Does the present scientific journal concept serve best science researchers needs?

The concept of scientific journals as we know them today has been invented some 150 years ago to fit the needs of scientists in the paper age: topical, peer reviewed (blind-blind), printed, sold by long term subscription contracts periodicals.

They are still there because the industry that grew over the 150 years, now an oligopole of a few huge international companies with about an annual turn of investment of some 30%, keeps it going, by long.term subscription contracts, by the scientists sticking unreflected to their habits, by their fear of career danger, by the pressure of an enormous amount of marketing, including political pressure, and by the simple fact, that a new service type, whichever, always has the problem to grow under the big trees.

So, as realists, we have to wait, until the big publishers slowly adapt and adjust an try out new service types, such as ‘open access articles’ on demand of the author, or even open access journals in parallel to the existing ones. Only when these will have enough revenue to replace the traditional one, will the boost of change improve.

With 17 years of the internet, we still don’t have such simple services, so needed by the scientists, such as

– ask some topical words and get all(!) the recent papers of other authors in the world on your screen to read and download. Would be really simple to realize (by mandate of the Research Institutions for their researchers to put a digital copy of any researcher’s paper online open access on the local repository); But the big Industry fights against it by pressing for new legislation (e.g. in the US by IPA and SOPA);
– ask for all recent papers of an author (or author group), and all the papers where they are cited , to be read and downloaded online;

– put research results immediately online by the Research Institution (before the peer reviewing), and let the results being checked by the whole international relevant science community in public, and immediately, instead of keeping the paper hidden until some peer reviewers have had time to read it.
In the paper age that made sense, because their was no quick and efficient way to inform the community beforehand and discuss it online;

– ask the author for the full scientific information (experimental) data, computer code, mathematical derivation steps to the result, sources drawn, – all of which might be necessary to redo the experiment, to check the validity of the result, to build on the findings effectively;

– ask for ‘professional scientific information’, by which I mean that a scientist who is expert in his field wants (immediately, free access, everything), wants the results of his colleagues in a form that he most effectively can build on it in his actual research; instead he gets papers who have long chapters on introduction to the field, history, the general method in the field, earlier work, long list of references, former work of the group etc., but the core of the new finding is given as nice to read sketch, but lacking enough details to make use of it, to build on it, to check it. No wonder, that clever authors, short on time, reuse the general chapters of their own older articles to copy and paste them in their newer ones. Nothing wrong with it, and the publishers know it and tolerate it; No wonder that even more clever authors cut their new research findings into small slices, each then written as a stand-alone paper of just marginal scientific contribution. And the frustrated referees have to read through all this marginal stuff; Surely, there are some attempts to overcome this, e.g. by a Summary Service, for example Papercore;

-ask for distributed collaborative research effort supporting tools such as jointly work on the screen on the development of mathematical derivations by a community of experts; by jointly working in a distributed collaborative moderated research effort of a group of scientists using e.g. a WiKi, so that anyone can join and see;

-ask for: given I am on travel in a town, where are the geographically next researchers in my field; (but see an example: say you are a Metal Physics researcher and you are at the moment physically at Aachen, Germany, then use PhysNet and push the button “i” to get the Neighbour Institutes abroad);

– ask the commercial Publishers to be eligible to read your own by them published papers: most will charge you 30 Dollars per paper, even if it is only one page;

To cure this is all too easy to establish, given the enormous financial means poured by the governments into the scientific journal sector, but instead it is locked into the printed age business model of the Scientific Publishers; The motors of the necessary change to the digital age in the scientific publishing area should be the Science Ministries, the Governments,- but instead they do not understand and lump the scientific sector into the more general belletristic market and apply the copyright laws suitable there (where authors live from their work and the work is for private use) to the scientific sector (where authors are paid to do research as effective as possible, and the researchers are to be best informed to be able to do their research, which is their professional task).

