Why Darwin's God is the God of the gaps.

 

Francis Collins’s The Language of God 15 Years On

Jonathan Witt@JonathanRWitt

Francis Collins’s bestselling The Language of God turned 15 this year, and with the author back in the news, it’s a good time to review his case for theistic Darwinism and consider what 15 years of subsequent research have done to strengthen or undermine those arguments. 

He became a household name in 2000 when he and Craig Venter announced that their teams had together successfully mapped the 3.1 billion letters of the human genetic code. The Language of God appeared six years later, making a case for both Darwinian evolution and a transcendent Creator.

The evolution Collins argues for involves no direct intelligent input after the origin of the universe until the origin of humans, and yet he also makes a case for a specifically Christian theism, arguing not only for a Creator but also for the possibility of miracles, the deity of Christ, and a literal resurrection. He insists that a scientist can believe these articles of Christian doctrine without checking his brain at the door.

The mainstream media emphasized the book’s insistence that Darwinism is no threat to Christianity and that Darwinism explains a range of physical evidence better than does either creationism or intelligent design. But what has gone begging for ink is a feature of the work hidden in plain sight: Francis Collins makes a scientific case for intelligent design.

According to the theory of intelligent design, which extends from the origin of matter to the origin of mind, an intelligent cause is the best explanation for certain features of the natural world. In chapter nine Collins argues against intelligent design in biology, a point the media duly emphasized; but elsewhere he argues that an intelligent cause is the best explanation for certain other features of the natural world.

Collins’s Case for Cosmic Design

He begins Chapter 3, “The Origins of the Universe,” by reviewing 20th century discoveries in physics and cosmology, many of which reinforce Christian teaching. For example, whereas scientists of the 19th century generally believed that the universe was eternal, a growing body of evidence in the 20th century convinced them that the universe began about 14 billion years ago, a theory, Collins notes, nicely in harmony with the biblical doctrine of creation ex nihilo — that is, creation out of nothing.

The chapter then summarizes the fine-tuning problem. This is the growing body of evidence suggesting that the physical constants of nature (including gravity, electromagnetism, and the mass of the universe) are exquisitely calibrated to allow for complex and even advanced life. A very tiny difference in any of these and life in the universe would be impossible.

Collins lists the three live explanations for fine tuning: (1) There are a multitude of universes in addition to our own, perhaps an infinite number, and at least one, ours, was bound to have the right physical constants for advanced life; (2) We’re just incredibly lucky; and (3) The physical constants look fine tuned because they were fine tuned. That is, they were designed.

He put his money on the third one, the design hypothesis, and he supports that conclusion by appeals to physical evidence and standard methods of scientific reasoning. Regarding the two non-design options, 1 and 2, he says, “On the basis of probability, option 2 is the least plausible. That then leaves us with option 1 and option 3. The first is logically defensible, but this near-infinite number of unobservable universes strains credulity. It certainly fails Occam’s Razor.”

Lest his guarded language obscure the fact that he’s chosen door number three, he adds, “It could be argued … that the Big Bang itself seems to point strongly toward a Creator.”

His appeal to the Big Bang and the fine-tuned cosmos serves as one of his main design arguments in the book. We should pause and register the significance of this. In our present intellectual climate, where scientists have been harassed and even fired for advocating intelligent design, and the idea is routinely attacked in news stories and popular books by “new atheists” such as Richard Dawkins and Daniel Dennett, it’s no small matter that a bestselling book by the former head of the Human Genome Project, and subsequently the head of the National Institutes of Health, makes a scientific case for intelligent design.

Collins’s Flaw

Why hasn’t this garnered more media attention? In part because Collins accepts the misleading description of ID that many of its critics employ. According to them, intelligent design is a purely negative argument aimed primarily against biological evolution, and is coupled to a fallacious God-of-the-gaps theology.

These ID critics insist that design theorists poke holes in Darwinism and then, in a rush to judgment, insist that the holes prove that God designed life. More broadly, they claim that ID proponents supposedly argue from our present ignorance of any adequate material cause of certain natural phenomena directly to intelligent design.

