JERRY BERGMAN  The latest issue of the popular science magazine, Discover,[i]  contains an article titled “Everything Worth Knowing About Evolution.” The article begins by claiming that over 350 million years ago our fish ancestors traded aquatic for terrestrial life, implying that this conclusion is science when it actually is problematic speculation.


 

The latest issue of the popular science magazine, Discover,[i]  contains an article titled “Everything Worth Knowing About Evolution.” The article begins by claiming that over 350 million years ago our fish ancestors traded aquatic for terrestrial life, implying that this conclusion is science when it actually is problematic speculation. The article includes four illustrations that were drawn to portray the theory of evolution from sea to land. The problem is, the illustrations look like four separate modern day creatures and show little evidence of gradual evolution from the first drawing to the last one. One could take four living animals, which it looks like the artist did, and produce a very similar set of pictures.

Photos of humpback whale with calf courtesy Illustra Media / Dave Anderson

The confidence of the headline is shattered when one reads the article. For example, the author admits that “The tetrapods’ move to land has long been one of the great evolutionary puzzles” and then added “Researchers have yet to find the species that can link early fishapods with fully terrestrial tetrapods.” This theory of evolution from water to land is proposed only because, since life is presumed to have first evolved in the water, and life now abundantly exists on land, in spite of the lack of evidence, life must have evolved from water to land.

The tetrapods’ move to land has long been one of the great evolutionary puzzles.

The only presumed physical evidence of evolution from water to land is fossil bones, not visceral organs, which means that we have only a small percent of the putative physical evidence. Furthermore, the fossil evidence that we have is rarely a complete skeleton. Most often it consists of bone fragments that have to be assembled, which itself is a daunting task. It is true that organs and organ systems can be inferred from bones, but this process is very problematic. As a result, conflicting interpretations exist among scholars.

The alleged sequence is largely artistic license. Illustration courtesy Illustra Media.

After marine life evolved to become terrestrial, evolutionists postulate that terrestrial animals evolved to again become marine life, such as the cetaceans including whales. Again, the theory is postulated only because the alternatives, such as aquatic fish evolving into whales, is even more problematic. The problem of terrestrial mammals re-evolving into marine life is enormously problematic. Although Professor Pyenson,[ii] Curator of Fossil Marine Mammals at the Smithsonian, wrote, the “evolution of cetaceans is one of the best examples of macroevolution documented from the fossil record,” when we analyze the changes required in the anatomy and physiology, clear problems are obvious.

One obvious example is that the body size changes required to evolve from a small terrestrial mammal to a whale are enormous—from a 50-pound dog-sized animal to a 300,000-pound sea animal, or 6,000 times larger, and from an animal a few feet long to a 100-foot-long animal. The tongue of a blue whale alone weighs as much as an elephant. Changes required to evolve from a land to a sea animal require not only size modifications, but major design changes in every body organ and structure.

Illustration courtesy Illustra Media.

For example, the heart size increase requires evolving a heart from the size of a human fist to one close to the size of a Volkswagen Beetle. The heart valves would have to evolve from those smaller than the size of a dime to the size of an automobile tire rim. A human heart beats about 70 times a minute, a whale heart only nine times a minute, but the force of each beat is many times stronger in a whale than that in humans. This requires major design changes in the entire circulatory system. The fact is, “How and why baleen [and other whales] evolved is one of the greatest mysteries of marine mammal evolution, with even Charles Darwin himself speculating upon its beginnings in his On the Origin of Species.”[iii]


[i] Gemma Tarlach. When we left the Water. Discover Magazine. July-August, 2017, pp. 44-47.

[ii] Nicholas Pyenson. 2017. The Ecological Rise of Whales Chronicled by the Fossil Record. Current Biology. 27(11):R558-R564.

[iii] Felix Georg Marx, David Hocking, And Travis Park. 2016. The evolution of the baleen in whales. https://phys.org/news/2016-11-evolution-baleen-whales.html. November.

Resource: Creation-Evolution Headlines https://crev.info/

 

JERRY BERGMAN  It has long been believed that the sperm tail is a very simple structure, mostly a tail that wags to propel the sperm forward to reach the egg. Textbooks pictured this structure as a simple string like filament much thinner than a human hair. It was observed that the sperm tail produced harmonic bending waves, thus they were said to cause the sperm to swim like a tadpole. The bigger question then was, what was in the sperm head?


 

It has long been believed that the sperm tail is a very simple structure, mostly a tail that wags to propel the sperm forward to reach the egg. Textbooks pictured this structure as a simple string like filament much thinner than a human hair. It was observed that the sperm tail produced harmonic bending waves, thus they were said to cause the sperm to swim like a tadpole. The bigger question then was, what was in the sperm head?

