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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blog, insofar as it seems to believe both in science and the importance of intellectual imagination, uncompromised by out of date emotions such as the impulse toward conventional religious beliefs, national aggression as a part of patriotism, and so on.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.
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Clinton’s CGI shows UN how to do it

September 26th, 2007

Giving is good, and Clinton leads world in how to get it done

$1 billion pledged by Norway and Holland

Bigger targets get more but fantasy meme maintains hold

billclintonpresident.jpgAs noisy helicopters overhead herald the arrival of international leaders to the UN Assembly, former President Clinton’s Clinton Global Initiative, his ambitious initiative leading prominent corporate chieftains and political leaders in many private projects to fight global poverty and ills, entered Round III today in Manhattan.

In a remarkably short time, Clinton has established himself as the world leader in coaxing and pressuring business and political leaders to contribute personal projects to raising up the lives of the underprivileged around the world.

In fact, if the business and political leaders who attend his jamboree don’t pony up and follow through, they are not invited back:

Attendees are required to make specific commitments to address one of the topics and report back to President Clinton on the progress made throughout the course of the year. Attendees who do not make or keep their commitment will not be invited to attend future meetings.

Here’s the gen this morning issued by CGI as we prepare to go down there and swim among the rich and influential whales, sharks, porpoises and small fry from the press.

Notice the improvement in balance that is being achieved by the Clinton effort, which is accelerating the spread of charitable rescue efforts in Africa and elsewhere well beyond AIDS to other ills. While the African First Ladies are banding together to make sure that as many pregnant black Africans as possible get the drugs they need to combat the HIV meme, the ten million children who die annually from pneumonia, sepsis, diarrhea, malaria, malnutrition and newborn complications globally are going to be the target of a special effort called Survive Until Five, which is going to spend nearly four times as much:

Clinton kicked off the third annual meeting of the Clinton Global Initiative (CGI) with over one thousand leaders of business, government and non-governmental organizations representing over 70 countries and including 52 current and former heads of state. During the opening session, Clinton announced five new commitments, including over $1 billion by the Norwegian and Dutch Governments to reduce maternal and child mortality.

“I’m gratified today because it’s clear to me that this model of philanthropy and giving, which began as an experiment in 2005, has proven itself in only two short years. Since our first meeting, more than 600 commitments have been made by CGI members, impacting 100 countries and millions of lives,” he said. “In its third year, CGI is evidence of something that I have always believed— that people are inherently generous, that giving makes you feel good, and that the only thing most of us are looking for is an opportunity to make a difference.”…

Save the Children US and UK
Save the Children and its partners will create a Survive to 5 campaign, driving awareness and action on behalf of the almost 10 million children who die annually from pneumonia, sepsis, diarrhea, malaria, malnutrition and newborn complications globally. Former US Senate Majority Leader, William Frist, will serve as the chair of the campaign as part of Save the Children’s commitment to global leadership will work closely with key governments to significantly reduce preventable child deaths. The five-year campaign will launch in fall 2007 and is estimated to cost $75 million.

Maureen Mwanawasa, First Lady of Zambia
The Organization of African First Ladies Against HIV/AIDS, and their President, the First Lady of Zambia, Mrs. Maureen K. Mwanawasa, will champion the expansion of programs and funding for the Prevention of Mother-to-Child-Transmission (PMTCT) of HIV/AIDS. Supported by $20 million over 2 years, their “Save the Unborn Child” campaign and will be implemented by 40 African First Ladies in their respective countries and will save millions of lives by preventing one of the most easily preventable forms of HIV/AIDS transmission.

Clinton kicked off the third annual meeting of the Clinton Global Initiative (CGI) with over one thousand leaders of business, government and non-governmental organizations representing over 70 countries and including 52 current and former heads of state. During the opening session, Clinton announced five new commitments, including over $1 billion by the Norwegian and Dutch Governments to reduce maternal and child mortality.

“I’m gratified today because it’s clear to me that this model of philanthropy and giving, which began as an experiment in 2005, has proven itself in only two short years. Since our first meeting, more than 600 commitments have been made by CGI members, impacting 100 countries and millions of lives,” he said. “In its third year, CGI is evidence of something that I have always believed— that people are inherently generous, that giving makes you feel good, and that the only thing most of us are looking for is an opportunity to make a difference.”

Joining President Clinton in the opening panel discussion, titled The Need for Global Action which explored the capacity of businesses, governments, and NGOs to collaboratively develop and implement global solutions, were the President of the Republic of the Philippines, Gloria Macapagal-Arroyo; Vice President Al Gore; President and CEO of Wal-Mart Stores, Inc., H. Lee Scott Jr.; Archbishop Desmond Tutu; and President of The World Bank Group, Robert B. Zoellick.

President Clinton announced the launch of MyCommitment.org, an interactive website challenging everyone to take action, make commitments and grow a grassroots movement around public service.

“This year, in an effort to inspire millions of people to engage in citizen service, we’ve developed a new online tool to help those who want to give back do so, either in their own communities or half a world away,” President Clinton said. “MyCommitment.org is intended to provide people across the globe with the opportunity to give to others as well as to tell others their stories of giving.”

The commitments made during the opening session included:

* The Partnership for Maternal, Newborn and Child Health: The governments of Norway and the Netherlands are committing $1 billion and $175 million respectively to launch “Deliver Now for Women and Children,” a campaign aimed at a two-thirds reduction in the rate of child mortality and three-quarters reduction in maternal mortality by 2015.
* Florida Power & Light: FP&L is investing $2.4 billion in energy efficiency and renewable energy projects. As part of the project, FP&L will build new solar power plants that are expected to reduce CO2 emissions by more than 2 million tons over 5 years, they will also provide smart meters to their customers along with an education program designed to help customers reduce their carbon footprint.
* The Darfur Project: PNC Foundation, Blue Mountain Capital, TONIC, the Bridge Foundation, Goldman Sachs Foundation and Merrill Lynch are partnering in a $2 million commitment funding eight airlifts to take much needed humanitarian relief to Darfur and Chad. The flights will be made available for partner organizations wanting to send essential supplies, with the first four flights completed by the end of the year.
* Scojo Reading Glass Microfranchises: In this $1.57 million commitment the Scojo Foundation is committing to more than triple the scale of its program for training entrepreneurs in developing countries to sell affordable reading glasses by expanding to ten additional countries. In total 3,000 entrepreneurs will develop new sources of income providing 300,000 people with new glasses and other eye care products.
* Interpeace: Partnering with President Ramos-Horta and the Peace and Democracy Foundation, Interpeace is investing $1.2 million to implement a nation-wide program designed to enable the Timorese to become the architects of their own future by empowering them to identify the underlying drivers of the violence and un-rest in their communities and to find ways of addressing them in a non-violent and sustainable manner.

Among the additional CGI commitments expected to be announced today:

GLOBAL HEALTH

Save the Children US and UK
Save the Children and its partners will create a Survive to 5 campaign, driving awareness and action on behalf of the almost 10 million children who die annually from pneumonia, sepsis, diarrhea, malaria, malnutrition and newborn complications globally. Former US Senate Majority Leader, William Frist, will serve as the chair of the campaign as part of Save the Children’s commitment to global leadership will work closely with key governments to significantly reduce preventable child deaths. The five-year campaign will launch in fall 2007 and is estimated to cost $75 million.

Maureen Mwanawasa, First Lady of Zambia
The Organization of African First Ladies Against HIV/AIDS, and their President, the First Lady of Zambia, Mrs. Maureen K. Mwanawasa, will champion the expansion of programs and funding for the Prevention of Mother-to-Child-Transmission (PMTCT) of HIV/AIDS. Supported by $20 million over 2 years, their “Save the Unborn Child” campaign and will be implemented by 40 African First Ladies in their respective countries and will save millions of lives by preventing one of the most easily preventable forms of HIV/AIDS transmission.

Merck & Co.
Merck will establish a $375.5 million program providing access to its HPV vaccine, Gardasil, in lowest-income countries. By donating a minimum of three million doses of the vaccine over a five-year period Merck will ensure that an estimated 1 million women receive the three-dose regimen and are protected from cervical cancer and other HPV-related diseases. This initiative is an extension of a 2006 CGI commitment by Merck to donate rotavirus vaccine to the Nicaraguan Government in an effort to cover every newborn in the country for three years.

CARE USA
Acting as a convener and catalyst, CARE USA will mobilize a global coalition of public and private entities to make sustainable improvements in maternal health and the nutritional status of children under the age of two. These coalitions will, through CARE’s signature eight-year program, “Empowering Women for Good Health,” develop services for low-income women that will help them realize their rights to a safe pregnancy and childbirth, as well as provide information and resources that will help new mothers give their babies a healthy start. The program will be globally focused and has the potential to reach 70+ countries where CARE works. It is anticipated that project implementations will occur in 10 countries in sub-Saharan Africa, South Asia, and Central and South America.

EDUCATION

BRAC, Nike, NoVo and the Bill & Melinda Gates Foundation
BRAC USA, as well as the Nike, NoVo and the Bill and Melinda Gates Foundation, are mobilizing $271 million to provide education opportunities ranging from primary schooling to graduate degrees and life skills training to 7.5 million children over the next five years in Bangladesh, Afghanistan, Tanzania, Uganda and Southern Sudan. The project hopes to mirror the success of last year’s $250 million commitment to provide comprehensive health, education, microfinance and empowerment programs to individuals in five African countries.

Academy for Educational Development
The Academy for Educational Development (AED) will increase the access and quality of education for girls in Liberia, Southern Sudan, Tanzania, Ethiopia, Equatorial Guinea, Guinea and other African countries. Their Leadership for Education and African Development (LEAD) project will introduce the tools necessary to update the local curriculum and teaching methods to enhance community participation and improve education quality. The project’s goal is to significantly improve the educational opportunities of at least 3 million children by 2015.

Center for Development and Population Activities
CEDPA commits to improving the education and health situations of 20,000 South African girls by adapting its successful life skills curriculum and proven youth development framework to townships in Southern Africa. Utilizing the support of anonymous private funding, CEDPA will expand its programs from its five pilot sites by working closely with local partners to successfully integrate its programs into each location.

POVERTY ALLEVIATION

National Geographic Society
National Geographic, working with partners Ashoka and the U.N. World Tourism Organization, will launch the Global Geotourism Network in March, 2008 to encourage tourism that sustains or enhances the geographical character of a place. Over the next three years the Network will develop a series of initiatives including two geotourism summits, the Ashoka Changemakers Competition to identify innovators and social entrepreneurs, an annual Places Rated destination stewardship survey distributed through National Geographic readers, and a specially designated website offering local tourism services and products.

XL Results Foundation/The Hunger Project
XL Results Foundation will contribute $5 million to implement a five-year strategy, to build the capacity of 50,000 elected women leaders who are directly responsible for improving access to health, education, nutrition and higher incomes for 15 million people in rural India. The project will also mobilize local populations to increase the effectiveness of local government, build federations of elected women leaders for advocacy and action and mobilize the power of the media to create public support for strengthening local democracy. Each million dollars raised enables The Hunger Project to provide training and ongoing support to 20,000 elected women representatives, who in turn will mobilize the energies of more than 6 million rural people for poverty eradication.

Hashoo Foundation
In December 2007, the Hashoo Foundation will launch the Honeybee Production project in the Northern Areas and Chitral (NAC) regions of Pakistan, which are amongst the poorest and most isolated in the country. Women account for 55% of honeybee producers in the NAC, but receive only 35% of the total income generated by honeybee production. With a strong focus on developing the production of by-products and creating linkages with markets, the Honeybee Project will allow local women to increase their income and provide for themselves and their dependants while expanding their future prospects.

ENERGY & CLIMATE CHANGE

Pratt Industries
In a $1 billion commitment Pratt Industries will build at least three new paper mills, four waste-to-energy plants and 30 materials recovery facilities over the next decade. Working with municipalities and sanitation departments it aims to avoid millions of tons of CO2 emissions.

Equator Environmental, LLC
Equator Environmental commits $100 million to establish a private equity fund investing in projects that are environmentally friendly, sustainable and directly preserve ecological assets. By monetizing these “eco-products” the fund will enhance the viability of the natural environment and showcase the importance of ecosystem preservation.

Green for All
Through the ground-breaking “Green for All” initiative, The Ella Barker Center for Human Rights is committing to help lead 250,000 Americans out of poverty and into “green-collar” jobs. With the continued growth in the building, solar, urban forestry, and bio-fuels sectors, a highly-trained “green-collar” workforce is needed to meet rising demand. Green for All will advocate for a national commitment to greater job training, employment and entrepreneurial opportunities – especially for people from disadvantaged communities. This transition could boost the U.S. economy, generating new opportunities for wealth and work.

American Council on Renewable Energy (ACORE)
With funding from Rockefeller Brothers Fund, ACORE is committing to advance a more robust policy and economic case for renewable energy solutions and amplifying influential voices to strengthen public understanding of climate change. The commitment will create RECAP-the Renewable Energy Communications and Policy (RECAP) program-a three-year campaign that will put forward critical policy and economic analysis on energy supply, environment and climate, economic development and jobs, and national security. This unique work builds on ACORE’s 2006 commitment to host a world meeting on renewable energy, which has now been successfully funded, and is scheduled to be held as the Washington International Renewable Energy Conference (WIREC 2008) on March 4-6, 2008 in Washington, D.C.

