Tag Archive for: teleological argument

The DNA replisome is one of the most remarkable molecular machines, involving a complex of different proteins, each of which is very specifically crafted to fulfill its role in the process of replicating the genome in preparation for cell division. The rate of DNA replication has been measured at a whopping 749 nucleotides per second[1] and the error rate for accurate polymerases is believed to be in the range of 10-7 and 10-7, based on studies of E. coli and bacteriophage DNA replication.[2]

One of the best animations of this incredible process is this one by Australian animator Drew Berry. It is difficult to look at an animation such as this (which is drastically over-simplified) and not come away with the strong intuition that such an intricately choreographed machine is the product of masterful engineering. Stable and functional protein structures are astronomically rare in combinatorial sequence space, and DNA replication requires many of them. But not just any old stably folding proteins will do. These proteins have to be crafted very particularly in order to perform their respective jobs. Indeed, when one focuses on specific proteins, it takes the design intuition to new heights. For example, see these beautiful animations of topoisomerasehelicase, and DNA polymerase. One paper summarizes the engineering prowess of DNA replication thus [3]:

Synthesis of all genomic DNA involves the highly coordinated action of multiple polypeptides. These proteins assemble two new DNA chains at a remarkable pace, approaching 1000 nucleotides (nt) per second in E. coli. If the DNA duplex were 1 m in diameter, then the following statements would roughly describe E. coli replication. The fork would move at approximately 600km/hr (375 mph), and the replication machinery would be about the size of a FedEx delivery truck. Replicating the E. coli genome would be a 40 min, 400 km (250 mile) trip for two such machines, which would, on average make an error only once every 170 km (106 miles). The mechanical prowess of this complex is even more impressive given that it synthesizes two chains simultaneously as it moves. Although one strand is synthesized in the same direction as the fork is moving, the other chain (the lagging strand) is synthesized in a piecemeal fashion (as Okazaki fragments) and in the opposite direction of overall fork movement. As a result, about once a second one delivery person (i.e. polymerase active site) associated with the truck must take a detour, coming off and then rejoining its template DNA strand, to synthesize the 0.2km (0.13 mile) fragments.[3]

Irreducible Complexity on Steroids

DNA replication is an example of what we might call “irreducible complexity on steroids.” Genome duplication is a prerequisite of differential survival, which is necessary for the process of natural selection to even work. Thus, one can hardly appeal to natural selection to account for the origins of DNA replication without assuming the existence of the very thing one is attempting to explain. It is difficult to envision a viable replication system that is simpler than the DNA replisome shown in the animation above. Though the RNA world scenario (which maintains that RNA-based life predates life based on DNA and proteins) is a popular hypothesis, problems abound for this scenario, as has been discussed many times in various other publications (e.g., Meyer, Signature in the Cell, Ch. 14). For example, one of the foremost challenges is the inherent instability of RNA (being single-stranded, and possessing an additional 2’ OH group, rendering it prone to hydrolysis). RNA polymers are therefore extremely unlikely to have survived in the early earth environment for long enough to be of much value. Second, when RNA forms complementary base pairs to fold back on itself, part of the molecule no longer presents an exposed strand that can serve as a template for copying. Thus, there is a physical limitation on the capability of RNA to self-replicate.

A further reason why the DNA replication machinery exhibits irreducible complexity on steroids is that, by being so primitive, it is far more difficult to envision any kind of co-optation scenario than it would be for a system that arose much later, such as bacterial flagella. With the flagellum, one can at least point to alternative functions that might be performed by a number of the flagellar components (such as the Type-III Secretion System). However, with DNA replication, it is unclear what other systems any of the components might be co-opted from – since any other system would need to have arisen after the origins of DNA replication.

An even more striking enigma is that, across the three domains of life, the key enzymes (in particular, the replicative polymerases) are not homologous, which has led to the suggestion that DNA replication may have arisen more than once independently.[4] This observation sits more comfortably on a design paradigm than on one committed to naturalism.

Which Components Are Essential for DNA Replication?

