As a graduate student and a postdoc, I spent countless hours in the lab doing research. Part of my work involved performing biochemical assays—laboratory procedures designed to measure the activities of biomolecules and biochemical systems.

To get our assays to work properly, we had to carefully design and optimize each test before executing it with exacting precision in the laboratory. Optimizing these assays was no easy feat. It could take weeks of painstaking effort to get the protocols just right.

My experiences working in the lab taught me some important lessons that I carry with me today as a Christian apologist. One of these lessons has to do with optimization. Optimized systems don’t just happen, whether they are laboratory procedures, manufacturing operations, or well-designed objects or devices. Instead, optimization results from the insights and efforts of intelligent agents, and therefore serves as a sure indicator of intelligent design.

As it turns out, nearly every biochemical system appears to be highly optimized. For me, this fact indicates that life stems from a Mind. And as life scientists continue to characterize biochemical systems, they keep discovering more and more examples of biochemical optimization, as recent work by a large team of collaborators working at the Earth-Life Science Institute (ELSI) in Tokyo, Japan, illustrates.¹

These researchers uncovered more evidence that the twenty amino acids encoded by the genetic code possess the optimal set of physicochemical properties. If not for these properties, it would not be possible for the cell to build proteins that could support the wide range of activities required to sustain living systems. This insight gives us important perspective into the structure-function relationships of proteins. It also has theological significance, adding to the biochemical case for a Creator.

Before describing the ELSI team’s work and its theological implications, a little background might be helpful for some readers. For those who are familiar with basic biochemistry, just skip ahead to Why These Twenty Amino Acids?

Background: Protein Structure

Proteins are large, complex molecules that play a key role in virtually all of the cell’s operations. Biochemists have long known that the three-dimensional structure of a protein dictates its function. Because proteins are such large, complex molecules, biochemists categorize protein structure into four different levels: primary, secondary, tertiary, and quaternary structures.

Figure 1: The Four Levels of Protein Structure. Image credit: Shutterstock

• A protein’s primary structure is the linear sequence of amino acids that make up each of its polypeptide chains.
• The secondary structure refers to short-range three-dimensional arrangements of the polypeptide chain’s backbone arising from the interactions between chemical groups that make up its backbone. Three of the most common secondary structures are the random coil, alpha (α) helix, and beta (β) pleated sheet.
• Tertiary structure describes the overall shape of the entire polypeptide chain and the location of each of its atoms in three-dimensional space. The structure and spatial orientation of the chemical groups that extend from the protein backbone are also part of the tertiary structure.
• Quaternary structure arises when several individual polypeptide chains interact to form a functional protein complex.

Background: Amino Acids

The building blocks of proteins are amino acids. These compounds are characterized by having both an amino group and a carboxylic acid bound to a central carbon atom. Also bound to this carbon are a hydrogen atom and a substituent that biochemists call an R group.

Figure 2: The Structure of a Typical Amino Acid. Image credit: Shutterstock

The R group determines the amino acid’s identity. For example, if the R group is hydrogen, the amino acid is called glycine. If the R group is a methyl group, the amino acid is called alanine.

Close to 150 amino acids are found in proteins. But only 19 amino acids (plus 1 imino acid, called proline) are specified by the genetic code. Biochemists refer to these 20 as the canonical set.

Figure 3: The Protein-Forming Amino Acids. Image credit: Shutterstock

A protein’s primary structure forms when amino acids react with each other to form a linear chain, with the amino group of one amino acid combining with the carboxylic acid of another to form an amide linkage. (Sometimes biochemists call the linkage a peptide bond.)

Figure 4: The Chemical Linkage between Amino Acids. Image credit: Shutterstock

The repeating amide linkages along the amino acid chain form the protein’s backbone. The amino acids’ R groups extend from the backbone, creating a distinct physicochemical profile along the protein chain for each unique amino acid sequence. To first approximation, this unique physicochemical profile dictates the protein’s higher-order structures and, hence, the protein’s function.

Why These Twenty Amino Acids?

