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Last post Author Topic: Peer Review and the Scientific Process  (Read 56708 times)

IainB

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Govt. agencies (UK) use peer review to discourage scientific skepticism
« Reply #75 on: March 30, 2014, 10:40:33 PM »
Here's a  :Thmbsup: to integrity and this group of 30 UK scientists who may have risked their careers by putting their names to this open letter.
(Copied below sans embedded hyperlinks/images.)
Quote
30 Scientists Call For More Challenges To ‘Prevailing Orthodoxies’
Date: 20/03/14     The Guardian

Government agencies use peer review to discourage open-ended inquiries and serious challenges to prevailing orthodoxies.

“Science is the belief in the ignorance of experts,” said Richard Feynman in the 1960s. But times change. Before about 1970, academics had access to modest funding they could use freely. Industry was similarly enlightened. Their results included the transistor, the maser-laser, the electronics and telecommunications revolutions, nuclear power, biotechnology and medical diagnostics galore that enriched the lives of virtually everyone; they also boosted 20th-century economic growth.

After 1970, politicians substantially expanded academic sectors. Peer review’s uses allowed the rise of priorities, impact etc, and is now virtually unavoidable. Applicants’ proposals must convince their peers that they serve national policies and are the best possible uses of resources. Success rates are about 25%, and strict rules govern resubmissions. Rejected proposals are usually lost. Industry too has lost its taste for the unpredictable. The 500 major discoveries, almost all initiated before about 1970, challenged mainstream science and would probably be vetoed today. Nowadays, fields where understanding is poor are usually neglected because researchers must convince experts that working in them will be beneficial.

However, small changes would keep science healthy. Some are outlined in Donald Braben’s book, Promoting the Planck Club: How Defiant Youth, Irreverent Researchers and Liberated Universities Can Foster Prosperity Indefinitely. But policies are deeply ingrained. Agencies claiming to support blue-skies research use peer review, of course, discouraging open-ended inquiries and serious challenges to prevailing orthodoxies. Mavericks once played an essential role in research. Indeed, their work defined the 20th century. We must relearn how to support them, and provide new options for an unforeseeable future, both social and economic. We need influential allies. Perhaps Guardian readers could help?

Donald W Braben University College London
John F Allen Queen Mary, University of London
William Amos University of Cambridge
Richard Ball University of Edinburgh
Tim Birkhead FRS University of Sheffield
Peter Cameron Queen Mary, University of London
Richard Cogdell FRS University of Glasgow
David Colquhoun FRS University College London
Rod Dowler Industry Forum, London
Irene Engle United States Naval Academy, Annapolis
Felipe Fernández-Armesto University of Notre Dame
Desmond Fitzgerald Materia Medica
Pat Heslop-Harrison University of Leicester
Dudley Herschbach Harvard University, Nobel Laureate
H Jeff Kimble Caltech, US National Academy of Sciences
Sir Harry Kroto FRS Florida State University, Tallahassee, Nobel Laureate
James Ladyman University of Bristol
Nick Lane University College London
Peter Lawrence FRS University of Cambridge
Angus MacIntyre FRS Queen Mary, University of London
John Mattick Garvan Institute of Medical Research, Sydney
Beatrice Pelloni University of Reading
Martyn Poliakoff FRS University of Nottingham
Douglas Randall University of Missouri
David Ray Bio Astral Limited
Sir Richard J Roberts FRS New England Biolabs, Nobel Laureate
Ken Seddon Queen’s University of Belfast
Colin Self University of Newcastle
Harry Swinney University of Texas, US National Academy of Sciences
Claudio Vita-Finzi FBA Natural History Museum

The Guardian, 18 March 2014

GWPF Newsletter   
©2013 The GWPF. All Rights Reserved. Information published on this website is for educational use only.   
_______________________

References:

IainB

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Re: Peer Review and the Scientific Process
« Reply #76 on: April 26, 2014, 11:09:06 AM »
A curious paper on psychology by one Prof Lewandowsky at the Univ. of Western Australia was recently retracted by its publishers, Frontiers, and for cogent reasons.
As reported here, the Lewandowsky retraction raises issues on Peer Review.
Quote
Climate Papers Without Peer
by Tony Thomas 6-4-14

Want your, er, highly innovative research to get lots of attention, the sort that keeps those grants coming? You could do worse than start with some kind words from a peer-reviewer whose work is glowingly cited in your own paper. After that, apply for the next batch of grants

Peer review is claimed to be the gold standard for scientific papers. Yet in the establishment climate science world, “peer review” operates differently. Professor Stephan Lewandowsky’s now-retracted paper Recursive Fury, about conspiracy-mindedness of “deniers”, raises a few issues about peer reviewing.
(Read the rest at the link.)

IainB

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Re: Peer Review and the Scientific Process
« Reply #77 on: May 26, 2014, 09:54:26 AM »
Interesting twitter discussion: What is peer review exactly?

IainB

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Re: Peer Review and the Scientific Process
« Reply #78 on: June 14, 2014, 06:41:44 AM »
I recall having read something about this "new discovery" earlier this year with considerable skepticism, and wondering whether it wasn't just another case of rushing something newsworthy/marketable (good for raising research funds) into print in Nature before properly peer reviewing it - especially as some of the media reports had pictures of this attractive girly-girl Japanese PhD student in a white lab coat, surrounded by Hello Kitty memorabilia or something, in her lab/office. She had apparently made the discovery and was grateful that her professor had "believed" in her despite the rest of the department's scientists apparently thinking she was a harebrained crackpot, or something.

