. He states, “These are processes with both similarities and differences. I also don’t think that mutations in one or a few genes will ever make a good model for the many, many genes involved in domestication.”2

Adding to this skepticism is the fact that nobody has anything beyond a speculative explanation for why humans would domesticate themselves in the first place.

Genetic Differences Support the Idea of Human Exceptionalism

Regardless of the mechanism that produced the genetic differences between modern and archaic humans, this work can be enlisted in support of human uniqueness and exceptionalism.

Though the claim of human exceptionalism is controversial, a minority of scientists operating within the scientific mainstream embrace the idea that modern humans stand apart from all other extant and extinct creatures, including Neanderthals and Denisovans. These anthropologists argue that the following suite of capacities uniquely possessed by modern humans accounts for our exceptional nature:

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

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

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

In effect, these qualities could be viewed as scientific descriptors of the image of God, if one adopts a resemblance view for the image of God.

This study demonstrates that, at a genetic level, modern humans appear to be uniquely designed to be friendlier, more cooperative, and less aggressive than other hominins—in part accounting for our capacity to form complex hierarchical social structures.

To put it differently, the unique capability of modern humans to form complex, social hierarchies no longer needs to be inferred from the fossil and archaeological records. It has been robustly established by comparative genomics in combination with laboratory studies.

A Creation Model Perspective on Human Origins

This study not only supports human exceptionalism but also affirms RTB’s human origins model.

RTB’s biblical creation model identifies hominins such as Neanderthals and the Denisovans as animals created by God. These extraordinary creatures possessed enough intelligence to assemble crude tools and even adopt some level of “culture.” However, the RTB model maintains that these hominids were not spiritual creatures. They were not made in God’s image. RTB’s model reserves this status exclusively for Adam and Eve and their descendants (modern humans).

Our model predicts many biological similarities will be found between the hominins and modern humans, but so too will significant differences. The greatest distinction will be observed in cognitive capacity, behavioral patterns, technological development, and culture—especially artistic and religious expression.

The results of this study fulfill these two predictions. Or, to put it another way, the RTB model’s interpretation of the hominins and their relationship to modern humans aligns with “mainstream” science.

But what about the similarities between the genetic fingerprint of modern humans and the genetic changes responsible for animal domestication that involve BAZ1B and genes under its influence?

Instead of viewing these features as traits that emerged through parallel and independent evolutionary histories, the RTB human origins model regards the shared traits as reflecting shared designs. In this case, through the process of domestication, modern humans stumbled upon the means (breeding through artificial selection) to effect genetic changes in wild animals that resemble some of the designed features of our genome that contribute to our unique and exceptional capacity for cooperation and friendliness.

It is true: studying the domestication process does, indeed, tell us something exceptionally important about who we are.

Resources

Endnotes
  1. Matteo Zanella et al., “Dosage Analysis of the 7q11.23 Williams Region Identifies BAZ1B as a Major Human Gene Patterning the Modern Human Face and Underlying Self-Domestication,” Science Advances 5, no. 12 (December 4, 2019): eaaw7908, doi:10.1126/sciadv.aaw7908.
  2. Michael Price, “Early Humans Domesticated Themselves, New Genetic Evidence Suggests,” Science (December 4, 2019), doi:10.1126/science.aba4534.

Reprinted with permission by the author

Original article at:

https://reasons.org/explore/blogs/the-cells-design

Ancient DNA Indicates Modern Humans Are One-of-a-Kind

By Fazale Rana – February 19, 2020

The wonderful thing about tiggers
Is tiggers are wonderful things!
Their tops are made out of rubber
Their bottoms are made out of springs!
They’re bouncy, trouncy, flouncy, pouncy
Fun, fun, fun, fun, fun!
But the most wonderful thing about tiggers is
I’m the only one!1

With eight grandchildren and counting (number nine will be born toward the end of February), I have become reacquainted with children’s stories. Some of the stories my grandchildren want to hear are new, but many of them are classics. It is fun to see my grandchildren experiencing the same stories and characters I enjoyed as a little kid.

Perhaps my favorite children’s book of all time is A. A. Milne’s (1882–1956) Winnie-the-Pooh. And of all the characters that populated Pooh Corner, my favorite character is the ineffable Tigger—the self-declared one-of-a-kind.

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A. A. Milne. Credit: Wikipedia

For many people (such as me), human beings are like Tigger. We are one-of-a-kind among creation. As a Christian, I take the view that we are unique and exceptional because we alone have been created in God’s image.

For many others, the Christian perspective on human nature is unpopular and offensive. Who are we to claim some type of special status? They insist that humans aren’t truly unique and exceptional. We are not fundamentally different from other creatures. If anything, we differ only in degree, not kind. Naturalists and others assert that there is no evidence that human beings bear God’s image. In fact, some would go so far as to claim that creatures such as Neanderthals were quite a bit like us. They maintain that these hominins were “exceptional,” just like us. Accordingly, if we are one-of-a-kind it is because, like Tigger, we have arrogantly declared ourselves to be so, when in reality we are no different from any of the other characters who make their home at Pooh Corner.

Despite this pervasive and popular challenge to human exceptionalism (and the image-of-God concept), there is mounting evidence that human beings stand apart from all extant creatures (such as the great apes) and extinct creatures (such as Neanderthals). This growing evidence can be marshaled to make a scientific case that as human beings we, indeed, are image bearers.

As a case in point, many archeological studies affirm human uniqueness and exceptionalism. (See the Resources section for a sampling of some of this work.) These studies indicate that human beings alone possess a suite of characteristics that distinguish us from all other hominins. I regard these qualities as scientific descriptors of the image of God:

  • Capacity for symbolism
  • Ability for open-ended manipulation of symbols
  • Theory of mind
  • Capacity to form complex, hierarchical social structures

Other studies have identified key differences between the brains of modern humans and Neanderthals. (For a sample of this evidence see the Resources section.) One key difference relates to skull shape. Neanderthals (and other hominins) possessed an elongated skull. In contradistinction, our skull shape is globular. The globularity allows for the expansion of the parietal lobe. This is significant because an expanded parietal lobe explains a number of unique human characteristics:

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

Again, I connect these scientific qualities to the image of God.

Now, two recent studies add to the case for human exceptionalism. They involve genetic comparisons of modern humans with both Neanderthals and Denisovans. Through the recovery and sequencing of ancient DNA, we have high quality genomes for these hominins that we can analyze and compare to the genomes of modern humans.

While the DNA sequences of protein-coding genes in modern human genomes and the genomes of these two extant hominins is quite similar, both studies demonstrate that the gene expression is dramatically different. That difference accounts for anatomical differences between humans and these two hominins and suggests that significant cognitive differences exist as well.

Differences in Gene Regulation

To characterize gene expression patterns in Neanderthals and Denisovans and compare them to modern humans, researchers from Vanderbilt University (VU) used statistical methods to develop a mathematical model that would predict gene expression profiles from the DNA sequences of genomes.2 They built their model using DNA sequences and gene expression data (measured from RNA produced by transcription) for a set of human genomes. To ensure that their model could be used to assess gene expression for Neanderthals and Denisovans, the researchers paid close attention to the gene expression pattern for genes in the human genome that were introduced when modern humans and Neanderthals presumably interbred and compared their expression to human genes that were not of Neanderthal origin.

blog__inline--ancient-dna-indicates-modern-humans-2The Process of Gene
Expression.
Credit: Shutterstock

With their model in hand, the researchers analyzed the expression profile for nearly 17,000 genes from the Altai Neanderthal. Their model predicts that 766 genes in the Neanderthal genome had a different expression profile than the corresponding genes in modern humans. As it turns out, the differentially expressed genes in the Neanderthal genomes failed to be incorporated into the human genome after interbreeding took place, suggesting to the researchers that these genes are responsible for key anatomical and physiological differences between modern humans and Neanderthals.

The VU investigators determined that these 766 deferentially expressed genes play roles in reproduction, forming skeletal structures, and the functioning of cardiovascular and immune systems.

Then, the researchers expanded their analysis to include two other Neanderthal genomes (from the Vindija and Croatian specimens) and the Denisovan genome. The researchers learned that the gene expression profiles of the three Neanderthal genomes were more similar to one another than they were to either the gene expression patterns of modern human and Denisovan genomes.

This study clearly demonstrates that significant differences existed in the regulation of gene expression in modern humans, Neanderthals, and Denisovans and that these differences account for biological distinctives between the three hominin species.

Differences in DNA Methylation

In another study, researchers from Israel compared gene expression profiles in modern human genomes with those from and Neanderthals and Denisovans using a different technique. This method assesses DNA methylation.3 (Methylation of DNA downregulates gene expression, turning genes off.)

Methylation of DNA influences the degradation process for this biomolecule. Because of this influence, researchers can determine the DNA methylation pattern in ancient DNA by characterizing the damage to the DNA fragments isolated from fossil remains.

Using this technique, the researchers measured the methylation pattern for genomes of two Neanderthals (Altai and Vindija) and a Denisovan and compared these patterns with genomes recovered from the remains of three modern humans, dating to 45,000 years in age, 8,000 years in age, and 7,000 years in age, respectively. They discovered 588 genes in modern human genomes with a unique DNA methylation pattern, indicating that these genes are expressed differently in modern humans than in Neanderthals and Denisovans. Among the 588 genes, researchers discovered some that influence the structure of the pelvis, facial morphology, and the larynx.