Research has revealed that the set of amino acids used to build proteins is universal. In other words, the proteins found in every organism on Earth are made up of the same canonical set.

Biochemists have long wondered: Why these 20 amino acids?

In the early 1980s biochemists discovered that an exquisite molecular rationale undergirds the amino acid set used to make proteins.² Every aspect of amino acid structure has to be precisely the way it is for life to be possible. On top of that, biochemists concluded that the set of 20 amino acids possesses the “just-right” physical and chemical properties that evenly and uniformly vary across a broad range of size, charge, and hydrophobicity (water resistance). In fact, it appears as if the amino acids selected for proteins seem to form a uniquely optimal set of 20 amino acids compared to random sets of amino acids.³

With these previous studies as a backdrop, the ELSI investigators wanted to develop a better understanding of the optimal nature of the universal set of amino acids used to build proteins. They also wanted to gain insight into the origin of the canonical set.

To do this they used a library of 1,913 amino acids (including the 20 amino acids that make up the canonical set) to construct random sets of amino acids. The researchers varied the set sizes from 3 to 20 amino acids and evaluated the performance of the random sets in terms of their capacity to support: (1) the folding of protein chains into three-dimensional structures; (2) protein catalytic activity; and (3) protein solubility.

They discovered that if a random set of amino acids included even a single amino acid from the canonical set, it dramatically out-performed random sets of the same size without any of the canonical amino acids. Based on these results, the researchers concluded that each of the 20 amino acids used to build proteins stands out, possessing highly unusual properties that make them ideally suited for their biochemical role, confirming the results of previous studies.

An Evolutionary Origin for the Canonical Set?

The ELSI researchers believe that—from an evolutionary standpoint—these results also shed light as to how the canonical set of amino acids emerged. Because of the unique adaptive properties of the canonical amino acids, the researchers speculate that “each time a CAA [canonical amino acid] was discovered and embedded during evolution, it provided an adaptive value unusual among many alternatives, and each selective step may have helped bootstrap the developing set to include still more CAAs.”⁴

In other words, the researchers offer the conjecture that whenever the evolutionary process stumbled upon one of the amino acids in the canonical set and incorporated it into nascent biochemical systems, the addition offered such a significant evolutionary advantage that it became instantiated into the biochemistry of the emerging cellular systems. Presumably, as this selection process occurred repeatedly over time, members of the canonical set would be added, one by one, to the evolving amino acid set, eventually culminating in the full canonical set.

Scientists find further support for this scenario in the following observation: some of the canonical amino acids seemingly play a more important role in optimizing smaller sets of amino acids, some play a more important role in optimizing intermediate size sets of amino acids, and others play a more prominent role in optimizing larger sets. They argue that this difference may reflect the sequence by which amino acids were added to the evolving set of amino acids as life emerged.

On the surface, this evolutionary explanation is not unreasonable. But more careful consideration of the idea raises concerns. For example, just because a canonical amino acid becomes incorporated into a set of amino acids and improves its adaptive value doesn’t mean that the resulting set of amino acids could produce the range of proteins with the solubility, foldability, and catalytic range needed to support life processes. Intuitively, it seems to me as a biochemist, that there must be a threshold for the number of canonical amino acids in any set of amino acids for it to have the range of physicochemical properties needed to build all the proteins needed to support minimal life.

I also question this evolutionary scenario because some of the amino acids that optimize smaller sets would not have been the ones present initially on the early Earth because they cannot be made by prebiotic reactions. Instead, many of the amino acids that optimize smaller sets can only be generated through biosynthetic routes that must have emerged much later in any evolutionary scenario for the origin of life.⁵ This limitation also means that the only way for some of the canonical amino acids to become incorporated into the canonical set is that multi-step biosynthetic routes for those amino acids evolved first. But if the full canonical set isn’t available, then it is questionable if the proteins needed to catalyze the biosynthesis of these amino acid would exist, resulting in a chicken-and-egg dilemma.

In light of these concerns, is there a better explanation for the highly optimized canonical set of amino acids?

A Creator’s Role?