But this isn’t so. Design theorists in biology do offer an extensive critique of Darwinian theory, including various contemporary variations on it, but they also offer positive evidence for intelligent design. They argue from our growing knowledge of the natural world (in biology, chemistry, physics, and cosmology), and from our knowledge of the only kind of cause known produce information or irreducibly complex machines (both found at the cellular level): intelligent agents.

Collins accuses design theorists of making arguments from ignorance, but actually it is Collins and other critics of intelligent design who do so when they make certain bad-design argument for blind evolution over against intelligent design. Collins does so, for instance, when he argues that the presence of “junk DNA” strongly suggests a blind evolutionary process rather than anything a divine engineer would have created. That argument rested on scientists’ ignorance of what purpose might be served by DNA that doesn’t code for proteins. But in the intervening years researchers have discovered numerous functional roles for this non-coding DNA. 

To his credit Collins eventually conceded that his use of the term “junk DNA” was misguided. “I’ve stopped using the term,” he told Wired magazine. And as biologist Jonathan Wells notes, “Since then, the evidence for function in non-protein-coding DNA has vastly increased. The first line of one recent article in a scientific journal is, “The days of ‘junk DNA’ are over.”

Chapter 3 of The Language of God contains another argument from ignorance. Collins refers to the “backward wiring” of the vertebrate eye, characterizing it as flawed from an engineering perspective because it forces light to pass through the nerves and blood vessels on its way to the eye’s light sensors. He says this bungled design is evidence for neo-Darwinism’s catch-as-catch-can evolutionary process, and evidence against the idea that a wise designer optimally engineered this organ. “The design of the eye does not appear on close inspection to be completely ideal,” he writes, and its imperfection seems “to many anatomists to defy the existence of truly intelligent planning of the human form.”

This is a favorite argument of Dawkins’s, and of Darwinists generally. However, geneticist Michael Denton and others have shown that the wiring improves oxygen flow, an important advantage not achievable by the tidier approach demanded by Dawkins. They have called attention to this point repeatedly, but The Language of God shows no evidence that Collins is aware of it. He neither addresses it nor so much as mentions it. (Dawkins and other Darwinists generally avoid discussing it.) In this case, then, it’s an argument from ignorance of why the vertebrate eye might benefit from “backward wiring,” and the ignorance appears almost willful.

Collins’s Flagellum

Collins also betrays unfamiliarity with the work of leading design theorists in the way he handles the scientific controversy surrounding a microscopic rotary engine called the bacterial flagellum. The flagellum is a favorite of design theorists because they are convinced that attempts to explain its origin apart from design are manifestly inadequate, and because images of the flagellum practically scream design.

In his book Darwin’s Black Box, Lehigh University biochemist Michael Behe made this sophisticated molecular machine famous by arguing that it was “irreducibly complex” and therefore evidence of design. He used the simple mechanism of a mousetrap as an example of irreducible complexity. If any part of the mousetrap is missing (the base, spring, hammer, holding bar, or catch), the trap cannot work. The mousetrap, then, is irreducibly complex. It is either complete, or it is not a functioning mousetrap.

In the same way, the bacterial flagellum, composed of dozens of protein machines, needs every one of them in place or it doesn’t work.

Here is how irreducible complexity relates to evolutionary theory: A conscious designer can pull together several non-functioning parts and assemble them into a functional whole, but blind evolution — which excludes intelligent guidance — must progress by one slight, random functional mutational improvement at a time. So how could such a process build an irreducibly complex motor one part at a time if the motor cannot propel at all until all its parts are in place?

Using the arguments of leading evolution apologist Kenneth Miller and others, Collins suggests that nature could have co-opted simpler molecular machines to create the bacterial flagellum, and he points to the “type three secretory apparatus” as evidence of such an indirect pathway (p. 192). But as it turns out, and as design theorists have emphasized, there are three crucial problems with this explanation.

One, the micro-syringe at best accounts for only ten proteins, leaving thirty or more unaccounted for; and these other thirty proteins are not found in any other living system. Second, as a wider body of literature suggests, the system probably developed after the more complicated flagellum, not the other way around.