The researchers think that differences in gene expression may explain the anatomical differences between modern humans and Neanderthals. They also think that this result indicates that Neanderthals lacked the capacity for speech.

What Is the Relationship between Modern Humans and Neanderthals?

These two genetic studies add to the extensive body of evidence from the fossil record, which indicates that Neanderthals are biologically distinct from modern humans. For a variety of reasons, some Christian apologists and Intelligent Design proponents classify Neanderthals and modern humans into a single group, arguing that the two are equivalent. But these two studies comparing gene regulation profiles make it difficult to maintain that perspective.

Modern Humans, Neanderthals, and the RTB Human Origins Model

RTB’s human origins model regards Neanderthals (and other hominins) as creatures made by God, without any evolutionary connection to modern humans. These extraordinary creatures walked erect and possessed some level of intelligence, which allowed them to cobble together tools and even adopt some level of “culture.” However, our model maintains that the hominins were not spiritual beings made in God’s image. RTB’s model reserves this status exclusively for modern humans.

Based on our view, we predict that biological similarities will exist among the hominins and modern humans to varying degrees. In this regard, we consider the biological similarities to reflect shared designs, not a shared evolutionary ancestry. We also expect biological differences because, according to our model, the hominins would belong to different biological groups from modern humans.

We also predict that significant cognitive differences would exist between modern humans and the other hominins. These differences would be reflected in brain anatomy and behavior (inferred from the archeological record). According to our model, these differences reflect the absence of God’s image in the hominins.

The results of these two studies affirm both sets of predictions that flow from the RTB human origins model. The differences in gene regulation between modern human and Neanderthals is precisely what our model predicts. These differences seem to account for the observed anatomical differences between Neanderthals and modern humans observed from fossil remains.

The difference in the regulation of genes affecting the larynx is also significant for our model and the idea of human exceptionalism. One of the controversies surrounding Neanderthals relates to their capacity for speech and language. Yet, it is difficult to ascertain from fossil remains if Neanderthals had the anatomical structures needed for the vocalization range required for speech. The differences in the expression profiles for genes that control the development and structure of the larynx in modern humans and Neanderthals suggests that Neanderthals lacked the capacity for speech. This result dovetails nicely with the differences in modern human and Neanderthal brain structure, which suggest that Neanderthals also lacked the neural capacity for language and speech. And, of course, it is significant that there is no conclusive evidence for Neanderthal symbolism in the archeological record.

With these two innovative genetic studies, the scientific support for human exceptionalism continues to mount. And the wonderful thing about this insight is that it supports the notion that as human beings we are the only ones who bear God’s image and can form a relationship with our Creator.

Resources

Behavioral Differences between Humans and Neanderthals

Biological Differences between Humans and Neanderthals

Endnotes
  1. Richard M. Sherman and Robert B. Sherman, composers, “The Wonderful Thing about Tiggers” (song), released December 1968.
  2. Laura L. Colbran et al., “Inferred Divergent Gene Regulation in Archaic Hominins Reveals Potential Phenotypic Differences,” Nature Evolution and Ecology 3 (November 2019): 1598-606, doi:10.1038/s41559-019-0996-x.
  3. David Gokhman et al., “Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan,” Science 344, no. 6183 (May 2, 2014): 523–27, doi:1126/science.1250368; David Gokhman et al., “Extensive Regulatory Changes in Genes Affecting Vocal and Facial Anatomy Separate Modern from Archaic Humans,” bioRxiv, preprint (October 2017), doi:10.1101/106955.

Reprinted with permission by the author

Original article at:

https://reasons.org/explore/blogs/the-cells-design

Cave Art Tells the Story of Human Exceptionalism

By Fazale Rana – February 5, 2020

Comic books intrigue me. They are a powerful storytelling vehicle. The combination of snapshot-style imagery, along with narration and dialogue, allows the writer and artist to depict action and emotion in a way that isn’t possible using the written word alone. Comic books make it easy to depict imaginary worlds. And unlike film, comics engage the reader in a deeper, more personal way. The snapshot format requires the reader to make use of their imagination to fill in the missing details. In this sense, the reader becomes an active participant in the storytelling process.

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Figure 1: Speech Bubbles on a
Comic Strip Background. Credit:
Shutterstock

In America, comics burst onto the scene in the 1930s, but the oldest comics (at least in Europe) trace their genesis to Rodolphe Töpffer (1799-1846). Considered by many to be “the father of comics,” Töpffer was a Swiss teacher, artist, and author who became well-known for his illustrated books—works that bore similarity to modern-day comics.

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Figure 2: Rodolphe Töpffer, Self
Portrait, 1840. Credit: Wikipedia

Despite his renown, Töpffer wasn’t the first comic book writer and artist. That claim to fame belongs to long forgotten artists from prehistory. In fact, recent work by Australian and Indonesian researchers indicates that comics as a storytelling device dates to earlier than 44,000 years ago.

Seriously!

These investigators discovered and characterized cave art from a site on the Indonesian island of Sulawesi that depicts a pig and buffalo hunt. Researchers interpret this mural to be the oldest known recorded story1 —a comic book story on a cave wall.

This find, and others like it, provide important insight into our origins as human beings. From my perspective as a Christian apologist, this discovery is important for another reason. I see it as affirming the biblical teaching about humanity: God made human beings in his image.

The Find

Leading up to this discovery, archeologists had already identified and dated art on cave walls in Sulawesi and Borneo. This art, which includes hand stencils and depictions of animals, dates to older than 40,000 years in age and is highly reminiscent of the cave art of comparable age found in Europe.

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Figure 3: Hand Stencils from a Cave
in Southern Sulawesi. Credit:
Wikipedia.

In December 2017, an archeologist from Indonesia discovered the hunting mural in a cave (now called Leang Bulu’ Sipong 4) in the southern part of Sulawesi. The panel presents the viewer with an ensemble of pigs and small buffalo (called anoas), endemic to Sulawesi. Most intriguing about the artwork is the depiction of smaller human-like figures with animal features such as tails and snouts. In some instances, the figures appear to be holding spears and ropes. Scholars refer to these human-animal depictions as therianthropes.

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Figure 4: Illustration of a Pig Deer
Found in a Cave in Southern
Sulawesi. Credit: Wikipedia.

Dating the Find

Dating cave art can be notoriously difficult. One approach is to directly date the charcoal pigments used to make the art using radiocarbon methods. Unfortunately, the dates measured by this technique can be suspect because the charcoal used to make the art can be substantially older than the artwork itself.

Recently, archeologists have developed a new approach to date cave art. This method measures the levels of uranium and thorium in calcite deposits that form on top of the artwork. Calcite is continuously deposited on cave walls due to hydrological activity in the cave. As water runs down the cave walls, calcium carbonate precipitates onto the cave wall surface. Trace amounts of radioactive uranium are included in the calcium carbonate precipitates. This uranium decays into thorium, hence the ratio of uranium to thorium provides a measure of the calcite deposit’s age and, in turn, yields a minimum age for the artwork.

To be clear, this dating method has been the subject of much controversy. Some archeologists argue that the technique is unreliable because the calcite deposits are an open system. Once the calcite deposit forms, water will continue to flow over the surface. The water will solubilize part of the calcite deposit and along with it the trace amounts of uranium and thorium. Thus, because uranium is more soluble than thorium we get an artificially high level of thorium. So, when the uranium-thorium ratio is measured, it may make it appear as if the cave art is older than it actually is.

To ensure that the method worked as intended, the researchers only dated calcite deposits that weren’t porous (which is a sign that they have been partially re-dissolved) and they made multiple measurements from the surface of the deposit toward the interior. If this sequence of measurements produced a chronologically consistent set of ages, the researchers felt comfortable with the integrity of the calcite samples. Using this method, the researchers determined that the cave painting of the pig and buffalo hunt dates to older than 43,900 years.

Corroborating evidence gives the archeologists added confidence in this result. For example, the discovery of archeological finds in the Sulawesi cave site that were independently dated indicate that modern humans were in the caves between 40,000 to 50,000 years ago, in agreement with the measured age of the cave art.

The research team also noted that the animal and the therianthropes in the mural appear to have been created at the same time. This insight is important because therianthropes don’t appear in the cave paintings found in Europe until around 10,000 years ago. This observation means that it is possible that the therianthropes could have been added to the painting millennia after the animals were painted onto the cave wall. However, the researchers don’t think this is the case for at least three reasons. First, the same artistic style was used to depict the animals and therianthropes. Second, the technique and pigment used to create the figures is the same. And third, the degree of weathering is the same throughout the panel. None of these features would be expected if the therianthropes were a late addition to the mural.

Interpreting the Find

The researchers find the presence of therianthropes in 44,000+ year-old cave art significant. It indicates that humans in Sulawesi not only possessed the capacity for symbolism, but, more importantly, had the ability to conceive of things that did not exist in the material world. That is to say, they had a sense of the supernatural.