Optimality of the universal set of protein amino acids finds explanation if life stems from a Creator’s handiwork. As noted, optimization is an indicator of intelligent design, achieved through foresight and preplanning. Optimization requires inordinate attention to detail and careful craftsmanship. By analogy, the optimized biochemistry epitomized by the amino acid set that makes up proteins rationally points to the work of a Creator.

Is There a Biochemical Anthropic Principle?

This discovery also leads to another philosophical implication: It lends support to the existence of a biochemical anthropic principle.

The ELSI researchers speculate that no matter the starting point in the evolutionary process, the pathways will all converge at the canonical set of amino acids because of the acids’ unusual adaptive properties. In other words, the amino acids that make up the universal set of protein-coding amino acids are not the outworking of an historically contingent evolutionary process, but instead seem to be fundamentally prescribed by the laws of nature. To put it differently, it appears as if the canonical set of amino acids has been preordained in some way.⁶ One of the study’s authors, Rudrarup Bose, suggests that “Life may not be just a set of accidental events. Rather, there may be some universal laws governing the evolution of life.”⁷

Though I prefer to see the origin of life as a creation event, it is important to recognize that even if one were to adopt an evolutionary perspective on life’s origin, it looks as if a Mind is responsible for jimmy-rigging the process to a predetermined endpoint. It looks as if a Mind purposed for life to be present in the universe and structured the laws of nature so that, in this case, the uniquely optimal canonical set of amino acids would inevitably emerge.

Along these lines, it is remarkable to think that the canonical set of amino acids has the precise properties needed for life to exist. This “coincidence” is eerie, to say the least. As a biochemist, I interpret this coincidence as evidence that our universe has been designed for a purpose. It is provocative to think that regardless of one’s perspective on the origin of life, the evidence converges toward a single conclusion: namely that life manifests from an intelligent agent—God.

Resources

• The Cell’s Design: How Chemistry Reveals the Creator’s Artistry by Fazale Rana (book)

The Optimality of Biochemical Systems

• “The Genetic Code: Simply the Best” by Fazale Rana (article)
• “The Optimal Design of the Genetic Code” by Fazale Rana (article)
• “Biochemical Synonyms Optimized, Part 1” by Fazale Rana (article)
• “Biochemical Synonyms Optimized, Part 2” by Fazale Rana (article)
• “Protein Amino Acids Form a “Just-Right” Set of Building Blocks” by Fazale Rana (article)
• “Why These 20 Amino Acids” by Fazale Rana (article)
• “Optimal Design of Metabolism” by Fazale Rana (article)
• “Metabolism: A Cascade of Design” by Fazale Rana (article)

The Biochemical Anthropic Principle

• “How the Central Dogma of Molecular Biology Points to Design” by Fazale Rana (article)
• “The Logic of DNA Replication Makes a Case for Intelligent Design” by Fazale Rana (article)
• “Protein Amino Acids Form a “Just-Right” Set of Building Blocks” by Fazale Rana (article)
• “Why These 20 Amino Acids” by Fazale Rana (article)
• “A Periodic Table for Protein Structures Reveals Biochemical Design” by Fazale Rana (article)
• “Biochemical Grammar Communicates the Case for Creation” by Fazale Rana (article)
• “Molecular Logic of the Electron Transport Chain Supports Creation,” by Fazale Rana (article)
• “Fatty Acids Are Beautiful” by Fazale Rana (article)

I have a problem with the Star Wars movies. Each saga film opens with the famous words, “In a galaxy far, far away.” We astronomers have observed thousands of far, far away galaxies and, unfortunately for Luke Skywalker and friends, none possess the features that support advanced life. Our Milky Way Galaxy is the only known life-friendly galaxy.

The list of characteristics necessary for life is long. In the last few weeks, months, and years astronomers have discovered yet another feature of the Milky Way Galaxy (MWG) that makes it uniquely qualified to host advanced life. It possesses a supermassive black hole like no other.

As I explained in last week’s blog, a supermassive black hole has a mass that exceeds one million times the Sun’s mass. All medium, large, and giant galaxies possess a supermassive black hole (SMBH) in the central part of their core. From just outside their event horizons, these SMBHs emit deadly radiation that renders advanced life impossible in these galaxies. Sometimes this radiation is so powerful that it renders advanced life impossible in all galaxies within its vicinity.

