Deconstructing Modern alchemy.

Top Five Problems with Current Origin-of-Life Theories

Casey Luskin December 12, 2012 5:01 PM

Last summer I published a list of the "Top Ten Problems with Darwinian Evolution." Since that time, some readers have requested a list of major problems with theories seeking to explain the chemical origin of life. There are numerous problems, but here's my list of the top 5:

Problem 1: No Viable Mechanism to Generate a Primordial Soup.

According to conventional thinking among origin-of-life theorists, life arose via unguided chemical reactions on the early Earth some 3 to 4 billion years ago. Most theorists believe that there were many steps involved in the origin of life, but the very first step would have involved the production of a primordial soup -- a water-based sea of simple organic molecules -- out of which life arose. While the existence of this "soup" has been accepted as unquestioned fact for decades, this first step in most origin-of-life theories faces numerous scientific difficulties.

In 1953, a graduate student at the University of Chicago named Stanley Miller, along with his faculty advisor Harold Urey, performed experiments hoping to produce the building blocks of life under natural conditions on the early Earth.¹ These "Miller-Urey experiments" intended to simulate lightning striking the gasses in the early Earth's atmosphere. After running the experiments and letting the chemical products sit for a period of time, Miller discovered that amino acids -- the building blocks of proteins -- had been produced.

For decades, these experiments have been hailed as a demonstration that the "building blocks" of life could have arisen under natural, realistic Earthlike conditions,² corroborating the primordial soup hypothesis. However, it has also been known for decades that the Earth's early atmosphere was fundamentally different from the gasses used by Miller and Urey.

The atmosphere used in the Miller-Urey experiments was primarily composed of reducing gasses like methane, ammonia, and high levels of hydrogen. Geochemists now believe that the atmosphere of the early Earth did not contain appreciable amounts of these components. UC Santa Cruz origin-of-life theorist David Deamer explains in the journal Microbiology & Molecular Biology Reviews:

This optimistic picture began to change in the late 1970s, when it became increasingly clear that the early atmosphere was probably volcanic in origin and composition, composed largely of carbon dioxide and nitrogen rather than the mixture of reducing gases assumed by the Miller-Urey model. Carbon dioxide does not support the rich array of synthetic pathways leading to possible monomers...³

Likewise, an article in the journal Science stated: "Miller and Urey relied on a 'reducing' atmosphere, a condition in which molecules are fat with hydrogen atoms. As Miller showed later, he could not make organics in an 'oxidizing' atmosphere."⁴ The article put it bluntly: "the early atmosphere looked nothing like the Miller-Urey situation."⁵ Consistent with this, geological studies have not uncovered evidence that a primordial soup once existed.⁶

There are good reasons why the Earth's early atmosphere did not contain high concentrations of methane, ammonia, or other reducing gasses. The Earth's early atmosphere is thought to have been produced by outgassing from volcanoes, and the composition of those volcanic gasses is related to the chemical properties of the Earth's inner mantle. Geochemical studies have found that the chemical properties of the Earth's mantle would have been the same in the past as they are today.⁷ But today, volcanic gasses do not contain methane or ammonia, and are not reducing.

A paper in Earth and Planetary Science Letters found that the chemical properties of the Earth's interior have been essentially constant over Earth's history, leading to the conclusion that "Life may have found its origins in other environments or by other mechanisms."⁸ So strong is the evidence against pre-biotic synthesis of life's building blocks that in 1990 the Space Studies Board of the National Research Council recommended that origin-of-life investigators undertake a "reexamination of biological monomer synthesis under primitive Earthlike environments, as revealed in current models of the early Earth."⁹

Because of these difficulties, some leading theorists have abandoned the Miller-Urey experiment and the "primordial soup" theory. In 2010, University College London biochemist Nick Lane stated that the primordial soup theory "doesn't hold water" and is "past its expiration date."¹⁰ Instead, he proposes that life arose in undersea hydrothermal vents. But both the hydrothermal vent and primordial soup hypotheses face another major problem.

Problem 2: Forming Polymers Requires Dehydration Synthesis

Assume for a moment that there was some way to produce simple organic molecules on the early Earth. Perhaps they did form a "primordial soup," or perhaps these molecules arose near some hydrothermal vent. Either way, origin-of-life theorists must then explain how amino acids or other key organic molecules linked up to form long chains (polymers) like proteins (or RNA).

Chemically speaking, however, the last place you'd want to link amino acids into chains would be a vast water-based environment like the "primordial soup" or underwater near a hydrothermal vent. As the National Academy of Sciences acknowledges, "Two amino acids do not spontaneously join in water. Rather, the opposite reaction is thermodynamically favored."¹¹ In other words, water breaks down protein chains into amino acids (or other constituents), making it very difficult to produce proteins (or other polymers) in the primordial soup.

Problem 3: RNA World Hypothesis Lacks Confirming Evidence

Let's assume, again, that a primordial sea filled with life's building blocks did exist on the early Earth, and somehow it formed proteins and other complex organic molecules. Origin-of-life theorists believe that the next step in the origin of life is that -- entirely by chance -- more and more complex molecules formed until some began to self-replicate. From there, they believe Darwinian natural selection took over, favoring those molecules which were better able to make copies. Eventually, they assume, it became inevitable that these molecules would evolve complex machinery -- like that used in today's genetic code -- to survive and reproduce.

Have modern theorists explained how this crucial bridge from inert nonliving chemicals to self-replicating molecular systems took place? Not at all. In fact, even Stanley Miller readily admitted the difficulty of explaining this in Discover Magazine:

Even Miller throws up his hands at certain aspects of it. The first step, making the monomers, that's easy. We understand it pretty well. But then you have to make the first self-replicating polymers. That's very easy, he says, the sarcasm fairly dripping. Just like it's easy to make money in the stock market -- all you have to do is buy low and sell high. He laughs. Nobody knows how it's done.¹²

The most prominent hypothesis for the origin of the first life is called the "RNA world." In living cells, genetic information is carried by DNA, and most cellular functions are performed by proteins. However, RNA is capable of both carrying genetic information and catalyzing some biochemical reactions. As a result, some theorists postulate the first life might have used RNA alone to fulfill all these functions.

