Monthly Archives: July 2012

#openaccess TOWIG (The Only Way Is Greold) – or are there others? Some suggestions

I'd hoped to blog about something other than Open Access – such as developing intelligent software for reading the scientific literature (and I shall). However things have niggled away and I have to get them and other ideas out before I can go back to writing code .

  • I have been invited as an OKF representative to a (invitation-only I think) meeting run by the Royal Society "Workshop on 'Revaluing Science in the Digital Age' 2-4 September 2012 at Chicheley Hall (Royal Soc). No idea how long I speak for, but I am expected to contribute a "provocation". No doubt more later.
  • A recent post ( ) to the OKFN open-access list [0] by Katie Foxall of Katie runs a discipline/community-based journal which is toll-free and APC-free (in simple language anyone can read it for free and authors don't have to pay charges). She writes:

    I haven't posted before but have been following the discussions [on OKFN open-access]with much interest and have founds the info and links provided by various people really useful. I run an open access cancer journal which has no author fees - we are currently mainly supported by charity funding but the journal has been growing at a great rate this year so I'm looking into accessing any funding that might be out there to support open access publishing. The reality is that we will have to start charging author fees at some point if we can't get more funding and we really don't want to do that as providing a free service for the oncology community is very important to us.

    So does anyone know whether there is anything like SCOAP3 [the consortium for High Energy Physics publishing] in the field of medical publishing?

To many of us this sounds entirely natural and desirable – after all that's how many journals started and – IMO – this often represents the best of science communication – a community-to-community process rather than the anonymous capitalist scholarly presses. So for me, part of the issue is whether #openaccess can solve Katie's problem.

If we go to the traditional approaches "Green and Gold") there are many words and some – but limited – progress. The publication of the Finch report and the RCUK policy on Open Access have engendered a huge amount of "debate" in the open access fora (such as the GOAL open access list ) and more recently and possibly more digestibly on Google+ Unfortunately much of this is politico-religious and revolves round "The Only Way Is Green" [1] and oh-no-it-isn't "The Only Way is Gold". (Hence the humpty-dumptyism of the title Gree-old). The "debate" consists of a lot of shouting and more recently withdrawal of cooperation: (Summary – Stevan Harnad said one thing and then changed his mind and attacks the RCUK and Finch and with his fellow-thinkers me if I dare to post on GOAL).

So my starting point is that Green and Gold (besides being almost meaningless terms operationally – like "democracy" or "healthy") have serious flaws and are not a solution to Katie's problem. Why do I say that? (I remain a supporter of BMC and Gulliver Turtle and PLoS and IUCr and EGU).

The problem is that they are C19/20 solutions in the C21. They glorify the "article". They are based on a very university-centric – and often arrogant – approach. They have very little scope for C21 ("Web 2/3.0"). There is no feeling of community if you publish a Gold article. There is no feeling of community in self-archiving a Green article. It's a chore. They are often predicated more on glory-for-the-authors than communicating to the electronic world. The end result is an "impact factor" not a community of practice.

Contrast this with Open Street Map. . This creates top-quality up-to-date maps for the whole world – in many cases better than the existing commercial products. And for many years (and maybe still true) it didn't even have a bank account. It has 250,000+ supporters who love doing it. The simple message – if you create a world community (not just an ivory-tower one) you can change the world.

Wikipedia has also done that. For that reason many academics hate and denounce it. "It can't be good because it's free and created by non-specialist volunteers. It has no peer-review" (wrong). It is against the laws of academia to create a volunteer-based high-quality zero-cash encyclopedia. Of course it's not zero-cost now, and we have JimmyW's face asking us to donate, but that's C21.

So can this translate to community journals without Gre-old? I think we can and I think we should try.

To start I highly recommend reading - which gives a factual, readable, account of how a journal can be run with virtually no cash.

LeCun (editor of Journal of Machine Learning Research (JMLR), ) "The best publications in my field are not only open access, but completely free to the readers and to the authors."

To supporters of the multi-billion dollar faceless publishing industry – like Kent Anderson of the Scholarly Kitchen – this is impossible.

I'm not entirely clear how JMLR is supported, but there is financial and infrastructure support going on, most likely from MIT. The servers are not "marginal cost = 0″ — as a computer scientist, you surely understand the 20-25% annual maintenance costs for computer systems (upgrades, repairs, expansion, updates). MIT is probably footing the bill for this. The journal has a 27% acceptance rate, so there is definitely a selection process going on. There is an EIC, a managing editor, and a production editor, all likely paid positions. There is a Webmaster. I think your understanding of JMLR's financing is only slightly worse than mine — I don't understand how it's financed, but I know it's financed somehow. You seem to believe in fairies.