Third, even if nature had on hand all the right protein parts to make a bacterial flagellum, something or someone would still need to assemble them in the precise temporal order the way cars are assembled in factories. How are such tasks presently accomplished? As biologist Scott Minnich and philosopher of science Stephen Meyer explain, “To choreograph the assembly of the parts of the flagellar motor, present-day bacteria need an elaborate system of genetic instructions as well as many other protein machines to time the expression of those assembly instructions.”

Collins never mentions any of this. In these and other instances, he comes across as having never engaged the best arguments for intelligent design in biology. To briefly note one other example, he muffs the issue of testability, mistakenly asserting that ID arguments are not testable.

These constitute significant weaknesses in Collins’s case against intelligent design, but as I will show tomorrow, perhaps the most glaring one is this: he flatly contradicts himself at crucial points.

Editor’s note: This essay is a substantially revised and updated version of a book review that first appeared in Touchstone Magazine.

Greek fire: a brief history.

 Greek fire was an incendiary weapon used by the Roman Empire beginning c. 666. Used to set fire to enemy ships, it consisted of a combustible compound emitted by a flame-throwing weapon. Some historians believe it could be ignited on contact with water, and was probably based on naphtha and quicklime. The Byzantines typically used it in naval battles to great effect, as it could supposedly continue burning while floating on water. The technological advantage it provided was responsible for many key Byzantine military victories, most notably the salvation of Constantinople from the first and second Arab sieges, thus securing the Empire's survival.

The impression made by Greek fire on the western European Crusaders was such that the name was applied to any sort of incendiary weapon, including those used by Arabs, the Chinese, and the Mongols. However, these mixtures used formulas different from that of Byzantine Greek fire, which was a closely guarded state secret. Byzantines also used pressurized nozzles to project the liquid onto the enemy, in a manner resembling a modern flamethrower.

Although usage of the term "Greek fire" has been general in English and most other languages since the Crusades, original Byzantine sources called the substance a variety of names, such as "sea fire" (Medieval Greek: πῦρ θαλάσσιον pŷr thalássion), "Roman fire" (πῦρ ῥωμαϊκόν pŷr rhōmaïkón), "war fire" (πολεμικὸν πῦρ polemikòn pŷr), "liquid fire" (ὑγρὸν πῦρ hygròn pŷr), "sticky fire" (πῦρ κολλητικόν pŷr kollētikón), or "manufactured fire" (πῦρ σκευαστόν pŷr skeuastón).

The composition of Greek fire remains a matter of speculation and debate, with various proposals including combinations of pine resin, naphtha, quicklime, calcium phosphide, sulfur, or niter. In his history of Rome, Titus Livy describes priestesses of Bacchus dipping fire into the water, which did not extinguish, "for it was sulphur mixed with lime."

Why I turned my back on the new Gods

 The human brain is hardwired for worship. Thus there are no atheists in the absolute sense. Even those claiming to be absolute atheists. We are only atheists with respect to our neighbors' Gods but each of us thinks of our own Gods as real,as worthy for reasons that satisfy us if not our associates.

One of the main reasons that I find the appeals of 'nontheists' so unpersuasive is that I once sacrificed at the altar of the Gods they are calling me to and forsook them on account of the superiority of the original God JEHOVAH. Nationalism (black nationalism to be specific),politics, money, intellectuals,chance and necessity,pleasure. They all failed to keep their promises.

One notable way that JEHOVAH has shown his superiority is that he is the only God who has taught his people to live in peace. If as God one cannot bring peace to ones own community of followers how can we trust you to bring peace universally.

Revelation15:4PHB"Who will not reverence you, LORD JEHOVAH, and glorify your name? For you alone are holy. Therefore, all the nations will come and will worship before you, because you are true.”

Minimalism with Chinese characteristics?

