The Devil in the Detail | fanismissirlis

The Devil in the Detail | fanismissirlis

A post by Fanis Missirlis on matters arising from our letter: Allen JF, Missirlis F (2012) Queen Mary: nobody expects the Spanish Inquisition. Lancet 379 (9828): 1785.

Who guards the guardians? And what happens if meta-guardians themselves have something to hide?

Research Assessment and REF

What is ‘research output’? Can it be measured? If so, how? What are its ‘metrics’? from Allen JF (2010) Research and how to promote it in a university. Future Medicinal Chemistry 2: 15-20.

What must one do to avoid being made redundant…?
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Fascination of Plants University of Greenwich 2015

17 April. My pleasure to help provide the solar energy demonstration.

Dr Iskander M. Ibrahim demonstrates the power of sunlight with the famous solar-powered train set.  The demonstration was devised as part of my inaugural lecture, thinking outside the green box.  On this sunny April day in Chatham the train could be driven by sunlight rather than artificial light.  The unshaded silicon photovoltaic panel produced quite enough power to derail the train.

image1Source: Fascination of Plants University of Greenwich 2015 | Facebook

The Bucket or the Searchlight?

“The Bucket and the Searchlight: Two Theories of Knowledge” from Sir Karl Popper presents two views of knowledge. We advance knowledge in research and disseminate knowledge in teaching. How we undertake these tasks depends on which view we take.

The bucket theory underlies many mistakes. Notably in universities.

I raised Popper’s essay in two papers published in 2001, illustrated nicely with cartoons by my daughter, Sarah. The cartoon data to be scooped up or interrogated, according to one’s viewpoint, are from DNA microarrays. Today I’d think more of genomics, perhaps GWAS, while the microarray example is not entirely outdated. Think, perhaps, transcriptomics and RNA-seq.

The Bucket. A theory of knowledge. Data are scooped up, at random. Collect as many as possible.

The race continues – the race to acquire a bigger bucket than anyone else, one large enough for “big data”. The bigger the bucket, the more expensive, and the more attractive the bucket theory becomes to the clowns and crooks who hold that research output is not knowledge, but grant income. Then there is factory science, as described by Sydney Brenner.

‘So we now have a culture which is based on everything must be high-throughput,’ Brenner continued. ‘I like to call it low-input, high-throughput, no-output biology’.

I suppose high-throughput biology is roughly equivalent to equipping the bucket-brigade with a hosepipe. Or water-cannon. The truly ambitious now divert rivers to fill reservoirs.

And the race continues, in teaching, to fill students’ empty buckets as quickly and completely as possible, while obsessively trying to gauge how much they’ve retained. The examination as dipstick.

What a waste of time. And energy. And money. And human potential.

While all the while the searchlight is there for us to use, to share, and to pass on.

The Searchlight. A theory of knowledge. Data are examined to see how they compare with the prediction of an hypothesis. Its prediction is on the clipboard.

Popper, K.R. The Bucket and the Searchlight: Two Theories of Knowledge. Appendix to ‘Objective Knowledge. An Evolutionary Approach’. Oxford University Press, Oxford. 1972.

Allen, J.F. (2001) Bioinformatics and discovery: induction beckons again. Bioessays 23: 104-107.

Allen, J.F. (2001) In silico veritas – Data-mining and automated discovery: the truth is in there. EMBO Reports 2: 542-544.

The Many Worlds Interpretation

Sober reflection may be required after my paean of praise for physicists in the post In Our Time, The Photon.

Too many worlds is a thought-provoking Aeon article by Philip Ball.

Nobody knows what happens inside quantum experiments. So why are some so keen to believe in parallel universes?

Apparently there is a strongly held view that simplicity and elegance trump falsifiability, and there are an indefinite number of parallel universes in which everything that can happen does happen. The problem is that we are inhabit just one of these, and can know nothing of any of the others.

Scientific method: Defend the integrity of physics by George Ellis and Joseph Silk (Nature, 16 December 2014) proposes that physics is becoming undermined by untestable theory. Any hypothesis is only as good as the evidence that supports it.

As card-carrying Popperian, I am with Ellis and Silk. However, all seem to agree that the Copenhagen model won’t do. The question is: what can we put in its place?