Some archeologists believe that the cave art reflects shamanic beliefs and visions. If this is the case, then it suggests that the therianthropes in the painting may reflect spirit animal helpers who ensured the success of the hunt. The size of the therianthropes supports this interpretation. These animal-human hybrids are depicted as much smaller than the pigs and buffalo. On the island of Sulawesi, both the pig and buffalo species in question were much smaller than modern humans.

Because this artwork depicts a hunt involving therianthropes, the researchers see rich narrative content in the display. It seems to tell a story that likely reflected the mythology of the Sulawesi people. You could say it’s a comic book on a cave wall.

Relationship between Cave Art in Europe and Asia

Cave art in Europe has been well-known and carefully investigated by archeologists and anthropologists for nearly a century. Now archeologists have access to a growing archeological record in Asia.

Art found at these sites is of the same quality and character as the European cave art. However, it is older. This discovery means that modern humans most likely had the capacity to make art even before beginning their migrations around the world from out of Africa (around 60,000 years ago).

As noted, the discovery of therianthropes at 44,000+ years in age in Sulawesi is intriguing because these types of figures don’t appear in cave art in Europe until around 10,000 years ago. But archeologists have discovered the lion-man statue in a cave site in Germany. This artifact, which depicts a lion-human hybrid, dates to around 40,000 years in age. In other words, therianthropes were part of the artwork of the first Europeans. It also indicates that modern humans in Europe had the capacity to envision imaginary worlds and held belief in a supernatural realm.

Capacity for Art and the Image of God

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. So, too, does our capacity for storytelling. As humans, we seem to be obsessed with both. Art and telling stories are manifestations of symbolism and open-ended generative capacity. 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 them within one another to create alternate possibilities.

As a Christian, I believe that our capacity to make art and to tell stories is an outworking of the image of God. As such, the appearance of art (as well as other artifacts that reflect our capacity for symbolism) serves as a diagnostic for the image of God in the archeological record. That record provides the means to characterize the mode and tempo of the appearance of behavior that reflect 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 make our first appearance as a species.

So, when did art (and symbolic capacity) first appear? Did art emerge suddenly? Did it appear gradually? Is artistic expression unique to human beings or did other hominins, such as Neanderthals, produce art too? Answers to these questions are vital to our case for human exceptionalism and, along with it, the image of God.

When Did the Capacity for Art First Appear?

Again, the simultaneous appearance of cave art in Europe and Asia indicates that the capacity for artistic expression (and, hence, symbolism) dates back to the time in prehistory before humans began to migrate around the world from out of Africa (around 60,000 years ago). This conclusion gains support from the recent discovery of a silcrete flake from a layer in the Blombos Cave that dates to about 73,000 years old. (The Blombos Cave is located around 150 miles east of Cape Town, South Africa.) A portion of an abstract drawing is etched into this flake.2

Linguist Shigeru Miyagawa believes that artistic expression emerged in Africa earlier than 125,000 years ago. Archeologists have discovered rock art produced by the San people that dates to 72,000 years ago. This art shares certain elements with European cave art. 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.3

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

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

In other words, the evidence indicates that our capacity for symbolism emerged at the time that our species first appears in the fossil record. Some archeologists claim that Neanderthals displayed the capacity for symbolism as well. If this claim proves true, then human beings don’t stand apart from other creatures. We aren’t special.

Did Neanderthals Have the Capacity to Create Art?

Claims of Neanderthal artistic expression abound in popular literature and appear in scientific journals. However, a number of studies question these claims. When taken as a whole, the evidence indicates that Neanderthals were cognitively inferior to modern humans.

So, when the evidence is considered as a whole, only human beings (modern humans) possess the capability for symbolism, open-ended generative capacity, and theory of mind—in my view, scientific descriptors of the image of God. The archeological record affirms the biblical view of human nature. It is also worth noting that the origin of our symbolic capacity seems to arise at the same time that modern humans appear in the fossil record, an observation I would expect given the biblical account of human origins.

Like the comics that intrigue me, this narrative resonates on a personal level. It seems as if the story told in the opening pages of the Old Testament is true.

Resources

Cave Art and the Image of God

The Modern Human Brain

Could Neanderthals Make Art?

Endnotes
  1. Maxime Aubert et al., “Earliest Hunting Scene in Prehistoric Art,” Nature 576 (December 11, 2019): 442–45, doi:10.1038/s41586-019-1806y.
  2. Shigeru Miyagawa, Cora Lesure, and Vitor A. Nóbrega, “Cross-Modality Information Transfer: A Hypothesis about the Relationship among Prehistoric Cave Paintings, Symbolic Thinking, and the Emergence of Language,” Frontiers in Psychology 9 (February 20, 2018): 115, doi:10.3389/fpsyg.2018.00115.
  3. Christopher S. Henshilwood et al., “An Abstract Drawing from the 73,000-Year-Old Levels at Blombos Cave, South Africa,” Nature 562 (September 12, 2018): 115–18, doi:10.1038/s41586-018-0514-3.

Reprinted with permission by the author

Original article at:

https://reasons.org/explore/blogs/the-cells-design

But Do Watches Replicate? Addressing a Logical Challenge to the Watchmaker Argument

By Fazale Rana – January 22, 2020

Were things better in the past than they are today? It depends who you ask.

Without question, there are some things that were better in years gone by. And, clearly, there are some historical attitudes and customs that, today, we find hard to believe our ancestors considered to be an acceptable part of daily life.

It isn’t just attitudes and customs that change over time. Ideas change, too—some for the better, some for the worst. Consider the way doing science has evolved, particularly the study of biological systems. Was the way we approached the study of biological systems better in the past than it is today?

It depends who you ask.

As an old-earth creationist and intelligent design proponent, I think the approach biologists took in the past was better than today for one simple reason. Prior to Darwin, teleology was central to biology. In the late 1700s and early to mid-1800s, life scientists viewed biological systems as the product of a Mind. Consequently, design was front and center in biology.

As part of the Darwinian revolution, teleology was cast aside. Mechanism replaced agency and design was no longer part of the construct of biology. Instead of reflecting the purposeful design of a Mind, biological systems were now viewed as the outworking of unguided evolutionary mechanisms. For many people in today’s scientific community, biology is better for it.

Prior to Darwin, the ideas shaped by thinkers (such as William Paley) and biologists (such as Sir Richard Owen) took center stage. Today, their ideas have been abandoned and are often lampooned.

But, advances in my areas of expertise (biochemistry and origins-of-life research) justify a return to the design hypothesis, indicating that there may well be a role for teleology in biology. In fact, as I argue in my book The Cell’s Design, the latest insights into the structure and function of biomolecules bring us full circle to the ideas of William Paley (1743-1805), revitalizing his Watchmaker argument for God’s existence.

In my view, many examples of molecular-level biomachinery stand as strict analogs to human-made machinery in terms of architecture, operation, and assembly. The biomachines found in the cell’s interior reveal a diversity of form and function that mirrors the diversity of designs produced by human engineers. The one-to-one relationship between the parts of man-made machines and the molecular components of biomachines is startling (e.g., the flagellum’s hook). I believe Paley’s case continues to gain strength as biochemists continue to discover new examples of biomolecular machines.

The Skeptics’ Challenge

Despite the powerful analogy that exists between machines produced by human designers and biomolecular machines, many skeptics continue to challenge the revitalized watchmaker argument on logical grounds by arguing in the same vein as David Hume.1 These skeptics assert that significant and fundamental differences exist between biomachines and human creations.

In a recent interaction on Twitter, a skeptic raised just such an objection. Here is what he wrote:

“Do [objects and machines designed by humans] replicate with heritable variation? Bad analogy, category mistake. Same one Paley made with his watch on the heath centuries ago.”

In other words, biological systems replicate, whereas devices and artefacts made by human beings don’t. This difference is fundamental. Such a dissimilarity is so significant that it undermines the analogy between biological systems (in general) and biomolecular machines (specifically) and human designs, invalidating the conclusion that life must stem from a Mind.

This is not the first time I have encountered this objection. Still, I don’t find it compelling because it fails to take into account manmade machines that do, indeed, replicate.

Von Neumann’s Universal Self-Constructor

In the 1940s, mathematician, physicist, and computer scientist John von Neumann (1903–1957) designed a hypothetical machine called a universal constructor. This machine is a conceptual apparatus that can take materials from the environment and build any machine, including itself. The universal constructor requires instructions to build the desired machines and to build itself. It also requires a supervisory system that can switch back and forth between using the instructions to build other machines and copying the instructions prior to the replication of the universal constructor.

Von Neumann’s universal constructor is a conceptual apparatus, but today researchers are actively trying to design and build self-replicating machines.2 Much work needs to be done before self-replicating machines are a reality. Nevertheless, one day machines will be able to reproduce, making copies of themselves. To put it another way, reproduction isn’t necessarily a quality that distinguishes machines from biological systems.