Tang ping (Chinese: 躺平; pinyin: tǎng píng; lit. 'lying flat') is a lifestyle choice and social protest movement in China by some young people in China who reject societal pressures for hard work or even overwork (such as the 996 working hour system, which is generally regarded as a rat race with ever diminishing returns), and instead choose to "lie down flat and get over the beatings" via a low-desire, more indifferent attitude towards life. Novelist Liao Zenghu described "lying flat" as a resistance movement, and The New York Times called it part of a nascent Chinese counterculture.

Unlike the hikikomori in Japan (who are socially withdrawn), these young Chinese people who subscribe to "lying flat" are not socially isolated, but merely choose to lower their ambitions and simplify their goals, still being fiscally productive for their own essential needs, and prioritize psychological health over materialism.

Wiliam Shakespeare: a brief history.

 William Shakespeare (bapt. 26 April 1564 – 23 April 1616) was an English playwright, poet, and actor, widely regarded as the greatest writer in the English language and the world's greatest dramatist. He is often called England's national poet and the "Bard of Avon" (or simply "the Bard"). His extant works, including collaborations, consist of some 39 plays, 154 sonnets, three long narrative poems, and a few other verses, some of uncertain authorship. His plays have been translated into every major living language and are performed more often than those of any other playwright. They also continue to be studied and reinterpreted.

Shakespeare was born and raised in Stratford-upon-Avon, Warwickshire. At the age of 18, he married Anne Hathaway, with whom he had three children: Susanna and twins Hamnet and Judith. Sometime between 1585 and 1592, he began a successful career in London as an actor, writer, and part-owner of a playing company called the Lord Chamberlain's Men, later known as the King's Men. At age 49 (around 1613), he appears to have retired to Stratford, where he died three years later. Few records of Shakespeare's private life survive; this has stimulated considerable speculation about such matters as his physical appearance, his sexuality, his religious beliefs, and whether the works attributed to him were written by others.

Shakespeare produced most of his known works between 1589 and 1613. His early plays were primarily comedies and histories and are regarded as some of the best work produced in these genres. He then wrote mainly tragedies until 1608, among them Hamlet, Romeo and Juliet, Othello, King Lear, and Macbeth, all considered to be among the finest works in the English language. In the last phase of his life, he wrote tragicomedies (also known as romances) and collaborated with other playwrights.

Many of Shakespeare's plays were published in editions of varying quality and accuracy in his lifetime. However, in 1623, two fellow actors and friends of Shakespeare's, John Heminges and Henry Condell, published a more definitive text known as the First Folio, a posthumous collected edition of Shakespeare's dramatic works that included all but two of his plays. Its Preface was a prescient poem by Ben Jonson that hailed Shakespeare with the now famous epithet: "not of an age, but for all time".

The most insulting aspect of the E.C.T lie.

Acts17:28KJV"For in him we live, and move, and have our being;..."

The doctrine of eternal conscious torment of the irreformably wicked has the necessary effect of making JEHOVAH God the main accessory to eternal corruption. 

As the quoted text shows there is no life(consciousness or motion) apart from God. Thus the eternal life that would make the eternal corruption suggested by this doctrine possible could only come from him. The scriptures assure us that JEHOVAH'S holiness precludes his perpetual enabling of sin. 

Indeed death is the end of sin.

James1:15KJV"Then when lust hath conceived, it bringeth forth sin: and sin, when it is finished, bringeth forth death. 16Do not err, my beloved brethren"

Note that death is the finish of sin. There is no sin after death. 

Romans6:7KJV"For he that is dead is freed from sin"

Thus there is no intermediate state between death and resurrection in which the wicked continue to sin. For the wicked to continue sinning perpetually JEHOVAH would need to resurrect them to perpetual life a promise only held out to the righteous.

Romans7,8KJV" them who by patient continuance in well doing seek for glory and honour and immortality, eternal life: 8But unto them that are contentious, and do not obey the truth, but obey unrighteousness, indignation and wrath,

The purpose of God's divine wrath is to bring a permanent end to wrongdoing and wrong desires not to perpetually enable them.

John2:17KJV"And the world passeth away and the LUST thereof ;BUT he that doeth the will of God abideth forever." 