So I was somewhat unsurprised to read in slashdot.org:
Japanese Stem Cell Debacle Could Bring Down Entire Center
(Copied below sans embedded hyperlinks/images.)
Quote
sciencehabit (1205606) writes
Shutting down the research center at the heart of an unfolding scientific scandal may be necessary to prevent a recurrence of research misconduct, according to a report released at a press conference in Tokyo today. A committee reviewing conduct at the RIKEN Center for Developmental Biology (CDB) in Kobe, Japan, found lax oversight and a failure on the part of senior authors of two papers in Nature outlining a surprisingly simple way of reprogramming mature cells into stem cells. The committee surmised that a drive to produce groundbreaking results led to publishing results prematurely. "It seems that RIKEN CDB had a strong desire to produce major breakthrough results that would surpass iPS cell research," the report concludes, referring to another type of pluripotent stem cell. "One of our conclusions is that the CDB organization is part of the problem," said committee chair Teruo Kishi Kishi. He recommends a complete overhaul of CDB, including perhaps restructuring it into a new institute. "This has to be more than just changing the nameplate."

IainB

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Re: Peer Review and the Scientific Process
« Reply #79 on: June 24, 2014, 09:24:40 PM »
There has been some discussion in this thread regarding the publication of "bad"/fraudulent science, and how peer review seems incapable of improving the situation and in some cases may actually aggravate it.
In the UK, the MPs in the House of Commons are having a "links day" in which MPs will get together with scientists to discuss the issue of trust in science. Though somewhat belated, this is arguably a Very Good Thing for science.
Trust largely arose as an issue due to the revelations of "Climategate" in 2009 (and again in 2011) - the publication of swathes of emails hacked from the servers at the UK's UEA CRU (University of East Anglia Climate Research Unit) which highlighted what were described as somewhat unscientific/fraudulent goings-on, and the scientists apparently narrowly avoided being put through a Royal Commission of Enquiry on the matter. One outcome from this was a relatively serious collapse of the public's trust in the scientists involved - in the UK and abroad. (This is discussed in its many aspects in the DC Forum in the Basement section - Thermageddon? Postponed!.)

The Bishop Hill blog has a post describing the proposed Links, and in it makes some very pertinent points about the relevance/use of peer review in science and especially the implications where outputs from that science are subsequently fed, along with statistically insignificant data, into a policy development process.
(Copied below sans embedded hyperlinks/images.)
Quote
Parliamentary links day
The House of Commons is having a "links day" in which MPs will get together with scientists to discuss the issue of trust in science. Mark Walport and Paul Nurse will be speaking. I've been following the tweets on the #linksday2014 hashtag and they are a mixed bunch so far.

For example, we learn that Nicola Gulley, the editorial director of the Institute of Physics opined that:

    ...peer review key to maintaining trust in science. No crisis but a lack of understanding of this process.


You can see why someone working in the peer-reviewed journal sector might be keen on peer reviewed science, but for many readers at BH and many others uninvolved with the climate debate, peer review - its ineffectiveness, the superficial aura of "correctness" it gives, and the problem of gatekeeping - are the source of mistrust in science not a solution to it.

On the other hand Mark Walport has apparently been emphasising that science is only one input into the policy process, which is undoubtedly true and a rebuke to the scientivists and activists who constantly criticise politicians for "ignoring" scientists.

When you think about it, there's a link between these two themes. As we know, the peer reviewed evidence demonstrates conclusively that peer review is virtually useless at finding error and fraud (see discussion in The Hockey Stick Illusion). Clearly then, those advocating use of peer reviewed science in the policymaking process must be incorporating non-peer-reviewed elements into their thinking in order to overcome the peer-reviewed evidence that peer-reviewed evidence is no better than non-peer-reviewed evidence.

I'm not sure what conclusions we should draw from this though.
________________________________________
Update on Jun 24, 2014 by Registered CommenterBishop Hill
Paul Nurse is currently speaking at the event. Somewhat predictably he is still airing his GWPF conspiracy theories, as revealed in a tweet by James Wilsdon:

    Paul Nurse warns against taking science advice from “shadowy organisations who refuse to declare their funders.”

Readers will recall the Met Office's scientific advice to Parliament: first telling them that recent changes in global mean surface temperature were statistically significant and then, when pressed for their calculations, prevaricating, then confessing that the changes were not statistically significant and then without apparently batting an eyelid claiming that they did not rely on such statistical analyses.

No doubt these are the kinds of people that Sir Paul feels should be giving scientific advice to politicians.
________________________________________
Update on Jun 24, 2014 by Registered CommenterBishop Hill
More from Sir Paul via the twitter hashtag:

    Parliamentarians, journalists & scientists need to work better together; will increase public trust in science.

(If the press don't hold anyone to account, we can persuade the public of anything).

    "Trust in science key to maintaining democracy" SirPaulNurse @royalsociety rounding off discussions on science & public trust.

(Huh?)

    Uncertainty in scientific issues must be reflected in policy advice says Sir Paul Nurse.

(I'm looking forward to the Royal Society saying that the rise in surface temperatures is not statistically significant).

This Links thing could be encouraging in terms of showing a will to get to the truth which is at the heart of the matter, and it would seem like a good opportunity to take the bull by the horns. However, given the changeable political situation in the UK and the preparatory positioning statements of some of the players (as indicated in the post), I am unsure as to whether the MPs will actually have the bottle to do it. We shall see.

Renegade

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Re: Peer Review and the Scientific Process
« Reply #80 on: June 29, 2014, 09:21:12 PM »
Again about trust...

http://www.psmag.com...-gums-science-84564/

Quote
How the Sugar Industry Gums Up Science

It goes over a bit how "science" is a bitter joke in the hands of the sugar industry shills.

The article links here:

http://blog.ucsusa.o...ebate-at-the-fda-564

Where, thankfully, we can see that there are people that actually care about shilling in science.

Still, I think the most important methodology in modern science is "follow the money", which is an incredibly sad thing.
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IainB

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More of this makes a mockery of "science".
(Copied below sans embedded hyperlinks/images.)
Quote
Scholarly journal retracts 60 articles, smashes ‘peer review ring’ - The Washington Post
By Fred Barbash July 10
Updated

Every now and then a scholarly journal retracts an article because of errors or outright fraud. In academic circles, and sometimes beyond, each retraction is a big deal.