It is interesting to me that a description of von Neumann’s universal constructor bears remarkable similarity to a description of a cell. In fact, in the context of the origin-of-life problem, astrobiologists Paul Davies and Sara Imari Walker noted the analogy between the cell’s information systems and von Neumann’s universal constructor.3 Davies and Walker think that this analogy is key to solving the origin-of-life problem. I would agree. However, Davies and Walker support an evolutionary origin of life, whereas I maintain that the analogy between cells and von Neumann’s universal constructor adds vigor to the revitalized Watchmaker argument and, in turn, the scientific case for a Creator.

In other words, the reproduction objection to the Watchmaker argument has little going for it. Self-replication is not the basis for viewing biomolecular machines as fundamentally dissimilar to machines created by human designers. Instead, self-replication stands as one more machine-like attribute of biochemical systems. It also highlights the sophistication of biological systems compared to systems produced by human designers. We are a far distance away from creating machines that are as sophisticated as the machines found inside the cell. Nevertheless, as we continue to move in that direction, I think the case for a Creator will become even more compelling.

Who knows? With insights such as these maybe one day we will return to the good old days of biology, when teleology was paramount.

Resources

Biomolecular Machines and the Watchmaker Argument

Responding to Challenges to the Watchmaker Argument

Endnotes
  1. “Whenever you depart, in the least, from the similarity of the cases, you diminish proportionably the evidence; and may at last bring it to a very weak analogy, which is confessedly liable to error and uncertainty.” David Hume, “Dialogues Concerning Natural Religion,” in Classics of Western Philosophy, 3rd ed., ed. Steven M. Cahn, (1779; repr., Indianapolis: Hackett, 1990), 880.
  2. For example, Daniel Mange et al., “Von Neumann Revisited: A Turing Machine with Self-Repair and Self-Reproduction Properties,” Robotics and Autonomous Systems 22 (1997): 35-58, https://doi.org/10.1016/S0921-8890(97)00015-8; Jean-Yves Perrier, Moshe Sipper, and Jacques Zahnd, “Toward a Viable, Self-Reproducing Universal Computer,” Physica D: Nonlinear Phenomena
     97, no. 4 (October 15, 1996): 335–52, https://doi.org/10.1016/0167-2789(96)00091-7; Umberto Pesavento, “An Implementation of von Neumann’s Self-Reproducing Machine,” Artificial Life 2, no. 4 (Summer 1995): 337–54, https://doi.org/10.1162/artl.1995.2.4.337.
  3. Sara Imari Walker and Paul C. W. Davies, “The Algorithmic Origins of Life,” Journal of the Royal Society Interface 10 (2013), doi:10.1098/rsif.2012.0869.

Reprinted with permission by the author

Original article at:

https://reasons.org/explore/blogs/the-cells-design

The Flagellum’s Hook Connects to the Case for a Creator

By Fazale Rana – January 8, 2020

What would you say is the most readily recognizable scientific icon? Is it DNA, a telescope, or maybe a test tube?

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Figure 1: Scientific Icons. Image credit: Shutterstock

Marketing experts recognize the power of icons. When used well, icons prompt consumers to instantly identify a brand or product. They can also communicate a powerful message with a single glance.

Though many skeptics question if it’s science at all, the intelligent design movement has identified a powerful icon that communicates its message. Today, when most people see an image the bacterial flagellum they immediately think: Intelligent Design.

This massive protein complex powerfully communicates sophisticated engineering that could only come from an Intelligent Agent. And along these lines, it serves as a powerful piece of evidence for a Creator’s handiwork. Careful study of its molecular architecture and operation provides detailed evidence that an Intelligent Agent must be responsible for biochemical systems and, hence, the origin of life. And, as it turns out, the more we learn about the bacterial flagellum, the more evident it becomes that a Creator must have played a role in the origin and design of life—at least at the biochemical level—as new research from Japan illustrates.1

The Bacterial Flagellum

This massive protein complex looks like a whip extending from the bacterial cell surface. Some bacteria have only a single flagellum, others possess several flagella. Rotation of the flagellum(a) allows the bacterial cell to navigate its environment in response to various chemical signals.

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Figure 2: Typical Bacteria with Flagella. Image credit: Shutterstock

An ensemble of 30 to 40 different proteins makes up the typical bacterial flagellum. These proteins function in concert as a literal rotary motor. The flagellum’s components include a rotor, stator, drive shaft, bushing, universal joint, and propeller. It is essentially a molecular-sized electrical motor directly analogous to human-produced rotary motors. The rotation is powered by positively charged hydrogen ions flowing through the motor proteins embedded in the inner membrane.

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Figure 3: The Bacterial Flagellum. Image credit: Wikipedia

The Bacterial Flagellum and the Revitalized Watchmaker Argument

Typically, when intelligent design proponents/creationists use the bacterial flagellum to make the case for a Creator, they focus the argument on its irreducibly complex nature. I prefer a different tact. I like to emphasize the eerie similarity between rotary motors created by human designers and nature’ bacterial flagella.

The bacterial flagellum is just one of a large number of protein complexes with machine-like attributes. (I devote an entire chapter to biomolecular machines in my book The Cell’s Design.) Collectively, these biomolecular machines can be deployed to revitalize the Watchmaker argument.

Popularized by William Paley in the eighteenth century, this argument states that as a watch requires a watchmaker, so too, life requires a Creator. Following Paley’s line of reasoning, a machine is emblematic of systems produced by intelligent agents. Biomolecular machines display the same attributes as human-crafted machines. Therefore, if the work of intelligent agents is necessary to explain the genesis of machines, shouldn’t the same be true for biochemical systems?

Skeptics inspired by atheist philosopher David Hume have challenged this simple, yet powerful, analogy. They argue that the analogy would be compelling only if there is a high degree of similarity between the objects that form the analogy. Skeptics have long argued that biochemical systems and machines are too dissimilar to make the Watchmaker argument work.

However, the striking similarity between the machine parts of the bacterial flagellum and human-made machines cause this objection to evaporate. New work on flagella by Japanese investigators lends yet more support to the Watchmaker analogy.

New Insights into the Structure and Function of the Flagellum’s Universal Joint

The flagellum’s universal joint (sometimes referred to as the hook) transfers the torque generated by the motor to the propeller. The research team wanted to develop a deeper understanding of the relationship between the molecular structure of the hook and how the structural features influence its function as a universal joint.

Comprised of nearly 100 copies (monomers) of a protein called FlgE, the hook is a curved, tube-like structure with a hollow interior. FlgE monomers stack on top of each other to form a protofilament. Eleven protofilaments organize to form the hook’s tube, with the long axis of the protofilament aligning to form the long axis of the hook.

Each FlgE monomer consists of three domains, called D0, D1, and D2. The researchers discovered that when the FlgE monomers stack to form a protofilament, the D0, D1, and D2 domains of each of the monomers align along the length of the protofilament to form three distinct regions in the hook. These layers have been labeled the tube layer, the mesh layer, and the spring layer.

During the rotation of the flagellum, the protofilaments experience compression and extension. The movement of the domains, which changes their spatial arrangement relative to one another, mediates the compression and extension. These domain movements allow the hook to function as a universal joint that maintains a rigid tube shape against a twisting “force,” while concurrently transmitting torque from the motor to the flagellum’s filament as it bends along its axis.

Regardless of one’s worldview, it is hard not to marvel at the sophisticated and elegant design of the flagellum’s hook!

The Bacterial Flagellum and the Case for a Creator

If the Watchmaker argument holds validity, it seems reasonable to think that the more we learn about protein complexes, such as the bacterial flagellum, the more machine-like they should appear to be. This work by the Japanese biochemists bears out this assumption. The more we characterize biomolecular machines, the more reason we have to think that life stems from a Creator’s handiwork.

Dynamic properties of the hook assembly add to the Watchmaker argument (when applied to the bacterial flagellum). This structure is much more sophisticated and ingenious than the design of a typical universal joint crafted by human designers. This elegance and ingenuity of the hook are exactly the attributes I would expect if a Creator played a role in the origin and design of life.

Message received, loud and clear.

Resources

The Bacterial Flagellum and the Case for a Creator

Can Intelligent Design Be Part of the Scientific Construct?

Endnotes
  1. Takayuki Kato et al., “Structure of the Native Supercoiled Flagellar Hook as a Universal Joint,” Nature Communications 10 (2019): 5295, doi:10.1038/s4146.

Reprinted with permission by the author

Original article at:

https://reasons.org/explore/blogs/the-cells-design

Genome Code Builds the Case for Creation

By Fazale Rana – December 18, 2019

A few days ago, I was doing a bit of Christmas shopping for my grandkids and I happened across some really cool construction kits, designed to teach children engineering principles while encouraging imaginative play. For those of you who still have a kid or two on your Christmas list, here are some of the products that caught my eye:

These building block sets are a far cry from the simple Lego kits I played with as a kid.

As cool as these construction toys may be, they don’t come close to the sophisticated construction kit cells use to build the higher-order structures of chromosomes. This point is powerfully illustrated by the insights of Italian investigator Giorgio Bernardi. Over the course of the last several years, Bernardi’s research teams have uncovered design principles that account for chromosome structure, a set of rules that he refers to as the genome code.1

To appreciate these principles and their theological implications, a little background information is in order. (For those readers familiar with chromosome structure, skip ahead to The Genome Code.)

