Tag Archive for: Biology

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 Al Serrato

“Let me see if I understand,” I said to my daughter’s high school biology teacher. “The human eye is the evolutionary product of a light-sensitive spot on the skin. Is that right?”

“Right,” she said.

“And by evolution, you mean a mindless, random process that didn’t really have an end in mind. In other words, there was no “designer” for the eye or the body for that matter. Am I getting that right?”

“Right again,” she replied.

But how could an undirected process produce such highly functional complexity, I wondered aloud. She gave me a look that said, “you really don’t have the time or, probably, the background to understand, so do we really have to go there?”

We did, and I persisted, trying another tack that I had been wondering about for a while.

“Okay, well let me ask you just a few questions” I countered. “Would you agree that evolution as you understand it is a gradual process of adaptation over time, where changes that are advantageous accumulate?”

“Yes,” came her quick reply.

“Would you agree that over time these gradual adaptations would lead to the development of complex systems, such as organ systems?”

“Yes, that makes sense,” she said.

“Would you also agree,” I pressed, “that, generally speaking, the more complex the system, the longer it would take for these gradual adaptations to evolve so that a complex system would take longer to evolve than a less complex system?”

“Yes.” The response was a bit slower, more thoughtful.

Shifting gears a bit, I asked, “In the field of human biology, would you agree that generally speaking, the human female reproductive system is considerably more complex than its male counterpart?”

“I’m not sure what you mean,” she queried.

“Well,” I started, “the male half of the equation involves dividing cells to get to 23 chromosomes and providing a, uh, delivery mechanism. The female system involves the production of eggs, the delivery of the eggs to a specific location, the means for implantation, and if that occurs, the creation of a placenta that is fine-tuned to support the development of the life that is growing. The whole system must work in conjunction with the woman’s body, provide for correction of any mistakes occurring to minimize miscarriages, screen the fetus from harmful substances in the woman’s blood, connect the fetus to the mother by means of a two-way umbilical cord, and provide a method for the baby to be safely delivered into the world. More amazingly, the two systems must somehow recognize each other and work together, so that the 23 chromosomes from each half form a single cell that has the complete instructions for a new human life to begin. This seems like a pretty complex, interconnected, and interdependent system requiring multiple components to work just right. And yet it does work right millions and millions of times.”

“I suppose there’s something to that, but” she hesitated, “what’s your point?” Her tone matched her more serious expression.
“Just this,” I responded. “What exactly were all those men doing generation after generation waiting for the first fully functional female to evolve?”

She stared at me, no doubt wondering whether I was trying to mock her. But, though my question was of course facetious, I wanted to know where my logic was flawed. After all, the premises seem valid. If designed, it makes perfect sense that God could create a system in which some parts are more complex than others, and still have them work together for a purpose. But how could mammalian sexual reproduction – involving separate male and female individuals -ever evolve simultaneously? I wanted to know where that very first human male and very first human female came from. She took a deep breath and began her answer…. and it didn’t have anything to do with God.

“Well, it didn’t work that way,” she said. “Evolution occurred gradually, over time, as the predecessors to humans slowly began to change.”

“Fair enough,” I responded. “So, tell me about that first pair of monkeys, the very first male and female monkey from which you say we evolved.”

“Well,” she began, formulating her thoughts, “it didn’t work that way.” I gave her a quizzical look and she continued. “Those predecessors also evolved slowly, over time, from still more primitive forms of life.”

I was patient. “Like what?” I asked. I don’t think anyone had pressed her for answers like this, but after all I wasn’t worried about getting a grade. My daughter, on the other hand, probably wouldn’t be too thrilled about dad’s efforts at higher learning. Luckily, she wasn’t nearby.

In answer, the teacher started to explain that monkeys had evolved from still lower forms of life. It was a long process with smaller animals making adaptations, adding features, becoming larger. It all sounded quite vague and fuzzy, as she painted the picture of a planet teeming with life of various kinds, widely dispersed, and being driven by this engine of evolution.
I tried to stay on track with her. Then she made the jump that I was expecting – she started talking about life emerging from the primitive seas. Single-celled life forms that began to replicate and pass their DNA on to the next generation. She paused when she saw me starting to shake my head.

