Science Guardian

Truth, beauty and paradigm power in science and society

I am Nicolaus Copernicus, and I approve of this blog

News, views and reviews measured against professional literature in peer reviewed journals (adjusted for design flaws and bias), well researched books, authoritative encyclopedias (not the bowdlerized Wiki entries on controversial topics) and the investigative reporting and skeptical studies of courageous original thinkers among academics, philosophers, researchers, scholars, authors, filmmakers and journalists.

Supporting the right of exceptional minds to free speech, publication, media coverage and funding against the crowd prejudice, leadership resistance, monetary influences and internal professional politics of the paradigm wars of cancer, HIV(not)AIDS, evolution, global warming, cosmology, particle physics, macroeconomics, information technology, religions and cults, health, medicine, diet and nutrition.

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I am Albert Einstein, and I heartily approve of this blog, insofar as it seems to believe both in science and the importance of intellectual imagination, uncompromised by out of date emotions such as the impulse toward conventional religious beliefs, national aggression as a part of patriotism, and so on.   As I once remarked, the further the spiritual evolution of mankind advances, the more certain it seems to me that the path to genuine religiosity does not lie through the fear of life, and the fear of death, and blind faith, but through striving after rational knowledge.   Certainly the application of the impulse toward blind faith in science whereby authority is treated as some kind of church is to be deplored.  As I have also said, the only thing that ever interfered with my learning was my education. I am Freeman Dyson, and I approve of this blog, but would warn the author that life as a heretic is a hard one, since the ignorant and the half informed, let alone those who should know better, will automatically trash their betters who try to enlighten them with independent thinking, as I have found to my sorrow in commenting on "global warming" and its cures.
Many people would die rather than think – in fact, they do so. – Bertrand Russell.

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Nicholas Wade driven to humor by science fraud

But the fallibility of journal review is now public


The reaction of sophisticated but good men in the scientific arena, who are aware of the way science may be twisted by human nature but find it impossible to understand because they would never do it themselves, is to relieve their embarrassment with humor.

This is probably why we are served up an amusing piece of satire today (Tues Jan 17) by Nicholas Wade in the Tuesday Science section, One Last Question: Who Did the Work?:

The article shown at left from a future issue of the Journal of Imaginary Genomics, annotated in the manner required by Science’s proposed reforms, has been released ahead of its embargo date.

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The New York Times

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January 17, 2006

One Last Question: Who Did the Work?

By NICHOLAS WADE

In the wake of the two fraudulent articles on embryonic stem cells published in Science by the South Korean researcher Hwang Woo Suk, Donald Kennedy, the journal’s editor, said last week that he would consider adding new requirements that authors “detail their specific contributions to the research submitted,” and sign statements that they agree with the conclusions of their article.

A statement of authors’ contributions has long been championed by Drummond Rennie, deputy editor of The Journal of the American Medical Association, and is already required by that and other medical journals.

But as innocuous as Science’s proposed procedures may seem, they could seriously subvert some traditional scientific practices, such as honorary authorship. Explicit statements about the conclusions could bring to light many reservations that individual authors would not otherwise think worth mentioning.

The article shown at left from a future issue of the Journal of Imaginary Genomics, annotated in the manner required by Science’s proposed reforms, has been released ahead of its embargo date.

* Copyright 2006The New York Times Company

This is the image referred to, which unfortunately probably cannot be made legible in this blog, as far as we know.

It contains various footnotes on contributions such as “1. I supplied the midwife toad cells used in this experiment, on condition that my name was included as co-author.” and 2. “I was riding in the elevator with Dr. Lysenko one day and gave him an idea about spring wheat; he very graciously said that he would add my name to his next paper.”

This light relief follows a heavier Wade piece on Sunday, tackling the difficult topic of what should be done to guard the virtue of science more effectively, indicated on the front of The Week In Review as “Iffy Science: Journals are the cops. But they’re not well armed”, Crumpled Papers: Lowering Expectations at Science’s Frontier”, which tries to explain that journal articles are fallible.

In this piece, Nicholas Wade, who in person certainly looks like the right mix of gentleman and professor that one imagines all science reporters ideally to be, makes an admission which goes far to explain the great hidden debacle in HIV?AIDS.

