Sunday, November 13, 2011

A review of peer review

After much experience of the process I have little respect for it. It should screen out egregious errors and make reporting more complete but it often does not even do that. I am not alone in such a negative opinion. Judith Curry, a recovering Warmist, has gathered some comments by others on the process and put her own conclusion at the end of it. One of the critics she quotes complains that the process holds up publication of his papers by 9 months. He's lucky. In my experience a delay of 2 years is not uncommon, even where a paper is accepted with only minor requests for revision. An excerpt below -- JR
But the truth is that peer review as practiced in the 21st century biomedical research poisons science. It is conservative, cumbersome, capricious and intrusive. It slows down the communication of new ideas and discoveries, while failing to accomplish most of what it purports to do. And, worst of all, the mythical veneer of peer review has created the perception that a handful of journals stand as gatekeepers of success in science, ceding undue power to them, and thereby stifling innovation in scientific communication.

So begins a post “Peer review is f***ed up” on the blog it is NOT junk, by evolutionary biologist Michael Eisen. Some excerpts:
There are too many things that are wrong with this process, but I want to focus on two here:

1) The process takes a really long time. In my experience, the first round of reviews rarely takes less than a month, and often take a lot longer, with papers sitting on reviewers’ desks the primary rate-limiting step. But even more time consuming is what happens after the initial round of review, when papers have to be rewritten, often with new data collected and analyses done. For typical papers from my lab it takes 6 to 9 months from initial submission to publication.

The scientific enterprise is all about building on the results of others – but this can’t be done if the results of others are languishing in the hands of reviewers, or suffering through multiple rounds of peer review. There can be little doubt that this delay slows down scientific discovery and the introduction to the public of new ways to diagnose and treat disease [this is something Pat Brown and I have talked about trying to quantify, but I don't have anything yet].

2) The system is not very good at what it purports to do. The values that people primarily ascribe to peer review are maintaining the integrity of the scientific literature by preventing the publication of flawed science; filtering of the mass of papers into to identify those one should read; and providing a system for evaluating the contribution of individual scientists for hiring, funding and promotion. But it doesn’t actually do any of these things effectively.

The kind of flawed science that people are most worried about are deceptive or fraudulent papers, especially those dealing with clinical topics. And while I am sure that some egregious papers are prevented from being published by peer review, the reality is that with 10,000 or so journals out there, most papers that are not obviously flawed will ultimately get published if the authors are sufficiently persistent. The peer reviewed literature is filled with all manner of crappy papers – especially in more clinical fields. And even the supposedly more rigorous standards of the elite journals fail to prevent flawed papers from being published (witness the recent Arsenic paper published by Science). So, while it might be a nice idea to imagine peer review as some kind of defender of scientific integrity – it isn’t.

And even if you believed that peer review could do this – several aspects of the current system make it more difficult. First, the focus on the importance of a paper in the publishing decision often deemphasizes technical issues. And, more importantly, the current system relies on three reviewers judging the technical merits of a paper under a fairly strict time constraint – conditions that are not ideally suited to recognize anything but the most obvious flaws. In my experience the most important technical flaws are uncovered after papers are published. And yet, because we have a system that places so much emphasis on where a paper is published, we have no effective way to annotate previously published papers that turn out to be wrong: once a Nature paper, always a Nature paper.

JC comments: During the past few weeks, we have seen two interesting examples of peer review: the pre-publication extended peer review of the BEST papers, and the post-publication extended peer review of the Ludecke et al. papers. The extended peer review in the blogosphere was far more substantial than the papers were likely to receive in the normal peer review process. In both instances, the extended peer review of these papers conducted in the blogosphere were not part of the formal peer review process. Scientists who do not check the blogs might be completely unaware that this extended peer review has occurred.

I am a big fan of preprint servers such as ArXiv, and also the online discussion journals such as Atmospheric Chemistry and Physics. ACPD actually posts the reviews along with the paper, and allows people to comment during the peer review process. Extending this to include blog discussions on the paper would be great.

