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Commentary

The Economist: some problems with the peer-review process

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From The Economist, of all places.

Excerpt:

The idea that the same experiments always get the same results, no matter who performs them, is one of the cornerstones of science’s claim to objective truth. If a systematic campaign of replication does not lead to the same results, then either the original research is flawed (as the replicators claim) or the replications are (as many of the original researchers on priming contend). Either way, something is awry.

It is tempting to see the priming fracas as an isolated case in an area of science—psychology—easily marginalised as soft and wayward. But irreproducibility is much more widespread. A few years ago scientists at Amgen, an American drug company, tried to replicate 53 studies that they considered landmarks in the basic science of cancer, often co-operating closely with the original researchers to ensure that their experimental technique matched the one used first time round. According to a piece they wrote last year in Nature, a leading scientific journal, they were able to reproduce the original results in just six. Months earlier Florian Prinz and his colleagues at Bayer HealthCare, a German pharmaceutical giant, reported in Nature Reviews Drug Discovery, a sister journal, that they had successfully reproduced the published results in just a quarter of 67 seminal studies.

Let’s take a look at some of the problems from the article.

Problems with researcher bias:

Other data-heavy disciplines face similar challenges. Models which can be “tuned” in many different ways give researchers more scope to perceive a pattern where none exists. According to some estimates, three-quarters of published scientific papers in the field of machine learning are bunk because of this “overfitting”, says Sandy Pentland, a computer scientist at the Massachusetts Institute of Technology.

Problems with journal referees:

Another experiment at the BMJ showed that reviewers did no better when more clearly instructed on the problems they might encounter. They also seem to get worse with experience. Charles McCulloch and Michael Callaham, of the University of California, San Francisco, looked at how 1,500 referees were rated by editors at leading journals over a 14-year period and found that 92% showed a slow but steady drop in their scores.

As well as not spotting things they ought to spot, there is a lot that peer reviewers do not even try to check. They do not typically re-analyse the data presented from scratch, contenting themselves with a sense that the authors’ analysis is properly conceived. And they cannot be expected to spot deliberate falsifications if they are carried out with a modicum of subtlety.

Problems with fraud:

Fraud is very likely second to incompetence in generating erroneous results, though it is hard to tell for certain. Dr Fanelli has looked at 21 different surveys of academics (mostly in the biomedical sciences but also in civil engineering, chemistry and economics) carried out between 1987 and 2008. Only 2% of respondents admitted falsifying or fabricating data, but 28% of respondents claimed to know of colleagues who engaged in questionable research practices.

Problems releasing data:

Reproducing research done by others often requires access to their original methods and data. A study published last month inPeerJ by Melissa Haendel, of the Oregon Health and Science University, and colleagues found that more than half of 238 biomedical papers published in 84 journals failed to identify all the resources (such as chemical reagents) necessary to reproduce the results. On data, Christine Laine, the editor of the Annals of Internal Medicine, told the peer-review congress in Chicago that five years ago about 60% of researchers said they would share their raw data if asked; now just 45% do. Journals’ growing insistence that at least some raw data be made available seems to count for little: a recent review by Dr Ioannidis which showed that only 143 of 351 randomly selected papers published in the world’s 50 leading journals and covered by some data-sharing policy actually complied.

Critics of global warming have had problems getting at data before, as Nature reported here:

Since 2002, McIntyre has repeatedly asked Phil Jones, director of CRU, for access to the HadCRU data. Although the data are made available in a processed gridded format that shows the global temperature trend, the raw station data are currently restricted to academics. While Jones has made data available to some academics, he has refused to supply McIntyre with the data. Between 24 July and 29 July of this year, CRUreceived 58 freedom of information act requests from McIntyre and people affiliated with Climate Audit. In the past month, the UK Met Office, which receives a cleaned-up version of the raw data from CRU, has received ten requests of its own.

Why would scientists hide their data? Well, recall that the Climategate scandal resulted from unauthorized release of the code used to generate the data used to promote global warming alarmism. The leaked code showed that the scientists had been generating faked data using a “fudge factor”.

