Helium shortage

For those who follow the news, though helium is rather common in the solar system, it is rare on earth. The shortages were predicted some years ago, and were put off only by the Pentagon agreeing to put some of its strategic reserve into the market.

We now face the first self-inflicted shortage: helium is now rationed in the UK. Self-inflicted, because we waste it, e.g., balloons and no recovery of the gas at point of use. This of course is all down to cost, and testimony, in a small way, to the failure of applying market principles across the board without any strategic consideration.

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Of nanoparticles, cells and polyanions

Of nanoparticles, cells and polyanions

It is the end of semester 2 so it’s marking season. Since we double mark (a good thing), the final year research projects are marked by both supervisor and an assessor, a member of staff who is not involved in the project. One of the projects I marked was Gemma Carolan’s on “How do SmartFlares RNA detection probes reach the cytosol? Available are the PDF of report, and posts here and here.

I had a sense of déjà vu while reading the project – the clear endosomal location of the SmartFlares, regardless of the DNA sequences brought me back to the days when antisense was the technology of the future for medicine.

While evaluating new technology it is useful to go back and look at other high flying technology. The reality is that it takes decades before we know whether the promise (and hype) were justified; this is true for any hot topic from stem cells to nanoparticles and graphene.

Antisense effects can be mediated by RNAse H, an enzyme that specifically cleaves RNA-DNA duplexes and which protects our cells from RNA viruses. There are other mechanisms, e.g., interference with splicing or translation, but the RNAse-H mediated transcript degradation should be central to many antisense effects. There were many papers reporting specific effects (evidenced by differences between sense, antisense and scrambled oligonucleotides sequences). These certainly contributed to success of individuals and of institutions, e.g., in UK Research Assessment Exercise and grant awards.

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Responding to questions raised on PubPeer

I am a fan of PubPeer, as it provides a forum for discussion between authors and the wider community, something I have discussed in a number of posts (two examples being here and here). Two days ago, My colleague Mike Cross came by my office, having just delivered a pile of exam scripts for second marking (it’s exam and marking season), asking if I had seen a comment on our paper on PubPeer. I had not – too many e-mails and too busy to look at incoming!
So I looked at the question, which relates to panels in two figures being identical in our paper on neuropilin-1 and vascular endothelial growth factor A (VEGFA) – indeed they are labelled as being identical.

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Self-righting or sinking?

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.

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When rigour deserts science we are left with quackery

Update June 5
Standards, who needs them? I am just back from the E-MRS spring meeting in Strasbourg, which was most enjoyable, though someone seems to have forgotten about the “Spring” bit. Meanwhile, out in the world of science we continue to witness ridiculous decisions regarding manipulated and falsified data by journals and a quite stunning self-justification by a materials scientist who looks to be the next serial fraudster.

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Stripy nanoparticles: update from MIT ombudsman

The assiduous reader will recall that on March 22 I formally contacted MIT regarding the re-use of images in multiple papers by Francesco Stellacci. This includes one instance of an image being re-used to describe a different experiment, which so far has resulted in a correction.
MIT have got back to me stating that they don’t have a report for me yet (I guess Friday was a deadline for delivery of an interim decision), but will get back to me at the end of May. Like many of us, MIT will have their hands full dealing with financial fallout. Nonetheless, I hope that this does not distract them too much from the necessity to ensure academic integrity. I look forward to hearing from them in due course, though depending on their interim decision, I may be bound by confidentiality.

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PhD position available on “Short- and long-range structure of the extracellular matrix

http://www.intelliagence.fr/Page/Offer/ShowOffer.aspx?popup=1&OfferId=47887&rwndrnd=0.9729958744719625.

either go through the ABG website, the University of Liverpool website or contact Dave Fernig directly.

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Data re-use warrants correction at Nature Materials

A number of events are worthy of a post, but the most urgent to bring to my readers’ attention is a development at Nature Materials. They have issued a correction to the 2008 paper by Francesco Stellacci, Nature Materials 7, 588 – 595 (2008). Thanks to Pep (despite stating he would no longer comment on this blog) for pointing this out in a comment on my blog entitled “Responses-to-evidence-of-self-plagiarism“. I have raised the issue of data re-use multiple times (no pun intended!) including these posts:

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Still no stripes: debate spreads to the Times Higher Education

There was an article on “Stripy Nanoparticles” in the Times Higher (THE) by Paul Jump on Jan 10. It was followed by a series of comments. Most of the comments (a substantial number from anonymous commentators) reckon that there is no evidence for stripes on nanoparticles.

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Stripy nanoparticles revisited

Raphael’s paper in Small on the likeliness (or lack of) of ligands self-assembling into stripes on nanoparticles is finally published. As Raphael notes, this took three years (plus six months at journals that would not touch the paper). Hats off to Small for letting science work as it should, that is through debate.

However, the process is slooooow. Why? Simply because we no longer operate in the agora where everyone meets regularly. Consequently, it is possible for substantial delay to occur whilst editors request a right of reply, something over which journal editors have no control. As Raphael’s Head of Department, I would say that this makes the process quite destructive with respect to the career of young tenure track staff who need to get papers out just to stay in the system. So, as ever, the established have a lever over the unestablished.

So how does a Head of Department judge such a polemic and come to a decision that has to be defended in discussions with senior management, when we justify budgets, hirings, tenure decisions and so on? My initial approach was to discuss some of the underlying techniques, such as scanning probe microscopy, with which I am familiar, with leading technical experts outside my own institution and the nanoparticle field. This allowed me to appreciate the limits of measurement and so come to an independent view. The upshot is I defended Raphael’s position and now senior management appreciate the importance of Raphael’s contribution to scientific debate.

Where now? Polemic aside, what I would like to see is experts in the measurements, who will not be in the nanoparticle field, to weigh in with their views and, importantly, advice. In this way the community will gain with respect to making technically challenging measurements, be it by scanning probe microscopy, spectroscopy or some other technique. We might then be able to make some progress.

Finally, one should always remember that science is a series of progressive approximations. Newton is “wrong”, but works fine to get you to Mars and back. I don’t think this has been put better than by Richard Feynman in his 1964 lecture from which we have this excerpt, entitled “The Key to Science“.

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