But there are many problems with this hypothesis.

For one, the first RNA molecules would have to arise by unguided, non-biological chemical processes. But RNA is not known to assemble without the help of a skilled laboratory chemist intelligently guiding the process. New York University chemist Robert Shapiro critiqued the efforts of those who tried to make RNA in the lab, stating: "The flaw is in the logic -- that this experimental control by researchers in a modern laboratory could have been available on the early Earth."¹³

Second, while RNA has been shown to perform many roles in the cell, there is no evidence that it could perform all the necessary cellular functions currently carried out by proteins.¹⁴

Third, the RNA world hypothesis can't explain the origin of genetic information.

RNA world advocates suggest that if the first self-replicating life was based upon RNA, it would have required a molecule between 200 and 300 nucleotides in length.¹⁵ However, there are no known chemical or physical laws that dictate the order of those nucleotides.¹⁶ To explain the ordering of nucleotides in the first self-replicating RNA molecule, materialists must rely on sheer chance. But the odds of specifying, say, 250 nucleotides in an RNA molecule by chance is about 1 in 10¹⁵⁰ -- below the "universal probability bound," a term characterizing events whose occurrence is at least remotely possible within the history of the universe.¹⁷ Shapiro puts the problem this way:

The sudden appearance of a large self-copying molecule such as RNA was exceedingly improbable. ... [The probability] is so vanishingly small that its happening even once anywhere in the visible universe would count as a piece of exceptional good luck.¹⁸

Fourth -- and most fundamentally -- the RNA world hypothesis can't explain the origin of the genetic code itself. In order to evolve into the DNA/protein-based life that exists today, the RNA world would need to evolve the ability to convert genetic information into proteins. However, this process of transcription and translation requires a large suite of proteins and molecular machines -- which themselves are encoded by genetic information.

All of this poses a chicken-and-egg problem, where essential enzymes and molecular machines are needed to perform the very task that constructs them.

Problem 4: Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code. 

To appreciate this problem, consider the origin of the first DVD and DVD player. DVDs are rich in information, but without the machinery of a DVD player to read the disk, process its information, and convert it into a picture and sound, the disk would be useless. But what if the instructions for building the first DVD player were only found encoded on a DVD? You could never play the DVD to learn how to build a DVD player. So how did the first disk and DVD player system arise? The answer is obvious: a goal-directed process -- intelligent design -- is required to produce both the player and the disk.

In living cells, information-carrying molecules (such as DNA or RNA) are like the DVD, and the cellular machinery that reads that information and converts it into proteins is like the DVD player. As in the DVD analogy, genetic information can never be converted into proteins without the proper machinery. Yet in cells, the machines required for processing the genetic information in RNA or DNA are encoded by those same genetic molecules -- they perform and direct the very task that builds them.

This system cannot exist unless both the genetic information and transcription/translation machinery are present at the same time, and unless both speak the same language. Not long after the workings of the genetic code were first uncovered, biologist Frank Salisbury explained the problem in a paper in American Biology Teacher:

It's nice to talk about replicating DNA molecules arising in a soupy sea, but in modern cells this replication requires the presence of suitable enzymes. ... [T]he link between DNA and the enzyme is a highly complex one, involving RNA and an enzyme for its synthesis on a DNA template; ribosomes; enzymes to activate the amino acids; and transfer-RNA molecules. ... How, in the absence of the final enzyme, could selection act upon DNA and all the mechanisms for replicating it? It's as though everything must happen at once: the entire system must come into being as one unit, or it is worthless. There may well be ways out of this dilemma, but I don't see them at the moment.¹⁹

The same problem confronts modern RNA world researchers, and it remains unsolved. As two theorists observed in a 2004 article in Cell Biology International:

The nucleotide sequence is also meaningless without a conceptual translative scheme and physical "hardware" capabilities. Ribosomes, tRNAs, aminoacyl tRNA synthetases, and amino acids are all hardware components of the Shannon message "receiver." But the instructions for this machinery is itself coded in DNA and executed by protein "workers" produced by that machinery. Without the machinery and protein workers, the message cannot be received and understood. And without genetic instruction, the machinery cannot be assembled.²⁰

Problem 5: No Workable Model for the Origin of Life

Despite decades of work, origin-of-life theorists are at a loss to explain how this system arose. In 2007, Harvard chemist George Whitesides was given the Priestley Medal, the highest award of the American Chemical Society. During his acceptance speech, he offered this stark analysis, reprinted in the respected journal Chemical and Engineering News:

The Origin of Life. This problem is one of the big ones in science. It begins to place life, and us, in the universe. Most chemists believe, as do I, that life emerged spontaneously from mixtures of molecules in the prebiotic Earth. How? I have no idea.²¹

Many other authors have made similar comments. Massimo Pigliucci states: "[I]t has to be true that we really don't have a clue how life originated on Earth by natural means."²² Or as science writer Gregg Easterbrook wrote in Wired, "What creates life out of the inanimate compounds that make up living things? No one knows. How were the first organisms assembled? Nature hasn't given us the slightest hint. If anything, the mystery has deepened over time."²³

Likewise, the aforementioned article in Cell Biology International concludes: "New approaches to investigating the origin of the genetic code are required. The constraints of historical science are such that the origin of life may never be understood."²⁴ That is, they may never be understood unless scientists are willing to consider goal-directed scientific explanations like intelligent design.

References:

[1.] See Stanley L. Miller, "A Production of Amino Acids under Possible Primitive Earth Conditions," Science, 117: 528-529 (May 15, 1953).

[2.] See Jonathan Wells, Icons of Evolution: Why Much of What We Teach About Evolution Is Wrong, (Washington D.C.: Regnery, 2000); Casey Luskin, "Not Making the Grade: An Evaluation of 19 Recent Biology Textbooks and Their Use of Selected Icons of Evolution," Discovery Institute (September 26, 2011).