Therefore we have to wait for a new Government, which understands the scientific needs, and understands, that funding scientific needs effectively, drawn from the researcher’s necessities, and not from habits and history, with a new copyright which derives the new legislation from the needs of the researchers, not from the wishes for a good revenue from an Industry of the paper age. In Germany that is most easily seen: All the major Scientific Institutions form a Coalition for Action ‘Copyright for Education and Research’, and even are forming an Infrastructure for Copyright in Science and Education.

But the present Government seems to form a firm coalition with the lobby organization of the Publishing Industry, instead of going the natural path: ask for needs of the Nation for research first, what the scientists need, and then put through effective legislation to assure and enable this; history tells that with a reliable legal frame given, Industry will be flexible and adjust and come up with fitting business models. It could be so simple. Even the money is there: Scientific Information Management costs are less than 1% of the research costs, but with the lack of an effective scientific information much of the research effort could be in vain.

Eberhard R. Hilf 26th January 2012

Panton Fellowships: What they are about and how to apply

#pantonfellowships #pantonprinciples

In 2010 we launched the Principles of Open Scientific Data and, because we met more than once in the Panton Arms we called them the “Panton Principles”. Since then “Panton” has started to become a brand for Openness. We’ve now had 6 Panton discussions with people who champion Open Data, and we are creating Panton Papers to support the discussion and formulation of ideas in Open Data.

Now we take this a major step forward. The idea to create Fellowships came from Jonathan Gray and he and I worked up an application to the Open Society Foundations (previously called OSI ) . We were delighted that in November the OSF told us that the grant had been successful, and we thank them.

The idea of the fellowships is to support scientists to develop activities in Open Data. The remit is deliberately broad as we want to encourage novel approaches. The details are given here. with an excerpt:

We firmly believe that “open data means better science“. Panton Fellowships have been created in order to support scientists – particularly graduate students and early-stage career scientists – to explore this idea, and to tackle those barriers which currently prevent science data from being made open.

Dr Cameron Neylon, of the Panton Fellowships Advisory Board, commented on the ‘real potential’ of the Fellowships to influence practice surrounding open data in the scientific community. ‘Panton Fellowships will allow those who are still deeply involved in research to think closely about the policy and technical issues surrounding open data’, observed Dr Neylon. By allowing scientists the scope both to explore the ‘big picture’ – gathering evidence to promote discussion throughout the community – and also to work on specific technical solutions to individual problems, the Panton Fellowship scheme has the potential to make a real impact upon the practice of open data in science.

Panton Fellows will have the freedom to undertake a range of activities, and prospective applicants are encouraged to formulate their own work plan. As Fellows will continue to be employed and/or study at their current institution, activities undertaken for the Panton Fellowship should ideally complement and enhance their existing work.

Fellowships will be held for one year, and will have a value of £8k p.a. For more details and information on how to apply, please visit

The Panton philosophy is increasingly adopted by promoters of Openness and as an example BiomedCentral have donated us banner advertising on their pages.

I am really looking forward to reading the applications!

Marcus Hanwell: The way ahead for CML and the community


Marcus Hanwell (Kitware) reported from the #semphyssci working group which was looking at how to grow the development and use of CML in the community. One of the great excitements of the Workshop is the agreement among participants that CML is valuable, worth developing and that they will put the effort in to make it happen.

There are several ways to develop a successful information infrastructure:

  • Commercial entrepreneurship, typified by Gates and Jobs – and also Google and Facebook. Build the products that people want and sell them. Failure is common, but the market doesn’t care WHO succeeds.
  • Design by committee. In many cases this works. CIF, W3C are committee-based, managed, successful. Failure is often common, normally because committees are very slow. I’ve sat on ISO committees – nuff said. It’s very difficult to get innovation.
  • Benevolent Dictator For Life (BDFL). Linux, Python are examples of this. It depends crucially on the energy, vision, political skills, etc. of the BDFL.
  • Leaderless meritocracy. Almost always requires an oligarchy of small number of hardworking, disciplined, drivers. Overlaps with (3).


