A recent article on bioarchiv “Amending published articles: time to rethink retractions and corrections?” puts forwards ideas on how we might change the way we deal with retractions and corrections.

I would like to thank the authors for a most useful article. There is a lot I do not agree with, and that is surely the point of writing the article. Stimulating discussion is how we arrive at some consensus, though such consensus can only be temporary, as continued change is inevitable.

Note that the article represents the views of the authors, not necessarily those of COPE. Moreover, COPE has guidelines. Bringing breaches of these to a journal’s attention generally results in a shrug of the shoulders (e.g., here). So while the COPE guidelines are useful, they have no teeth. Perhaps this is a good thing, because the changes of science communication continue and it is more than likely that very soon we will have a world of science operating at two, very different regimes.

Regime 1: content of papers is key, place of publication unimportant. This is the current direction of much of the English speaking world.

Regime 2: JIF and glamour journals rule the roost, which is the status some European countries and much of Asia.

However, over time, budgets and financial pressure from large funders, some with international reach (e.g., Wellcome Trust, Bill and Melinda Gates Foundation) means that Regime 2 is likely to falter.


Now onto the article itself.

At the centre of the article is the statement “A lack of willingness to engage in proper post publication correction and amendment…” (Page 3, start of section “A fundamental underlying problem”). This paragraph then states that retraction is tainted, claiming that retractions for honest reasons (we got something wrong) are confounded by dishonest ones (we made up the data). The authors do not cite any evidence for this, but there is evidence, documented, for example, on Retraction Watch.

The evidence I am aware of does not agree.

Honest retractions, which on Retraction Watch are tagged by “Doing the right thing” do not tar authors with the brush of fraud. There is an upwell of sympathy from the community, because we are all too aware how easy it is to get something wrong. On occasion the authors publish how they tracked down the problem; when authors are alerted by a reader of a problem, the reader is more often than not thanked. This only enhances the reputation of the authors in terms of the community’s understanding of the rigour of their research and pushes their future papers higher up a lab’s reading list.

Dishonest retractions are often marked by a long period of obfuscation by the journal AND the authors. For example, look at the delay in The Lancet retracting Wakefield’s fraudulent claims of a link between the MMR vaccine and autism, the still standing paper on arsenate DNA, and how Nature dealt with the STAP stem cell papers (e.g.,  here). We often see corrections (sometimes colloquially termed “mega corrections”, because of the number of figures involved) of data that are fraudulent, to allow authors to find/produce the ‘right’ figure. This I do not agree with.

Retraction means what it says. That it can be a pejorative is down to the fact that most retractions are due to dishonesty, though as I note above, the honest are not tarred by the same brush by the community. If we substitute a neutral word, this too will gain a pejorative flavour, because the underlying problem will remain: most retractions are due to dishonesty. So using a different word will not solve the problem perceived by the authors. Alerting readers that there is ‘concern’ and an investigation is fine, and Pubpeer allows this in a most transparent manner: one can read the concerns of readers, look at the evidence and make up one’s mind. Critical evaluation of the evidence is our job, putting in some sort of filter isn’t going to do science any good. Note that obfuscation by journals and authors is the reason for Pubpeer’s popularity.

The solution to the problem is simple and lies in a different direction: open data. It is still possible to be dishonest in the context of open data, but more difficult and also much easier to spot.

The argument is also made that correcting the literature and investigating fraud should be separate. How can they? The paper is after all integral to the evidence that fraud has or has not occurred and the prime motive (paper = promotion/grant); open data means that individuals can use their critical and analytical faculties to make up their own mind, a platform for communicating one’s analyses, such as Pubpeer, provides the means to access more brains, which is always beneficial. An investigatory committee will likely need the analyses performed by the community.

Of course we all ‘make up data’ every day in the sense of model building, hypothesis generation and generally shooting the bull. We don’t publish this.  So publishing is the key step in scientific fraud, since one is communicating fiction as factual observation. I think the argument made in the paper relies on the idea that the ‘literature’ is somehow distinct from the rest of the process of science. It isn’t, never was and never will be. Communication is at the heart of science.

So what sort of amendments should be allowed? Errata and corrigenda (both make sense as production can result in errors), but no more. The more categories we have, the more game playing will occur by the dishonest journals and authors and we will be none the wiser.

That leaves version control. Should we embrace this? To me the answer is not entirely clear.

Preprint to print.  Yes, it is interesting to readers to see the genesis of the work.

Data: these will have accession numbers/DOIs. In curated databases, there is clear version control and a trail, though the investment in curation of databases is lamentable and we could do much much better. For some reason this is not regarded as ‘cutting edge, innovative, etc. This is a problem for the community to resolve. In the ‘wild’ (other open data) full version control may be less likely and patchy.

