It's Design all the way down III

The Puzzle of Perfection, Thirty Years On

Evolution News & Views July 31, 2015 3:18 AM 

Thirty years ago in his book Evolution: A Theory in Crisis, Michael Denton (above) posed "The Puzzle of Perfection" as a challenge to Darwinism. He described molecular machines in the cell as phenomena inexplicable by chance. He predicted that what was known in 1985 was sure to grow, concluding:

It would be an illusion to think that what we are aware of at present is any more than a fraction of the full extent of biological design. In practically every field of fundamental biological research ever-increasing levels of design and complexity are being revealed at an ever-increasing rate. The credibility of natural selection is weakened, therefore, not only by the perfection we have already glimpsed but by the expectation of further as yet undreamt of depths of ingenuity and complexity. (Denton, p. 82)

If the design argument is scientifically credible, it should get stronger with time. The counter-position of natural selection should correspondingly weaken. Was the perfection of cellular machines an illusion in 1985? Has Darwinian theory risen to the challenge in the meantime? Denton's prediction was made before details of ATP synthase, the bacterial flagellum, and kinesin had come to light (see Denton's 2014 description of kinesins and myosins here). And two recent papers suggest that, if anything, the evidence for design has only grown stronger.

The authors of the first paper, published in PNAS, seem hesitant to use the word "perfect" in their description of ATP synthase, the machine that generates energy currency for most cellular processes in all living things (see our animation of this amazing machine here). They use "near-perfect" in the title and throughout the paper:

ATP synthase produces most of the ATP in respiratory and photosynthetic cells. It is a rotary motor enzyme and its catalytic portion F₁-ATPase hydrolyzes ATP to drive rotation of the central γ subunit. Efficiency of chemomechanical energy conversion by this motor is always near-perfect under different ATP hydrolysis energy (ΔG_ATP) conditions. [Emphasis added.]

Any deviation from perfection, however, could be due to experimental error. In their graph, the error bars transverse the slope for 100 percent efficiency (that is, for conversion of chemical energy to mechanical work). It may well be as close to perfect as is physically possible. What's even more striking is that this "near-perfect" level of efficiency is maintained throughout a "broad range" of operation conditions.

The authors found a "simple" model that maintains this near-perfect efficiency. In the F₁ subunit of ATP synthase, where ATP is synthesized or dissociated (depending on the direction of energy flow), they deduced a spring mechanism that generates a "sawtooth" pattern of mechanical work. The spring automatically adjusts for varying conditions:

The chemomechanical energy conversion efficiency of F1 is close to 100% under various ΔG_ATP conditions. The torque profile found here explains how F₁ achieves this remarkable task. Fig. 5C illustrates how F₁ responds to the increase of [ATP] andadjusts its mechanical work accordingly. The equilibrium constants for nucleotide bindings/dissociations are functions of the γ angle. Therefore, as [ATP] is increased, the angular position of binding/dissociation of ATP shifts to the left (Fig. 5C, red arrow) at the point where the spring is shorter. The shorter the spring becomes, the greater the force to extend becomes because of the nature of a spring (Fig. 5B). This shift invariably increases the area of the sawtooth, that is, the mechanical work. This study shows that the following two properties of the torque profile of the F₁ motor ensure ∼100% energy conversion under various ΔG_ATP conditions: (i) shift of the angular positions of binding/dissociation of substrates according to their concentrations and (ii) changing its force (torque) according to the angular position of substrate binding/dissociation, which isreadily accomplished by a simple spring.

Since each of three catalytic sites has this mechanism, there are three springs in the motor. The "sawtooth" is the torque profile, consisting of three steep jumps and linear descents during each catalytic turnover. The shape of the sawtooth adjusts according to concentration or binding angle because of spring-like action inside the machine. It is "simple" only in the author's model to explain the observations. But hey -- if a simple mechanism achieves perfection, who's complaining? The authors didn't disparage this complex machine's efficiency. They twice called it "remarkable." By the way, is anyone surprised to hear that neither Darwin nor evolution is mentioned in the paper?

Perfection in Gene Translation

The second paper explores the amazing process of gene translation. A set of twenty machines helps translate the genetic code into the protein code. It's a shame the set doesn't have a cool name. They are called the "amino-acyl tRNA synthetases." Fortunately, we can call them aaRS for short. Their job is to read the transfer-RNA (tRNA) triplet codons and charge them with the appropriate amino acids. When the charged tRNAs match up with the messenger RNA (mRNA) codons in the ribosome (if the aaRS's did their job accurately), the correct string of amino acids links up to build a protein. The aaRS enzymes are the keys to the genetic code. They link the DNA code to the protein code.

