Nature and the Sunday Sport

The paper by Steven Sherwood has been agitating those of a green disposition in recent days, with all sorts of wailing on Twitter about how we're going to hit four degrees of warming by the end of the century. This is certainly the story that Nature gave out in its press release:

Global average temperatures will rise at least 4°C by 2100 and potentially more than 8°C by 2200 if carbon dioxide emissions are not reduced according to new research published in Nature. Scientists found global climate is more sensitive to carbon dioxide than most previous estimates.

The research also appears to solve one of the great unknowns of climate sensitivity, the role of cloud formation and whether this will have a positive or negative effect on global warming.

Click to read more ...

Economist on science

The Economist has a fascinating article on the failings of science and peer review which is a nice synthesis of many of the principal critiques that global warming sceptics have been expounding for years. So we hear about Ioannidis's suggestion that most scientific papers are wrong, Fiona Godlee's famous study that showed that peer review was largely a waste of time, and the lack of replication of most studies. It's almost a rewrite of Chapter 15 of The Hockey Stick Illusion.

While it's nice to have one's positions supported by such an august journal, you do have to wonder how the powers that be at the Economist can continue to support revolutionary policy changes on the basis of a system as pathetic as academic peer review. Don't get me wrong - if academics find it useful to peer review each others' work that's OK with me, but we need a much, much higher hurdle before academic papers are deemed worthy of affecting public policy. Independent replication is only the bare minimum required.

Replication, schmeplication

The Scientist reports on the failure of many scientific papers to include enough information to allow others to replicate the results.

Reproducibility is a hallmark of good science. However, despite the fact that most scientific journals require authors to list the resources used in their experiments, almost half of the papers examined in a new study failed to specify all of the items needed to replicate the findings. The study was published Thursday (September 5) in the journal PeerJ.

From the looks of it, the papers studied were mainly in the life sciences, but this is clearly just as much an issue for climatology. Unless you are an scientivist, of course, in which case replication means being able to reach vaguely similar results using different, but equally obscure methods.

Moriarty on peer review

The University of Nottingham's Phil Moriarty has written an excellent piece in Times Higher Education looking at post-publication peer review, whether through official channels or via blogs.

Responding last year to criticism of their field in the wake of the serial fraud committed by Diederik Stapel, three social psychologists - Wolfgang Stroebe, Tom Postmes and Russell Spears - published a paper in Perspectives on Psychological Science, titled “Scientific Misconduct and the Myth of Self-Correction in Science”. This provided compelling evidence that, across the disciplines, peer review fails to root out fraud. This is worrisome enough. Yet even basic errors in the literature can now be extremely difficult to correct on any reasonable timescale.

Meanwhile, Jonathan Jones points us to this post - at once appalling and hilarious - about just how difficult publishing comments has become.

Lew two in doo-doo

As readers no doubt know, a few days ago, Stephan Lewandowsky's "Conspiricy Ideation" paper was removed from the publisher's website without explanation. Now, perhaps in response to criticism from the respected Retraction Watch site, that explanation has appeared:

This article, first published by Frontiers on 18 March 2013, has been the subject of complaints. Given the nature of some of these complaints, Frontiers has provisionally removed the link to the article while these issues are investigated, which is being done as swiftly as possible and which Frontiers management considers the most responsible course of action. The article has not been retracted or withdrawn. Further information will be provided as soon as possible. Thank you for your patience.

Marcott in freefall

It has only taken days for some serious question marks to be raised about the Marcott hockey stick. McIntyre has posted here about the mystery surrounding the methodology and here about the curious lack of a similar 20th century uptick in Marcott's PhD thesis on which the Science paper appears to have been based. Willis Eschenbach notes that many of the proxies used fail the paper's own criteria for inclusion, David Middleton has raised further questions based on examination of individual proxies. Don Easterbrook has further concerns here.