SMBH in the Milky Way
If the radiation from SMBHs in other galaxies is deadly, then why can’t we say the same of the radiation from the SMBH in our galaxy? Part of the answer to this question is that the MWG possesses an exceptionally low-mass SMBH. Its SMBH weighs in at only 4.02±0.16 million solar masses.¹ This low mass establishes a limit on how much deadly radiation can emanate from the MWG’s SMBH.

Our local SMBH’s low mass is truly extraordinary. Astronomers have determined consistent correlations between four different galaxy characteristics and the respective masses of the galaxies’ SMBHs:

1. Number of globular clusters orbiting about the galaxy²
2. Mass of the galaxy’s central bulge³
3. Luminosity of the galaxy⁴
4. Velocity dispersion (range of velocities) of the stars in the galaxy’s central bulge⁵

A globular cluster is a very dense array of 100,000–10,000,000 stars (see figure 1). A galaxy’s central bulge refers to its core, where the density of stars is equal to, or near, that of a globular cluster’s star density (see figure 2). The velocity of the gas in the galaxy’s central bulge is directly proportional to the mass of its SMBH. Gas velocity can be difficult to measure. Fortunately, the velocity dispersion of stars in a central bulge is easier to measure and has been demonstrated to correlate tightly with the gas velocity.

Figure 1: Omega Centauri Globular Cluster. Image credit: European Southern Observatory

Figure 2: Central Bulge of the NGC 3344. The central bulge is the solid white, oval-shaped region. For most galaxies, the central bulge contains about half the galaxy’s stars. Image credit: NASA/ESA/Hubble Space Telescope/STScI

However, astronomers Kastytis Zubovas and Andrew King have demonstrated that SMBH mass measurements differ based on the type of host galaxy.⁶ For example, these correlations indicate higher SMBH masses for supergiant elliptical galaxies in the cores of large galaxy clusters than they do for elliptical field galaxies that exist outside of, or on the fringes of, galaxy clusters. Likewise, these correlations indicate higher SMBH masses for elliptical field galaxies than they do for spiral galaxies. And among spiral galaxies, other astronomers have shown that spiral galaxies manifesting a central bar structure tend to possess slightly less-massive SMBHs than do spiral galaxies without a central bar structure.⁷

Because the MWG is a spiral galaxy that possesses a central bar structure (see figure 3), astronomers would expect an SMBH mass somewhat lower than what the four correlations would otherwise indicate based on the average properties of the known population of galaxies. However, the MWG possesses a much lower SMBH mass than what this small adjustment would imply.

Figure 3: Structure of the Milky Way Galaxy. This map of the MWG was constructed from observations across the electromagnetic spectrum of multiple components of the galaxy. Image credit: NASA/JPL-Caltech/R. Hurt

The mass of the Andromeda Galaxy’s SMBH is in agreement with the four correlations. Since the MWG possesses the same mass as Andromeda (the total mass for both = 1.5 trillion solar masses)⁸ and both are spiral galaxies with a bar,⁹ the MWG’s SMBH should be about the same mass. Instead, it measures to be about twenty times less massive.

Optimal SMBH
That the MWG’s SMBH is twenty times less massive than the SMBHs in other galaxies of the same size and structure means that our galaxy’s SMBH has about twenty times less potential to emit deadly radiation from the regions just outside its event horizon. That factor of twenty times is one reason why advanced life is possible in the MWG.

Another important reason why advanced life can exist in the MWG is that its SMBH is very quiet at present. The quantity and the intensity of deadly radiation emitted by an SMBH depend on how much gas, dust, comets, asteroids, planets, and/or stars are being drawn toward the SMBH’s event horizon. SMBHs in nearby galaxies consume a solar-type star on average about once every 100,000 years.¹⁰ When that happens, a bright flare lasting several months pours out deadly radiation throughout the galaxy. Stars smaller than the Sun get consumed in these galaxies about once every 10,000 years, resulting in deadly radiation lasting several days to weeks. These galaxies also consume molecular clouds of gas on time scales ranging from once a century to once every few millennia that likewise result in the emission of deadly radiation lasting days to weeks.