Elsewhere, leaked e-mailed from global warmists revealed that they do indeed suppress articles that are critical of global warming alarmism:

As noted previously, the Climategate letters and documents show Jones and the Team using the peer review process to prevent publication of adverse papers, while giving softball reviews to friends and associates in situations fraught with conflict of interest. Today I’ll report on the spectacle of Jones reviewing a submission by Mann et al.

Let’s recall some of the reviews of articles daring to criticize CRU or dendro:

I am really sorry but I have to nag about that review – Confidentially I now need a hard and if required extensive case for rejecting (Briffa to Cook)
…
If published as is, this paper could really do some damage. It is also an ugly paper to review because it is rather mathematical, with a lot of Box-Jenkins stuff in it. It won’t be easy to dismiss out of hand as the math appears to be correct theoretically, (Cook to Briffa)
…
Recently rejected two papers (one for JGR and for GRL) from people saying CRU has it wrong over Siberia. Went to town in both reviews, hopefully successfully. (Jones to Mann)

One last quote from the Economist article. One researcher submitted a completely bogus paper to many journals, and many of them accepted it:

John Bohannon, a biologist at Harvard, recently submitted a pseudonymous paper on the effects of a chemical derived from lichen on cancer cells to 304 journals describing themselves as using peer review. An unusual move; but it was an unusual paper, concocted wholesale and stuffed with clangers in study design, analysis and interpretation of results. Receiving this dog’s dinner from a fictitious researcher at a made up university, 157 of the journals accepted it for publication.

Dr Bohannon’s sting was directed at the lower tier of academic journals. But in a classic 1998 study Fiona Godlee, editor of the prestigious British Medical Journal, sent an article containing eight deliberate mistakes in study design, analysis and interpretation to more than 200 of the BMJ’s regular reviewers. Not one picked out all the mistakes. On average, they reported fewer than two; some did not spot any.

The Economist article did not go into the problem of bias due to worldview presuppositions, though. So let me say something about that.

A while back Casey Luskin posted a list of problems with peer review.

Here was one that stuck out to me:

Point 5: The peer-review system is often biased against non-majority viewpoints.
The peer-review system is largely devoted to maintaining the status quo. As a new scientific theory that challenges much conventional wisdom, intelligent design faces political opposition that has nothing to do with the evidence. In one case, pro-ID biochemist Michael Behe submitted an article for publication in a scientific journal but was told it could not be published because “your unorthodox theory would have to displace something that would be extending the current paradigm.” Denyse O’Leary puts it this way: “The overwhelming flaw in the traditional peer review system is that it listed so heavily toward consensus that it showed little tolerance for genuinely new findings and interpretations.”

Recently, I summarized a podcast on the reviewer bias problem featuring physcist Frank Tipler. His concern in that podcast was that peer-review would suppress new ideas, even if they were correct. He gave examples of this happening. Even a paper by Albert Einstein was rejected by a peer-reviewed journal. Elsewhere, Tipler was explicitly told to remove positive references to intelligent design in order to get his papers published. Tipler’s advice was for people with new ideas to bypass the peer-reviewed journal system entirely.

Speaking about the need to bypass peer-review, you might remember that the Darwinian hierarchy is not afraid to have people sanctioned if they criticize Darwinism in peer-reviewed literature.

Recall the case of Richard Sternberg.

Excerpt:

In 2004, in my capacity as editor of The Proceedings of the Biological Society of Washington, I authorized “The Origin of Biological Information and the Higher Taxonomic Categories” by Dr. Stephen Meyer to be published in the journal after passing peer-review. Because Dr. Meyer’s article presented scientific evidence for intelligent design in biology, I faced retaliation, defamation, harassment, and a hostile work environment at the Smithsonian’s National Museum of Natural History that was designed to force me out as a Research Associate there. These actions were taken by federal government employees acting in concert with an outside advocacy group, the National Center for Science Education. Efforts were also made to get me fired from my job as a staff scientist at the National Center for Biotechnology Information.