Ideas about how sperm cells work date from their discovery by Leeuwenhoek in the 17th century. It was once widely believed that there exists a little person inside of every sperm cell head that traveled to the mother’s womb. The womb’s only role was to feed the child as it grew into a baby. This view was called preformationism. Another preformationist idea held that it was the egg that contained a little person that would begin to grow into a baby once the sperm initiated conception.

Preformationist view vs modern structural discoveries

When it was recognized that the formation of a child required both a sperm (the smallest cell in the body) and an egg (the largest cell in the body), it was realized that reproduction was far more complex than once thought. Next, the parts of the sperm were studied. Researchers observed that the head contained mostly 23 haploid chromosomes. The first part of the tail, they found, contained mitochondria, the powerhouses of the cell that produce ATP. The rest of the tail consisted of a long thread-like structure. That ‘simple’ thread, the tail, is at last now being revealed by more detailed observations, and it turns out to be amazingly complex!

Research around 1968 proved that the sperm tail—properly called a flagellum—consists of a complex system of sliding filaments that are connected by elastic springs resembling cylinder-like structures. The cross-linked filament bundles, found both in cilia and flagella, are ubiquitous in life. Scientists also found evidence that this system contains a scaffold, the function of which is to enable the sperm to swim in the hostile environment necessary to reach the egg in the Fallopian tube. It was also discovered that the basic sperm tail design is very similar in most animal species. No evidence was found for it having evolved from a simple structure in primitive animals to a complex structure in higher animals.

The Latest Wiggle

New research published in 2017 has discovered that the tail system is far more complex than thought 50 years ago. The front design is vital to transmit information to distant parts of the tail to enable it to function as an effective unit for steering and propelling the sperm to its end goal.[i] The system works by complex elasto-hydrodynamics that we can only briefly outline here. Each tail is programmed to produce slightly different movements in order for the sperm to reach the egg. Scientists learned some of the details of this system partly by physically moving parts of dead sperm tails and designing mathematical models of the motion.

Any one movement in this complex sequence appears to be able to trigger motion right through to the distant parts of the tail.

One mechanism is counter-bending of a passive flagellum that instigates a compensatory counter-curvature in the section that it is connected to.[ii] The researchers found that movement, which begins near the sperm’s head, is transmitted along the interconnected system, creating controlled oscillatory movement along the tail’s full length.[iii]  The tail “utilizes interconnected elastic spring structures to transmit mechanical information from the front to the distant parts of the tail, helping it to bend appropriately and ultimately swim toward an egg.”[iv]

The sections within the tail communicate by sensing the front of the tail near the section that contains the mitochondria. Each section in turn responds to information in front of it to synchronize their motions. The sperm tail mechanism first creates a sliding motion between the filaments inside the cylindrically arranged structure, producing the tail bending. Movement in this complex sequence triggers motion down to the distant parts of the tail. Even with these revelations, researchers are only beginning to understand what goes on. Phys.org says,

“The mechanism of a sperm tail first creates a sliding motion between filaments, inside this cylindrically arranged structure, finally resulting in a tail bending, a bit like the piston that converts back and forth motion in to [sic] rotation of the wheel on a train. Any one movement in this complex sequence appears to be able to trigger motion right through to the distant parts of the tail.

“The big question now is, are particular springs in the tail coupled-up to transmit specific biomechanical information, and just [do] these ‘rowers’ self-organize?

It turns out that the design of the sperm tail is just as complex as the design of the bacteria flagellum, which is well known to Darwin skeptics as an icon of intelligent design. Both are complex well-designed structures, one located on a so-called simple primitive organism, and the other on the sperm of the most complex organism known, namely humans.

This example illustrates a trend in biology. When structures do not seem very difficult to evolve, further research shows them to be far more complex and, consequently, much more difficult to explain by unguided evolution. What appear to be simple structures, such as sperm tails, on further investigation are shown to be far more complex, requiring a good understanding of biomechanics, especially elasto-hydrodynamics.

If Darwin were alive today, would he still try to explain such complex phenomena with his theory of gradual transmutation via natural selection? In 1859, when he suggested that all life was the result of slow, gradual variations (now thought to come from genetic mistakes), he could not have known the intricacies of sexual reproduction down to the tip of a sperm tail. Those who know today have no such excuse.

[i] “The mechanical properties of sperm tails revealed,” https://phys.org/news/2017-05-mechanical-properties-sperm-tails-revealed.html

[ii] Coy, Rachel and Hermes Gadêlha. 2017. The counterbend dynamics of cross-linked filament bundles and flagella, Journal of the Royal Society Interface. 14(130):1-10. May 31.

rsif.royalsocietypublishing.org/lookup/doi/10.1098/rsif.2017.0065

[iii] Phys.org, Ibid.

[iv] Phys.org, Ibid.