Now comes word of a journal retracting 60 articles at once.

The reason for the mass retraction is mind-blowing: A “peer review and citation ring” was apparently rigging the review process to get articles published.

You’ve heard of prostitution rings, gambling rings and extortion rings. Now there’s a “peer review ring.”

The publication is the Journal of Vibration and Control (JVC). It publishes papers with names like “Hydraulic engine mounts: a survey” and “Reduction of wheel force variations with magnetorheological devices.”

The field of acoustics covered by the journal is highly technical:

    Analytical, computational and experimental studies of vibration phenomena and their control. The scope encompasses all linear and nonlinear vibration phenomena and covers topics such as: vibration and control of structures and machinery, signal analysis, aeroelasticity, neural networks, structural control and acoustics, noise and noise control, waves in solids and fluids and shock waves.

JVC is part of the SAGE group of academic publications.

Here’s how it describes its peer review process:

[The journal] operates under a conventional single-blind reviewing policy in which the reviewer’s name is always concealed from the submitting author.
All manuscripts are reviewed initially by one of the Editors and only those papers that meet the scientific and editorial standards of the journal, and fit within the aims and scope of the journal, will be sent for peer review.  Generally, reviews from two independent referees are required.

An announcement from SAGE published July 8 explained what happened, albeit somewhat opaquely.

In 2013, the editor of JVC, Ali H. Nayfeh, became aware of people using “fabricated identities” to manipulate an online system called SAGE Track by which scholars review the work of other scholars prior to publication.

Attention focused on a researcher named Peter Chen of the National Pingtung University of Education (NPUE) in Taiwan and “possibly other authors at this institution.”

After a 14-month investigation, JVC determined the ring involved “aliases” and fake e-mail addresses of reviewers — up to 130 of them — in an apparently successful effort to get friendly reviews of submissions and as many articles published as possible by Chen and his friends. “On at least one occasion, the author Peter Chen reviewed his own paper under one of the aliases he created,” according to the SAGE announcement.

The statement does not explain how something like this happens. Did the ring invent names and say they were scholars? Did they use real names and pretend to be other scholars? Doesn’t anyone check on these things by, say, picking up the phone and calling the reviewer?

In any case, SAGE and Nayfeh confronted Chen to give him an “opportunity to address the accusations of misconduct,” the statement said, but were not satisfied with his responses.

In May, “NPUE informed SAGE and JVC that Peter Chen had resigned from his post on 2 February 2014.”

Each of the 60 retracted articles had at least one author and/or one reviewer “who has been implicated in the peer review” ring, said a separate notice issued by JVC.

Efforts by The Washington Post to locate and contact Chen for comment were unsuccessful.

The whole story is described in a publication called “Retraction Watch” under the headline: “SAGE Publications busts ‘peer review and citation ring.’”

“This one,” it said, “deserves a ‘wow.’”

Update: Some additional information from the SAGE statement: “As the SAGE investigation drew to a close, in May 2014 Professor Nayfeh’s retirement was announced and he resigned his position as Editor-in-Chief of JVC….Three senior editors and an additional 27 associate editors with expertise and prestige in the field have been appointed to assist with the day-to-day running of the JVC peer review process. Following Professor Nayfeh’s retirement announcement, the external senior editorial team will be responsible for independent editorial control for JVC.”

Note to readers: Thanks for pointing out my grammatical error. No excuses.

There’s a follow to this story here.

Renegade

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Re: Peer Review and the Scientific Process
« Reply #82 on: July 12, 2014, 03:02:41 AM »
Yay. The supposed results of the skeptical process need to be skeptically questioned because... just... ::facepalm::
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IainB

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Re: Peer Review and the Scientific Process
« Reply #83 on: August 18, 2014, 03:44:15 AM »
Interesting item in Hacker News from peerj.com. It's a link to a .PDF file.
Quote
A surge of p-values between 0.040 and 0.049 in recent decades (but negative results are increasing rapidly too).

It is known that statistically significant results are more likely to be published than results that are not statistically significant.  However, it is unclear whether negative results are disappearing from papers, and whether there exists a ‘hierarchy of sciences’ with the social sciences publishing more positive results than the physical sciences.  Using Scopus, we conducted a search in the abstracts of papers published between 1990 and 2014, and calculated the percentage of papers reporting marginally positive results (i.e., p-values between 0.040 and 0.049) versus the percentage of papers reporting marginally negative results (i.e., p-values between 0.051 and 0.060).  The results indicate that negative results are not disappearing, but have actually become 4.3 times more prevalent since 1990.  Positive results, on the other hand, have become 13.9 times more prevalent since 1990.  We found no consistent support for a ‘hierarchy of sciences’.  However, we did find large differences in reporting practices between disciplines, with the reporting of p-values being 60.6 times more frequent in the biological sciences than in the physical sciences.  We argue that the observed longitudinal trends may be caused by negative factors, such as an increase of questionable research practices, but also by positive factors, such as an increasingly quantitative research focus. ...

