Category Archives: Science & Study

Seeing the Wonder of Transparency

I was pouring liquid laundry detergent into the washer when I realized, “Hey, it’s clear!” In that moment I became entranced by the wonder of transparency. Through research, I discovered not only how much ingenuity and engineering is involved in making something transparent, but also that transparency is a highly valued aesthetic property in consumer products. Making things like clear cleaning products requires detailed planning and precise chemical composition. Any contaminant makes the product worthless.

Vision also requires a transparent medium—beginning with the eye and extending out into the cosmos. And thankfully, humans enjoy finely tuned transparency, as the following hierarchy—from the macro-level sky perspective to the micro-level inner eye view—powerfully demonstrates.

Transparent Atmosphere and Instruments

Outer space is clear and filled with invisible dark energy. This transparent “nothingness” (it’s really a “something”) provides a backdrop for the great cosmic choreography we know as astronomy—the dance of planets and galaxies, suns and moons, and all we know of the material world, including Earth. This intergalactic space allows photons (light particles) to travel at the speed of light for billions of years to our telescopes. Gas clouds could blot out the view were it not for superwinds from the high-energy light of ancient massive stars. Also, our solar system’s just-right location between the Milky Way Galaxy’s spiral arms provides an ideal window for observing the heavens.

Earth’s atmosphere, as we know it, is also transparent. The planet’s early atmosophere was hazy and thick with methane. Gradually it cleared up thanks to oxygenating life-forms and, thus, the Sun, moon, and stars became visible, filling the sky with otherworldly beauty and providing natural timekeepers.

Even our equipment for observing the cosmos requires optical telescopes furnished with clear glass lenses and reflective mirrors in order to collect and capture photons. Silicon dioxide, the key component used in making optical glass, possesses unique chemical properties that give it the necessary clarity. Oxygen bridge bonds between silicon atomsprevent it from crystallizing upon heating and cooling at normal temperatures, which would cloud the lens. In other words, just-right chemistry allows us to build powerful telescopes that extend our scope of vision.

Clear Eyeballs

Our transparent atmosphere and clear eyeballs allow photons to reach the retina—making possible the wonder of vision. But first, light must travel through several protein structures. The cornea (the “pinhole to the world) protects the rest of the eye even as it allows light to enter. This means all five layers of the cornea must be transparent. The outermost corneal epithelium is made of cells that are constantly produced and shed every week. Next is a dense fibrous sheet of connective tissue called Bowman’s layer. Third, the corneal stroma is the thickest layer. It is composed of collagen fibrils, the regular arrangement and uniform spacing of which is what enables the cornea to be perfectly clear. Descemet’s membrane, the fourth layer, begins as a very thin membrane that gradually thickens throughout life. Finally, the innermost corneal endothelium is bathed in the clear aqueous humor that fills the space between the cornea and the iris and pupil. Behind the cornea is the crystalline lens. It changes shape to bend light (refraction is another convenient property of light) to form a clear image on the retina. Here is the key point: all of these structures must retain their transparency in a dynamic biochemical environment within the eyeball or blindness will result.

Two ocular fluids—aqueous humor and vitreous humor—bathe the eyeball and also must be transparent. Aqueous humor is a thin, clear, watery fluid that fills the eye’s anterior and posterior chambers. It nourishes the cornea and lens by supplying nutrients. High pressures can result in glaucoma while low pressure can distort eye structures and degrade vision. Vitreous humor is the fluid-like gel located in the posterior chambers of the eyes. It is 98–99 percent water with trace amounts of collagen protein and other chemical constituents. Dynamic chemical processes within each cell must keep this fluid’s ion concentrations within a very narrow range or blindness would set in quickly.

If water were not transparent to visible light—hence, appearing clear—ocular fluids would cloud our vision. Water’s transperancy is a complex topic that requires deeper physics. Nevertheless, clear water is perfect for bathing eyeballs!