Note the contrast the wrong desires characteristic of the present civilisation are as transient as the present age itself ,but the one accepting JEHOVAH'S help in being transformed inwardly so as to become the sort fit for a place in his new world will exists perpetually.

Why the origin of evolution deconstructs Darwinism.

Oh-So-Close to Self-Replication

Granville Sewell

In my video “A Summary of the Evidence for Intelligent Design,” I claim that with all our advanced technology we are still not close to designing any type of self-replicating machine. Instead, that is still pure science fiction. When we add technology to such a machine, to bring it closer to the goal of reproduction, I said, we only move the goalposts, because now we have a more complicated machine to reproduce. So how could we imagine that such a machine could have arisen by pure chance? In “Why Evolution is Different,” I further invited viewers to imagine that we were somehow able to design, for example, self-replicating cars. The duplication errors that would inevitably arise as these cars reproduced themselves would surely result in rapid devolution, I claimed. Who could imagine that they could eventually accumulate into major advances in automobile evolution? 

A Very Different Question

In a post here (“The First ‘Simple’ Self-Replicator?”), I tried to explain why self-replicating machines are so far beyond current human technology, by imagining trying to design something as “simple” as a self-replicating cardboard box. Take an empty cardboard box, I said, and build a completely automated factory inside which can produce empty cardboard boxes. The factory would, I presume, at least need to have some metal parts to cut and fold the cardboard and a motor with a battery to power these parts. But since the box now only builds empty boxes, it is not a self-replicator. So we would need to add another factory that could automatically produce a box with an empty box-building factory inside, and that factory would be enormously more complicated. But this box is still not a self-replicator because the box it builds can only build empty boxes, so now we need to add more technology to build a factory that builds the empty box-building factory, and then…. All of this ignores, of course, the very difficult question of where the box gets the cardboard and metals and other raw materials needed to supply its factories.

A commenter at Stephen Meyer’s Facebook page said it was “not true” that we are not close to building a self-replicator, and pointed to this video of a device built at Cornell University that can produce copies of itself…as long as humans keep feeding it certain high-tech blocks. According to the Cornell news story:

One of the dreams of both science fiction writers and practical robot builders has been realized, at least on a simple level: Cornell University researchers have created a machine that can build copies of itself….. Their robots are made up of a series of modular cubes — called “molecubes” — each containing identical machinery and the complete computer program for replication. The cubes have electromagnets on their faces that allow them to selectively attach to and detach from one another, and a complete robot consists of several cubes linked together. 

Subject to Interpretation

So I stand corrected: although human engineers are still not able to design self-replicating machines, we are oh-so-close. All that is left is to add a factory to the Cornell device so it can produce for itself the molecubes that humans keep building and feeding them. Well, of course then we would have to add a factory that could produce this molecube-producing factory. And then…

The Cornell story goes on to argue that “self-replication” is a term subject to different interpretations, and that the Cornell device is at least a “proof-of-concept.” Well, although the definition in the Wikipedia article linked above says it must “use raw materials found in the environment,” maybe it is possible to water down the definition of self-replication to where this device could be said to be close to self-replication. But it certainly has no relevance whatever to how the first life formed…unless of course origin-of-life researchers find evidence that the early Earth was rich in high-tech blocks. 

Chiang kai chek: a brief history.

 Chiang Kai-shek, Wade-Giles romanization Chiang Chieh-shih, official name Chiang Chung-cheng, (born October 31, 1887, Fenghua, Zhejiang province, China—died April 5, 1975, Taipei, Taiwan), soldier and statesman, head of the Nationalist government in China from 1928 to 1949 and subsequently head of the Chinese Nationalist government in exile on Taiwan.

Chiang was born into a moderately prosperous merchant and farmer family in the coastal province of Zhejiang. He prepared for a military career first (1906) at the Baoding Military Academy in North China and subsequently (1907–11) in Japan. From 1909 to 1911 he served in the Japanese army, whose Spartan ideals he admired and adopted. More influential were the youthful compatriots he met in Tokyo; plotting to rid China of the Qing (Manchu) dynasty, they converted Chiang to republicanism and made him a revolutionary.