Renegade

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Re: Peer Review and the Scientific Process
« Reply #84 on: August 27, 2014, 11:02:27 PM »
If the below turns out to be correct, it's going to be pretty damning against the CDC and "peer review" as we have it now.

http://ireport.cnn.com/docs/DOC-1164794

Quote
Fraud at the CDC uncovered, 340% increased risk of autism hidden from public

More...
http://www.naturalne...C_whistleblower.html

Quote
Vaccine bombshell: CDC whistleblower reveals cover-up linking MMR vaccines to autism in African-Americans



http://www.naturalne...C_whistleblower.html

Quote
A medical conspiracy of epic proportions stands to bring down the entire vaccine house of cards following the revelation that the U.S. Centers for Disease Control and Prevention (CDC) censored key data linking the MMR vaccine to autism. A top CDC researcher-turned-whistleblower has come forward with the truth about a study that the CDC has long claimed proves the safety of MMR, when in fact it actually shows the exact opposite.

http://www.canarypar...t-news&Itemid=50

Quote
Rob Schneider Demands Answers on CDC MMR Fraud   

In light of the revelation that Dr. William Thompson, senior scientiest at CDC, has admitted guilt in hiding data that found that black males are 340% more likely to have an autism diagnosis when given the MMR before age 3, Rob Schneider has written to the office of the Governor of California, Jerry Brown, to assure himself that Brown is aware of the fraud, and to demand answers and actions to protect California children.

http://www.rawstory....changed-autism-data/

Quote
Actor and anti-vaxxer Rob Schneider: I have proof the CDC ‘fraudulently changed’ autism data

Actor and anti-vaccine advocate Rob Schneider contacted California Gov. Jerry Brown’s office (D) claiming to possess documents showing that the Centers for Disease Control has hidden data showing Black children are at a particularly high risk of developing autism from vaccines.

According to the anti-vaccine site The Canary Party, Schneider stated in his letter to deputy legislative secretary Lark Park that he was “compelled” to share his proof of a CDC report the agency suppressed and “fraudulently changed.”

“One disturbing disclosure, AFRICAN AMERICAN CHILDREN were and still are THREE HUNDRED AND FIFTY PERCENT more likely to develop Autism under the current Vaccine MMR schedule,” Schneider wrote. “This according to the original CDC study in 2001.”


On the flip side, here's the "debunk":

http://www.scienceba...rican-american-boys/

Quote
Here we go again.

Regular readers who pay attention to the antivaccine movement almost can’t help but have noticed that last week there was a lot of activity on antivaccine websites, blogs, and Facebook pages, as well as Twitter and Instagram feeds. For all I know, it’s all out there on Pinterest (which I’ve never really understood), Tumblr, and all those other social media sites that I don’t check much, if at all. In particular, it’s been exploding under the Twitter hashtags #CDCwhistleblower, #CDCfraud, and #CDCPantsOnFire. It’s almost impossible to have missed it if you’re plugged in and pay attention to crank websites, as many skeptics do, but here are a selection of the main stories going around over the last few days:

And:

http://scienceblogs....rsy-continues-apace/

Quote
Here it is, Tuesday already, and the antivaccine underground is still on full mental jacket alert over the biggest story the antivaccine movement has seen in a while. Fortunately, it’s a story that’s been largely ignored by the mainstream media, which tells me that maybe, just maybe, the mainstream media has figured out that it shouldn’t give undue credence to cranks. I’m referring, of course, to the claim that the CDC has for 13 years been covering up smoking gun evidence that the MMR vaccine when administered before 36 months causes autism in African-American males.

It's a developing story, so I suppose there's not much to do but wait until more analysis comes out.

If it does turn out that there was fraud, then we have some pretty nasty stuff to deal with.

I've not looked too deeply into it, so I have no idea about what is or isn't correct there. It could all just be complete nonsense, but, considering (source):

http://www.ncbi.nlm.....gov/pubmed/21623535
http://www.ncbi.nlm.....gov/pubmed/24354891
http://www.ncbi.nlm.....gov/pubmed/12145534
http://www.ncbi.nlm.....gov/pubmed/21058170
http://www.ncbi.nlm.....gov/pubmed/15527868

It may not be.

It's not like medical cover-ups haven't happened before.

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IainB

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Re: Peer Review and the Scientific Process
« Reply #85 on: August 27, 2014, 11:45:25 PM »
Yes, I read about this and remain skeptical in the absence of solid proof, either way.

IainB

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Everything We Know Is Wrong
« Reply #86 on: August 29, 2014, 08:11:33 AM »
A surprising programme from BBC Radio 4: Everything We Know Is Wrong (click on link to download/hear the programme)
Quote
Written notes:
Every day the newspapers carry stories of new scientific findings. There are 15 million scientists worldwide all trying to get their research published. But a disturbing fact appears if you look closely: as time goes by, many scientific findings seem to become less true than we thought. It's called the "decline effect" - and some findings even dwindle away to zero.

A highly influential paper by Dr John Ioannidis at Stanford University called "Why most published research findings are false" argues that fewer than half of scientific papers can be believed, and that the hotter a scientific field (with more scientific teams involved), the less likely the research findings are to be true. He even showed that of the 49 most highly cited medical papers, only 34 had been retested and of them 41 per cent had been convincingly shown to be wrong. And yet they were still being cited.

Again and again, researchers are finding the same things, whether it's with observational studies, or even the "gold standard" Randomised Controlled Studies, whether it's medicine or economics. Nobody bothers to try to replicate most studies, and when they do try, the majority of findings don't stack up. The awkward truth is that, taken as a whole, the scientific literature is full of falsehoods.

Jolyon Jenkins reports on the factors that lie behind this. How researchers who are obliged for career reasons to produce studies that have "impact"; of small teams who produce headline-grabbing studies that are too statistically underpowered to produce meaningful results; of the way that scientists are under pressure to spin their findings and pretend that things they discovered by chance are what they were looking for in the first place. It's not exactly fraud, but it's not completely honest either. And he reports on new initiatives to go through the literature systematically trying to reproduce published findings, and of the bitter and personalised battles that can occur as a result.

Producer/Presenter: Jolyon Jenkins.


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Re: Peer Review and the Scientific Process
« Reply #87 on: August 29, 2014, 08:09:56 PM »
Yes, I read about this and remain skeptical in the absence of solid proof, either way.

The issue is mired down with too much baggage. The best one can hope for is just a gamble.
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Re: Peer Review and the Scientific Process
« Reply #88 on: August 29, 2014, 08:12:16 PM »
A surprising programme from BBC Radio 4: Everything We Know Is Wrong (click on link to download/hear the programme)
Quote
Written notes:
Every day the newspapers carry stories of new scientific findings. There are 15 million scientists worldwide all trying to get their research published. But a disturbing fact appears if you look closely: as time goes by, many scientific findings seem to become less true than we thought. It's called the "decline effect" - and some findings even dwindle away to zero.