Figure 1: A three-dimensional reconstruction of alpha beta-crystallin, a protein molecule protecting vision. Image credit: Dept. of Chemistry, Technische Universitaet Muenchen (TUM).

Protected Vision

Finely tuned features of the eye continue down one more micro level as we examine protein molecules that make up the eye’s structures. A concentrated mix of several proteins make up the human eye. Protective proteins in the lens prevent the structural proteins from clumping into cataracts, which cause blurry vision. One of these proteins is called alpha beta-crystallin (ab-crystallin), a globular molecule made of 24 subunits, like a perforated soccer ball (see figure 1). It chaperones (assists) other proteins and belongs to a group of small heat-shock proteins that prevent clumping under stress conditions. Without this process blindness would result.

Our Bright Future

Natural vision can be obscured by gas clouds in deep space, vapor clouds in the sky, or cataracts in the eye. That these obfuscations are relatively rare is a wonder which defies material explanation. As the Bible points out in 1 Corinthians 13:12 (ESV), humans can experience clouded spiritual vision as well.

For now we see in a mirror dimly, but then face to face. Now I know in part; then I shall know fully, even as I have been fully known.

1 Corinthians 13:12, ESV

I believe such spiritual blindness can obscure human ability to appreciate the exquisite design in the details of nature and of our bodies. The finely tuned physics, exquisitely engineered chemistry, and precisely regulated physiology behind the transparency that makes vision possible shows that planning, purpose, and powerful reasoning must be in play. May we diligently learn and communicate these elegant discoveries so they will be clear to everyone.

Original article: Seeing the Wonder of Transparency


More Anthropic Reasons for the Extreme Fine-Tuning of Dark Energy

Years ago, in a paper published in the Astrophysical Journal, theoretical physicist Lawrence Krauss referred to dark energy as presenting “the most extreme fine-tuning problem known in physics.”1 Dark energy is energy embedded in the universe’s space surface that makes up about 70 percent of all the stuff of the universe (see figure 1). Krauss determined that the fine-tuning level is more extreme than one part in 10120! He has been joined by several other theoretical physicists who conclude that the required fine-tuning of dark energy is “the most difficult problem in physics.”The obvious question is does this most difficult problem point to a causal agent with the capacity to fine-tune to a degree far, far beyond anything we humans are capable of manifesting?


Figure 1: Relative abundance components of the universe.

Dark energy is the dominant factor controlling cosmic expansion. The larger the constant or constants governing dark energy, the more rapidly the universe expands from the cosmic creation event.

If the constant(s) governing dark energy is much larger than what we observe, then galaxies and stars will never form. If the constant(s) governing dark energy is much smaller than what we observe, then too much of the matter of the universe collapses into black holes and neutron stars.

Galaxies and stars of any kind will not form in the universe if the value of the dark energy constant, Λ, is greater than a hundred times more than what astronomers observe. However, a team of nine astrophysicists led by Luke Barnes used detailed computer simulations to demonstrate that increases in the value of Λ, even by a factor of 10–20 times, has only a small effect on star formation history and efficiency.3 The reason for such a small effect is that the rate of star formation in our universe peaks when the universe is about 3.5 billion years old, which is well before Λ would begin to accelerate the expansion rate of the universe. In fact, Barnes et al. showed that galaxies and stars will form in the universe even for values of Λ as high as 50 times greater than the observed value. This factor of 50 caused some astronomers to question the anthropic nature of Λ, the implication that Λ was personally fine-tuned (designed) to an extreme degree to make possible the existence of human beings in the universe.

Now, two papers have been published that establish that Λ must be fine-tuned to a very extreme degree after all. In the most recent issue of the journal Astrobiology, a team of six Japanese astrophysicists led by Tomonori Totani provides calculations that show that Λ must be as small as what we observe to prevent advanced life from being wiped out by lethal radiation from nearby supernovae (see figure 2).4 Totani’s team demonstrated that as the value of Λ increases from the observed value to 50 times the observed value, the density of stars in the universe proportionately increases. With an increase in the density of stars comes an increase in the number of nearby supernova eruptions in the vicinity of a planet that could potentially support advanced life.