Resource: Creation-Evolution Headlines https://crev.info

ADNAN OKTAR   The theory of evolution claims that a particular species transforms into a brand-new species with very small changes. However, to prove such a claim it is necessary to find proof of these transitional species with the aforementioned changes and to present them as scientific evidence. 


 

The theory of evolution claims that a particular species transforms into a brand-new species with very small changes. However, to prove such a claim it is necessary to find proof of these transitional species with the aforementioned changes and to present them as scientific evidence. The alleged transitional species must originate from an imaginary ancestor species and possess new developing organs, systems or limbs. However, such imaginary transformations, which involve trial and error and are claimed to have lasted for millions of years, will result in an unsuccessful transitional species with half-limbs or missing organs. It is interesting that THERE IS NOT EVEN A SINGLE TRANSITIONAL FORM in the fossil record that would bear witness to such changes. Contrary to the expectations of evolutionists, the fossil record is instead full of species with intact and complete organs and systems. This shows us that the millions of species we have witnessed so far all had the same characteristics 100 million years ago.

There is NO CHAOS in the fossil records

It can be expected that a world governed by coincidences would bring along chaos as well. In such an imaginary system, it is impossible for species to have symmetry or aesthetics. Even the existence of life itself would be impossible in a world prevailed by coincidences. Mutations, claimed to be the so-called mechanism of evolution, lead to distortions and deficiencies in DNA, and as a result, distorted and irregular structures, defects in organs and systems occur. According to the claim of evolution, we should frequently encounter fossil samples of different species that have undergone mutation, and therefore have not survived and went extinct. However, there is not even a single sample of it.

This fact, posing a problem for the evolutionists, was first admitted by Charles Darwin:

“Why if species have descended from other species by insensibly fine gradations, do we not everywhere see INNUMERABLE transitional forms? Why is not all nature in CONFUSION instead of the species being, as we see them, WELL DEFINED?” (Charles Darwin, The Origin of Species, p.108)

Despite being the founder of the theory, Darwin admitted that the fossils, witnessing the history of life, were not confusing and that the fossils were perfectly in order. Strange- looking transitional species have never existed throughout history. The very moment a species appeared in the fossil record, they had intact organs and symmetrical limbs.

There is no such thing as “Innumerable Transitional Species”

We always find fossil samples of complete and intact species in the fossil record. Some of them belong to species that emerged with perfect limbs and organs, and then went extinct, and some belong to existent species that emerged millions of years ago with their perfect and present appearance. As claimed by evolutionists, the intermediate forms, which developed intermediate features that proved to be disadvantageous and caused the extinction of that species, certainly do not exist. The fossil record offers NOT A SINGLE FOSSIL OF AN INTERMEDIATE FORM.

According to the claim of evolution, the number of imaginary transitional species is supposed to be geometric multiples of the number of species known today. The so-called evolutionary tree must be full of unsuccessful species and must have innumerable subsections that have ceased to exist. This number could have been expressed in the trillions. Charles Darwin always emphasized that the amount of transitional species, which he hoped for but never found its existence, is INNUMERABLE:

INNUMERABLE transitional forms must have existed, why we not find them embedded in COUNTLESS NUMBERS IN THE CRUST OF THE EARTH?.. Why then is not EVERY GEOLOGICAL FORMATION AND EVERY STRATUM full of such intermediate links?” (Charles Darwin, The Origin of Species, p.172-280)

As Darwin pointed out, if the claim of evolution were true, almost every geological stratum would be full of such unsuccessful attempts, namely strange-looking transitional forms. These imaginary transitional life forms, trillions of which should be found in every fossil layer thus far excavated, should have been encountered by now; however, the situation is exactly the opposite. Fossils refute evolution by not showing a single transitional form.

The fact that species have remained unchanged

Paleontology, the study of fossils, reveals that species have not changed and have always remained stable throughout the time they remained on earth. The famous evolutionist paleontologist Niles Eldredge also stated that this is an undeniable fact:

Stasis is now abundantly well documented as the preeminent paleontological pattern in the evolutionary history of species. (Niles Eldredge, Reinventing Darwin, 1995, p. 77 – http://bevets.com/equotese.htm)

It is an obvious fact that species emerged on the earth fully developed and have remained unchanged throughout their existence. This is a situation that can never be contradicted by any paleontologist and is always confessed. One of the leading evolutionists, American paleontologist and science historian Stephen Jay Gould, wrote the following about these two most prominent features of the fossil record:

The history of most fossil species includes two features particularly inconsistent with gradualism:

(1) Stasis. Most species exhibit no directional change during their tenure on earth. They appear in the fossil record looking much the same as when they disappear; morphological change is usually limited and directionless.