A highly influential paper by Dr John Ioannidis at Stanford University called "Why most published research findings are false" argues that fewer than half of scientific papers can be believed, and that the hotter a scientific field (with more scientific teams involved), the less likely the research findings are to be true. He even showed that of the 49 most highly cited medical papers, only 34 had been retested and of them 41 per cent had been convincingly shown to be wrong. And yet they were still being cited.

Again and again, researchers are finding the same things, whether it's with observational studies, or even the "gold standard" Randomised Controlled Studies, whether it's medicine or economics. Nobody bothers to try to replicate most studies, and when they do try, the majority of findings don't stack up. The awkward truth is that, taken as a whole, the scientific literature is full of falsehoods.

Jolyon Jenkins reports on the factors that lie behind this. How researchers who are obliged for career reasons to produce studies that have "impact"; of small teams who produce headline-grabbing studies that are too statistically underpowered to produce meaningful results; of the way that scientists are under pressure to spin their findings and pretend that things they discovered by chance are what they were looking for in the first place. It's not exactly fraud, but it's not completely honest either. And he reports on new initiatives to go through the literature systematically trying to reproduce published findings, and of the bitter and personalised battles that can occur as a result.

Producer/Presenter: Jolyon Jenkins.



Interesting. I suppose that it sort of explains why medical advice changes every few years. Yesterday X was great, and today X is bad.
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IainB

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Re: Peer Review and the Scientific Process
« Reply #89 on: August 30, 2014, 10:10:58 PM »
Yes, it could explain such medical "fads", but the more informed amongst us would probably have woken up to those years ago.
The paper seems to be well substantiated (independently observable evidence and reference sources) and thus generally provable/TRUE. There's nothing especially new about it per se, except that it has been reported on by the BBC - infamous for promulgating their religio-political bias and for pushing pseudo-science (e.g., Rotherham, 28Gate, etc.). I suspect they produced the programme by mistake - it probably missed going through their usual internal censorship gate.

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Re: Peer Review and the Scientific Process
« Reply #90 on: August 31, 2014, 08:06:52 AM »
There's nothing especially new about it per se, except that it has been reported on by the BBC - infamous for promulgating their religio-political bias and for pushing pseudo-science (e.g., Rotherham, 28Gate, etc.). I suspect they produced the programme by mistake - it probably missed going through their usual internal censorship gate.

Hahah! ;D

Yep. Probably.

My favourite BBC gaffe is them reporting WTC 7 collapsing well before it did with WTC 7 still standing in the background.

But, Russia and China have "state run media" and we over here in freedom-land have "public television". Let's all repeat that now...
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Freedom is the right to be wrong, not the right to do wrong. - John Diefenbaker

IainB

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Re: Peer Review and the Scientific Process
« Reply #91 on: August 31, 2014, 11:45:34 AM »
My favourite BBC gaffe is them reporting WTC 7 collapsing well before it did with WTC 7 still standing in the background.
Yes, I never did understand how they did that. However, by definition, a gaffe is "an embarrassing blunder", so is is it correct to call accurately predicting a nearby future event a gaffe?   :tellme:
I would have thought that knowing the news before it happens would be a highly regarded/desirable skill in media circles.

IainB

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Re: Peer Review and the Scientific Process
« Reply #92 on: September 17, 2014, 03:20:08 AM »
This looks like a novel idea. It's an opinion article proposing the criminalising of "serious scientific misconduct" (awaiting legal definition...) in New Scientist. Not all a bad idea, I would have thought.
I am surprised that NS are publishing this though, as they have over the years arguably published their share of scientific garbage and some of it might have fitted into the awaited definition of SSM.
Hmm. Mind you, if SSM were criminalised, then NS would presumably be blameless...ahhh, I see now. Cunning plan. All care and no responsibility?
(Copied below sans embedded hyperlinks/images.)
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It's time to criminalise serious scientific misconduct - opinion - 15 September 2014 - New Scientist
    15 September 2014 by Rachel Nuwer

Research misconduct degrades trust in science and causes real-world harm. As such, it should be a crime akin to fraud, argues Richard Smith

Why should research misconduct be illegal?
After 30 years of observing how science deals with the problem, I have sadly come to the conclusion that it should be a crime, for three main reasons. First, in a lot of cases, people have been given substantial grants to do honest research, so it really is no different from financial fraud or theft. Second, we have a whole criminal justice system that is in the business of gathering and weighing evidence – which universities and other employers of researchers are not very good at. And finally, science itself has failed to deal adequately with research misconduct.

How can we recognise honest mistakes?
It's quite difficult. Clearly not every minor misconduct should be regarded as a crime. And as with all laws, it will take time to establish what merits prosecution and what can be dealt with by a reprimand. But we know peer review doesn't detect all misconduct. If research seems wrong or impossible, we start with the assumption that it's just an honest mistake and then look into it. You can sometimes detect fraud statistically, because if you invent data you tend to come up with a recurrent pattern. But in most cases, it is detected because somebody blows a whistle.

Are there cases in which you think researchers should have been prosecuted?
There are cases where someone demonstrated intent, not simply made a horrible mistake. For example, I was involved in the case of a researcher named Malcolm Pearce, who published two papers in the British Journal of Obstetrics and Gynaecology. One was a case report of successfully re-implanting an ectopic pregnancy into a patient's womb and another was a randomised trial about treating recurrent miscarriage. It turned out the case study patient did not exist, and there was also no record that he had actually conducted this randomised trial. Those aren't honest errors. The facts speak for themselves.