[3.] David W. Deamer, "The First Living Systems: a Bioenergetic Perspective," Microbiology & Molecular Biology Reviews, 61:239 (1997).

[4.] Jon Cohen, "Novel Center Seeks to Add Spark to Origins of Life," Science, 270: 1925-1926 (December 22, 1995).

[5.] Ibid.

[6.] Antonio C. Lasaga, H. D. Holland, and Michael J. Dwyer, "Primordial Oil Slick," Science, 174: 53-55 (October 1, 1971).

[7.] Kevin Zahnle, Laura Schaefer, and Bruce Fegley, "Earth's Earliest Atmospheres," Cold Spring Harbor Perspectives in Biology, 2(10): a004895 (October, 2010) ("Geochemical evidence in Earth's oldest igneous rocks indicates that the redox state of the Earth's mantle has not changed over the past 3.8 Gyr"); Dante Canil, "Vanadian in peridotites, mantle redox and tectonic environments: Archean to present," Earth and Planetary Science Letters, 195:75-90 (2002).

[8.] Dante Canil, "Vanadian in peridotites, mantle redox and tectonic environments: Archean to present," Earth and Planetary Science Letters, 195:75-90 (2002) (internal citations removed).

[9.] National Research Council Space Studies Board, The Search for Life's Origins (National Academy Press, 1990).

[10.] Deborah Kelley, "Is It Time To Throw Out 'Primordial Soup' Theory?," NPR (February 7, 2010).

[11.] Committee on the Limits of Organic Life in Planetary Systems, Committee on the Origins and Evolution of Life, National Research Council, The Limits of Organic Life in Planetary Systems, p. 60 (Washington D.C.: National Academy Press, 2007).

[12.] Stanley Miller quoted in Peter Radetsky, "How Did Life Start?" Discover Magazine (Nov., 1992).

[13.] Richard Van Noorden, "RNA world easier to make," Nature News (May 13, 2009).

[14.] See Stephen C. Meyer, Signature in the Cell: DNA and the Evidence for Intelligent Design, p. 304 (New York: HarperOne, 2009).

[15.] Jack W. Szostak, David P. Bartel, and P. Luigi Luisi, "Synthesizing Life," Nature, 409: 387-390 (January 18, 2001).

[16.] Michael Polanyi, "Life's Irreducible Structure," Science, 160 (3834): 1308-1312 (June 21, 1968).

[17.] See William A. Dembski, The Design Inference: Eliminating Chance through Small Probabilities (Cambridge University Press, 1998).

[18.] Robert Shapiro, "A Simpler Origin for Life," Scientific American, pp. 46-53 (June, 2007).

[19.] Frank B. Salisbury, "Doubts about the Modern Synthetic Theory of Evolution," American Biology Teacher, 33: 335-338 (September, 1971).

[20.] J.T. Trevors and D.L. Abel, "Chance and necessity do not explain the origin of life," Cell Biology International, 28: 729-739 (2004).

[21.] George M. Whitesides, "Revolutions In Chemistry: Priestley Medalist George M. Whitesides' Address," Chemical and Engineering News, 85: 12-17 (March 26, 2007).

[22.] Massimo Pigliucci, "Where Do We Come From? A Humbling Look at the Biology of Life's Origin," in Darwin Design and Public Education, eds. John Angus Campbell and Stephen C. Meyer (East Lansing, MI: Michigan State University Press, 2003), p. 196.

[23.] Gregg Easterbrook, "Where did life come from?," Wired, p. 108 (February, 2007).

[24.] J.T. Trevors and D.L. Abel, "Chance and necessity do not explain the origin of life," Cell Biology International, 28: 729-739 (2004).

Every bit as "sapien" as his brothers.

A Deep and Abiding Need for Neanderthals to Be Stupid. Why?

Denyse O'Leary July 21, 2014 5:10 AM 

When Neanderthal man was first classified, he satisfied a felt need for a separate, intellectually inferior human species, fleshing out (so to speak) the Ascent of Man. But there has been a significant change in his status in recent years, as researchers began separating what we see from what we think ought to be or must be true.

The editors of the British newspaper The Guardian, for example, recently reappraised Neanderthals' intelligence in the light of evidence of their use of pigments and decorative shells. (They used red ochre pigment 250,000 years ago.) Some apparently used feathers as decorations and others built houses from mammoth bones, featuring carvings and pigments.

They chipped tools for various jobs as well, to be sure (and made string), and organized their living spaces by task. Curiously, when one research group meticulously reproduced both Neanderthal and early modern human tools, according to Stone Age methods, and then used them for customary tasks of the day, they found that, contrary to sixty years of textbook orthodoxy, "early stone tool technologies developed by modern humans were no more efficient than those used by Neanderthals." Neanderthals tended to have bigger hands, which may have created the impression of comparative clumsiness. At any rate, their leather working tools were like those in use today. They also reworked their tools, perhaps to avoid wasted effort. Some argue that they learned such skills from homo sapiens (current humans), but, if so, they had to grasp the underlying concepts in order to do so.

Neanderthals were also a seafaring people. One paleoanthropologist found their distinctive stone tools on the island of Crete in 2008. They were omnivores like ourselves, probably ate fish, and apparently used medicinal plants as well.

More significantly, Neanderthal paintings of seals havebeen found (an "academic bombshell"). Also, perhaps inevitably, jewelry and makeup. As one researcher puts it, "The findings show that our long-lost cousins were cognitively advanced from the get-go, long before modern humans appeared in Europe."

Did Neanderthals speak? Some say yes, and thus attempt to argue that language involves no great leap in human cognition; language is all just more Darwinian gradualism (as in half a noun or three quarters of a verb?). Others say yes for a different reason; Neanderthals were mostly right-handed and "No animals other than humans show such a bias toward right-handedness." While it is reasonable to assume that they could speak, given their other cultural activities, the "right-handedness" thesis doesn't sound like the surest evidence.