Figure 2: Supernova 1994D in the Galaxy NGC 4536. At the height of its supernova eruption, Supernova 1994D (lower left) was as bright as all the rest of the more than 100 billion stars in the NGC 4536 galaxy.

A number of research studies establish that high-energy gamma and cosmic rays from a core-collapse supernova within 10 parsecs (32.6 light-years) of Earth would prove lethal for all terrestrial animals and especially for human beings.5 For the solar neighborhood the expected number of such nearby supernova events is 1 per 500,000,000 years.6 For global human civilization to be possible terrestrial animals must be abundant throughout the past 400,000,000 years. Therefore, Totani’s group concludes that for global human civilization to be possible the value of Λ cannot be significantly larger than the observed value.

As it is, humans must live in a large spiral galaxy and in a fine-tuned location in a large spiral galaxy for the frequency of lethal supernova events to be less than 1 per 500,000,000 years. If we were located in one of the much more common spheroidal or elliptical galaxies, or if we were closer to our galaxy’s bulge or one of our galaxy’s globular clusters or spiral arms, we would be exposed to a much higher frequency of lethal supernova events. That higher frequency would rule out our possible existence. This limitation on our location within the universe yields another reason why the value of Λ cannot be any greater than what astronomers observe.

A separate research study establishes that the value of Λ cannot be any smaller than what we observe. A paper published in Physical Review Letters by five theoretical astrophysicists led by Tsvi Piran showed that in a universe where Λ does not presently dominate the control of the cosmic expansion rate (true if Λ is just the tiniest smaller in value than what we observe) the density of dwarf galaxies skyrockets.7 In such a universe, a planet like Earth would be exposed to a lethal-to-animals gamma-ray burst event at a rate much higher than 1 per 400,000,000 years. Consequently, for our existence to be possible the value of Λ cannot be any smaller than what astronomers observe.

The bottom line is that dark energy really does present scientists with the most extreme fine-tuning problem known in physics. If the value of Λ were the slightest bit greater, nearby supernovae would have ruled out our existence. If the value of Λ were the slightest bit lesser, nearby gamma-ray burst events would have ruled out our existence. Thus, the value of Λ ranks as the most spectacular measurable scientific evidence for the supernatural, super-intelligent design of the universe to make possible the existence of human beings.

Original article: More Anthropic Reasons for the Extreme Fine-Tuning of Dark Energy

Scientific Discovery and God: Planet Earth, Part 3

In the first two parts of this series (see here and here) I discussed how secular scientists, given their naturalistic worldview, expected to discover that we live in an eternal—and therefore uncaused—universe, as well as in an ordinary solar system. Yet on both scores scientists were surprised by what scientific advances revealed. In both cases, the great contrast for scientists who hold a purely secular worldview is that the universe’s and solar system’s features seem to best comport with the expectations of theism over atheistic naturalism.

In this article I will briefly discuss how the specific expectations of secular scientists concerning Earth’s characteristics were also very different from what science has shown. Again, the results follow a similar pattern of favoring the expectations of one worldview over another.

The Rare Earth Hypothesis

The consensus of secular scientists a half-century ago was that the earth is not a special planet, but rather a mediocre one, with no rare or unique significance. Many scientists thought that since Earth is not at the center of the universe, then it is merely ordinary. For example, in the 1970s and 1980s scientists like Carl Sagan and Frank Drake described the Earth as a typical rocky planet in a nonexceptional place in an ordinary galaxy.

However, this initial expectation has been challenged. The rare Earth hypothesis holds that the earth is distinct as a planet and may even be special. University of Washington scientists Peter D. Ward and Donald Brownlee have led the way in representing this perspective in their book Rare Earth: Why Complex Life Is Uncommon in the Universe.