I have nothing to offer. However, important questions about the nature of reality and of ourselves clearly coincide in deciding how to interpret quantum mechanics.

I still wish I were a physicist. I have consistently sought unifying principles in biology, biochemistry, and evolution, while believing that nothing can advance understanding if it fails to make predictions about observations that could, in principle, demonstrate that it is false. I act on the assumptions that we all inhabit the same single World, and that we can, if we are honest with each other and ourselves, share our experiences of it, thus increasing our understanding; pushing forward the boundaries of knowledge; seeing more deeply into nature. The alternative seems absurd. And, in fact, dangerous.

Nevertheless, both physicists and biologists eventually run up against the insight that there is a problem in understanding how we can know things in the first place. There, I am endorse Philip Ball’s closing comment.

Here, after all, is a theory that seems to allow everything conceivable to happen. To pretend that its only conceptual challenge is that it leads to scenarios like the plot of Sliding Doors (1998) shows a puzzling lacuna in the formidable minds of its advocates. Perhaps they should stop trying to tell us that philosophy is dead.

In Our Time, The Photon

What an informative and inspiring edition of BBC Radio 4 – In Our Time, The Photon on 12 February.

Steve Jones sometimes refers to biologists as having “physics envy”. I suffer from this. Steve suggests it is because biologists know that physicists are cleverer than they are. Hard to know. However, as a group, physicists use terms clearly and consistently, and don’t waste time on trivial disagreement. They seem to wish to understand each other, and always strive to know how the world really is.

I’d intended to write on my own experience as a guest, last May 15, on In Our Time. BBC Radio 4 – In Our Time, Photosynthesis. I’ll try to get back to this. Just for now, let me record that Melvyn Bragg – surely the perfect host and chairman – wrote:

I think it was John Allen who said that the United States aerospace industry is giving quite substantial support to research into photosynthesis. The reason that NASA is interested is because they are looking for ways in which they can identify on the surface of planets what may be the origins of life as we know it. Seems a terrifically oblique way to subsidise science, but in my view, the more oblique the better. John ended the programme with a wonderful quotation from Priestley about the practical discovery of photosynthesis. It was, he said, as a result of Priestley’s curiosity. All of Priestley’s research was curiosity-driven. Again and again research has been curiosity-driven.

I’ve picked up from academics over the past few years a feeling, sometimes of sadness, sometimes approaching despair, that that sort of research – i.e. intellectual curiosity, knowledge for the sake of knowledge – is not in favour at the moment. Why on earth have we become a box-ticking, bureaucratic, over-managed society wherever you look? Why don’t we follow the talent, instead of (as in the case of universities and elsewhere) driving the talent out because of ways of managing which only make sense in some sterile boardroom…?

How strongly I agree.

How clearly is Melvyn’s last point illustrated by subsequent events.

Sir Paul Nurse on Conjectures and Refutations

BBC Radio 3 – The Essay, The Book that Changed Me, Sir Paul Nurse on Conjectures and Refutations

Broadcast Friday 23 Jan 2015 22:45

My own revelation of the insight of Karl Popper came from second-year tutorials with Colin McClare, a lecturer in Biophysics at King’s College London. I had the temerity to argue with my tutor. He won. He was right.

I began with The Logic of Scientific Discovery, and read it from cover to cover. Conjectures and Refutations came next.

It continues to amaze me that so many people responsible for making decisions on science, funding, and research priorities seem not to have understood that “Hypotheses are nets – he who casts will catch”.

And that the purpose of every experiment is to test an hypothesis.

Nobel winners say scientific discovery ‘virtually impossible’ due to funding bureaucracy – Telegraph


Nobel winners say scientific discovery ‘virtually impossible’ due to funding bureaucracy

Major scientific discovery is being hindered because of the peer preview system, Nobel Prize winning scientists have warned

10:30PM BST 02 Jun 2014

Major scientific discoveries of the 20th Century would not have happened under today’s funding rules, Nobel Prize winning scientists have warned.

More than 30 leading scientists including four Nobel Laureates have written to The Telegraph deploring the current system of granting funding for scientific research.

They said that: “Sustained open-ended enquiries in controversial or unfashionable fields are virtually forbidden today and science is in serious danger of stagnating.”