By comparison, the MWG’s SMBH produces tiny flares that last only hours but occur on an almost daily basis.¹¹ In 2012, a team of three astronomers demonstrated that being surrounded by super-Oort clouds of comets and asteroids explains the near-continual high radiation activity from regions outside the event horizons of SMBHs in active galactic nuclei. It is likely that some kind of Oort cloud surrounds all SMBHs.¹² A relatively modest Oort cloud surrounding the MWG’s SMBH explains the observed tiny frequent flares.¹³

As several astronomers have noted, the MWG’s nucleus is exceptionally quiet and has been for billions of years.¹⁴ The low mass of our galaxy’s SMBH, the tiny size of its surrounding Oort cloud, and the lack of merger events with large- and medium-sized dwarf galaxies over the past several billion years explain why life has survived and thrived on Earth throughout the past 3.8 billion years. That the activity level just outside the event horizon of the MWG’s SMBH has been extremely quiet throughout the past 10,000 years explains why global human civilization has flourished.

Our galaxy’s SMBH is like no other. It is exquisitely fine-tuned and designed to make possible not only the existence of human beings but also the existence of global high-technology civilization. Apparently, Someone wanted billions of humans to exist and to possess high-technology and to use that technology for a specified purpose.

Featured image: Artist’s Conception of a Supermassive Black Hole
Image credit: NASA/JPL-Caltech

Large terrestrial mammals bring delight to everyone. Such pleasure explains why zoos, wild animal parks, and safaris are so popular. It also explains why so many of us enjoy the close encounters we experience with wild terrestrial mammals when we visit national parks and wilderness areas. To add to our enjoyment, a paper¹ published in a little-known science journal, Acta Oecologica, provides research showing that we humans are living at an especially optimal time to experience and benefit from large terrestrial mammals.

Genesis 1:24–27 declares that God created large terrestrial mammals before he created human beings. Job 38:39–39:25 selects six different kinds of terrestrial mammals for special mention: the lion, the goat, the deer, the donkey, the ox, and the horse. As I explain in Hidden Treasures in the Book of Job, God created and designed the different species of modern large-bodied terrestrial mammals to serve and please humans beings and to play a critical role in launching and sustaining our civilization.²

Advanced global technology would not have been possible without the terrestrial mammals described in the book of Job. Evidence for this conclusion is not just biblical but also scientific. On those continents (Australia, North America, and South America) where colonizing humans quickly wiped out the resident donkeys, oxen, horses, and other large-bodied terrestrial mammals, the descendants of those humans found themselves unable to advance beyond stone-age technology and unable to develop a large population. To overcome these obstacles it required Europeans importing the missing species of mammals.

Climate Stability and Mammal Density
Even on those continents where humans hadn’t wiped out the terrestrial mammals critical for launching civilization, large-scale organized civilization did not begin right away. There was a time lag of several tens of thousands of years caused, in large part, by Earth’s being in the grip of an ice age. The four scientists who wrote the paper in Acta Oecologica offered additional reasons why.

The team of four first cite and describe several research studies that demonstrate how “climate has played a key role in shaping the geographic patterns of biodiversity.”³ Then they used a macroecological approach to assess—for terrestrial mammals living in mid- and high-latitude northern hemisphere regions—species richness, range sizes, adult body sizes, average lifespans, and average litter sizes from the end of the last glacial maximum 19,000 years ago to the present.

The researchers found that for subregions in both Eurasia and North America there was a strong correlation between the number density of terrestrial mammals and the degree of climate stability in the subregion. They also noted that the greater the climate instability of a subregion, the smaller the average body size of the terrestrial mammals dwelling there and the greater the geographic range size for each mammal species.