There it has been clear for some time that a precipitate claim (that HIV was the cause of AIDS). made even before the papers were published supposedly supporting it, became established as a profitable paradigm before any post publication review was done, and has proved immovable and flourishing, rather like a huge tumor on the body of science, in the face of numerous journal reviews that are so damning that they would normally, like surgery, excise and kill it.

The contrast between the fallibility of Dr. Hwang’s claims and the general solidity of scientific knowledge arises from the existence of two kinds of science – a distinction that is often blurred when new advances are reported first by scientific journals and then by the news media. There is textbook science and frontier science, and the two types carry quite different expiration dates.

Textbook science is material that has stood the test of time and can be largely relied upon. It may include findings made just a few years ago, but which have been reasonably well confirmed by other laboratories.

Science from the frontiers of knowledge, on the other hand, is wild, untamed and often either wrong or irrelevant to future research. A few years after they are published, most scientific papers are never cited again.

This is quite an admission of journal fallibility, but this is the line that is emerging in comments by science editors as they get caught by fraud these days, as Wade reports. He acknowledges very clearly that peer reviewing is really “rough screening” which if tightened up, “could retard the pace of scientific advance.”

Scientific journals try to impose order on the turbulent flow of new claims by having expert reviewers assess their merit. But even at the best journals, reviewers provide only a rough screen. Many papers slip through that later turn out to be innocently wrong. A few, like Dr. Hwang’s, are found to be fraudulent.

This rough screening serves a purpose. Tightening it up, in a vain attempt to produce instant textbook science, could retard the pace of scientific advance.

He goes on to note that since a journal’s imprimatur is no guarantee of truth, and claims can only be confirmed by other labs after a time, which means that it is no longer news, journalists have a problem, since they are quite likely to write up findings which turn out to be flawed.

Perhaps it is time for them to recognize this fact, he suggests.

Tightening up the reviewing system may remove some faults but will not erase the inescapable gap between textbook science and frontier science. A more effective protection against being surprised by the likes of Dr. Hwang might be for journalists to recognize that journals like Science and Nature do not, and cannot, publish scientific truths. They publish roughly screened scientific claims, which may or may not turn out to be true.

Of course, this is not what most science journalists want to do – write up stories of the news in science with caveats saying that it all might not be true. Why bother their sources or their readers with that deflating fact? Hard to imagine how it could be done to any more meaningful extent than it already is, anyway. Small wonder Wade doesn’t suggest what form this new caution would take, in a world where the Web forces ever shorter deadlines on science news. But we certainly agree they should and can acknowledge the fact that big claims have to be confirmed, as they often do.

In the end, though, the responsibility belongs to the journals, and they should put their house in order as far as possible. Wade points out that JAMA (the Journal of the American Medical Association) has already instigated the reforms that Science is proposing, where individual authors take explicit responsibility for their part in the work and in the conclusion of a paper. This is working well.

But some medical journals, like The Journal of the American Medical Association, already require authors to state who did what. The system works very well, said Drummond Rennie, the journal’s deputy editor and the instigator of the idea. Requiring authors to specify that they agree with the conclusions leads to conservative statements, a result that is also beneficial, in Dr. Rennie’s view.

Anyhow the important thing is that it is finally being publicly admitted and emphasized that the scientific literature is not infallible, and that all claims should be tested and reviewed.

It’s the reviewing part which is the key in HIV?AIDS, of course, and this is not really mentioned yet. Claims which can be tested in repeat experiments will not last long. It is the theoretical claims which amount to a way of interpreting new data, data which are not necessarily challenged in themselves, which are the tricky problem. HIV?AIDS is the prime example.

Most people have no idea of the power and quality of the reviews that have rejected HIV as the cause of AIDS. A new theoretical claim may resist review for a very long time it appears, even if the review is done and done well, and done repeatedly, if the new claim gets established too firmly with political and economic advantages.

Perhaps the newly perceived fallibility of journals will help awaken people to the idea that challenges to existing paradigms should not be too easily dismissed as heresies which challenge the bible of science, as they are in HIV?AIDS. As many Nobel prizes show, the paradigm challenger may be right.

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January 15, 2006

IDEAS & TRENDS: Crumpled Papers; Lowering Expectations at Science’s Frontier

By NICHOLAS WADE

THERE is considerable disorder in heaven when stem-cell scientists are chided by the Roman Catholic Church for the folly of pursuing ”miracle cures.” But such are the paradoxes generated by the implosion of a South Korean researcher’s widely believed claims to have created human embryonic stem cells from patients.