A common model is for a BDFL to create an initial prototype and then for (1) or (2) to take some role – either complete or partial.

Henry and I have been BDFL for CML for nearly 20 years. We’ve never wanted to be self-important and so much of the work has been low-key. Unlike ICT where new developments are welcomed both in terms of new ideas and new markets, chemistry regards new ideas with suspicion. There’s a large chemical information industry (content and software) which is almost completely out of touch with the 21st Century. There’s a few sparks, but most are based on the concepts of possessing content and building walled gardens, and of developing monolithic applications. Both are failing. But so far almost no interest from the chemical information market in semantics. The result is that we have had to build the ecosystem ourselves.

Now it’s changing. This meeting #semphyssci has shown that there is not only a desire for the CML ecosystem, but also a willingness to develop it. That’s why I invited the National Laboratories to this meeting and I’d like to congratulate them on their commitment. The mechanisms are yet to be worked out but I have no doubt it will happen.

An aside: Four years ago I went to CERN ( to talk to Salvatore Mele about open access publishing. SCOAP3 ( would cost some tens of millions of dollars but change the model of publishing to a scientist-centered one, rather than a publisher-centered one. Salvatore took me to the Large Hadron Collider, pointed to a hole 100 metres deep and said “last week we lowered 500 million Euros worth of instrument down the hole. We know how to make large projects work” (with the implication that open access was only a middle-sized project).

I have already welcomed Marcus and Kitware’s commitment to Open Source, Open Access and collaborative models of information infrastructures. These will inevitably triumph and the current ecosystem will adapt or die. Even their lawyers will not be able to enforce sustainability – the market will simply move on. And CML will be part of the new market. Because that’s a central part of the new market – free flow or raw data and ideas, managed by semantics.

And CML is currently the only system which supports chemical semantics across the major subdisciplines – especially in this context spectra, computation and solid-state.

Marcus coordinated the working group on the vision and ecosystem of CML and here’s his presentation I have snipped from this – I think it’s rather fun compared with just the flat presentation of slides!

0:00 overview and value of CML

1:15 creating CML ecosystem

4:45 Resources for developers using CML

6:50 End-user applications (maybe whitepaper)

8:20 wish list for new tools

9:20 Features of community

10:20 future meetings

11:00 exercise in validation

Latest Article Alert from BMC Infectious Diseases

The latest articles from BMC Infectious Diseases, published between 26-Dec-2011 and 25-Jan-2012For articles which have only just been published, you will see a ‘provisional PDF’ corresponding to the accepted manuscript.A fully formatted PDF and full text (HTML) version will be made available soon.DebateThe definition of HIV-associated neurocognitive disorders: are we overestimating the real

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The latest articles from BMC Medical Research Methodology, published between 26-Dec-2011 and 25-Jan-2012For articles which have only just been published, you will see a ‘provisional PDF’ corresponding to the accepted manuscript.A fully formatted PDF and full text (HTML) version will be made available soon.Research articlePrediction intervals for future BMI values of individual children – a

Bug love: The fascinating story of the fig wasp

About 10 years ago, I had quite a scare when my high school biology teacher warned us away from figs because their insides were crawling with wasps. Some internet research revealed that this claim was only partly true, so I continued along my fig-consuming way without thinking much more of it.

That is, until today, when we published a paper titled “Moving your sons to safety: galls containing male fig wasps expand into the centre of figs, away from enemies,” which made me look deeper into this symbiotic relationship – and now I’m eager to share all the creepy crawly details I found.

The short story is that fig wasps lay their eggs inside the fruit, where they hatch and mate. The female then crawls out of the fig, through a tunnel chewed by the male, and eats her way into a new fig to lay her eggs. In the process, she loses her wings and antennae and dies, trapped, inside the new fig, which she has also pollinated.

As for the caveats: there are also species of self-pollinating figs, which do not require the wasps, and species of parasitic fig wasps that game the system, taking advantage of the figs as incubators without doing their pollination duty. (I’m still not sure which ones make it to the supermarket though.)

