Is Fossil-Associated Cholesterol a Biomarker for a Young Earth?

fossilassociatedcholesterol

BY FAZALE RANA – OCTOBER 24, 2018

Like many Americans, I receive a yearly physical. Even though I find these exams to be a bit of a nuisance, I recognize their importance. These annual checkups allow my doctor to get a read on my overall health.

An important part of any physical exam is blood work. Screening a patient’s blood for specific biomarkers gives physicians data that allows them to assess a patient’s risk for various diseases. For example, the blood levels of total cholesterol and the ratio of HDLs to LDLs serve as useful biomarkers for cardiovascular disease.

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Figure 1: Cholesterol. Image credit: BorisTM. Public domain via Wikimedia Commons, https://commons.wikimedia.org/wiki/File:Cholesterol.svg.

As it turns out, physicians aren’t the only ones who use cholesterol as a diagnostic biomarker. So, too, do paleontologists. In fact, recently a team of paleontologists used cholesterol biomarkers to determine the identity of an enigmatic fossil recovered in Precambrian rock formations that dated to 588 million years in age.1 This diagnosis was possible because they were able to extract low levels of cholesterol derivatives from the fossil. Based on the chemical profile of the extracts, researchers concluded that Dickinsonia specimens are the fossil remains of some of the oldest animals on Earth.

Without question, this finding has important implications for how we understand the origin and history of animal life on Earth. But young-earth creationists (YECs) think that this finding has important implications for another reason. They believe that the recovery of cholesterol derivatives from Dickinsonia provides compelling evidence that the earth is only a few thousand years old and the fossil record results from a worldwide flood event. They argue that there is no way organic materials such as cholesterol could survive for hundreds of millions of years in the geological column. Consequently, they argue that the methods used to date fossils such as Dickinsonia must not be reliable, calling into question the age of the earth determined by radiometric techniques.

Is this claim valid? Is the recovery of cholesterol derivatives from fossils that date to hundreds of millions of years evidence for a young earth? Or can the recovery of cholesterol derivatives from 588 million-year-old fossils be explained in an old-earth paradigm?

How Can Cholesterol Derivatives Survive for Millions of Years?

Despite the protests of YECs, for several converging reasons the isolation of cholesterol derivatives from the Dickinsonia specimen is easily explained—even if the specimen dates to 588 million years in age.

The research team did not recover high levels of cholesterol from the Dickinsonia specimen (which would be expected if the fossils were only 3,000 years old), but trace levels of cholestane (which would be expected if the fossils were hundreds of millions of years old). Cholestane is a chemical derivative of cholesterol that is produced when cholesterol undergoes diagenetic changes.

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Figure 2: Cholestane. Image credit: Calvero. (Self-made with ChemDraw.) Public domain via Wikimedia Commons, https://commons.wikimedia.org/wiki/File:Cholestane.svg.

Cholestane is a chemically inert hydrocarbon that is expected to be stable for vast periods of time. In fact, geochemists have recovered steranes (other biomarkers) from rock formations that date to 2.8 billion years in age.

The Dickinsonia specimens that yielded cholestanes were exceptionally well-preserved. Specifically, they were unearthed from the White Sea Cliffs in northwest Russia. This rock formation has escaped deep burial and geological heating, making it all the more reasonable that compounds such as cholestanes could survive for nearly 600 million years.

In short, the recovery of cholesterol derivatives from Dickinsonia does not reflect poorly on the health of the old-earth paradigm. When the chemical properties of cholesterol and cholestane are considered, and given the preservation conditions of the Dickinsonia specimens, the interpretation that these materials were recovered from 588-million-year-old fossil specimens passes the physical exam.

Resources

Featured image: Dickinsonia Costata. Image credit: https://commons.wikimedia.org/wiki/File:DickinsoniaCostata.jpg.

Endnotes

  1. Ilya Bobrovskiy et al., “Ancient Steroids Establish the Ediacaran Fossil Dickinsonia as One of the Earliest Animals,” Science 361 (September 21, 2018): 1246–49, doi:10.1126/science.aat7228.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/10/24/is-fossil-associated-cholesterol-a-biomarker-for-a-young-earth

Further Review Overturns Neanderthal Art Claim

furtherreviewoverturns

BY FAZALE RANA – OCTOBER 17, 2018

As I write this blog post, the 2018–19 NFL season is just underway.