The prestige journals such as Nature, Science, and PNAS do not allow any pre-publication of the paper and serve a gate-keeping role in determining “significance.” Personally I am not a fan of this approach, but it seems to have worked in terms of generating high impact factors for these journals.


Air Pollution: Bad For Health, But Good For Planet?

Give people a silly premise and they can logically draw all sorts of bizarre conclusions from it. We see below that the global warming scare leads some people to arrive at the bizarre conclusion that air pollution is a good thing!

Cleaning up the air, while good for our lungs, could make global warming worse. That conclusion is underscored by a new study, which looks at the pollutants that go up smokestacks along with carbon dioxide.

These pollutants are called aerosols and they include soot as well as compounds of nitrogen and sulfur and other stuff into the air. Natalie Mahowald, a climate researcher at Cornell University, says so far, scientists have mostly tried to understand what those aerosols do while they're actually in the air.

"There are so many different kinds of aerosols and they have many different sources," she says. "Some warm and some cool. But in the net, humans are emitting a lot of extra aerosols, and they tend to cool for the most part."

As we clean up the aerosols, which we really want to do for public health reasons, we are going to be perhaps causing ourselves more trouble in terms of the climate situation.

The aerosols reflect sunlight back into space, or they stimulate clouds that keep us cool. But it turns out that's not all they do. These aerosols also influence how much carbon dioxide gets drawn out of the air by plants on land and in the sea.

"They can add nutrients, for example, to the oceans or to the land," Mahowald says. "But also while they're in the atmosphere they can change the climate, and so that also can impact the amount of carbon the land or the ocean can take up. So there are quite a few different ways that aerosols can interact."

In an article published in Science magazine, she concludes that those effects add up to quite a bit. At the moment, aerosols are not only helping reduce global warming by cooling the atmosphere, but they're helping reduce the amount of carbon dioxide that stays in the air once we emit it.

That's good news for now — it means the planet isn't heating up quite as fast as it could. But that's bad news looking down the road a little bit. That's because many aerosols make people sick — heart and lung disease in particular. So some nations are now in the process of trying to rein them in.


"Dangerous" climate change?

This is a slightly edited version of a comment Richard Betts left on the discussion forum. I thought it was quite challenging to much of what we hear about climate change in the mainstream media and therefore worthy of posting here as a header post. (Richard, for anyone visiting for the first time, is head of climate change impacts at Britain's Met Office).

Most climate scientists* do not subscribe to the 2 degrees "Dangerous Climate Change" meme (I know I don't). "Dangerous" is a value judgement, and the relationship between any particular level of global mean temperature rise and impacts on society are fraught with uncertainties, including the nature of regional climate responses and the vulnerability/resilience of society. The most solid evidence for something with serious global implications that might happen at 2 degrees is the possible passing of a key threshold for the Greenland ice sheet, but even then that's the lower limit and also would probably take centuries to take full effect. Other impacts like drought and crop failures are massively uncertain, and while severe negative impacts may occur in some regions, positive impacts may occur in others. While the major negative impacts can't be ruled out, their certainty is wildly over-stated.

While really bad things may happen at 2 degrees, they may very well not happen either - especially in the short term (there may be a committment to longer-term consequences such as ongoing sea level rise that future generations have to deal with, but imminent catastrophe affecting the current generation is far less certain than people make out. We just don't know.

The thing that worries me about the talking-up of doom at 2 degrees is that this could lead to some very bad and expensive decisions in terms of adaptation. It probably is correct that we have about 5 years to achieve a peak and decline of global emissions that give a reasonable probability of staying below 2 degrees, but what happens in 10 years' time when emissions are still rising and we are probably on course for 2 degrees? If the doom scenario is right then it would make sense to prepare to adapt to the massive impacts expected within a few decades, and hence we'd have to start spending billions on new flood defences, water infrastructure and storm shelters, and it would probably also make sense for conservationists to give up on areas of biodiversity that are apparently "committed to extinction" - however all these things do not make sense if the probability of the major impacts is actually quite small.