The Clinton Global Initiative is a project of the William J. Clinton Foundation that brings together a community of global leaders to devise and implement innovative solutions to some of the world’s most pressing challenges. CGI has approximately 1,000 members, diverse and influential leaders from all over the world, who make tangible commitments to create or support projects within CGI’s areas of focus. During the three-day Annual Meeting, attendees participate in workshops and meetings focused on four main topics: Global Heath, Education, Poverty Alleviation, and Energy & Climate Change. Attendees are required to make specific commitments to address one of the topics and report back to President Clinton on the progress made throughout the course of the year. Attendees who do not make or keep their commitment will not be invited to attend future meetings.More later, with details of any interaction with the topmost figures of key influence in the world encountered at this great event.

Political non-science: Frog (5)

September 21st, 2007

Iowa Tara’s trashing of critics betrays ignorance of science history

Science is reason and evidence, not democracy

Deplorable inaccuracies about a fine lady

froggie.jpgOK, back to the Poison Dart Frog, our image for the laborious trashing of the critics of the wingless HIV∫AIDS paradigm by Tara C. Smith of Iowa and Steve P. Novella of Yale at the Public Library of Science under the misleading title HIV Denial in the Internet Era.

The smokescreen of misconceived notions about the HIV critics and about science pumped out by this tract is nothing new.

Knocking the credentials of the HIV critics naturally occurs to defenders, perhaps, when their attitudes are drawn from uncritical acceptance of authority more than from their own investigations, as this paper suggests.

In general, HIV paradigm promoters choose to defend the science of HIV∫AIDS with political rather than scientific counter attacks, and this essay with its studious avoidance of the scientific debate is a fine example, since the authors make it explicit. The authors claim that the non peer reviewed Web pages they refer to at the NIH and CDC do the scientific debunking of the critics for them, but since those pages are not peer reviewed, they make it hard not to conclude that the real problem these defenders have is that they lack faith in the science and/or lack the answers to defend it directly.

We would say that their attempt to support the conventional wisdom with diversionary replies is a gift to the critics, since objective onlookers are provided with evidence of insecurity, historical misunderstanding and belligerent defensiveness that suggest that the critics are on the right track.

This is why we feel that a blow by blow deconstruction is worthwhile, since this unusually lengthy and “worked up” series of political potshots now on display at the NSF Public Library of Science offers a rare chance to make a thorough reply to the propaganda, for a change. This seems preferable to ignoring it as beneath serious consideration, and letting it sit like a slow release AZT pill into the bloodstream of the national discourse. Better to offer a complete antidote rather than allow this to happen, as it so often does because the expert and high level critics of HIV and AIDS, such as the distinguished Peter Duesberg, or the fiery Harvey Bialy, find it distasteful to deal with such ignorant trashing of their position as peer-reviewed elite commentators, and would rather occupy themselves with more constructive activities than responding to material which no intelligent student of science can take seriously.

This is why in a spirit of self sacrifice we offer our own deconstruction of the Frog, realizing that seasoned observers of this long drawn out battle such as the witty MacDonald will not find our series of posts on it very original; but we hope that it will be useful to newcomers to the arena, one obscure to so many people such as Hank Campbell for lack of of media coverage.

Saddling up the camels for this trek across this intellectual desert, we will now go through the claims of the text one by one. Here they are:

1. Implication that any paradigm debunking is by definition invalid

froganalyzed.jpgIt may seem remarkable that, 23 years after the identification of the human immunodeficiency virus (HIV), there is still denial that the virus is the cause of acquired immune deficiency syndrome (AIDS). This denial was highlighted on an international level in 2000, when South African president Thabo Mbeki convened a group of panelists to discuss the cause of AIDS, acknowledging that he remained unconvinced that HIV was the cause [1]. His ideas were derived at least partly from material he found on the Internet [2]. Though Mbeki agreed later that year to step back from the debate [3], he subsequently suggested a re-analysis of health spending with a decreased emphasis on HIV/AIDS [4].

Response: On the contrary, there is nothing at all surprising in the fact that few people outside the field of HIV∫AIDS, and not everyone in it, know that there is still a serious question that the virus HIV is the cause of AIDS after 23 years, because there has been effective official and institutional censorship, some explicit, including the leading media, of the news.

That any public criticism still exists despite the huge pressure against challenging HIV=AIDS should tell you, in fact, that something is rotten in the state of Denmark, especially when a seasoned politician leading the most advanced country in Africa looks into the question for himself, rather than depending solely on advisors, and is then sufficiently alarmed to call a special panel of science professionals from both sides to resolve the issue, because he has been directed via the Internet to relevant and authoritative material in the peer reviewed mainstream scientific literature which is not being reported in the media, and then resists tremendous political and media pressure to go along and conform to the paradigm, and instead frees up his health policy from total dependence on the suspect paradigm claim, after it is neither proven nor justified by its supporters at the special panel he called to review it. For that is the story of what has happened in South Africa.

2. Just quoting the skeptics is enough to show them up

greenandbblackpoisondart.jpegThe false premise of the entire text of this essay is established at the start by the clear suggestion that it is enough to quote the statements and behavior of the skeptics to show how laughable they are, and that quoting and replying to any of their scientific objections is not necessary.

Response: This assumption is by definition scientifically naive since any familiarity with the history of science and medicine, not to mention simple logic, will indicate that science advances paradigm by paradigm, with the old replaced by the new and improved as a result of fresh data and thinking, much to the surprise and chagrin of people who assume that the consensus of conventional scientists is a validation of their belief. By definition all replaced paradigms reign by overwhelming consensus until they are overthrown by revisionists, who as Schopenhauer and others have pointed out, are inevitably first ridiculed, then violently opposed, and finally joined by their opponents who will claim they knew their new paradigm was right all the time.

Every truth passes through three stages before it is recognized: In the first it is ridiculed. In the second, it is opposed. In the third it is regarded as self-evident. – Arthur Schopenhauer.

(see the page of this and other salutary Quotations on Science, Politics and Beliefin the blog, indexed as a link in the list of Pages in the right margin).

3. Implication that any challengers are “dangerous” to the public interest, untutored in science and unqualified to discuss the issue

tiny-frog.jpgHIV denial has taken root in the general population and has shown its potential to frustrate public education efforts and adversely affect public funding for AIDS research and prevention programs. For example, the AIDS Coalition to Unleash Power (ACT UP) was for many years on the front lines of AIDS education and activism. But now a San Francisco chapter of the group has joined the denialist movement, stating on its Web site that “HIV does not cause AIDS… HIV antibody tests are flawed and dangerous…AIDS drugs are poison” (http://www.actupsf.com/aids/index.htm). In 2000 the chapter wrote letters to every member of Congress asking them to stop funding research into HIV [5]. ACT UP San Francisco’s position has been condemned by other ACT UP chapters, such as ACT UP Philadelphia and ACT UP East Bay (http://www.actupny.org/indexfolder/actupgg.html). Rock stars have weighed in on the topic. Members of the group “The Foo Fighters” provided music for a soundtrack of the recent documentary, “The Other Side of AIDS” (http://www.theothersideofaids.com/), which questions whether HIV is the cause of AIDS. The band has spread its message that HIV does not cause AIDS at concerts [6], and it lists the HIV denial group “Alive and Well” as a worthy cause on its Web site (http://www.foofighters.com/community_cause.html).

Response: Defending against paradigm challenges by labeling them a danger to public remedial measures begs the question who is right about the paradigm, rather than answering it. A political argument of this kind suggests that the scientific defense is not strong enough to stand by itself, an implication that this whole essay carries.

That respectable people who normally would be expected to follow mainstream institutional and professional authority especially in matters of science and medicine turn against it so decisively, especially after long trusting the paradigm and fighting for it as in the case of ACTUP San Franscisco, tells us that there must be persuasive arguments against the claim of authority which have led them to take a public stand against it in the face of social sanctions and penalties of all kinds, including this kind of scorn.

Since the lay dissenters quoted take an active part by publicly insisting on paradigm review, in the case of the Foo Fighters at the risk of losing some of their audience, their public stand indicates that they take the issue very seriously and are not merely superficially deluded fools who persist out of sheer iconoclasm, especially when they assert factually detailed views on their web pages, as in the case of ACT UP San Franscisco.

4. Misleading characterization of challengers and their arguments as below the level of peer-reviewed literature

largepoison-frog.jpgAs these challenges to mainstream theories have largely occurred outside of the scientific literature, many physicians and researchers have had the luxury of ignoring them as fringe beliefs and therefore inconsequential. Indeed, the Internet has served as a fertile and un-refereed medium to spread these denialist beliefs. The Group for the Scientific Reappraisal of the HIV/AIDS Hypothesis (“Reappraising AIDS”) noted, “Thanks to the ascendance of the internet, we are now able to reinvigorate our informational campaign” [7]. The Internet is an effective tool for targeting young people, and for spreading misinformation within a group at high risk for HIV infection.

Response: This attempt to stain the critics objections as unable to meet the standards of peer review, and thus able to find self-publication only on the Internet, is 100% inappropriate and misleading. The opposite is correct.

The challenge to the mainstream HIV∫AIDS theory was initiated and pursued at the highest level of the scientific literature by the senior expert in the relevant field, retrovirology, and repeatedly survived (and thus was doubly validated by) the fiercest and most hostile peer reviewers, who knew perfectly well their own backsides were on the line if they let any of the material through, but they were unable to prove it incorrect or even questionable. All their objections were met before publication.

The critique of the paradigm published by this expert retrovirologist, Peter Duesberg, from 1987 to 2003 has never been countered effectively in the top journals where it has appeared, where no peer-reviewed rebuttal has been attempted, despite a promise to do so by Gallo at the Proceedings of the National Academy, where the longest fundamental debunking took place in 1988.

Duesberg’s review and rejection of the paradigm thus stands as the best and most validated peer-reviewed science in the matter, even though, politically speaking, the paradigm bandwagon has steered around it, and while intensely resisting any media coverage of the reviews, delivered every scientist riding on it to the unusually large HIV∫AIDS trough at the NIH, where every now and then they raise their heads and cry, No review necessary! Any questioning dangerous! before resuming feeding again.

If anything the fringe pseudoscience is not the HIV∫AIDS paradigm refutation by its critics, but the initially politically established, never scientifically substantiated, soon professionally reviewed and rejected ruling paradigm of HIV=AIDS, purveyed by its leading scientists and officials such as John Moore, Mark Wainberg and Anthony Fauci who act as despots of the field banning media coverage of paradigm critics and are enthusiastically joined in this by outsiders such as Tara and Steve who naively imagine they are defending good science.

The critics occupy the fringes of publication on the Internet only because print and television editors know better than to assign articles on the topic, even if they have the resources and inclination to investigate science, for fear of misunderstanding, ridicule, and alienating the NIAID, where the policy announced in print in an AAAS newsletter by director Anthony Fauci early on was that no reporter who raised the topic of the reviews that rejected HIV in the literature would have his or her calls returned.

With editors uniformly playing the role of establishment gatekeepers the Internet is indeed the only public venue readily available for the distribution of this information, information which in its ability to explain the paradoxes and insults to common sense and good science inherent in the standard model of HIV=AIDS has such power to suggest that revision is necessary, and that the drugs are suspect and dangerous, that the paradigm promoters justifiably view it as “dangerous”, and rightly so, to the funding of the paradigm, and try to deflect it with political misdirection such as calling it ‘pseudoscience’. If the critics are right the danger is to their welfare, clearly, and not to the welfare of patients, who will benefit. It is hard to imagine that anyone who genuinely believes that the case for HIV=AIDS is rock solid scientifically would fear and smear those call for open debate.

5. Misrepresenting promotional fact sheets as peer reviewed science

cricket-frog.jpgTwo excellent online fact sheets have been prepared to counter many of the most commonly used arguments to deny HIV causation of AIDS [8,9]; as such, we will not discuss these in this article. Instead, we will review the current intellectual strategies used by the HIV denial movement. Although other forms of science denial will not be specifically discussed, the characteristics described below apply to many other forms of popular denial, including denial of evolution, mental illness, and the Holocaust.

Response: The official fact sheets referred to are not peer-reviewed, and are not a valid excuse for avoiding any mention of the specifics of the scientific debunking of the paradigm by critics.

Nor are the objections of the critics vitiated by whatever “intellectual strategies” the authors might like to discern in a supposed “HIV denial movement”, both of which phrases imply that the battle is a political one, when in fact it is only a political one because the defenders of the paradigm resist the free and open purely scientific review demanded by the critics.

There is very little coordination among the disparate and widely scattered sources of paradigm rebuttal, such as this blog, or the many individuals and groups around the world listed in the Accurate/Helpful section of our link index on the right. Rather, there appears to be much more coordination in the consistent, in fact universal refusal of the many individuals and institutions working with the globally entrenched paradigm to countenance any questioning at all, let alone respect any critics, who are countered with media censorship, funding and tenure refusals, and active smearing and disinformation at AIDSTruth, the New York Times and multiple media outlets.

To repeat, our pair of paradigm defenders in stating their purpose neatly evade the need to produce any kind of scientific rebuttal by quoting the NIAID Factsheet and the site AIDSTruth.org of John P. Moore as sources of rebuttal, when neither is peer-reviewed and the latter site very seriously misleading in its science, as this blog has often pointed out in earlier posts, most egregiosuly including statements where scientists contradict their own research, most notoriously Nancy Padian and her attempt to disown her landmark study demonstrating “HIV positivity” does not transmit between the sexes.