During the course of any NFL season, several key games are decided by a controversial call made by the officials. Nobody wants the officials to determine the outcome of a game, so the NFL has instituted a way for coaches to challenge calls on the field. When a call is challenged, part of the officiating crew looks at a computer tablet on the sidelines—reviewing the game footage from a number of different angles in an attempt to get the call right. After two minutes of reviewing the replays, the senior official makes his way to the middle of the field and announces, “Upon further review, the call on the field . . .”

Recently, a team of anthropologists from Spain and the UK created quite a bit of controversy based on a “call” they made from working in the field. Using a new U-Th dating method, these researchers age-dated the artwork in caves from Iberia. Based on the age of a few of their samples, they concluded that Neanderthals produced cave paintings.1 But new work by three independent research teams challenges the “call” from the field—overturning the conclusion that Neanderthals made art and displayed symbolism like modern humans.

U-Th Dating Method

The new dating method under review measures the age of calcite deposits beneath cave paintings and those formed over the artwork after the paintings were created. As water flows down cave walls, it deposits calcite. When calcite forms, it contains trace amounts of U-238. This isotope decays into Th-230. Normally, detection of such low quantities of the isotopes would require extremely large samples. Researchers discovered that by using accelerator mass spectrometry, they could get by with 10-milligram samples. And by dating the calcite samples with this technique, they produced minimum and maximum ages for the cave paintings.2

Call from the Field: Neanderthals Are Artists

The team applied their dating method to the art found in three cave sites in Iberia (ancient Spain): (1) La Pasiega, which houses paintings of animals, linear signs, claviform signs, and dots; (2) Ardales, which contains about 1,000 paintings of animals, along with dots, discs, lines, geometric shapes, and hand stencils; and (3) Maltravieso, which displays a set of hand stencils and geometric designs. The research team took a total of 53 samples from 25 carbonate formations associated with the cave art in these three cave sites. While most of the samples dated to 40,000 years old or less (which indicates that modern humans were the artists), three measurements produced minimum ages of around 65,000 years, including: (1) red scalariform from La Pasiega, (2) red areas from Ardales, and (3) a hand stencil from Maltravieso. On the basis of the three measurements, the team concluded that the art must have been made by Neanderthals because modern humans had not made their way into Iberia at that time. In other words, Neanderthals made art, just like modern humans did.

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Figure: Maltravieso Cave Entrance, SpainImage credit: Shutterstock

Shortly after the findings were published, I wrote a piece expressing skepticism about this claim for two reasons.

First, I questioned the reliability of the method. Once the calcite deposit forms, the U-Th method will only yield reliable results if none of the U or Th moves in or out of the deposit. Based on the work of researchers from France and the US, it does not appear as if the calcite films are closed systems. The calcite deposits on the cave wall formed because of hydrological activity in the cave. Once a calcite film forms, water will continue to flow over its surface, leeching out U (because U is much more water soluble than Th). By removing U, water flowing over the calcite will make it seem as if the deposit and, hence, the underlying artwork is much older than it actually is.3

Secondly, I expressed concern that the 65,000-year-old dates measured for a few samples are outliers. Of the 53 samples measured, only three gave age-dates of 65,000 years. The remaining samples dated much younger, typically around 40,000 years in age. So why should we give so much credence to three measurements, particularly if we know that the calcite deposits are open systems?

Upon Further Review: Neanderthals Are Not Artists

Within a few months, three separate research groups published papers challenging the reliability of the U-Th method for dating cave art and, along with it, the claim that Neanderthals produced cave art.4 It is not feasible to detail all their concerns in this article, but I will highlight six of the most significant complaints. In several instances, the research teams independently raised the same concerns.