Neanderthals are also said by some to have had "a deep-seated sense of compassion" There is some evidence that they cared for invalids. One 500,000-year-old Homo heidelbergensis fossil (a group now generally classed with Neanderthals) was of an individual too old to hunt, probably a hunchback who needed a cane for support. At about 45, he was the most elderly ancient human found at the time, and the evidence suggests that, in an unsparing environment, others must have cared for him. Less believably, some have tried to psychoanalyze Neanderthal man, claiming, for example, that he couldn't have told a "walks-into-a-bar" joke. But how would we know?

Generally, we only know what we find that early peoples actually did; we can't know what they might have done or been unable to do under counterfactual circumstances. But one commentator, science writer Michael Shermer, offers a defense of a standard Darwinian view:

... there is almost no evidence that Neanderthals would have ever "advanced" beyond where they were when they disappeared 30,000 years ago. Even though paleoanthropologists disagree about a great many things, there is near total agreement in the literature that Neanderthals were not on their way to becoming "us."¹

Shermer repeated his views on Neanderthals last week in a debate with Stephen Meyer on the Michael Medved Show. Their tools and culture did not change, he informs us, for more than 200,000 years. That, says paleoanthropologist Richard Leakey, is "a technological stasis that seems to deny the workings of the fully human mind."²

Does it? Prehistoric and non-literate cultures in general are static compared to modern ones. There is a good reason for that. When life depends almost entirely on unpredictable natural events, static culture feels like an insurance policy: "Our ancestors always did things this way, and they survived!" Aid workers from technologically advanced societies struggle with this attitude in poor remote communities to this day. Yet no one supposes that the struggling peoples who cling to such a view do not have a "fully human mind." What they don't have is psychological room for error.

Shermer insists that such advances as Neanderthals made were the result of contact with current humans. As for burying their dead in a fetal position, strewn with flowers, he cites authorities who suggest that graves "may have been dug simply to remove corpses from habitation areas" and that the choice of the fetal position was merely a "desire to dig the smallest possible burial trench" (and not because the mourners thought that the dead might be reborn).

The clincher, in his view, is that we have not yet found a Neanderthal site where "grave goods" (food, jewelry, etc.) were left with the departed. No, but some researchers have noted that, curiously, child burials featured "generally more elaborate graves than older individuals." This points to some sort of belief, though we may never know what it was.

One must ask, given all the things we have discovered recently about Neanderthals, what if we do find the sort of grave goods he specifies? Would that change his view? Possibly not. He feels that we, the "glorious contingency," won out over the Neanderthals, because we are smarter:

Had Neanderthals won and we lost, there is every reason to believe that they would still be living in a stone-age culture of hunting, fishing, and gathering, roaming the hinterlands of Europe in small bands of a couple of dozen individuals, surviving in a world without towns and cities, without music and art, without science and technology ... a world so different from our own that it is almost inconceivable.

In fact, quite apart from the fact that Neanderthals appear to have been part of our own families, they have persistently failed to be as stupid as Shermer's account needs. Increasing numbers of finds are breaking down the supposed differences between them and other early humans. As one paleontologist puts it, "The historical downgrading of our Neanderthal cousins has gone well beyond the scientific."

It's not clear, however, that "the scientific" was driving the need to downgrade Neanderthal man so much as a Darwinian anthropology that is at odds with the archaeology.

Editor's note: Here are links to the whole "Science Fictions: Human Evolution" series to date.

References Cited:

(1) Michael Shermer, quoted in Bruce L. Gordon and William A. Dembski, The Nature of Nature: Examining the Role of Naturalism in Science (Wilmington, DE: ISI Books, 2011), p. 452.

Believe it or not.

Civil war

Law enforcement in the United States

Armed and dangerous

No-knock raids, assault weapons and armoured cars: America’s police use paramilitary tactics too often

EARLY one morning a team of heavily armed police officers burst into the home of Eugene Mallory, an 80-year-old retired engineer in Los Angeles county. What happened next is unclear. The officer who shot Mr Mallory six times with a submachine gun says he was acting in self-defence—Mr Mallory also had a gun, though he was in bed and never fired it. Armed raids can be confusing: according to an investigation, the policeman initially believed that he had ordered Mr Mallory to “Drop the gun” before opening fire. However, an audio recording revealed that he said these words immediately after shooting him. Mr Mallory died. His family are suing the police.

Such tragedies are too common in America. One reason is that the police have become more militarised. Raids by Special Weapons and Tactics (SWAT) units used to be rare: according to Peter Kraska of Eastern Kentucky University there were only about 3,000 a year in the early 1980s. Now they are routine: perhaps 50,000 a year (see article).

Some of the uses to which SWAT teams are put defy belief. In Maryland paramilitary police have been sent to break up illegal poker games; in Iowa, to arrest people suspected of petty fraud; in Arizona, to crack down on cockfighting.These teams, whose members wear body armour and are equipped with military-style weapons, were originally intended to tackle only the most dangerous criminals, such as murderers or hostage-takers. Now they are most commonly used to serve search warrants in drug-related cases. The police raided Mr Mallory’s home, for example, because they thought they would find a methamphetamine factory there. Instead they found two marijuana plants, belonging to a stepson who had a California medical-marijuana licence.

America’s courts tend to smile on SWAT tactics. They have ruled that police may enter a home without knocking if announcing their presence might give a criminal a chance to destroy evidence, for example by flushing drugs down the toilet. Such “no-knock” raids carry the advantages of surprise—and the disadvantages.

Having armed men burst into one’s home is terrifying. Startled citizens may assume they are being burgled—the “flash-bang” grenades that SWAT teams toss in to (temporarily) blind and deafen their targets tend to add to the confusion. Some people shoot back, with tragic consequences. Radley Balko, a campaigning journalist, has identified more than 50 innocent civilians who have been killed in SWAT raids.

Two factors have pushed the American police to militarise. First, thanks to the “war on terror”, there is plenty of money available for big weapons. Between 2002 and 2011 the Department of Homeland Security handed out a whopping $35 billion in grants to state and local police. In addition, the Pentagon supplies surplus military hardware to police forces at virtually no cost. That is why the quiet little town of Keene, New Hampshire has an armoured personnel carrier called a BearCat, which the local police chief said might be used to protect its pumpkin festival.

