Apparently if you're a Darwin sceptic,even when you're right you're wrong

A Pretty Sharp Edge: Reflecting on Michael Behe's Vindication                       

Ann Gauger July 28, 2014 3:59 AM

I am writing a post that shouldn't have to be written. It's about Dr. Michael Behe's book The Edge of Evolution, what it predicted, how that prediction was confirmed, and how his detractors continue to quibble and obfuscate, claiming that even if he was right he was still somehow wrong. That's not the way scientists are supposed to operate.

In science, theory that explains data and makes a prediction that is experimentally verified is considered to be confirmed. That's the way it is supposed to work. Einstein's general theory of relativity, Mendeleev's periodic table, and many other theories have been verified this way.

Now let's look at Behe's theory. Malaria is a devastating disease caused by the parasiteP. falciparum. These parasites are quick to develop resistance to most drugs, but they have had a hard time overcoming chloroquine, requiring more than ten years to develop resistance. In fact, sixty years since the drug's introduction, and after more than 10²⁰malarial parasites total, resistance to chloroquine has developed fewer than ten times. Why?

In The Edge of Evolution, Behe proposed an answer. His explanation -- his hypothesis, if you will -- is simple. The mutation rate of P. falciparum is roughly 1 in 10⁸ mutations per base pair per parasite. There are on average 10¹² parasites in the human body -- that's enough for more than a thousand copies of every possible single mutation to exist somewhere in each infected person. So if resistance required only one mutation, it should have appeared in a few days. However, it took more than a decade for resistance to emerge. Behe argued that therefore at least two mutationsmust be required for the parasite to develop resistance to chloroquine. Furthermore, those two mutations must each be of no use as single mutations, and those two mutations must be present together in the same organism in order to confer resistance to the drug.

Why did Behe make these predictions? It's a simple calculation, really. If two simultaneous mutations are required for resistance, the rate of that double mutation occurring can be calculated by multiplying the single rates together. That makes the rate for two mutations roughly 1 in 10¹⁶ mutations per base pair per parasite. To find those two mutations would require many more trials than are available among the 10¹² parasites in each person infected. However, 10²⁰parasites (the total present in a single year) represent more than enough opportunity for that double mutation to occur.

His critics focus on Behe's use of the word "simultaneous." Getting two simultaneous mutations is ridiculous, they say, and so multiplying two rates together is ridiculous. 

Maybe the two mutations happened simultaneously, meaning together in the same molecule in one generation. It is possible. Maybe the mutations happened one at a time. We don't know. Parasites carrying single mutations on the path to resistance (meaning they have no resistance yet) are sickly, though, because those single mutations have damaged an essential function. They and their offspring might survive and reproduce long enough for a second mutation to occur, but it seems unlikely. Most of the time they will simply be out-competed by their non-mutant siblings.

Another critique Behe's opponents offer is that Behe just doesn't understand evolution. Theremust be some cumulative adaptive path that would take the parasite to drug resistance. In support they offer Joe Thornton's work with hormone receptors, where his lab evolved a hormone receptor from its "ancestral" form by a series of selective steps. Thus there can't be an edge to evolution as sharp as just two mutations, they say. What the critics don't say is that the first step is not a selectable step. It's a gully across the road to new function that must be crossed by jumping.

The same is true about the path to chloroquine resistance. First of all, common sense says if there were a selective path with each mutation conferring increasing resistance, it would happen quickly, much more quickly than in a decade. But more importantly, a recent paper by Summers et al. has shown by experiment that two mutations, neither of them conferring any resistance by themselves, are the first steps of chloroquine resistance. (One mutation is required by all pathways; then either of two other mutations can be used to bring about resistance.) This is a more like a canyon than a gully. Two mutations must be present together in the same molecule to confer resistance to chloroquine. Call it "occurring simultaneously" or not. The effect is the same, and Behe is right and his critics are wrong. 

Ironically, recent work has shown the same thing with regard to hormone receptors. Carroll et al.(2011) reported that at the base of the pathway to evolve the ancient hormone receptor there are two mutations (a gene duplication plus point mutation) that must occur before any further evolution is possible. Harms and Thornton then showed that these mutations are the only way forward. There is no other road to take, no way around the canyon. It sounds remarkably like the malarial resistance pathway, doesn't it?

