January 2015

The hiatus is over!

No, I'm not talking about how last year was the hottest (globally) on record. It's been almost two years since my last post here, but I'm intending to end the silence. I have actually been doing a lot of reading and listening of one form or another, along with a few comments here and there, especially on twitter. One reason I haven't felt an urgent need to write has been a couple of excellent new entrants in the climate blogosphere:

Lead Guest Editor of a Special Issue!!!

I thought I ought to share a recent incoming email with the world... I know this is a widespread problem, but the coincidence of this appearing just as I was thinking about Gerlich, Tscheuschner and Monckton made posting this one a little irresistible :)

Invitation to Propose a Special Issue and be the Lead Guest Editor

Dear [...]

SciencePG (http://www.sciencepublishinggroup.com) is one of the worldwide publishers who is dedicated to promoting exchange of knowledge and advancing technological innovation. Special Issue is a part of SciencePG and plays an important role of its rapid development. Acquiring that you have once published a paper titled COMMENT ON "FALSIFICATION OF THE ATMOSPHERIC CO2 GREENHOUSE EFFECTS WITHIN THE FRAME OF PHYSICS" on the theme of Greenhouse effect; climate; thermodynamics in INTERNATIONAL JOURNAL OF MODERN PHYSICS B, SciencePG believes you must have great achievements in your research field and sincerely invites you to propose a Special Issue and be its Lead Guest Editor.

Oxygen causes cancer while sunspots kill - what science can we trust these days?

A paper recently appeared in the open access peer-reviewed journal PeerJ titled Lung cancer incidence decreases with elevation: evidence for oxygen as an inhaled carcinogen. It makes the hard-to-believe claim that the oxygen we breathe is a cause of lung cancer. This is pretty far from my own expertise. Can I trust this result? Reading the paper I find it seems to have done the sort of statistical tests I would expect, checking for a long list of other possible factors including such things as radon and UV exposure (as well as of course cigarette smoking). Maybe they missed an important factor (cosmic ray exposure? levels of some other carcinogens that vary with elevation?) but the analysis looks pretty reasonable to me.

I know nothing about the authors or their previous publication history. Their institutions are reasonably well-known (University of Pennsylvania, UC San Francisco). In the paper they declare "no funding for this work" which is a little suspicious - most good science is done with some sort of external funding. What about the journal? PeerJ is a new entrant (launched in February 2013), focused on Biological and Medical sciences, with a very different business model from traditional journals. But it claims to be applying rigorous peer review. I have some first-hand knowledge of that as a co-author (among many) on a paper being considered for publication in that journal - we had a pretty thorough first round of review by external referees.

What about external commentary on this oxygen-causes-cancer paper? There was quite wide positive coverage presumably following a university or journal press release, for example this report from EurekAlert!. The only negative response I could find was this one from Fiona Osgun at Cancer Research UK which concludes "this paper is an interesting read certainly, but definitely doesn’t tell us that oxygen causes lung cancer" - her primary complaint seems to be they likely didn't take smoking fully into account due to issues with the years for which data was acquired in the study.

Who to trust here? Unfortunately it's very unclear at the moment. To me this doesn't look like either the journal or authors were "behaving badly" - at worst they might have made some honest mistake that will be understood as this research is followed up on. At best - well, maybe we now understand another source of cancer risk. But maybe I'm way off base - like I said, this isn't a field I'm at all familiar with!

A second recent paper in a similar vein is Solar activity at birth predicted infant survival and women's fertility in historical Norway published in the quite-prestigious 350-year-old Proceedings of the Royal Society B (impact factor 5.683). This is again a statistical study of correlations, this time between solar activity (sunspot counts) at date of birth and various metrics of survival and fertility. Again the authors seem to have accounted for a variety of possibly confounding factors - the science looks reasonable to me (far from an expert in this field). The authors themselves are from the "Norwegian University of Science and Technology" in Trondheim which seems like a respectable place. The journal is clearly among the most well-regarded in the world. There's no sign of bad behavior by either author or journal here.

So what about reactions? The paper received pretty wide-spread media coverage, again essentially parroting a (positive) press release, with occasional quotes from other scientists expressing doubts about the mechanism. The only lengthy critical response I could find was this one by Richard Telford, and his critique of the UV mechanism appears quite devastating. Norwegians have very little UV exposure in the first place, and cloud and regional variability is much more significant than the solar cycle effect. His suggested explanations for the paper (assuming the authors and journal did not behave badly):

The first is that some property of the data causes the statistical methods (which look good) to fail unexpectedly. The second is chance – one of the 5% of results that appear to be statistically significant at the p = 0.05 level when the null hypothesis is true.

There is a third possibility - that some other mechanism than UV variation is mediated by the solar cycle and has an impact on life expectancy etc in Norway (and perhaps elsewhere).

So do I trust this one? Given the strength of the one critique, right now I feel most likely the authors have made some sort of honest mistake. But again I'm way outside my own expertise, it is really hard to know what's right.