(2) Sudden appearance. In any local area, a species does not arise gradually by the steady transformation of its ancestors; it appears all at once and ‘fully formed.’ (S. J. Gould, “Evolution’s Erratic Pace”, Natural History, vol. 86, May 1977)

Gould again continues his confessions in an article in the Natural History magazine as follows:

Statis, or non-change of most fossil species during their lengthy geological lifespans, was tacitly acknowledged by all paleontologists, but almost never studied explicitly… The overwhelming prevalence of stasis became an embarrassing feature of the fossil record, but left as a manifestation of nothing (that is, non-evolution). (S.J. Gould, “Cordelia’s Dilemma,” Natural History, 1993, p. 15)

 

Atlas of Creation and Fossils Say ‘We Have Not Changed’

As is seen, comparing fossils with their living counterparts and showing that they have not undergone any change is nothing but disclosing a well-known fact to the public. This fact, which has always been withheld from the public, reached and was spread to the public at large through the Atlas of Creation, the magnum opus of the author Adnan Oktar, writing under the pen name Harun Yahya. Paleontology has shown that species do not emerge slowly in millions of years as claimed, but that they emerge miraculously, in their perfect forms. With the work of Mr. Adnan Oktar, the findings and fossils that have been hidden from the public for so many years have been revealed at last and the secrets of the evolutionists have been shown for all the world to see.

Although this extraordinary piece of work exhibits only about 2,000 fossils in detailed photographs, the number of classified fossils that are stored in repositories in universities or in museums with date tags, is about 700 million. The fact that some evolutionists, who feel upset about these facts write stories about merely three or four fossils out of the thousands mentioned in the Atlas and try to make unfair criticisms shows just how desperate they actually are. These criticisms are far from being scientific and typically do not go beyond ill-advised sarcasm as obviously, in the scientific literature, there are thousands of other examples of the fossils in question.

Seeking Imaginary Ancestors through Mathematics

Evolutionists claim that humans share a common ancestor with chimpanzees. Speculations go on and on, one day claiming that chimpanzees are closer to humans, and the next the bonobos. While there is no evidence of any transformation, according to what exactly can Darwinists establish a relationship between those two? At this point, evolutionists produce statistical formula that they invented from scratch and which have no scientific validity.

The deception here is based on the comparison of some selected base-pairs of specific genes of the two species. Here it should not be assumed that all the codes of the two species’ genomes have been compared one by one. This fact is better understood when we examine this trick used to create the imaginary family tree:

When studies of genetic similarity between man and apes are conducted, only certain genes are compared. For example, while drawing the family tree of living primates, 34,927 base pairs of 54 genes were considered.[1] There are about 25,000 genes in the human body and not all of them are compared here.

Evolutionists initially claimed that there is a 1% difference between the chimpanzee and the human genome, but later this difference was generally accepted as 4%; this rate corresponds to about 35 million nucleotides. Evolutionists are in search of an imaginary mechanism in which this difference is made up. Therefore, they suggest mutations that altered the DNA, added or subtracted codes, all of which would completely harm the organism. They claim that history worked backwards like this and that mutations worked regularly, and had only beneficial effects all the time- which in fact is impossible – and thus they make fake calculations about the dates when the two species may have split. There is no fossil of the imaginary common ancestor, and there are no intermediate species either; nevertheless, evolutionists present calculations, which do not have scientific validity, as if they are true under the rubric of “prediction” to the public. The imaginary data, entered into a computer on the basis of this claim, is executed under the name of the Bayes formula and the lie that they can reach out to their imaginary common ancestor that existed some five to seven million years ago as a result of the calculations made through this imaginary data, is put forth.

 

The Bayesian Approach in Statistics and Scientific Errors Arisen from Presupposition

The Bayesian formula used in some statistical calculations enables a retrospective analysis of a particular claim. The Bayesian formula is used to calculate conditional probabilities. So if a person claims that ‘two species were derived from a common ancestor’, the formula works to verify this fake hypothesis and calculates how many millions of years must elapse to make up the 35 million nucleotide difference. In reality, however, the 35 million nucleotide difference has never been made up, but the formula provides a result because the claim is entered in this way. Therefore, the Bayesian approach is regarded as a scale of a person’s belief for any fact rather than physical evidence.

As we can see, the gaps in the genes are closed in the minds through computer formulas, and the history of life is arbitrarily written. It is evident that such studies, carried out through the postulate of ‘evolution exists’, have no scientific aspect and completely serve ideological purposes. This mentality, which is far from being able to explain how even a single gene, encoded with information, emerged by itself, uses genetics as a cover.

Paleontology, histology, biochemistry and all other branches of science reveal that life is so complex that it is not possible for it to have come about by pure chance. All species, a single cell – and even a single protein belonging to these species – constitute indisputable proof for the infinite knowledge and power of God.

 

[1] A Molecular Phylogeny of Living Primates Perelman P, Johnson WE, Roos C, Seuánez HN, Horvath JE, et al. (2011) A Molecular Phylogeny of Living Primates. PLOS Genetics 7(3): e1001342.https://doi.org/10.1371/journal.pgen.1001342

FAZALE RANA  Why do I think God exists? In short: The elegance, sophistication, and ingenuity of biochemical systems—and their astonishing similarity to man-made systems—convinces me that God is responsible for life’s origin and design.