So how sharp is the edge of evolution? For the malarial parasite P. falciparum, the edge of evolution for chloroquine resistance is two mutations: one specific mutation and either one of two other mutations. These mutations have to occur together, and they have to be there before any other mutations can have any effect. If the parasite doesn't have these two mutations, it remains chloroquine-sensitive. But as we have seen, getting two mutations can take a long time. It happens relatively quickly for malaria because of its huge population size. For us and other animals it may take an extremely long time.

That sounds like a pretty sharp edge of evolution to me.

Behe predicted this requirement for two mutations seven years ago. All continuing criticism now sounds like sniping and quibbling over terminology. Maybe those quibbling and sniping can't see they are wrong. Maybe they don't understand how science works and what counts as evidence. Or, and this is more likely, they will never admit that Behe is right and they are wrong.

Why all the doubt?

Natural selection and the S.D.L algorithm.

Is Natural Selection Like a Computer Algorithm?

Evolution News & Views July 23, 2014 5:24 AM

Analogies can be useful, but they can also distract from what's really important. Consider a simple example. Say you are at a playground, and you hear a steady din of children's voices at play. You notice that the sound has spectral characteristics: a particular frequency range, dynamic range, and time variation, with occasional spikes. As a scientist, you produce a mathematical model to characterize the sound spectrum. You even make a prediction: the addition of n more children will cause the intensity to rise, but not the average pitch. Finding confirmation, you call your model the Weighted Playground Spectral Algorithm (WPSA) and publish it in a journal, where you apply it to galactic spectra. What have you done?

While your model might be useful in some contexts, it obscures what is most important about the playground: the minds, emotions and needs of the children and their parents. A star's light is not in the same ballpark (or playground) as a child calling out cheerfully, "Daddy! Watch me slide down the slide!" Yet we see a similar fallacy in a Commentary for PNAS by Nicholas H. Barton, Sebastian Novak, and Tiago Paixão of the Institute of Science and Technology in Austria. They compare evolution to computer science.

In "Diverse forms of selection in evolution and computer science," the authors notice that a particular mathematical model, the Multiplicative Weights Update Algorithm (MWUA) used in computer science, seems to fit some evolutionary scenarios, too. Launching from a paper by Chastain et al. called "Algorithms, Games and Evolution," they find this similarity interesting, and perhaps fruitful.

The astonishing diversity of complex adaptations that we see in the living worldhas been produced by natural selection, over ∼ 3.5 billion years of evolution. Information from the largely random survival and reproduction of past organisms has accumulated to produce genomes that are precisely fitted to diverse environments. In PNAS, Chastain et al. show that natural selection on freely recombining populations is equivalent to the multiplicative weights update algorithm (MWUA), an efficient optimization algorithm that has been discovered many times in computer science, statistics, and economics. Whether this equivalence explains the extraordinary effectiveness of natural selection, or conversely, of artificial algorithms, depends on one's perspective. Perhaps surprisingly, theoretical results in population genetics and in computer science look quite different, even when they deal with essentially the same questions. Thus, the equivalence identified by Chastain et al. allows these different results to be transferred between fields in both directions. (Emphasis added.)

The obvious problem with this line of thinking is that evolution has no algorithm! By definition, it is aimless, unguided, and mindless -- unlike an economist, statistician, or computer scientist. Like the playground voices compared to stellar spectra, any similarities will surely be swamped by more important differences. We also see that the commenters assume natural selection created all the "astonishing diversity of complex adaptations" in the living world, forcing them to try to fit an intelligent-design algorithm on what they believe originated by chance. Here's how Chastain et al. commit the same question-begging error:

Even the most seasoned students of evolution, starting with Darwin himself, have occasionally expressed amazement that the mechanism of natural selection has produced the whole of Life as we see it around us. There is a computationalway to articulate the same amazement: "What algorithm could possibly achieve all this in a mere three and a half billion years?" In this paper we propose an answer: We demonstrate that in the regime of weak selection, the standard equations of population genetics describing natural selection in the presence ofsex become identical to those of a repeated game between genes played according to multiplicative weight updates (MWUA), an algorithm known in computer science to be surprisingly powerful and versatile. MWUA maximizes atradeoff between cumulative performance and entropy, which suggests a new view on the maintenance of diversity in evolution.

