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Posts Tagged ‘Research integrity’


I need a “Bullshit-O-Meter”, which would determine the purity of bovine excrement that at times heads my way. In a previous post, “Why doesn’t the sun go around the earth?”, I put forth my views on the case brought by Fazlul Sarkar that aims to lift the anonymity of PubPeer. This led to an e-mail from Weishi Meng, which starts (note I have redacted the co-addressee).

“Dear Drs. XXX and Fernig, (more…)

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Dear Dr Worms,
I write this letter in a personal capacity to express my views on the letter you sent to Dr Amaya Moro-Martin on behalf of the ESF, regarding her opinion piece in Nature. Note the word “opinion” and refer to Article 10 of the European Convention on Human Rights (on page 11, it is only two very short paragraphs) (more…)

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A recent post at Retraction Watch revealed that Fazlul Sarkar of Wayne State University is behind the attempt to lift the anonymity of commenters at PubPeer
The Spectroscope has posted The REAL threat to PubPeer is a real threat to science communication.

I agree entirely. (more…)

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On December 31 2013 I posted my New Year’s resolution: to only review manuscripts from open access or learned society journals.

My reasoning was that open access will only be the norm if we stop giving that which is most precious, our time, to closed access journals. I really think the wider community needs to start to be selective in reviewing. It is far easier to implement than the radical re-alignment of library journal subscriptions. (more…)

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Last week at Retraction Watch (RW) there was a post on a paper in elife by Andrew Stern, Arturo Casadevall, Grant Steen, and Ferric Fang that put a figure on the cost of research misconduct, using misconduct officially identified by the ORI.

A number of comments on RW, including my own, highlighted that the study necessarily (because it had to use hard data) resulted in an underestimate of the financial cost of misconduct by a least a factor of 10. I thought it useful to summarise my views in what follows. (more…)

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The end of this week has seen two very insightful postings on science and governance by Stephen Curry and Neuroskeptic.

Stephen Curry’s post “Who governs science” has what is for me a pithy summary of how science works: “No-one is in charge … …. That structure, or rather, lack of structure has not been arrived at by design but reflects the organic emergence of the scientific enterprise over the past several hundred years… …It poses challenges for good governance but is at the same time a source of great strength.

(more…)

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This post has been stimulated by a post on PubPeer entitled “A crisis of trust
This post should be required reading for all engaged in research and in the management of the institutions involved in research, including funders and journal editors. I made a brief comment, relating to a sentence that is some way down the post:

“This could be done if together we invert the burden of proof. It should be your responsibility as a researcher to convince your peers, not theirs to prove you wrong”. (more…)

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Inspiration for this post comes from various sources, including Arjun Raj’s posts on the STAP papers (here and here) and that by The Spectroscope (here)
and my previous posts on the question of whether science does self-right.

I take issue with the trivialisation of data fabrication. (more…)

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A rather one sided debate on stripy nanoparticles is taking place over on PubPeer and on Raphaël’s blog

An individual (“unregistered”) is engaging a good old Gish Gallop, having a hard squint in the dark and seeing patterns. It happens.

I have suggested that “unregistered” should turn their efforts to something more mundane, which is to explain the re-use of data across a number of paper from the Stellacci group.
(more…)

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Gradually, the structural problems in sciences are making their way to the surface. There have been articles in newspapers, The Economist and other magazines around the world on the subject. These are stimulated by the constant dripping of information and studies that sit awkwardly with the perceived notion of how science functions.

The high profile controversies tend to catch our attention, simply because of a sense of outrage amongst the wider community that nothing has been done to fix the problem, or that the fixes have been inadequate. Despite the outrage, it remains the case that only a very few are willing to put their head above the parapet and say something. There has been an interesting discussion of this on Athene Donald’s blog here.

Not surprisingly, the “reproducibility question” has gained quite a lot of traction( e.g., here and here). This leads to a simple question: what qualifies as a reproduction?

I argue that an important aspect of reproduction is that it is not necessarily actual reproduction, but a re-examination of observations made with better methods, which includes analytical tools. I have two examples of how scientists deal with the changing landscape of data and their interpretation in these circumstances. The first example is an instance of good practice and is common (or should be). The second seems to ignore the past and the clear message provided by the new data.

Example 1
This is from an excellent 2012 paper in Journal of Biological Chemistry that we discussed (again) in a recent lab meeting. It deals with the molecular basis for one member of the fibroblast growth factor family, FGF-1, being a universal ligand. That is, FGF-1 can bind all FGF receptor isoforms, whereas other FGFs show clear restriction in their specificity. These differences must lie in the structural basis of the recognition of the FGF ligand, the FGF receptor and the heparan suflate co-receptor. The first model put forward by Moosa Mohamadi was superseded in his 2012 paper, when he and his group obtained higher resolution structures of the complexes. This is a great step forward, as FGFs are not just important to basic biology, but they also impact on a wide range of diseases, as well as tissue homeostasis and regeneration. I highlight the following from the paper:
To quote (page 3073, top right column)
“Based on our new FGF1-FGFR2b and FGF1-FGFR1c structures, we can conclude that the promiscuity of FGF1 toward FGFR isoforms cannot be attributed to the fact that FGF1 does not rely on the alternatively spliced betaC’-betaE loop of FGFR for binding as we initially proposed (31).”

This paper provides a great example of how science progresses and is how we should all deal with the normal refinement of data and the implications of such refinements.

Example 2
This is from the continued discussions on whether the ligands on the surface of gold nanoparticles can phase separate into stripes. This has been the subject of a good many posts on Raphael Lévy’s blog (from here to here), following his publication a year ago of his paper entitled “Stripy nanoparticles revisited“, as well as commentary here and elsewhere.

Some more papers from Stellacci and collaborators have been published in 2013. The entire oeuvre has been examined in detail by others, with guest posts on Raphael Lévy’s blog (most recent here) and comments on PubPeer relating to a paper on ArXiv that takes apart the entire body of evidence for stripes.

What is quite clear, even to a non-specialist, is that the basics of experimental science had not been followed in the Stellacci papers on the organisation of ligands on nanoparticles published from 2004 to 2012. These basics include the importance of signal being greater than noise and ensuring that experimental data sample at sufficient depth to avoid interpolation; note that in no cases did instrumentation limitation require interpolation. This might happen to any of us, we are, after all “enthusiasts”.

To conclude, I refer to my quote from Seneca “Errare humanum est sed perseverare diabolicum

This excellent advice is clearly being followed by one FGF lab. It would be good if this advice was adopted more generally across science. When we see real data and analysis (the hard stuff) that challenges our previous data and interpretations, we should all be happy to change these. This is how science (should) move forward. If everyone did this, then there would be no discussion regarding reproducibility. When we see more of the same stuff, without a clear hypothesis testing experiment, we are veering towards metaphysics.

Metaphysics is not science. I note that when data are hidden, so that analysis is restricted, we again enter the realm of metaphysics – hence, for example, the call for open access to clinical trials data.

Links with some relevance to the Seneca’s advice, reproducibility and so on:
There is an excellent post at The Curious Wavefunction’s Sci Am blog
PubPeer: here and here
Neuroskeptic’s post at Discover
Chembark’s post in response to an ACS Nano editorial on reporting misconduct.

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