These scientifically corrupted sites cannot weigh in the balance against the peer-reviewed rejections of the paradigm in the highest journals in science by one of the most respected practitioners of retrovirology, Peter Duesberg, who is universally respected for his own work by his peers, even those who resist his HIV=AIDS critique, for the quality of all his research and publications, which have never been questioned, except for the extremely high quality critique he has made of HIV=AIDS theory, which has led those of his colleagues who are its promoters to shun him, rather than answer him, which in itself is a signal of how much they fear his view. But none of them has ever called him personally anything but a fine scientist.

6. Misinformation peddled as fact

tomatofrog.jpegOne of the prominent HIV denial groups currently is Christine Maggiore’s “Alive and Well” (formerly “HEAL,” Health Education AIDS Liaison) (http://www.aliveandwell.org/). Maggiore’s life story is at the center of this group. Diagnosed with HIV in 1992, Maggiore claims she has since been symptom-free for the past 14 years without the use of antiretroviral drugs, including protease inhibitors [10]. She has risen to prominence, and been embroiled in controversy, in recent years after giving birth to and openly breast-feeding her two children, Charles and Eliza Jane. She had neither child tested for HIV, and did not take antiretroviral medication during her pregnancy or subsequent breast-feeding [11]. Eliza Jane died in September 2005 of HIV-related pneumonia [12], though Maggiore remains unconvinced that HIV had any role in her daughter’s death [13], and continues to preach her message to other HIV-positive mothers.

Response: This paragraph is misleading on the facts, which it misstates in prejudicial terms. Whether Christine Maggiore was ever HIV positive remains a question, with her critics now saying she was not. Her resistance to treatment with standard medication would be understandable, even if she hadn’t read deeply into the paradigm issue and written a very thorough book debunking it.

The hounding of Maggiore on the false assumption she betrayed her daughter by not having her tested for HIV is deplorable, since the tragedy of Maggiore’s child Eliza Jane was that she suffered a rapidly fatal allergic shock reaction to an antibiotic, and had no AIDS symptoms, contrary to claims by the coroner. She did not suffer from HIV∫AIDS nor did she die from it, since she did not test HIV positive after death, and her T cell count was quite remarkably high.

The lynch mob treatment of Christine Maggiore in the aftermath of this tragedy by misinformed people has been one of the worst episodes of this wretched affair, and it may reasonably be labeled a disgrace that reputable scientists such as Tara and Steven should blindly join in this perfidy, where naivete is no excuse.

7. Mistaken belief that science is a democracy, decided by the authority of consensus

greentreefrog.jpegThat HIV is the primary cause of AIDS is the strongly held consensus opinion of the scientific community, based upon over two decades of robust research. Deniers must therefore reject this consensus, either by denigrating the notion of scientific authority in general, or by arguing that the mainstream HIV community is intellectually compromised. It is therefore not surprising that much of the newer denial literature reflects a basic distrust of authority and of the institutions of science and medicine. In her book, Christine Maggiore thanks her father Robert, “who taught me to question authority and stand up for what’s right” [10]. Similarly, mathematical modeler Dr. Rebecca Culshaw, another HIV denier, states: “As someone who has been raised by parents who taught me from a young age never to believe anything just because ‘everyone else accepts it to be true,’ I can no longer just sit by and do nothing, thereby contributing to this craziness” [17].

Response: All established paradigms are naturally and inevitably based on wide consensus, but all advances of a major order in science and medicine involve overturning that consensus. Science is not a democracy, and its questions are not decided by vote. It is decided by gathering research data and by reasoning, in open debate, on the meaning of the data, and this free discussion is the life blood of good science. The worst sign of a paradigm which has gone past its due date is the fierce resistance which gathers to prevent its overthrow by rejecting criticism.

Any time anyone calls for repressing any view in science, as the HIV=AIDS promoters do, they betray their lack of understanding of how science develops. When scientists or institutions foreclose debate by refusing to review any data or interpretation called into question in the peer reviewed literature, they abandon science itself, which dies if questioning dies, and becomes religion.

Authority and consensus might reflect the best judgment of the current leaders of a field, but consensus is always subject to the myriad social and psychological influences listed at the top of this blog. These may influence the peer-reviewed literature too, but with all its flaws it’s the best measure of the validity of a paradigm that we have, and that is why this blog reviews the paradigm in the light of the literature, which lies unread by most defenders of the faith, including it seems clear, Tara and Steven.

To be continued.

Sloppy science everywhere

September 21st, 2007

Hotz at Journal initiates wave of media coverage of error in science

Hotter the field, the more bias

Most studies wrong

error-sign.jpegAttentive perusers of this modest blog may have noticed that we recently expanded its subhead to include the thought that while we base our critique of the public claims of Robert Gallo, Anthony Fauci, John P. Moore, Mark Wainberg, Nancy Padian and other highly decorated generals of the HIV∫AIDS salvation army on the peer-reviewed literature, a certain caveat is in order.

Not everything which finds its way into science and medical journals, even the top ones, is totally reliable, because even if the authors are not conscious of being emotionally flawed human beings subject to all the warping influences listed in the blogo above, their best efforts would still include bad design, inadvertent error and unconscious “data management”, perhaps because they make false assumptions at the start of the study, a habit which is universal in HIV∫AIDS.

As we have mentioned earlier one of the more distinguished scientists we have been privileged to interview, the renowned Harvard researcher and Nobel prize winner Walter Gilbert, once confided to us that whenever he embarked on a new investigation prompted by someone else’s paper he would always try to repeat the experiment himself, and was surprisingly often chagrined to find that he couldn’t.

And in our early efforts to report on the objections raised by the equally distinguished retrovirology researcher Peter Duesberg of Berkeley to the theoretical kite flown by Robert Gallo in 1984 in AIDS, the unlikely notion that the ugly and fatal new syndrome of immune collapse was cause by an infectious virus eventually labeled Human Immunodeficiency Virus, unfortunately immediately backed by the federal government and thus rendered sacrosanct, we were taken aback by the deep analysis of papers in HIV∫AIDS that the Berkeley professor frequently explained to us privately which showed they were badly done and poorly argued and as a result entirely misleading, even if one accepted the uncritical assumption that they were all based upon, that HIV was the right culprit for the new and appalling disease.

Politely ignoring a huge problem

We also noted, however, that in arguing against the HIV=AIDS paradigm, professor Duesberg did not at first rely on exposing the shoddiness of the papers that resulted from it. He would directly undermine the paradigm by accepting the data and conclusions of the literature, and then show how the paradigm did not stack up – in fact was contradicted by the very papers that were claimed to shore it up.

Only later was he forced to show how many major results were based on poorly designed studies which were misinterpreted, an obligation unfairly thrust upon him in answering the somewhat specious demand, Well if it isn’t HIV, what is it that causes AIDS, then? The demand is specious because so much of the literature is based on the assumption that it is HIV which is the villain in the drama, that most of it will have to be redone without that assumption to nail down the real and obviously multiple causes of immune failure in all five continents, with all their disparate symptoms and epidemiology.

A mudslide of articles about error

Anyhow we are pleased to notice that a rash of articles came out this week publicizing this little noticed fact, that it is not simply fraud which occasionally corrupts the peer-reviewed literature, it is the inadequacy of peer review, which often lets go by papers which should have been corrected or redone, whose conclusions are unreliable.

Needless to say, one of the marks of the horrendously incompetent science reporting carried out in the media – reporting that mostly doesn’t rise above the level of noting down and publishing what sources say without it passing through the critical faculties of the reporter, assuming that these even exist, let alone actually double checking it with critics in the traditional manner observed in every other field of public affairs – is that none of the top reporters whose specialty HIV=AIDS is, with the exception of HIV skeptic Celia Farber in Harpers, and of course HIV skeptic Liam Scheff elsewhere, has shown any interest whatsoever in the possibility that research in the field is questionable.

It is as if they either didn’t know, or have given the NIAID under the firm control of Lasker winner Dr Anthony Fauci a free pass, for some reason, possibly one associated with the undeniable hostility of that public servant to such notions.

How wrong it is to assume that published, peer reviewed science is scripture engraved in tablets of stone is well known to those familiar with the Baltimore scandal, where Nobelist David Baltimore blocked retraction of an incorrect paper with his name on it for years until three Congressional investigations finally prised his protective grip from it. Whether error or knowing fraud (by the lead author, not Baltimore) was involved was not quite made clear, but the subsequent book by Daniel Kevles exonerated Dr Baltimore sufficiently that having been ignominiously kicked out of the presidency of Rockefeller University, eventually the renowned researcher was able to be reinstated in the eyes of the public with the presidency of Caltech, from which he recently retired, where professor Kevles also moved from Yale.

Hotz’ hot column points to Ioannidis’s white hot essay

But fraud is not an interesting subject to contemplate, even if the cases of it which are occasionally exposed in the public prints are often spectacular, as in the case of the downfall of the Korean gentleman recently. The important point is that bad but not intentionally fraudulent science gets into print even in the top journals, as HIV/AIDS has shown in its own spectacular fashion, and science reporters seem universally unaware of this possibility. Now however, we have more than one article suddenly acknowledging this problem.

The first was last Friday, when the Wall Street Journal printed a column by Robert Lee Hotz, Most Science Studies Appear to Be Tainted By Sloppy Analysis, reporting on the work of John Ioannidis, an epidemiologist who studies research methods at the University of Ioannina School of Medicine in Greece and Tufts University in Medford, Mass.

ioannidis.jpgIoannidis has documented how the conclusions of thousands of peer-reviewed research papers may be invalid because the research is inept. In fact, he is the star of the Public Library of Science, where his stunningly honest essay of 2005, Why Most Published Research Findings Are False is their most downloaded technical paper, which is clearly what prompted Hotz’ column.

The essay is a strong contrast with Tara C. Smith and Steven Novella’s froglike masterpiece which we are deconstructing here when more important matters do not obtrude, as in the case of this exemplary piece of research based, logically sound, statistically formulated and politically sophisticated scientific commentary:

Summary

There is increasing concern that most current published research findings are false. The probability that a research claim is true may depend on study power and bias, the number of other studies on the same question, and, importantly, the ratio of true to no relationships among the relationships probed in each scientific field. In this framework, a research finding is less likely to be true when the studies conducted in a field are smaller; when effect sizes are smaller; when there is a greater number and lesser preselection of tested relationships; where there is greater flexibility in designs, definitions, outcomes, and analytical modes; when there is greater financial and other interest and prejudice; and when more teams are involved in a scientific field in chase of statistical significance. Simulations show that for most study designs and settings, it is more likely for a research claim to be false than true. Moreover, for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias….

Published research findings are sometimes refuted by subsequent evidence, with ensuing confusion and disappointment. Refutation and controversy is seen across the range of research designs, from clinical trials and traditional epidemiological studies [1–3] to the most modern molecular research [4,5]. There is increasing concern that in modern research, false findings may be the majority or even the vast majority of published research claims [6–8]. However, this should not be surprising. It can be proven that most claimed research findings are false. …..

Bias

First, let us define bias as the combination of various design, data, analysis, and presentation factors that tend to produce research findings when they should not be produced…..

Corollary 4: The greater the flexibility in designs, definitions, outcomes, and analytical modes in a scientific field, the less likely the research findings are to be true. Flexibility increases the potential for transforming what would be “negative” results into “positive” results, i.e., bias, u.…..


Corollary 5: The greater the financial and other interests and prejudices in a scientific field, the less likely the research findings are to be true. Conflicts of interest and prejudice may increase bias, u. Conflicts of interest are very common in biomedical research [26], and typically they are inadequately and sparsely reported [26,27]. Prejudice may not necessarily have financial roots. Scientists in a given field may be prejudiced purely because of their belief in a scientific theory or commitment to their own findings. Many otherwise seemingly independent, university-based studies may be conducted for no other reason than to give physicians and researchers qualifications for promotion or tenure. Such nonfinancial conflicts may also lead to distorted reported results and interpretations. Prestigious investigators may suppress via the peer review process the appearance and dissemination of findings that refute their findings, thus condemning their field to perpetuate false dogma. Empirical evidence on expert opinion shows that it is extremely unreliable [28].


Corollary 6: The hotter a scientific field (with more scientific teams involved), the less likely the research findings are to be true….

Most Research Findings Are False for Most Research Designs and for Most Fields

Claimed Research Findings May Often Be Simply Accurate Measures of the Prevailing Bias

Traditionally, investigators have viewed large and highly significant effects with excitement, as signs of important discoveries. Too large and too highly significant effects may actually be more likely to be signs of large bias in most fields of modern research. They should lead investigators to careful critical thinking about what might have gone wrong with their data, analyses, and results.

Of course, investigators working in any field are likely to resist accepting that the whole field in which they have spent their careers is a “null field.” However, other lines of evidence, or advances in technology and experimentation, may lead eventually to the dismantling of a scientific field….

How Can We Improve the Situation?

Is it unavoidable that most research findings are false, or can we improve the situation? A major problem is that it is impossible to know with 100% certainty what the truth is in any research question….

Large-scale evidence is also particularly indicated when it can test major concepts rather than narrow, specific questions. A negative finding can then refute not only a specific proposed claim, but a whole field or considerable portion thereof. Selecting the performance of large-scale studies based on narrow-minded criteria, such as the marketing promotion of a specific drug, is largely wasted research.

What matters is the totality of the evidence. Diminishing bias through enhanced research standards and curtailing of prejudices may also help. However, this may require a change in scientific mentality that might be difficult to achieve.

