Archive for the ‘Blogosphere’ Category

My previous entry on this subject, “Research Integrity“, was stimulated by the breaking news in October 2011 of problems surrounding publications from Prof. Melendez when he was at NUS. I have recently discovered that, following an internal investigation at the University of Liverpool, Prof. Melendez resigned from the University some months ago (late autumn or during the winter, I am not entirely sure). I am not au fait with the legal niceties, but I think the University should be proud that it has managed to resolve effectively the issue at Liverpool.

Update 3 November 2013 The links to Abnormal Science and Science Fraud are dead.

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UoL-A*STAR agreement signed

A lot of effort on both sides culminated today in the signing of a MOU between the University and A*STAR’s Graduate Academy on formalising research links through the ARAP programme. This provides the means for joint research between A*STAR Research Institutes and Liverpool through the University’s PhD students spending a 24 month research attachment in Singapore. With a good number of projects in the pipeline through the efforts of PIs on both sides, we can now look forward to the exciting bit, actually doing the work!

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Scientific misconduct has fascinated me, since I was a PhD student. A number of frauds were exposed around that time, including that of Phil Spector, a graduate student in Ephraim’s Racker’s lab. Racker subsequently wrote a fascinating article in Nature where he dissects what he believes to be the main characteristics of fraudsters.

It is extremely important to separate misconduct, or to use the colloquial term, fraud, from mistake and artefact. Mistakes happen, particularly at the cutting edge of science and in interdisciplinary research. Artefacts are there, lying in wait equally for the unwary and the well prepared. Though embarrassing, real scientists own up to their mistakes.
However, there is a class of people, I guess those with inflated egos and/or misplaced ambition, who defend artefact well beyond reason and refuse to admit to error. This is one end of the fraud spectrum. This spectrum then extends into data manipulation and data creation. In all instances I would use the term “fraud”, not “scientific fraud”. There is nothing scientific about the fraud, it is just plain old simple fraud. It is also completely against what should be the normal process of science, which is the rigorous examination and debate of information and ideas. However, temptation is substantial: journal editors watch their impact factors nervously, promotion and hiring committees look at the gloss (what is the impact factor of a candidate’s publications, as opposed to actually reading some of these publications and considering their actual impact as pieces of scientific output). Governments and funding agencies contribute, by promoting views of excellence that can be misguided. We see this in the UK through the stress placed on REF/RAE, which can only be an imperfect exercise and, if too rigid, risks disenfranchising substantial amounts of excellent research.

There have been a fair number of scientific frauds. The result was that in the USA the Office of Research Integrity has been set up. ORI is pretty unique and a model that should be replicated elsewhere. It combines fraud investigation with education. Most fraud is preventable. However, lab members often prefer to keep quiet. I guess it is difficult to speak up against someone one sees everyday. In addition, pressures on PIs mean that they often lose track of what is their actual job: PI. Pressures on the young to get tenure don’t help either.
So we have, perhaps, created a system where what is most surprising is not that fraud happens, but that it isn’t more common. So there is clearly plenty of good in science.

It should also be noted that most frauds go undetected or more correctly, no one bothers to right the ship, because they feel the work will be forgotten soon enough. How many Photoshopped half tones do we see in papers and react by simply not reading any further or ignoring those particular data in the paper? In instances where fraud is publicised, this seems to be either due to the scale (in terms of number of papers, taxpayer’s funds spent, perceived importance of the scientific findings) and/or due to the stature of the scientist involved. However, even when data have been clearly tinkered with in a manner that is not acceptable, e.g., clear evidence of cutting and pasting bands in a Western blot, this is not the end: it is possible to wriggle out, though not without tarnishing one’s reputation.

Enough for now – I recommend the links to OSI and the OSI video and these really should be a “must watch” for scientists in training.

In the meantime, if you want to know what not to read, I recommend these two WordPress blogs.

Retraction Watch does just that: it highlights papers that are retracted, a most excellent and useful service to the community.

Abnormal Science catalogued published data that should not have been published. It has not been active since February 2012, but is a very interesting insight, including some of the major recent cases of fraud, such as that by Melendez.

Update 3 November 2013 The links to Abnormal Science and Science Fraud are dead

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Dave’s Guide to a PhD

I have finally got around to putting this document up – it is on the “Lab” page.

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Many years ago the SETI@home project was born. I think the idea came from some earlier projects that harnessed people’s computers when they were idle to calculate Pi to a new record. SETI@home sifted through radio telescope data for signals from ET. The amount of data was huge, the calculations more so. The answer was to use distributed computing: you signed up and then when your computer was idle it worked on a small part of the problem, The SETI@home project then put the bits together and managed the entire dataset. The idea took off, lots of people joined and then some new projects arose, all needing vast amounts of computing power.

Then software changed and I lost track of this, until a week or so ago when SETI@home sent me an e-mail. Now they use the open source BOINC platform, which you download onto your computer. You then choose a project(s) you would like to contribute to and that is it.

So far I am very impressed by BOINC. Seamless and does not get in the way at all – in fact it is quite “retiring” in terms of using processor time.