Does scientific misconduct often cause real social harm?
To begin with, there is the loss of confidence in science. But another example of clear, obvious harm is the infamous MMR-vaccine paper by Andrew Wakefield that was published in The Lancet. It suggested that the vaccine was a cause of autism, and that idea absolutely took off, causing dramatic drops in childhood vaccinations. This in turn caused outbreaks of diseases such as measles. Eventually, when claims in the paper were proven to be false, The Lancet retracted it.

These types of things often ruin researchers' careers. Is that punishment enough?
There are many examples in which researchers have simply carried on with their careers. I believe scientists should be held to a higher standard. Those who commit research misconduct cannot be trusted. It's too easy to be tempted into ignoring or destroying data that undermines your work. It may seem an inhuman way to be, but a true scientist is delighted when his or her favourite hypothesis is destroyed by good data.

This article appeared in print under the headline "Lawless labs no more"

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Richard Smith edited the BMJ from 1991 to 2004. He is a founding member of the Committee on Publication Ethics, a former trustee of the UK Research Integrity Office and author of The Trouble with Medical Journals (CRC Press, 2006)

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Re: Peer Review and the Scientific Process
« Reply #93 on: October 14, 2014, 07:45:03 PM »
Here's a bit of an interesting bit on censored science:

http://www.projectce...ides-health-threats/

Here's an excerpt:

Quote
Monsanto is not alone in trying to silence its critics. As Rachel Aviv of the New Yorker and Amy Goodman of Democracy Now! reported, after fifteen years of research, Tyrone Hayes, University of California–Berkeley professor of integrative biology, determined that Syngenta’s herbicide atrazine causes sexual abnormalities in frogs and could cause the same problems for humans. The company now known as Syngenta hired Hayes to research atrazine in 1997. But when his findings ran contrary to their interests, they refused to allow him to publish and instead worked to discredit him. He left Syngenta in 2001, but continued to research the harmful effects of atrazine on the endocrine system.

Court documents from a class action lawsuit against Syngenta show how the company sought to smear Hayes’s reputation and to prevent the Environmental Protection Agency from banning the profitable chemical, which is already banned by the European Union. The company’s public relations team drafted a list of four goals. Reporter Rachel Aviv wrote, “The first was ‘discredit Hayes.’ In a spiral-bound notebook, Syngenta’s communications manager, Sherry Ford, who referred to Hayes by his initials, wrote that the company could ‘prevent citing of TH data by revealing him as noncredible.’ He was a frequent topic of conversation at company meetings. Syngenta looked for ways to ‘exploit Hayes’ faults/problems.’ ‘If TH involved in scandal, enviros will drop him,’ Ford wrote.”

Yet again, science is often about religio-political positions (or profit - which is often the core of political positions) rather than actual evidence.
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Freedom is the right to be wrong, not the right to do wrong. - John Diefenbaker

IainB

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Re: Peer Review and the Scientific Process
« Reply #94 on: October 18, 2014, 12:54:58 AM »
^^ Some people (not me, you understand) might say that if there was a devil, it could well look like Monsanto, but I couldn't possibly comment.
"By their fruits ye shall know them."

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Re: Peer Review and the Scientific Process
« Reply #95 on: October 18, 2014, 02:30:36 AM »
^ Searching for "Monsatan":

https://www.google.c...num=100&tbm=isch

the-t-shirt-whore-Monsatan-Monsanto-Evil-black-womens-ladies-t-shirt.pngPeer Review and the Scientific Process

And so many, many more...

Rumour has it that they don't serve GMOs in their cafeteria. Hm...
Slow Down Music - Where I commit thought crimes...

Freedom is the right to be wrong, not the right to do wrong. - John Diefenbaker

IainB

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A new Decalogue for Peer Review and the Scientific Process
« Reply #96 on: November 03, 2014, 03:53:18 PM »
Here is some sage advice on thinking from Bertrand Russell, in regard to teaching, and which could equally well be applied to science and peer review. I have copied it below from an RSS feed I subscribe to at brainpickings.org: (well worth a read)
(Copied below sans embedded hyperlinks/images.)
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British philosopher, mathematician, historian, and social critic Bertrand Russell endures as one of the most intellectually diverse and influential thinkers in modern history, his philosophy of religion in particular having shaped the work of such modern atheism champions as Christopher Hitchens, Daniel Dennett, and Richard Dawkins. From the third volume of The Autobiography of Bertrand Russell: 1944-1969 comes this remarkable micro-manifesto, entitled A Liberal Decalogue — a vision for responsibilities of a teacher, in which Russell touches on a number of recurring themes from pickings past — the purpose of education, the value of uncertainty, the importance of critical thinking, the gift of intelligent criticism, and more.
It originally appeared in the December 16, 1951, issue of The New York Times Magazine, at the end of the article “The best answer to fanaticism: Liberalism.”
__________________________
Perhaps the essence of the Liberal outlook could be summed up in a new decalogue, not intended to replace the old one but only to supplement it. The Ten Commandments that, as a teacher, I should wish to promulgate, might be set forth as follows:
  • 1. Do not feel absolutely certain of anything.
  • 2. Do not think it worth while to proceed by concealing evidence, for the evidence is sure to come to light.
  • 3. Never try to discourage thinking for you are sure to succeed.
  • 4. When you meet with opposition, even if it should be from your husband or your children, endeavor to overcome it by argument and not by authority, for a victory dependent upon authority is unreal and illusory.
  • 5. Have no respect for the authority of others, for there are always contrary authorities to be found.
  • 6. Do not use power to suppress opinions you think pernicious, for if you do the opinions will suppress you.
  • 7. Do not fear to be eccentric in opinion, for every opinion now accepted was once eccentric.
  • 8. Find more pleasure in intelligent dissent than in passive agreement, for, if you value intelligence as you should, the former implies a deeper agreement than the latter.
  • 9. Be scrupulously truthful, even if the truth is inconvenient, for it is more inconvenient when you try to conceal it.
  • 10. Do not feel envious of the happiness of those who live in a fool’s paradise, for only a fool will think that it is happiness.