Finally, instead of chasing statistical significance, we should improve our understanding of the range of R values—the pre-study odds—where research efforts operate [10]. Before running an experiment, investigators should consider what they believe the chances are that they are testing a true rather than a non-true relationship. Speculated high R values may sometimes then be ascertained. As described above, whenever ethically acceptable, large studies with minimal bias should be performed on research findings that are considered relatively established, to see how often they are indeed confirmed. I suspect several established “classics” will fail the test [36].

Nevertheless, most new discoveries will continue to stem from hypothesis-generating research with low or very low pre-study odds. We should then acknowledge that statistical significance testing in the report of a single study gives only a partial picture, without knowing how much testing has been done outside the report and in the relevant field at large.

Human error in papers

Here is how Hotz in Most Science Studies Appear to Be Tainted By Sloppy Analysis told the many readers of the pragmatic Wall Street Journal about this problem, thus ensuring that many investors, lawyers, and other people who need realistic information about scientific claims of world pandemics are now aware that scientists’ pronouncements, and their published literature, may have to be double checked for accuracy, since the New York Times has a habit of not bothering to do so, not having the money or inclination to employ factcheckers since it trusts its reporters to get it right, since they have instant access after all to the top gurus of every field, and judging from their public appearances do not appear to be overworked:

Most Science Studies Appear to Be Tainted By Sloppy Analysis

We all make mistakes and, if you believe medical scholar John Ioannidis, scientists make more than their fair share. By his calculations, most published research findings are wrong.

Dr. Ioannidis is an epidemiologist who studies research methods at the University of Ioannina School of Medicine in Greece and Tufts University in Medford, Mass. In a series of influential analytical reports, he has documented how, in thousands of peer-reviewed research papers published every year, there may be so much less than meets the eye.

These flawed findings, for the most part, stem not from fraud or formal misconduct, but from more mundane misbehavior: miscalculation, poor study design or self-serving data analysis. “There is an increasing concern that in modern research, false findings may be the majority or even the vast majority of published research claims,” Dr. Ioannidis said. “A new claim about a research finding is more likely to be false than true.”

The hotter the field of research the more likely its published findings should be viewed skeptically, he determined.

…”There is an increasing concern that in modern research, false findings may be the majority or even the vast majority of published research claims,” Dr. Ioannidis said. “A new claim about a research finding is more likely to be false than true.”

Hotz dug around and found plenty of agreement with what Ioannidis is saying, and plenty of material to confirm what the Greek American researcher has found in his many reports:

Take the discovery that the risk of disease may vary between men and women, depending on their genes. Studies have prominently reported such sex differences for hypertension, schizophrenia and multiple sclerosis, as well as lung cancer and heart attacks. In research published last month in the Journal of the American Medical Association, Dr. Ioannidis and his colleagues analyzed 432 published research claims concerning gender and genes (Drs. Nikolaos A. Patsopoulos, Athina Tatsioni and John Ioannidis analyzed claims of genetic risk and sex differences in “Claims of Sex Differences: An Empirical Assessment in Genetic Associations,”3 (abstract; login required for full text) published in the Journal of the American Medical Association last month).

Upon closer scrutiny, almost none of them held up. Only one was replicated.

What’s going wrong? The key problem is one most observers of science are well aware of, and that is that science advances hypothesis by hypothesis, which tends to translate into hope by hope, and the data tends to support a new hypothesis unless studies are carefully done to banish that effect:

Statistically speaking, science suffers from an excess of significance. Overeager researchers often tinker too much with the statistical variables of their analysis to coax any meaningful insight from their data sets. “People are messing around with the data to find anything that seems significant, to show they have found something that is new and unusual,” Dr. Ioannidis said.

In the U. S., research is a $55-billion-a-year enterprise that stakes its credibility on the reliability of evidence and the work of Dr. Ioannidis strikes a raw nerve. In fact, his 2005 essay “Why Most Published Research Findings Are False” remains the most downloaded technical paper that the journal PLoS Medicine has ever published.

“He has done systematic looks at the published literature and empirically shown us what we know deep inside our hearts,” said Muin Khoury, director of the National Office of Public Health Genomics at the U.S. Centers for Disease Control and Prevention. “We need to pay more attention to the replication of published scientific results.”

Every new fact discovered through experiment represents a foothold in the unknown. In a wilderness of knowledge, it can be difficult to distinguish error from fraud, sloppiness from deception, eagerness from greed or, increasingly, scientific conviction from partisan passion. As scientific findings become fodder for political policy wars over matters from stem-cell research to global warming, even trivial errors and corrections can have larger consequences.

Still, other researchers warn not to fear all mistakes. Error is as much a part of science as discovery. It is the inevitable byproduct of a search for truth that must proceed by trial and error. “Where you have new areas of knowledge developing, then the science is going to be disputed, subject to errors arising from inadequate data or the failure to recognize new matters,” said Yale University science historian Daniel Kevles. Conflicting data and differences of interpretation are common.

Now in his well worded piece Hotz comes to the point where HIV/AIDS critics will sit up and applaud:(our boldface)

To root out mistakes, scientists rely on each other to be vigilant. Even so, findings too rarely are checked by others or independently replicated. Retractions, while more common, are still relatively infrequent. Findings that have been refuted can linger in the scientific literature for years to be cited unwittingly by other researchers, compounding the errors.

Stung by frauds in physics, biology and medicine, research journals recently adopted more stringent safeguards to protect at least against deliberate fabrication of data. But it is hard to admit even honest error. Last month, the Chinese government proposed a new law to allow its scientists to admit failures without penalty. Next week, the first world conference on research integrity convenes in Lisbon.

Overall, technical reviewers are hard-pressed to detect every anomaly. On average, researchers submit about 12,000 papers annually just to the weekly peer-reviewed journal Science. Last year, four papers in Science were retracted. A dozen others were corrected.

No one actually knows how many incorrect research reports remain unchallenged.

Earlier this year, informatics expert Murat Cokol and his colleagues at Columbia University sorted through 9.4 million research papers at the U.S. National Library of Medicine published from 1950 through 2004 in 4,000 journals. By raw count, just 596 had been formally retracted, Dr. Cokol reported.

“The correction isn’t the ultimate truth either,” Prof. Kevles said.

Well, how many were wrong? That is the unanswered question. If all the papers on HIV/AIDS were immediately retracted because HIV is clearly not involved in causing immune collapse, Science would be crippled as a reference source, and science would lose much of its credibility. An honest error on the part of the editors, perhaps, but inexcusable as long as they claim the role of the gatekeepers and the watchdogs of science.

All of this speaks for the credibility of the well qualified critics of the paradigm in HIV=AIDS and the unusual attention they have paid to the quality of the research papers which support it, where they have found a remarkable level of data mismanagement, poor design and misleading conclusions. Yet their case is typically dismissed by paradigm defenders such as Tara Smoth of Iowa, Steve Connall of Yale, John P. Moore of Weill Cornell with scorn and derision, rather than scientific arguments. The public likewise assumes that the literature is thoroughly validated by peer review.

Now the public has been informed by one prominent newspaper, perhaps the most trusted daily now, that something is rotten in the state of science, and that they should proceed with caution before dismissing all challenges to mainstream science as if they were all ignorant creationism. After all, it is clear now that the paradigm HIV causes AIDS would have been universally discredited long ago but for the papers universally based on the assumption they are used to support.

What’s to be done?

Most people, including almost all the scientists in a field, are unlikely to examine a paper closely enough to find its faults. One wonders just how many beliefs would be dashed if they did. Dr Ioannidis has already found that the new paradigm that the sexes differ in their risk of disease according to their gender is based on 432 studies of which only one was able to be replicated and proven valid.

It is difficult to know what to trust until all the papers on a topic are thoroughly reviewed for bias, and there is no field where bias is so blatant as HIV/AIDS, where scientists such as Moore and Wainberg are so proud of it that Wainberg has suggested imprisonment for the reviewers.

Apparently in one later paper in another PLoS Medicine article earlier this year, Ramal Moonesinghe and Muin Khoury at the U.S. Centers for Disease Control and Prevention demonstrated that the likelihood of a published research result being true increases when that finding has been repeatedly replicated in multiple studies. The article is: “Most Published Research Findings Are False — But a Little Replication Goes a Long Way.

But with bias and preconceptions playing a big part obviously repetition is not enough. Raising the level of awareness among scientists and the public of the fallibility of science is key. Lets hope that the Conference last week in the world capital of port, the world’s most delicious liqueur, started some greater awareness of the problem and improvement of the situation in science. The European Science Foundation and the Office of Research Integrity held a world conference on research integrity in Lisbon, Portugal, Sept. 16-19, 2007, which included papers on best practices, training researchers, and the role played by academic journals).

Gee, we wondered if anyone mentioned HIV/AIDS in this context? Not only is it a field where bias in favor of the unproven and unsubstantiated hypothesis is so rife that every paper is imbued with it, and researchers flaunt their bias as if it was a badge of honor, but as regards testing drugs, there haven’t been any controls in any study after the AZT study was called to a sudden halt twenty years ago because the benefit was so powerfully assumed by gay activists that they insisted that the scientists release the drug immediately without further testing because it would be unfair to withhold it from the placebo control group, who were already finding ways to take it.

This blatant lack of controls is one reason why the drugs in AIDS are not recognized as being as lethal as general studies of the welfare of patients show they are, with half of current AIDS deaths due to the drugs and not to AIDS proper, whatever the cause of that is.

Of course, to those unaware that the scientific literature is subject to human error, that last phrase will come as a surprise.

Here is Hotz’s piece for reference:
September 14, 2007

SCIENCE JOURNAL
By ROBERT LEE HOTZ

Most Science Studies
Appear to Be Tainted
By Sloppy Analysis
September 14, 2007; Page B1

We all make mistakes and, if you believe medical scholar John Ioannidis, scientists make more than their fair share. By his calculations, most published research findings are wrong.

Dr. Ioannidis is an epidemiologist who studies research methods at the University of Ioannina School of Medicine in Greece and Tufts University in Medford, Mass. In a series of influential analytical reports, he has documented how, in thousands of peer-reviewed research papers published every year, there may be so much less than meets the eye.

These flawed findings, for the most part, stem not from fraud or formal misconduct, but from more mundane misbehavior: miscalculation, poor study design or self-serving data analysis. “There is an increasing concern that in modern research, false findings may be the majority or even the vast majority of published research claims,” Dr. Ioannidis said. “A new claim about a research finding is more likely to be false than true.”

The hotter the field of research the more likely its published findings should be viewed skeptically, he determined.

Take the discovery that the risk of disease may vary between men and women, depending on their genes. Studies have prominently reported such sex differences for hypertension, schizophrenia and multiple sclerosis, as well as lung cancer and heart attacks. In research published last month in the Journal of the American Medical Association, Dr. Ioannidis and his colleagues analyzed 432 published research claims concerning gender and genes.
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RECOMMENDED READING

–by Robert Lee Hotz
[Recommended Reading] Drs. Nikolaos A. Patsopoulos, Athina Tatsioni and John Ioannidis analyzed claims of genetic risk and sex differences in “Claims of Sex Differences: An Empirical Assessment in Genetic Associations,”3 (abstract; login required for full text) published in the Journal of the American Medical Association last month.
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Dr. John Ioannidis argued that false findings may be the majority of published research claims, in “Why Most Published Research Findings Are False,”4 in the PLoS Medicine journal, in August 2005.
* * *
In another PLoS Medicine article earlier this year, Ramal Moonesinghe and Muin Khoury at the U.S. Centers for Disease Control and Prevention demonstrated that the likelihood of a published research result being true increases when that finding has been repeatedly replicated in multiple studies. The article is: “Most Published Research Findings Are False — But a Little Replication Goes a Long Way.”5
* * *
The Office of Research Integrity6 promotes integrity in biomedical and behavioral research supported by the U.S. Public Health Service at about 4,000 institutions world-wide.
* * *
The European Science Foundation and the Office of Research Integrity are holding a world conference on research integrity7 in Lisbon, Portugal, Sept. 16-19, 2007. The invited researchers will be presenting papers on best practices, training researchers, and the role played by academic journals.
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Upon closer scrutiny, almost none of them held up. Only one was replicated.

Statistically speaking, science suffers from an excess of significance. Overeager researchers often tinker too much with the statistical variables of their analysis to coax any meaningful insight from their data sets. “People are messing around with the data to find anything that seems significant, to show they have found something that is new and unusual,” Dr. Ioannidis said.

In the U. S., research is a $55-billion-a-year enterprise that stakes its credibility on the reliability of evidence and the work of Dr. Ioannidis strikes a raw nerve. In fact, his 2005 essay “Why Most Published Research Findings Are False” remains the most downloaded technical paper that the journal PLoS Medicine has ever published.

“He has done systematic looks at the published literature and empirically shown us what we know deep inside our hearts,” said Muin Khoury, director of the National Office of Public Health Genomics at the U.S. Centers for Disease Control and Prevention. “We need to pay more attention to the replication of published scientific results.”

Every new fact discovered through experiment represents a foothold in the unknown. In a wilderness of knowledge, it can be difficult to distinguish error from fraud, sloppiness from deception, eagerness from greed or, increasingly, scientific conviction from partisan passion. As scientific findings become fodder for political policy wars over matters from stem-cell research to global warming, even trivial errors and corrections can have larger consequences.

Still, other researchers warn not to fear all mistakes. Error is as much a part of science as discovery. It is the inevitable byproduct of a search for truth that must proceed by trial and error. “Where you have new areas of knowledge developing, then the science is going to be disputed, subject to errors arising from inadequate data or the failure to recognize new matters,” said Yale University science historian Daniel Kevles. Conflicting data and differences of interpretation are common.