Lead signatory Prof Donald Braben, professor of earth sciences at University College London, had published a book on how difficult it has become in the last 30 years to get research funded.

He warned that all the major funding institutions now use a system of peer preview in which anonymous members in the same field consider the proposal and decide if it should go ahead.

Prof Braben said: “The major scientific discoveries of the 20th Century would not have happened under today’s rules, they would not get funding now.

“It is very difficult to get a discussion together on this matter because everyone has to acquiesce.”

His book documents the 500 major discoveries of the 20th Century.

He says that Max Planck would not have made his quantum mechanics discoveries and Peter Mitchell would not have discovered the energy currency in biology had they been put through today’s funding rules.

The letter continued: “Peer preview is now virtually unavoidable and its bureaucratic, protracted procedures are repeated for every change in direction or new phase of experimentation or whatever the applicant might subsequently propose.

“Many scientists privately deplore these policies but their professional standing often depends on their acquiescence.”

Prof Braben’s book ‘Promoting the Planck Club: How defiant youth, irreverent researchers and liberated universities can foster prosperity indefinitely, is published by Wiley.

Co-signatories on the letter include: John F Allen, Queen Mary, University of London; William Amos, University of Cambridge; Richard Ball, University of Edinburgh; Tim Birkhead FRS, University of Sheffield; Peter Cameron, Queen Mary, University of London; Richard Cogdell FRS, University of Glasgow; and David Colquhoun University College London.

As well as Nobel Laureates, John Hall, University of Colorado; Dudley Herschbach, Harvard University; Sir Harry Kroto, Florida State University, and Sir Richard J Roberts FRS, New England Biolabs.

The damaging bureaucracy of academic peer preview – Telegraph


The damaging bureaucracy of academic peer preview

Academic funding agencies should support research in unfashionable fields

 10:35PM BST 02 Jun 2014
SIR – Under current policies, academic researchers must submit their proposals to a small group of their closest competitors – their peers – for consideration before they might be funded. Peers selected by funding agencies are usually allowed to deliver their verdicts anonymously. They assess the proposal’s suitability for funding, whether it would be the best possible use of the resources requested, and determine, if it were successful, the probability that it might contribute to the national economy in some way. If the answers are satisfactory the proposal has roughly a 25 per cent chance of being funded.

Peer preview is now virtually unavoidable and its bureaucratic, protracted procedures are repeated for every change in direction or new phase of experimentation or for whatever an applicant might subsequently propose. Consequently, support for research that might lead to major new scientific discoveries is virtually forbidden nowadays, and science is in serious danger of stagnating. Many scientists privately deplore these policies but their professional standing often depends on their acquiescence – a catch-22 that effectively diminishes public opposition to the policies. We call upon funding agencies to support sustained, open-ended research in unfashionable fields.

Donald W Braben
University College London

John F Allen
Queen Mary, University of London

William Amos
University of Cambridge

Richard Ball
University of Edinburgh

Tim Birkhead
FRS, University of Sheffield

Peter Cameron
Queen Mary, University of London

Richard Cogdell FRS
University of Glasgow;

David Colquhoun FRS
University College London;

Rod Dowler
Industry Forum, London

Irene Engle
United States Naval Academy, Annapolis;

Felipe Fernández-Armesto
University of Notre Dame

Desmond Fitzgerald
Materia Medica

John Hall
University of Colorado, Nobel Laureate

Pat Heslop-Harrison
University of Leicester

Dudley Herschbach
Harvard University, Nobel Laureate

H Jeff Kimble
Caltech, US National Academy of Sciences

Sir Harry Kroto FRS
Florida State University, Nobel Laureate

James Ladyman
University of Bristol

Peter Lawrence FRS
University of Cambridge

Angus MacIntyre FRS
Queen Mary, University of London

John Mattick FAA
Garvan Institute of Medical Research, Sydney

Beatrice Pelloni
University of Reading

Douglas Randall
University of Missouri

David Ray
Bio Astral Limited

Sir Richard J Roberts FRS
New England Biolabs, Nobel Laureate

Ken Seddon
Queen’s University of Belfast

Colin Self
University of Newcastle

Harry Swinney
University of Texas, US National Academy of Sciences;

Claudio Vita-Finzi FBA
Natural History Museum