So while I do agree that climate change is a serious issue and it makes sense to try to avoid committing the planet to long-term changes, creating a sense of urgency by over-stating imminent catastrophe at 2 degrees could paint us into a corner when 2 degrees does become inevitable.

*I prefer to distinguish between "climate scientists" (who are mainly atmospheric physicists) and "climate change scientists" who seem to be just about anyone in science or social science that has decided to see what climate change means for their own particular field of expertise. While many of these folks do have a good grasp of climate science (atmospheric physics) and the uncertainties in attribution of past events and future projections, many sadly do not. "Climate change science" is unfortunately a rather disconnected set of disciplines with some not understanding the others - see the inconsistencies between WG1 and WG2 in IPCC AR4 for example. We are working hard to overcome these barriers but there is a long way to go.


Britain's fruit and nuts are ripening 18 days earlier than a decade ago due to warmer weather

Pesky that there has in fact been NO warming in the last decade -- so if there IS any real change it is certainly not due to warming

Fruit and nuts from British trees are ripening an average of 18 days earlier than a decade ago. Figures from the Woodland Trust suggest that the changing climate is altering the patterns of a range of trees.

The trend has been seen across a dozen species, with acorns ripening 13 days earlier than they did between 2000 and 2002; beech nuts 19 days earlier; and rowan berries almost a month ahead of schedule.

Experts believe the shift is down to the trees flowering earlier in the face of warmer springs.

Professor Tim Sparks, nature adviser for the Trust, said: ‘There is a suggestion that the average ripening dates have some correlation with mean temperatures recorded for April, so we presume that the link is through earlier flowering leading to earlier ripening.

‘However, to see such a uniform advance across so many species is most unusual and we need many years’ more data from the public to try to better understand the reasons for these changes.’ [Good to see that someone has got a brain]

The Trust said the changes may mean that wildlife will have access to more food earlier – but the reserves could then be depleted earlier in the winter.

It added that 2011 would go down on record as a ‘mast year’, or bumper crop, for beech and oak trees, possibly as a result of the early, hot spring.

The charity is urging people to plant a million trees for its Jubilee Woods project to mark the Queen’s diamond jubilee.


Lying Penn State President Fired

Steve McIntyre

His lack of any ethics finally caught up with him

On the same day that Nature published yet another editorial repudiating public examination of the conduct of academic institutions, Penn State President Graham Spanier was fired from his $813,000/year job for failing to ensure that a proper investigation was carried out in respect to pedophilia allegations in Penn State’s hugely profitable football program. The story is receiving massive coverage in North America because the iconic Penn State football coach, Joe Paterno, was also fired today.

CA readers are aware of Spanier’s failure to ensure proper investigation of Climategate emails and his untrue puffs about the ineffective Penn State Inquiry Committee, reported at CA here and by the the Penn State Collegian as follows:

Graham Spanier addressed the inquiry and the panel’s work during the Board of Trustees meeting on Jan. 22. Penn State President Spanier is quoted as saying:

“I know they’ve taken the time and spent hundreds of hours studying documents and interviewing people and looking at issues from all sides,” Spanier said.

Spanier’s claims were totally untrue. Not only did the Inquiry Committee fail to “look at issues from all sides”, they didn’t even interview or take evidence from critics – as they were required to do under the applicable Penn State policy. As I reported at CA at the time:

The only interviews mentioned in the report (aside from Mann) are with Gerry North and Donald Kennedy, editor of Science. [Since they are required to provide a transcript or summary of all interviews, I presume that the Inquiry did not carry out any other interviews.] What does Donald Kennedy know about the matter? These two hardly constitute “looking at issues from all sides”. [A CA reader observed below that "North [at a Rice University event] admitted that he had not read any of the EAU e-mails and did not even know that software files were included in the release.”] They didn’t even talk to Wegman. Contrary to Spanier’s claim, they did not make the slightest effort to talk to any critic or even neutral observer.