To root out mistakes, scientists rely on each other to be vigilant. Even so, findings too rarely are checked by others or independently replicated. Retractions, while more common, are still relatively infrequent. Findings that have been refuted can linger in the scientific literature for years to be cited unwittingly by other researchers, compounding the errors.

Stung by frauds in physics, biology and medicine, research journals recently adopted more stringent safeguards to protect at least against deliberate fabrication of data. But it is hard to admit even honest error. Last month, the Chinese government proposed a new law to allow its scientists to admit failures without penalty. Next week, the first world conference on research integrity convenes in Lisbon.

Overall, technical reviewers are hard-pressed to detect every anomaly. On average, researchers submit about 12,000 papers annually just to the weekly peer-reviewed journal Science. Last year, four papers in Science were retracted. A dozen others were corrected.

No one actually knows how many incorrect research reports remain unchallenged.

Earlier this year, informatics expert Murat Cokol and his colleagues at Columbia University sorted through 9.4 million research papers at the U.S. National Library of Medicine published from 1950 through 2004 in 4,000 journals. By raw count, just 596 had been formally retracted, Dr. Cokol reported.

“The correction isn’t the ultimate truth either,” Prof. Kevles said.

Email me at ScienceJournal@wsj.com9.
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Here for reference is the complete essay by Ionnadis, Why Most Published Research Findings Are False. The boldface is added by NAR to highlight key passages:
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PLoS Medicine
A peer-reviewed, open-access journal published by the Public Library of Science

ESSAY

Why Most Published Research Findings Are False

John P. A. Ioannidis

Summary

There is increasing concern that most current published research findings are false. The probability that a research claim is true may depend on study power and bias, the number of other studies on the same question, and, importantly, the ratio of true to no relationships among the relationships probed in each scientific field. In this framework, a research finding is less likely to be true when the studies conducted in a field are smaller; when effect sizes are smaller; when there is a greater number and lesser preselection of tested relationships; where there is greater flexibility in designs, definitions, outcomes, and analytical modes; when there is greater financial and other interest and prejudice; and when more teams are involved in a scientific field in chase of statistical significance. Simulations show that for most study designs and settings, it is more likely for a research claim to be false than true. Moreover, for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias. In this essay, I discuss the implications of these problems for the conduct and interpretation of research.

Competing Interests: The author has declared that no competing interests exist.

Citation: Ioannidis JPA (2005) Why Most Published Research Findings Are False. PLoS Med 2(8): e124 doi:10.1371/journal.pmed.0020124

Published: August 30, 2005

Copyright: © 2005 John P. A. Ioannidis. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abbreviation: PPV, positive predictive value

John P. A. Ioannidis is in the Department of Hygiene and Epidemiology, University of Ioannina School of Medicine, Ioannina, Greece, and Institute for Clinical Research and Health Policy Studies, Department of Medicine, Tufts-New England Medical Center, Tufts University School of Medicine, Boston, Massachusetts, United States of America. E-mail: jioannid@cc.uoi.gr

Published research findings are sometimes refuted by subsequent evidence, with ensuing confusion and disappointment. Refutation and controversy is seen across the range of research designs, from clinical trials and traditional epidemiological studies [1–3] to the most modern molecular research [4,5]. There is increasing concern that in modern research, false findings may be the majority or even the vast majority of published research claims [6–8]. However, this should not be surprising. It can be proven that most claimed research findings are false. Here I will examine the key factors that influence this problem and some corollaries thereof.

Modeling the Framework for False Positive Findings

Several methodologists have pointed out [9–11] that the high rate of nonreplication (lack of confirmation) of research discoveries is a consequence of the convenient, yet ill-founded strategy of claiming conclusive research findings solely on the basis of a single study assessed by formal statistical significance, typically for a p-value less than 0.05. Research is not most appropriately represented and summarized by p-values, but, unfortunately, there is a widespread notion that medical research articles should be interpreted based only on p-values. Research findings are defined here as any relationship reaching formal statistical significance, e.g., effective interventions, informative predictors, risk factors, or associations. “Negative” research is also very useful. “Negative” is actually a misnomer, and the misinterpretation is widespread. However, here we will target relationships that investigators claim exist, rather than null findings.

It can be proven that most claimed research findings are false.

As has been shown previously, the probability that a research finding is indeed true depends on the prior probability of it being true (before doing the study), the statistical power of the study, and the level of statistical significance [10,11]. Consider a 2 × 2 table in which research findings are compared against the gold standard of true relationships in a scientific field. In a research field both true and false hypotheses can be made about the presence of relationships. Let R be the ratio of the number of “true relationships” to “no relationships” among those tested in the field. R is characteristic of the field and can vary a lot depending on whether the field targets highly likely relationships or searches for only one or a few true relationships among thousands and millions of hypotheses that may be postulated. Let us also consider, for computational simplicity, circumscribed fields where either there is only one true relationship (among many that can be hypothesized) or the power is similar to find any of the several existing true relationships. The pre-study probability of a relationship being true is R/(R + 1). The probability of a study finding a true relationship reflects the power 1 − β (one minus the Type II error rate). The probability of claiming a relationship when none truly exists reflects the Type I error rate, α. Assuming that c relationships are being probed in the field, the expected values of the 2 × 2 table are given in Table 1. After a research finding has been claimed based on achieving formal statistical significance, the post-study probability that it is true is the positive predictive value, PPV. The PPV is also the complementary probability of what Wacholder et al. have called the false positive report probability [10]. According to the 2 × 2 table, one gets PPV = (1 − β)R/(R − βR + α). A research finding is thus more likely true than false if (1 − β)R > α. Since usually the vast majority of investigators depend on α = 0.05, this means that a research finding is more likely true than false if (1 − β)R > 0.05.

Table 1. Research Findings and True Relationships

What is less well appreciated is that bias and the extent of repeated independent testing by different teams of investigators around the globe may further distort this picture and may lead to even smaller probabilities of the research findings being indeed true. We will try to model these two factors in the context of similar 2 × 2 tables.

Bias

First, let us define bias as the combination of various design, data, analysis, and presentation factors that tend to produce research findings when they should not be produced. Let u be the proportion of probed analyses that would not have been “research findings,” but nevertheless end up presented and reported as such, because of bias. Bias should not be confused with chance variability that causes some findings to be false by chance even though the study design, data, analysis, and presentation are perfect. Bias can entail manipulation in the analysis or reporting of findings. Selective or distorted reporting is a typical form of such bias. We may assume that u does not depend on whether a true relationship exists or not. This is not an unreasonable assumption, since typically it is impossible to know which relationships are indeed true. In the presence of bias (Table 2), one gets PPV = ([1 − β]R + uβR)/(R + α − βR + u − uα + uβR), and PPV decreases with increasing u, unless 1 − β ≤ α, i.e., 1 − β ≤ 0.05 for most situations. Thus, with increasing bias, the chances that a research finding is true diminish considerably. This is shown for different levels of power and for different pre-study odds in Figure 1.
Figure 1. PPV (Probability That a Research Finding Is True) as a Function of the Pre-Study Odds for Various Levels of Bias, u

Panels correspond to power of 0.20, 0.50, and 0.80.

Table 2. Research Findings and True Relationships in the Presence of Bias

Conversely, true research findings may occasionally be annulled because of reverse bias. For example, with large measurement errors relationships are lost in noise [12], or investigators use data inefficiently or fail to notice statistically significant relationships, or there may be conflicts of interest that tend to “bury” significant findings [13]. There is no good large-scale empirical evidence on how frequently such reverse bias may occur across diverse research fields. However, it is probably fair to say that reverse bias is not as common. Moreover measurement errors and inefficient use of data are probably becoming less frequent problems, since measurement error has decreased with technological advances in the molecular era and investigators are becoming increasingly sophisticated about their data. Regardless, reverse bias may be modeled in the same way as bias above. Also reverse bias should not be confused with chance variability that may lead to missing a true relationship because of chance.

Testing by Several Independent Teams

Several independent teams may be addressing the same sets of research questions. As research efforts are globalized, it is practically the rule that several research teams, often dozens of them, may probe the same or similar questions. Unfortunately, in some areas, the prevailing mentality until now has been to focus on isolated discoveries by single teams and interpret research experiments in isolation. An increasing number of questions have at least one study claiming a research finding, and this receives unilateral attention. The probability that at least one study, among several done on the same question, claims a statistically significant research finding is easy to estimate. For n independent studies of equal power, the 2 × 2 table is shown in Table 3: PPV = R(1 − βn)/(R + 1 − [1 − α]n − Rβn) (not considering bias). With increasing number of independent studies, PPV tends to decrease, unless 1 − β < α, i.e., typically 1 − β < 0.05. This is shown for different levels of power and for different pre-study odds in Figure 2. For n studies of different power, the term βn is replaced by the product of the terms βi for i = 1 to n, but inferences are similar. Figure 2. PPV (Probability That a Research Finding Is True) as a Function of the Pre-Study Odds for Various Numbers of Conducted Studies, n Panels correspond to power of 0.20, 0.50, and 0.80. Table 3. Research Findings and True Relationships in the Presence of Multiple Studies Corollaries A practical example is shown in Box 1. Based on the above considerations, one may deduce several interesting corollaries about the probability that a research finding is indeed true. Corollary 1: The smaller the studies conducted in a scientific field, the less likely the research findings are to be true. Small sample size means smaller power and, for all functions above, the PPV for a true research finding decreases as power decreases towards 1 − β = 0.05. Thus, other factors being equal, research findings are more likely true in scientific fields that undertake large studies, such as randomized controlled trials in cardiology (several thousand subjects randomized) [14] than in scientific fields with small studies, such as most research of molecular predictors (sample sizes 100-fold smaller) [15]. Corollary 2: The smaller the effect sizes in a scientific field, the less likely the research findings are to be true. Power is also related to the effect size. Thus research findings are more likely true in scientific fields with large effects, such as the impact of smoking on cancer or cardiovascular disease (relative risks 3–20), than in scientific fields where postulated effects are small, such as genetic risk factors for multigenetic diseases (relative risks 1.1–1.5) [7]. Modern epidemiology is increasingly obliged to target smaller effect sizes [16]. Consequently, the proportion of true research findings is expected to decrease. In the same line of thinking, if the true effect sizes are very small in a scientific field, this field is likely to be plagued by almost ubiquitous false positive claims. For example, if the majority of true genetic or nutritional determinants of complex diseases confer relative risks less than 1.05, genetic or nutritional epidemiology would be largely utopian endeavors.

Corollary 3: The greater the number and the lesser the selection of tested relationships in a scientific field, the less likely the research findings are to be true. As shown above, the post-study probability that a finding is true (PPV) depends a lot on the pre-study odds (R). Thus, research findings are more likely true in confirmatory designs, such as large phase III randomized controlled trials, or meta-analyses thereof, than in hypothesis-generating experiments. Fields considered highly informative and creative given the wealth of the assembled and tested information, such as microarrays and other high-throughput discovery-oriented research [4,8,17], should have extremely low PPV.

Corollary 4: The greater the flexibility in designs, definitions, outcomes, and analytical modes in a scientific field, the less likely the research findings are to be true. Flexibility increases the potential for transforming what would be “negative” results into “positive” results, i.e., bias, u. For several research designs, e.g., randomized controlled trials [18–20] or meta-analyses [21,22], there have been efforts to standardize their conduct and reporting. Adherence to common standards is likely to increase the proportion of true findings. The same applies to outcomes. True findings may be more common when outcomes are unequivocal and universally agreed (e.g., death) rather than when multifarious outcomes are devised (e.g., scales for schizophrenia outcomes) [23]. Similarly, fields that use commonly agreed, stereotyped analytical methods (e.g., Kaplan-Meier plots and the log-rank test) [24] may yield a larger proportion of true findings than fields where analytical methods are still under experimentation (e.g., artificial intelligence methods) and only “best” results are reported. Regardless, even in the most stringent research designs, bias seems to be a major problem. For example, there is strong evidence that selective outcome reporting, with manipulation of the outcomes and analyses reported, is a common problem even for randomized trails [25]. Simply abolishing selective publication would not make this problem go away.

Corollary 5: The greater the financial and other interests and prejudices in a scientific field, the less likely the research findings are to be true. Conflicts of interest and prejudice may increase bias, u. Conflicts of interest are very common in biomedical research [26], and typically they are inadequately and sparsely reported [26,27]. Prejudice may not necessarily have financial roots. Scientists in a given field may be prejudiced purely because of their belief in a scientific theory or commitment to their own findings. Many otherwise seemingly independent, university-based studies may be conducted for no other reason than to give physicians and researchers qualifications for promotion or tenure. Such nonfinancial conflicts may also lead to distorted reported results and interpretations. Prestigious investigators may suppress via the peer review process the appearance and dissemination of findings that refute their findings, thus condemning their field to perpetuate false dogma. Empirical evidence on expert opinion shows that it is extremely unreliable [28].