Today’s paper explores some of the differences in egg-laying behavior between pollinating, symbiotic wasps and non-pollinating, parasitic wasps. Non-pollinating wasps not only take advantage of the fig, but sometimes also kill the larvae of pollinating wasps. In response to this threat, it appears that pollinator wasps have developed some defense mechanisms, including the location and sex ratio of eggs laid, the authors report.

Wasps aside, I also learned a surprising piece of information about figs themselves. They are not fruits, but are actually something called an “inflorescence,” or a cluster of flowers. It’s just that the flowers are hidden on the inside: each crunchy little seed in a fig represents one flower. To make it more complicated, there are three different types of flowers: male, short female, and long female. Female fig wasps can only reach and lay their eggs in the short female flowers, so the long female flowers are left to develop fig seeds, allowing both the fig and the wasp to prosper.

Image source: Mundoo via Flickr

First Announcement: Berlin 10 Open Access Conference to be held in Stellenbosch, South Africa

Stellenbosch University, in partnership with the Max Planck Society and the Academy of Science for South Africa, has the pleasure of announcing that the prestigious Berlin 10 Open Access Conference will be held in Stellenbosch, South Africa. This will be the first time that the Berlin Open Access Conference will be held in Africa. As is tradition with the conference, it will explore the transformative impact that open, online access to research can have on scholarship, scientific discovery, and the translation of results to the benefit of the public.

The Conference will be held at the Wallenberg Research Centre, Stellenbosch Institute for Advanced Study (STIAS). STIAS is situated on the historic Mostertsdrift farm in the heart of Stellenbosch.

Conference date: 7-8 November 2012

Pre-conference date: 6 November 2012

The theme, programme, speakers and other relevant information will become available in forthcoming announcements which will also be available on the conference website (

Andrew Walker: Fantastic Mr FoX II


Andrew Walker (video ) presented “FoX, CML, and semantic tools for atomistic simulation” at the Semantic Physical Science symposium. Andrew has taken on from Toby White as the “Doctor Who” of FoX, the FORTRAN library for managing XML input and output. FoX allows for domain-specific XML conventions and supports a subset of CML (scalar/array/matrix, module/list, and molecule). There are now about 12 codes which have substantial conversion to allow CML output.

In this presentation Andrew describes the philosophy and current status of FoX.

Here I’ll take time to thank Andrew for continuing the work on FoX. Without that I don’t think we could expect groups such as PNNL and Daresbury to commit to supporting CML. There is now a critical mass of users and new features are clearly worth the investment.

The Time-annotated talk (on VIMEO you can click times)

0:00 Intro and data management

1:00 traditional example, glue code

2:00 Code in FORTRAN, require XML. Only tool C compiler

3:00 options

3:30 FORTRAN-XML is most attractive choice

3:50 Homage to Toby White and Alberto Garcia


5:30 Benefit of XML

6:00 example of XML code

6:40 benefits of XML

7:00 CML convention for atomistic simulation

8:00 overview of FoX

8:50 Codes using FoX – about 12

10:00 SIESTA tests new version against CML

11:00 example of output transformations (uses XSLT)

11:50 SIESTA output

12:30 Jmol output

12:50 AMBER example

13:50 Where to get FoX and completely reusable (BSD licence) with mailing list.

14:36 end (and some questions)

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Call for withdrawal of labour from publishers in favour of the US Research Works Act

Gary Hall posts a call for withdrawal of labor from publishers in favour of the US Research Works Act, which would make it impossible for the U.S. government to require public access to the published results of research that it funds:

Among the publishers of critical and cultural theory on this list are:

Sage (who publish numerous journals in the area including Theory, Culture and Society and New
Media and Society)

Palgrave Macmillan (publisher of Feminist Review

Stanford University Press

Fordham University Press

Harvard University Press

NYU Press

Cambridge University Press