Once again, they first assume evolution, then try to force-fit an intelligently designed algorithm (MWUA) onto the whole of life. This is fallacious. It takes a mind to assign weights, play games to win, and run algorithms. It takes a mind to recognize a tradeoff, measure performance, and counteract entropy. A mindless world is incapable of such things. The authors have merely transferred their own mental activity onto a world that they must assume, being Darwinists, is blind and uncaring. Barton and colleagues never quite catch the absurdity of the comparison:

Although computer science and evolutionary biology appear to be very different fields, there are some surprisingly close parallels, which are apparent if one thinks of natural selection as providing a general algorithm by which populations can efficiently learn about their environment. Although the questions in each field differ, there are common themes -- not least, how rapidly can evolutionary algorithms act? In computer science terms, what is the complexity of anevolutionary algorithm, or in other words, how does the runtime scale with thedimensionality of the environment, genome size, population size, and so on? It is striking that, although these different fields deal with similar problems, their theoretical structures are quite different, giving an opportunity for fruitful transfer.

The only algorithm possible for evolutionary theory is what we might dub (after Berlinski) the SDLA: the "Sheer Dumb Luck" Algorithm. Unfortunately, that algorithm is weighted heavily in favor of entropy and extinction. We would hope that Darwinists would not try to transfer their algorithm back onto the computer scientists. It may be too late for the economists.

Without their halos

Bad Science Muckrakers Question the Big Science Status Quo

Among the American public, trust in professional scientists and scientific journals is declining. Yet an overwhelming majority still believes that science “remains a source for good in the world.” Could the public be on to something? Medical-doctor-turned-journalistIvan Oransky thinks so. And it’s a growing problem.

As editor and publisher of Retraction Watch, a closely followed industry blog that tracks peer-reviewed journal articles withdrawn from publication, Oransky is raising awareness of the impact that competition for grants and career advancement is having on the quality of the science being produced. Far from being above the fray and immune to corrupting influences, “Scientists are just as human as anyone else,” says Oransky. And increasingly, “People are starting to see scientists the way they really are.”One of the deeper problems is the publish-or-perish fight for resources, tenure, and prestige among the elite scientists whose living depends on maintaining the trust of the taxpayers who foot their bills. “Publication is the coin of the realm in academia,” says Oransky. “If you want to get tenure, if you want to get grants, if you want get promoted, if you want to get exposed to companies that might license your products, you have to publish in top journals.”

The academic pecking order is based on the number of papers a scientist gets published in high impact factor journals, that is, journals whose papers are heavily cited by other scientists. And yet, “The vast majority of scientific publications are never cited. There are something like 30,000 [published papers] a week.” How many of those can be first rate? How much second- and third-rate science is being funded? And how can we know?

The surge of publications is a direct result of the tsunami of money that washed over the industry between 1998 and 2003 with the doubling of the National Institutes of Health (NIH) budget. “It was a gold rush,” says Oransky. “What scientists did was grow their labs so they can produce more papers so they can get more grants.”

But, like a real gold rush, the bonanza couldn’t go on forever. So, asks Oransky, “What happens to all those folks when the doubling stops?” NIH funding has currently leveled out at between $30 billon and $40 billion a year, depending on how you count it. In an era of stagnant budgets, competition for limited funding has become cutthroat. That has led some scientists to take shortcuts. And that, in turn, has caused retractions to soar.

That’s a serious problem. As Oransky explains, “A retraction means there is something deeply wrong” with a given academic paper. “About two thirds of the time, that’s actually something that’s considered misconduct – the official federal definition of which is falsification, fabrication, or plagiarism.”

Another major problem is that many study results cannot be reliable reproduced. Oransky cites a famous paper by Dr. John Iaonnidis, “Why most published research findings are false,” that shows the inherent biases and the flawed statistical analyses built into most “hypothesis driven” research, resulting in publications that largely represent “accurate measures of the prevailing bias.”

To make matters worse, private research dollars are being choked off by ill-conceived regulations, making researchers even more dependent on government grants, as Dr. Thomas Stossel at Harvard Medical School points out.

Stossel calls overly restrictive conflict of interest regulations “a damaging solution in search of a problem.” A self-described “typical academic socialist, totally living on grants for the first third of my career,” Stossel says his eyes were opened in 1987, when he was asked to serve on the scientific advisory board of Biogen (now Biogen IDEC), a fledgling biotech startup that went on to become a tremendous success. “I realized how fundamentally honest business people are compared to my academic colleagues, who’d run their grandmothers over for recognition.”

While working with Biogen, Stossel learned how difficult it was to translate academic research into products that actually help people. “It was during that time that conflict of interest mania emerged.” In 1988 Harvard Medical School instituted the first conflict of interest rules, largely as a result of an incident at the Mass Eye and Ear infirmary that was sensationalized by The Boston Globe.