Although State Senator Piccola had written to Penn State President Spanier asking him to ensure that “the university must deploy its fullest resources to conduct an investigation of this case”, the Inquiry Committee decided that the investigation committee should not investigate three of the four charges “synthesized” by the inquiry committee and, as a result, despite the request of Piccola and others, no investigation was ever carried out Penn State on any of the key issues e.g the “trick… to hide the decline”, Mann’s role in the email deletion enterprise organised by Phil Jones or the failure to report adverse data which the House Energy and Commerce Committee had asked about (but not investigated by the NAS panel, whose terms of reference were sabotaged by Ralph Cicerone, President of NAS).

When told by the subsequent Investigation Committee that they weren’t investigating the substantive charges, Richard Lindzen told the committee,

“It’s thoroughly amazing. I mean these issues are explicitly stated in the emails. I’m wondering what’s going on?”

Clive Crook of the Atlantic Monthly mercilessly criticized Penn State for their fatuous findings that success in bringing revenue to the university and accolades from peers necessarily meant that misconduct was precluded:

The Penn State inquiry exonerating Michael Mann — the paleoclimatologist who came up with “the hockey stick” — would be difficult to parody. Three of four allegations are dismissed out of hand at the outset: the inquiry announces that, for “lack of credible evidence”, it will not even investigate them. …

You think I exaggerate?

This level of success in proposing research, and obtaining funding to conduct it, clearly places Dr. Mann among the most respected scientists in his field. Such success would not have been possible had he not met or exceeded the highest standards of his profession for proposing research…

Had Dr. Mann’s conduct of his research been outside the range of accepted practices, it would have been impossible for him to receive so many awards and recognitions, which typically involve intense scrutiny from scientists who may or may not agree with his scientific conclusions…

Clearly, Dr. Mann’s reporting of his research has been successful and judged to be outstanding by his peers. This would have been impossible had his activities in reporting his work been outside of accepted practices in his field.

In short, the case for the prosecution is never heard. Mann is asked if the allegations (well, one of them) are true, and says no.

In the case of Climategate, President Spanier apparently saw nothing wrong with reasoning that equated revenue generation with virtue and accepted the report.

In such a febrile environment, the likelihood of wilful blindness in respect to the far more profitable football program was that much greater and that appears to have been what happened. Even though a Penn State staff member witnessed a rape of a 10-year old by a more senior Penn State official, the junior Penn State staff member did not intervene at the time and investigation by more senior Penn State officials appears to have been cursory until a recent grand jury. (For example, they don’t appear to have bothered even identifying or interviewing the victims.)

It’s hard not to transpose the conclusions of the Penn State Climategate “investigation” into Penn State’s attitude towards misconduct charges in their profitable football program:

This level of success on the football field and revenue generated from it, clearly places Coaches Paterno and Sandusky among the most respected professionals in their field. Such success would not have been possible had he not met or exceeded the highest standards of their profession in operating a football program…

Had Coach Paterno or Coach Sandusky’s conduct of their program been outside the range of accepted practices, it would have been impossible for them to receive so many awards and recognitions, which typically involve intense scrutiny from peers who may or may not agree with his program …

Spanier planned to introduce Michael Mann at an invited lecture next February. I guess that someone else will make the introduction.

Spanier was fired not because of any personal role in the Sandusky football scandal, but because of negligence on his part in ensuring that the allegations were properly investigated. This was not the only case in which Spanier failed to ensure proper investigation of misconduct allegations. As noted above, Spanier had falsely reported to the Penn State trustees and the public that the Penn State Inquiry Committee had properly interviewed critics and had examined the Climategate documents and issues “from all sides”.


Some realism from a Warmist

He knows that reliance on "renewables" is a fantasy

Environmentalists who believe a massive global investment in renewable energy is the answer to future demands are “smoking dope,” International Energy Agency Deputy Executive Director Richard Jones said on Wednesday.

He was responding to Greenpeace Canada accusations that the IEA was taking an “intellectually and morally inconsistent” stand by supporting pipelines and the oilsands sector while scolding world leaders about climate change inaction.

Pipeline megaprojects, and the oilsands bitumen that would be carried by proposed energy arteries from Alberta to B.C.’s west coast and to Texas, are important components of global energy security, Jones said.