So those are some of the issues to consider when thinking about the peer-review process. My view is that peer-reviewed evidence does count for something in a debate situation, but as you can see from the Economist article, it may not count for as much as it used to. I think my view of science in general has been harmed by what I saw from physicist Lawrence Krauss in his third debate with William Lane Craig. If a scientist can misrepresent another scientist and not get fired by his employer, then I think we really need to be careful about the level of honesty in the academy.

Commentary

Reformation Day celebrates the supremacy of Scripture and reason in theology

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The Ligonier Ministries web site has a summary of the event that kicked off the Reformation.

Excerpt:

On October 31, 1517, Martin Luther tacked up 95 theses on the church door at Wittenberg. With this act, he hoped to provoke a discussion among the scholars about the abuses of the indulgences by the Roman Catholic Church. He was not trying to create a public furor by any means, but within a fortnight, these theses had spread through the country like wildfire. The last thing Luther had in mind was to start some kind of major controversy, but nevertheless major controversy did begin.

From the discussions at Wittenberg, the disputations began to accelerate and escalate. Copies of the theses reached Rome and critical meetings were scheduled with the young monk. In these debates, Luther was maneuvered into proclaiming publicly that he had questions about the infallibility of church councils and also that he thought that it was possible that the pope could err. In 1520 a papal encyclical was issued which condemned Martin Luther as a heretic. Luther burned the document in a public bonfire and his defiance before the church was now a matter of record.

In response, Martin Luther picked up his pen to challenge the entire penitential system of the Roman Catholic Church, which undermined in principle the free remission of sins that is ours in the gospel. By doing so, he was unswervingly advocating his commitment to sola fide, the doctrine of justification by faith alone.

In 1521, Luther was summoned to the Imperial Diet, an authoritative meeting that involved the princes of the church, called by the Emperor of the Holy Roman Empire to be held in the city of Worms in Germany. Luther was an outlaw. For him to appear at the Diet was to risk his very life; therefore, he was given safe conduct by the Emperor to attend. With a few friends, Luther traveled from Wittenberg to Worms. The eyewitnesses of that episode tell us that when Luther’s little covered wagon appeared around the corner of the bend, there were lookouts posted in the church tower at Worms. All the people were agog waiting for the arrival of this notorious person. When Luther’s caravan was sighted, people were throwing their hats in the air, blowing trumpets, and creating all the fanfare of the arrival of the hero. It was the 16th century answer to a ticker-tape parade.

Things, however, became very solemn in a hurry because the next day he appeared before the Diet. His books were stacked on a table in the room, and he was asked and ordered to recant of his writings. This surprised Luther because he thought he was going to have an opportunity to defend his writings; but the only question really of any importance that was asked of him was this: “Are these your writings?” And when he said yes, they said, “Are you ready to recant of them?”

Hollywood has their version of Luther standing there boldly with his fist in the air saying, “Here I stand!” and so on. But instead he dropped his chin on his chest and muttered something that nobody could understand, so they asked him to speak up. “What did you say?” He said, “May I have 24 hours to think about it.” And so Luther was granted a reprieve of 24 hours to return to his room to contemplate the seriousness of this occasion.

The prayer that Luther wrote in that ensuing 24-hour period was one of the most moving prayers I have ever read in my life. In that prayer, Luther cried out for God in his sense of total loneliness fearing that God had abandoned him, and proclaimed, “O Lord, I am Thine, and the cause is Thine, give me the courage to stand.”

And on the morrow, Luther was called once again back to the court and was told to reply to the question. He said to the Diet, “Unless I am convinced by sacred Scripture or by evident reason, I cannot recant, for my conscience is held captive by the Word of God, and to act against conscience is neither right nor safe. Here I stand. I can do no other. God help me.” And with that there was an instant uproar.