Anderson's comments (and it's worth reading the comment thread) read like a sceptic of heavier-than-air flight: "Publishing requires fees – it is theoretically impossible to run a no-fee journal". Read how every time his "argument" is countered he plays-the-man-rather-than-the-ball (a soccer term). "You failed to fill in a tax return for the journal so this proves you cannot run a journal without fees".

So to Katie my suggestions would be:

  • Resist rushing into conventional solutions. You sell your soul if you involve a commercial publisher (look at all the "Society" publishers who are now controlled by for-profit publishers). [2]
  • Look to collaborate with others. There is no reason why JMLR and ecancer shouldn't share infrastructure development, for example.
  • Be open (as you have been) and ask for help and advice. There is a lot going.

So reader, if you have a bright idea for how new methods in #scholpub can be developed bring them forward. And if you can help to develop new ways of running almost-cash-free journals I think there will be people interested in helping get this off the ground.

NOW I can get back to writing code


[0] The OKFN open-access list has much of its input from outside academia and has a collaborative and innovative approach.

[1] There is a reality program in the UK called often abbreviated to TOWIE. I don't watch it and it has no other relation to Open Access other than the cadence of the title.

[2] In a later post I shall compare scholarly publishing to banks – both of course are highly respectable, ultra-efficient, scandal-free, publicly loved, high-value-providers and respected.

I ask Elsevier for their list of articles published as “hybrid Open Access”

Scientists can pay up to 5000 USD for an "Open Access" article in Elsevier journals (i.e. published normally in a toll-access journal but free to read). Leaving aside whether this is good value I wish to know what the authors get for their money. In particular since the authors presumably wish me to be able to read them, Elsevier must make it easy for me to find them.


I ask the Director of Universal Access how I can find the articles and how they can be identified by readers:


To: "Wise, Alicia (ELS-OXF) [Director of Universal Access]" <>,

Dear Director of Universal Access,
I am interested in articles published in toll-access Elsevier journals as "authors-pays Open Access" often called "hybrid Gold".  See, for example,

for the Lancet (for which the price is 400 GBP (ca 600 USD) per page (and 3000-5000 USD for articles in other journals). I am interested in all subjects, not just Biomedical.
I would be grateful if you could answer the following questions:
* What , if any, is Elsevier's precise name for this scheme and where is it described?
* how many articles in total have been published under this scheme?
* what explicit licence, if any, is used on the articles?
* how are the articles labelled in the Elsevier journal (i.e. how is the licence and the Open Access information made apparent)?
* where is the machine-readable list of all articles published under this scheme?  I wish to download and analyze all of them.

Thanks in advance for your answers. I shall be making the results Openly available as I shall be contributing to public discussion on this matter in a few weeks.

Jimmy Wales is fighting for British rights; he/we needs your help

People don't realise that we are in the middle of a global fight for our electronic rights – lose them and we sink into the digital dark ages. The following story is so appalling that Jimmy Wales (of Wikipedia) is lobbying us Britons to fight. The story is here

Hi, I am Jimmy Wales, founder of Wikipedia, and if you care about justice and the future of Internet freedom, Demand Progress and I need your help.  This will only take a few seconds, but you can really help us change things for the better.

Richard O'Dwyer is a 24 year old British student at Sheffield Hallam University in the UK. He is facing extradition to the USA and up to ten years in prison, for creating a website - – which linked (similarly to a search-engine) to places to watch TV and movies online.

O'Dwyer is not a US citizen, he's lived in the UK all his life, his site was not hosted there, and most of his users were not from the US. America is trying to prosecute a UK citizen for an alleged crime which took place on UK soil.

The Internet as a whole must not tolerate censorship in response to mere allegations of copyright infringement. As citizens we must stand up for our rights online.

Please sign on at right here to join me in demanding that British authorities refuse to extradite O'Dwyer, and that US officials cease persecuting him.

This is M*ck*y M**se imperialism of the worst kind. It's the attitude that is espoused by supporters of ACTA, SOPA, CETA and the never-ending hydras. It's made easier by the lobbying of publishers of all sorts (including scholarly publishers) to restrict digital freedom for purely monetary gains.

There can only be one winner. If you don't fight for freedom, then who will. To paraphrase:

"First they came for Richard O'Dwyer, then they came for … " but you know the rest. Over-the-top? No. digital imperialism is erosive of human well being.

So I wrote to my MP, Julian Huppert. He'll already know about this:

Dear Julian,

I expect you know that Richard O'Dwyer is being prosecuted for
providing hyperlinks to TV sites. (The full story is presented by Jimmy
Wales, the new government adviser on Open Data)
I , like him, am appalled (a) that this could be considered illegal and
(b) that the UK government can so easily give in to foreign powers.

If we do not fight this type of injustice we shall have little
independence as individuals or as a country.