“Wait a sec,” I said. “You’re getting ahead of me, or perhaps more precisely, you’re moving back too far. I’ll grant you that life first began in the seas, but even if I grant you the ‘primordial soup’ theory, you’re still making quite a jump. What I want to focus on are the first male and female land mammals. If we wind the clock back, there must be a point on the early Earth in which there are no mammals walking the land. None whatsoever. Whatever life exists, it hasn’t yet evolved to sexually reproducing, warm-blooded mammals. Before that point, maybe there’s life in the sea, but the land is barren; after that point, the land begins to get populated. You with me?”

She nodded.

“I’d like to know what model science has to explain how that first began. That first couple.”

She was still formulating an answer, so I pressed on. “I can understand that once you have thousands of fully functioning mammals that over time they may begin to change, especially if subjected to some environmental challenge. That makes perfect sense, whether it is directed by the genes, as I believe was designed into them, or whether it’s a random process. But tell me how the first pair appeared on the land.”

I was hoping to get an answer, because I had been wondering for a while how Darwinists made sense of that rather large step, from single-celled asexually reproducing life to complex, sexually producing mammals. But it was not to be. “Coach.” We both looked in the direction of the voice. The bio teacher was also a coach, and someone was trying to get her attention. She smiled and said, “Let’s continue this later.” Was that a look of relief that crossed her features? Probably, I eventually decided. We never did finish the conversation.

Perhaps Darwinists have a plausible model for this transition, but I have yet to hear it. Instead, what I have heard is always along the lines of what’s recounted above – vague and fuzzy references to a planet teeming with evolving life, and then a jump to the oceans, where DNA first appears. But this jump appears to be a “just so” story, with a vague promise that someday science will make it all clear, will discover these missing links that just “must be there.” But common sense, and reason, tell me that when those original sexually reproducing mammals first appeared on Earth, they were able to reproduce in that fashion immediately, making use of an incredibly complex and interdependent system, a system that has all the hallmarks of design. And a system that couldn’t take long periods of time to evolve because, unless it’s working properly and completely on day one, there won’t be a next-generation upon which evolution could act.

Perhaps, like Frank Turek puts it, I just don’t have enough faith to be an atheist. Until I do, then, I guess I’ll just keep believing that the incredible complexity of life is what it appears to be – the telltale sign of an intelligent designer that set it all in motion for a purpose. After all, every time I see a complex, highly organized, interdependent system – like a watch or a plane or a car – I don’t struggle trying to figure out how it assembled itself. So, why do people struggle so hard when it comes to something even more complex – like life?

Why indeed.

Recommended resources related to the topic:

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)

Stealing From God by Dr. Frank Turek (Book)

Answering Stephen Hawking & Other Atheists MP3 and DVD by Dr. Frank Turek 

God’s Crime Scene: The Case for God’s Existence from the Appearance of Design (mp4 Download Set) by J. Warner Wallace 

God’s Crime Scene: The Case for God’s Existence from the Appearance of Design in Biology DVD Set by J. Warner Wallace

 

__________________________________________________________________________________________________________________________________________________

Al Serrato earned his law degree from the University of California at Berkeley in 1985. He began his career as an FBI special agent before becoming a prosecutor in California, where he continues to work. An introduction to CS Lewis’ works sparked his interest in Apologetics, which he has pursued for the past three decades. He got his start writing Apologetics with J. Warner Wallace and Pleaseconvinceme.com. 

 

Play

By Steve Williams 

I can see the fingerprints of God when I look at you I can see the fingerprints of God and I know its true you’re a masterpiece that all creation quietly applauds and you’re covered with the fingerprints of God

~from Fingerprints of God, by Stephen Curtis Chapman

The common scientific view of the “hardware of life” (that is, the physical components of living systems) is, as Biologist Richard Dawkins puts it, “the study of complicated things that give the appearance of having been designed for a purpose.” (The Blind Watchmaker, 1986).