The Autobiography of Bertrand Russell is a treasure trove of wisdom in its entirety — highly recommended.

IainB

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Re: Peer Review and the Scientific Process
« Reply #97 on: November 23, 2014, 09:37:34 PM »
There have been several scientific frauds covered in this discussion thread, and today I was reading a new review of one of the biggest such frauds - a fraud with an effective lifetime that spanned approx. 40 years, even getting into school textbooks on prehistory as a bona fide discovery of palaeontology: Piltdown Man: Untangling One of the Most Infamous Hoaxes in Scientific History—Blog—The Appendix
What is especially interesting here is that several very distinguished scientists apparently collaborated in this deliberate fraud, in peer review and invention, and even today we are not entirely sure about the "why"/motivation for doing it. The urge that some scientists evidently sometimes succumb to - to create a fraud - is nothing particularly new or peculiar to modern-day science, though the motives are not necessarily fully understood or the same in each case.
(The review is copied below sans embedded hyperlinks/images.)
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Piltdown Man: Untangling One of the Most Infamous Hoaxes in Scientific History

Posted by Lydia Pyne on May 16, 2014

Few scientific forgeries have captured the scientific and public imaginations as completely as that of the 1912 Piltdown Man hoax. While examples of blatant fraud can be found in many scientific disciplines over the centuries, out-and-out forgeries and hoaxes prove to be relatively rare. The Piltdown Man is one of the most studied and least resolved incidents in the history of paleoanthropology – an episode surrounded by mystery and intrigue.

It would seem that just about everyone who is anyone in the paleo-community of the last sixty years has a theory about who perpetrated the fossil hoax; why it lasted as long as it did (forty years); and what Piltdown meant (and means) to paleoanthropology. Suspects charged with perpetrating the hoax have included the fossil’s discoverer Charles Dawson, scientific notables like William J. Sollas and Sir Arthur Keith, and even Sir Arthur Conan Doyle and the philosopher Pierre Teilhard de Chardin.
Piltdown

A 1915 group portrait by John Cooke, Charles Dawson and others associated with the Piltdown find. Wikimedia Commons

In the first decade of twentieth-century, the fledgling discipline had few fossils to hang its science on. A couple of Neanderthal skulls, a few specimens from France, some scattered skeletal elements from around Europe, a skull from Australia – to say nothing of Eugene Dubois’s famous 1891 find in Java (which he termed Pithecanthropus erectus) which firmly established Southeast Asia as an epicenter of human evolution for the scientific communities of Europe. Equally as debated as the geographic origin of human ancestry was the evolutionary sequence of “human-like” traits and the order that these traits appear in the fossil record. For the early twentieth-century paleo-community, the question of whether brains (read: a surrogate for culture) developed before or after bipedalism (read: non-cultural anatomy) occupied a good proportion of paleo-research efforts.

The Piltdown material itself came to the attention of British intellectuals, like paleontologist Arthur Smith Woodward, via the British Museum upon the fossil’s excavation in 1912. The Piltdown fossil consisted of a mandibular fragment (the lower jaw) as well as portions of the crania (the skull), recovered from the Piltdown gravels of East Sussex by antiquarian Charles Dawson. The find was promptly and rather grandiosely named Eoanthropus dawsoni.
Piltdown

Skull of the “Eoanthropus Dawsoni” (Piltdown Man). Wellcome Images

Woodward claimed that the find pointed to a “missing link” in the chain of human evolution – a fossil that could be reconstructed as a human ancestor with a large brain. This would have been a testament to the long-term significance of culture and intellectual prowess in the evolution of Homo sapiens.

Woodward wasn’t alone in his interpretation. The Piltdown fossils became readily accepted by the paleo-community. Indeed, many fossils found in subsequent decades (such as the 1925 Taung Child in South Africa) were ignored due to the influence of Piltdown. Even prominent American paleontologist Henry Fairfield Osborn (then-president of the American Museum of Natural History) declared the skull and jaw a perfect fit and the specimen fascinating.
Piltdown

A photograph by John Frisby of Uckfield, showing excavations at the Piltdown gravels in 1912. Standing centre left in the picture is the white-bearded figure of Arthur Smith Woodward and working in the trench on the right is Charles Dawson, the local solicitor who had "discovered" the skull of "Piltdown Man." Photo and caption courtesy of http://www.photohist...ssex.co.uk/index.htm.
Piltdown

Arthur Smith Woodward and Uckfield photographer John Frisby inspect the excavations at Piltdown in 1912. Arthur Smith Woodward was a palaeontologist and Keeper of Geology at the Natural History Museum in South Kensington. http://www.photohist...ssex.co.uk/index.htm

In 1953, a committee of sorts convened to evaluate the growing dissatisfaction with the fossil and the evidence against it being legitimate. In the end, “fossil” was demonstrated to comprise three “modern” species – a human skull, an orangutan jaw, and chimpanzee teeth. The teeth had been filed down and the entire set of bones stained with an iron solution. A few scientists in the early days of the fossil’s fame (like Franz Weidenreich, discoverer of the 1930s fossils ascribed to the so-called Peking Man) declared the fossil a forgery, but it wasn’t until 40 years after the fossil’s entry into the paleo community that is was exposed for what it was.

But what was it? A forgery? A hoax? A joke? A gross error in bending facts to fit a theory?