What protein components that are involved in DNA replication are indispensable for function? First, there is the DNA polymerase that actually performs the copying of each strand. Without it, no replication would take place at all. But, the DNA polymerase is unable to begin replication without the presence of a free 3’ OH (hydroxyl) group. Thus, another enzyme — a form of RNA polymerase called a primase — creates a short RNA fragment (called a primer) from which the DNA polymerase can extend (unlike DNA polymerase, the primase does not require the presence of a free 3’ OH group). Thus, in the absence of the primase enzyme, no RNA primers would be laid down on either the leading or lagging strand, and DNA replication would be unable to commence. Furthermore, the DNA polymerase itself has to be attached to the DNA by a ring-shaped protein known as a sliding clamp (which prevents it from falling off the DNA template strand). But, the sliding clamp cannot directly attach to the DNA on its own. Instead, a protein complex called the clamp loader mediates the loading of the sliding clamp onto the DNA at the replication fork, utilizing the energy from ATP hydrolysis to open the sliding clamp ring and load it onto the DNA. In the absence of the sliding clamp or clamp loader, the DNA polymerase would frequently fall off the DNA template, rendering it extremely inefficient.

Of course, the replication process cannot begin unless the DNA double helix is unzipped, and this is accomplished by the enzyme helicase, which breaks the hydrogen bonds along the DNA molecule, thereby opening up and exposing the two strands for replication by the polymerase. In its absence, the DNA polymerase will stall, unable to separate the strands that lie ahead.

Even with the helicase enzyme separating the two strands, the strands are likely to reanneal during the copying process. Enter the single-stranded binding proteins which bind to the exposed DNA strands, preventing them from re-annealing during copying. Without them, the DNA strands would bind together again before they were able to be copied.

The topoisomerase enzymes are necessary for removing supercoils that are induced by the torsional stress. They do so by cutting one strand, passing the other strand through the gap, and then resealing the break. In the absence of the topoisomerase enzymes, the DNA would eventually break, thereby hindering the DNA replication process.

Because of the anti-parallel nature of DNA (and the fact that the DNA polymerase can only replicate in a 5’ to 3’ direction), one strand, the lagging strand, has to be replicated backwards (in order for the replication fork to move in a single direction). This is done discontinuously in small sections. RNA primers are laid down by primase, and from those are synthesized short fragments of DNA known as Okazaki fragments. The RNA primers are then removed and replaced with DNA, and the Okazaki fragments are stitched together by the enzyme ligase. We have already discussed the necessity of the primase enzyme for synthesizing RNA primers. It may be added that, in the absence of the RNA excision enzymes (which remove the RNA primers), the RNA fragments would remain covalently attached to the newly replicated fragments of DNA. Moreover, in the absence of ligase (which links the Okazaki fragments together), the newly replicated strands would remain as fragments.

If the removal of any of the aforementioned components would render the DNA replication machinery non-functional, how could such a system come about through an undirected Darwinian step-wise pathway, preserving selective utility at every step along the way? Whatever process produced the DNA replisome had to know where the target was. Such a cause would have to be teleological in nature.

A Paradigm of Design

The DNA replication machinery represents one of the most extraordinary examples of nanotechnology found in the cell. In any other realm of experience, such a complex and delicate arrangement of parts would be immediately recognized as reflecting conscious intent — that is, as being the product of a mind. Why should such an inference be disallowed when examining biological systems? For more detail on this fascinating molecular machine, see my interview on it from last summer on ID the Future. I also published an earlier series (more than a decade ago) exploring the various protein components in more detail. You can find these here:

If you enjoyed the animation by Drew Berry linked at the beginning of this article, here is a more detailed animation, produced by Oxford University Press. Here is a second animation which reveals how the DNA polymerases are coupled so that they can move in the same direction.

References: 

[1] McCarthy D, Minner C, Bernstein H, Bernstein C. DNA elongation rates and growing point distributions of wild-type phage T4 and a DNA-delay amber mutant. J Mol Biol. 1976 Oct 5;106(4):963-81.

[2] Schaaper RM. Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli. J Biol Chem.1993 Nov 15;268(32):23762-5.

[3] Baker TA, Bell SP. Polymerases and the replisome: machines within machines. Cell. 1998 Feb 6;92(3):295-305.