The Protestant Reformation emphasizes the responsibility of each person to become familiar with what the Bible teaches for themselves and to make sense of it using the laws of logic for themselves. There is an enormous focus on the individual and individual’s responsibility to puzzle theology out for himself, using the tools available to him: reason, science, Scripture, history.  The Reformation put forward the famous five Solas: “Sola Scriptura” (Scripture Alone); “Sola Gratia” (Grace Alone); “Sola Fide” (Faith Alone); “Solus Christus” (Christ Alone); and “Soli Deo Gloria” (To God Alone Be Glory).

My friend J.W. Wartick has a post about the effects of the Reformation on society as a whole.

Here’s one of the effects: (links removed)

Capitalism had already begun before the European Reformations, having its renewal start in Italian city states in the 12th Century (for a detailed and extremely interesting discussion of this, see Rodney Stark, The Victory of Reason, 71ff). The Reformation, however, provided a place for capitalism to flourish. John Calvin’s thought touched upon nearly every contemporary problem, and one of these was usury (money lending at interest). Focusing upon the cultural context of the prohibition of usury in the Hebrew Scriptures, Calvin argued that his contemporary cultural context provided a way for usury to work without being necessarily wrong. Lending money in such a fashion was essential for the later development of capitalism (Alister McGrath, Reformation Thought: An Introduction, 259-260).

The Reformation also paved the way for a “Protestant Work Ethic.” Martin Luther’s notion of the “priesthood of all believers” demolished the hard distinction between the “temporal” and “spiritual” realm which dominated the thought of the church at the time. By breaking down this barrier, hard labor was elevated. It was no longer seen as an inferior life to that of monastic withdrawal; rather, any type of work could be pleasing to God (McGrath, 256-258). In contemporary churches, one can often hear about how the engineer, the retail worker, the auto worker, and the like should all utilize their skills to the glory of God. Such thinking came directly from the Reformation.

The Reformation also kick-started science, because nature held secrets about God’s existence and character.

Excerpt:

Without the Reformation, modern science would probably have developed in any event because of the ethos of rationality and the doctrine of creation conducive to it. The Reformation, however, hastened the development by criticizing scholasticism and by putting emphasis on the direct observation of nature. Luther has been called the Copernicus of theology while, on the other hand, Copernicus has been called the Luther of astronomy. Indeed, Thomas Sprat, an Anglican clergyman and an early member of the Royal Society, emphasized that there was a reformation, some would say revolution, in both philosophy and theology [3]. In natural philosophy or science, questions about nature were no longer answered primarily by quoting Aristotle and the Scholastics, but by turning to observation of and experimentation on nature itself. Similarly, after the Reformation, Protestants no longer answered questions in theology primarily by quoting scholastic philosophers and theologians, but by turning directly to the Bible. Luther interpreted Scripture by asking: what is the clear and straightforward meaning of the text? Scientists interpret nature in the simplest way using the minimum number of hypotheses.

Luther believed that the world was beginning a new age, which would bring not only a reform of religion but a new appreciation of nature. In his informal “Table Talk” he said,

We are at the dawn of a new era, for we are beginning to recover the knowledge of the external world that was lost through the fall of Adam. We now observe creatures properly …. But by the grace of God we already recognize in the most delicate flower the wonders of divine goodness and omnipotence [4].

In the last part of this statement, Luther paraphrased the words of the Apostle Paul in his letter to the Romans (Rom. 1:20).

Luther was open to the authentic scientific advances of his age [5]. He appreciated the mechanical inventions of his day.

He accepted the use of medicine in treating disease and is quoted as having said [6],

It’s our Lord God who created all things and they are good. Wherefore it’s permissible to use medicine, for it is a creature of God.

To someone who said that it is not permissible for a Christian to use medicine, Luther replied rhetorically, “Do you eat when you are hungry?” According to Andrew White [7], this attitude of Luther made the Protestant cities of Germany more ready than others to admit anatomical investigation and dissection.

Luther accepted astronomy as a science, but rejected astrology as a superstition because it cannot be confirmed by demonstration. Astrology, according to Luther, is idolatry and violates the first commandment. He was both amused and distressed by Melanchthon’s interest in astrology, a belief system that was widely accepted at the time [8].