There are twenty normal amino acids in proteins, but 64 possible combinations of triplet codons from the four DNA bases. The aaRS enzymes have to be able to handle situations where one amino acid may correspond to one to six codons. Not all codons link up with equal ease (there may be reasons for that). That's enough to make an aaRS enzyme's job hard, but it also has to discriminate between similar amino acids, like valine and isoleucine. (Remember, molecular machines have no eyes. This occurs in the dark, by touch.) Additionally, the aaRS enzymes have to work fast.

The d-value is a measure of the system's accuracy, with the maximum representing perfect accuracy. But like the auto mechanic dealing with a frantic businessman with a repair emergency, there's a trade-off: "You want it done fast, or you want it done right?" Since d-values can vary by a factor of 400, some situations could bring translation to a halt if accuracy is of paramount concern.

A team of four from Uppsala University, also publishing in PNAS, examined this trade-off problem. They found that cells are much more clever providing both accuracy and speed than anyone knew 30 years ago. First, a little history from 1957:

The existence of maximal accuracy limits (d values) in amino acid discrimination by an amino acid-selecting protein wassuggested years ago by Linus Pauling. He proposed that these dvalues would be very small for pairs of similar amino acids. For discrimination between valine and isoleucine he estimated a dvalue of 10, leading to the proposal of high intracellular amino acid substitution error frequency, which turned out not to be true. We now know that Pauling greatly underestimated the d value by which the isoleucine-specific aa-tRNA synthetase (IleRS) discriminates against valine, but the notion of d-value limits for enzymatic selections has since continued to guide experimental research on replication, transcription, and genetic code translation.

In fact, the discovery of substrate proofreading was inspired by the challenge of how to transcend the accuracy limits postulated by Pauling.

So there you have it. The cell has a way to get both arms of the tradeoff. First, it goes as fast as it can. Then, other molecular machines proofread the result! Here is a clear case where the expectation of design perfection inspired a major discovery. Somehow, the author's Lamarckian explanation is unconvincing:

From our results we suggest that proofreading has evolved in bacterial protein synthesis to minimize damage on the bacterial proteome by amino acid substitution errors due to initial tRNA selection error hot spots as identified here and maybe others that remain to be found from larger datasets.

While one shares their hope that "future extensions will serve as an inspiration and testing ground for theoretical approaches to explain the accuracy of codon reading," approaches based on design theory are bound to be much more productive than evolutionary approaches that hope perfection might be reached by blind processes.

The Puzzle of Perfection, c. 2015

As these papers illustrate, Denton was right. His "expectation of further as yet undreamt of depths of ingenuity and complexity" has been amply fulfilled.

But it's not just seen in the realm of molecular machines. Throughout all biology -- from the tiniest bacterial cell to the greatest of multicellular organisms -- we see exceptional ingenuity and complexity of design.

Illustra's new film Living Waters includes a wonderful example of an "engineering problem" that was solved ingeniously in the male reproductive organs of the humpback whale. The testes would have had to move inside the body cavity when the whale supposedly evolved from a land mammal, but the heat inside would have killed sperm cells, causing sterility -- the end of the line in evolution. We don't want to give away the solution before you watch the film; suffice it to say that Biologic Institute evolutionary biologist Richard Sternberg, who studied the situation, calls it "an elegant solution to the problem; it's beautiful. It's anatomically complex."

In the film, Tim Standish shows another example of design perfection in salmon, which can discriminate odors at the level of parts per trillion, recalling combinations of odors they had memorized as juveniles.

As Sternberg concludes, the flip side of Darwin's proposal of natural selection as a designer substitute is that "things look designed -- because they are designed." Whether in a whale or a bacterial cell, "things look too optimal," he adds, "to have been cobbled together by some haphazard mechanism."

The invincible scroll II

The Bible—A Remarkable Story of Survival

THE Bible is the most widely distributed book in history—an estimated 4.8 billion copies have already been circulated. In 2007 alone, more than 64,600,000 copies were produced. To put that into perspective, consider that the best-selling work of fiction that year had an initial printing of 12 million copies in the United States.

On its way to becoming the world’s most published book, the Bible survived many hazards. Down through history, it has been banned and burned, and those who would translate it have been oppressed and killed. Yet, one of the greatest threats to the continued existence of the Bible was, not the sudden heat of persecution, but the slow process of decay. Why so?

The Bible is a compilation of 66 smaller books, the oldest of which were written or compiled over 3,000 years ago by members of the nation of Israel. The original writers and those who copied the texts recorded the inspired messages on perishable materials, such as papyrus and leather. None of the original writings have yet been discovered. But thousands of ancient copies of small and large sections of the books of the Bible have been unearthed. A fragment of one of these books, the Gospel of John, dates to within just a few decades of the original document written by the apostle John.