[4] Leipe DD, Aravind L, Koonin EV. Did DNA replication evolve twice independently? Nucleic Acids Res. 1999 Sep 1;27(17):3389-401; and Brown JR, Doolittle WF. Archaea and the prokaryote-to-eukaryote transition. Microbiol Mol Biol Rev. 1997 Dec;61(4):456-502.

Recommended Resources:

Why Science Needs God by Dr. Frank Turek (DVD and Mp4)

Science Doesn’t Say Anything, Scientists Do by Dr. Frank Turek (DVD, Mp3, and Mp4)

Oh, Why Didn’t I Say That? Does Science Disprove God? by Dr. Frank Turek (DVD and Mp4)

I Don’t Have Enough Faith to Be an Atheist (Paperback), and (Sermon) by Norman Geisler and Frank Turek

 


Dr. Jonathan McLatchie is a Christian writer, international speaker, and debater. He holds a Bachelor’s degree (with Honors) in forensic biology, a Masters’s (M.Res) degree in evolutionary biology, a second Master’s degree in medical and molecular bioscience, and a Ph.D. in evolutionary biology. Currently, he is an assistant professor of biology at Sattler College in Boston, Massachusetts. Dr. McLatchie is a contributor to various apologetics websites and is the founder of the Apologetics Academy (Apologetics-Academy.org), a ministry that seeks to equip and train Christians to persuasively defend the faith through regular online webinars, as well as assist Christians who are wrestling with doubts. Dr. McLatchie has participated in more than thirty moderated debates around the world with representatives of atheism, Islam, and other alternative worldview perspectives. He has spoken internationally in Europe, North America, and South Africa promoting an intelligent, reflective, and evidence-based Christian faith.

This article was originally published on March 21st, 2024, at Evolution News & Science Today.

And republished at: https://bit.ly/4f6pp5q

By Mark McGee

I was comfortable as an atheist. I could do anything I wanted to do (or could get away with) and laugh at the masses of people stuck in the merry-go-round of belief in a “higher power.” I laughed at them privately, with friends, and publicly on my radio talk show. So, it came as quite a surprise when I heard that science might support creation of the heavens and the earth by “God.” That was stuff of my childhood, certainly nothing to concern myself as an informed adult, but there it was staring me in the face – creation science.

In the early 1970s people like Dr. John Meyer of the University of Louisville (Physiology and Biophysics), Dr. Malcolm Cutchins of Auburn University (Aerospace Engineering), Dr. Kenneth Cummings with the U.S. Consultants Fisheries Service in LaCrosse, Wisconsin (Research Biologist), Dr. Thomas Barnes of the University of Texas, El Paso (Physics), Dr. David Boylan of Iowa State University (Dean, College of Engineering), Dr. Arthur Wilder-Smith of the University of Illinois Medical School Center, University of Geneva School of Medicine, and University of Bergen School of Medicine (Doctorates in Physical Organic Chemistry and Pharmacological Sciences), and Dr. Edward Blick of the University of Oklahoma (Aerospace, Mechanical and Nuclear Engineering) were supporting creationism using science as evidence. I found that very interesting since my observation of Christians at the time was they were not educated nor informed in the “sciences.”

The man who introduced me to the fact that many scientists believed in creation had been a professor of Civil Engineering at Rice University in the 1940s and had received his Ph.D. in Hydraulic Engineering at the University of Minnesota. Dr. Henry Morris taught at several universities during the 1950s and 60s and helped start the Creation Research Society in the early 60s. He co-wrote The Genesis Flood with Dr. John Whitcomb, which included his belief in the literal interpretation of the world-wide cataclysmic flood that killed all life on earth except for those who rode out the flood in the Ark built by Noah and his sons. Thus, the reason for Dr. Morris’ visit to Florida as he prepared to search for the Ark on Mt. Ararat. All of this seemed ridiculous to me, so I invited Dr. Morris to appear on my radio show in a special two-hour edition where we would dig into the claims of a creator God who destroyed most life on the planet with water.

One of Dr. Morris’ evidences about creationism was the “fine-tuning” of the universe. By that he meant the earth was the only physical place in the universe capable of sustaining higher forms of life. Dr. Morris pointed to the earth’s unique hydrosphere, atmosphere, and lithosphere as some of the evidence for that, along with the position of the earth in its distance from the sun and how the earth’s moon and other planets and moons in our solar system orbited the sun in a way that benefited life on earth and served as a protective shield to most of the damaging elements hurtling through space.