I was struck by Rob Wilson's comments about the paper a couple of days ago. He had only given it a brief read and alarm bells were already sounding. Rob is an expert in the area, but even for me, the paper did not pass the sniff test.

What does it say about Science that it would publish such a paper?

Shutting down the police

An article at Forbes discusses the recent closing down of the Science Fraud website, a crowdsourced effort to expose scientific misconduct, particularly in the life sciences.

Reading between the lines, the site's owner was a little careless with the reputations of some of those who came under suspicion and the ensuing legal threats did for his site. It looks as though he's going to try again, but utilising a different structure and a different approach.

That sounds like a good idea. Science, being a process that is operated by fallible human beings with perverse incentives, desperately needs policing by outsiders. It looks as though the life sciences will get their neighbourhood cop. Let's hope the physical sciences can develop one too.

Phil Trans B says end of world nigh

The Royal Society's elevation of Paul Ehrlich to the ranks of the fellowship last year was a surprising development, given the great doomsayer's predeliction for being entirely wrong about everything. Many noted at the time that Ehrlich shares Paul Nurse's interest in the global population figures and wondered whether Ehrlich's election as a fellow was connected to Nurse's election as president. As I understand it, however, new fellows are appointed after a vote of the existing fellowship, so presumably there was in fact broad support for Ehrlich's candidacy. There is no accounting for taste.

Anthony Watts recently noted the publication of a new Ehrlich paper in the Royal Society's Phil Trans B, in which full vent is given to the tale of environmental doom that he has been getting so badly wrong for the last 30 years. Is this kind of millenarian nonsense new for Royal Society Journals? I certainly have no conception of their stable of publications as being particularly full of woo in the way that, say, Nature is. Have I missed anything?

A new kind of journal

Richard Smith, former editor of the BMJ, describes an interesting new biomedical journal called F1000Research.

F1000Research, will post papers, including opinion pieces and case reports as well as clinical trials and other studies, within hours of them being submitted. If a study includes data then the authors must make it available—as the BMJ is now insisting on for clinical trials. With F1000Research the data will be available through the website. The data are citable, and the creators of the data will be credited when their data are used for new studies.

Sounds excellent. I wonder if this kind of thing will catch on in climatology?

Smith's article is here.

Quote of the day

There are so many areas where there is still real uncertainty, where there is legitimate debate that occurs in good faith. That's expressed in the peer-reviewed literature and in the debates that scientists have with each other at scientific meetings.

Fair-minded promoter of free open debate in the peer reviewed literature, Michael E Mann, quoted at the Atlantic.

While it was easy to make sure that the worst papers . . . didn’t see the light of the day at [Journal of Climate], it was inevitable that such papers might slip through the cracks at GRL.

An apparently unrelated Michael E Mann in the Climategate emails.

Markonis and Koutsoyiannis

Demetris Koutsoyiannis emails to point me to his new paper. Markonis and Koutsoyiannis (Surveys of Geophysics) takes a look at climate variability over periods spanning nine orders of magnitude.

We overview studies of the natural variability of past climate, as seen from available proxy information, and its attribution to deterministic or stochastic controls. Furthermore, we characterize this variability over the widest possible range of scales that the available information allows, and we try to connect the deterministic Milankovitch cycles with the Hurst–Kolmogorov (HK) stochastic dynamics. To this aim, we analyse two instrumental series of global temperature and eight proxy series with varying lengths from 2 thousand to 500 million years. In our analysis, we use a simple tool, the climacogram, which is the logarithmic plot of standard deviation versus time scale, and its slope can be used to identify the presence of HK dynamics. By superimposing the climacograms of the different series, we obtain an impressive overview of the variability for time scales spanning almost nine orders of magnitude—from 1 month to 50 million years. An overall climacogram slope of −0.08 supports the presence of HK dynamics with Hurst coefficient of at least 0.92. The orbital forcing (Milankovitch cycles) is also evident in the combined climacogram at time scales between 10 and 100 thousand years. While orbital forcing favours predictability at the scales it acts, the overview of climate variability at all scales suggests a big picture of irregular change and uncertainty of Earth’s climate.