On some level, the Piltdown “fossil” is all of these things. However, it is also an important lesson not only about early twentieth-century science's search for a missing link, but also our own. In a discourse where chains, links, and linearity are treated not only as helpful metaphors ("the Great Chain of Being," "the Tree of Life"), but as actual explanation for biological phenomenon, Piltdown Man serves as a reminder that missing links can also be invented ones.
Piltdown

A reconstruction of the Piltdown man in three quarters profile. Wellcome Images

Acknowledgments: The author would like to acknowledge the Pennoni Honors College, Drexel University and the generous time and conversations of Dr. Francis Thackery (University of Witwatersrand.)
Recommended Links
    The Piltdown Inquest by Charles Blinderman
    Piltdown: A Scientific Forgery by Frank Spencer
    Bones of Contention by Roger Lewin

IainB

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The Peer Review Scam: Why not review your own paper?
« Reply #98 on: November 28, 2014, 06:39:54 AM »
I thought this was a spoof at first, but no, it's true. Not sure whether this shouldn't be in the silly humour thread as well...it certainly gave me larf.
(Copied below sans embedded hyperlinks/images.)
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The Peer Review Scam: Why not review your own paper?
If you suffer from an uncontrollable urge to claim that peer review is a part of The Scientific Method (that’s you Matthew Bailes, Pro VC of Swinburne), the bad news just keeps on coming.  Now, we can add the terms “Peer Review Rigging” to “Peer-review tampering”, and “Citation Rings”.

Not only do personal biases and self-serving interests mean good papers are slowed for years and rejected for inane reasons, but gibberish gets published, and in some fields most results can’t be replicated. Now we find (is anyone surprised?) that some authors are even reviewing their own work. It’s called Peer-Review-Rigging. When the editor asks for suggestions of reviewers, you provide pseudonyms and bogus emails. The editor sends the review to a gmail type address, you pick it up, and voila, you can pretend to be an independent reviewer.

One researcher, Hyung-In Moon, was doing this to review his own submissions. He was caught because he sent the reviews back in less than 24 hours. Presumably if he’d waiting a week, no one would have noticed.
Nature reports: “THE PEER-REVIEW SCAM”

Authors: Cat Ferguson, Adam Marcus and Ivan Oransky are the staff writer and two co-founders, respectively, of Retraction Watch in New York City.

Moon’s was not an isolated case. In the past 2 years, journals have been forced to retract more than 110 papers in at least 6 instances of peer-review rigging. What all these cases had in common was that researchers exploited vulnerabilities in the publishers’ computerized systems to dupe editors into accepting manuscripts, often by doing their own reviews. The cases involved publishing behemoths Elsevier, Springer, Taylor & Francis, SAGE and Wiley, as well as Informa, and they exploited security flaws that — in at least one of the systems — could make researchers vulnerable to even more serious identity theft. “For a piece of software that’s used by hundreds of thousands of academics worldwide, it really is appalling,” says Mark Dingemanse, a linguist at the Max Planck Institute for Psycholinguistics in Nijmegen,

Even Moon himself thinks the editors should “police the system against people like him”.

“editors are supposed to check they are not from the same institution or co-authors on previous papers.”

That would rule out half the publications in the climate science world.

The worst case involved 130 papers:

….a case that came to light in May 2013, when Ali Nayfeh, then editor-in-chief of the Journal of Vibration
and Control, received some troubling news. An author who had submitted a paper to the journal told Nayfeh that he had received e-mails about it from two people claiming to direct contact with authors, and — strangely —the e-mails came from generic-looking Gmail accounts rather than from the professional institutional accounts that many academics use (see ‘Red flags in review’). Nayfeh alerted SAGE, the company in Thousand Oaks, California, that publishes the journal. The editors there e-mailed both the Gmail addresses provided by the tipster, and the institutional addresses of the authors whose names had been used, asking for proof of identity and a list of their publications. One scientist responded — to say that not only had he not sent the e-mail, but he did not even work in the field.

This sparked a 14-month investigation that  came to involve about 20 people from SAGE’s editorial, legal and production departments. It showed that the Gmail addresses were each linked to accounts with Thomson Reuters’ ScholarOne, a publication-management system used by SAGE and several other publishers, including Informa. Editors were able to track every paper that the person or people behind these accounts had allegedly written or reviewed, says SAGE spokesperson Camille Gamboa. They also checked the wording of reviews, the details of author-nominated reviewers, reference lists and the turnaround time for reviews (in some cases, only a few minutes). This helped the investigators to ferret out further suspicious-looking accounts; they eventually found 130. As they worked through the list, SAGE investigators realized that authors were both reviewing and citing each other at an anomalous rate. Eventually, 60 articles were found to have evidence of peer-review tampering, involvement in the citation ring or both.

Those 60 papers were retracted.

Nature, of course, is happy to air problems that mostly apply to its competitors. When will Nature admit that namecalling, and failures of logic and reason are every bit as damaging to science as rank corruption?

Ht to Willie.

IainB

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US legislature decrees that science must be scientific.
« Reply #99 on: December 01, 2014, 07:14:41 AM »
Interesting. It's the Secret Science Reform Act of 2014. A very concise bill - doesn't seem to mandate anything regarding the peer review process, but goes straight to the heart of the matter.
Again, I'm not sure whether this shouldn't be in the silly humour thread as well... :-[
(Copied below sans embedded hyperlinks/images.)
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Abuse of Science in Texas
By Anne LeHuray

On November 19, 2014, the House of Representatives passed HR 4012, the Secret Science Reform Act of 2014. The bill would prohibit the US Environmental Protection Agency from regulations based on “science that is not transparent or reproducible.” Hooray! Reproducibility is the touchstone of science.  Transparency is the way to ensure that scientists who want to reproduce another scientist’s results can try to do so. No scientist anywhere would argue against reproducibility, nor should any scientist argue that research results used to make regulatory decisions (such as drug approvals, emission limits, product bans) be exempt from transparency. Unfortunately, transparency has not always been a priority.  Examples of the current reproducibility crisis in the sciences can be found here, here, here, here, and here. A requirement to use transparent, reproducible science should apply to all government agencies, not just EPA. The government need not replicate the science itself, just make sure the information needed for reproducibility is readily available. Just one of the many examples from the pavement coatings industry’s decade-long effort to obtain data from the U.S. Geological Survey illustrates the point. ... (Read more at the link.)