Unfortunately, Dawkins (like many others in his field) has succumbed to a logically fallacious assumption that a supernatural explanation is not within the “pool of live options” to explain this appearance of design. Why not? Well, to summarize the common opinions of materialists like Dawkins, it’s “not science”. But what is “Science”?

Louis Pasteur once said “Religions, philosophies, atheism, materialism, or its opposite–none of these is relevant to the matter…I might even add that, scientifically speaking, I am indifferent to them all. The question is purely one of fact”. In other words, science should be “the un-biased search for truth” without philosophical preconceptions. That definition was always the ancient understanding of the term.

Since the so-called “Enlightenment” that swept through Europe in the 1700’s, and especially since the proposal of Darwin’s Theory of Evolution in 1859, however, intellectual activists have been trying to add the qualifying concept of “within naturalistic explanations” to the definition. What that means, in effect, is the addition of a bias to the search for truth.

This bias first “got its legs” from the writings of an apparently bitter atheistic Scottish philosopher named David Hume in the 1700’s. Hume proposed a set of reasons why the supernatural should be ruled be ruled out of consideration as an explanatory mechanism. Not long afterwards, these reasons were shown to be fallacious (we’ll examine this in a later chapter), but at the time, it was as if Europe was eager to unfetter itself from religion, and atheism blossomed somewhat throughout the continent.

Most modern philosophers (even agnostic ones) find Hume’s arguments to be almost laughably illogical, but many atheists unknowingly cite him today as if he was “the Christ” of their belief system. For a full-length treatment of this subject, see John Earman’s book Hume’s Abject Failure, but suffice it to say for the moment that modern humankind has nowhere near a broad enough scope of reality to eliminate the possibility of the supernatural. To the contrary, there are many things in our experience that defy naturalistic explanations.

The philosophical name of the most common scientific form of atheism is “Materialism”, and it claims that not only is there no God, but that there is nothing even like God in the universe. Although it has taken root within the Biological sciences, it has done so to a much lesser extent within Astronomy, Philosophy, and Physics. Many Americans would probably be surprised to know that polls show that the percentage of PhD’ed scientists overall who identify themselves as Christians and who go to church is roughly the same as the percentage in the population at large. Unfortunately, the small minority who identify themselves as atheists is much louder and more aggressive though, so they exert a disproportionate influence on the media, academic standards committees and the like.

Luckily for all who respect unbiased inquiry, many Philosophers who are experts in logic by definition (logic being a subset of Philosophy), have objected vociferously, especially in the past 40 years, to this effort, and have recognized that the scientific method is at stake. As I wrote before, it seems that the key element that catalyzed this mindset since the late 1800’s is Charles Darwin’s Theory of Evolution. Biologists became so enamored with it over the years that they invested heavily in deepening and entrenching their paradigms based on that assumption, and are not willing to consider that major problems have developed within it. Pride in Biology, and a reluctance to admit being wrong might be a factor. One has to wonder if there are spiritual and carnal reasons that admitting the mere possibility of the existence of the metaphysical is so daunting to some. Since Darwinian Evolution seems to be the lynchpin of this type of thinking, let’s take a hard look at it.

The concept of life arising from non-life by random chance is called “abiogenesis”. This concept is the “creation story” of Darwinian Evolution. But what are the odds of the building blocks of life coming together by random chance in a way to provide even the possibility of life? Harold Morowitz, an agnostic Yale University physicist, created mathematical models by imagining broths of living bacteria that were superheated until all the complex chemicals were broken down into basic building blocks. After cooling the mixtures, Morowitz used physics calculations to conclude that the odds of a single bacterium reassembling by chance is one in 10100,000,000,000. (1) Wow! How can we grasp such a large statistic? Well, it’s more likely that one would win the state lottery every week for a million years by purchasing just one ticket each week!