“The transmission of the text of the Hebrew Bible [Old Testament] is of extraordinary exactitude, without parallel in Greek and Latin classical literature.”—Professor Julio Trebolle Barrera

Why is it remarkable that any copies of the Bible have survived? And how accurately do modern Bibles reflect the messages recorded by the original writers?

What Happened to Other Ancient Documents?

The survival of the Bible is extraordinary, considering what happened to the writings of nations contemporary with the Israelites. The Phoenicians, for instance, were neighbors of the Israelites during the first millennium B.C.E. These sea traders spread their alphabetic writing system throughout the Mediterranean area. They also profited from an extensive papyrus trade with Egypt and the Greek world. Even so, the National Geographic magazine observes regarding the Phoenicians: “Their writings, mostly on fragile papyrus, disintegrated—so that we now know the Phoenicians mainly by the biased reports of their enemies. Although the Phoenicians themselves reportedly had a rich literature, it was totally lost in antiquity.”

What about the writings of the ancient Egyptians? The hieroglyphics they carved or painted on temple walls and elsewhere are well-known. The Egyptians are also famous for developing papyrus as a writing material. However, regarding Egyptian records written on papyrus, Egyptologist K. A. Kitchen says: “It has been estimated that some 99 percent of all papyri written from circa 3000 down to the advent of Greco-Roman times have perished completely.”

What about Roman records that were written on papyrus? Consider this example. According to the book Roman Military Records on Papyrus, Roman soldiers were apparently paid three times a year, and a record of the pay was made on papyrus pay vouchers. It is estimated that during the 300 years from Augustus (27 B.C.E.–14 C.E.) to Diocletian (284-305 C.E), there were 225,000,000 individual pay records. How many have survived? Only two have been found that are legible.

Why have so few ancient documents written on papyrus survived? Perishable materials, such as papyrus and another common writing material, leather, decay quickly in damp climates. The Anchor Bible Dictionary says: “Because of the climate, papyrus documents from this period [the first millennium B.C.E.] are likely to be preserved only if they are in a dry desert and in a cave or shelter.”

What About the Bible Texts?

The original Bible books were evidently written on material as fragile as that used by the Phoenicians, Egyptians, and Romans. Why, then, did the material contained in the Bible survive to become the world’s most published book? Professor James L. Kugel provides one reason. He says that the original writings were copied “many, many times even within the biblical period itself.”

How do modern translations of the Bible compare with ancient manuscripts? Professor Julio Trebolle Barrera, a member of the team of experts charged with studying and publishing the ancient manuscripts known as the Dead Sea Scrolls, says: “The transmission of the text of the Hebrew Bible is of extraordinary exactitude, without parallel in Greek and Latin classical literature.” Respected Bible scholar F. F. Bruce says: “The evidence for our New Testament writings is ever so much greater than the evidence for many writings of classical authors, the authenticity of which no one dreams of questioning.” He continues: “If the New Testament were a collection of secular writings, their authenticity would generally be regarded as beyond all doubt.” Certainly, the Bible is a remarkable book. Do you make time to read it each day.

On Jesus's resurrection body.

After Jesus’ Resurrection, Was His Body Flesh or Spirit?

The Bible’s answer

The Bible says that Jesus “was put to death in the flesh but made alive [resurrected] in the spirit.”—1 Peter 3:18; Acts 13:34; 1 Corinthians 15:45;2 Corinthians 5:16.

Jesus’ own words showed that he would not be resurrected with his flesh-and-blood body. He said that he would give his “flesh in behalf of the life of the world,” as a ransom for mankind. (John 6:51; Matthew 20:28) If he had taken back his flesh when he was resurrected, he would have canceled that ransom sacrifice. This could not have happened, though, for the Bible says that he sacrificed his flesh and blood “once for all time.”—Hebrews 9:11, 12.

If Jesus was raised up with a spirit body, how could his disciples see him?

• Spirit creatures can take on human form. For example, angels who did this in the past even ate and drank with humans. (Genesis 18:1-8; 19:1-3) However, they still were spirit creatures and could leave the physical realm.—Judges 13:15-21.
• After his resurrection, Jesus also assumed human form temporarily, just as angels had previously done. As a spirit creature, though, he was able to appear and disappear suddenly. (Luke 24:31; John 20:19, 26) The fleshly bodies that he materialized were not identical from one appearance to the next. Thus, even Jesus’ close friends recognized him only by what he said or did.—Luke 24:30, 31, 35; John 20:14-16; 21:6, 7.
• When Jesus appeared to the apostle Thomas, he took on a body with wound marks. He did this to bolster Thomas’ faith, since Thomas doubted that Jesus had been raised up.—John 20:24-29.