In 1911, upon hearing of revolutionary outbreaks in China, Chiang returned home and helped in the sporadic fighting that led to the overthrow of the Manchus. He then participated in the struggles of China’s republican and other revolutionaries in 1913–16 against China’s new president and would-be emperor, Yuan Shikai.

After these excursions into public life, Chiang lapsed into obscurity. For two years (1916–17) he lived in Shanghai, where he apparently belonged to the Green Gang (Qing Bang), a secret society involved in financial manipulations. In 1918 he reentered public life by joining Sun Yat-sen, the leader of the Nationalist Party, or Kuomintang. Thus began the close association with Sun on which Chiang was to build his power. Sun’s chief concern was to reunify China, which the downfall of Yuan had left divided among warring military satraps. Having wrested power from the Qing, the revolutionists had lost it to indigenous warlords; unless they could defeat these warlords, they would have struggled for nothing.

Shortly after Sun Yat-sen had begun to reorganize the Nationalist Party along Soviet lines, Chiang visited the Soviet Union in 1923 to study Soviet institutions, especially the Red Army. Back in China after four months, he became commandant of a military academy, established on the Soviet model, at Whampoa, near Guangzhou. Soviet advisers poured into Guangzhou, and at this time the Chinese communists were admitted into the Nationalist Party. The Chinese communists quickly gained strength, especially after Sun’s death in 1925, and tensions developed between them and the more conservative elements among the Nationalists. Chiang, who, with the Whampoa army behind him, was the strongest of Sun’s heirs, met this threat with consummate shrewdness. By alternate shows of force and of leniency, he attempted to stem the communists’ growing influence without losing Soviet support. Moscow supported him until 1927, when, in a bloody coup of his own, he finally broke with the communists, expelling them from the Nationalist Party and suppressing the labour unions they had organized

Meanwhile, Chiang had gone far toward reunifying the country. Commander in chief of the revolutionary army since 1925, he had launched a massive Nationalist campaign against the northern warlords in the following year. This drive ended only in 1928, when his forces entered Beijing, the capital. A new central government under the Nationalists, with Chiang at its head, was then established at Nanjing, farther south. In October 1930 Chiang became Christian, apparently at the instance of the powerful Westernized Soong family, whose youngest daughter, Mei-ling, had become his second wife. As head of the new Nationalist government, Chiang stood committed to a program of social reform, but most of it remained on paper, partly because his control of the country remained precarious. In the first place, the provincial warlords, whom he had neutralized rather than crushed, still disputed his authority. The communists posed another threat, having withdrawn to rural strongholds and formed their own army and government. In addition, Chiang faced certain war with Japan, which, after seizing Manchuria (Northeast Provinces) in 1931, showed designs upon China proper. Chiang decided not to resist the coming Japanese invasion until after he had crushed the communists—a decision that aroused many protests, especially since a complete victory over the communists continued to elude him. To give the nation more moral cohesion, Chiang revived the state cult of Confucius and in 1934 launched a campaign, the so-called New Life Movement, to inculcate Confucian morals.

In December 1936 Chiang was seized by one of his generals who believed that Chinese forces should concentrate on fighting the Japanese instead of the communists. Chiang was held captive for some two weeks, and the Sian (Xian) Incident, as it became known, ended after he agreed to form an alliance with the communists against the Japanese invaders. In 1937 the mounting conflict between the two countries erupted into war (see Sino-Japanese War). For more than four years China fought alone until it was joined by the Allies, who with the exception of the Soviet Union declared war on Japan in 1941. China’s reward was an honoured place among the victors as one of the Big Four. But internally Chiang’s government showed signs of decay, which multiplied as it resumed the struggle against the communists after the Japanese surrendered to the United States in 1945. Civil war recommenced in 1946; by 1949 Chiang had lost continental China to the communists, and the People’s Republic of China was established. Chiang moved to Taiwan with the remnants of his Nationalist forces, established a relatively benign dictatorship over the island with other Nationalist leaders, and attempted to harass the communists across the Formosa Strait. The chastened Chiang reformed the ranks of the once-corrupt Nationalist Party, and with the help of generous American aid he succeeded in the next two decades in setting Taiwan on the road to modern economic development. In 1955 the United States signed an agreement with Chiang’s Nationalist government on Taiwan guaranteeing its defense. Beginning in 1972, however, the value of this agreement and the future of Chiang’s government were seriously called in question by the growing rapprochement between the United States and the People’s Republic of China. Chiang did not live to see the United States finally break diplomatic relations with Taiwan in 1979 in order to establish full relations with the People’s Republic of China. After his death in 1975 he was succeeded temporarily by Yen Chia-kan (C.K. Yen), who was in 1978 replaced by Chiang’s son Chiang Ching-kuo.

