Impending flood? Hold Onto Your Family!

antsWith the extreme weather we’ve witnessed all over the US this winter, some people may be planning new ways to stay safe in the event of a natural disaster. If we can’t learn to predict these extreme events (as some animals may be able to) we may take a moment to learn from some often overlooked creatures, in this case, Formica selysi ants.

A group of researchers in Switzerland studied this species of ants’ technique for surviving a flooding event. They found that these ants, which regularly inhabit flood plains in the Alps and the Pyrenees, are well-prepared and ready to act in the event of impending submersion. The ants quickly form a “collective structure” by physically grasping on to one another to create a floating platform and raft to safety when a flood comes. This technique keeps nest-mates together, protects the queen, and ensures the survival of the majority of the colony.

Predictably, the researchers observed  that the ants place their queen towards the center of the rafts, in the most protected position. However, instead of likewise protecting their young, the worker ants use the buoyant properties of the brood by placing them at the bottom of the raft where they act as floatation devices. The young suffer little or no mortality from this placement and serve as vital support for the rest of the colony when incorporated into the raft in this fashion. Check out the ants in action in the video below (and on our Youtube channel).

Although we may not be able to literally grab onto each other and float above the water when threatened with a flood, the principle is what might be important. Lesson learned: be prepared and gather your family and friends close to tackle whatever challenge is approaching together.

 

Citation: Purcell J, Avril A, Jaffuel G, Bates S, Chapuisat M (2014) Ant Brood Function as Life Preservers during Floods. PLoS ONE 9(2): e89211. doi:10.1371/journal.pone.0089211

Image: Figure 1 from doi:10.1371/journal.pone.0089211

 

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Nature News reports SCIgen gibberish papers; can we rely on conventional peer-review? Or can machines help?

Richard van Noorden has an important report

http://www.nature.com/news/publishers-withdraw-more-than-120-gibberish-papers-1.14763

Two science publishers have withdrawn more than 120 papers after a researcher in France identified them as computer-generated. According to Nature News, 16 fraudulent papers appeared in publications from Germany-based Springer, and more than 100 were published by the New York-based Institute of Electrical and Electronic Engineers (IEEE).

It’s not clear what the motive was – academic fraud? or a Sokal/Bohannon-like demo of the frailty of peer-review? But the immediate effect is to show that a large number of “peer-reviewed” scientific papers have flaws.

This should surprise no-one who understands the process of scientific publication. I will assert that, in principle, every published article has flaws. Most will be minor – typos in references or mislabelled diagrams or typos in tables or misdrawn chemical diagrams or countless other errors.

Consider a doctoral thesis – possibly  the most intensively peer-reviewed document that a scientist produces. The thesis is written knowing that failure may be absolute – a career could depend on it. It has taken months to prepare. Almost always the student has to revise it for “minor errors”. (My own thesis had a number and yet I have asked for it to be digitised at Oxford). Errors are ubiquitous.

There are roughly three absolute reviewers of scientific material:

  • The natural and physical world. Nature (not the journal) always wins. It is fair – God does not play dice – but neither does s/he tolerate errors. This is the ultimate arbiter. One of the strucures in my thesis was “wrong”. I discovered later that it was in a subgroup (Fd3) of the reported space group (Fd3m). This wasn’t trivial – it included a rare sort of twinning (which has given me minor eponymity) This is how science progresses. Science is a series of snapshots.
  • The computer.  It doesn’t lie. If you don’t get the same answer as someone else then either you or they or both have to find out where the problem is. It’s interesting that most of these fake papers were in the area of Computer Science. Properly reported CS should be very difficult to fake. Unfortunately much of it is very badly reported.
  • Humans. Human judgment is variable and changes with time. A “good” paper noes may be “bad” at a later stage and vice versa. An “exciting” one now may be shown to be uninteresting later or vice versa.  Science often changes by paradigm shifts and many of those were rejected when first published. Moving continents? ulcerating bacteria? charged species in solution? Examples of science that would have led to dismissal for lack of  ”impact”

The rush for immediate impact is anti-scientific as is the rush for multiple publications.

I doubt this will change.

But one thing that can help to reduce noise, error, fraud, duplication etc is the use of machines.

Machines can detect fraud (I shall show how shortly). Machines can detect errors – we have already shown this. Machines can reproduce (or fail to reproduce) computational science.  This could and should be done.

 

The problem is that it is a lot of work to set up the proper apparatus. And publishers don’t like that (I expect a few shining examples such as IUCr/Acta Crystallographica). It costs money to verify and check science. That eats into profits. And while publishers get paid for the number of papers they publish (and generally not the ones they reject) why bother?

Why do chemistry publishers not insist on machine readable spectra. It’s trivial.

Why do they not insist on machine readable chemical structures? That’s even more trivial.

Because it costs effort?

And worse – it means that the scientific literature becomes a semantic database. And that would never do, because it could replace the secondary databases that generate hundreds of millions of dollar income.

I and my friends could have all the tools to create higher quality chemistry, less fraud, more value. And that goes for many other sciences.

Machines can help authors… I’ve tried that for over 10 years. No progress.

Will the culture of publication change in my lifetime??

That’s up to you.

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New PLOS Open data policy

PLOS one logoPLOS has announced some changes to their publishing policies, and these changes are great news.  The new PLOS policies will go a significant way towards encouraging open data and open source.  Although the announcement itself is somewhat vague on the subject of source code, the actual PLOS One Sharing Policy is excellent:

…if new software or a new algorithm is central to a PLOS paper, the authors must confirm that the software conforms to the Open Source Definition, have deposited the following three items in an open software archive, and included in the submission as Supporting Information:

  • The associated source code of the software described by the paper. This should, as far as possible, follow accepted community standards and be licensed under a suitable license such as BSD, LGPL, or MIT (see http://www.opensource.org/licenses/alphabetical for a full list). Dependency on commercial software such as Mathematica and MATLAB does not preclude a paper from consideration, although complete open source solutions are preferred.
  • Documentation for running and installing the software. For end-user applications, instructions for installing and using the software are prerequisite; for software libraries, instructions for using the application program interface are prerequisite.
  • A test dataset with associated control parameter settings. Where feasible, results from standard test sets should be included. Where possible, test data should not have any dependencies — for example, a database dump.