  1. The U-Th method is unreliable because the calcite deposits are an open system. The concern that I raised was reiterated by two of the research teams for the same reason I expressed. The U-Th dating technique can only yield reliable results if no U or Th moves in or out of the system once the calcite film forms. The continued water flow over the calcite deposits will preferentially leech U from the deposit, making the deposit appear to be older than it is.
  2. The U-Th method is unreliable because it fails to account for nonradiogenic Th. This isotope would have been present in the source water producing the calcite deposits. As a result, Th would already be present in calcite at the time of formation. This nonradiogenic Th would make the samples appear to be older than they actually are.
  3. The 65,000-year-old dates for the three measurements from La Pasiega, Ardales, and Maltravieso are likely outliers. Just as I pointed out before, two of the research groups expressed concern that only 3 of the 53 measurements came in at 65,000 years in age. This discrepancy suggests that these dates are outliers, most likely reflecting the fact that the calcite deposits are an open system that formed with Th already present. Yet, the researchers from Spain and the UK who reported these results emphasized the few older dates while downplaying the younger dates.
  4. Multiple measurements on the same piece of art yielded discordant ages. For example, the researchers made five age-date measurements of the hand stencil at Maltravieso. These dates (66.7 kya [thousand years ago], 55.2 kya, 35.3 kya, 23.1 kys, and 14.7 kya) were all over the place. And yet, the researchers selected the oldest date for the age of the hand stencil, without justification.
  5. Some of the red “markings” on cave walls that were dated may not be art. Red markings are commonplace on cave walls and can be produced by microorganisms that secrete organic materials or iron oxide deposits. It is possible that some of the markings that were dated were not art at all.
  6. The method used by the researchers to sample the calcite deposits may have been flawed. One team expressed concern that the sampling technique may have unwittingly produced dates for the cave surface on which the paintings were made rather than the pigments used to make the art itself. If the researchers inadvertently dated the cave surface, it could easily be older than the art.

In light of these many shortcomings, it is questionable if the U-Th method to date cave art is reliable. After review, the call from the field is overturned. There is no conclusive evidence that Neanderthals made art.

Why Does This Matter?

Artistic expression reflects a capacity for symbolism. And many people view symbolism as a quality unique to human beings that contributes to our advanced cognitive abilities and exemplifies our exceptional nature. In fact, as a Christian, I see symbolism as a manifestation of the image of God. If Neanderthals possessed symbolic capabilities, such a quality would undermine human exceptionalism (and with it the biblical view of human nature), rendering human beings nothing more than another hominin. At this juncture, every claim for Neanderthal symbolism has failed to withstand scientific scrutiny.

Now, it is time for me to go back to the game.

Who dey! Who dey! Who dey think gonna beat dem Bengals!

Resources:

Endnotes

  1. L. Hoffmann et al., “U-Th Dating of Carbonate Crusts Reveals Neandertal Origin of Iberian Cave Art,” Science359 (February 23, 2018): 912–15, doi:10.1126/science.aap7778.
  2. W. G. Pike et al., “U-Series Dating of Paleolithic Art in 11 Caves in Spain,” Science 336 (June 15, 2012): 1409–13, doi:10.1126/science.1219957.
  3. Georges Sauvet et al., “Uranium-Thorium Dating Method and Palaeolithic Rock Art,” Quaternary International 432 (2017): 86–92, doi:10.1016/j.quaint.2015.03.053.
  4. Ludovic Slimak et al., “Comment on ‘U-Th Dating of Carbonate Crusts Reveals Neandertal Origin of Iberian Cave Art,’” Science 361 (September 21, 2018): eaau1371, doi:10.1126/science.aau1371; Maxime Aubert, Adam Brumm, and Jillian Huntley, “Early Dates for ‘Neanderthal Cave Art’ May Be Wrong,” Journal of Human Evolution (2018), doi:10.1016/j.jhevol.2018.08.004; David G. Pearce and Adelphine Bonneau, “Trouble on the Dating Scene,” Nature Ecology and Evolution 2 (June 2018): 925–26, doi:10.1038/s41559-018-0540-4.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/10/17/further-review-overturns-neanderthal-art-claim

Can Evolution Explain the Origin of Language?

canevolutionexplain

BY FAZALE RANA – OCTOBER 10, 2018

Oh honey hush, yes you talk too much
Oh honey hush, yes you talk too much
Listenin’ to your conversation is just about to separate us

—Albert Collins

He was called the “Master of the Telecaster.” He was also known as the “Iceman,” because his guitar playing was so hot, he was cold. Albert Collins (1932–93) was an electric blues guitarist and singer whose distinct style of play influenced the likes of Stevie Ray Vaughn and Robert Cray.

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Image: Albert Collins in 1990. Image Credit: Masahiro Sumori [GFDL (https://www.gnu.org/copyleft/fdl.html), CC-BY-SA-3.0 (https://creativecommons.org/licenses/by-sa/3.0/) or CC BY-SA 2.5 (https://creativecommons.org/licenses/by-sa/2.5)], from Wikimedia Commons.