Among the reasons for Chiang’s overthrow by the communists, one frequently cited is the corruption that he countenanced in his government; another was his loss of flexibility in dealing with changing conditions. Growing more rigid in his leadership over the years, he became less responsive to popular sentiment and to new ideas. He came to prize loyalty more than competence and to rely more on personal ties than on ties of organization. His dependence on a trusted clique also showed in his army, in which he favoured narrow traditionalists over many abler officers. Chiang initially maintained his position as republican China’s paramount leader by shrewdly playing off provincial warlords and possible Nationalist rivals against each other and later by his adroit cultivation of American military, diplomatic, and financial support for his regime. His overthrow by the communists can perhaps be traced to his strategy during World War II; he generally refused to use his U.S.-equipped armies to actively resist China’s Japanese occupiers and counted instead on the United States to eventually defeat Japan on its own. He chose rather to preserve his military machine until the time came to unleash it on the communists at the war’s end and then crush them once and for all. But by that point Chiang’s strategy had backfired; his passive stance against the Japanese had lost him the prestige and support among the Chinese populace that the communists ultimately gained by their fierce anti-Japanese resistance. The morale and effectiveness of his armies had decayed during their enforced passivity in southwestern China, while the communists had built up large, battle-hardened armies on the strength of their appeal to Chinese nationalist sentiment. Finally, it can be said that Chiang “lost China” because he had no higher vision or coherent plan for making the deep social and economic changes needed to bring Chinese society into the 20th century. From his purge of the Nationalists’ communist partners in 1927 and his subsequent alliance with the landowning and mercantile classes, Chiang inexorably followed an increasingly conservative path that virtually ignored the plight of China’s oppressed and impoverished peasantry. The peasants formed almost 90 percent of China’s population, though, and it was their support, as demonstrated by the communist victory, which proved crucial in once more establishing a strong central government that could achieve the modern unification of China.

Technology without a technologist?

 

Can New Proteins Evolve?

Douglas Axe@DougAxe

Editor’s note: This excerpt is from a chapter by Douglas Axe  in the newly released book The Comprehensive Guide to Science and Faith: Exploring the Ultimate Questions About Life and the Cosmos. 

What enables a long chain of linked amino acids to perform highly specific molecular functions with machine-like precision? The answer is machine-like structure. Figure 2 shows one example (among thousands) of these remarkable structures. The multipart machine depicted is an ATP synthase — an assembly of 22 protein molecules that produces the energy molecule ATP. Biochemists refer to this as an enzyme because it accomplishes a chemical conversion (making ATP from ADP). But it’s no exaggeration to call it a molecular machine as well. Operating as a sophisticated nano-generator, the ATP synthase has a rotor (consisting of the parts labeled c-ring, y, and E) that spins at 8,000 rpm!

Figure 2: Structure of a bacteria l ATP synthase. (A) Schematic diagram showing the protein parts. (B) Images of the ATP synthase, from different angles. obtained with a method called cryogenic electron microscopy. (C) Molecular details (not of concern here). This figure is token from H. Guo. T Suzuki. J.L. Rubinstein (2019) ‘Structure of a bacterial ATP synthase.’ eLife 2029:8:e43128. https://elifesciences.org/articles/43128/tfigl (accessed August 24, 2020), under CC BY 4.0 license.