While many skeptics readily acknowledge the remarkable designs of biochemical systems, they would disagree with my conclusion about God’s existence. Why? Because for every biochemical system I point to that displays beauty and elegance, they can point to one that seems to be poorly designed. In their view, these substandard designs reflect life’s evolutionary origin. They argue that evolutionary mechanisms kludged together the cell’s chemical systems through a historically contingent process that co-opted preexisting systems, cobbling them together to form new biochemical systems.

According to skeptics, one doesn’t have to look hard to find biochemical systems that seem to have been put together in a haphazard manner, and DNA replication appears to be an example of this. In many respects, DNA replication lies at the heart of the cell’s chemical operations. If designed by a Creator, this biochemical system, above all others, should epitomize intelligent design. Yet the DNA replication process appears to be unwieldy, inefficient, and unduly complex—the type of system evolution would generate by force, not the type of system worthy to be designated the product of the Creator’s handiwork.

Yet new work by Japanese researchers helps explain why DNA replication is the way it is.1 Instead of reflecting the cumbersome product of an unguided evolutionary history, the DNA replication process displays an exquisite molecular logic.

To appreciate the significance of the Japanese study and its implication for the creation/evolution controversy, a short biochemistry primer is in order. For readers who are familiar with DNA’s structure and the DNA replication process, you can skip the next two sections.

DNA

DNA consists of chain-like molecules known as polynucleotides. Two polynucleotide chains align in an antiparallel fashion to form a DNA molecule. (The two strands are arranged parallel to one another with the starting point of one strand in the polynucleotide duplex located next to the ending point of the other strand and vice versa.) The paired polynucleotide chains twist around each other to form the well-known DNA double helix. The cell’s machinery forms polynucleotide chains by linking together four different subunit molecules called nucleotides. The nucleotides used to build DNA chains are adenosine, guanosine, cytidine, and thymidine, famously abbreviated A, G, C, and T, respectively.

The nucleotide molecules that make up the strands of DNA are, in turn, complex molecules consisting of both a phosphate moiety, and a nucleobase (either adenine, guanine, cytosine, or thymine) joined to a 5-carbon sugar (deoxyribose).

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Image 1: Adenosine Monophosphate, a Nucleotide

Repeatedly linking the phosphate group of one nucleotide to the deoxyribose unit of another nucleotide forms the backbone of the DNA strand. The nucleobases extend as side chains from the backbone of the DNA molecule and serve as interaction points when the two DNA strands align and twist to form the double helix.
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Image 2: The DNA Backbone

When the two DNA strands align, the adenosine (A) side chains of one strand always pair with thymidine (T) side chains from the other strand. Likewise, the guanosine (G) side chains from one DNA strand always pair with cytidine (C) side chains from the other strand.

DNA Replication

Biochemists refer to DNA replication as a template-directed, semi-conservative process. By template-directed, biochemists mean that the nucleotide sequences of the “parent” DNA molecule function as a template, directing the assembly of the DNA strands of the two “daughter” molecules. By semi-conservative, biochemists mean that after replication, each daughter DNA molecule contains one newly formed DNA strand and one strand from the parent molecule.

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Image 3: Semi-Conservative DNA Replication

Conceptually, template-directed, semi-conservative DNA replication entails the separation of the parent DNA double-helix into two single strands. By using the base-pairing rules, each strand serves as a template for the cell’s machinery to use when it forms a new DNA strand with a nucleotide sequence complementary to the parent strand. Because each strand of the parent DNA molecule directs the production of a new DNA strand, two daughter molecules result. Each one possesses an original strand from the parent molecule and a newly formed DNA strand produced by a template-directed synthetic process.

DNA replication begins at specific sites along the DNA double helix, called replication origins. The DNA double helix unwinds locally at the origin of replication to produce what biochemists call a replication bubble. The bubble expands in both directions from the origin during the course of DNA replication. Once the individual strands of the DNA double helix unwind and are exposed within the replication bubble, they are available to direct the production of the daughter strand. The site where the DNA double helix continuously unwinds is called the replication fork. Because DNA replication proceeds in both directions away from the origin, there are two replication forks within each bubble.

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Image 4: DNA Replication

DNA replication can only proceed in a single direction, from the top of the DNA strand to the bottom. Because the strands that form the DNA double helix align in an antiparallel fashion with the top of one strand juxtaposed to the bottom of the other strand, only one strand at each replication fork has the proper orientation (bottom-to-top) to direct the assembly of a new strand, in the top-to-bottom direction. For this strand—referred to as the “leading strand”—DNA replication proceeds rapidly and continuously in the direction of the advancing replication fork.

