Simple Biological Rules Affirm Creation

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By Fazale Rana – September 4, 2019

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

To say that biological systems are complicated is an understatement.

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

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

Order in the Midst of Biochemical Complexity

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

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

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

Rules Govern Biological Systems

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

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

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

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

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

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

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

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

Mutualism and Ecosystem Stability

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

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

Mutualism Can Be Explained by a Simple Rule

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

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

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

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

Let me explain.

The Case for a Creator

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

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

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

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

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Figure: The Mathematical Universe. Image credit: Shutterstock.

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

A Case against Materialism

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

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

Is There a Biological Anthropic Principle?

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

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

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

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

Resources

The Argument from Math and Beauty

Designed for Discovery

The Biochemical Anthropic Principle

The Design of Intermediary Metabolism

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

Reprinted with permission by the author

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

ATP Transport Challenges the Evolutionary Origin of Mitochondria

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By Fazale Rana – August 21, 2019

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

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

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

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

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

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

The Endosymbiont Hypothesis

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

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

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

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Image: Endosymbiont Hypothesis. Image credit: Wikipedia

Evidence for the Endosymbiont Hypothesis

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

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

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

The Role of Mitochondria

Mitochondria serve cells in a number of ways, including:

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

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

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

 

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

ATP Production and Transport

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

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

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

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

The Problem ATP Transport Causes for The Endosymbiont Hypothesis

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

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

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

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

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

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

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

Two Alternative Models

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

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

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

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

Moving Forward, Or Moving Backward?

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

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

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

According to the authors, this means that:

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

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

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

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

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

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

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

Resources

Challenges to the Endosymbiont Hypothesis:

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

ATP Production and the Case for a Creator:

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

Reprinted with permission by the author

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

Does Information Come from a Mind?

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By Fazale Rana – August 14, 2019

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

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

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Image credit: Shutterstock

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

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

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

Information and the Case for a Creator

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

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

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

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

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

Is Biochemical Information Really Information?

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

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

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

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

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

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

Further Studies that Strengthen the Case for a Creator

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

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

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

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

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

Does Information Come from a Mind?

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

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

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

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

–Roland W. via Facebook

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

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

The type of information found in volcanic rocks and tree rings is different from the semantic information found in human languages. It is actually algorithmic information, meaning that it consists of a set of instructions. And technically, the rocks and tree rings don’t contain this information—they result from it.

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

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

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

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

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

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

Resources

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

Reprinted with permission by the author

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

New Insights into Endothermy Heat Up the Case for a Creator

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By Fazale Rana – August 7, 2019

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

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

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

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

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

An Explanation for Endothermy

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

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

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

Temperature and Immune System Function

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

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

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Figure: The Human Immune System. Image credit: Shutterstock

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

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

Fever Response in Ectotherms

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

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

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

Endothermy and Ectothermy Trade-Offs

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

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

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

Regulation of Body Temperature and the Case for a Creator

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

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

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

And I am chill with that.

Resources

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

Reprinted with permission by the author

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

Is SETI an Intelligent Design Research Program?

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By Fazale Rana – July 24, 2019

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

Skeptical Challenge

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

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

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

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

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

SETI and Intelligent Design

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

 

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Figure: Seth Shostak. Image credit: Wikipedia

 

According to Shostak,

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

Shostak goes on to say, “If we as SETI researchers admit this is so, it sounds as if we’re guilty of promoting a logical double standard. If the ID folks aren’t allowed to claim intelligent design when pointing to DNA, how can we hope to claim intelligent design on the basis of a complex radio signal?”2

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

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

Artificiality and Intelligent Design

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

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

Here are three ways I adopt this approach:

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

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

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

Resources

Endnotes
  1. Seth Shostak, “SETI and Intelligent Design,” Space.com (December 1, 2005), https://www.space.com/1826-seti-intelligent-design.html.
  2. Shostak, “SETI and Intelligent Design.”

Reprinted with permission by the author

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

Does Old-Earth Creationism Make God Deceptive?

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By Fazale Rana – July 17, 2019

“Are [vestigial structures] unequivocal evidence of evolution?

No. Are they reasonable evidence of evolution? Yes.

Ditto gene sequences.

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

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

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

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

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

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

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

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

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

Evidence for Evolution: Vestigial Structures

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

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Figure 1: Whale Pelvis. Image credit: Shutterstock

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

Evidence for Evolution: Shared Genetic Features

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

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

A Response to the Evidence for Evolution

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

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

Appearance of Age and the Appearance of Evolution

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

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

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

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

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

A Response to the Appearance of Evolution Challenge

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

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

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

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

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

Appearance of Design Fallacy

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

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

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

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

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

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

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

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

Theories Are Underdetermined by Data

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

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

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

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

Resources

Vestigial Structures Are Functional

Shared Genetic Features Reflect Design

Scientific Challenges for the Evolutionary Paradigm

Archetype Biology

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

Reprinted with permission by the author

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

Membrane Biochemistry Challenges Route to Evolutionary Origin of Complex Cells

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By Fazale Rana – July 10, 2019

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

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

Endosymbiont Hypothesis

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

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

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

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

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

Discovery of Lokiarchaeota

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

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

Challenges to the Endosymbiont Hypothesis

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

Lipid Divide

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

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

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

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

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

Lipid Divide Frustrates the Origin of Eukaryotic Cell Membranes

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

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

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

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

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

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

Can Lokiarchaeota Traverse the Lipid Divide?

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

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

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

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

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

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

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

More Lipid Divide Frustration

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

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

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

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

Resources

Challenges to the Endosymbiont Hypothesis

Support for a Creation Model for the Origin of Eukaryotic Cells

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

Reprinted with permission by the author

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

Ancient Mouse Fur Discovery with Mighty Implications

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By Fazale Rana – June 26, 2019

“What a mouse! . . . WHAT A MOUSE!”

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

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

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Figure 1: Mighty Mouse. Image credit: Wikipedia

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

Mouse Fur Discovery

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

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

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

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

Detection of 3-Million-Year-Old Pigment

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

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

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

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

Soft Tissues and the Scientific Case for a Young Earth

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

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

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

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

Preservation Mechanisms for Soft Tissues in Fossils

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

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

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

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

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

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

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

Resources

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

Satellite DNA: Critical Constituent of Chromosomes

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By Fazale Rana – June 26, 2019

Let me explain.

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

Getting Rid of the Junk

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

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

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

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

Junk in the Genome

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

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

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

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

Satellite DNA

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

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Figure: Chromosome Structure. Image credit: Shutterstock

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

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

What Was Thought to Be Junk Turns Out to Have Purpose

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

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

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

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

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

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

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

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

Is the Evolutionary Paradigm the Wrong Framework to Study Genomes?

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

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

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

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

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

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

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

Resources

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

Frog Choruses Sing Out a Song of Creation

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BY FAZALE RANA – JUNE 12, 2019

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

In Spanish, Rana means frog.

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

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Image: Five Ranitas. Image credit: Shutterstock

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

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

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

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

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

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

Frog Choruses: A Cacophony or a Symphony?

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

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

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

The Mathematical Structure of Frog Choruses

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

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

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

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

Use of Frog Choruses for Managing Data Traffic

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

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

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

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

Frog Choruses and the Argument from Beauty

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

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

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

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

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

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

Frog Choruses and the Converse Watchmaker Argument

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

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

The argument can be stated like this:

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

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

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

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

Resources

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

Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2019/06/12/frog-choruses-sing-out-a-song-of-creation