In response to the probabilities calculated by Morowitz, Robert Shapiro, author of Origins – A Skeptic’s Guide to the Creation of Life on Earth, wrote:

The improbability involved in generating even one bacterium is so large that it reduces all considerations of time and space to nothingness. Given such odds, the time until the black holes evaporate and the space to the ends of the universe would make no difference at all. If we were to wait, we would truly be waiting for a miracle. (2)

Sir Frederick Hoyle compared the probability of life arising by chance to lining up 1050 (ten with fifty zeros after it) blind people, giving each one a scrambled Rubik’s Cube, and finding that they all solve the cube at the same moment!

Biological “Hardware” (Complex Structure) Argument

  1. According to a leading Darwinist, the odds of component parts in close proximity assembling into a single-celled creature are 1 in 10100,000,000,000.
  2. According to probability theorists, anything with lower odds than 1 in 1050is mathematically impossible.
  3. Therefore, the spontaneous generation of life is mathematically impossible.

Regarding the origin of life, Francis Crick, winner of the Nobel Prize in biology for his work with the DNA molecule, stated in 1982:

An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going. (3)

Crick’s assessment of the hopelessness of the spontaneous generation of life on earth led him to subsequently postulate a theory called “Directed Panspermia”, which held that space aliens “seeded” life on earth. As Philip Johnson observed, “When a scientist of Crick’s caliber feels he has to invoke undetectable spaceman, it is time to consider whether the field of prebiological evolution has come to a dead end.” (4)

Ever since the discovery of DNA in 1953, the Darwinian Theory of Evolution has faced increasing challenges yearly as more and more evidence for the complexity of the cell has been discovered. In 1996, Dr. Michael Behe (professor of Biochemistry at Lehigh University) released a book entitled “Darwins’ Black Box”, which detailed an argument against Darwinian Evolution known as the “irreducible complexity” of biological structures and systems. In the 11 years since the publication of the book, it has been attacked from every angle by atheistic scientists, yet its central thesis has only gained strength, as the debate has exposed the weakness of Darwinian counter-arguments, and the naturalistic (atheistic) philosophical biases that lurk behind them.

Have you ever wondered if Charles Darwin himself would still believe in Darwinian Evolution (or macro-evolution) if he knew all of the evidence that has accumulated for and against it up to this time? Well, there is an interesting quote in which Darwin stated his own minimum standard for assessing whether or not his theory would withstand the tests of time:

If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. (5)

In Darwin’s day, it was assumed that cells were very simple. In the last half of the 20th century, however, it has come to light that inside each living cell are vastly complex molecular machines made up of various protein parts. Organs, which are made up of these complex cells, have also been shown to be much more complex than previously believed.

The blueprints for assembling the protein parts for cells and organs in correct timing and order are encoded into our DNA, which is similar to binary computer code, although it is quaternary (having 4 letters instead of 2). The density of the information encoded into DNA staggers the imagination; there is enough information-storing space in a half-teaspoon of DNA to store all of the assembly instructions for every creature ever made, and room left over to include every book ever written!

In addition to the incredible information-storing capacity in DNA, there are machines and systems in biology which vastly exceed mankind’s creative capacity in terms of their complexity. For example, the blood-clotting mechanism requires a sequence of 20 different proteins (each of which has an average chance of 1 in 8.03 x 10 to the 59th power of forming by random chance!) triggering one another like dominoes falling in order, until a fibrin mesh scaffolding is formed for the clot itself.

If you subtract any one single protein (regardless of where in the sequence of 20), this scaffolding fails to form, and no blood clot is possible. Without clotting, any creature with a circulatory system would bleed to death from a tiny wound, similarly to what happens to hemophiliacs.

Now think about how this compares to Darwin’s criterion for his own theory. Macro-evolution requires a mutation for every step, each of which needs to confer an advantage in surviving or creating offspring to be retained by natural selection. Even if we grant the creation of proteins by random chance (which is extremely unlikely), at steps 1, 2 ,3, 4, etc. on up to and through step 19, there is no advantage conferred toward the production of a blood clot until step 20 is completed! If you reduce the complexity by any single component (regardless of where in the sequence the single component is), the system doesn’t work, and has no reason to be retained by natural selection. This is Irreducible Complexity.