DNA replication can’t proceed along the strand with the top-to-bottom orientation until the replication bubble has expanded enough to expose a sizable stretch of DNA. When this happens, DNA replication moves away from the advancing replication fork. DNA replication can only proceed a short distance for the top-to-bottom oriented strand before the replication process has to stop and wait for more of the parent DNA strand to be exposed. When a sufficient length of the parent DNA template is exposed for a second time, DNA replication can proceed again, but only briefly before it has to stop again and wait for more DNA to be exposed. The process of discontinuous DNA replication takes place repeatedly until the entire strand is replicated. Each time DNA replication starts and stops, a small fragment of DNA is produced. Biochemists refer to these pieces of DNA (that will eventually comprise the daughter strand) as “Okazaki fragments,” named after the biochemist who discovered them. Biochemists call the strand produced discontinuously the “lagging strand,” because DNA replication for this strand lags behind the more rapidly produced leading strand.

One additional point: The leading strand at one replication fork is the lagging strand at the other replication fork, since the replication forks at the two ends of the replication bubble advance in opposite directions.

Before the newly formed daughter strands can be produced, a small RNA primer must be produced. The protein that synthesizes new DNA by reading the parent DNA template strand—DNA polymerase—can’t start production from scratch. It has to be primed. A massive protein complex, called the primosome, which consists of more than 15 different proteins, produces the RNA primer needed by DNA polymerase.

Once primed, DNA polymerase will continuously produce DNA along the leading strand. However, for the lagging strand, DNA polymerase can only generate DNA in spurts to produce Okazaki fragments. Each time DNA polymerase generates an Okazaki fragment, the primosome complex must produce a new RNA primer.

Once DNA replication is completed, the RNA primers are removed from the continuous DNA of the leading strand and the Okazaki fragments that make up the lagging strand. A protein called a 3’–5’ exonuclease removes the RNA primers. A different DNA polymerase fills in the gaps created by the removal of the RNA primers. Finally, a protein called a ligase connects all the Okazaki fragments together to form a continuous piece of DNA out of the lagging strand.

DNA Replication and the Case for Evolution

This cursory description of DNA replication clearly illustrates the complexity of this biochemical operation. (Many details of the process were left out of the discussion.) This description also reveals why biochemists view this process as cumbersome and unwieldy. There is no obvious reason why DNA replication proceeds as a semi-conservative, RNA primer-dependent, unidirectional process involving leading and lagging strands to produce DNA daughter molecules. Because of this uncertainty, skeptics view DNA replication as a chance outcome of a historically contingent process, kludged together from the biochemical leftovers of the RNA world.

If there is one feature of DNA replication that is responsible for the complexity of the process, it is the directionality of DNA replication—from top to bottom. At first glance, it would seem as if the process would be simpler and more elegant if replication could proceed in both directions. Skeptics argue that the fact that it doesn’t reflects the evolutionary origin of the replication process.

Yet work by the team from Sapporo, Japan indicates that there is an exquisite molecular rationale for the directionality of DNA replication.

Why DNA Replication Proceeds in a Single Direction

These researchers recognized an important opportunity to ask why DNA replication proceeds only in a single direction with the discovery of a class of enzymes that add nucleotides to the ends of transfer RNA (tRNA) molecules. (tRNA molecules ferry amino acids to the ribsosome during protein synthesis.) If damaged, tRNA molecules cannot properly carry out their role in protein production. Fortunately, there are repair enzymes that can fix damaged tRNA molecules. One of them is called Thg-1-like protein (TLP).

TLP adds nucleotides to damaged ends of tRNA molecules. But instead of adding the nucleotides top to bottom, the enzyme adds these subunit molecules to the tRNA bottom to top, the opposite direction of DNA replication.

By determining the mechanism employed by TLP during bottom-to-top nucleotide addition, the researchers gained important insight into the constraints of DNA replication. As it turns out, bottom-to-top addition is a much more complex process than the normal top-to-bottom nucleotide addition. Bottom-to-top addition is a cumbersome two-step process that requires an enzyme with two active sites that have to be linked together in a precise way. In contrast, top-to-bottom addition is a simple, one-step reaction that proceeds with a single active site. In other words, DNA replication proceeds in a single direction (top-to-bottom) because it is mechanistically simpler and more efficient.

One could argue that the complexity that arises by the top-to-bottom DNA replication process is a trade-off for a mechanistically simpler nucleotide addition reaction. Still, if DNA replication proceeded in both directions the process would be complex and unwieldy. For example, if replication proceeded in two directions, the cell would require two distinct types of primosomes and DNA polymerases, one set for each direction of DNA replication. Employing two sets of primosomes and DNA polymerases is clearly less efficient than employing a single set of enzymes.