Chromosomes

DNA and proteins interact to make chromosomes. Each chromosome consists of a single DNA molecule wrapped around a series of globular protein complexes. These complexes repeat to form a supramolecular structure resembling a string of beads. Biochemists refer to the “beads” as nucleosomes.

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Figure 1: Nucleosome Structure. Image credit: Shutterstock

The chain of nucleosomes further coils to form a structure called a solenoid. In turn, the solenoid condenses to form higher-order structures that constitute the chromosome.

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Figure 2: Chromosome Structure Image credit: Shutterstock

Between cell division events (called the interphase of the cell cycle), the chromosome exists in an extended diffuse form that is not readily detectable when viewed with a microscope. Just prior to and during cell division, the chromosome condenses to form its readily recognizable compact structures.

Biologists have discovered that there are two distinct regions—labeled euchromatin and heterochromatin for chromosomes in the diffuse state. Euchromatin is resistant to staining with dyes that help researchers view it with a microscope. On the other hand, heterochromatin stains readily. Biologists believe that heterochromatin is more tightly packed (and, hence, more readily stained) than euchromatin. They have also learned that heterochromatin associates with the nuclear envelope.

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Figure 3: Structure of the Nucleus Showing the Distribution of Euchromatin and Heterochromatin. Image credit: Wikipedia

The Genome Code

Historically, biologists have viewed chromosomes as consisting of compositionally distinct units called isochores. In vertebrate genomes, five isochores exist (L1, L2, H1, H2, and H3). The isochores differ in the composition of guanine- and cytosine-containing deoxyribonucleotides (two of the four building blocks of DNA). The GC composition increases from L1 to H3. Gene density also increases, with the H3 isochore possessing the greatest number of genes. On the other hand, the size of DNA pieces of compositional homogeneity decreases from L1 to H3.

Bernardi and his collaborators have developed evidence that the isochores reflect a fundamental unit of chromosome organization. The H isochores correspond to GC-rich euchromatin (containing most of the genes) and the L isochores correspond to GC-poor heterochromatin (characterized by gene deserts).

Bernardi’s research teams have demonstrated that the two groups of isochores are characterized by different distributions of DNA sequence elements. GC-poor isochores contain a disproportionately high level of oligo A sequences while GC-rich isochores harbor a disproportionately high level of oligo G sequences. These two different types of DNA sequence elements form stiff structures that mold the overall three-dimensional architecture of chromosomes. For example, oligo A sequences introduce curvature to the DNA double helix. This topology allows the double helix to wrap around the protein core that forms nucleosomes. The oligo G sequence elements adopt a topology that weakens binding to the proteins that form the nucleosome core. As Bernardi points out, “There is a fundamental link between DNA structure and chromatin structure, the genomic code.”2

In other words, the genomic code refers to a set of DNA sequence elements that:

  1. Directly encodes and molds chromosome structure (while defining nucleosome binding),
  2. Is pervasive throughout the genome, and
  3. Overlaps the genetic code by constraining sequence composition and gene structure.

Because of the existence of the genomic code, variations in DNA sequence caused by mutations will alter the structure of chromosomes and lead to deleterious effects.

The bottomline: Most of the genomic sequence plays a role in establishing the higher-order structures necessary for chromosome formation.

Genomic Code Challenges the Junk DNA Concept

According to Bernardi, the discovery of the genomic code explains the high levels of noncoding DNA sequences in genomes. Many people view such sequences as vestiges of an evolutionary history. Because of the existence and importance of the genomic code, the vast proportion of noncoding DNA found in vertebrate genomes must be viewed as functionally vital. According to Bernardi:

Ohno, mostly focusing on pseudo-genes, proposed that non-coding DNA was “junk DNA.” Doolittle and Sapienza and Orgel and Crick suggested the idea of “selfish DNA,” mainly involving transposons visualized as molecular parasites rather than having an adaptive function for their hosts. In contrast, the ENCODE project claimed that the majority (~80%) of the genome participated “in at least one biochemical RNA-and/or chromatin-associated event in at least one cell type.”…At first sight, the pervasive involvement of isochores in the formation of chromatin domains and spatial compartments seems to leave little or no room for “junk” or “selfish” DNA.3

The ENCODE Project

Over the last decade or so, ENCODE Project scientists have been seeking to identify the functional DNA sequence elements in the human genome. The most important landmark for the project came in the fall of 2012 when the ENCODE Project reported phase II results. (Currently, ENCODE is in phase IV.) To the surprise of many, the project reported that around 80 percent of the human genome displays biochemical activity—hence, function—with many scientists anticipating that that percentage would increase as phases III and IV moved toward completion.

The ENCODE results have generated quite a bit of controversy, to say the least. Some researchers accept the ENCODE conclusions. Others vehemently argue that the conclusions fly in the face of the evolutionary paradigm and, therefore, can’t be valid. Of course, if the ENCODE Project conclusions are correct, then it becomes a boon for creationists and intelligent design advocates.

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. These critics assert that, at most, about ten percent of the human genome is truly functional, with the remainder of the activity reflecting biochemical noise and experimental artifacts.

However, as Bernardi points out, his work (independent of the ENCODE Project) affirms the project’s conclusions. In this case, the so-called junk DNA plays a critical role in molding the structures of chromosomes and must be considered functional.

Function for “Junk DNA”

Bernardi’s work is not the first to recognize pervasive function of noncoding DNA. Other researchers have identified other functional attributes of noncoding DNA. To date, researchers have identified at least five distinct functional roles that noncoding DNA plays in genomes.

  1. Helps in gene regulation
  2. Functions as a mutational buffer
  3. Forms a nucleoskeleton
  4. Serves as an attachment site for mitotic apparatus
  5. Dictates three-dimensional architecture of chromosomes

A New View of Genomes

These types of insights are forcing us to radically rethink our view of the human genome. It appears that genomes are incredibly complex, sophisticated biochemical systems and most of the genes serve useful and necessary functions.

We have come a long way from the early days of the human genome project. Just 15 years ago, many scientists estimated that around 95 percent of the human genome consists of junk. That acknowledgment seemingly provided compelling evidence that humans must be the product of an evolutionary history. Today, 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 provides reasons to think that it is the handiwork of our Creator. A skeptic might wonder why a Creator would make genomes littered with so much junk. But if a vast proportion of genomes consists of functional sequences, then this challenge no longer carries weight and it becomes more and more reasonable to interpret genomes from within a creation model/intelligent design framework.

What a Christmas gift!

Resources

Junk DNA Regulates Gene Expression

Junk DNA Serves as a Mutational Buffer

Junk DNA Serves a Nucleoskeletal Role

Junk DNA Plays a Role in Cell Division

ENCODE Project

Studies that Affirm the ENCODE Results

Endnotes
  1. Giorgio Bernardi, “The Genomic Code: A Pervasive Encoding/Molding of Chromatin Structures and a Solution of the ‘Non-Coding DNA’ Mystery,” BioEssays 41, no. 12 (November 8, 2019), doi:10.1002/bies.201900106.
  2. Bernardi, “The Genomic Code.”
  3. Bernardi, “The Genomic Code.”

Reprinted with permission by the author

Original article at:

https://reasons.org/explore/blogs/the-cells-design

Mutations, Cancer, and the Case for a Creator


By Fazale Rana – December 11, 2019

Cancer. Perhaps no other word evokes more fear, anger, and hopelessness.

It goes without saying that cancer is an insidious disease. People who get cancer often die way too early. And even though a cancer diagnosis is no longer an immediate death sentence—thanks to biomedical advances—there are still many forms of cancer that are difficult to manage, let alone effectively treat.

Cancer also causes quite a bit of consternation for those of us who use insights from science to make a case for a Creator. From my vantage point, one of the most compelling reasons to think that a Creator exists and played a role in the origin and design of life is the elegant, sophisticated, and ingenious designs of biochemical systems. And yet, when I share this evidence with skeptics—and even seekers—I am often met with resistance in the form of the question: What about cancer?

Why Would God Create a World Where Cancer Is Possible?

In effect, this question typifies one of the most common—and significant—objections to the design argument. If a Creator is responsible for the designs found in biochemistry, then why are so many biochemical systems seemingly flawed, inelegant, and poorly designed?

The challenge cancer presents for the design argument carries an added punch. It’s one thing to cite inefficiency of protein synthesis or the error-prone nature of the rubisco enzyme, but it’s quite another to describe the suffering of a loved one who died from cancer. There’s an emotional weight to the objection. These deaths feel horribly unjust.

Couldn’t a Creator design biochemistry so that a disease as horrific as cancer would never be possible—particularly if this Creator is all-powerful, all-knowing, and all-good?

I think it’s possible to present a good answer to the challenge that cancer (and other so-called bad designs) poses for the design argument. Recent insights published by a research duo from Cambridge University in the UK help make the case.1

A Response to the Bad Designs in Biochemistry and Biology

Because the “bad designs” challenge is so significant (and so frequently expressed), I devoted an entire chapter in The Cell’s Design to addressing the apparent imperfections of biochemical systems. My goal in that chapter was to erect a framework that comprehensively addresses this pervasive problem for the design argument.