Let’s look at another example. The Bacterial Flagellum is a tail-like protein propeller attached to one end of a bacterium that propels the organism through its environment via rapid rotations (like a miniature outboard motor driving a whip in circular motion). It has components that are remarkably similar to a man-made outboard motor, such as a rotor, a U-joint, a stator, a driveshaft, a propeller, bushings, and O-rings.

There are at least 40 different protein parts required for the assembly of a flagellum. Many of the flagellar proteins control the construction process, switching the building phases on and off with chemical triggers at just the right times, and setting up construction in the proper sequence. It is an engineering marvel. If you deduct 1% of the parts, you don’t have a 99% functional bacterial flagellum; it becomes completely dysfunctional, and you have nothing but a hindrance (probably fatal) to any organism attached to it. The following picture hints at its complexity…

http://freethinkingministries.com/wp-content/uploads/2017/12/

Consider the fact that it is conservatively calculated that the odds of this incredible structure forming by random chance is 1 in 10 to the 1170th power. (6)  According to probability theorists, anything with a chance lower than 1 in 10 to the 50th power is mathematically impossible, so it doesn’t matter how much time you give it—it simply won’t occur by chance alone.

Just recently, a vastly more complex gear-driven, seven-engine, magnetic-guided flagellar bundle was discovered. Here is an piece on it from www.evolutionnews.org:

Souped-Up Hyperdrive Flagellum Discovered

Evolution News & Views December 3, 2012 5:05 AM

Get a load of this — a bacterium that packs a gear-driven, seven-engine, magnetic-guided flagellar bundle that gets 0 to 300 micrometers in one second, ten times faster than E. coli.

If you thought the standard bacterial flagellum made the case for intelligent design, wait till you hear the specs on MO-1, a marine bacterium described by Japanese researchers in the Proceedings of the National Academy of Sciences. Edited by Howard Berg, Harvard’s mastermind of flagellum reverse engineering, this paper describes the Ferrari of flagella.

Instead of being a simple helically wound propeller driven by a rotary motor, it is a complex organelle consisting of 7 flagella and 24 fibrils that form a tight bundle enveloped by a glycoprotein sheath…. the flagella of MO-1 must rotate individually, and yet the entire bundle functions as a unit to comprise a motility organelle.

To feel the Wow! factor, jump ahead to Figure 6 in the paper. It shows seven engines in one, arranged in a hexagonal array, stylized by the authors in a cross-sectional model that shows them all as gears interacting with 24 smaller gears between them. The flagella rotate one way, and the smaller gears rotate the opposite way to maximize torque while minimizing friction. Download the movie from the Supplemental Information page to see the gears in action.

Electron micrographs included in the paper show that the model is not unrealistic. These flagella really are tightly packed in a sheath, suggesting that the bundle acts like a gear-driven hyperdrive.

Here we have used electron cryotomography to visualize the 3D architecture of the sheathed flagella. The seven filaments are enveloped with 24 fibrils in the sheath, and their basal bodies are arranged in an intertwined hexagonal array similar to the thick and thin filaments of vertebrate skeletal muscles. This complex and exquisite architecture strongly suggests that the fibrils counter-rotate between flagella in direct contact to minimize the friction of high-speed rotation of individual flagella in the tight bundle within the sheath to enable MO-1 cells to swim at about 300 µm/s. (Emphasis added.)

At microbial level, that’s more than 10 body lengths per second. The authors were clearly excited by this engine, sounding like young men checking out high-performance cars, talking thrust, gear ratios and torque.

