Guest Post – Latest Discoveries in the Field of Structural Biology Point to Intelligent Design

The August 9, 2021 edition of Chemical and Engineering News (C&EN) featured a story in the field of structural biology entitled “How Transcription Gets Its Start.” Transcription is the biochemical process that occurs in every cell in the human body when protein synthesis is initiated. It is a complex series of steps that begin in the nucleus when a gene—a section on a strand of DNA—expresses instructions for a specific protein to be produced.  

In simple terms, the portion of the DNA molecule where the gene is located is unzipped resulting in a strand of mRNA (messenger RNA). mRNA can be thought of as a digital tape that contains a sequence of 3-letter codes called codons that dictate the precise sequence of amino acids for the protein it is about to produce.  

The mRNA leaves the nucleus and enters the site of protein synthesis called a ribosome. It is here that the codons are read and the specific amino acids are delivered by a second RNA molecule, tRNA (transfer RNA) which has its own 3-letter sequences called anti-codons that match the codons on the mRNA. The process continues; the ribosome continues assembling the amino acids one-by-one until the protein has been assembled according to the instructions originally encoded on the gene. 

To say that this process is stunning in its complexity is an understatement. It is nothing short of miraculous.

The C&EN article details the 20-plus years of efforts by several research groups from around the world to understand the initiation of transcription. They discovered it involves something called a preinitiation complex (PIC); an ensemble of transcription factors, an enzyme called RNA polymerase II (Pol II), more transcription factors, and a mediator complex that stabilizes the structure. In all there are about 75 different proteins.

In order to image the PIC, it first had to be produced. This entailed building “on years of painstaking work by research teams that not only established methods for isolating all of the PIC’s protein components in the lab but coaxed those pieces into assembling in just the right way, without the whole complex falling apart.”¹

There is a deeper, philosophical question here: How can such a complex molecular machine, crucial for the synthesis of proteins and hence life, be itself dependent on 75 different proteins for its function? Where did those proteins come from in the first place if there was no PIC to initiate protein synthesis?   

Or what came first—the chicken or the egg?

Douglas Axe, the author of Undeniable, How Biology Confirms Our Intuition That Life Is Designed, believes that it is examples such as this that make it obvious life was designed and not the result of blind, unguided chance.

“To explain how natural proteins, with their exquisite functions, could have appeared by accident is a monumental challenge,”² he writes. “When we see things working together that came about by bringing many parts together in the right way, we find it impossible not to ascribe these inventions to purposeful action, and this pits our intuition against the evolutionary account.”³

He gives an example dubbed “oracle soup” —a poke at the primordial soup—the “warm little pond” believed to be the birthplace of life on planet Earth that Darwin described in a letter to his friend, Joseph Hooker in 1871.⁴  Axe’s recipe calls for a large pot of broth and pasta letters, brought to a boil and then removed from the heat and allowed to cool. When the soup has cooled, “…Lift the lid to reveal a complete set of instructions for building something new and useful—worthy of a patent—all spelled out in pasta letters.”⁵

“How would we make sense of oracle soup if it were real? If we reflect on that for a moment, I think we would agree that no ordinary explanation would seem adequate for something so extraordinary. But if this is true, how can the evolutionary explanation of life not provoke that same skepticism?”⁶

I recently attended the inauguration ceremony of our university’s new president, delayed a year and a half by social distancing restrictions due to Covid19. One of the speakers, Dr. John Patrick, served as a medical missionary in Jamaica and Sub-Saharan Africa, where he studied malnutrition in children. He shared a story from when he had been invited as a guest lecturer of ethics at one of Cuba’s medical universities. The school’s director noticed how alert the students were during Dr. Patrick’s lectures and in order to better understand why this was, he challenged Dr. Patrick to a debate on the origins of life.

Dr. Patrick, always up for a good challenge, wrote on the board (in Spanish) “This sentence wrote itself.” The group of doctors and medical students debated the nonsense of such a statement for several minutes until finally Dr. Patrick erased the phrase This sentence and replaced it with DNA, adding “But you all believe this statement, don’t you?”

There was complete silence in the room, the point having been elegantly made.      

I have a similar thought-game that I play with students in an introductory chemistry class I teach. When we begin the study of protein synthesis, I show them a photograph of my necktie drawer before my wife spent an hour organizing it by folding all of the ties and neatly arranging them in three rows according to color. No student has ever thought that this happened by blind, unguided chance nor could it ever happen this way given any amount of time.