They argue that the universe is fundamentally hostile to complex life and that microbial life may be common. However, the evolution of biological complexity from simple life on Earth requires an exceptionally unlikely set of circumstances; therefore, complex life is probably extremely rare.

“[A]mong the essential criteria for life are a terrestrial planet with plate tectonics and oxygen, a large moon, magnetic field, a gas giant like Jupiter for protection and an orbit in the habitable zone of the right kind of star.”1

Not all scientists accept this rare Earth view, and some have criticized the hypothesis (see here). Yet scientists who embrace a purely naturalistic worldview expected Earth to prove to be commonplace, but instead they discovered viable reasons to think otherwise.

The rare Earth hypothesis seems to comport well with a theistic, even biblical, worldview, but appears unexpected and out of place from an atheistic, naturalistic perspective. So what would Earth look like if biblical theism were true? Evidently much like it appears right now.

In part four I’ll discuss the topic of human exceptionalism and what scientists anticipated and have discovered about it.

Original article: Scientific Discovery and God: Planet Earth, Part 3

Electron Transport Chain Protein Complexes Rev Up the Case for a Creator

As a little kid, I spent many a Saturday afternoon “helping” my dad work on our family car. What a clunker.

We didn’t have a garage, so we parked our car on the street in front of the house. Our home was built into a hillside and the only way to get to our house was to climb a long flight of stairs from the street.

I wasn’t very old at the time—maybe 6 or 7—so my job was to serve as my dad’s gofer. Instead of asking me to carry his toolbox up and down the flight of stairs, he would send me back and forth when he needed a particular tool. It usually went like this: “Fuz, go get me a screwdriver.” Up and down the stairs I would go. And, when I returned: “That’s the wrong screwdriver. Get me the one with the flat head.” Again, after I returned from another roundtrip on the stairs: “No, the one with the flat head and the blue handle.” Up and down the stairs I went, but again: “Why did you bring all of the screwdrivers? Take the rest of them back up the stairs and put them in the toolbox.” By the time he finished working on our car I was frustrated and exhausted.

Even though I didn’t have a lot of fun helping my dad, I did enjoy peering under the hood of our car. I was fascinated by the engine. From my vantage point as a little kid, the car’s engine seemed to be bewilderingly complex. And somehow my dad knew what to do to make the car run. Clearly, he understood how it was designed and assembled.

As a graduate student, when I began studying biochemistry in earnest, I was taken aback by the bewildering complexity of the cell’s chemical systems. Like an automobile engine, the cell’s complexity isn’t haphazard, but instead displays a remarkable degree of order and organization. There is an underlying ingenuity to the way biochemical systems are put together and the way they operate. And, for the most part, biochemists have acquired a good understanding of how these systems are designed.

Along these lines, one of the most remarkable and provocative insights into biochemical systems has been the discovery of protein complexes that serve the cell as molecular-scale machines and motors—many of which bear an eerie similarity to man-made machines. Two recent studies illustrate this stunning similarity by revealing new information about the structure and function of two protein complexes that are part of the electron transport chain: the F1-FATPase and respiratory complex I. These ubiquitous protein complexes are two of the most important enzymes in biology because of the central role they play in energy-harvesting reactions.


This well-studied protein complex plays a key role in harvesting energy for the cell to use. F1-FATPase is a molecular-scale rotary motor (see figure 1). The F1 portion of the complex is mushroom-shaped and extends above the membrane’s surface. The “button of the mushroom” literally corresponds to an engine turbine. The F1-FATPase turbine interacts with the part of the complex that looks like a “mushroom stalk.” This stalk-like component functions as a rotor.



Figure 1: A cartoon of the F1-FATPase rotary motor.

Located in the inner membrane of mitochondria, F1-FATPase makes use of a proton gradient across the inner membrane to drive the production of ATP (adenosine triphosphate), a high-energy compound used by the cell to power many of its operations. Because protons are positively charged, the exterior region outside the inner membrane is positively charged and the interior region is negatively charged. The charge differential created by the proton gradient is analogous to a battery and the inner membrane is like a capacitor.