The Reformation means good economics and good science, as well as good theology.

But theology still had some growing to do.

The challenges of the Reformers led to the development of the doctrine of middle knowledge, which reconciles divine sovereignty with human freedom and responsibility, solving a major problem with Reformed theology.

A very good book on middle knowledge is “Salvation and Sovereignty” by Kenneth Heathley. Highly recommended by Paul Gould.

Commentary

Christina Hoff Sommers: helping boys succeed in school

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An article from the leftist Time magazine by feminist Christina Hoff Sommers. (H/T Independent Women’s Forum)

Excerpt:

Being a boy can be a serious liability in today’s classroom. As a group, boys are noisy, rowdy and hard to manage. Many are messy, disorganized and won’t sit still. Young male rambunctiousness, according to a recent study, leads teachers to underestimate their intellectual and academic abilities. “Girl behavior is the gold standard in schools,” says psychologist Michael Thompson. “Boys are treated like defective girls.”

These “defective girls” are not faring well academically. Compared with girls, boys earn lower grades, win fewer honors and are less likely to go to college. One education expert has quipped that if current trends continue, the last male will graduate from college in 2068. In today’s knowledge-based economy, success in the classroom has never been more crucial to a young person’s life prospects. Women are adapting; men are not.

Some may say, “Too bad for the boys.” The ability to regulate one’s impulses, sit still and pay attention are building blocks of success in school and in life. As one critic told me, the classroom is no more rigged against boys than workplaces are rigged against lazy or unfocused workers. That is absurd: unproductive workers are adults — not 5- and 6-year-old children who depend on us to learn how to become adults. If boys are restive and unfocused, we must look for ways to help them do better.

She introduces three ideas to fix the problem, and here’s the third one:

In his delightful Boy Writers: Reclaiming their Voices, celebrated author and writing instructor Ralph Fletcher advises teachers to consider their assignments from the point of view of boys. Too many writing teachers, he says, take the “confessional poet” as the classroom ideal. Personal narratives full of emotion and self-disclosure are prized; stories describing video games, skateboard competitions or a monster devouring a city are not.

Peg Tyre’s The Trouble With Boys illustrates the point. She tells the story of a third-grader in Southern Californianamed Justin who loved Star Wars, pirates, wars and weapons. An alarmed teacher summoned his parents to school to discuss a picture the 8-year-old had drawn of a sword fight — which included several decapitated heads. The teacher expressed “concern” about Justin’s “values.” The father, astonished by the teacher’s repugnance for a typical boy drawing, wondered if his son could ever win the approval of someone who had so little sympathy for the child’s imagination.

Teachers have to come to terms with the young male spirit. As Fletcher urges, if we want boys to flourish, we are going to have to encourage their distinctive reading, writing, drawing and even joke-telling propensities. Along with personal “reflection journals,” Fletcher suggests teachers permit fantasy, horror, spoofs, humor, war, conflict and, yes, even lurid sword fights.

If boys are constantly subject to disapproval for their interests and enthusiasms, they are likely to become disengaged and lag further behind. Our schools need to work with, not against, the kinetic imaginations of boys to move them toward becoming educated young men.

Dr. Sommers participated in a recent debate where she argued in favor of allowing all-male schools against a radical feminist. That page has audio and a transcript as well.

My thoughts

I do think that women need to realize that boys have to be encouraged to do the different things that boys do, if we want boys to be engaged. The good things that boys do in society are not free – they need to be encouraged and not dismissed. Playing a wargame or an adventurous boardgame with a boy is good. Firing real guns with a boy is good. Playing adventurous role-playing games with a boy is good. Going to a war museum or on a camping trip with a boy is good. Watching patriotic war movies or adventurous movies with a boy is good. Reading military history and military biographies is good. Reading classical adventure novels with a boy is good. Listening to adventurous music with a boy is good. Even watching the news with a boy is good.

Nothing is free. We have to create the boys we want, and encourage them to be aggressive, active and righteous.