But how do long chains of linked amino acids form stable parts to make machines like this? The short answer is that it’s possible for the different amino acids to be arranged along the chain in such a way that the whole thing locks into a specific three-dimensional form. The process is called protein folding, with the term fold referring to the overall form. Figure 3 illustrates the basics.

I emphasized the word possible there for a reason. A random gene would specify a random sequence of amino acids, which would flop around without folding. Chains like that are rapidly broken back down into amino acids to keep them from interfering with cellular processes. Very special amino acid sequences are needed for protein chains to fold into stable structures. 

Measuring the Remarkable

It’s possible to measure just how special these sequences must be. Because random genes are hopeless, the best way to do this is to start with a natural gene that specifies a selectable trait by producing a protein that imparts this trait. Laboratory methods exist for introducing random mutations into the chosen gene. This can be done in a controlled way by restricting how many changes occur or by confining the mutations to a small portion of the gene. By starting with a gene that specifies a working protein and by controlling in this way the extent to which the gene is mutated, experimenters can produce large numbers of mutant versions of the gene, some of which will almost certainly still work.

Building on earlier work of this kind, I applied the method to a natural gene that enables bacteria to inactivate penicillin-like antibiotics. The trait in this case is antibiotic resistance, which is very easy to select for in the lab. First, one simply puts the bacteria on petri dishes with a small amount of penicillin. Cells carrying a mutant version of the gene specifying an enzyme that’s still able to break penicillin will form visible colonies on the petri dishes, whereas cells with inactive genes will die. I chose four clusters of amino acids, ten each, for my experiments. In each experiment, I heavily mutated the gene locations for one cluster, resulting in many mutant genes, each of which specified a mutant version of the enzyme with a jumble of amino acids in those ten locations. Of roughly 100,000 mutant genes tested per cluster, some were found to work in three of the clusters. None in the fourth. Testing more mutants presumably would have turned up some that worked in that fourth cluster. In any case, I was able to estimate from these results a fraction of mutants that work for each cluster, though this fraction is really an upper-bound estimate for the fourth cluster. 

Figure 3: The construction of proteins from amino acid s. Amino acids are linked one by one in the precise sequence specified by a gene, to form a long, flexible chainlike molecule (upper right). The amino-acid sequences specified by most natural genes have the highly special property of causing the who le chain to fold into a well-defined three-dimensional structure. an example of which is shown in the lower left. Scientists use simplified representations to make it easier to see the features of these folded protein structures. the most common one being the “ribbon” diagram. shown for the same protein (called beta-lactamase) in the lower right. Each coil in a ribbon diagram represents an element of structure called an alpha helix, and each arrow represent s a beta strand. These two elements make up most of the structures of all proteins. with the connections between the elements called turns or loops. Although the loops look floppy, like spaghetti. they usually have a firmly fixed structure just like the rest of the protein. (Reprinted from Undeniable, with permission.)

From these experimentally based estimates, I calculated the fraction of mutants that would be expected to work if the entire gene had been mutated in a similar way. This fraction is closely related to another fraction that carries a great deal of significance for protein evolution. But before we talk about what this important fraction turned out to be, let’s take some time to understand evolutionary thinking well enough to put this fraction in its proper context…..

Back to Proteins

Returning now to proteins, what do they add to the picture? The answer is that they exemplify the commonsensical principles by which we rightly reject purpose-free accounts of life. We can fully grasp and affirm these principles without turning to the subject of proteins (or any other technical subject), but in proteins we find elegant confirmation.

The important fraction I referred to above is the likelihood that a random chain of amino acids would have the special physical properties needed to fold into a stable structure that’s suitable for a particular function. Putting that in evolutionary terms, assuming a particular new capability that can be achieved with a new protein fold would benefit an organism, and that a genetic mistake in that organism has produced a gene sequence that differs substantially from what existed before, this fraction is the probability that the new gene happens to encode a new protein that performs the desirable new function. Using the results of my experiments on the penicillin-resistance enzyme, I estimated this probability to be in the ballpark of:

1/100,000,000,000,000,000,000,00