Reforming #scholpub: A fairy tale


On the [GOAL] Open Access mailing list Jean-Claude Guédon makes the clear point that the continued bickering about whether Gold or Green OA is best is holding Open Access back. I agree and I go further. Here's my diagnosis and a fairy-tale

  • The OA movement is fragmented, with no clear unified objective. We (if I can count myself a member of anything) resemble the People's Front of Judea and the Judean People's front. Every time I am lectured on why one approach is the only one I lose energy and the movement - if it is a movement - loses credibility. Until we get a unified body that fights for our rights we are ineffective.
  • Most people (especially librarians) are scared stiff of publishers and their lawyers.
  • There is a huge pot of public money (tens of billions in sciences) and it's easier to pay off the publishers than standing against them. There is no price control on publishing - publishers charge what they can get away with.
  • The contract between publishers and academics has completely broken down. The Finch report, the Hargreaves process have not thrown up a single constructive suggestion from toll-access publishers
  • senior people in universities don't care enough about the problem to challenge publishers. It's easier to put up student fees to pay the ransom. And many have accepted the Faustian bargain. (Here's an awful example of an LSE academic who "published" a paper only to have to wait TWO YEARS while th epubklishers typeset it. And her boss would rather NO ONE read it as long as LSE got the glory.
  • Young people are disillusioned and frightened.

So here's my fairy tale. It more likely to happen than universal green OA mandates. It's more likely to happen than a useful amount of Gold OA. It is technically trivial (My software can do it).

Fairy Tale:

  • The top 20 vice-chancellors (provosts, heads of institutions) in the world meet for 2 days (obviously somewhere nice).
  • They bring along a few techies (I'd go).
  • They agree that they will create copies of all the papers their faculty have published. (this is trivial as they are already collecting them for REF, etc. And if they can't , then I can provide software).
  • They reformat them to non-PDF.
  • They put them up on their university website.
  • They prepare to fight the challenge from the publishers.


  • they win the law suit. Because it's inconceivable that a judge (except in Texas) will find for the publishers.
  • Other universities will take the model and do it.

Total cost perhaps 1 million per university. It's cheaper than running our currently empty repositories. It's cheaper than hybrid fees.

There's only one thing missing:




Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge

Open Data – la Conference (2012-09-27). Data is truth.

I've had the privilege to be invited to an important European conference on Open Data in Paris As a start I have been asked to answer three questions, which I think will appear on a web page. [You'll see the same three questions answered from a Brazilian perspective – which I didn't read till I had given mine.] Because I do everything openly here are the questions and how I answered them.

I'd be grateful for comments.

1)      How Open Data can modify the current way of « doing » science, the actual epistemologic paradigm ?

I will interpret "epistemology" in a pragmatic way. If this doesn't answer your Q please come back. I will also concentrate on science. My discipline of chemistry is a good central pragmatic one, where there is relatively little philosophical discussion. Modern biology is also highly reductionist and I suspect much medicine, materials science, earth and environmental science is similar. I will exclude modern physics where multiverses and similar concepts are constrained by theory rather than data. Thus although I fully support Dirac ("it is more important to have beauty in one's equations than to have them fit experiment.") most science is not at this level.

Most science is based on a concept of shared truth and most of the scientists above believe that this has some tangible reality, represented by data. [I also exclude shared materials such as specimens, samples - which are also out of scope]. In the more physical sciences there is a belief that a given experiment can be replicated to provide the same data - if not then either the observation is flawed or the experiment does not address a single truth. Without data we are limited in how we share truth. In many cases we have to take the word of the scientist, which is a non-objective way of doing science. Apart from fraud, and sloppiness there is also unmeasured variation. And, without the data, we are unconsciously importing the values of the other scientist.

But there is also a growing realisation that we can, in principle, have access to all the world's scientific data. This creates a new type of scientist - the data-scientist. Tony Hey has popularised Jim Gray's "the Fourth Paradigm" to describe data-driven science. The principle of using other work is, of course, not new and goes back at least to Kepler. But the scale of possibilities changes this qualitatively - everyone can and should be, in part, a data-scientist. It is no longer acceptable not to know what machines can know.

But the practice of holding on to data for personal or institutional gain is still very strong, aided by laziness in publishing data. Despite the term "data deluge" there is an Open Data drought in many areas. Computational chemistry and materials probably consumes >> 1 billion EUR /year but almost none of the raw data is published although it's trivial by HEP standards - much would probably fit on a modern laptop.  Therefore until everyone has access to the world's shared knowledge we are still working in the twentieth century.

The primary check on truth is therefore data. 

2)      How can the Open Knowledge movement (and, in general, Open Data) be a vector of democratization of science ?