Second, the war on drugs creates perverse incentives. When the police find assets that they suspect are the proceeds of crime, they can seize them. Under civil asset-forfeiture rules, they do not have to prove that a crime was committed—they can grab first and let the owners sue to get their stuff back. The police can meanwhile use the money to beef up their own budgets, buying faster patrol cars or computers. All this gives them a powerful incentive to focus on drug crimes, which generate lots of cash, rather than, say, rape, which does not. This is outrageous. Citizens should not forfeit their property unless convicted of a crime; and the proceeds should fund the state as a whole, not the arm that does the grabbing.

Bang! Knock, knock...er, sorry, wrong house

The police do a difficult and dangerous job, and it is completely understandable that they do not wish to be outgunned by bad guys. A big show of force can sometimes deter criminals from starting a fight. And police departments are right to spend generously on defensive equipment such as body armour, which increases the chance that officers will come home alive.

Nonetheless, the militarisation of American law enforcement is alarming. The police are not soldiers. Armies are trained to kill the enemy; the police are supposed to uphold the law and protect citizens. They should use the minimum force necessary to accomplish those goals.

That does not mean getting rid of SWAT teams entirely. But it does mean restricting their use to situations where there are solid grounds to believe that the suspect involved is armed and dangerous. They should not be used to serve search warrants on non-violent offenders, or to make sure that strip joints are code-compliant, or in any circumstance where a knock on the door from a regular cop would suffice. The “war on drugs” is supposed to be a metaphor, not a real war.

From the print edition: Leaders

Seeking an amicable divorce?

Established churches

The palace and the desert

IS THE proper place of religion in the emperor's palace or in the world's toughest, poorest locations? That has been a hard question for Christianity at least since the fourth century of its existence. During that period, the faith was first tolerated, then adopted by the Roman empire; but some believers went to the opposite extreme and took up lives of poverty, prayer and self-discipline in barren, remote spots on the edge of the known world.

It's not just a scholarly debating point. In most historically Christian countries, one or more churches enjoy privileges inherited from the past which seem way out of proportion to the active followers they now command. Should they hang on to those perks or gracefully discard them? One country where this problem arises is England, where the state religion, Anglicanism, has been in the news twice this week, as I wrote in the print edition. On Monday, the Church's Synod voted in favour of women bishops, and today, (male) Anglican bishops were using their seats in Parliament to express their opposition to an assisted dying bill.

As with many British institutions, the power enjoyed by the Church of England is both entrenched and "soft"—it burns no heretics and generally deals emolliently with other sects and faiths, and with society as a whole. Still, at least two kinds of people are keen to see that power removed: principled secularists, who oppose religious privilege in all forms, and groups within the Church of England with a sharply defined vision which might be easier to pursue if the church were to cut loose from the state. These range from leftists like Giles Fraser who see links with the state as corrupting, to evangelicals who dream of an initially smaller, more vigorous body of believers which would not need to compromise with the social mainstream.

For some conservative evangelicals (those who take literally the Biblical passages about teaching as a male prerogative), the women-bishops issue probably reinforced their belief in the virtues of independence. Their camp caused a furore by blocking the proposal in November 2012, but some were apparently persuaded to change their minds this week because the earlier vote had shocked public opinion and made establishment seem less tenable. If preserving establishment were not an issue, then Synod members could arguably have followed their consciences, however idiosyncratic in the eyes of the world.

But there might be better reasons than that, from the church's point of view, for loosening the bonds. That view was put to me by Patrick Comerford, an Irish Anglican priest and theology lecturer. In his opinion, the English discussion about women bishops was disappointingly shallow at times; it had stressed the general need for gender equality in top positions, as though the English church was just a worldly bureaucracy. In the non-established Anglican churches of the British Isles (Wales, Scotland and Ireland), there was a more spiritual debate, unheeded by the secular world, about the church as an inclusive "body of Christ" and all three Celtic groups had marched ahead of their English brethren in blessing a female episcopate. Ireland's first woman bishop, Pat Storey, was consecrated last year.

So would it be a better idea, for everybody, if the Church of England were simply cut adrift? Frank Cranmer, a research fellow at Cardiff University and law-and-religion blogger, notes one interesting reason why that would be hard unless the church actively co-operated. In 1920, when the Anglican Church in Wales was disestablished, it was summarily deprived of any endowments which went back further than the 1660s. But since 1953, the European Convention on Human Rights has made that sort of arbitrary confiscation much harder: it is now "vastly more difficult to disendow an organisation against its wishes," Mr Cranmer thinks, in view of the ECHR's guarantee of the "peaceful enjoyment of property".

So in practice, the Church of England will probably not be separated from the state unless both sides want it. And the separation will be gradual; indeed it is happening already. Margaret Thatcher had some discretion in nominating the Archbishop of Canterbury; David Cameron does not. A bill is now going through parliament to terminate a bizarre arrangement under which some English home-owners can be required to help repair Anglican churches.

The question for the Church of England (and churches in a similiar position like those of Denmark and Norway) is whether the tide of separation should be accelerated or held back. To make a disappointingly secular point, you generally have a better chance of controlling a process if you push it forward rather than delaying it till the last moment.

Answering that knock.

A CONVERSATION WITH A NEIGHBOR

When Did God’s Kingdom Begin Ruling? (Part 1)

 

 

The following is a typical conversation that one of Jehovah’s Witnesses might have with a neighbor. Let us imagine that a Witness named Cameron has come to the home of a man named Jon.

“KEEP SEARCHING” FOR UNDERSTANDING

Cameron: Jon, I’ve really enjoyed the regular discussions we’ve been having about the Bible. * The last time we spoke, you raised a question about God’s Kingdom. You asked why Jehovah’s Witnesses believe that the Kingdom began ruling in the year 1914.