In both cases this state of uncertainty isn't bad - it's quite normal for science at the cutting edge to be ambiguous and uncertain. Scientific results that stand the test of time require confirmation by replication of studies like these under different conditions, testing the explanatory hypothesis via all the experimental and theoretical implications one can. When multiple lines of evidence all support the same picture of reality, then one can be fairly certain it is right. When we just have one line of evidence, in cases like this, it's fine and appropriate to be skeptical. Over time the truth should be sorted out.

Dubious physics articles cast doubt on new publishers...

In my last couple of posts I've been sharing some observations on the state of science communication these days, particularly problems with predatory publishers, overzealous publicity for ambiguous research, and the difficulty for an outsider in understanding what to trust in what's published in science these days. Bottom line: it's become much easier to communicate, but harder to know whether what's being communicated is worth paying attention to.

In this post I present two more cases of dubious publication - as these are in physics I'm rather more certain they are wrong. These have received a rather mixed collection of "post publication peer review" but in a fashion that I believe would leave the non-expert quite unaware they are not useful contributions to science.

Our first case study here is from the mega-journal PLOS ONE - "Implications of an absolute simultaneity theory for cosmology and universe acceleration" by Edward T. Kipreos, of the University of Georgia. PLOS ONE is an open access journal started in 2006 (2012 impact factor: 3.73); it is the world's largest journal by number of papers published, publishing original research across many fields. Published articles are reviewed for technical validity but as long as they pass that, it doesn't matter how important the reviewers or editors feel the article is. PLOS ONE doesn't publish many physics articles on the whole, but it has done a few along the lines of the above, for example this article that seeks to rework general relativity - probably equally dubious but one I have less background to assess.

What are we to make of Dr. Kipreos' article? Univeristy of Georgia seemed rather pleased with the publication. It also notes he is a molecular geneticist, not a physicist. Hmmm. Some version of the press release (with no comment from any actual physicists) spread quickly around the internet; the article lists 8522 "views" on the PLOS platform right now. Despite the promise of "post publication peer review", there is only one incomprehensible comment on PLOS ONE itself, and nothing in PubMed Commons or PubPeer.

I did track down two apparently knowledgeable critiques in blog form from physicists Brian Koberlein and Matthew R. Francis. There is no sign of any response or acknowledgement from Dr. Kipreos of the problems they raise.

As Dr. Francis notes, articles "proving" Einstein was wrong are extremely popular among the less-well-informed. I recall when I was a young man, probably about 12 after having read some account of special relativiely probably by Asimov, there was something that occurred to me that I thought I saw clearly, everybody must have overlooked it! I'd be famous, get a Nobel, etc. etc. When I tried explaining to my Dad (a chemist) he rather patiently suggested maybe I needed to study a bit more about it. Sure enough, when I understood it more, my insight had already been long accounted for.

Sadly, there are a few people who never seem to grow out of that stage of certainty that they've discovered something simple that others have missed. Physics journals routinely receive these "crackpot" papers - I've heard something like one in five papers submitted to journals that cover gravitation and relativistic physics are in that category. Their editors can spot these papers a mile away.

The Monckton equation

My last few posts have been on some examples of dubious scientific publications. Some publishers are bad actors. Some authors are naively over-confident and have found naive editors or publishers to match. Sometimes it can be hard to tell. The last case I'm going to look at here is perhaps the worst situation - where the authors are clearly behaving badly, and somehow made it through some form of peer review. This is the sort of thing that gets reported regularly on Retraction Watch, and also similar to the Gerlich and Tscheuschner case except that the journal in question is slightly more prestigious (G&T's journal, IJMP-B, has an impact factor of less than 0.5). And once again the topic is climate change.

The paper this time is Why models run hot: results from an irreducibly simple climate model by Christopher Monckton, Willie W.-H. Soon, David R. Legates, and William M. Briggs, published in Science Bulletin by Science China Press and Springer-Verlag. Given that Springer is about to merge with Nature, the break-down of reasonable peer review in this case indirectly reflects badly on one of the most prestigious journal brands in all of Science (Springer is of course also highly regarded).

Monckton and friends' paper has been widely criticized already by ... and Then There's Physics, Jan Perlwitz in two articles and from Roz Pidcock at the Carbon Brief who quotes various other scientists on the topic. Since the essential argument is barely changed from Monckton's 2008 Physics & Society (P&S) article that I found full of errors I thought it deserved a bit of post-publication attention from me also. It really is astonishing that this work was approved by an editor for what looks like a reasonable scientific journal.

At first sight this article isn't as obviously nutty as some of those I've discussed here previously - the graphics and tables seem to be well designed, the reference section looks fairly substantive. The mathematics is once again pure algebra with not a sign of an understanding of the calculus invented by Newton and Leibniz a few hundred years back - and we'll get back to that. But other than the overly simplistic math, the paper may not strike the experienced editor immediately as absurd.