We are in the middle of a titanic struggle between Openness and ( Closed + Apathy). If one wins it will survive for the rest of this century. But if we lose the freedom of the Net (e.g. HADOPI) we move to a dystopia similar to Orwell's 1984. Knowledge is the key component as openness is based on the power of knowledge. The recent EP vote against ACTA was a critical battle for Openness and its success was based on Net democracy / neutrality. The Net is our main defence against the creeping corporatism and apathy of modern "democracies" - we can find like-minded people, move rapidly and develop our resources communally while remaining within the law.

Open Data from government is extremely powerful. It's been very refreshing to see how governments *wish* to share data. Indeed they are often ahead of science in their technology and protocols.

In science we have several problems. Universities and public research labs are conservative and have failed to react to possibilities of change. Many have allowed their knowledge to be appropriated by commercial interests such as publishers and for the most part they don't care. They have huge amounts of public funding (I calculate that 100-1000 Billion USD is spent each year on public STM research).  They have little effective drive to share anything as their primary purpose is to compete against each other

So in the open movement we have to create approaches to destabilise this dystopia. I see Open Data and Open Software as liberating - I call my own software "liberation software" as it is designed to break down walled gardens by showing the value of communal data. The good news is that this type of approach is emerging in many places and is undoubtedly a "bottom-up" movement - people are sick of many current practices and believe that science will be better, faster, more productive and more valuable if Open.

3)      If you should summarize Open Data, its philosophy and its consequences, in one word, what would it be ?


(Free-as-in-speech, of course)
I think you can translate this to Liberty - with its cognate "libre" in languages other than English.


Freedom and Openness in Cambridge: ACTA and OKFN

I am really fortunate to live in Cambridge – it's where things happen . It's small enough to know people and large enough to consolidate things.

Today I left the car for its annual road test (MOT). We're in a small cul-de-sac with a mixed economy – residential and industry – which I like.

The garage (centre right) has just been taken over by two employees. It's great to do business with humans rather than amorphous businesses – and that's why we've had windows, fences, etc. done by local people.

They offered me coffee and we talked for over half an hour. I told them about the importance of Cambridge as a high-tech hub of Europe and then we went on to discuss ACTA. Outlined how I had written to MEPs and the vote was expected today. How democracy was increasingly bottom-up and how the Internet enabled people. And lots more.

And then to OKFN – although the OKF is global its heart is in Cambridge and it's of enormous importance to me. I believe the OKF is unique, and has the opportunity to change the world does things. It's enormously difficult – we have to have a vision where intangibles such as trust and community are the primary worth but where we manage to raise enough money to thrive and develop.

So here are some of the wonderful people who work with/for the OKFN:

And – breaking news


Europeans: Urge your MEPs to vote against ACTA. It’s easy!

It's essential that we defeat ACTA. It's not just about copyright but fundamental rights of individuals.

It takes a few minutes using

Here's what I wrote:


                                                  Monday 2 July 2012

Dear Andrew Duff, David Campbell Bannerman, Stuart Agnew, Vicky Ford,
Robert Sturdy, Geoffrey Van Orden and Richard Howitt,

Dear Cambridge MEPs

I would urge you very strongly to vote against ACTA next week.

A very good analysis is given by Glyn Moody
My added view is that defeating  ACTA  will be seen as similar to Magna
Carta, the Rights of Man, trial by jury and many other places where
Britain has pioneered reform of democracy and the rights of

If ACTA passes we are condemned to a century of digital darkness which
will spill over into many other aspects of our everyday life.

Yours sincerely,

Dr. Peter Murray-Rust



Immediate support from UKIP:

Dear Dr Murray-Rust

Thank you for your recent email, addressed to Stuart Agnew MEP.  I am
replying on his behalf.

Mr Agnew is a member of the UK Independence Party.  We are strongly opposed
to ACTA and the EU taking control of intellectual property rights and have
been for some time.

Please rest assured that we will continue to oppose it.

Best wishes,

Stuart Gulleford
Political Advisor to Stuart Agnew MEP

UK Independence Party
145 New London Road
Tel: 01245 266466
Fax: 01245 252071


PMR: This is democracy in action. Thanks UKIP! (There is a possible implication that they would support the UK taking control of our democratic rights, but we'll face that when we come to it!)

Understanding diagrams in scientific journals: I

Now that I am working with Ross Mounce on phylogenetic trees and related sciences I have to learn about what some of the diagrams mean. This is the first in hopefully a series of posts

Here's a diagram from BMC Evolutionary Biology

And here's one from from Molecular Phylogenetics and Evolution


So what is the main difference between them? I'd welcome reader's comments.


A number of people have commented that they cannot see the second image. This is very common. There is a simple, clear explanation. No-one has fully explained why yet.