Stossel characterizes this rationale as, “If I am paid by a corporation to do research, I am going to lie, cheat and steal.” Based on his experience at Biogen, he calls this a “total inversion of reality.” He notes that, “95 percent of the scientific papers retracted for falsification, fabrication, or plagiarism have no commercial connection.” And yet, conflict of interest rules continue to proliferate, choking off what could be a critical alternative to taxpayer funding.

In his farewell address, President Dwight Eisenhower warned of a day when, “because of the huge costs involved, a government contract becomes virtually a substitute for intellectual curiosity,” and “public policy could itself become the captive of a scientific-technological elite.”

Thanks to the work they are doing, Dr. Ivan Oransky and Dr. Thomas Stossel may help us heed Ike’s warning. They are my guests this week on RealClear Radio Hour. You can hear them describe the problem in their own words here.

Just enough religion to make us hate.

The end of Christianity in the Middle East could mean the demise of Arab secularism

In a Middle East rebuilt on intolerant ideologies, there is likely to be little place for beleaguered minorities

William Dalrymple

• The Guardian, Wednesday 23 July 2014 16.47 BST

The past decade has been catastrophic for the Arab world'sbeleaguered 12 million strong Christian minority. In Egypt revolution and counter-revolution have been accompanied by a series of anti-Copt riots, killings and church burnings. In Gaza and the West Bank Palestinian Christians are emigrating en masse as they find themselves uncomfortably caught between Netanyahu's pro-settler government and their increasingly radicalised Sunni neighbours.

In Syria most of the violence is along the Sunni-Alawite fault line, but stories of rape and murder directed at the Christian minority, who used to make up around 10% of the population, have emerged. Many have already fled to camps in Lebanon, Turkey or Jordan; the ancient Armenian community of Aleppo is reported to be moving en masse to Yerevan.

The worst affected areas of Syria are of course those controlled by Isis. Last weekend it issued a decree offering the dwindling Christian population of eastern Syria and northern Iraq a choice: convert to Islam or pay a special religious levy – the jizya. If they did not comply, "there is nothing to give them but the sword". The passing of the deadline led to possibly the largest exodus of Middle Eastern Christians since theArmenian massacres during the first world war, with the entire Christian community of Mosul heading off towards Kirkuk and the relative religious tolerance of the Kurdish zone.

Even before this latest exodus, at least two-thirds of Iraqi Christians had fled since the fall of Saddam. Christians were concentrated in Mosul, Basra and, especially, Baghdad – which before the US invasion had the largest Christian population in the Middle East. Although Iraq's 750,000 Christians made up only 7% of the pre-war population, they were a prosperous minority under the Ba'athists, as symbolised by the high profile of Tariq Aziz, Saddam's foreign minister, who used to disarm visiting foreign dignitaries by breaking into Onward, Christian Soldiers in Aramaic, the language of Jesus.

According to tradition it was St Thomas and his cousin Addai who brought Christianity to Iraq in the first century. At the Council of Nicea, where the Christian creed was thrashed out in AD325, there were more bishops from Mesopotamia than western Europe. The region became a refuge for those persecuted by the Orthodox Byzantines, such as theMandeans – the last Gnostics, who follow what they believe to be the teachings of John the Baptist. Then there was the Church of the East, which brought the philosophy of Aristotle and Plato, as well as Greek science and medicine, to the Islamic world – and hence, via Cordoba, to the new universities of medieval Europe.

Now almost everywhere Arab Christians are leaving. In the past decade maybe a quarter have made new lives in Europe, Australia and America. According to Professor Kamal Salibi, they are simply exhausted: "There is a feeling of fin de race among Christians all over the Middle East. Now they just want to go somewhere else, make some money and relax. Each time a Christian goes, no other Christian comes to fill his place and that is a very bad thing for the Arab world. It is Christian Arabs who keep the Arab world 'Arab' rather than 'Muslim'."

Certainly since the 19th century Christian Arabs have played a vital role in defining a secular Arab cultural identity. It is no coincidence that most of the founders of secular Arab nationalism were men like Michel Aflaq – the Greek Orthodox Christian from Damascus who, with other Syrian students freshly returned from the Sorbonne, founded the Ba'ath party in the 1940s – or Faris al-Khoury, Syria's only Christian prime minister. Then there were intellectuals like the Palestinian George Antonius, who in 1938 wrote in The Arab Awakening of the crucial role Christians played in reviving Arab literature and the arts after their long slumber under Ottoman rule.