The flow of positively charged hydrogen ions through the F0 component, embedded in the cell membrane, drives the rotation of the rotor. A rod-shaped protein structure that also extends above the membrane surface serves as a stator. This protein rod interacts with the turbine, holding it stationary as the rotor rotates.

The electrical current that flows through the channels of the F0 complex is transformed into mechanical energy, which then drives the rotor’s movement. A cam that extends at a right angle from the rotor’s surface causes displacements of the turbine. These back-and-forth motions are used to produce ATP.

Even though biochemists have learned a lot about this protein complex, they still don’t understand some things. Recently, a team of collaborators from the US determined the path that protons take as they move through the F0 component embedded in the inner membrane.1

To accomplish this feat, the research team trapped the enzyme complex into a single conformation by fusing the stator to the rotor. This procedure exposed the channels in the F0complex and revealed the precise path taken by the protons as they move across the inner membrane. As protons shuttle through these channels, they trigger conformational changes that drive the rotation of the rotor by one full turn for each proton as it moves through the channel.

Respiratory Complex I

Respiratory complex I serves as the first enzyme complex of the electron transport chain. This complex transfers high-energy electrons from a compound called nicotinamide adenine dinucleotide (NADH) to a small molecule associated with the inner membrane of mitochondria called coenzyme Q. The high-energy electrons of NADH are captured during glycolysis and the Kreb’s cycle, two metabolic pathways involved in the breakdown of the sugar, glucose.

During the electron-transfer process, respiratory complex I also transports four protons from the mitochondria’s interior across the inner membrane to the exterior space (figure 2). In other words, respiratory complex I helps to generate the proton gradient F1-FATPase uses to generate ATP. By some estimates, respiratory complex I is responsible for establishing about 40 percent of the proton gradient across the inner membrane.


Figure 2: A cartoon of the electron transport chain. 

Massive in size, 45 individual protein subunits comprise respiratory complex I. The subunits interact to form two arms, one embedded in the inner membrane and one extending into the mitochondrial matrix. The two arms are arranged to form an L-shaped geometry.


Figure 3: A cartoon of respiratory complex I.

The electron transfer process occurs in the peripheral arm that extends into the mitochondrial matrix (upward in figure 3). Conversely, the proton transport mechanism takes place in the membrane-embedded arm (to the right).

The mechanism of proton translocation across the inner membrane served as the focus of a study conducted by a research team from Oxford University in the UK.2 These researchers discovered that proton transport across the inner membrane is driven by the machine-like behavior of respiratory complex I. The process of transferring electrons through the peripheral arm results in conformational changes (changes in shape) in this part of the complex. This conformational change drives the motion of an alpha-helix cylinder like a piston in the membrane arm of the complex. The pumping motion of the alpha-helix causes three other cylinders to tilt and, in doing so, opens up channels for protons to move through the membrane arm of the complex.

Revitalized Watchmaker Argument

Biochemists’ discovery of enzymes with machine-like domains, as exemplified by F1-FATPase and respiratory complex I, revitalize the Watchmaker argument. Popularized by William Paley in the eighteenth century, this argument states that as a watch requires a watchmaker, so, too, does life require a Creator.

This simple yet powerful analogy has been challenged by skeptics like David Hume, who assert that the necessary conclusion of a Creator, based on analogical reasoning, is only compelling if there is a high degree of similarity between the objects that form the analogy. Skeptics have long argued that nature and a watch are sufficiently dissimilar so that the conclusion drawn from the Watchmaker argument is unsound.

But due to the striking similarity between the machine parts of these enzymes and man-made devices, the discovery of enzymes with domains that are direct analogs to man-made devices addresses this concern. Toward this end, it is provocative that the more we learn about enzyme complexes such as F1-FATPase, the more its machine-like character becomes apparent. It is also thought-provoking that as biochemists study the structure and function of protein complexes, new examples of analogs to man-made machines emerge. In both cases, the Watchmaker argument receives new vitality.