These three correlations demonstrate that food availability for terrestrial mammals must be tightly linked to climate stability. Indeed, the correlations were most strongly manifested for North American mammals. Since North America experienced much greater climate instability since the last glacial maximum than did Eurasia, these stronger correlations affirm that increased climate stability yields greater food supplies for terrestrial mammals, which in turn yields a greater density and diversity of mammals.

Earth’s Improbable Extreme Climate Stability
The last 2.6 million years has been marked by the most extreme long-term climate instability in the entire 3.8-billion-year history of life on Earth. The only exception has been the last 9,500 years—a period marked by extreme climate stability. The figure below shows the difference between the mean temperature variations (taken from Greenland’s ice sheet) of the past 9,500 years compared to the previous 8,000 years.

Figure 1: Temperature Variations for Mid-Greenland throughout the Past 17,000 Years. The temperature figures represent the surface air temperature in the central region of Greenland’s ice sheet. The blue curve shows the newly determined temperature record of the past 9,500 years. The purple curve shows the temperature record from 17,000–9,500 years ago derived from oxygen-18 isotope measures in ice cores drilled in the central region of Greenland’s ice sheet. The top arrow and the two dotted lines delineate the start and end times of the Younger Dryas cooling event. Data credit for blue curve: Shaun A. Marcott et al. and Andy May; Data credit for purple curve: United States Geological Survey; Diagram credit: Hugh Ross

In a previous series of blogs here,⁴ here,⁵ here,⁶ and here,⁷ I explained how a sequence of exquisitely fine-tuned circumstances and events—one would be justified in calling them miraculous—led to the past 9,500 years of extreme climate stability. Amazingly, the global mean temperature over the past 9,500 years has not varied by more than ±0.65°C.

Our period of extreme climate stability (less than four-thousandths of one percent of the duration of the climate instability period) has made possible large-scale specialized agriculture. Thanks to that food-production capacity, humans have established global high-technology civilization and a population of 7.5 billion. I describe ten more benefits we have accrued from the past 9,500 years of extreme climate stability in my book, Improbable Planet.⁸ Thanks to the four scientists’ research study, we can add one more to the list. Humans get to enjoy and benefit from terrestrial mammals, both domesticated and wild, at the greatest possible abundance and diversity. Next time you consume meat, milk, or cheese or wear a wool sweater or see a cute mammal on a wilderness trek, you now have scientific insight to motivate you to be grateful for this gift of extreme climate stability.

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 Theology, William 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.

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.

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.

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.

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

• The Cell’s Design: How Chemistry Reveals the Creator’s Artistry by Fazale Rana (book)
• “FYI: I. D. IN DNA Deciphering Design in the Genetic Code” by Fazale Rana (article)
• “The Genetic Code: Simply the Best” by Fazale Rana (article)
• “Mitochondria’s Deviant Genetic Code: Evolution or Creation?” by Fazale Rana (article)
• “Biochemical Synonyms Optimized, Part 1 of 2” by Fazale Rana (article)
• “Biochemical Synonyms Optimized, Part 2 of 2” by Fazale Rana (article)
• “Protein Amino Acids Form a ‘Just Right’ Set of Biological Building Blocks” by Fazale Rana (article)
• “Why These 20 Amino Acids?” by Fazale Rana (article)
• “The Optimal Design of Metabolism” by Fazale Rana (article)
• “Metabolism: A Cascade of Design” by Fazale Rana (article)

New work by scientists from Switzerland and the Netherlands provides increased evidence for the optimal design of the cell’s metabolic pathways. This optimization supports the notion that life stems from the work of an intelligent Agent.

One of the biggest shocks I experienced when we moved from Cincinnati to the Los Angeles area thirteen years ago was the traffic—and the complexity of the Southern California freeway system. (When you ask someone for directions, it sounds like a quarterback calling out signals at the line of scrimmage: take the 210 to the 57 to the 5 to the 55 to the… hut!)

Yet, in spite of the horrible traffic and complex directions, the well-designed freeway system makes it easy to navigate the greater Los Angeles area. Virtually all of the towns and cities are laid out on a grid, connecting major roadways to different regions of the Southland.

Conversely, cities on the east coast are laid out in a haphazard manner, in part because they were built hundreds of years ago, well before automobiles became the dominant means of transportation.