In the face of this challenge it is important to recognize that many so-called biochemical flaws are not genuine flaws at all. Instead, they arise as the consequences of trade-offs. In their cellular roles, many biochemical systems face two (or more) competing objectives. Effectively managing these opposing objectives means that it is impossible for every aspect of the system to perform at an optimal level. Some features must be carefully rendered suboptimal to ensure that the overall system performs robustly under a wide range of conditions.

Cancer falls into this category. It is not a consequence of flawed biochemical designs. Instead, cancer reflects a trade-off between DNA repair and cell survival.

DNA Damage and Cancer

The etiology (cause) of most cancers is complex. While about 10 percent of cancers have a hereditary basis, the vast proportion results from mutations to DNA caused by environmental factors.

Some of the damage to DNA stems from endogenous (internal) factors, such as water and oxygen in the cell. These materials cause hydrolysis and oxidative damage to DNA, respectively. Both types of damage can introduce mutations into this biomolecule. Exogenous chemicals (genotoxins) from the environment can also interact with DNA and cause damage leading to mutations. So does exposure to ultraviolet radiation and radioactivity from the environment.

Infectious agents such as viruses can also cause cancer. Again, these infectious agents cause genomic instability, which leads to DNA mutations.

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Figure: Tumor Formation Process. Image credit: Shutterstock

In effect, DNA mutations are an inevitable consequence of the laws of nature, specifically the first and second laws of thermodynamics. These laws make possible the chemical structures and operations necessary for life to even exist. But, as a consequence, these same life-giving laws also undergird chemical and physical processes that damage DNA.

Fortunately, cells have the capacity to detect and repair damage to DNA. These DNA repair pathways are elaborate and sophisticated. They are the type of biochemical features that seem to support the case for a Creator. DNA repair pathways counteract the deleterious effects of DNA mutation by correcting the damage and preventing the onset of cancer.

Unfortunately, these DNA repair processes function incompletely. They fail to fully compensate for all of the damage that occurs to DNA. Consequently, over time, mutations accrue in DNA, leading to the onset of cancer. The inability of the cell’s machinery to repair all of the mutation-causing DNA damage and, ultimately, protect humans (and other animals) from cancer is precisely the thing that skeptics and seekers alike point to as evidence that counts against intelligent design.

Why would a Creator make a world where cancer is possible and then design cancer-preventing processes that are only partially effective?

Cancer: The Result of a Trade-Off

Even though mutations to DNA cause cancer, it is rare that a single mutation leads to the formation of a malignant cell type and, subsequently, tumor growth. Biomedical researchers have discovered that the onset of cancer involves a series of mutations to highly specific genes (dubbed cancer genes). The mutations that cause cells to transform into cancer cells are referred to as driver mutations. Researchers have also learned that most cells in the body harbor a vast number of mutations that have little or no biological consequence. These mutations are called passenger mutations. As it turns out, there are thousands of passenger mutations in a typical cancer cell and only about ten driver mutations to so-called cancer genes. Biomedical investigators have also learned that many normal cells harbor both passenger and driver mutations without ever transforming. (It appears that other factors unrelated to DNA mutation play a role in causing a cancer cell to undergo extensive clonal expansion, leading to the formation of a tumor.)

What this means is that mutations to DNA are quite extensive, even in normal, healthy cells. But this factor prompts the question: Why is the DNA repair process so lackluster?

The research duo from Cambridge University speculate that DNA repair is so costly to cells—making extensive use of energy and cell resources—that to maintain pristine genomes would compromise cell survival. These researchers conclude that “DNA quality control pathways are fully functional but naturally permissive of mutagenesis even in normal cells.”2 And, it seems as if the permissiveness of the DNA repair processes generally have little consequence given that a vast proportion of the human genome consists of noncoding DNA.

Biomedical researchers have uncovered another interesting feature about the DNA repair processes. The processes are “biased,” with repairs taking place preferentially on the DNA strand (of the double helix) that codes for proteins and, hence, is transcribed. In other words, when DNA repair takes place it occurs where it counts the most. This bias displays an elegant molecular logic and rationale, strengthening the case for design.

Given that driver mutations are not in and of themselves sufficient to lead to tumor formation, the researchers conclude that cancer prevention pathways are quite impressive in the human body. They conclude, “Considering that an adult human has ~30 trillion cells, and only one cell develops into a cancer, human cells are remarkably robust at preventing cancer.”3

So, what about cancer?

Though cancer ravages the lives of so many people, it is not because of poorly designed, substandard biochemical systems. Given that we live in a universe that conforms to the laws of thermodynamics, cancer is inevitable. Despite this inevitability, organisms are designed to effectively ward off cancer.

Ironically, as we gain a better understanding of the process of oncogenesis (the development of tumors), we are uncovering more—not less—evidence for the remarkably elegant and ingenious designs of biochemical systems.

The insights by the research team from Cambridge University provide us with a cautionary lesson. We are often quick to declare a biochemical (or biological) feature as poorly designed based on incomplete understanding of the system. Yet, inevitably, as we learn more about the system we discover an exquisite rationale for why things are the way they are. Such knowledge is consistent with the idea that these systems stem from a Creator’s handiwork.

Still, this recognition does little to dampen the fear and frustration associated with a cancer diagnosis and the pain and suffering experienced by those who battle cancer (and their loved ones who stand on the sidelines watching the fight take place). But, whether we are a skeptic or a believer, we all should be encouraged by the latest insights developed by the Cambridge researchers. The more we understand about the cause and progression of cancers, the closer we are to one day finding cures to a disease that takes so much from us.

We can also take added encouragement from the powerful scientific case for a Creator’s existence. The Old and New Testaments teach us that the Creator revealed by scientific discovery has suffered on our behalf and will suffer alongside us—in the person of Christ—as we walk through the difficult circumstances of life.

Resources

Examples of Biochemical Trade-Offs

Evidence that Nonfunctional DNA Serves as a Mutational Buffer

Endnotes
  1. Serena Nik-Zainal and Benjamin A. Hall, “Cellular Survival over Genomic Perfection,” Science 366, no. 6467 (November 15, 2019): 802–03, doi:10.1126/science.aax8046.
  2. Nik-Zainal and Hall, 802–03.
  3. Nik-Zainal and Hall, 802–03.

Reprinted with permission by the author

Original article at:
https://reasons.org/explore/blogs/the-cells-design

Evolutionary Story Tells the Tale of Creation

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By Fazale Rana – December 4, 2019

Story Telling in the Evolutionary Paradigm

Storytelling isn’t just the purview of a mischievous kid facing the music in the principal’s office, it is part of the construct of science.

Recent work by a team of scientific investigators from the University of Florida (UF) highlights the central role that storytelling plays in evolutionary biology.1 In fact, it is not uncommon for evolutionary biologists to weave grand narratives that offer plausible evolutionary stories for the emergence of biological or behavioral traits. And, though these accounts seem scientific, they are often unverifiable scientific explanations.

Inspired by Rudyard Kipling’s (1865–1936) book of children’s origin stories, the late evolutionary biologist Stephen Jay Gould (1941–2002) referred to these evolutionary tales as just-so stories. To be fair, others have been critical of Gould’s cynical view of evolutionary accounts, arguing that, in reality, just-so stories in evolutionary biology are actually hypotheses about evolutionary transformations. But still, more often than not, these “hypotheses” appear to be little more than convenient fictions.

An Evolutionary Just-So Story of Moths and Bats

The traditional evolutionary account of ultrasonic sound detection in nocturnal moths serves as a case in point. Moths (and butterflies) belong to one of the most important groups of insects: lepidoptera. This group consists of about 160,000 species, with nocturnal moths comprising over 75 percent of the group.

Moths play a key role in ecosystems. For example, they serve as one of the primary food sources for bats. Bats use echolocation to help them locate moths at night. Bats emit ultrasonic cries that bounce off the moths and reflect back to the bats, giving these predators the pinpoint location of the moths, even during flight.

Many nocturnal moth species have defenses that help them escape predation by bats. One defense is ears (located in different areas of their bodies) that detect ultrasonic sounds. This capability allows the moths to hear the bats coming and get out of their way.

For nearly a half century, evolutionary biologists explained moths’ ability to hear ultrasonic sounds as the outworking of an “evolutionary arms race” between echolocating bats and nocturnal moths. Presumably, bats evolved the ability to echolocate, allowing them to detect and prey upon moths at night by plucking them out of the air in mid-flight. In response, some groups of moths evolved ears that allowed them to detect the ultrasonic screeches emitted by bats, helping them to avoid detection.

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Figure: Flying Pipistrelle bat. Image credit: Shutterstock

For 50 years, biologists have studied the relationship between echolocating bats and nocturnal moths with the assumption that this explanation is true. (I doubt Mr. Reynolds ever assumed my stories were true.) In fact, evolutionary accounts like this one provide evidence for the idea of coevolution. Advanced by Paul Ehrlich and Peter Raven in 1964, this evolutionary model maintains that ecosystems are shaped by species that affect one another’s evolution.