Corollary 6: The hotter a scientific field (with more scientific teams involved), the less likely the research findings are to be true.
This seemingly paradoxical corollary follows because, as stated above, the PPV of isolated findings decreases when many teams of investigators are involved in the same field. This may explain why we occasionally see major excitement followed rapidly by severe disappointments in fields that draw wide attention. With many teams working on the same field and with massive experimental data being produced, timing is of the essence in beating competition. Thus, each team may prioritize on pursuing and disseminating its most impressive “positive” results. “Negative” results may become attractive for dissemination only if some other team has found a “positive” association on the same question. In that case, it may be attractive to refute a claim made in some prestigious journal. The term Proteus phenomenon has been coined to describe this phenomenon of rapidly alternating extreme research claims and extremely opposite refutations [29]. Empirical evidence suggests that this sequence of extreme opposites is very common in molecular genetics [29].

These corollaries consider each factor separately, but these factors often influence each other. For example, investigators working in fields where true effect sizes are perceived to be small may be more likely to perform large studies than investigators working in fields where true effect sizes are perceived to be large. Or prejudice may prevail in a hot scientific field, further undermining the predictive value of its research findings. Highly prejudiced stakeholders may even create a barrier that aborts efforts at obtaining and disseminating opposing results. Conversely, the fact that a field is hot or has strong invested interests may sometimes promote larger studies and improved standards of research, enhancing the predictive value of its research findings. Or massive discovery-oriented testing may result in such a large yield of significant relationships that investigators have enough to report and search further and thus refrain from data dredging and manipulation.

Most Research Findings Are False for Most Research Designs and for Most Fields

In the described framework, a PPV exceeding 50% is quite difficult to get. Table 4 provides the results of simulations using the formulas developed for the influence of power, ratio of true to non-true relationships, and bias, for various types of situations that may be characteristic of specific study designs and settings. A finding from a well-conducted, adequately powered randomized controlled trial starting with a 50% pre-study chance that the intervention is effective is eventually true about 85% of the time. A fairly similar performance is expected of a confirmatory meta-analysis of good-quality randomized trials: potential bias probably increases, but power and pre-test chances are higher compared to a single randomized trial. Conversely, a meta-analytic finding from inconclusive studies where pooling is used to “correct” the low power of single studies, is probably false if R ≤ 1:3. Research findings from underpowered, early-phase clinical trials would be true about one in four times, or even less frequently if bias is present. Epidemiological studies of an exploratory nature perform even worse, especially when underpowered, but even well-powered epidemiological studies may have only a one in five chance being true, if R = 1:10. Finally, in discovery-oriented research with massive testing, where tested relationships exceed true ones 1,000-fold (e.g., 30,000 genes tested, of which 30 may be the true culprits) [30,31], PPV for each claimed relationship is extremely low, even with considerable standardization of laboratory and statistical methods, outcomes, and reporting thereof to minimize bias.
Table 4. PPV of Research Findings for Various Combinations of Power (1 − β), Ratio of True to Not-True Relationships (R), and Bias (u)

Claimed Research Findings May Often Be Simply Accurate Measures of the Prevailing Bias

As shown, the majority of modern biomedical research is operating in areas with very low pre- and post-study probability for true findings. Let us suppose that in a research field there are no true findings at all to be discovered. History of science teaches us that scientific endeavor has often in the past wasted effort in fields with absolutely no yield of true scientific information, at least based on our current understanding. In such a “null field,” one would ideally expect all observed effect sizes to vary by chance around the null in the absence of bias. The extent that observed findings deviate from what is expected by chance alone would be simply a pure measure of the prevailing bias.

For example, let us suppose that no nutrients or dietary patterns are actually important determinants for the risk of developing a specific tumor. Let us also suppose that the scientific literature has examined 60 nutrients and claims all of them to be related to the risk of developing this tumor with relative risks in the range of 1.2 to 1.4 for the comparison of the upper to lower intake tertiles. Then the claimed effect sizes are simply measuring nothing else but the net bias that has been involved in the generation of this scientific literature. Claimed effect sizes are in fact the most accurate estimates of the net bias. It even follows that between “null fields,” the fields that claim stronger effects (often with accompanying claims of medical or public health importance) are simply those that have sustained the worst biases.

For fields with very low PPV, the few true relationships would not distort this overall picture much. Even if a few relationships are true, the shape of the distribution of the observed effects would still yield a clear measure of the biases involved in the field. This concept totally reverses the way we view scientific results. Traditionally, investigators have viewed large and highly significant effects with excitement, as signs of important discoveries. Too large and too highly significant effects may actually be more likely to be signs of large bias in most fields of modern research. They should lead investigators to careful critical thinking about what might have gone wrong with their data, analyses, and results.

Of course, investigators working in any field are likely to resist accepting that the whole field in which they have spent their careers is a “null field.” However, other lines of evidence, or advances in technology and experimentation, may lead eventually to the dismantling of a scientific field. Obtaining measures of the net bias in one field may also be useful for obtaining insight into what might be the range of bias operating in other fields where similar analytical methods, technologies, and conflicts may be operating.

How Can We Improve the Situation?

Is it unavoidable that most research findings are false, or can we improve the situation? A major problem is that it is impossible to know with 100% certainty what the truth is in any research question. In this regard, the pure “gold” standard is unattainable. However, there are several approaches to improve the post-study probability.

Better powered evidence, e.g., large studies or low-bias meta-analyses, may help, as it comes closer to the unknown “gold” standard. However, large studies may still have biases and these should be acknowledged and avoided. Moreover, large-scale evidence is impossible to obtain for all of the millions and trillions of research questions posed in current research. Large-scale evidence should be targeted for research questions where the pre-study probability is already considerably high, so that a significant research finding will lead to a post-test probability that would be considered quite definitive. Large-scale evidence is also particularly indicated when it can test major concepts rather than narrow, specific questions. A negative finding can then refute not only a specific proposed claim, but a whole field or considerable portion thereof. Selecting the performance of large-scale studies based on narrow-minded criteria, such as the marketing promotion of a specific drug, is largely wasted research. Moreover, one should be cautious that extremely large studies may be more likely to find a formally statistical significant difference for a trivial effect that is not really meaningfully different from the null [32–34].

Second, most research questions are addressed by many teams, and it is misleading to emphasize the statistically significant findings of any single team. What matters is the totality of the evidence. Diminishing bias through enhanced research standards and curtailing of prejudices may also help. However, this may require a change in scientific mentality that might be difficult to achieve. In some research designs, efforts may also be more successful with upfront registration of studies, e.g., randomized trials [35]. Registration would pose a challenge for hypothesis-generating research. Some kind of registration or networking of data collections or investigators within fields may be more feasible than registration of each and every hypothesis-generating experiment. Regardless, even if we do not see a great deal of progress with registration of studies in other fields, the principles of developing and adhering to a protocol could be more widely borrowed from randomized controlled trials.

Finally, instead of chasing statistical significance, we should improve our understanding of the range of R values—the pre-study odds—where research efforts operate [10]. Before running an experiment, investigators should consider what they believe the chances are that they are testing a true rather than a non-true relationship. Speculated high R values may sometimes then be ascertained. As described above, whenever ethically acceptable, large studies with minimal bias should be performed on research findings that are considered relatively established, to see how often they are indeed confirmed. I suspect several established “classics” will fail the test [36].

Nevertheless, most new discoveries will continue to stem from hypothesis-generating research with low or very low pre-study odds. We should then acknowledge that statistical significance testing in the report of a single study gives only a partial picture, without knowing how much testing has been done outside the report and in the relevant field at large. Despite a large statistical literature for multiple testing corrections [37], usually it is impossible to decipher how much data dredging by the reporting authors or other research teams has preceded a reported research finding. Even if determining this were feasible, this would not inform us about the pre-study odds. Thus, it is unavoidable that one should make approximate assumptions on how many relationships are expected to be true among those probed across the relevant research fields and research designs. The wider field may yield some guidance for estimating this probability for the isolated research project. Experiences from biases detected in other neighboring fields would also be useful to draw upon. Even though these assumptions would be considerably subjective, they would still be very useful in interpreting research claims and putting them in context.

Box 1. An Example: Science at Low Pre-Study Odds

Let us assume that a team of investigators performs a whole genome association study to test whether any of 100,000 gene polymorphisms are associated with susceptibility to schizophrenia. Based on what we know about the extent of heritability of the disease, it is reasonable to expect that probably around ten gene polymorphisms among those tested would be truly associated with schizophrenia, with relatively similar odds ratios around 1.3 for the ten or so polymorphisms and with a fairly similar power to identify any of them. Then R = 10/100,000 = 10−4, and the pre-study probability for any polymorphism to be associated with schizophrenia is also R/(R + 1) = 10−4. Let us also suppose that the study has 60% power to find an association with an odds ratio of 1.3 at α = 0.05. Then it can be estimated that if a statistically significant association is found with the p-value barely crossing the 0.05 threshold, the post-study probability that this is true increases about 12-fold compared with the pre-study probability, but it is still only 12 × 10−4.

Now let us suppose that the investigators manipulate their design, analyses, and reporting so as to make more relationships cross the p = 0.05 threshold even though this would not have been crossed with a perfectly adhered to design and analysis and with perfect comprehensive reporting of the results, strictly according to the original study plan. Such manipulation could be done, for example, with serendipitous inclusion or exclusion of certain patients or controls, post hoc subgroup analyses, investigation of genetic contrasts that were not originally specified, changes in the disease or control definitions, and various combinations of selective or distorted reporting of the results. Commercially available “data mining” packages actually are proud of their ability to yield statistically significant results through data dredging. In the presence of bias with u = 0.10, the post-study probability that a research finding is true is only 4.4 × 10−4. Furthermore, even in the absence of any bias, when ten independent research teams perform similar experiments around the world, if one of them finds a formally statistically significant association, the probability that the research finding is true is only 1.5 × 10−4, hardly any higher than the probability we had before any of this extensive research was undertaken!

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How Fauci solved AIDS

September 19th, 2007

At AIDS panel, future Nobelist Fauci revealed way forward

Add HIV to boost T-cells, eliminate drugs

Long run danger remedied by normal health measures

fauci-white-coat.pngAs we were saying, we welcome the Lasker prize which Dr Anthony Fauci of NIAID has won, because we already recognized a year ago the extraordinary contribution that the well tailored director of the National Institute of Allergies and Infectious Diseases had earlier made quietly to the final solution of the world wide AIDS panic, at a New School panel in June last year.

For some reason, perhaps personal modesty, Dr Fauci had not informed the general public previously of his breakthrough in understanding, but merely communicated it to the Proceedings of the National Academy and included it in a chapter on the Immunology of AIDS he wrote for the textbook “Fundamental Immunology”, edited by William E. Paul MD and published by Lippincott, Williams and Wilkins in 2003 (p. 1295):

What Fauci confirmed to the few graduate students and working scientists who perused this book was that the result of HIV arriving in the human body was to touch off and maintain proliferation of T-cells, rather than killing them off.

What happens is that for a 56 fold (5600 per cent) gain in HIV early on CD4 T-cells drop maybe 6% but CD8 T-cells rise 20 per cent. The net increase is there until drugs are provided, in which case this beneficial effect is wiped out. If the drugs are stopped, then the benefit is once again felt.

The total outcome is hidden in the complexity of the immune system – there are other major factors involved in the standard and rather misleading T-cell count, such as rate of production, redistribution, longevity of cells, level of apoptosis and activation induced cell death – but these trends are clear, Fauci pointed out:

“Several investigators have demonstrated that there is an increase in CD4+ T-cell proliferation in both HIV and SIV infection. In certain studies, the enhanced T-cell proliferation that was observed during active disease was significantly decreased following the initiation of anti-retroviral therapy, and proliferation increased again in parallel with plasma viremia following the cessation of treatment in these individuals.

Read the Proceedings for genuine AIDS truths

Fauci’s reference is a paper by Lempicki R. A. et al. in the Proceedings of the National Academy of Sciences (97:13778-83, 2000). The Proceedings is the place where all those seriously interested in what is really going on in science should go, perhaps. It is after all, the place where Peter Duesberg’s definitive review and rejection of HIV as the cause of AIDS took place nearly two decades ago, a beautifully written and argued exposition with 200 footnoted references from mainstream literature which oddly enough has never been answered in the same journal, though the HIV=AIDS paradigm author Bob Gallo promised the editors he would do so.

Apparently Gallo preferred to do so from the safe bunker of the last chapters of Virus Hunting, his 1991 book three years later which was happily not subject to peer review, nor did it have to provide references, unlike Duesberg’s masterpiece, which was afterwards cited in Nobel prize winning biologist Walter Gilbert’s graduate class at Harvard as an exemplary paradigm challenge. But we digress, as usual for the benefit of newcomers to this issue.

Fauci explains what kills T cells

faucihairflat.jpgReturning to Dr Fauci’s brave and perspicacious statement drawing the attention of insiders to the efficacy of HIV in stimulating the immune system, and the negative impact of drugs, this seemed at such odds with the general assumption in HIV∫AIDS that HIV kills T-cells rather than adds to them, and that drugs are needed to defeat the virus at whatever cost, that when Dr Fauci and Mathilde Krim mounted the stage at the New School with Larry Kramer to celebrate 25 years of HIV∫AIDS a year ago June 19th, Robert Houston took the opportunity to ask Dr Fauci about it.

The question came as a rowdy audience of middle aged gays calmed down after upsetting Larry Kramer so much with their objections to him telling the representative of the New York Times that the Times didn’t cover the issue of HIV∫AIDS enough that he stalked off the stage.

His departure was a pity, for his long time friend Dr Fauci gave an extremely informative reply which heralded the final solution of the AIDS puzzle, suggesting both its cause and its cure.