Collins was known for his sense of humor and it often came through in his music. In one of Collins’s signature songs, Honey Hush, the bluesman complains about his girlfriend who never stops talking: “You start talkin’ in the morning; you’re talkin’ all day long.” Collins finds his girlfriend’s nonstop chatter so annoying that he contemplates ending their relationship.

While Collins may have found his girlfriend’s unending conversation irritating, the capacity for conversation is a defining feature of human beings (modern humans). As human beings, we can’t help ourselves—we “talk too much.”

What does our capacity for language tell us about human nature and our origins?

Language and Human Exceptionalism

Human language flows out of our capacity for symbolism. Humans have the innate ability to represent the world (and abstract ideas) using symbols. And we can embed symbols within symbols to construct alternative possibilities and then link our scenario-building minds together through language, music, art, etc.

As a Christian, I view our symbolism as a facet of the image of God. While animals can communicate, as far as we know only human beings possess abstract language. And despite widespread claims about Neanderthal symbolism, the scientific case for symbolic expression among these hominids keeps coming up short. To put it another way, human beings appear to be uniquely exceptional in ways that align with the biblical concept of the image of God, with our capacity for language serving as a significant contributor to the case for human exceptionalism.

Recent insights into the mode and tempo of language’s emergence strengthen the scientific case for the biblical view of human nature. As I have written in previous articles (see Resources) and in Who Was Adam?, language appears to have emerged suddenly—and it coincides with the appearance of anatomically modern humans. Additionally, when language first appeared, it was syntactically as complex as contemporary language. That is, there was no evolution of language—proceeding from a proto-language through simple language and then to complex language. Language emerges all at once as a complete package.

From my vantage point, the sudden appearance of language that uniquely coincides with the first appearance of humans is a signature for a creation event. It is precisely what I would expect if human beings were created in God’s image, as Scripture describes.

Darwin’s Problem

This insight into the origin of language also poses significant problems for the evolutionary paradigm. As linguist Noam Chomsky and anthropologist Ian Tattersall admit, “The relatively sudden origin of language poses difficulties that may be called ‘Darwin’s problem.’”1

Anthropologist Chris Knight’s insights compound “Darwin’s problem.” He concludes that “language exists, but for reasons which no currently accepted theoretical paradigm can explain.”2 Knight arrives at this conclusion by surveying the work of three scientists (Noam Chomsky, Amotz Zahavi, and Dan Sperber) who study language’s origin using three distinct approaches. All three converge on the same conclusion; namely, evolutionary processes should not produce language or any form of symbolic communication.

Chris Knight writes:

Language evolved in no other species than humans, suggesting a deep-going obstacle to its evolution. One possibility is that language simply cannot evolve in a Darwinian world—that is, in a world based ultimately on competition and conflict. The underlying problem may be that the communicative use of language presupposes anomalously high levels of mutual cooperation and trust—levels beyond anything which current Darwinian theory can explain . . . suggesting a deep-going obstacle to its evolution.3

To support this view, Knight synthesizes the insights of linguist Noam Chomsky, ornithologist and theoretical biologist Amotz Zahavi, and anthropologist Dan Sperber. All three scientists determine that language cannot evolve from animal communication for three distinct reasons.

Three Reasons Why Language Is Unique to Humans

Chomsky views animal minds as only being capable of bounded ranges of expression. On the other hand, human language makes use of a finite set of symbols to communicate an infinite array of thoughts and ideas. For Chomsky, there are no intermediate steps between bounded and infinite expression of ideas. The capacity to express an unlimited array of thoughts and ideas stems from a capacity that must have appeared all at once. And this ability must be supported by brain and vocalization structures. Brain structures and the ability to vocalize would either have to already be in place at the time language appeared (because these structures were selected by the evolutionary process for entirely different purposes) or they simultaneously arose with the capacity to conceive of infinite thoughts and ideas. To put it another way, language could not have emerged from animal communication through a step-evolutionary process. It had to appear all at once and be fully intact at the time of its genesis. No one knows of any mechanism that can effect that type of transformation.