As a little kid, peering under the hood of our family car and watching my father work on the engine convinced me that some really smart people who knew what they were doing designed and built that machine. In like manner, the remarkable machine-like properties displayed by many protein complexes in the cell make it rational to conclude that life comes from the work of a Mind.

Original article: Electron Transport Chain Protein Complexes Rev Up the Case for a Creator

We Are Living at the Optimal Terrestrial Mammal Moment

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.

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.

Original article: We Are Living at the Optimal Terrestrial Mammal Moment

Life’s Layers of Complexity: When All Isn’t All

Looking back on 2018, I give thanks for the blessings God has rained upon me. I can’t help but think how my vision of God’s goodness and glory have grown as I contemplate almost every aspect of creation in each new scientific study.

One thing that continues to amaze me is the staggering complexity of all things biological. Whether we’re looking at things as “simple” as genes and their regulatory elements, or basic life-supporting components such as photosynthesis, nitrogen fixation, or DNA replication, life is not simple by any measure.

It’s easy to miss life’s complexity. Daily routines don’t allow for much reflection, and biological complexities don’t fit into five-second soundbites. Admittedly, many of us are tempted to check out when topics become too detail-oriented. Additionally, scientific experimentation necessitates that we simplify complex systems and isolate various mechanisms in order to study individual components in cause-and-effect relationships. The detailed findings that reach peer-review publication are often reductionistic and further simplified by science writers and then given a provocative (and sometimes inaccurate) “hook” for the general public. We often have to look past the headlines—and sometimes beyond the detailed but limited findings—to appreciate the underlying complexities.

Complexity upon Complexity Everywhere We Look

I was impressed by three articles in Nature‘s December 6, 2018 issue, which reminded me of the near fathomless depths of complexity contributing to life’s staggering complexity.1 In the first article, researchers identify a mechanism involved in regulating repair of damaged DNA that depends on a specific protein called cyclin-dependent kinase 12 (CDK12). This article drew my attention to the extreme complexities of transcription and DNA damage responses employed in all cells to maintain genome integrity.

Mission Critical: DNA Repair

Our DNA is in constant need of repair. Cells are continually bombarded by various forms of ionizing radiation and they encounter other kinds of environmental stress (smoke, chemicals, UV light, etc.). Even normal cellular metabolism produces potentially damaging byproducts such as reactive oxygen species. Replication of DNA for cell proliferation results in DNA damage as well. Estimates suggest that every cell may experience 100,000 DNA damage events per day!2

Some of these events result in base modifications and damage to only one strand of the DNA double helix. Some damage leads to double-stranded breaks (DSB) in cellular DNA. Thankfully, cells contain complex systems for repairing DNA damage. Two main mechanisms of DNA repair allow for homologous recombination (HR) and non-homologous end-joining (NHEJ) at the sites of DSBs. HR maintains genomic integrity by utilizing sister chromatids to provide an unbroken and undamaged template for DNA repair. HR is a primary mechanism for repair when these sequences are most accessible (in S and G2 of the cell cycle).3 NHEJ, which is less rigorous in maintaining DNA sequence integrity, joins damaged ends together and sometimes introduces deletions (or insertions) at the site of repair. NHEJ functions through all stages of the cell cycle and is a major mechanism for post-mitotic repairs and for generating critical diversity in immune system proteins.4

Because DNA is the substance of heredity and the template for cellular processes, maintaining genomic sequence integrity is critical and requires myriad supporting players. More than 50 proteins are involved in DNA damage response (DDR), with some estimates of tens of thousands of copies of each.5 More recent omics studies estimate that thousands of gene products participate in DDR.6 The proteins serve a variety of functions that are highly spatially and temporally orchestrated. DDR takes place in intracellular foci described as highly dynamic giga-dalton (a billion atomic mass units) structures that can assemble and disassemble within minutes and are capable of simultaneously repairing multiple DNA lesions.7

“DNA repair is carried out by a plethora of enzymatic activities that chemically modify DNA to repair DNA damage including nucleases, helicases, polymerases, topoisomerases, recombinases, ligases, glycosylases, demethylases, kinases and phosphatases. These repair tools must be precisely regulated because each in its own right can wreck havoc on the integrity of DNA if misused or allowed to access DNA at the inappropriate time or place.”

