Posted on 03/19/2025 6:50:16 AM PDT by Heartlander
A few years ago, Chemical and Engineering News (C&EN) featured a story in the field of structural biology entitled “How Transcription Gets Its Start, in Pictures.” 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 begins 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.”
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?
To put it differently, 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,” 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.”
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. 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.” He asks:
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?
Dr. John Patrick served as a medical missionary in Jamaica and sub-Saharan Africa, where he studied malnutrition in children. At an event at my university, he shared a story from when he had been invited as a guest lecturer of ethics at one of Cuba’s medical schools. 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 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 inquiry through the 16th and 17th 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, which makes a convincing case for the Judeo-Christian 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.”
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, writes Meyer,
exclaimed that “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.
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, this way of thinking about faith and science became passé during the mid 19th century with the writings of Darwin, Marx, Nietzsche, and Freud — sometimes dubbed, “the four bearded god-killers.”
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, he explains how 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.
Consider the irony in the C&EN article: For 20 years, research groups in the U.S., Germany, and China, some of the most brilliant biochemists in the world, have been working in modern laboratories with advanced biological reagents, utilizing instrumentation to synthesize ever 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).
Editor’s note: We are delighted to welcome Gregory J. Rummo as a new contributor. He is a Lecturer in Chemistry at Palm Beach Atlantic University and an adjunct scholar at the Cornwall Alliance. Professor Rummo is author of the new book, Reaching Gen Z with the Gospel in the College Classroom: Awakening the Imago Dei in Gen Z (Wipf and Stock, 2025).
The 12 discoveries that have changed the debate about design:
List of Peer-Reviewed and Mainstream Scientific Publications Supporting Intelligent Design
Why Intelligent Design Is Not a “God of the Gaps’ Argument
A Positive, Testable Case for Intelligent Design
Comprehensive List of Factors of Fine-Tuning for Intelligent Life in the Universe
“some top scientists have claimed that the study of biology is based on Darwin’s unproved theory of evolution by natural selection, therefore biology is not a science, it is more of a faith & a pseudo science. It’s why nobody can challenge it because zealots control the debate & punish heretics.
Ironically, communists refused to teach Darwin because he was an aristocrat who got his idea of survival of the fittest from reading Malthus......thus our science textbooks from government schools we attended lied to us when they differentiated “social Darwinism” from Darwinism to claim the former was an illegitmate offspring of the later, when it fact Darwinism came from social Darwinism & they both are, in fact, the same thing.....which is why science today finds no room for religion.....because a lot of it is competing religion.
Galileo was not persecuted over religion, he was persecuted over science, because he challenged pagan philosopher Aristotle’s claim that the moon was a perfect sphere because telescopes showed its craters. The church had accepted Aristotle’s theory of celestial motion of perfect spheres, thus Galileo was a heretic because he challeged the authority of the Church over scientific theory accepted on faith.
It is a mystery why progressives who believe in love and unity which require metaphysics want our children to believe in survival of the fittest, which depends on circular logic and undermines their social and political aims. Does China teach Darwinism as fact in their schools, and can we claim that Chinese communists do not believe in science? Russians scientists actually refuted Darwin on scientistic grounds, as they observed cooperation among animals.....eg the bee hive. Communists often have claimed that communism itself is a science, it’s evolution......which probably is the real aim of those on the Left who insist on teaching Darwin’s theory of evolution by Natural Selection as fact, ie because they want science to refute the idea of the Fall in religion.....to eliminate belief in God through teaching of scientistic materialism. Progressives want to teach perpetual progress.....even though every species that ever went extinct once was the fittest, by definition.
Einstein made fun of Newton, by the way. Newton did not discover what he called gravity, he explained it in scientific terms. And Ann Coulter’s book “Godless” has an essential chapter about the Scopes Monkey trial about which most people only know about because of a Spencer Tracy movie that is a complete lie from beginning to end. Scopes was a substitute teacher who agreed to be prosecuted as a publicity stunt by the New York ACLU under a law that was not even criminal, but was merely prescriptive. It was a set up that allowed Clarence Darrow and William Jennings Bryan to get publicity over a subject the press wanted to come down a certain way——which is why the press narrative that came out of the trial had nothing to do with the trial or what it proved about faith, science and Reason.”-—unnamed source
This did not happen by chance.Even billions of years of happenstance could not create this.
And it is not only the exquisite orderliness and complication of protein synthesis that is miraculous. Countless systems within the human body--and everywhere else--are every bit as miraculous.
Minds capable of unravelling and comprehending these miracles also did not come about by happenstance.
i wrote the below commentary a few years ago, as well as gening up my own “pasta soup” example [further down in the text] several years ago as follows:
my commentary on an article about a book:
from the article:
“Though they used design analysis to discover functions, the study authors apparently eliminated the possibility of a Designer as the cause of these similar, energy-efficient structures in diverse organisms”
my commentary:
Nothing unusual there. All biological machinery, programming and processes at every level have to be described in mechanical terms because they are in fact machines.
Furthermore, practically every machine mankind “invents” is already present in some biological form in some biological creature. And not only that, it’s only until AFTER man has “invented” a particular kind of machine is man then able to recognize that which was previously a mystery in biology as being an example of the machine man just “invented”.