MO-1 is a magnetotactic bacterium capable of orienting its cell body along the geomagnetic field lines by using magnetosomes. The MO-1 cell has a flagellar apparatus with two lophotrichous [containing numerous flagella in] bundles. In contrast to peritrichously [flagella all over the cell] flagellated bacteria, MO-1 cells swim constantly in a helical trajectory toward magnetic north, and the trajectory changes from right-handed to left-handed without changes in velocity or direction. The cells are able to swim as fast as 300 μm/s, which is nearly 10-fold faster than E. coli and Salmonella. Although the flagella of the other types of bacteria usually work individually or by forming a loose bundle to produce thrust, the flagellar apparatus of MO-1 is a tight bundle of seven flagella enveloped in a sheath made of glycoproteins. This unique architecture appears to be essential for the smooth and high-speed swimming of MO-1.

They can’t see actual gears, of course, but physics demands that the mechanism of rotation must have something like it:

We hypothesize that, whereas each of the seven flagella has its torque-generating motor, the 24 fibrils counter rotate between the flagellar filaments to minimize the friction that would be generated if the flagella were directly packed together in a tight bundle. A schematic diagram representing our hypothesis is presented in Fig. 6. The flagella are represented as large brown gears and the fibrils are represented as small blue-green gears. The flagella and fibrils rotate counterclockwise and clockwise, respectively, as indicated by the arrows, to minimize friction (Movie S1). Although there is no direct evidence that the fibrils can rotate freely in the opposite direction as the flagellar filaments with which they are in direct contact, we think this is the simplest interpretation to explain the superior function afforded by the complex architecture of the MO-1 flagellar apparatus.

Considering the very tight packing of the 7 flagella and 24 fibrils that are in direct physical contact within the sheath, there appears to be no other way for the flagella to rotate at high speed without the counter rotation of the intervening fibrils. Although the fibrils and the surrounding sheath are in direct contact, the friction between them would be small because of the stocking-like flexibility of the sheath. This design must be playing an essential role in the fast, smooth rotation of the flagellar apparatus that allows the rapid swimming of MO-1.

With powerful evidence of design like this, did the researchers become converts to intelligent design? We can’t know, but would PNAS have printed such a paper without an obligatory tribute to unguided materialistic evolution? Evolution is not mentioned until the last paragraph:

Taken together, these features of the MO-1 flagellar apparatus represent an advanced level of evolution of a motility apparatus. It is also intriguing that the same pattern of an intertwined hexagonal array in two evolutionary distant systems: the basal bodies of flagella and fibrils of the MO-1 flagellar apparatus, and the thick and thin filaments in vertebrate skeletal muscle. Similar architectures of filamentous structures presumably evolved independently in prokaryotes and eukaryotes to fulfill the requirements for two very distinct mechanisms to generate motion: counter rotation and axial sliding.

OK, so the Darwinists got their offering, but it leaves a bad aftertaste: now, they have to believe that advanced mechanisms for generating motion evolved not just once, but twice — completely independent of each other. Thanks a lot, guys. Wait till the intelligent-design movement hears about this.

Oops, too late.

(http://www.evolutionnews.org/2012/12/souped-up_flage066921.html).

Going back to our previous subject, what if we just ignored the previously mentioned problems of forming the first cell, and assume that we’re starting the Darwinian process from the bacterial level and advancing to the human level? On page 153 of the book Who Was Adam?, Fazale Rana and Hugh Ross cite one of the world’s most prominent evolutionists, Dr. Francisco Ayala of UC Irvine, as calculating the minimal odds of human beings evolving from the bacterial level  to be 1 in 10 to the 1 millionth power. Three physicists, John Barrow, Brandon Carter and Frank Tipler, did roughly the same calculation but included some important factors that Ayala overlooked, and came up with the number 1 in 10 to the 24 millionth power. Again, according to probability theorists, any event with lower odds than 1 in 10 to the 50th power is mathematically impossible. Therefore unguided Darwinian evolution is mathematically impossible!

Reduced to a propositional argument, it might go like this:

Biological “Hardware” (Complex Structure) Argument

  1. According to leading Darwinists, odds of humans evolving from a single-celled creature are 1 in 1024,000,000.
  2. According to probability theorists, anything with lower odds than 1 in 1050is mathematically impossible.
  3. Therefore, Darwinian evolution of human beings is mathematically impossible.