He was commenting on his organization’s annual report that warns of stark consequences if the world doesn’t take far tougher action to reduce carbon emissions.

“We don’t have any inhibitions in saying we support the development of the oilsands because it’s an important resource,” Jones told The Journal.

The world is going to need energy from all sources in coming needs to meet rising demand, he said. He also noted that coal-fired power plants are the main source of global warming because they are “much dirtier” than the oilsands.

“Obviously we think over time fossil fuels should be phased out, but we recognize that for the foreseeable future there’s going to be major demand for oil and gas. And some of that demand might as well be filled by oilsands because of the security benefit.”

While he wouldn’t comment on the current debate over whether Canada’s oil can be considered “ethical,” the former senior U.S. diplomat and ex-ambassador to Kuwait agreed with the Canadian industry’s defenders that Canada represents a secure oil source.

“As an American I’d rather send my dollars to Canada than to Kuwait, even though I have a lot of friends in Kuwait. They’re in a pretty volatile part of the planet and who knows where that money might end up?”

He wouldn’t comment specifically on whether the IEA supports two controversial proposed megaprojects advanced by Calgary firms: TransCanada’s Keystone XL pipeline from Alberta to Texas, and Enbridge’s Northern Gateway project linking Alberta bitumen to Asian markets via Kitimat, B.C.

The Keystone proposal is now awaiting a politically-charged decision from President Barack Obama on whether it can proceed. The Northern Gateway proposal, widely criticized by B.C. aboriginal and environmental groups, is before the National Energy Board.

“In general we support pipelines because they increase the diversity of supply, and they make the systems more robust. And the more sources the consumers have, and the more markets producers have, increases the security of both.”

Greenpeace Canada analyst Keith Stewart said the IEA, funded by 28 member countries including the U.S. and Canadian governments, is being influenced by a political agenda.

He said the IEA’s endorsement of the oilsands and pipelines contradicts its warning Wednesday against allowing the buildup of a carbon-heavy infrastructure that raises the risk of catastrophic temperature increases later in the century.

“Allowing pipelines like Keystone XL or Gateway to go forward, along with the expansion of the tar sands necessary to fill them with high-carbon oil, is intellectually and morally inconsistent with stopping global warming,” Stewart said in a statement.

Greenpeace also slammed the IEA for proposing solutions that rely far too heavily on nuclear energy and unproven carbon capture and storage technology.

Instead, governments should focus on energy efficiency and renewable energy as replacements for coal, nuclear energy, and high-carbon sources like Canada’s bitumen, according to Greenpeace.

Jones said there’s no realistic way renewable energy sources can expand so dramatically by 2035.

“We think the people who just say, ‘you can wave a magic wand and replace all of these other technologies with renewables’ are smoking dope.”

Jones said the IEA’s decision to advance a less-ambitious plan to reduce carbon emissions, compared to a more aggressive proposal in 2009, is based on the failure at international gatherings to come to an agreement on putting a price on carbon.

Only the European Union, New Zealand and, as of this week, Australia have established carbon pricing systems. The IEA projects that South Korea will have its own system in 2015 and China in 2020.

Neither Canada nor the U.S. are expected to establish carbon pricing at the national government level during this period, according to the report.

“Canada can’t do it because the Canadian market is linked to the U.S. through NAFTA (the North American Free Trade Agreement), and so Canada won’t do it unless the United States does it. And in the U.S. politically it looks pretty much dead in the water.

“There’s just unfortunately a lot of demagoguery on the issue in the U.S. right now.”



For more postings from me, see DISSECTING LEFTISM, TONGUE-TIED, EDUCATION WATCH INTERNATIONAL, POLITICAL CORRECTNESS WATCH, FOOD & HEALTH SKEPTIC, GUN WATCH, AUSTRALIAN POLITICS, IMMIGRATION WATCH INTERNATIONAL and EYE ON BRITAIN. My Home Pages are here or here or here. Email me (John Ray) here. For readers in China or for times when is playing up, there are mirrors of this site here and here


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