And while anyone would be considered insane if they proclaimed that all of man’s machines built in all of man’s existence were merely an accidental product of “nature” with no possibility of an intelligent designer or builder, the official, central dogma of “science” is a similarly insane proclamation that all of life in Earth’s biosphere (a situation a trillion times a trillion more complex than man’s puny accomplishments) is merely the mindless, capricious product of a grotesquely improbable and accidental “nature”.
again from the article about the book:
“So, after reading the book my current position of how life “evolved” is that we really don’t know. “
and my commentary:
But we can make an intelligent guess. All we have to do is analyze the one example we do have available to us of evolutionary intelligent design, namely the evolution of all that which has been created by mankind and how that has occurred, and then comparing that to the structures and processes we ourselves have “invented”.
In fact, we see the same design principles, structures and processes embodied in biologic life that we ourselves have used to create our own manosphere, which includes the totality of all man-made machines, systems, infrastructure and processes on earth.
We see the principle of modular construction in life, as embodied by the endosymbiotic origin of mitochondria. We see the reuse of common structures and processes throughout large numbers of highly varying life forms and at multiple levels. We see that chromosomes are a form of computer programming using chemical codons for coded data bytes and ribosomes as the computer.
We see on Earth that simpler life forms existed before more complex lifeforms, and that there has in fact been an evolutionary progression from simpler to more complex life forms over time, just as we’ve seen the evolution of discrete component digital computing evolve in the late 1940’s to the current massively integrated forms we have only 70 years later. Of course, when I use the word “evolution”, I mean “intelligently directed evolution”, not accidental evolution, with the latter of course actually being an oxymoron.
I’ve intensely studied computer programming, biologic processes and mechanisms and many other sciences for that matter, and to me, there is no doubt whatsoever that we and all other living parts of the earth’s biosphere were deliberately made by a higher intelligence than our own, and made in the same fashion as what we ourselves have made and how we made it, that is, as a collective consciousness, building on and improving work from previous generations. When the first stone was knapped to make an arrowhead, we did not know how to make the Internet, but now we do.
Personally, I believe we were made by a collective of beings somewhat similar to ourselves and only thousands of years (or maybe much less) more advanced than ourselves, a process that begun a few billion years ago on Earth. And yes, that belief does indeed beg the question as to where THAT bunch of beings came from, but personally, I am satisfied just to know the penultimate source of where we came from and not necessarily where everything came from for all of time.
[Secondarily, of course, is the apparent miraculous survival for billions of years of the collective consciousness that made us, and then thirdly, what was the nature of THEIR collective consciousness evolution and do they still exist, and if so, what form?]
my example of “pasta soup”:
as a life-long computer scientist, systems designer and programmer, as well as a lifelong student of the molecular life sciences, it’s crystal clear that life on earth could NOT have arisen by flipping an atomic coin an astronomical gazillions of times ...
the intra-cellular nano-machinery and mechanisms are mind-blowingly similar to computing machinery, programmatic data, and principles of data coding, such as modular coding and reuse of code ... it’s simply undeniable that cellular functioning consists of an unimaginably intricate set of very clever machines constructed from organic molecular parts ... and anyone who pretends that all of that happened by accident is either an ignorant fool or a liar or both ...
Some “scientists” claim to believe that lightning and cosmic rays zapified a primordial soup in ammonia-rich oceans, producing the complex molecules that formed the precursors to life. Others believe that chemical reactions at deep-sea hydrothermal vents gave rise to cell membranes and simple cellular pumps.
In other words, the massively sophisticated molecular machinery of single-cell organisms simply arose spontaneously as fully functional units after bombarding mud puddles with lightening and cosmic rays for a few hundred million years.
And, btw, the current THEORY of evolution is really no different than the previous “discredited” 19th century “spontaneous generation” theory that life arose spontaneously from mud puddles. The ONLY difference is the amounts of time involved in the two theories ... plus some extra mumbo-jumbo about lightening, cosmic rays and sea water ...
And if you believe the above, then you should have no problem at all with believing that a Panasonic CF-54 laptop computer with Windows 7 operating system could arise spontaneously if we simply ground a bunch of said laptops into powder along with a bunch of powered DVDs of the Windows Operating system and filled a large number of beakers with those powders, put some sea water in, and then bombarded the laptop soup in the beakers with lightening and cosmic rays for a few hundred million years while shaking the beakers.
Eventually, we might obtain some resisters and capacitors, but then they would evolve into integrated circuit chips, which would eventually EVOLVE all by themselves into CPU and GPU chips, and then motherboards, and then laptops (with operating systems) after being bombarded by cosmic rays for a very long time after the first resisters and capacitors appeared.
If organic life formed by accident in a similar scenario, then certainly there should be no problem with obtaining the laptop and operating system in a like fashion, because after all, the laptop and OS are a few thousand trillion times simpler than, say, a single cell of the Homo Sapiens species. In fact, we should obtain the laptop and OS much much faster because they are so much simpler.
Psalm 14:1
“ Transcription is the biochemical process that occurs in every cell in the human body when protein synthesis is initiated.”
Transcription is transcribing DNA to RNA. The produced RNA is called a transcript.
Protein synthesis is called translation which occurs at the ribosome.
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