—Alberto Ciccia and Stephen Elledge

HR and NHEJ are not simple processes. The choice of which one is utilized depends on multiple factors, of which many, if not most, remain unidentified. As it turns out CDK12 may be one contributing regulator favoring implementation of HR repair. But in order to understand how CDK12 may be contributing to HR, we need to understand another layer of complexity, that of cellular transcription.

Transcribing DNA to RNA

Transcription is the rewriting of DNA into RNAs which serve as regulators of cellular processes and templates for protein production. Transcription involves another myriad of players, highly orchestrated, within a process that takes place remarkably fast and continually within every cell.8 In eukaryotic cells, RNA polymerase II (Pol II) transcribes DNA into pre-mRNAs. The 12-component Pol II complex in mammals does not act alone in initiating, elongating, or terminating transcription. Pol II requires several general transcription factors for binding the DNA promoter and recruiting the Pol II complex to the DNA promoter. Many additional proteins and protein complexes are needed for Pol II elongation and termination.9Furthermore, many more proteins are involved in co-transcriptionally and post-transcriptionally modifying pre-mRNA transcripts into mRNAs.

CDK12 and HR Repair

One of the 12 subunits of Pol II, RPB1, serves many critical functions in transcription and processing of mRNAs. CDK12, the star of the first article, functions to phosphorylate (post-translationally modify) RPB1 at a specific site (Ser-2 residue in the C-terminal heptad repeat).10

In the Nature report, the researchers present data that demonstrates that CDK12-dependent phosphorylation of Pol II contributes to Pol II’s transcription elongation and results in an increase in full-length mRNAs that encode many of the HR repair proteins. Without this phosphorylation event, transcription in many HR repair genes (and others) is prematurely terminated at internal poly-adenylation (IPA) sites located in introns upstream of the 3′-most exon. If transcription terminates at IPAs, full-length pre-mRNAs are not transcribed, and full-length HR proteins are not produced.

The researchers “conclude that the primary role of CDK12 is to suppress IPAs genome-wide and to promote expression of distal (full-length) isoforms.”11 This effect impacts multiple genes, but it seems CDK12 has a more profound effect on HR repair genes. “Our data suggest that the cumulative effect of multiple, high-sensitivity IPAs in HR genes accounts for the downregulation of their full-length isoforms. . . We propose that the combined effect of strong downregulation of multiple gene products within the same functional pathway causes the HR-deficient phenotypes observed upon CDK12 loss.”12

That means when CDK12 is present, Pol II elongation continues to the distal polyadenylation site in many genes, and specifically results in a functional HR repair pathway. These findings demonstrate a role for CDK12 in the phosphorylation of Pol II that regulates the production of essential HR repair proteins and suggests that regulation of CDK12 may be one factor affecting the selection of HR (over NHEJ) in a system of staggering complexity.

Complexity’s “Wow” Factor

In the second and third Nature articles (which I won’t unpack here), additional layers of complexity for sustaining and propagating life are brought to the fore. Just briefly, the second article highlights complex spatial and mechanotransductive signals that affect cell fate during development and differentiation. Mechanical signals like stretching and confinement affect cellular processes and cellular development and ultimately cell fates (in this case, pancreatic cell type) of pluripotent and multipotent stem cells.13 In the third article, researchers examine the maintenance and protection of the methylation status of oocyte genomes necessary for proper progression of embryogenesis. That is, they look at the effect of DNA modifications (not affecting the DNA sequence) and the regulation of those modifications by at least three critical proteins: Stella, UHRF1, and DNMT1.14 Each of those proteins, in turn, serves various critical roles at different stages and in different cell types. The signals, molecules, and mechanisms regulating these functions are astoundingly complex and only partially understood but are critical for proper development and life.