Now, these two sets of odds (totaling to 1 in 10100,024,000,000) seem overwhelming to say the least; why would scientists insist that creations like these could have come about by evolution? To re-iterate, it seems that biological science has become dominated by atheistic philosophers. Science is “a search for truth”, but the oligarchy in control in this day and age is trying to change that to “a search for truth by naturalistic (atheistic) means”. To them, the idea of God is unacceptable, so science cannot consider even the possibility that God created this universe and all that is in it.

Take a look at the following quote by prominent Darwinist Richard Lewontin, and consider whether his viewpoint is logically sound. Unfortunately, this quote seems to be representative of how many Darwinists think, and how they want everyone else to think:

Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. (7)

One wonders why such a concerted effort is made to deny the metaphysical into the pool of live options. Perhaps the following quote by another prominent Darwinist named Aldous Huxley provides some insight:

I had motives for not wanting the world to have meaning; consequently assumed that it had none, and was able without any difficulty to find satisfying reasons for this assumption … For myself, as no doubt, for most of my contemporaries, the philosophy of meaninglessness was essentially an instrument of liberation.  The liberation we desired was simultaneous liberation from a certain political and economic system, and liberation from a certain system of morality.  We objected to the morality because it interfered with our sexual freedom. (8)

Now, just for fun, look at the following Bible passage, and think about how it relates to the quotes above:

For since the creation of the world His invisible attributes, His eternal power and divine nature, have been clearly seen, being understood through what has been made, so that they are without excuse.

For even though they knew God, they did not honor Him as God or give thanks, but they became futile in their speculations, and their foolish heart was darkened. Professing to be wise, they became fools. –Romans 1:20-22.

Perhaps this is a good place to ponder a quote from Nobel-Prize winning organic chemist Christian de Duve:

If you equate the probability of the birth of a bacteria cell to chance assembly of its atoms, eternity will not suffice to produce one… Faced with the enormous sum of lucky draws behind the success of the evolutionary game, one may legitimately wonder to what extent this success is actually written into the fabric of the universe. (9)

God has indeed left His signature in nature in its irreducible complexity and fine-tuning. Darwinism has failed repeatedly when tested as an explanation for the existence of life. Hundreds of scientists have recognized this and have signed a document called the “Dissent from Darwinism” (http://www.dissentfromdarwin.org/) to express their disagreement with philosophical naturalism dominating science through Darwinism. We simply need to “have eyes to see, and ears to hear”, and stop listening to atheistic philosophers disguised as scientists, who try to insist that the supernatural or metaphysical is off-limits for science. “Reasonable faith” is going in the same direction to which the evidence is pointing. The teachings of the Bible, understood properly, merge perfectly with science.

 


This article is chapter 3 From What Your Atheist Professor Doesn’t know (But Should), by Steve Williams

Original Blog Source: http://bit.ly/2Ch6MsY

Questions related to origins are some of the most divisive in the church today: How old is the earth? Is there good evidence for intelligent designDid God use evolution?Sadly, rather than discussing differences in a sober and gracious manner, conversations are often characterized by defensiveness, misunderstanding, and personal attacks. What a shame!

But this need not be the case. The recent book Old-Earth or Evolutionary Creation?demonstrates that leading voices in the origins debate can come together and wrestle over big questions of faith and science with both “gentleness and respect” (1 Peter 3:15).

This book is the culmination of a decade-long formal conversation between scientists, philosophers, and theologians from the old-earth creationist organization Reasons to Believe (RTB) and evolutionary creation (theistic evolution) organization BioLogos, as well as a group of Southern Baptist (SB) seminary professors.

One of the Southern Baptist moderators describes the major purposes of the book as demonstrating that “two creationist organizations can strongly disagree with one another while treating one another with Christian charity, respect, and a willingness to seriously consider the merits of an opposing position.”[1] This mission was clearly accomplished in the book.

If you are interested in questions of the interaction between science and faith, then this book is a must-read. Even if you hold to a young-earth position, which is not represented in this book, you will find the give-and-take invaluable.