Fine-Tuning of the Universe

One of the evidences presented by scientists who believe in creation is known as “fine-tuning.” Dr. Lawrence Henderson of Harvard College and Harvard Medical School wrote about the concept of fine-tuning a century ago in his book The Fitness of the Environment (1913). Other scientists who made scientific discoveries used in the development of the theory of fine-tuning (prior to 1971) included Dr. Hermann Weyl of ETH Zurich (where he was a colleague of Albert Einstein) and Princeton University (Mathematical Physics), Sir Arthur Eddington of the University of Cambridge (Astrophysics), Nobel Prize winner (Physics) Dr. Paul Dirac of the University of Cambridge, University of Miami, and Florida State University, Dr. Carl Brans of Princeton University and Loyola University (Mathematical Physics), and Dr. Robert Dicke of Princeton University (Physics, Astrophysics, Atomic Physics).

The idea of fine-tuning, as was explained to me, is that of the universe being fine-tuned for “life”. Could the universe be so highly tuned for life that the earth was the only place in the universe that could support it? What had we learned from our exploration of the universe through powerful telescopes straining to see as far as many miles and light years as possible? Did we see other planets supporting life? NASA had launched many rockets into space by 1971 looking for signs of life. Did we have “proof of life” in another part of our galaxy or the universe? Not to say that space exploration wouldn’t find life out there somewhere, someday, but it seemed at the time as if we were alone in the universe.

Some of the “large number coincidences” (also known as large numbers hypothesis) were extraordinary in the study of the universe. I traced it back to the early part of the 20th century to something Dr. Hermann Weyl wrote – “the ratio of the electron radius to the electron’s gravitational radius is of the order of 1040. The ratio of the electron radius to the world radius may be of similar proportions”  (H. Weyl. 1919. Ann. der Physik S9129). Eddington, Dirac, and Dicke built on Weyl’s idea of coincidences between extremely large numbers from different origins. Were those coincidences because of the slow change of evolution or something more purposeful?

As an atheist who gladly accepted evolution as the “truth,” I did not believe there was any purpose to life. Why would there be any purpose to billions of years of evolution with its slow process of “natural” selection? There wasn’t. I had no purpose. People I knew had no purpose. The world I lived in had no purpose. I was the product of a more highly evolved life form and could use lower life forms to my advantage. I could also take advantage of similar life forms, but at a certain risk of other life forms taking advantage of me. It was a bit tricky, but I was figuring it out as I went along.

But what if there was a life form that was much higher than humans? What if that higher life form existed in another dimension than the one we experienced? What if that higher life form made demands on humans even as humans made demands on lower life forms?  What if that higher life form had created lower life forms for a purpose? If so, what was the purpose? Was it to take advantage of us in the same way we took advantage of other life forms? Or something else?

I had never looked at life in that way before. Things were so simple in my world. Eat, grow, dominate, reproduce, lose strength and ability to dominate, die. Things only became difficult if something or someone tried to keep me from eating, growing, dominating, and reproducing. Get in my way and I’ll shut you down. That was my basic belief about life at the time. The possibility of something greater than the human race making demands on us got my attention in a big way.

The process of researching something in 1971 was different than today. There was no publicly-accessible Internet, no cable TV with hundreds of channels filled with information, no smart phones and tablets with apps, no personal computers with quick and easy access to the vast online libraries of the world, and no email. If you wanted to research something you spent hours at a library, or purchased books and other materials at bookstores or ordered them through catalogs. I spent a lot of time at libraries.

The more I read, the more I wondered if I had missed something – something big. What if I was wrong? What if the universe was so finely tuned that evolution could not have done it? What if a “higher life form” had designed and created the universe with a purpose? If so, how could I know the purpose? It was an important time in my life. I sensed I was at a crossroads. I didn’t know what it would mean for my life, but I needed to know the truth. Something was pulling me to figure it out.

Would the argument of a finely-tuned universe be enough to change my mind about the existence of God? If that was the only evidence for the existence of God, it might not have been enough. However, there were many more arguments to come. More about those next time.

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