Fauci’s Final Solution in AIDS

facuimikehand-upo.jpgHere’s how it went. Houston asked his question as follows, both flattering the two exceptional scientists and armed with the reference to the Fauci written statement if for some reason the great man saw fit to deny it.

Houston: We have two of the most distinguished scientists in the world on AIDS on this panel and I would like to ask a basic scientific question. How does HIV cause AIDS? Does it do so by directly killing T-cells, as the New York Times science writers seem to tell us, or do you think it does it in the opposite way: by causing T-cells to multiply – and by overactivating the immune system?

And this is how Dr Fauci explained how HIV boosted the immune system, rather than crippled it, having identified drugs as the real cause of T-cell decline in his written review earlier:

Fauci: Well… It does it in both ways. I don’t want to waffle with you on that but it is very, very clear that HIV is related to a very aberrant turning on and activation of T-cells. When T-cells are sustained in their activation – because every time anybody in this room gets an immune response to a benign virus or bacteria your immune system activates (he draws line going up in air with his hand) and then it goes down again (draws line in the air going down again) to the base line.

We like the Freudian slip here in calling HIV a ‘benign” virus, but we may have misheard Fauci – readers can check for themselves when we put the video up on YouTube shortly for the admiration of all.

Here Fauci has confirmed that when HIV is responded to by the immune system, the T-cells are activated to drive it out, and indeed, reference to the Lempicki paper will, as Robert Houston has shown here in the last comment attached to our earlier post nominating Fauci for the Nobel, for a 56-fold rise in HIV viral load between early and intermediate levels of infection, CD4 T-cells decline not very much (around 6% in the chart), while CD8 T-cells rise 20 per cent, for a combined rise of 11%. Now Fauci continued:

When you have a high level of viremia with a lot of activation you just drive the immune system to an aberrant form of activation that leads to the death of a cell, even cells which don’t directly get infected with HIV. They die by a process called apoptosis, meaning essentially they die a suicidal type death.

Here the director of NIAID for 23 years is bringing in cell suicide as a means of explaining how T-cells do die in the face of HIV. Apoptosis is indeed the last refuge of HIV∫AIDS paradigm promoters in their anxiety to explain how it is that HIV might be causing immune collapse by killing T-cells, when there is no discernible biological activity along these lines detected by any researcher in the 23 years of exceptionally well funded HIV∫AIDS research.

The problem is that until Dr Fauci in this reply confirmed that this was the case, doubters had wondered what the evidence was that there was any more cell suicide than normal when the body is aiming for homeostasis, ie returning to the normal balance in the proportions of the constituents of the blood. Cell suicide is a normal process here, and with the levels being maintained, as Dr Fauci confirms, it is hard to see how it is killing off so many T-cells that the immune system collapses.

claudius-ptolemy.jpgThe difficulty that conjuring up cell suicide is intended to solve is that there is no evidence of any mechanism by which HIV directly kills T-cells, which was the original premise of Robert Gallo’s theory that HIV was the cause of the immune collapse of AIDS. The evidence is that HIV does not kill T-Cells, so enthusiasts for the well funded paradigm had to come up with indirect ways it might get rid of T-cells.

Apoptosis is the best they could come up with, which didn’t present any great difficulty to the army of officials, politicians, activists, health workers, journeyman scientists and dying AIDS patients who were told of this solution perhaps because none of them had heard of Ptolemy the Egyptian, who managed to work out elliptical orbits that could predict the movements of the planets even though he assumed that the Sun went around the Earth, rather than vice versa. The indirect mechanisms by which HIV is said to work its fatal effects on T-cells are the elliptical trajectories of the HIV∫AIDS explanation of AIDS.

Now, however, the director of NIAID sums it all up in one beautiful breakthrough concept which accounts, finally, for the ultimate decline and fall of the human immune system after years of responding to HIV by making T-cells which effectively drive out the virus in a matter of weeks, reducing it to minimal levels of as little as one to five active virions per milliliter, impossible to detect without PCR.

Why does it all change? Steam is key

pcousyn-steam_engine.jpgThe puzzle has always been, why does the immune system collapse in five ten or even twenty years, if it has got rid of virtually all virus within six weeks. Fauci now ‘explains’:

You can wind up depleting your T-cells by direct infection and those cells dying or just a burst of aberrant activation and also some elimination by the immune system of infected cells. So it’s not a unified concept; there’s multifactorial ways in which you drain your T-cells and then after a few years you just run out of steam.

sink.jpegIn other words, Dr Fauci is prepared to throw everything including the kitchen sink into the mix. Those who say that HIV doesn’t kill T-cells are wrong, it does kill them by “direct infection” somehow. Then you have more killed by cell suicide after a “burst of aberrant activation”. Finally – here is the key at last – the immune system just “runs out of steam”.

Dr Fauci’s Solution to AIDS

Robert Houston confesses that he failed to follow up his question because he was prepared only for Fauci to deny that T-cells proliferated when faced with HIV. What we wish he had done is congratulate Fauci for a conceptual framework which tells us how to defeat AIDS.
Unless we misunderstand him, here is his solution to HIV∫AIDS:

1. With even a dramatic leap in viral load, the T-cells divide faster in response. The end result is that CD 8 T-cell count goes up substantially, with no significant decline in CD 4 T-cell count.

2. So if there is any concern that the immune system is weak, simply add more HIV.

3. Remove ARV drugs, and T-cells will multiply and return to excess levels again.

4. After defeating HIV is a matter of weeks and then maintaining this success for up to twenty years, somehow the immune system might run of steam.

5. But as Dr Fauci’s choice of phrase implies this loss of steam can surely be prevented with proper exercise, nutrition, fresh air, travel and all other general health stimulants, including the renewed optimism that comes from knowing there is a solution – the Fauci Solution to AIDS.

But since the Lasker winner didn’t actually mention this last point explicitly perhaps we can check with him at the lunch where he will accept his prize, surrounded by the members of the medical and economic establishment, of which he has long been a fully paid up member.

faucihandsinair.jpgSo after years of the whole world left confused and supporting antiretroviral drugs as the only defense against the deadly effect of HIV, we have Dr Fauci to thank for telling us that on the contrary, it is HIV rather than drugs which benefit the immune system.

Of course, it must be acknowledged that both Robert Gallo, and two years later Peter Duesberg, were the first to point out that HIV was harmlessly involved in AIDS. But neither of them detected the fact that it was actually beneficial to AIDS patients.

Gallo, of course, proved that HIV was not the cause of AIDS with his 1984 papers showing it was occurring in only one third of sick AIDS patients, with pre-AIDS patients having it more often, suggesting it was a possible antidote. Now Anthony Fauci has found why – HIV stimulates the immune system – and he has also noticed that drugs have a negative impact.

Considering that the drug companies involved in HIV∫AIDS have a considerable interest in this revision of the paradigm, we feel that Anthony Fauci is showing considerable moral fortitude in revealing these insights in public in front of gay activists, who were already a noisy crowd and most of them funded by the drug companies.

Luckily, however, none of them noticed.

Fauci wins Lasker

September 17th, 2007

Deserves it for his power to explain biological threats, says award

One step towards Nobel for revealing HIV is harmless after all, we say

fauci190.jpgFans of Dr Anthony Fauci, the smoothly tailored director of NIAIDS since 1984, will be pleased to hear he has won the Lasker award.

This is one step nearer the Nobel we heralded earlier here at New AIDS Review, a prize we thought the good doctor deserved for his contributions to our understanding of the solution to AIDS.

After all, his meta review of the grand puzzle in AIDS, how HIV can possibly cause the syndrome without showing any sign whatsoever of relevant biological activity, contained the thrilling revelation that the best antidote to HIV may be HIV itself!

For Fauci noted in that masterwork that the main effect of HIV when it arrives in the bloodstream was to excite the production of greater levels of T cells than normal, ie prompted them to proliferate rather than kill them.

This honest admission that HIV might act as its own cure was modestly communicated only to the National Academy and not to the general public, but since it indicated that an endlessly expensive effort to find a vaccine might not be needed after all, and that the lethal AIDS drugs could be thrown in the trash, we felt it was quite important.

Now the Times backs our contention that Fauci deserves nomination for a trip to Stockholm by reporting with apparent approval that the Lasker will be awarded to the great bureaucrat this year, for his services in facilitating counter measures to AIDS all these years.

September 16, 2007
4 Winners of Lasker Medical Prize
By LAWRENCE K. ALTMAN

Two surgeons who developed prosthetic heart valves that have prolonged the lives of millions of people are among the winners of this year’s Lasker awards, widely considered the nation’s most prestigious medical prizes.

Drs. Alain Carpentier, 74, of the Georges Pompidou hospital in Paris, and Albert Starr, 81, of the Providence Health System in Portland, Ore., are among three American and one French scientists to win the awards, the Albert and Mary Lasker Foundation announced yesterday.

The third, Dr. Ralph M. Steinman, 64, of Rockefeller University in Manhattan, discovered a cell that starts a cascade of immune responses that defend the body against microbes. The cell is now the basis of experimental therapies for cancer and many other diseases.

The fourth winner, Dr. Anthony S. Fauci, 66, is an internationally known immunologist who is being honored as the principal architect of two major Bush administration programs: the President’s Emergency Plan for AIDS Relief, or Pepfar, and Project Bioshield, which seeks to improve countermeasures against potential bioterror agents.

Dr. Fauci, who has directed the National Institute of Allergy and Infectious Diseases since 1984, marshaled scientific evidence to construct the United States’ responses to these two global crises. The Lasker Foundation also cited Dr. Fauci for his role “in explaining issues of great concern like the science behind emerging biological hazards” to the public.

The prestigious Lasker is the harbinger of the Nobel – 72 of the winners have gone on to the Nobel as well – for such great men as Fauci, but for the moment he will have to be happy with the limited renown of the US prize, and will at least be able to pocket a nice piece of change in addition to his royal stipend at NIAID.

Dr. Steinman and Dr. Fauci will each receive $150,000 and Dr. Starr and Dr. Carpentier will each receive $75,000.

Here at NAR we feel vindicated since we suggested to Dr Anthony Fauci when we met him last year, (in the Washington HIVNET meeting where all those he funds to pursue trials of AIDS drugs in Africa gathered to hear him assure them that he would make sure their money came through) that we cover him as a “hero of AIDS’, and were surprised when after several moment’s thought he declined the flattering invitation.

Since Fauci is cited for his helpfulness in “explaining issues of great concern” maybe we will now put up his remarkable answer to Robert Houston at the panel at the New School later in 2006 when he and Mathilde Krim celebrated 25 years of HIV∫AIDS with Larry Kramer, until the gay playwright activist walked off the stage in a huff, when Houston rescued the two by hailing their importance as scientists and asking Fauci how he thought HIV killed T cells.

Dr Fauci’s answer was most informative and we will give the text here shortly after putting the video up on YouTube, in recognition of the signal honor to be extended to Dr Fauci in New York when he next visits.

We can honestly say it is one of the most helpful explanations we have heard any of the paradigm protectors give in public, since Dr Robert Gallo (a double Lasker winner) gave his renowned prize lectures at Columbia University.

When you read and/or hear it you will see what we mean.

Frog (4):Derek Price saw it all

September 14th, 2007

Why human factors spoil science

PLoS authors get it wrong, wielding paradigm as religious belief

Top paradigm critic, elite, peer-reviewed, authoritative, responsible – and stampeded over

derekdesollaprice.jpgAs readers of the evolving blog heading may have noted, we are having trouble finding space to list all the human factors which nowadays interfere with science as a pure and principled search for truth (All contributions welcome:-)).

The fundamental reason for the human factor – politics, bias, and “data management”- being a worse problem than ever before in the history of science is that small science has become Big Science with a vengeance over the last half century.

As huge sums have flowed in and been spent, with attendant and burgeoning publicity and coverage in media and book publishing, science as a practice has morphed from an individual vocation to a group profession, and inevitably it has been adulterated with the attitudes and interests of people who like to inhabit a big institutional framework sustained by large amounts of funding from Washington and Wall Street. Annual direct and associated spending on the HIV∫AIDS paradigm is reckoned at $7 billion a year by one count, for example.

Derek saw it coming

All these problems of the changing nature of science and scientists were foreseen long ago by Yale’s Derek J. De Solla Price, the historian of science, in his powerful little book Little Science Big Science, based on four 1962 Pegram Lectures given at the Brookhaven National Laboratory. Just to quote one paragraph (here broken up):

“I suggest that all those characteristics (first born, lost one parent, etc) apply to people who became eminent in the days of Little Science and that we do not yet have much inkling of whatever new characteristics have been elicited by the change to the new conditions of Big Science.

Many of the personality traits found formerly seem to be consistent with the hypothesis that many scientists turned to their profession for an emotional gratification that was otherwise lacking. If this is true, be it only a partial explanation, one can still see how cataclysmic must be the effect of changing the emotional rewards of the scientific life.

If scientists were, on the whole, relatively normal people, just perhaps more intelligent or even more intelligent in some special directions, it would not be so difficult. But since it appears that scientists are especially sensitive to their modes of gratification and to the very personality traits that have made them become scientists, one must look very carefully at anything which tampers with and changes these systems of reward.

Any such change will make Big Scientists people of very different temperament and personality from those we have become accustomed to as traditional among Little Scientists.”

This paragraph evokes a radical change in temperament and approach to science between old and new science and scientists. Some would say this is perfectly exemplified in HIV∫AIDS by Peter Duesberg and Robert Gallo, the former a vocational scientist unwilling to sacrifice any principles of scientific truthseeking for earthly rewards, the latter a career scientist occupying the opposite end of the spectrum in all his glory as a one time celebrity globetrotter. One indication of which type a scientist may be is the number of papers to which his name attached beyond the number that it is humanly possible for one individual to write. Gallo had 930 papers to his credit by 2002.