If the UF team’s work is to be believed, then it turns out that the story recounting the evolutionary arms race between nocturnal moths and echolocating bats is fictional. As team member Jesse Barber, a researcher who has studied bats and moths, complains, “Most of the introductions I’ve written in my papers [describing the coevolution of bats and moths] are wrong.”2

An Evolutionary Study on the Origin of Moths and Butterflies

To reach this conclusion, the UF team generated the most robust evolutionary tree (phylogeny) for lepidopterans to date. They also developed an understanding of the timing of events in lepidopteran natural history. They were motivated to take on this challenge because of the ecological importance of moths and butterflies. As noted, these insects play a central role in terrestrial ecosystems all over the world and coevolutionary models provide the chief explanations for their place in these ecosystems. But, as the UF researchers note, “These hypotheses have not been rigorously tested, because a robust lepidopteran phylogeny and timing of evolutionary novelties are lacking.”3

To remedy this problem, the researchers built a lepidopteran evolutionary tree from a data set of DNA sequences that collectively specified 2,100 protein-coding genes from 186 lepidopteran species. These species represented all the major divisions within this biological group. Then, they dated the evolutionary timing of key events in lepidopteran natural history from the fossil record.

Based on their analysis, the research team concluded that the first lepidopteran appeared around 300 million years ago. This creature fed on nonvascular plants. Around 240 million years ago, lepidopterans with tubelike proboscises (long, sucking mouthpiece) appeared, allowing these insects to extract nectar from flowering plants.

These results cohere with the coevolutionary model that the first lepidopterans fed internally on plants and, later, externally, as they evolved the ability to access nectar from plants. Flowering plants appear around 260 million years ago, which is about the time that the tubelike proboscis appears in lepidopterans.

But perhaps the most important and stunning finding from their study stems from the appearance of hearing organs in moths. It looks as if these organs arose independently 9 separate times—around 80 to 90 million years ago—well before bats began to echolocate. (The earliest known bat from the fossil record with the capacity to echolocate is around 45 to 50 million years old.)

The UF investigators uncovered another surprising result related to the appearance of butterflies. They discovered that butterflies became diurnal (active in the daytime) around 98 million years ago. According to the traditional evolutionary story, butterflies (which are diurnal) evolved from nocturnal moths when they transitioned to daytime activities to escape predation of echolocating bats, which feed at night. But as with the origin of hearing organs in moths, the transition from nocturnal to diurnal behavior occurred well before the first appearance of echolocating bats and seems to have occurred independently at least two separate times.

It Just Isn’t So

The UF evolutionary biologists’ study demonstrates that the coevolutionary models for the origin of hearing organs in moths and diurnal behavior of butterflies—dominant for over a half century in evolutionary thought—are nothing more than just-so stories. They appear to make sense on the surface but are no closer to the truth than the tales I would weave in Mr. Reynolds’ office.

In light of this discovery, the research team posits two new evolutionary models for the origin of these two traits, respectively. Now scientists think that the evolutionary emergence of hearing organs in moths may have provided these insects the capacity for auditory surveillance of their environment. Their capacity to hear may have helped them detect the low-frequency sounds of flapping bird wings, for example, and avoid predation. Presumably, these same hearing organs later evolved to detect the high-frequency cries of bats. As for the evolutionary origin of diurnal behavior characteristic of butterflies, researchers now speculate that butterflies became diurnal to take advantage of flowers that bloom in the daytime.

Again, on the surface, these explanations seem plausible. But one has to wonder if these models, like their predecessors, are little more than just-so stories. In fact, this study raises a general concern: How much confidence can we place in any evolutionary account? Could it be that other evolutionary accounts are, in reality, good stories, but in the end will turn out to be just as fanciful as the stories written by Rudyard Kipling?

In and of itself, recognizing that many evolutionary models could just be stories doesn’t provide sufficient warrant for skepticism about the evolutionary paradigm. But it does give pause for thought. Plus, two insights from this study raise real concerns about the capacity of evolutionary processes to account for life’s history and diversity:

  1. The discovery that ultrasonic hearing in moths arose independently nine separate times
  2. The discovery that diurnal behavior in butterflies appeared independently in at least two separate instances

Convergence

Evolutionary biologists use the term convergence to refer to the independent origin of identical or nearly identical biological and behavioral traits in organisms that cluster into unrelated groups.

Convergence isn’t a rare phenomenon or limited to the independent origin of hearing organs in moths and diurnal behavior in butterflies. Instead, it is a widespread occurrence in biology, as evolutionary biologists Simon Conway Morris and George McGhee document in their respective books Life’s Solution and Convergent Evolution. It appears as if the evolutionary process routinely arrives at the same outcome, time and time again.4 In fact, biologists observe these repeated outcomes at the ecological, organismal, biochemical, and genetic levels.

From my perspective, the widespread occurrence of convergent evolution is a feature of biology that evolutionary theory can’t explain. I see the widespread occurrence of convergence as a failed scientific prediction of the evolutionary paradigm.

Convergence Should Be Rare, Not Widespread

In effect, chance governs biological and biochemical evolution at its most fundamental level. Evolutionary pathways consist of a historical sequence of chance genetic changes operated on by natural selection, which, too, consists of chance components. The consequences are profound. If evolutionary events could be repeated, the outcome would be dramatically different every time. The inability of evolutionary processes to retrace the same path makes it highly unlikely that the same biological and biochemical designs should appear repeatedly throughout nature.5

In support of this view, consider a 2002 landmark study carried out by two Canadian investigators who simulated macroevolutionary processes using autonomously replicating computer programs. In their study, the computer programs operated like digital organisms.6 The programs could be placed into different “ecosystems” and, because they replicate autonomously, they could evolve. By monitoring the long-term evolution of these digital organisms, the two researchers determined that evolutionary outcomes are historically contingent and unpredictable. Every time they placed the same digital organism in the same environment, it evolved along a unique trajectory.

In other words, given the historically contingent nature of the evolutionary mechanisms, we would expect convergence to be rare in the biological realm. Yet, biologists continue to uncover example after example of convergent features—some of which are quite astounding.

Bat Echolocation and Convergence

Biologists have discovered one such example of convergence in the origin of echolocating bats. Echolocation appears to have arisen two times independently: once in microbats and once in Rhinolophidae, a superfamily of megabats.7 Prior to this discovery, reported in 2000, biologists classified Rhinolophidae as a microbat based on their capability to echolocate. But DNA evidence indicates that this superfamily has greater affinity to megabats than to microbats. This result means that echolocation must have originated separately in the microbats and Rhinolophidae. Researchers have also shown that the same genetic and biochemical changes occurred in microbats and megabats to create their echolocating ability. These changes appear to have taken place in the gene prestin and in its protein-product, prestin.8

In other words, we observe two outcomes: (1) the traditional evolutionary accounts for coevolution among echolocating bats, nocturnal moths, and diurnal butterflies turned out to be just-so stories, and (2) the convergence observed in these three groups stands as independent and separate instances of failed predictions of the evolutionary paradigm.

Convergence and the Case for Creation

If the widespread occurrence of convergence can’t be explained through evolutionary theory, then how can it be explained?

It is not unusual for architects and engineers to redeploy the same design features, sometimes in objects, devices, or systems that are completely unrelated to one another. So, instead of viewing convergent features as having emerged through repeated evolutionary outcomes, we could understand them as reflecting the work of a divine mind. From this perspective, the repeated origins of biological features equate to the repeated creations by an intelligent Agent who employs a common set of solutions to address a common set of problems facing unrelated organisms.

Now that’s a story even Mr. Reynolds might believe.

Resources

Convergence of Echolocation

The Historical Contingency of the Evolutionary Process

Endnotes
  1. Akito Y. Kawahara et al., “Phylogenomics Reveals the Evolutionary Timing and Pattern of Butterflies and Moths,” Proceedings of the National Academy of Sciences, USA 116, no. 45 (November 5, 2019): 22657–63, doi:10.1073/pnas.1907847116.
  2. Ed Yong, “A Textbook Evolutionary Story about Moths and Bats Is Wrong,” The Atlantic (October 21, 2019), https://www.theatlantic.com/science/archive/2019/10/textbook-evolutionary-story-wrong/600295/.
  3. Kawahara et al., “Phylogenomics.”
  4. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).
  5. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W. W. Norton & Company, 1990).
  6. Gabriel Yedid and Graham Bell, “Macroevolution Simulated with Autonomously Replicating Computer Programs,” Nature 420 (December 19, 2002): 810–12, doi:10.1038/nature01151.
  7. Emma C. Teeling et al., “Molecular Evidence Regarding the Origin of Echolocation and Flight in Bats,” Nature 403 (January 13, 2000): 188–92, doi:10.1038/35003188.
  8. Gang Li et al., “The Hearing Gene Prestin Reunites Echolocating Bats,” Proceedings of the National Academy of Sciences, USA 105, no. 37 (September 16, 2008): 13959–64, doi:10.1073/pnas.0802097105.

Reprinted with permission by the author

Original article at:
https://reasons.org/explore/blogs/the-cells-design

Evolution of Antibiotic Resistance Makes the Case for a Creator

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By Fazale Rana – November 27, 2019

It isn’t that hard to imagine, because antibiotics weren’t readily available for medical use until after World War II. And since that time, widespread availability of antibiotics has revolutionized medicine. However, the ability to practice modern medicine is being threatened because of the rise of antibiotic-resistant bacteria. Currently, there exists a pressing need to understand the evolution of antibiotic-resistant strains and to develop new types of antibiotics. Surprisingly, this worthy pursuit has unwittingly stumbled upon evidence for a Creator’s role in the design of biochemical systems.