There was a time when a researcher working on “Problem A” would on occasion provide a simple title for a succession of papers:

Problem A: paper I

Problem A: paper II

and so on.

The papers in the series do not replace each other; each provides new evidence and likely a modified interpretation of “Problem A”. However, many journals decided that such practice was not good, I guess in part because the title was not sufficiently tabloid-like. Maybe this is a way forward?

As for a ‘living article’, that is the job of encyclopedias. As my generation of scientists retire, rather than write a book summarizing our field, many of us are likely to spend our dotage editing Wikipedia. This will change many aspects of science.

Positions open

Two postdoc positions are available in my lab.

Both are part of the larger, European Commission-funded FET-Open programme, ArrestAD, which has recently been funded.

Position 1 aims to characterise heparin-binding proteins in Alzhiemer’s disease.

Position 2 aims to develop inhibitors to Golgi sulfotransferases.

For both positions, feel free to contact me directly by e-mail for informal discussions.

Kick-off meeting


The ArrestAD team had its kick off meeting in Paris on 5 January 2017. This was held on Paris, the base of our coordinator, Dulcé Papy-Garcia and was hosted by the APHP in the Espace Scipion. Team members from outside Paris stayed at the Hotel La Demeure  situated nearby and though on the Boulevard St Marcel, nice and quiet.

The kick off meeting started with a presentation form our coordinator, which provided the backdrop for the day. Science presentations from the participants then followed. These provided an overview of the position of the field of the participant and then summarised research plans. In a multidisciplinary project, one cannot be fully up to speed with the other fields, so we all learned a lot. The more technical part of these presentations gave us an opportunity to discus the nuts and bolts of our research plans and how these fitted together. It…

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At a primary school during break 28 children are playing a peaceful, if somewhat idiosyncratic ball game, with a ball bought by the 6 oldest kids.

Theresa has recently joined the school. She is not happy and and screams from the edge of the game “LISTEN”.

27 kids stop playing and look at Theresa.

Theresa “We will play My game NOT yours”

27 kids resume their peaceful game.

Theresa screams “I will take my ball away”.

But it isn’t her ball, so she goes off to sulk.

Next day she isn’t at the school. The 27 continue their game, developing it, as they mature.

2017 Resolution

A little late this year, but then there are many calendars, so it is surely the start of the New Year for someone, somewhere, today.

Three years ago I made a simple resolution for the New Year, which was not to review for commercial closed access journals. I developed this in 2015 (and here) when I decided to change my publishing priorities and avoid commercial closed access journals.  This was pretty much already happening, so painless. My two caveats relating to publication are important, if you collaborate extensively, simply because many colleagues live in countries where Impact Factor rules their lives. Thus, when I am not the PI and in editorial control of the work, but merely a contributor, then I suggest alternatives, but I do not dig my heels in. For my students and postdocs who originate from these many countries the Learned Society and Open Access alternatives have pretty much solved the problem, in that they have decent impact factors, and their career progression will not be impeded.

I have also been experimenting with preprints for some time and now, along with Open Data. So the 2016 resolution adds preprints and Open Data. All papers where I am sole PI and have, therefore, the full decision-making power on publication (and also full responsibility for the paper) will be first submitted as preprints and data will be fully accessible.

What is interesting is the development of the change in publication culture. There are still many wedded to the notion that the “Top” journals are those with the highest impact factor, despite the fact that there is no evidence to support this conclusion. Witness the article in Nature reporting the excellent decision by the Gates Foundation, which stipulates that worked funded by the Gates Foundation cannot be published in journals that are not properly open access and open data compliant. To paraphrase the Nature headline:

“Shock Horror, Gates stops researchers publishing in Top journals aka ours”.

The implication that a paper in Nature is worth more than one in The Biochemical Journal or PlosOne to name two other good journals of many is ludicrous. Only when the paper is read can one decide whether it is excellent, good or poor, and then it takes time (=years) for the full scientific impact to be recognised. There are plenty of papers in ALL journals that are worse than poor, ample evidence is provided by a quick scan of Pubpeer; Nature for one has a lot to do to put its house in order.

So preprints and Open Data it is. I would encourage all my colleagues to follow suit.

Back to the trees

The state of the Brexit debate reminded me of “The Evolution Man” (a very funny read by Roy Lewis, also entitled “The Evolution Man or why I ate my father”), which is centred on a protohomonim family that invents many new things, including fire and cooking. Uncle Vanya, whose teeth are not what they were, loves to come down from the trees and eat cooked meat, but he castigates all progress and his catchphrase is “Back to the trees”.


Uncle Vanya is a prototypical Brexiter. He would die if were not for the invention of cooking by his brother’s family, because poor teeth mean reduced consumption of raw food, which can only result in death. Uncle Vanya is a true mirror of the Brexiter in the UK and their homologues elsewhere. Despite reality check after reality check, they continue to fantasise about a world that cannot exist.