There is an interesting link to a discussion at BH here. That conversation ended when Prof Koutsoyiannis told commenters that he was unable to respond to further questions since the answers were contained in a draft paper that he had going through the peer review process at the time:

As per the “opportunity” to discuss the scientific part, I am afraid it must wait some time. We have produced some results related to your questions, but I do not wish to discuss them before we have them officially published. In this case the peer review may take some months or years, considering the necessary rejections.

This paper is the result. The discussion thread dates back a year, so you can see that the peer review process has been at least that long. The paper was rejected by Geophysical Research Letters and Nature Geoscience (the peer review comments are available here) although as DK notes in the discussion thread, those of his papers rejected by mainstream climate journals tend to be the ones most cited after finding a home in some less "plugged" publication.

(Hurst Kolmogorov dynamics are explained here)

The problem of pal review

The Committee on Publication Ethics has just recently reported on recent cases of misconduct it has dealt with, some of which are very interesting. This one in particular struck a familiar note, with an author of a paper trying to game the system by having his paper reviewed by sympathetic colleagues. In fact he even created sockpuppet reviewers.

On noticing a high volume of submissions from corresponding author A, editor X flagged up concerns with the preferred reviewers being suggested and their comments. Author A had in most cases suggested the same preferred reviewers for each submission, preferred reviewer accounts had non-attributable email addresses, comments were being returned very quickly (within 24 hours) and were often brief and positive, largely restricted to grammatical changes. All preferred reviewers favoured immediate acceptance or acceptance subject to minor revisions.

Click to read more ...

British research goes open source

All scientific research funded by the UK taxpayer is to become open source, according to an article in the Guardian. It seems that academics will be required to pay the fees to make their papers freely available.

Since few journals will solely publish papers by UK academics, this presumably means that the scientific publishers will retain the library subscriptions which are the bedrock of their profits, while gaining a massive windfall in the shape of open access fees for much of their content.

A good day to be a scientific publisher I think.

Potty-mouthed Nature

Here is an extraordinary example of the depths to which academic journals are willing to go in support of the great green cause.

Count how many times Bain et al use the "d-word" in their paper on attitudes towards AGW - it certainly looks as if the authors intended to generate offence and controversy rather than truth and light. Hilariously, the authors are writing about how to convert people to the green cause!

I think it's pretty interesting that the editors have decided to give their backing to this kind of thing. One almost wonders if they are struggling for readers and need to try to get some attention. Of course it has long been clear that Nature has been so corrupted by greenery as to put a question mark over all of its output. This latest paper is just confirmation of what we already knew.

(As ever, do not respond in kind)

Update on Jun 18, 2012 by Bishop Hill

I've written to the editor, Rory Howlett:

Dear Dr Howlett

I have written a blog post on the Bain et al paper you have recently published. I found it quite surprising that a reputable journal would publish an article that contained so much offensive language.

http://www.bishop-hill.net/blog/2012/6/18/potty-mouthed-nature.html

I was wondering if you would care to comment on your decision to publish the article in this form. Did the editorial team consider asking the authors to use less incendiary language? Do you view your journal as having a role in encouraging civilised debate? Do you have policies on offensive language?

Thanks for your attention.

Update on Jun 22, 2012 by Bishop Hill

One of the authors of the paper has responded at WUWT. It's accepted terminology apparently.

Gatekeeping continues

Hans von Storch interviews Reiner Grundmann about his recent Climategate paper. It looks as though gatekeeping of inconvenient climate papers extends to some of the social science journals too:

One editor responsible for handling my manuscript was apologetic about the negative verdict, pointing out that the topic was too hot to handle for some referees in the field. He thought it was very difficult in the current situation to get such material published. I took this as a strong indication that the politicization of climate change had had an effect in STS scholarship, something which is not thematized sufficiently in the community.