If the Islamic state proclaimed by Isis turns into a permanent, Christian-free zone, it could signal the demise not just of an important part of the Arab Christian realm but also of the secular Arab nationalism Christians helped create. The 20th century after 1918, which saw the creation of the different Arab national states, may well prove to be a blip in Middle Eastern history, as the old primary identifiers of Arab identity, religion and qabila – tribe – resurface.

It is as if, after a century of flirting with imported ideas of the secular nation state, the region is reverting to the Ottoman Millet system (from the Arabic millah, literally "nation"), which represented a view of the world that made religion the ultimate marker of identity, and classified Ottoman subjects by their various sectarian religious "nations".

Despite sizeable Christian populations holding on in Lebanon, Jordan and Egypt, there is likely to be little place for Christian Arabs in a Middle East rebuilt on intolerant ideologies like those of Isis. Their future is more likely to resemble that of the most influential Christian Arab intellectual of our day, Edward Said. Born in Jerusalem at the height of Arab nationalism in 1935, Said died far from the turmoil of the Middle East in New York in 2003. His last collection of essays was appropriately entitledReflections On Exile.

• The headline of this article was amended on 24 July 2014.

The first casualty/Collateral damage V

In Gaza, Hamas fighters are among civilians. There is nowhere else for them to go

Lines are blurred when a guerrilla war is fought in as dense a place as Gaza but the IDF's HQ is also surrounded by civilians

• • Harriet Sherwood in Jerusalem
  • The Guardian, Thursday 24 July 2014 20.55 BST

Israel's accusation that Hamas is using civilians as human shields has grown increasingly strident as the war in Gaza worsens.

The charge is laid relentlessly by political and military leaders and media commentators, repeated in conversations by members of the public and echoed in the comments of foreign politicians and diplomats. On the other side of the conflict, the accusation is vigorously denied by Hamas and others in Gaza.

The truth is lost amid the propaganda battle being waged alongside the shells, bombs, guns and rockets. What is certain is that the picture is more complicated than either side claims.

Deliberately placing non-combatants in and around targets to deter enemy attack – the definition of human shields – is illegal under international law.

The Geneva conventions state: "The presence or movements of the civilian population or individual civilians shall not be used to render certain points or areas immune from military operations, in particular in attempts to shield military objectives from attacks or to shield, favour or impede military operations. The parties to the conflict shall not direct the movement of the civilian population or individual civilians in order to attempt to shield military objectives from attacks or to shield military operations."

International law also bans the use of medical units or prisoners of war to deter enemy attack.

However, even if Hamas were violating the law on this matter, it would not legally justify Israel's bombing of areas where civilians are known to be.

"Any violation of these prohibitions shall not release the parties to the conflict from their legal obligations with respect to the civilian population and civilians, including the obligation to take the precautionary measures," the conventions say.

Israel claims Hamas routinely uses hospitals, mosques, schools and private homes to launch rockets at Israel, store weapons, hide command and control centres, shelter military personnel, and conceal tunnel shafts. This is their justification for targeting such places, despite the legal requirement to ensure its attacks are proportional, distinguish between military and civilian objects, and avoid civilian casualties.

Israel says it gives due notice of attack – by phone, text messages, leaflet drops and "warning missiles" – to give civilians the chance to leave.

A typical statement from the Israel Defence Forces, issued in the past few days, says: "While the IDF does everything that it can to avoid civilian casualties, Hamas deliberately puts Palestinian civilian lives in danger. Hamas hides weapons and missile launchers in densely populated areas. Instead of keeping its citizens out of harm's way, Hamas encourages and even forces Gazans to join its violent resistance against Israel. It sends men, women and children directly into the line of fire to be used as human shields for terrorists."

On Wednesday, the IDF released a series of maps purporting to show Hamas military sites close to – but not in – schools, hospitals, mosques and residential buildings. It also released video, which it said showed militants using an ambulance to flee after coming under attack by IDF troops, and said the grounds and vicinity of al-Wafa hospital in Gaza City had been "repeatedly utilised by Hamas and the Palestinian Islamic Jihad as a command centre, rocket-launching site, and a post enabling terrorists to open fire at soldiers".

Israel has repeatedly targeted the rehabilitation hospital during the course of the conflict, finally destroying the heavily damaged and, by then, empty building on Wednesday.

But the hospital's director rejected the Israeli assertion that the hospital had been used for military purposes by Hamas or other militant groups. In a statement, Basman Alashi said: "Israel has targeted our hospital based on false and misleading claims. They are targeting medical facilities, the wounded, the sick and our children, all over the Gaza Strip. They want us to know that nowhere is safe."