Ironically, if DNA replication could proceed in two directions, there still would be a leading and a lagging strand. Why? Because bottom-to-top replication is a two-step process and would proceed more slowly than the single step of top-to-bottom replication. In other words, the assembly of the DNA strand in a bottom-to-top direction would lag behind the assembly of the DNA strand that traveled in a top-to-bottom direction.

Bidirectional DNA replication would also cause another complication due to a crowding effect. Once the replication bubble opens, both sets of replication enzymes would have to fit into the replication bubble’s constrained space. This molecular overcrowding would further compromise the efficiency of the replication process. Overcrowding is not an issue for unidirectional DNA replication that proceeds in a top-to-bottom direction.

The bottom line: In light of this new insight, it is hard to argue that DNA replication has been cobbled together via a historically contingent pathway. Instead, it is looking more and more like a process ingenuously designed by a Divine Mind.

 

ADNAN OKTAR  The basic structural unit of creatures, the cell, is incredibly complex enough to leave people amazed. Just like the existence of a single cell, the harmony and cooperation in the cell is very impressive. As the structure of the cell and systems in it are further investigated and new details are found, this perfect order is seen more clearly.

FAZALE RANA  Before joining Reasons to Believe in 1999, I spent seven years working in R&D at a Fortune 500 company, which meant that I spent most of my time in a chemistry laboratory alongside my colleagues trying to develop new technologies with the hope that one day our ideas would become a reality, making their way onto store shelves.

From time to time, my work would be interrupted by an urgent call from one of our manufacturing plants. Inevitably, there was some crisis requiring my expertise as a chemist to troubleshoot. Often, I could solve the plant’s problem over the phone, or by analyzing a few samples sent to my lab. But, occasionally, the crisis necessitated a trip to the plant. These trips weren’t much fun. They were high pressure, stressful situations, because the longer the plant was offline, the more money it cost the company.

But, once the crisis abated, we could breathe easier. And that usually afforded us an opportunity to tour the plant.

It was a thrill to see working assembly lines manufacturing our products. These manufacturing operations were engineering marvels to behold, efficiently producing high-quality products at unimaginable speeds.

The Cell as a Factory

Inside each cell, an ensemble of manufacturing operations exists, more remarkable than any assembly line designed by human engineers. Perhaps one of the most astounding is the biochemical process that produces proteins—the workhorse molecules of life. These large complex molecules work collaboratively to carry out every cellular operation and contribute to the formation of all the structures within the cell.

Subcellular particles called ribosomes produce proteins through an assembly-line-like operation, replete with sophisticated quality control checkpoints. (As discussed in The Cell’s Design, the similarity between the assembly-line production of proteins and human manufacturing operations bolsters the Watchmaker argument for God’s existence.)

Ribosomes

About 23 nanometers in diameter, ribosomes play a central role in protein synthesis by catalyzing (assisting) the chemical reactions that form the bonds between the amino acid subunits of proteins. A human cell may contain up to half a million ribosomes. A typical bacterium possesses about 20,000 of these subcellular structures, comprising one-fourth the total bacterial mass.

Two subunits of different sizes (comprised of proteins and RNA molecules) combine to form a functional ribosome. In organisms like bacteria, the large subunit (LSU) contains 2 ribosomal RNA (rRNA) molecules and about 30 different protein molecules. The small subunit (SSU) consists of a single rRNA molecule and about 20 proteins. In more complex organisms, the LSU is formed by 3 rRNA molecules that combine with around 50 distinct proteins and the SSU consists of a single rRNA molecule and over 30 different proteins. The rRNAs act as scaffolding that organizes the myriad ribosomal proteins. They also catalyze the chain-forming reactions between amino acids.

Ribosomes Make Ribosomes

Before a cell can replicate, ribosomes must manufacture the proteins needed to form more ribosomes—in fact, the cell’s machinery needs to manufacture enough ribosomes to form a full complement of these subcellular complexes. This ensures that both daughter cells have the sufficient number of protein-manufacturing machines to thrive once the cell division process is completed. Because of this constraint, cell replication cannot proceed until a duplicate population of ribosomes is produced.

Is There a Rationale for Ribosome Structure?

Clearly, ribosomes are complex subcellular particles. But, is there any rhyme or reason for their structure? Or are ribosomes the product of a historically contingent evolutionary history?

New work by researchers from Harvard University and Uppsala University in Sweden provides key insight into the compositional make up of ribosomes, and, in doing so, help answer these questions.1

As part of their research efforts, the Harvard and Uppsala University investigators were specifically trying to answer several questions related to the composition of ribosomes, including:

  1. Why are ribosomes made up of so many proteins?
  2. Why are ribosomal proteins nearly the same size?
  3. Why are ribosomal proteins smaller than typical proteins?
  4. Why are ribosomes made up of so few rRNA molecules?
  5. Why are rRNA molecules are so large?
  6. Why do ribosomes employ rRNA as the catalyst to form bonds between amino acids, instead of proteins which are much more efficient as enzymes?