Jon: Yes, I was reading one of your publications, and it said that God’s Kingdom started ruling in 1914. That made me curious because you say that you base all of your beliefs on the Bible.

Cameron: That’s right, we do.

Jon: Well, I’ve read through the Bible myself. But I can’t remember ever seeing a passage that mentioned the year 1914. So I went to an online Bible and did a search for “1914.” Sure enough, the search engine said: “0 results.”

Cameron: I have to commend you on two counts, Jon. First, that you’ve read through the entire Bible. You must really love God’s Word.

Jon: I do. There’s nothing like it.

Cameron: I agree. Second, I want to commend you for turning to the Bible when trying to find an answer to your question. You did exactly what the Bible encourages us to do: “Keep searching” for understanding. * It’s good that you are putting forth effort like that.

Jon: Thank you. I do want to keep learning. In fact, I dug around a little more and found some information about 1914 in this book we’ve been studying. It mentions a dream that a king had—it was about a big tree that was cut down and then grew back or something like that.

Cameron: Ah, yes. That’s the prophecy recorded in Daniel chapter 4. It involves a dream that King Nebuchadnezzar of Babylon had.

Jon: Yes, that’s the one. I read the prophecy over and over. But to be honest, I still don’t see what it has to do with God’s Kingdom or the year 1914.

Cameron: Actually, Jon, even the prophet Daniel didn’t understand the full meaning of what he was inspired to record!

Jon: Really?

Cameron: Yes. Here at Daniel 12:8, he says: “Now as for me, I heard, but I could not understand.”

Jon: I’m not the only one then. That makes me feel a little better.

Cameron: The truth is, Daniel didn’t understand because it was not yet God’s time for humans to discern completely the meaning of the prophecies in the book of Daniel. But now, in our time, we can understand them more fully.

Jon: Why do you say that?

Cameron: Well, notice what we read in the very next verse. Daniel 12:9 says: “The words are to be kept secret and sealed up until the time of the end.” So these prophecies would only be understood much later, during “the time of the end.” And as we will soon discuss in our Bible study, all evidence indicates that we are now living in that time period. *

Jon: So, can you explain the prophecy in Daniel to me?

Cameron: I’ll do my best.

NEBUCHADNEZZAR’S DREAM

Cameron: To begin, let me briefly summarize what King Nebuchadnezzar saw in his dream. Then we can talk about what it means.

Jon: OK.

Cameron: In the dream, Nebuchadnezzar saw an enormous tree that reached all the way to heaven. Then he heard God’s messenger command that the tree be cut down. However, God said for its rootstock to be left in the ground. After a period of “seven times,” the tree would grow again. * This prophecy initially applied to King Nebuchadnezzar himself. Although he was a prominent king—like the tree that reached clear to heaven—he was cut down for “seven times.” Do you remember what happened?

Jon: No, I don’t recall.

Cameron: That’s all right. The Bible shows that Nebuchadnezzar lost his sanity, evidently for seven years. During that time, he was unable to rule as king. But at the end of the seven times, Nebuchadnezzar regained his sanity and started ruling again. *

Jon: OK, I’m with you so far. But what does all of this have to do with God’s Kingdom and the year 1914?

Cameron: In a nutshell, this prophecy has two fulfillments. The first fulfillment happened when King Nebuchadnezzar’s rulership was interrupted. The second fulfillment involved an interruption of God’s rulership. So it is this second fulfillment that is related to God’s Kingdom.

Jon: How do you know that the prophecy has a second fulfillment in regard to God’s Kingdom?

Cameron: For one thing, we find an indication in the prophecy itself. According to Daniel 4:17, the prophecy was given “so that people living may know that the Most High is Ruler in the kingdom of mankind and that he gives it to whomever he wants.” Did you notice the expression “the kingdom of mankind”?

Jon: Yes, it says that “the Most High is Ruler in the kingdom of mankind.”

Cameron: Right. Who do you suppose is “the Most High”?

Jon: I guess that’s talking about God.

Cameron: Correct. So that tells us that this prophecy is not only about Nebuchadnezzar. It also involves “the kingdom of mankind”—that is, God’s rulership over mankind. And that makes sense when we look at the prophecy in its context.

Jon: What do you mean?

THE BOOK’S CENTRAL THEME

Cameron: Time and again, the Bible book of Daniel develops a central theme. It keeps pointing forward to the establishment of God’s Kingdom under the rulership of his Son, Jesus. For example, let’s turn back a couple of chapters. Would you please read Daniel 2:44?

Jon: OK. It says: “In the days of those kings the God of heaven will set up a kingdom that will never be destroyed. And this kingdom will not be passed on to any other people. It will crush and put an end to all these kingdoms, and it alone will stand forever.”

Cameron: Thank you. Would you say that this verse sounds as if it is referring to God’s Kingdom?

Jon: Hmm. I’m not sure.

Cameron: Well, notice that it says that this Kingdom “will stand forever.” That’s true of God’s Kingdom, but it’s not something that we can say of any human government, can we?

Jon: No, I guess not.

Cameron: Here’s another prophecy in the book of Daniel that points to God’s Kingdom. It’s the prophecy recorded at Daniel 7:13, 14. Regarding a future ruler, the prophecy says: “To him there were given rulership, honor, and a kingdom, that the peoples, nations, and language groups should all serve him. His rulership is an everlasting rulership that will not pass away, and his kingdom will not be destroyed.” Is there anything in this prophecy that sounds familiar?

Jon: It mentions a kingdom.

Cameron: That’s right. And not just any kingdom. Notice it says that this Kingdom would have authority over “peoples, nations, and language groups.” In other words, this Kingdom would have global rulership.

Jon: I didn’t pick up on that, but you’re right. It does say that.

Cameron: Also, notice what else the prophecy says: “His rulership is an everlasting rulership that will not pass away, and his kingdom will not be destroyed.” That sounds a lot like the prophecy we just read at Daniel 2:44, doesn’t it?

Jon: Yes, it does.