He added: "I hope things calm down as soon as possible. It's painful to see what's happening and that the hospital has become a target for military attacks."

The UN's discovery of arms caches in two of its schools in the past week has given Israel's assertions credence. "UNRWA [the UN agency for Palestinian refugees] immediately informed all relevant parties and issued a statement strongly condemning the abuse of its premises," said a spokesman, Chris Gunness. The UN agency UNRWA's shelters have been shelled on four occasions in recent days, despite officials giving precise coordinates to the IDF.

Israel also claimed that Hamas had forced civilians to remain in the Gaza City neighbourhood of Shujai'iya after the IDF warned them to evacuate ahead of its assault on Sunday. Civilians were being "held as hostages", said Peter Lerner, an IDF military spokesman.

These claims have not been backed up by independent reporting from international journalists covering the war from Gaza. Instead, dispatches from the ground have presented complex reasons why some residents did not evacuate from Shujai'iya and other areas targeted by the IDF. Many said nowhere in Gaza was safe, so they saw little point in abandoning their homes.

Others cited worries about not knowing the identities of people who would be their new neighbours; they could be evacuating a familiar neighbourhood for one that was a militant stronghold and others were simply too terrified to go out on the streets. Many media reports said there was no evidence of coercion by Hamas.

In fact, tens of thousands of people have fled their homes for what they hope is a safer place. UNRWA reports that more than 140,000 people have sought shelter in its properties; churches and mosques have been overwhelmed by displaced civilians; the grounds of the Shifa hospital in Gaza City have begun to resemble a makeshift refugee camp. These families are in fear of their lives, but they overwhelmingly cite Israeli bombing and shelling as the cause, rather than threats from Hamas.

Gaza is one of the most overcrowded places on earth. Almost two million people are crammed into a strip of land just 25 miles long and between three and a half and seven miles wide – roughly the same size as the Isle of Wight. In general there are few opportunities to leave; and in the midst of a conflict such as this, there is no exit.

The current war is not being fought on a conventional battlefield. Israel is pounding Gaza from the air, and its troops are increasingly fighting battles against a guerrilla army in densely populated urban areas – which constitute much of the Gaza Strip. As Israeli tanks and troops push further into the towns and cities, it is increasingly likely that Hamas will launch attacks from positions close to civilian buildings.

The separation between "civilian" and "military" in Gaza is much more blurred than with a conventional army – both physically and in the Gazan psyche. Hamas and other militants are embedded in the population. Their fighters are not quartered in military barracks, but sleep at night in their family homes. While it is not difficult to find antipathy to Hamas on the streets of Gaza in quiet times, most people defend their "right to resist" – and under such sustained military attack, support for Hamas rises.

Israel, meanwhile, does not have an unblemished record in the use of human shields. In 2010, two soldiers were convicted in an IDF military court of using an 11-year-old Palestinian boy as a human shield in its 2008-09 operation in Gaza. The pair ordered the child to search bags they suspected of being booby-trapped.

It was the first conviction of what is known within the IDF as the "neighbour procedure" – forcing civilians to assist troops in military operations. Investigations by news organisations and human rights groups have suggested the IDF has used Palestinians as human shields in operations in both Gaza and the West Bank.

Meanwhile, in response to Israel's assertions that Hamas situates its military centres in civilian areas, some have pointed out that the IDF's headquarters, the Kiriya, is in central Tel Aviv, surrounded by a hospital, blocks of flats, shopping centres and offices.

The invincible scroll.

The Bible—A Remarkable Story of Survival

 

 

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

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

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

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

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

What Happened to Other Ancient Documents?

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

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

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

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

What About the Bible Texts?

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

How do modern translations of the Bible compare with ancient manuscripts? Professor Julio Trebolle Barrera, a member of the team of experts charged with studying and publishing the ancient manuscripts known as the Dead Sea Scrolls, says: “The transmission of the text of the Hebrew Bible is of extraordinary exactitude, without parallel in Greek and Latin classical literature.” Respected Bible scholar F. F. Bruce says: “The evidence for our New Testament writings is ever so much greater than the evidence for many writings of classical authors, the authenticity of which no one dreams of questioning.” He continues: “If the New Testament were a collection of secular writings, their authenticity would generally be regarded as beyond all doubt.” Certainly, the Bible is a remarkable book. Do you make time to read it each day?—1 Peter 1:24, 25.

Still in existence today are some 6,000 handwritten copies of the Hebrew Scriptures, or Old Testament, and some 5,000 copies of the Greek Scriptures, or New Testament

 

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).