Metabolic Pathways
Metabolism refers to the myriad chemical reactions that occur in organisms necessary to sustain life. Metabolic activity makes it possible for life-forms to extract energy from the environment and construct life’s components. These processes allow organisms to grow, reproduce, maintain biological structures, and respond to changes in the environment. Metabolic reactions include the production and breakdown of proteins and RNA molecules, DNA replication, and the assembly of cell membranes and cell walls.

Additionally, metabolism involves reactions of small molecules. A significant number of metabolic reactions produce small molecules used by the cell’s machinery as building blocks to assemble proteins, DNA, RNA, and cell membrane bilayers. On the other hand, some metabolic activities breakdown compounds like glucose and other sugar molecules into smaller molecules to provide energy for the cell’s operations. Some metabolic activities prepare materials the cell no longer needs (cellular waste) for elimination. Other reactions detoxify materials that are harmful to the cell.

Within the cell’s interior, metabolic processes are often organized like city streets into routes or pathways comprised of a series of chemical reactions. These reactions transform a starting compound into a final product via a series of small, stepwise chemical changes. Each step in a metabolic route is mediated by a protein (called an enzyme) that assists in the chemical transformation. These pathways can be linear, branched, or circular. An example of a linear pathway is glycolysis, which is illustrated in figure 1 below.

Figure 1. Image credit: https://en.wikipedia.org/wiki/File:Glycolysis.jpg

The chemical components that form part of a particular metabolic sequence sometimes take part in other metabolic pathways. These shared compounds cause metabolic pathways to be interconnected and networked together. The sum total of metabolic processes represents a complex, reticulated web of chemical reactions, each one catalyzed by an enzyme. Figure 2 below shows (in a highly schematic way) the major
metabolic pathways in the cell and some ways that they interconnect.

Figure 2. Image credit:
https://en.wikipedia.org/wiki/File:Metabolism_790px_partly_labeled.png

Given the vast complexity of the cell’s metabolism, (go here for a detailed depiction of the cell’s metabolic pathways) it’s easy to envision how evolutionary processes could have poorly matched the pathways together, bit by bit, over a vast period of time—just like the random layout of some cities in the eastern United States.

However, a number of recent reports point out that metabolic pathways in the cell appear to be designed exquisitely, rather than haphazardly. (For more details, go here and here.)

A new study further highlights the optimality of the cell’s metabolic systems.² Using the multi-dimension optimization theory, researchers evaluated the performance of the metabolic systems of several different bacteria. The data generated by monitoring the flux (movement) of compounds through metabolic pathways (like the movement of cars along the roadways ) allowed researchers to assess the behavior of cellular metabolism. They determined that metabolism functions optimally for a system that seeks to accomplish multiple objectives. It looks as if the cell’s metabolism is optimized to operate under a single set of conditions. At the same time, it can perform optimally with relatively small adjustments to the metabolic operations when the cell experiences a change in condition.

This latest study illustrates that biochemical systems are highly optimized. Optimization is a hallmark feature of man-made designs, and it requires planning and deliberate effort to achieve such optimization. So, by analogy, one could argue that the optimization of biochemical systems reflects the work of an intelligent Agent—a Creator. (See my book, The Cell’s Design, for a more detailed presentation of this argument.)

During speaking events, I am frequently complimented for my “phenomenal memory.” People are impressed by the relative ease with which I quote Bible passages from memory or recall the details of arcane scientific discoveries made decades ago. However, my wife, Kathy, has a different opinion. She is amazed by my “spectacular memory lapses.” Thirty seconds after answering the phone I forget who called or what the call was about. Furthermore, she often needs to remind me of the names of close friends and relatives. Now, however, thanks to some recent scientific breakthroughs, I can attempt to explain to Kathy that there are advantages to being able to forget.

The discovery of the benefit of memory lapses arises from research on rodents. Rodents (short-legged mammals) are listed in Genesis 1 as one of three sets of land mammals that God created especially to assist human beings.¹ In the launch of civilization rodents provided humanity with an effective, economic source of clothing. No other set of animals produces luxuriant fur at such low cost.