Zahavi’s work centers on understanding the evolutionary origin of signaling in the animal world. Endemic to his approach, Zahavi divides natural selection into two components: utilitarian selection (which describes selection for traits that improve the efficiency of some biological process—enhancing the organism’s fitness) and signal selection (which involves the selection of traits that are wasteful). Though counterintuitive, signal selection contributes to the fitness of the organism because it communicates the organism’s fitness to other animals (either members of the same or different species). The example Zahavi uses to illustrate signal selection is the unusual behavior of gazelles. These creatures stot (jump up and down, stomp the ground, loudly snort) when they detect a predator, which calls attention to themselves. This behavior is counterintuitive. Shouldn’t these creatures use their energy to run away, getting the biggest jump they can on the pursuing predator? As it turns out, the “wasteful and costly” behavior communicates to the predator the fitness of the gazelle. In the face of danger, the gazelle is willing to take on risk, because it is so fit. The gazelle’s behavior dissuades the predator from attacking. Observations in the wild confirm Zahavi’s ideas. Predators most often will go after gazelles that don’t stot or that display limited stotting behavior.

Animal signaling is effective and reliable only when actual costly handicaps are communicated. The signaling can only be effective when a limited and bounded range of signals is presented. This constraint is the only way to communicate the handicap. In contrast, language is open-ended and infinite. Given the constraints on animal signaling, it cannot evolve into language. Natural selection prevents animal communication from evolving into language because, in principle, when the infinite can be communicated, in practice, nothing is communicated at all.

Based in part on fieldwork he conducted in Ethiopia with the Dorze people, Dan Sperber concluded that people use language to primarily communicate alternative possibilities and realities—falsehoods—rather than information that is true about the world. To be certain, people use language to convey brute facts about the world. But most often language is used to communicate institutional facts—agreed-upon truths—that don’t necessarily reflect the world as it actually is. According to Sperber, symbolic communication is characterized by extravagant imagery and metaphor. Human beings often build metaphor upon metaphor—and falsehood upon falsehood—when we communicate. For Sperber, this type of communication can’t evolve from animal signaling. What evolutionary advantage arises by transforming communication about reality (animal signaling) to communication about alternative realities (language)?

Synthesizing the insights of Chomsky, Zahavi, and Sperber, Knight concludes that language is impossible in a Darwinian world. He states, “The Darwinian challenge remains real. Language is impossible not simply by definition, but—more interestingly—because it presupposes unrealistic levels of trust. . . . To guard against the very possibility of being deceived, the safest strategy is to insist on signals that just cannot be lies. This rules out not only language, but symbolic communication of any kind.”4

Signal for Creation

And yet, human beings possess language (along with other forms of symbolism, such as art and music). Our capacity for abstract language is one of the defining features of human beings.

For Christians like me, our language abilities reflect the image of God. And what appears as a profound challenge and mystery for the evolutionary paradigm finds ready explanation in the biblical account of humanity’s origin.

Is it time for our capacity for conversation to separate us from the evolutionary explanation for humanity’s origin?

Resources:

Endnotes

  1. Johan J. Bolhuis et al., “How Could Language Have Evolved?” PLoS Biology 12 (August 2014): e1001934, doi:10.1371/journal.pbio.1001934.
  2. Chris Knight, “Puzzles and Mysteries in the Origins of Language,” Language and Communication 50 (September 2016): 12–21, doi:10.1016/j.langcom.2016.09.002.
  3. Knight, “Puzzles and Mysteries,” 12–21.
  4. Knight, “Puzzles and Mysteries,” 12–21.
Reprinted with permission by the author
Original article at:
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2018/10/10/can-evolution-explain-the-origin-of-language

The Optimal Design of the Genetic Code

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BY FAZALE RANA – OCTOBER 3, 2018

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

–William Paley, Natural Theology

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

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

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

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

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

Proteins

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

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

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Figure 1: The Amino Acids. Image credit: Shutterstock

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

DNA

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

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

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

The Genetic Code

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

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

Sixty-four codons make up the genetic code. Because the code only needs to encode 20 amino acids, some of the codons are redundant. That is, different codons code for the same amino acid. In fact, up to six different codons specify some amino acids. Others are specified by only one codon.

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

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

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Figure 3: The Genetic Code. Image credit: Shutterstock

The Optimal Genetic Code

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

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

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

Frameshift Mutations

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

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Figure 4: Types of Mutations. Image credit: Shutterstock

The Genetic Code Is Optimized to Withstand Frameshift Mutations

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

The Genetic Code Is Optimized to Harbor Multiple Overlapping Codes

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

The Genetic Code and the Case for a Creator

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

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

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

Resources

Endnotes

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