So which problem(s)? A matter of taste, though SETI@home captures my imagination. Happily, one can contribute to more than one and with our computers doing virtually nothing most of the time (writing this consumes very little of the resource of my laptop).

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Building on the existing Pancreatic Biomedical Research Unit, Prof. Robert Sutton has successfully led a proposal for a new NIHR Biomedical Research Unit, focussed on acute pancreatitis, chronic pancreatitis and pancreatic cancer. NIHR have agreed to fund this translational research effort at the level of £1.3 M a year for 5 years. Prof. Sutton somehow managed to cross all the disciplinary boundaries (from bionanotechnology to clinical trials) that separated him and his cohort of co-investigators and pulled together a very strong proposal. After review by an International panel of experts, NIHR came to the conclusion that the proposal met its criteria for funding, which are based on excellence in seven areas:
1. The quality, volume and breadth of internationally-excellent biomedical and translational research
and researchers;

2. Existing research capacity, and plans for increasing capacity including training;

3. The strength of the forward strategic plan and ability to generate a step-change in capacity to
undertake experimental research in the relevant priority area;

4. The relevance of the research portfolio to the health of patients and the public;

5. The track record in translating advances in basic biomedical research into clinical research, and
pulling through basic biomedical research findings into benefits for patients, the public and the

6. The strength of the strategic partnerships, including those with industry and other NIHR-funded
research Infrastructure;

7. Value for money.

The impact of acute pancreatitis, chronic pancreatitis and pancreatic cancer is severe and large numbers of people die from these diseases. They are difficult to diagnose and it is difficult to predict how badly patients will be affected. There is a complete lack of drug treatments for pancreatitis and shortage of drugs for pancreatic cancer. Liverpool University has the largest research programme in pancreatic diseases in the UK, partnering the largest pancreatic digestive diseases service, at the Royal Liverpool and Broadgreen University Hospital NHS Trust, where there are excellent facilities for safe clinical research. There is also a strong track record of working with industry and working with other leading clinical centres on new tests, new methods to see inside the human body and developing new treatments. The new Pancreas Biomedical Research Unit in Liverpool will build on our previous Unit to give clinical research in this area a real chance of major success, by translating research advances into improved patient care. Once new tests and new treatments are shown to work, they must then be developed further by industry to provide to the wider world, to the benefit of both the health and wealth of the country.

Now for the exciting part, putting our plans into action!

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ICMAT is over

ICMAT finished on Friday; the symposium on Frontiers in Optical Bio-imaging and Microscopy was very enjoyable. The Symposium got off to a good start on Monday, with speakers keeping to time and good questions from the audience. Happily, Jon Hobley and Martin Lear had secured a budget for refreshments, which was strategically deployed on the fist evening over posters. This helped the core of attendees and the speakers to mix and ensured a vibrant symposium for the next three days. The “graveyard shift”, the last session of the symposium, was well attended and had some very stimulating talks from very different fields. So good, we all went off for a beer after to discuss model organisms and imaging!

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Cat herding a success

I had likened the organisation of visits to seven Research Institutes in A*STAR on Wednesday to cat herding – an impossible job given academics’ preference for freedom! On Saturday morning at 10 am all 25 of us assembled in the lobby of the Holiday Inn for a first debrief on the visits to A*STAR, NUS and NTU. Overall a success, we had all had got real traction on future collaborations at several, if not all, of these institutions.
This was an experiment for the university. In the past we have sent a small high level delegation and the success of the venture then depended on people with existing contacts at the partner institution. Here we sent a lot of people out, including a substantial number of early career staff.
The conclusion was that the experiment worked well. One lesson is that we really have to have inside contacts to build such visits, so that individuals can drill down in 1 to 1 meetings to the details of projects and get to know each other sufficiently to develop these projects in the future. So our contacts within A*STAR, NUS and NTU were vital to the success of the enterprise. A personal lesson is that if you are the University person helping a contact organise a visit, you need to arrive a week early and expect a very substantial workload in the course of that week!
I am really looking forward to future visits to Singapore and having a cohort of research students going in both directions.

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We lose a pioneer

Dr. Nathan Sharon has passed away. He pioneered studies on glycoconjugates and lectins and made seminal contributions to the field of glycobiology. Dr. Sharon’s contributions are not only to the scientific literature, but also in communicating the importance of science to the lay public. For his long-lasting contributions to understanding glycoconjugates and the functions of lectins in biological systems, the Society for Glycobiology awarded him the 2008 Rosalind Kornfeld Award for Lifetime Achievement in Glycobiology

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Countdown to “workshop”

The A*STAR University of Liverpool workshop is taking shape. Virtually everything has been done by Jon Hobley at IMRE. Without his help it would never have seen the light of day. So Sunday was devoted to basic secretarial work, pulling together itineraries for 20 academic staff, extracting 20 CVs from one large PDF and sending e-mails left right and centre to A*STAR investigators across nine Research Institutes.

So far so good and we are in good shape, a few final details to figure out with Jon on Monday, including the venue for dinner! Somewhere convivial where people can mix. My own preference would be a Hawker Centre, a brilliant Singaporean invention, perfectly designed for stimulating networking, but probably not to everyone’s taste.
then on to NUS, followed by NTU on Friday and a reception at the British Embassy.

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