Today, rodents serve humanity’s need for medical advances. Rodent DNA is remarkably similar to human DNA. Hence, they make an excellent laboratory proxy for humans. Moreover, because of rodents’ small size, short generation times, the ease with which they adapt to crowded conditions, and their broad diet spectrum, scientists can perform medical experiments on tens of thousands of mice, rats, and others for relatively little cost.

In the ongoing search for cures to dyslexia, Alzheimer’s disease, and other forms of dementia, several different teams of researchers are again turning to rodents for answers.² The researchers noted with much astonishment that the molecular pathways the brain uses to form long-term memories are virtually identical in rodents and humans. This similarity allows scientists to genetically engineer mice in order to alter the molecular pathways in attempt to improve the memory of mice—with the hope that eventually the same can be done for humans.

So far, four neuroscience research teams have discovered that by inducing slight differences at the molecular level they can achieve in mice dramatic improvements in learning and memory.³ Some scientists go so far to claim they are “improving on evolution.”⁴ In fact, the “improvements” already have launched a black market for “intellectual steroids” on university campuses and high-tech firms. But, like the steroids used by athletes, do these chemical enhancements of cognitive abilities come with unexpected costs?

Ongoing research with super-smart mice indicates that enhancing the cognitive capacities of normal mice indeed has deleterious side effects. These include greater physical and mental stress, chronic pain, and increased cancer risk. And there are cognitive side effects as well.

The problem observed with the super-smart mice is that they seem to remember too much. In some strains fear responses kick in even in reaction to benign stimuli. Other strains have no trouble solving a difficult maze but fail to solve simple mazes. The problem seems to be that the cognitively enhanced mice remember too much irrelevant information.

The super-smart mice manifest an uncanny resemblance to a very rare cognitive disorder in humans. In the 1920s, Russian newspaper reporter Solomon Shereshevsky had such a perfect memory that he never needed to take notes. In fact, after a single reading of Dante’s Divine Comedy, Shereshevsky could recite the entire poem by heart. However, his mind was so fixated on particulars that he could not grasp metaphors. He was unable to comprehend the imagery in the poems he was reciting.

Apparently, the ability to forget is an important cognitive attribute. Years ago, a research team demonstrated through computer models that slight imperfections in memory are necessary for humans to see connections between different but related events.⁵

Researchers are now drawing the conclusion that the brains of normal mice and normal humans manifest optimized memory designs. As for humans, our memory systems allow us to both particularize and generalize, to engage in concrete, literal thinking but also to think abstractly and metaphorically. Such consistent optimization is the hallmark of a supernatural, super-intelligent Creator, not the outcome of naturalistic evolution.

God has created the human race with a diversity of memorization and forgetfulness abilities so that, by dividing our labor and specializing, we can work together to achieve great accomplishments. In this context it would be unwise and harmful to attempt to improve upon God’s optimal designs. However, just like physical steroids have given relief to humans suffering from physical disorders, so, too, mental steroids hold great promise to cure the maladies of the mind, such as Alzheimer’s disease and dementia. For these marvelous medical advances we again can thank our Creator for the manner in which He designed rodents in advance of our creation to serve us.

TNRTB Archive – Retained for reference information

A new study confirms declarations in the Bible (e.g. Job 39 and Psalm 104) that God creates life with optimal designs in the ecological relationships between plants and animals. Researchers found that protecting forests in the Peruvian Amazon from species-specific herbivores resulted in certain forest species crowding out others. Evidently, the great diversity of herbivore species, with many of them specializing on just one or two plant species, promotes both the health and the diversity of plant species by ensuring that each plant species remains confined to the habitats for which it is best suited. This delicate ecological balance reflects the wisdom of an intelligent Creator.

• Paul V. A. Fine, Italo Mesones, and Phyllis D. Coley, “Herbivores Promote Habitat Specialization by Trees in Amazonian Forests,” Science 305 (2004): 663-68.
• https://www.sciencemag.org/cgi/content/abstract/305/5684/663