Cameron: Let’s briefly review what we’ve discussed so far. The prophecy in Daniel chapter 4 was given so that people would know that “the Most High is Ruler in the kingdom of mankind.” This in itself indicates that the prophecy has a bigger fulfillment than just the one involving Nebuchadnezzar. And throughout the book of Daniel, we find prophecies about the establishment of God’s Kingdom under the rulership of his Son. Do you think it’s reasonable to conclude, then, that this prophecy in Daniel chapter 4 also has something to do with God’s Kingdom?

Jon: I suppose so. But I still don’t see the connection with 1914.

“LET SEVEN TIMES PASS”

Cameron: Well, let’s go back to King Nebuchadnezzar. He was represented by the tree in the first fulfillment of the prophecy. His rulership was interrupted when the tree was chopped down and left for seven times—that is, when he lost his sanity for a period of time. That period of seven times ended when Nebuchadnezzar regained his sanity and resumed his rulership. In the second fulfillment of the prophecy, God’s rulership would be interrupted for a period of time—but not because of any deficiency on God’s part.

Jon: What do you mean?

Cameron: In Bible times, the Israelite kings who ruled in Jerusalem were said to sit on “Jehovah’s throne.” * They represented God in governing his people. So the rulership of those kings was really an expression of God’s rulership. In time, however, most of those kings became disobedient to God and most of their subjects followed suit. Because of the Israelites’ disobedience, God allowed them to be conquered by the Babylonians in 607 B.C.E. From that time on, no more kings represented Jehovah in Jerusalem. In that sense, then, God’s rulership was interrupted. Are you with me so far?

Jon: I think so.

Cameron: So 607 B.C.E. marked the beginning of the seven times, or the period when God’s rulership would be interrupted. At the end of the seven times, God would install a new ruler to represent Him—this time, someone in heaven. That’s when the other prophecies we read about in Daniel would be fulfilled. So the big question is: When did the seven times end? If we can answer that question, we will know when God’s Kingdom began ruling.

Jon: I see. Let me guess—the seven times ended in 1914?

Cameron: Exactly! You got it.

Jon: But how do we know that?

Cameron: Well, during his earthly ministry, Jesus indicated that the seven times had not yet ended. * So they must be a very long period of time. The seven times started hundreds of years before Jesus came to earth, and they continued until sometime after he returned to heaven. Remember, too, that the meaning of the prophecies in Daniel was not to become clear until “the time of the end.” * Interestingly, during the late 1800’s, sincere students of the Bible were moved to examine this and other prophecies very carefully. They began to discern that the seven times would end in the year 1914. And major world events since then confirm that 1914 was indeed the year that God’s Kingdom began ruling in heaven. It was the year when this world entered its last days, or the time of the end. Now, I know this is probably a lot to digest . . .

Jon: Yes. I’m definitely going to have to go over this again to get it all straight.

Cameron: Don’t worry. It took me a while to see how all the pieces fit together too. But at the very least, I hope our discussion has helped you to see that Jehovah’s Witnesses do base their beliefs about the Kingdom on the Bible.

Jon: For sure. I’ve always been impressed with how you rely on the Bible for your beliefs.

Cameron: And I can see that you have a similar desire. As I said, this is a lot to take in all at once. You probably still have some questions. For example, we’ve established that the seven times relate to God’s Kingdom and that they began in 607 B.C.E. But how, exactly, do we know that these seven times ended in 1914? *

Jon: Yes, I’m wondering about that.

Cameron: The Bible itself helps us to determine the precise length of the seven times. Would you like to examine that topic the next time I’m here? *

Jon: That sounds good.

Do you have a particular Bible subject that you have wondered about? Are you curious about any of the beliefs or religious practices of Jehovah’s Witnesses? If so, do not hesitate to ask one of Jehovah’s Witnesses. He or she will be pleased to discuss such matters with you.

On the edge.

So, Michael Behe Was Right After All; What Will the Critics Say Now?

Casey Luskin July 16, 2014 1:30 PM

 

 

 

A new paper in Proceedings of the National Academy of Sciences USA has vindicated Michael Behe in one of the central controversies over his 2007 book The Edge of Evolution. Behe already reported here on the paper, which found that multiple mutations, at least two, are required to confer resistance to the drug chloroquine on malaria parasites:

A minimum of two mutations sufficed for (low) CQ transport activity, and as few as four conferred full activity. ... The findings presented here reveal that the minimum requirement for (low) CQ transport activity in both the ET and TD lineages of CQR PfCRT is two mutations.

(Summers et al., "Diverse mutational pathways converge on saturable chloroquine transport via the malaria parasite's chloroquine resistance transporter," Proceedings of the National Academy of Sciences USA, Vol. 111: E1759-E1767 (April 29, 2014) (emphasis added).)

Why does it matter? As Dr. Behe explained, this was a major point of contention among critics of his book. They claimed that Behe mistakenly thought chloroquine resistance required multiple simultaneous mutations, when in actuality it could arise through sequential mutations, each conferring a successively greater resistance-advantage. It can no longer be denied that the critics were dead wrong: chloroquine resistance does not arise at all until two mutations or more are present.

(To be precise, the paper found that the two minimum mutations break down as follows: one specific mutation is needed, plus a second mutation that's also needed which can occur in one of two locations. As the paper puts it, "Given that all known PfCRT haplotypes contain either N75E/D or N326D, these results indicate that PfCRT acquires the ability to transport CQ via one of two main mutational routes, both of which entail the introduction of K76T plus the replacement of an asparagine (N75 or N326) with an acidic residue.")

From the Beginning, the Critics Mischaracterized Behe

The critics were wrong from the outset. Behe's argument in The Edge of Evolution didn't depend on whether chloroquine resistance arose in a stepwise manner, or only after multiple mutations accumulated. His argument was based upon an empirically observed data point from public health studies which found that chloroquine resistance arose in about 1 in every 10²⁰ organisms. He had a strong citation for this empirical observation: Nicholas White, "Antimalarial Drug Resistance," Journal of Clinical Investigation, Vol. 113: 1084-1092 (2004). He called the mutations (whatever they were) that caused chloroquine resistance a "chloroquine complexity cluster" or CCC. Whatever molecular mechanisms may be behind a CCC, empirical data showed that 10²⁰ cells are required in order to produce one. Behe pointed out that if a trait required the molecular equivalent of two CCC's before providing any advantage, then that would pose major problems for Darwinian evolution.