These three very different studies all contribute to the fundamental complexities required for sustaining and propagating all animal life. I look at these biological processes in sheer wonder and awe at the complexities involved in fundamental processes for sustaining and propagating life. It comes as no surprise that many of the mechanisms and molecular players are highly conserved within various organisms—from yeast to human beings. These functions are critical for sustaining and propagating life—so, of course, living organisms share these critical functions.

Our ability to apply basic research findings from yeast, flies, and mice for human care and creation care is a magnificent byproduct of God’s providence in creating life according to shared molecular archetypes and fundamental processes. These and other fundamental, common features (such as the DNA code) point to God’s goodness and his providence in caring for creation and human well-being. These shared features do not (or need not) point to shared ancestral origins. Their discovery requires no broad evolutionary narrative. And to imagine that they come from unaided naturalistic processes requires broad speculations as to how these staggering complexities may have originated—speculations that never include specifics on how complex, interdependent networks of systems are established or how novel genes are produced. Reductionistic views and oversimplification (even in complex, peer-reviewed research reports) neglect underlying complexities.

When “All” Isn’t All

While reading a recent Science News article, I was struck by this tendency to over-simplify yet again. The article addresses unexpected findings of paternal mitochondrial DNA inheritance. In it, the author states, “DNA in a cell’s nucleus is inherited equally from both parents and contains all the genetic instructions for building a body.” Reading this, one probably thinks, “Well, of course it does. DNA contains all the genetic instructions for building a body.” But is it true? Is parental DNA all the instructions needed for life? Well, technically speaking, no.

As the three Nature articles above point out, the system comes preloaded with (1) not only genomes regulated by epigenetic modifications but also with regulatory RNAs often post-transcriptionally and differentially modified and expressed to varying degrees, (2) proteins with relevant and variable cellular localizations, expression levels, glycosylation statuses and post-translational modifications, and (3) cells elegantly set with various capacities for mechanical transduction signaling (including force responses to gravity and proximity-type detection that can sense, not just variable force, but directional differences). All of these molecular components bear additional information for cell development and replication and are necessary for the growth, development, and reproduction of living cells and creatures. These all (not to mention the critical role for mitochondria, which have their own DNA) carry information necessary for building a body. These components also accompany and are all necessary for accessing the genetic instructions in nuclear DNA. In scientific terms, the information in DNA is necessary but not sufficient for building a body. So “all” isn’t all.

God’s Fingerprints

I often say that the data can fit almost any scenario for life’s origins with varying degrees of plausibility. Data can fit an evolutionary narrative or a progressive creation narrative. My evolution-advocating colleagues argue that evolution explains all these features, but I really don’t see it the same as they do. I actually find the scope of evolution fairly limited and, the more I study, I see appeals to evolutionary just-so stories growing more incredulous.

These studies convince me even more that life requires life of similar levels of complexity to propagate and sustain itself. Life, it seems, only ever comes from life, and science has produced no data that supports a contradictory claim. Life comes from life always and everywhere we look.

These reports point ever more clearly to common features of mind-boggling complexity necessary for fundamental life-sustaining and propagating cellular processes. But what a remarkable testament to the glory of God. God’s providence seems clear. As scientists make these discoveries and test their viability in animals and yeast, they unlock applications for human biology and other areas of creation stewardship. As I consider these things, I am led to worship God for his glory demonstrated throughout the complex array of life’s interdependent systems and for his magnificent foresight and infinite, clever brilliance. We, and all life, are walking miracles of absurd complexities that shout often without words, “Glory to God!”

Original article: Life’s Layers of Complexity: When All Isn’t All

Michael Heiser — Supernatural Intelligence and the World’s Governing Authorities (Excerpt)

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It really is shocking how illiterate the modern Church is about its own manual.

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