The sadly predictable hyping of things nano reached a nadir recently with the promotion of silver nanoparticles (aka “silver bullet”) as a treatment for ebola virus. There has been a great discussion of this and other aspects of silver nanoparticles by Andrew Maynard (here, here for ebola and here for the essential Risk Bites video).

It may surprise some, but until a few weeks ago, there was no simple, direct published method to quantify non-destructively silver nanoparticles. Yet, the non-destructive quantification of silver nanoparticles is essential to any experiment that aims to prepare and use these in a biological context. Without it any experimental work is likely to be qualitative and simple things, such as determining the stoichiometry of functonalisation, become difficult. Indeed, so important is simple quantification of nanoparticles that we validated and published a method for gold nanoparticles in 2007 that has been very well received by the community and which we use daily in the lab.

A few weeks ago all this changed, when Paul Free in Singapore published a method in The Analyst entitled A rapid method to estimate the concentration of citrate capped silver nanoparticles from UV-visible light spectra to quantify silver nanoparticles by uv-vis spectrometry. Like the previous work on gold, it is based on Mie theory. The present work on silver uses an elegant bit of lateral thinking by Paul Free, which allowed him to measure the amount of silver using the product of a reaction with cyanide and a cyanide ion selective electrode, a critical step in the work. Multiple experimental validations using different techniques and theory round off what I think will prove to be a most useful paper for the field – it works, it is simple, all you need is a uv-vis spectrometer and knowledge of the diameter of the silver nanoparticles and you can figure out the concentration.

After pulling the wrong lottery ticket at publisher X, the paper has found a happy home at The Analyst, a publication of the Royal Society of Chemistry. Such a happy home that the RSC decided this was to be one of their “HOT” papers, though this appellation always brings images of charred pages and the end of civilisation to my mind!

I wanted to go Open Access, but the Singapore team were constrained by budget and the antediluvian practice of using impact factor as part of the metric for determining career progression there. Nonetheless, the paper will be available in due course in the A*STAR and University of Liverpool repositories and in the meantime a short e-mail to any of the authors will guarantee a PDF by return – the electronic equivalent of a “request-a-print” in the days of paper and snail mail, but a lot faster.

I hope that now we will see an increase in quantitative experiments in biology with silver nanoparticles. Despite the hype, they do have really interesting properties. They release Ag+ ions, which are toxic to bacteria and perhaps some viruses (see links to Andrew Maynard’s musings on the subject), and they have a much stronger photoactivity compared to gold, so an interesting material to work with.

Update 22 August 2014
Paul has placed the pre-publication PDF at Research Gate. This does look useful and though I have resisted (resisted makes it look like a conscious decision, it is more a question of activation energy/inertia/procrastination…) it looks like I should invest some time and put my closed access papers up there.

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.

It is obvious from the number of papers that are retracted for what is data fabrication, e.g., image manipulation, data duplication and re-use of data to describe different experiment, that ORI only investigates a small proportion of what is likely misconduct. Moreover, considerable misconduct is beyond the time limit of ORI. There is also misconduct elsewhere on the planet.

A while back I did a rough calculation based on the total number of retractions at RW and the fraction that were for what we can term “correct” reasons, that is a genuine mistake, rather than data fabrication. These are categorised under the “Doing the right thing” tag at Retraction Watch and make up less than 5% of all retractions. Of course RW tracks all retractions, not just ones with US authors, but RW has tags that would allow this calculation to be done afresh for papers with US authors. However, the costs of misconduct to the US do not arise only from papers with US based authors.

So my 10-fold multiplier is a guesstimate, based on less than 5% of papers at RW featuring for the right reasons, rather than misconduct, and the number of papers that are corrected, rather than retracted. Given that several such papers may be authored by the same PI, I ended up with 10x.

So the financial cost is higher than estimated in the elife paper.

In terms of human cost, which in my view is far higher than the financial cost, we can consider (in no particular order):

- Some students and postdocs will accept the poison of misconduct dished out by the PI gladly, since this allows them to progress their careers. The human cost here is that we train charlatans, who go on to teach and train other young people.

- Other students and postdocs will rightly refuse to take this poison. This is likely to drive them out of science, since the weak have no chance against the powerful. There are plenty of instances of this documented in various blogs across the web.

-The desperation induced in a young scientist trying to replicate fraudulent work published in a “top” journal. I have had direct experience of this many years ago at another institution and it really knocks your self-confidence and self-esteem. I would count myself as particularly resilient. My view is that this is another route for driving inexperienced people out of science, unknowingly give them a project that is in fact not possible.

- Send a whole bunch of people in labs around the world barking up the wrong tree, costs resources across many labs and leads also to problems with the actual young researchers attempting to do the experiments. This may also break a PI in terms of acquiring outputs required for subsequent grant funding.

-In the extreme we have suicide. Jonathan Eissen’s post on the subject of the suicide of his father, the result of his being requested to investigate potential misconduct, is incredibly moving. Most recently we have the suicide of one of the authors on the STAP cell papers.

-Fraudulent clinical trials can lead to patient death. There are well-documented cases.

So the cost is higher and may not be possible to quantify. It is a cost that we should not incur.

Policing the police

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.

Continue Reading »

The burden of proof

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”. Continue Reading »

What is that ship?

Living in a port, there is always movement on the river. What is that ship, where did it come from, where might it be going? The answer is here, a website I stumbled across courtesy of @livuniwx, the Liverpool University weather station twitter feed.

Real-time update of shipping

This is a great companion to Flight Radar: a real-time map of planes in the air across the world.

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. Continue Reading »

Kat’s paper on the interactions of neuropilin-1 with a heparan sulfate mimetic library of modified heparins is now published in The PeerJ
Continue Reading »


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