It's a simple calculation. Behe observed that if 10²⁰ organisms were required to obtain one CCC, then the square of that amount -- 10⁴⁰ organisms -- would be required to evolve a trait that required two CCC's before providing any advantage. However, as Behe observed, a total of only 10⁴⁰ organisms have lived on Earth over the entire history of the planet. As Behe put it:

Recall that the odds against getting two necessary, independent mutations are the multiplied odds for getting each mutation individually. What if a problem arose that required a cluster of mutations that was twice as complicated as a CCC? (Let's call it a double CCC.) For example, what if instead of the several amino acid changes needed for chloroquine resistance in malaria, twice that number were needed? In that case the odds would be that for a CCC times itself. Instead of 10²⁰ cells to solve the evolutionary problem, we would need 10⁴⁰ cells. Workers at the University of Georgia have estimated that about a billion billion trillion (10³⁰) bacterial cells are formed on the earth each and every year. ... If that number has been the same over the entire several-billion-year history of the world, then throughout the course of history there would have been slightly fewer than 10⁴⁰ cells, a bit less than we'd expect to need to get a double CCC. The conclusion, then, is that the odds are slightly against even one double CCC showing up by Darwinian processes in the entire course of life on earth.

(Michael Behe, The Edge of Evolution: The Search for the Limits of Darwinism, p. 135 (Free Press, 2007).)

Behe inferred, based upon the great rarity of a CCC evolving, that it was a trait that probably required multiple mutations. Behe's argument didn't turn on that inference, but it was a reasonable one. Richard Dawkins himself used exactly the same sort of reasoning in other contexts to infer that a trait required multiple mutations to evolve.

Will Ken Miller, Jerry Coyne, Paul Gross, Nick Matzke, Sean Carroll, Richard Dawkins, and PZ Myers Now Apologize to Michael Behe?

Behe's critics misread him as saying that a single CCC necessarily required multiple simultaneous mutations, and castigated Behe for allegedly ignoring the possibility of a single CCC arising via sequential mutations. For example:

• Kenneth Miller: "It would be difficult to imagine a more breathtaking abuse of statistical genetics. Behe obtains his probabilities by considering each mutation as an independent event, ruling out any role for cumulative selection, and requiring evolution to achieve an exact, predetermined result." (Nature, 2007)
• Paul Gross: "Behe assumes simultaneous mutations at two sites in the relevant gene, but there is no such necessity and plenty of evidence that cumulativeness, rather than simultaneity, is the rule. As Nature's reviewer (Kenneth R. Miller) notes, 'It would be difficult to imagine a more breathtaking abuse of statistical genetics.'" (The New Criterion, 2007)


• Jerry Coyne: "Behe requires all of the three or four mutations needed to create such an interaction to arise simultaneously. ... If it looks impossible, this is only because of Behe's bizarre and unrealistic assumption that for a protein-protein interaction to evolve, all mutations must occur simultaneously, because the step-by-step path is not adaptive." (The New Republic, 2007)


• Nick Matzke: "Here is the flabbergasting line of argument. First, Behe admits that CQR evolves naturally, but contends that it requires a highly improbable simultaneous double mutation, occurring in only 1 in 10²⁰ parasites. ... The argument collapses at every step." (Trends In Ecology and Evolution, 2007)


• Sean Carroll: "Behe's main argument rests on the assertion that two or more simultaneous mutations are required for increases in biochemical complexity and that such changes are, except in rare circumstances, beyond the limit of evolution. .. Examples of cumulative selection changing multiple sites in evolving proteins include ... pyrimethamine resistance in malarial parasites (6) -- a notable omission given Behe's extensive discussion of malarial drug resistance. (Science, 2007)


• Richard Dawkins: "If correct, Behe's calculations would at a stroke confound generations of mathematical geneticists, who have repeatedly shown that evolutionary rates are not limited by mutation." (New York Times, 2007)


• And then of course there's PZ Myers. He made much the same criticisms, and also wrote:

  Behe isn't just a crackpot who thinks he has a novel explanation for an evolutionary mechanism -- he's a radical anti-evolutionist extremist who rejects the entire notion of the transformation of species by natural processes. ... Most of the arguments are gussied up versions of the kind of handwaving, ignorant rationalizations you'd get from some pomaded fundagelical Baptist minister who got all his biology from the Bible, not at all what you'd expect from a tenured professor of biochemistry at a good university -- throwing in an occasional technical gloss or mangled anecdote from the literature is only a gloss to fool the rubes.

All these critics were wrong. You get no resistance to chloroquine whatsoever unless at least two mutations are present to begin with. You might be able to get some cumulative selection after that, where successive mutations improve resistance up to a certain point. It is, however, by definition a multimutation feature.

Behe reasonably inferred that chloroquine resistance requires multiple mutations. He was right. His critics misunderstood his argument and thought this inference was a crucial plank in his reasoning. It wasn't. But it now turns out that the position Behe's critics attributed to him, and then railed against, was itself correct. Even a single CCC apparently requires multiple mutations before conferring any advantage. In fact, it's probably very close to the "edge" of evolution that Behe identified in his book.

Is an apology from Behe's critics then forthcoming? In a world where debates were conducted with the goal of discovering truth rather scoring points, it sure ought to be. Unfortunately, I'm not sure we live in that world.

What we'll probably get is nothing more than PZ Myers's concession, offered in the context of the rant quoted above:

Fair enough; if you demand a very specific pair of amino acid changes in specific places in a specific protein, I agree, the odds are going to be very long on theoretical considerations alone, and the empirical evidence supports the claim of improbability for that specific combination.

Well, that's more or less what's required to generate chloroquine resistance. We'll gladly take this -- i.e., simply being proven right -- in lieu of an apology.