While much could be said about the book, the most valuable part to me was that it surfaces key underlying assumptions that drive how both sides interpret the evidence. RTB and BioLogos frequently agree on the scientific facts, but their conclusions vary because they bring different philosophical and theological lenses to the data. Let me offer a couple examples.

The Interaction Between Science and Scripture

First, both organizations approach the philosophical question of the interaction of science and Scripture differently. RTB holds a soft-concordist view, which means they believe there is some overlap between biblical claims and science. Specifically, they believe science confirms some Scriptural claims such as the origin of the universe (Gen 1:1) and the unique creation of Adam (Gen 2:7).

On the other hand, BioLogos writer Jim Stump looks at the natural world through two different lenses—scientific and personal (chapter 6). Thus he doesn’t expect any overlap between scientific claims and Scripture because, from his perspective, the two operate on different levels of explanation.

There are also theological differences at the heart of how they interpret the interaction between Scripture and science. Writing for BioLogos, John Walton argues that God does not convey more meaning in Scripture than the original authors intended (except when NT authors add meaning to OT writers, which is an example of further divine inspiration). Thus, he is not tempted to look for modern scientific claims in ancient Scripture.

On the other hand, RTB philosopher Ken Samples argues that there can be deeper truths in Scripture beyond the intention of the original authors. Thus, he (and the RTB team) is inclined to look for scientific clues that find modern confirmation. In both cases, their underlying assumptions shape how they reconcile the interaction between science and Scripture.

Common Descent or Common Design?

Second, the two organizations have different assumptions about how God acts in the natural world. BioLogos is committed to natural mechanisms as driving the evolutionary process. Answering a question related to the size of their “tent,” BioLogos president Deborah Haarsma responds:

Someone who disagrees with common ancestry would be outside the BioLogos tent. However, we welcome debate within BioLogos on questions currently debated in the scientific community, such as the relative importance of various natural mechanisms in evolution and whether genes or organisms are most central to the evolutionary story.”[2]

In contrast, RTB scholars believe that science can validate God’s direct involvement in physical history. Astrophysicist Jeff Zweerink explains:

RTB affirms that just as the descriptions of the exodus and the battle of Jericho (Josh 6) give details that archaeologists and historians can validate, the creation accounts in Genesis 1-2, Job 38-41, Psalm 8, and elsewhere describe physical events that scientists can validate.”[3]

As a result of these differences, they tend to evaluate the evidence for evolution differently. For instance, Darrell Falk argues that one of the most compelling arguments for evolution is the genetic “scars” that exist in humans and chimps in the same location in the genome, which he says can only be explained by common ancestry.

In contrast, Fuz Rana believes genetic scars can also be explained by common design. He gives the example of a scar found on the tip of your finger because of a common initiation rite. In this case, the cut serves a common function for all club members, even if it seems purposeless and accidental to outsider observers. He interprets genetic “scars” through the same design framework.

My point is not to the debate the issue here (my own perspective is much closer to RTB, which I have laid out in my book with William Dembski, Understanding Intelligent Design). Rather, to simply highlight how powerfully assumptions shape—not determine—how people interpret the data.

Much more could be said about this book. I enjoyed the chapters on the historical Adam, human evolution, methodological naturalism, natural evil, and more. In these cases, as the two above, the discussion clarifies underlying assumptions. To me, this is worth the price of the book.

Given both the quality of the content, and the generous spirit of interaction in this book, I hope it is just the beginning of many more common projects yet to come.

Sean McDowell, Ph.D. is a professor of Christian Apologetics at Biola University, best-selling author, popular speaker, part-time high school teacher, and the Resident Scholar for Summit Ministries, California. Follow him on Twitter: @sean_mcdowell and his blog: seanmcdowell.org.

[1] Old-Earth or Evolutionary Creation? Discussing Origins with Reasons to Believe and BioLogos, ed. Kenneth Keathley, J.B. Stump, and Joe Aguirre (Downers Grove, IL: IVP Academic, 2017), 7.

[2] Ibid., 21.

[3] Ibid., 114.