Alexander Fleming (1881–1955) discovered the first antibiotic, penicillin, in 1928. But it wasn’t until Ernst Chain, Howard Florey, and Edward Abraham purified penicillin in 1942 and Norman Heatley developed a bulk extraction technique in 1945 that the compound became available for routine medical use.

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Figure 1: Alexander Fleming. Image Credit: Wikipedia

Prior to this time, people often died from bacterial infections. Complicating this vulnerability to microbial pathogens was the uncertain outcome of many medical procedures. For example, patients often died after surgery due to complications arising from infections.

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Figure 2: A generalized structure for penicillin antibiotics. Image credit: Shutterstock

Bacterial Resistance Necessitates New Antibiotics

Unfortunately, because of the growing threat of superbugs—antibiotic-resistant strains of bacteria—health experts around the world worry that we soon will enter into a post-antibiotic era in which modern medicine will largely revert to pre-World War II practices. According to Dr. David Livermore, laboratory director at Public Health England, which is responsible for monitoring antibiotic-resistant strains of bacteria, “A lot of modern medicine would become impossible if we lost our ability to treat infections.”1

Without antibiotics, people would routinely die of infections that we easily treat today. Abdominal surgeries would be incredibly risky. Organ transplants and chemotherapy would be out of the question. And the list continues.

The threat of entering into a post-antibiotic age highlights the desperate need to develop new types of antibiotics. It also highlights the need to develop a better understanding of evolutionary processes that lead to the emergence of antibiotic resistance in bacteria.

Recently, a research team from Michigan State University (MSU) published a report that offers insight into the latter concern. These researchers studied the evolution of antibiotic resistance in bacteria that had been serially cultured in the laboratory for multiple decades in media that was free from antibiotics.2 Through this effort, they learned that the genetic history of the bacterial strain plays a key role in its acquisition of resistance to antibiotics.

This work has important implications for public health, but it also carries theological implications. The decades-long experiment provides evidence that the elegant designs characteristic of biochemical and biological systems most likely stem from a Creator’s handiwork.

The Long-Term Evolution Experiment

To gain insight into the role that genetic history plays in the evolution of antibiotic resistance, the MSU researchers piggy-backed on the famous Long-Term Evolution Experiment (LTEE) at Michigan State University. Inaugurated in 1988, the LTEE is designed to monitor evolutionary changes in the bacterium E. coli, with the objective of developing an understanding of the evolutionary process.

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Figure 3: A depiction of E. coli. Image Credit: Shutterstock

The LTEE began with a single cell of E. coli that was used to generate twelve genetically identical lines of cells. The twelve clones of the parent E. coli cell were separately inoculated into a minimal growth medium containing low levels of glucose as the only carbon source. After growing overnight, an aliquot (equal fractional part) of each of the twelve cultures was transferred into fresh growth media. This process has been repeated every day for about thirty years. Throughout the experiment, aliquots of cells have been frozen every 500 generations. These frozen cells represent a “fossil record” of sorts that can be thawed out and compared to current and other past generations of cells.

Relaxed Selection and Decay of Antibiotic Resistance

In general, when a population of organisms no longer experiences natural selection for a particular set of traits (antibiotic resistance, in this case), the traits designed to handle that pressure may experience functional decay as a result of mutations and genetic drift. This process is called relaxed selection.

In the case of antibiotic resistance, when the threat of antibiotics is removed from the population (relaxed selection), it seems reasonable to think that antibiotic resistance would decline in the population because in most cases antibiotic resistance comes with a fitness cost. In other words, bacterial strains that acquire antibiotic resistance face a trade-off that makes them less fit in environments without the antibiotic.

Genetic History and the Re-Evolution of Antibiotic Resistance

In light of this expectation, the MSU researchers wondered how readily bacteria that have experienced relaxed selection can overcome loss of antibiotic resistance when the antibiotic is reintroduced to the population.

To explore this question, the researchers examined the evolution of antibiotic resistance in the LTEE ancestor by exposing it to a set of different antibiotics and compared its propensity to acquire antibiotic resistance with four strains of E. coli derived from the LTEE ancestor (that underwent 50,000 generations of daily growth and transfer into fresh media in the absence of exposure to antibiotics).

As expected, the MSU team discovered that 50,000 generations of relaxed selection rendered the four strains more susceptible to four different antibiotics (ampicillin, ceftriaxone, ciprofloxacin, and tetracycline) compared to the LTEE ancestor. When they exposed these strains to the different antibiotics, the researchers discovered that acquisition of antibiotic resistance was idiosyncratic: some strains more readily evolved antibiotic resistance than the LTEE ancestor and others were less evolvable.

Investigators explained this difference by arguing that during the period of relaxed selection some of the strains experienced mutations that constrained the evolution of antibiotic resistance, whereas others experienced mutations that potentiated (activated) the evolution of antibiotic resistance. That is, historical contingency has played a key role in the acquisition of antibiotic resistance. Different bacterial lineages accumulated genetic differences that influence their capacity to evolve and adapt in new directions.

Historical Contingency

This study follows on the heels of previous studies that demonstrate the historical contingency of the evolutionary process.3 In other words, chance governs biological and biochemical evolution at its most fundamental level. As the MSU researchers observed, evolutionary pathways consist of a historical sequence of chance genetic changes operated on by natural selection (or that experience relaxed selection), which, too, consists of chance components.

Because of the historically contingent nature of the evolutionary process, it is highly unlikely that the same biological and biochemical designs should appear repeatedly throughout nature. In his book Wonderful Life, Stephen Jay Gould used the metaphor of “replaying life’s tape.” If one were to push the rewind button, erase life’s history, and then let the tape run again, the results would be completely different each time.4

The “Problem” of Convergence

And yet, we observe the opposite pattern in biology. From an evolutionary perspective, it appears as if the evolutionary process independently and repeatedly arrived at the same outcome, time and time again (convergence). As evolutionary biologists Simon Conway Morris and George McGhee point out in their respective books Life’s Solution and Convergent Evolution, identical evolutionary outcomes are a widespread feature of the biological realm.5

Scientists see these repeated outcomes at ecological, organismal, biochemical, and genetic levels. To illustrate the pervasiveness of convergence at the biochemical level, I describe 100 examples of convergence in my book The Cell’s Design.6

From my perspective, the widespread occurrence of convergent evolution is a feature of biology that evolutionary theory can’t genuinely explain. In fact, given the clear-cut demonstration that the evolutionary process is historically contingent, I see the widespread occurrence of convergence as a failed scientific prediction for the evolutionary paradigm.

Evolution in Bacteria Doesn’t Equate to Large-Scale Evolution

The evolution of E. coli in the LTEE doesn’t necessarily validate the evolutionary paradigm. Just because such change is observed in a microbe doesn’t mean that evolutionary processes can adequately account for life’s origin and history, and the full range of biodiversity.

Convergence and the Case for Creation

Instead of viewing convergent features as having emerged through repeated evolutionary outcomes, we could understand them as reflecting the work of a divine Mind. In this scheme, the repeated origins of biological features equate to the repeated creations by an intelligent Agent who employs a common set of solutions to address a common set of problems facing unrelated organisms.

Sadly, many in the scientific community are hesitant to embrace this perspective because they are resistant to the idea that design and purpose may play a role in biology. But, one can hope that someday the scientific community will be willing to move into a post-evolution future as the evidence for a Creator’s role in biology mounts.

Resources

The Historical Contingency of the Evolutionary Process

Microbial Evolution and the Validity of the Evolutionary Paradigm

Endnotes
  1. Sarah Bosley, “Are You Ready for a World without Antibiotics?” The Guardian, August 12, 2010, https://www.theguardian.com/society/2010/aug/12/the-end-of-antibiotics-health-infections.
  2. Kyle J. Card et al., “Historical Contingency in the Evolution of Antibiotic Resistance after Decades of Relaxed Selection,” PLoS Biology 17, no. 10 (October 23, 2019): e3000397, doi:10.1371/journal.pbio.3000397.
  3. Zachary D. Blount et al., “Historical Contingency and the Evolution of a Key Innovation in an Experimental Population of Escherichia coli,” Proceedings of the National Academy of Sciences USA 105, no. 23 (June 10, 2008): 7899-7906, doi:10.1073/pnas.0803151105.
  4. Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York: W.W. Norton & Company, 1990).
  5. Simon Conway Morris, Life’s Solution: Inevitable Humans in a Lonely Universe (New York: Cambridge University Press, 2003); George McGhee, Convergent Evolution: Limited Forms Most Beautiful (Cambridge, MA: MIT Press, 2011).
  6. Fazale Rana, The Cell’s Design: How Chemistry Reveal the Creator’s Artistry (Grand Rapids, MI: Baker, 2008).

Reprinted with permission by the author

Original article at:
https://reasons.org/explore/blogs/the-cells-design