However, the one loophole is that they allow for code that runs on closed source platforms in “common use by the readership”  (e.g. MATLAB), although it must run without dependencies on proprietary or otherwise unobtainable ancillary software.  That “common use” loophole could potentially be a mile wide in some fields.  Is Gaussian a common use platform in computational chemistry and therefore exempt from this new policy?   If so, the policy is a bit toothless.  I’d like to see the limits and bounds of the “common use” loophole more clearly stated.

The announcement makes PLOS ONE a much more attractive place to send our next paper.

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MDPI and Beall – further comments from a “brainwashed Brit”

After my recent post on MDPI there has been a flurry of comments on this blog and I have also received a few private mails. Some are accusatory either of me or other correspondents.

To clarify my position:

  • I have been aware of MDPI for ca 16 years and have no indication that they are other than a reputable scientific publisher. I have 2-3 times corresponded  with them.
  • I wrote “I have no personal involvement with MDPI”. This was poorly phrased – I mean to say I have no financial interest in MDPI nor am I involved in any way in the running of the company.
  • A month ago I accepted an invitation to be on the editorial board of the journal Data. I approve of what Data is setting out to do and I intend to take an active interest – making comments and suggestions where appropriate. I do not approve of editorial boards who simply provide names.  I intended to announce my membership on this blog.
  • I have been invited to contribute an article to a special issue edited by Bjoern Brembs and continue to do so.

I have worked extensively on material in the 3 journals Molecules, Materials and Metabolites because it is well presented and I believe it to be honest science. This does not involve MDPI, although I have told them what I am doing.

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I note that there are a great number of accusations about what various people have been doing, some implying fraud or near-criminal activity. I know nothing more of these (that is what the phrase “no personal involvement” was intended to address.) I do not intend to try to find out more about these. I shall not respond to them and may decline to post some of them.

  • I shall continue to mine the content from MDPI journals and publish the resulting science. I can do this with or without the cooperation of MDPI. I shall report the science objectively.
  • I shall continue to be an active member of the board of Data.

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I remark that the scholarly publishing industry has a turnover of ca 10-15 Billion dollars. Profit margins are very high. I am not surprised that there are low quality journals. Elsevier’s “Fractals, Solitons and Chaos” is a case in point (see Wikipedia for objective analysis). How many libraries have bought that? What chccks are there on quality? none.

I have argued for many years that Open Access needs a regulatory organ and been generally shouted down. The OA community is now reaping the harvest of its lack of care in standards – the (mis)label “Open Access” costs far more dollars than marginal publishers. Had the OA community created a system whereby MDPI or any other publisher could get formally certified they would not need to be have to defend themselves.

No good can come from single people who set themselves up as self-appointed arbiters, be they Beall or Harnad.  Criticising single articles (as Retraction Watch does or the chemical blogosphere) is admirable – especially as the discussion is open and different points of view are accepted. However Beall writes:

This post is a good example of how Brits in particular and Western Europeans in general have been brainwashed into thinking that individuals should not make any assertions and that any statements, pronouncements, etc. must come from a committee, council, board, or the like. This suppression of individuality is emblematic of the intellectual decline of Western Europe. This suppression is laying the foundation for the erosion of individual rights in Europe and the forced imposition of groupthink throughout the continent.

This immediately shows Beall’s total lack of objectivity. He gave an indication earlier with a white paper effectively attacking Open Access as a capitalist plot (or an anti-capitalist one – I couldn’t work out which). My nationality is irrelevant. Beall’s language verges on the nationalist – the nationality of the proprietor of MDPI (Chinese) is irrelevant for me – the question is does s/he run and host an effective operation.

Murray-Rust’s statement “I have no personal involvement with MDPI” is not reflective of the facts. Indeed, he is listed as serving on the editorial board of one of MDPI’s many (empty) journals, the journal Data. See: http://www.mdpi.com/journal/data/editors (Peter, if you did not know that you were listed here, please let me know, because this is a common practice, adding people to editorial boards without their permission. Otherwise, please explain your statement that you lack involvement with MDPI.)

I have explained this above

It would be great if SPARC were to list predatory publishers and journals, but it and most OA organizations pretend that predatory publishers don’t exist because they are afraid to admit that their OA fantasies are … just fantasies. OASPA’s membership list functions as sort of a white list, so if you don’t like my list, use OASPA.

The word “fantasy” immediately removes any chance or rational discourse.

MDPI is becoming an increasingly controversial publisher. This controversy will rub off on authors who publish there, and in the long run, I think most will wish they had published in a higher quality venue. Authors should make decisions as individuals (while they still can) and do what’s best for themselves as researchers. I am saying that for most individual researchers, MDPI is not a good choice, and you ought to consider a better-quality venue.

“controversial” is a subjective term and irrelevant. It is possible to whip up opinion against an organisation and, where the organisation depends on trust, this can be very difficult to refute. Beall has built a  list of publishers of questionable ethics and practices. Initially I felt it was useful, though I disliked the word “predatory” as it applies to many closed access publishers – they just use different tactics. I now have no regard for Beall’s list which I consist consists of personal prejudices (some of them nationalist).

I shall not write more on this topic. I shall write on Data and I shall write on content extraction.