Consensus merely means current

We are concerned here, in this obscure but, we hope, eventually influential blog, with this vast social change in science from one very specific point of view: the abysmal lack of understanding among the new order of scientists of how science actually works in ruthlessly replacing its paradigms as it advances, paradigms which naturally sit atop wide consensus before they are so rudely interrupted by better analysis and data.

For what are paradigms after all but the umbrella assumptions under which all who toil in the rice paddies and fields at the bottom of the mountains of science do their work. Journeymen scientists typically never question these ruling beliefs, and why should they? If they did they would never accomplish any work. In a way therefore paradigms serve as the religions of science, and indeed they are often defended in the same irrational manner as religious beliefs.

The stampede of the sheep

sheep-flock.jpgBut these are the sentiments of followers, the congregation rather than the priests. Consensus in science merely means temporary wisdom, it turns out. As paradigms are modified or replaced – stomach ulcers are found to be produced by bacteria, not stress, for example – consensus shifts eventually from old to new. Unfortunately, this group shift is a lot slower and stickier than the shift of thinking individuals.

This is why Jonathan Swift remarked, “When a true genius appears, you can know him by this sign: that all the dunces are in a confederacy against him. ” The fools imagine that current consensus is scriptural authority and always get in the way of anyone with a new and better idea, imagining that they are putting down error, when this may not be the case. If the credentials of the apparently crackpot original thinker are good enough, you first have to examine his case thoroughly and with an open mind.

Paradigms, it seems, are maintained by groups and changed by clever individuals, who often seem off the wall to the army of conventional scientists that naturally opposes them. Individuals are the mountain goats among the sheep, who find something new and better, and then find they have to suffer through all the resistance and scorn offered by believers whose built in assumptions are threatened, not to mention their investment in the old. When those who are successful finally reap their Nobel, they typically have bitter stories to tell of the vicissitudes of their younger days, where paradigm defenders who control peer reviewed publication block their papers and hurl the intellectual equivalent of fiery tar balls and dead cows over the ramparts of their castle at the invaders.

The influx of power and money has magnified the resistance to change beyond measure, because the investment in the old has built up bigger pyramids than ever before. In the case of HIV∫AIDS, moreover, the leaders of the field have implemented active discouragement of media coverage to an unprecedented degree, so many scientists and most heard of the challenge, let alone its merits.

This was demonstrated by Hank Campbell, a contributor at scienceblogging who runs a “thermal analysis” company, recently: “Did you know there was even a debate about whether or not HIV causes AIDS? I didn’t. You might as well have walked up and told me puppies and free money don’t cause happiness – I was that shocked – but a debate there is and I learned about it when I read an editorial in PLoS ( Public Library of Science) Medicine titled HIV Denial in the Internet Era….I had quite literally no idea this was even an issue before I saw the editorial.”

But paradigm protectors such as John P. Moore and Anthony Fauci benefit from the fundamental trend as well. For in modern times, defenders of paradigms are ever more entrenched in vast systems and elite institutions, running invisible colleges which make belief in their paradigm a requirement of club membership. Loss of that highly privileged and rewarding membership can be crippling financially and socially in a way which imposes and fosters unthinking loyalty to whatever paradigm is in place, whatever scientists may privately think.

Why Peter failed to move the pyramid

goatmountainbig.jpegAs the experience of Peter Duesberg demonstrates, even the best scientist in a field whose worth is officially and universally acknowledged can be defeated by the politics of the monsters that the influx of billions into science has created, if the leaders of a profitable paradigm and their vast sea of followers close ranks against him.

For any challenge to the paradigm is a challenge to the system, and those who live by it, for a modern paradigm is an institutionalized belief, as deeply rooted in its secular church as any religion, as rewarding and protective and as stoutly defended by its foot soldiers as Christian or Muslim beliefs.

When Duesberg’s critique first appeared in Cancer Research three years after the HIV∫AIDS paradigm was established, the pyramid was already immovable. The endorsement of the theory by the federal government was made clear at the 1984 press conference, so federal funding had been diverted exclusively to the new solution for almost three years.

Many papers since, culminating in 2003 – see Duesberg’s Papers on HIV∫AIDS – had less and less effect, as the HIV∫AIDS pyramid became one of the new wonders of the world, inflating to a size greater than the Cheops pyramid of Egypt, and as immovable.

That is why the very specific purpose of this blog is this:

To defend good science against the unscientific assumption that challenging institutionalized beliefs in science is by definition wrong.

On the contrary, it is how science evolves. While we all have to be very careful in examining major novelty, which can easily attract spurious enthusiasm in the media via premature press conferences, as in the classic examples of cold fusion and HIV in AIDS, we must remember also that science progresses by replacing paradigms, and that the ever larger built in resistance to change in big science must not be allowed to take over, as it has in HIV∫AIDS.

There the above assumption that critics must be wrong has taken over so completely that the attitude to paradigm critics is reflex scorn, insults and ostracism, all of it deaf to scientific points. It reminds one of church leaders condemning the Monty Python movie, Life of Brian, without having seen it. “You don’t have to go into a pig sty to know that it stinks!”

The ruling assumption of the Tara essay is bad science

frog.jpegAnd nowhere do we have a better example of that thoughtless assumption in action than our favorite Frog, the Library of Science essay by Tara Smith of Iowa and Steven Connall of Yale on “HIV Denial in the Internet Era”, which scorns the heretics of HIV∫AIDS by pretending that their case is nothing but uninformed comment on the Web by ignoramuses.

All of it is written in the belief that the critics of HIV in AIDS are so wrong in tilting against consensus that there is no need to mention their objections in detail. In fact, simply recording their points and their behavior is enough to demonstrate they must be making some kind of error by challenging what ‘everyone knows’.

That is why we now hurry back to list the objections that any person familiar with the history of science and medicine will make to the essay, which in its many misstatements offers a chance to correct all the misconceptions that obscure the case of the critics in the censored debate on the validity of believing in the HIV∫AIDS paradigm, that HIV is an infectious virus which collapses the immune system and causes AIDS.

Cont. next Frog post (5)

Paradigm buster dies

September 11th, 2007

Says “I Love You” as last words, then conks

Alex counted, reported colors, shapes, materials for Irene, even ordered breakfast

But no recursive logic, humanity’s defenders rush to point out

Sad news today. After a brilliant, 31 year academic and show biz career as a student of language and television star on PBS and BBC, Irene Pepperberg’s research subject Alex passed away in the night, last Thursday.

alexparrot.jpgHe knew his colors and shapes, he learned more than 100 English words, and with his own brand of one-liners he established himself in TV shows, scientific reports, and news articles as perhaps the world’s most famous talking bird.

But last week Alex, an African Grey parrot, died, apparently of natural causes, said Dr. Irene Pepperberg, a comparative psychologist at Brandeis University and Harvard who studied and worked with the parrot for most of its life and published reports of his progress in scientific journals. The parrot was 31.

Scientists have long debated whether any other species can develop the ability to learn human language. Alex’s language facility was, in some ways, more surprising than the feats of primates that have been taught American Sign Language, like Koko the gorilla, trained by Penny Patterson at the Gorilla Foundation/Koko.org in Woodside, Calif., or Washoe the chimpanzee, studied by R. Allen and Beatrice Gardner at the University of Nevada in the 1960s and 1970s….

Even up through last week, Alex was working with Dr. Pepperberg on compound words and hard-to-pronounce words. As she put him into his cage for the night last Thursday, Dr. Pepperberg said, Alex looked at her and said: “You be good, see you tomorrow. I love you.”

He was found dead in his cage the next morning, and was determined to have died late Thursday night.

We have known about and admired Alex for a long time, but we were never surprised by his facility with words, since we have long owned an African Grey, who is both affectionate and knows exactly what is going on.

However, we haven’t taught her to order breakfast yet, which was the most human-like feat Alex managed, in our book. Reportedly Irene would ask Alex what he wanted for breakfast, and Alex might say “Apple!’ If he was then brought a banana, he would say “No banana! Apple!”

No, no, humans are still superior!

As Benedict Carey reports Alex was a paradigm buster who pushed the envelope of what bird brains were thought capable of (by scientists), and seemed to surpass both Koko the gorilla and Washoe the chimp in some ways.

But note the resistance that some people put up to any idea that a parrot might compete with a human child. They rush to point out that Alex lacked “recursive logic”, and “grammatical structure”, as if they were defending a fence between humans and the rest of the animal world.

Dr. Pepperberg prompted Alex to learn about 150 words, which he could put into categories, and to count small numbers, as well as colors and shapes. “The work revolutionized the way we think of bird brains,” said Diana Reiss, a psychologist at Hunter College who works with dolphins and elephants. “That used to be a pejorative, but now we look at those brains — at least Alex’s — with some awe.”

Other scientists, while praising the research, cautioned against characterizing Alex’s abilities as human. The parrot learned to communicate in basic expressions — but it did not show the sort of logic and ability to generalize that children acquire at an early age, they said. “There’s no evidence of recursive logic, and without that you can’t work with digital numbers or more complex human grammar,” said David Premack, a professor emeritus of psychology at the University of Pennsylvania.

We prefer to think of the differences as a spectrum in which different abilities merge into one another like the colors in a rainbow, so that we are simply farther along in a continuum where animals and it seems birds and other creatures do have much more in common with us that we have allowed in the past.

bootsieupsodedown.jpgWe used to sit with guests and while they were all still sitting down and we hadn’t yet noticed any signs of incipient departure, our African Grey would suddenly pipe up “Goodbye! Goodbye!” and it would become clear that indeed they were just about ready to take their leave. The parrot could read body language very well. Bootsie (left) was reading cues, she didn’t give them the cue to leave, we assure you.

Does anyone except Irene and other African Grey owners care about Alex’s departure? Seems so. It is currently the top story on the “e-mailed” list at the Times.

We are just sorry to recall how much trouble Irene and Alex had gaining funding for one of the most interesting research projects around. But that’s the fate of paradigm busters.

Here is the story in the Times, Alex, a Parrot Who Had a Way With Words, DiesThe New York Times
September 10, 2007
Alex, a Parrot Who Had a Way With Words, Dies
By BENEDICT CAREY

He knew his colors and shapes, he learned more than 100 English words, and with his own brand of one-liners he established himself in TV shows, scientific reports, and news articles as perhaps the world’s most famous talking bird.

But last week Alex, an African Grey parrot, died, apparently of natural causes, said Dr. Irene Pepperberg, a comparative psychologist at Brandeis University and Harvard who studied and worked with the parrot for most of its life and published reports of his progress in scientific journals. The parrot was 31.

Scientists have long debated whether any other species can develop the ability to learn human language. Alex’s language facility was, in some ways, more surprising than the feats of primates that have been taught American Sign Language, like Koko the gorilla, trained by Penny Patterson at the Gorilla Foundation/Koko.org in Woodside, Calif., or Washoe the chimpanzee, studied by R. Allen and Beatrice Gardner at the University of Nevada in the 1960s and 1970s.

When, in 1977, Dr. Pepperberg, then a doctoral student in chemistry at Harvard, bought Alex from a pet store, scientists had little expectation that any bird could learn to communicate with humans. Most of the research had been done in pigeons, and was not promising.

But by using novel methods of teaching, Dr. Pepperberg prompted Alex to learn about 150 words, which he could put into categories, and to count small numbers, as well as colors and shapes. “The work revolutionized the way we think of bird brains,” said Diana Reiss, a psychologist at Hunter College who works with dolphins and elephants. “That used to be a pejorative, but now we look at those brains — at least Alex’s — with some awe.”

Other scientists, while praising the research, cautioned against characterizing Alex’s abilities as human. The parrot learned to communicate in basic expressions — but it did not show the sort of logic and ability to generalize that children acquire at an early age, they said. “There’s no evidence of recursive logic, and without that you can’t work with digital numbers or more complex human grammar,” said David Premack, a professor emeritus of psychology at the University of Pennsylvania.

Dr. Pepperberg used an innovative approach to teach Alex. African Greys are social birds, and pick up some group dynamics very quickly. In experiments, Dr. Pepperberg would employ one trainer to, in effect, compete with Alex for a small reward, like a grape. Alex learned to ask for the grape by observing what the trainer was doing to get it; the researchers then worked with the bird to help shape the pronunciation of the words.

Alex showed surprising facility. For example, when shown a blue paper triangle, he could tell an experimenter what color the paper was, what shape it was, and — after touching it — what it was made of. He demonstrated off some of his skills on nature shows, including programs on the BBC and PBS. He famously shared scenes with the actor Alan Alda on the PBS series, “Look Who’s Talking.”

Like parrots can, he also picked up one-liners from hanging around the lab, like “calm down,” and “good morning.” He could express frustration, or apparent boredom, and his cognitive and language skills appeared to be about as competent as those in trained primates. His accomplishments have also inspired further work with African Grey parrots; two others, named Griffin and Arthur, are a part of Dr. Pepperberg’s continuing research program.

Even up through last week, Alex was working with Dr. Pepperberg on compound words and hard-to-pronounce words. As she put him into his cage for the night last Thursday, Dr. Pepperberg said, Alex looked at her and said: “You be good, see you tomorrow. I love you.”

He was found dead in his cage the next morning, and was determined to have died late Thursday night.


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