The level of fantasy is quite remarkable. For example, Andrea Leadsom stated that a central plank of the new Brexit UK economy would be tea, biscuits and marmalade. Many of the ingredients are produced elsewhere; oranges, sugar (if from cane), wheat (ours having too low a protein content, we need to cut our flour with that made from imported wheat) and, of course, tea itself. Global warming will be insufficient to allow us to growth these crops in the UK. Our 18th Century ventures into greenhouse culture of exotic fruits only succeeded due to Dutch help. Worse, a few meters of sea level rise (coming late this century) will wipe out a substantial part of our wheat belt (go to http://geology.com/sea-level-rise/ select 3 m and check out East Anglia). Salinity from one little flood will cause havoc with yields.


The refusal to engage in any sort of debate and to acknowledge that a number of things do not add up is seen in the HE Bill’s passage through Parliament. Outright rejection of all amendments from opposition MPs, despite the obvious fact that one possible future outcome of the Bill, is a UK version of Lysenkoism, a consequence of which was mass starvation in the USSR. It would seem appropriate for Parliament to consider such an outcome and ensure new legislation is proof against it.


Threads relating to the Article 50 court case are quite remarkable –  Brexiters paint this as Remainers whingeing and filibustering. Ears are firmly shut against the fact there are indeed points of law the relate deeply to our democracy – can the executive remove statutory rights of citizens without the agreement of Parliament? If it can, then the Parliamentary democracy that we are ceases to exist. We may, as a nation, agree on this course, but surely it merits discussion?


This refusal to listen and engage in constructive debate is worse than in the most opinionated toddler.


The term “post truth’ has been coined. This is a euphemism. It is simple delusional lying. The motivations behind the behaviour will vary in individuals. Two clues come from the political importance of panis et circenses in the Roman Republic and 1984. Those in power and with ambitions of power will look to all means to provide at least the illusion that bread and circuses are more plentiful and better than before.  In a time when they are manifestly not (austerity), build an illusion.  For the illusion to work, you need to be at war. Permanent war is the dream of political power seekers (as opposed to political problem solvers). So create an enemy that is permanent, weak and unable to fight back: the immigrant.


So this is where we are. Raging toddlers at the helm, with a posse of toddlers in tow. The outcome? We cannot tell, but there are two extremes.


The power ambitious continue to run the country (=Brexit). The consequence will be a decline in the UK as an economic, intellectual and political power. While the break up of the UK is not a given, it is certain that over time the country (UK or England and Wales) will become less attractive and net emigration will result: our best and brightest will leave, when their personal circumstances allow and few will wish to come.


The problem solving politicians come to the fore. No Brexit, some hard truths to swallow about being British (where are the billions of tax unpaid by that small number of wonderful patriotic citizens of ours?) and a lot of hard work (e.g., getting 90% of that tax into the treasury). The country then becomes extremely attractive and we will need take leadership of solving the problems that cause masses of people to leave their homes: war, global warming, etc.


So delusional toddlerdom or work.


I did say I was going to leave. I will at some point if the country choses delusional toddlerdom. Toddlers are great, but if you let them rule the home, you are lost.

Monty Python sum up what I think here. Leave voters?  A dose of Derek and  Clive might be useful.

Otherwise, some thoughts on the Brexit referendum

1. We now have our freedom they trumpet. From what? Where is this new freedom of mine? Not being able to travel and work freely across 27 other countries? Not being able to travel because we are too poor to afford the cheapest Ryanair deal? No one from Leave is able to say what freedoms I gain in exchange for those I have lost.

2. There is plenty of room at the bottom. We had the 5th largest economy in the world, because we were part of the EU. We are now the 6th. I am no fan of the square mile, but the big financial houses are making contingency plans. Once made, even if we remain, they will see the benefit of derisking operations and shifting some of them elsewhere in the EU. If we do leave, they are gone. As for what is left of manufacturing, building business takes years. Cut off that business and it’s benefit street for you. The country can head down through the relegation zone into the conference and below. It takes 25 to 50 years to rebuild and you never get back what you had.

3. But we have all our money back. Sure, but it’s peanuts and isn’t enough to fix the potholes. Check the estimates for fixing the UK’s basic infrastructure. Plus, our brilliant chancellor has hypothecated our taxes, so he is using taxes he will collect in coming years to pay the bills today. That way he doesn’t have to collect tax from the tax-dodgers, like his good pro-Brexit mate who owns the Daily Mail. The country was in financial trouble in 2008, it has been borrowing heavily since in a variety of ways and now is broke, broke, broke. Any money will go into George Osbourne’s black hole.