The lesson is clear: someone intelligent, with an eye for color and a skill for artfully folding fabric, was behind the organized arrangement. One could say that my wife was acting as an intelligent designer.  

Belief in God as The Intelligent Designer was the starting point for much of scientific enquiry through the sixteenth  and seventeenth  centuries. 

“The great pioneers in physics—Newton, Galileo, Kepler, Copernicus—devoutly believed themselves called to find evidences of God in the physical world,” writes Stephen C. Meyer in The Return of the God Hypothesis, his latest book in which he makes a convincing case for the Judeo-Christin origins of modern science. “The founders…assumed that if they studied nature carefully, it would reveal its secrets. Their confidence in this assumption was grounded in both the Greek and the Judeo-Christian idea that the universe is an orderly system—a cosmos not a chaos.”⁷

This cosmos described as a “world with a blueprint” was open to the great, searching minds of science. Take for example the astronomer Johannes Kepler (1571-1630) who wrote:

“God wanted us to recognize” natural laws and God made this possible “by creating us after his own image so that we could share in his own thoughts.” Thus, the assumption that a rational mind with a will had created the universe gave rise to two ideas—contingency and intelligibility—which in turn, provided a powerful impetus to study nature with confidence that such study would yield understanding.⁸

This powerful impetus to study nature goes hand in hand with curiosity and critical thinking, often leading to the deeper, philosophical questions about life’s origin and meaning.

Tragically, Faith-Science became passe during the mid-nineteenth century with the writings of Darwin, Marx, Nietzsche and Freud—sometimes dubbed, “the four bearded god-killers.”⁹

Venki Ramakrishnan was one of three collaborators awarded the Nobel Prize in chemistry in 2009 for studies in the function and structure of the ribosome. Writing in Gene Machine, The Race To Decipher The Secrets Of The Ribosome, his own research led him to ponder the deeper question of life’s origins.

How life began is one of the great remaining mysteries of biology… the problem [is] that in nearly all forms of life, DNA [carries] genetic information but DNA itself [is] inert and made by a large number of protein enzymes, which [require] not only RNA but also the ribosome to make these enzymes. Moreover, the sugar in DNA, deoxyribose, [is] made from ribose by a large, complicated protein. Nobody [can] understand how the whole system could have started.¹⁰

Well, almost nobody.

Consider the irony in the C&EN article: For 20 years, research groups in the US, Germany and China, comprised of some of the most brilliant biochemists in the world have been working in modern laboratories with advanced biological reagents, utilizing instrumentation to synthesize even larger and more complicated biomechanical machines in order to image and elucidate the structure of the PIC.

Or to put it another way: Groups of intelligent designers have been working in intelligently designed laboratories, using intelligently designed starting materials and intelligently designed instrumentation to elucidate the structure of one of the biomechanical machines involved in the early stages of protein synthesis.    

Clearly it is worth pondering the question asked by God himself to Job in the Old Testament book that bears his name: “Where were you when I laid the earth’s foundation? Tell me, if you understand,” (Job 38:4 NIV). 

1. Howes, Laura, “How transcription gets it start,” Chemical & Engineering News, Aug. 9, 2021, CEN.ACS.ORG
2. Axe, Douglas, Undeniable How Biology Confirms Our Intuition That Life Is Designed, (Harper Collins Publishers, New York, NY, 2016), 81
3. Douglas, Undeniable How Biology Confirms Our Intuition That Life Is Designed, 87
4. Darwin to Joseph Hooker, 1871 as recorded in a footnote in The Life and Letters of Charles Darwin, Including an Autobiographical Chapter, ed. Francis Darwin, vol. 3 (London: John Murray, 1887), 18 (footnote from “Undeniable” p. 277)
5. Douglas, Undeniable How Biology Confirms Our Intuition That Life Is Designed 16
6. Douglas, Undeniable How Biology Confirms Our Intuition That Life Is Designed,16
7. Stephen C. Meyer,The Return of the God Hypothesis, (New York: Harper Collins,  2021).
8. Hodgson, The Christian Origin of Science,” Logos, 145 (quotation from The Return of the God Hypothesis, Stephen C. Meyer, p. 25) 
9. Martin E. Marty,. “Freud and Other ‘God-Killers’ Are Here to Stay” Oct. 2, 2017, Chicago Divinity School, https://divinity.uchicago.edu/sightings/articles/freud-and-other-god-killers-are-here-stay
10. Venki Ramakrishnan, , Gene Machine, (NY: Basic Books, 2018).