Of course, miracles like the Shroud of Turin are also widely believed. But scientific claims are meant to belong to a different category of truth: They are the certified knowledge of a community of scholars who have rigorously tested their ideas through experiment and mutual criticism.

How then can the fraudulent claims by Dr. Hwang Woo Suk have been accepted by Science, a leading journal that rejects most papers submitted to it? How can the community of stem-cell scientists have allowed a very visible claim to have stood unchallenged in their field for 20 months? Little wonder that Richard Doerflinger, an official of the United States Conference of Catholic Bishops, ridiculed the dreams of therapeutic cloning in a statement last week, scoffing that scientists were chasing miracle cures ”in pursuit of this mirage.”

The contrast between the fallibility of Dr. Hwang’s claims and the general solidity of scientific knowledge arises from the existence of two kinds of science — a distinction that is often blurred when new advances are reported first by scientific journals and then by the news media. There is textbook science and frontier science, and the two types carry quite different expiration dates.

Textbook science is material that has stood the test of time and can be largely relied upon. It may include findings made just a few years ago, but which have been reasonably well confirmed by other laboratories.

Science from the frontiers of knowledge, on the other hand, is wild, untamed and often either wrong or irrelevant to future research. A few years after they are published, most scientific papers are never cited again.

Scientific journals try to impose order on the turbulent flow of new claims by having expert reviewers assess their merit. But even at the best journals, reviewers provide only a rough screen. Many papers slip through that later turn out to be innocently wrong. A few, like Dr. Hwang’s, are found to be fraudulent.

This rough screening serves a purpose. Tightening it up, in a vain attempt to produce instant textbook science, could retard the pace of scientific advance.

But the roughness of the proceedings is not prominently advertised by journal editors, except when cases of blatant fraud are detected, whereupon they proclaim that peer review cannot reasonably be expected to detect fraud. They do not protest so much when newspapers report their journals’ claims as if they were certifiably true. Because of Science’s authority, Dr. Hwang’s claims to have cloned human embryonic cells were prominently reported and presented to the public as if they were important breakthroughs.

But any new advance belongs to frontier science, which is inherently fallible, and a journal’s imprimatur, though worth something, is no guarantee of truth. An advance only becomes solid when other laboratories have confirmed it, by which time it is no longer news. This presents a serious problem for journalists: many scientific claims, including those in leading journals, turn out to be overstated or wrong, and science reporting that presents these journals’ products as gospel is likely to be misleading.

Scientists and journal editors are, of course, well aware of the tentative nature of frontier science. As Donald Kennedy, the editor of Science, observed when the Hwang case first broke, journals often publish work that is innocently wrong. ”The public needs to understand that the journals and peer review are not perfect,” he said.

But last week Dr. Kennedy announced he was considering revising the journal’s publication procedures, though not with any great hope of preventing future cases of fraud. He suggested that authors would be required to state in writing their specific contributions to a report, a reform perhaps aimed at Dr. Gerald Schatten of the University of Pittsburgh. Dr. Schatten accepted senior authorship of — and thus responsibility for — one of Dr. Hwang’s papers, even though Dr. Schatten had performed none of the experiments and was not in a position to vouch for them. All the work was done in Seoul.

A second proposed change is to have all authors state that they agree with an article’s conclusions.

Both procedures may seem to include a certain potential for generating strife. Each author could overstate his or her contribution, arousing the wrath of all the others. Some authors may think a conclusion too timid, while others consider it an overstatement.

But some medical journals, like The Journal of the American Medical Association, already require authors to state who did what. The system works very well, said Drummond Rennie, the journal’s deputy editor and the instigator of the idea. Requiring authors to specify that they agree with the conclusions leads to conservative statements, a result that is also beneficial, in Dr. Rennie’s view.

Tightening up the reviewing system may remove some faults but will not erase the inescapable gap between textbook science and frontier science. A more effective protection against being surprised by the likes of Dr. Hwang might be for journalists to recognize that journals like Science and Nature do not, and cannot, publish scientific truths. They publish roughly screened scientific claims, which may or may not turn out to be true.

* Copyright 2006 The New York Times Company

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