4. UKIP is a lie. Does anyone actually think that an individual as corrupt as Nigel Farage, whose only job is a UK MEP, wants to sacrifice his substantial tax free income from his MEP seat, as well as his wife’s tax free income – he employs her at European taxpayers’ expense? If we Leave, he loses his job and so does his wife. I very much doubt that our Nige wants to travel economy with the rest of us stinking peasants or claim benefit. Remember he has no other job and isn’t going to get one – he has repeatedly failed to get a seat in Parliament. Answer that one.

5. Leave was a lie. No one leading the Leave campaign thought they would win, but they acted like it and you followed, venting your frustration at the London elite. Who are the London elite? Well they include the leaders of the Leave campaign. They had no plan, no idea what to do and also no idea of what is required to Leave.

6. What is required to leave?
(i) Invoke Article 50
(ii) Perhaps ratification by parliament, because the referendum was advisory and parliament was and is sovereign (Brussels never had any sovereignty).
(iii) Ratification by the Scottish Parliament and probably the Northern Ireland Assembly. This is written into the devolution laws passed by the UK Parliament.

7. There are a lot of angry people in the UK, because their future, for which they have worked their socks off has been taken away. In the UK, they are taking action to save what they can from the sinking ship. Consider this: Ian Paisley’s son, a good Unionist, has publicly stated that the people of Northern Ireland should take out Irish passports. Once you make people consider the impossible, they realize it has significant advantages. The irony of the Conservative and Unionist Party possibly causing a future reunification of Ireland will not be lost on those who know a little history. In any event there will be an exodus from the UK and you won’t get their jobs, because you are not qualified. There is no one able to replace them, because we don’t train enough people. A good many of the young we do train will emigrate, as this is no longer ‘their’ country.

8. There are a lot of angry people in the EU and elsewhere. Junker is pissing in the wind when he says he wants to start leave negotiations now (remember, our government has to invoke article 50). However, the 27 member states are really pissed off at us. This is not a good starting point for any negotiation, whether we remain or leave. Elsewhere in the world? Well they are simply re-targeting their business, looking to shift their factory into one of the other 27 countries.

How did we get here?

9. The Thatcher-Major-Blair-Cameron project to destroy the working class bears its fruit. Note I include Blair here, because more production jobs were lost during his time as PM, and he was no friend of Trades Unions. The groundwork was laid by Thatcher, through destruction of heavy industry and Trades Unions, and enabling the take over of British companies (GD Searle, Wellcome, Cadbury’s to name a few). Alongside the economic destruction is social destruction, particularly in terms of values and the importance of education as a means of social and economic betterment.

10. TV media with Reithian principles have been replaced by a dystopian feed of bread and circuses. The latter were always there, but with just a few TV channels, there was plenty of other material. Now this is so diluted as to have little effect.

11. Most other media belong to tycoons (nothing new there) with an agenda – their agenda is to make money and they need political control. So they promote weak and venal politicians.

12. Previously politicians were happy to sacrifice members of the armed forces, but not the country. Now politicians are willing to sacrifice all for their own ambitions. I may be wrong, and I would appreciate a comment on this from a historian. My feeling is that it has been over a century (perhaps even before Cromwell’s revolution?) since politicians (or monarchs) have been willing to sacrifice large swathes of the country for their own ambition.

Where next?

13. Article 50 has not been invoked – see here for a lucid analysis by David Allen Green. This analysis suggests that it will never be invoked. The argument rests entirely on reading the Lisbon Treaty and from a legal standpoint and is absolutely correct.

14. However, politics is not the law and political pressure can result in very stupid decisions. It is clear that as of yesterday the other 27 EU countries were pretty pissed off with the UK. This has been brewing since the time of Thatcher, few or no countries have been as annoying as the UK at the negotiating table.

Edit 26 June: an excellent analysis of the balance of law and political pressure is here.

15. We have lost our voice in Brussels, since Lord Hill has resigned as the UK government appointed Commissioner.

16. We have no government, virtually no opposition and the civil service have no idea what to do. Cameron has resigned. Osbourne seems to have gone fishing. The ministers and MPs on the Leave bus are hiding under the duvet. Corbyn remains paralysed or looking for political gain in the narrow sense. Only one politician in England has stood up – Sadiq Khan, but with respect, he is only mayor of London, not a government minister. He can try to stabilize the ship, but he is not at the helm. Politicians in Scotland and Northern Ireland are considering their options.

Time to shift a few deckchairs. Or consider a rosier view here, to which I subscribe to some extent.

Update 22.25: Excellent new piece by David Allen Green on his Jack of Kent blog. The issues now are perhaps a little simpler: Brexit has flushed into the open the fascist side of the UK; is there a politician (for we clearly have no stateswomen or statesmen) likely to succeed David Cameron willing to actually invoke article 50?