Ribosome Composition Is Optimal for Efficient Production of Ribosomes

Using mathematical modeling, the Harvard and Uppsala University investigators discovered that if ribosomal proteins were larger, or if these biomolecules were variable in size, ribosome production would be slow and inefficient. Building ribosomes with smaller, uniform-size proteins represents the faster way to duplicate the ribosome population, permitting the cell replication to proceed in a timely manner.

These researchers also learned that if the ribosomal proteins were any shorter, inefficient ribosome production also results. This inefficiency stems from biochemical events needed to initiate protein production. If proteins are too short, then the initiation events take longer than the elongation processes that build the protein chains.

The bottom line: The mathematical modeling work by the Harvard and Uppsala University research team indicates that the sizes of ribosomal proteins are optimal to ensure the most rapid and efficient production of ribosomes. The mathematical modeling also determined that the optimal number of ribosomal proteins is between 50 to 80—the number of ribosomal proteins found in nature.

Ribosome Composition Is Optimal to Produce a Varied Population of Ribosomes

The insights of this work have bearing on the recent discovery that within cells a heterogeneous population of ribosomes exists, not a homogeneous one as biochemists have long thought.2 Instead of every ribosome in the cell being identical, capable of producing each and every protein the cell needs, a diverse ensemble of distinct ribosomes exists in the cell. Each type of ribosome manufactures characteristically distinct types of proteins. Typically, ribosomes produce proteins that work in conjunction to carry out related cellular functions. The heterogeneous makeup of ribosomes contributes to the overall efficiency of protein production, and also provides an important means to regulate protein synthesis. It wouldn’t make sense to use an assembly line to make both consumer products, such as antiperspirant sticks, and automobiles. In the same manner, it doesn’t make sense to use the same ribosomes to make the myriad proteins, performing different functions for the cell.

Because ribosomes consist of a large number of small proteins, the cell can efficiently produce heterogeneous populations of ribosomes by assembling a ribosomal core and then including and excluding specific ribosomal proteins to generate a diverse population of ribosomes.3 In other words, the protein composition of ribosomes is optimized to efficiently replicate a diverse population of these subcellular particles.

The Case for Creation

The ingenuity of biochemical systems was one of the features of the cell’s chemistry that most impressed me as a graduate student (and moved me toward the recognition that there was a Creator). And the latest work by researchers on ribosome composition from Harvard and Uppsala Universities provides another illustration of the clever way that biochemical systems are constructed. The composition of these subcellular structures doesn’t appear to be haphazard—a frozen accident of a historically contingent evolutionary process—but instead is undergirded by an elegant molecular rationale, consistent with the work of a mind.

The case for intelligent design gains reinforcement from the optimal composition of ribosomal proteins. Quite often, designs produced by human beings have been optimized, making this property a telltale signature for intelligent design. In fact, optimality is most often associated with superior designs.

As I pointed out in The Cell’s Design, ribosomes are chicken-and-egg systems. Because ribosomes are composed of proteins, proteins are needed to make proteins. As with ingenuity and optimality, this property also evinces for the work of intelligent agency. Building a system that displays this unusual type of interdependency requires, and hence, reflects the work of a mind.

On the other hand, the chicken-and-egg nature of ribosome biosynthesis serves as a potent challenge to evolutionary explanations for the origin of life.

The Challenge to Evolution

Because ribosomes are needed to make the proteins needed to make ribosomes, it becomes difficult to envision how this type of chicken-and-egg system could emerge via evolutionary processes. Protein synthesis would have to function optimally at the onset. If it did not, it would lead to a cycle of auto-destruction for the cell.

Ribosomes couldn’t begin as crudely operating protein-manufacturing machines that gradually increased in efficiency—evolving step-by-step—toward the optimal systems, characteristic of contemporary biochemistry. If error-prone, ribosomes will produce defective proteins—including ribosomal proteins. In turn, defective ribosomal proteins will form ribosomes even more prone to error, setting up the auto-destruct cycle. And in any evolutionary scheme, the first ribosomes would have been error-prone.

The compositional requirement that ribosomal proteins be of the just-right size and uniform in length only exacerbates this chicken-and-egg problem. Even if ribosomes form functional, intact proteins, if these proteins aren’t the correct number, size, or uniformity then ribosomes couldn’t be replicated fast enough to support cellular reproduction.

In short, the latest insights in the protein composition of ribosomes provides compelling reasons to think that life must stem from a Creator’s handiwork.

 

 

If you were asked to guess the number of all trees in the world, what would your answer be? 10 million? 250 million? 250 billion? No, none of them is the answer. According to the latest researches, there are a total of 3.1 trillion trees in our world. This is quite a big number… In fact, you have to add 11 zeros next to the number of 3.1 to get this number.

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