John F. Allen's Blog at

10th June 2015

The Devil in the Detail | fanismissirlis

Filed under: About science,About universities,Diary — John Allen @ 10:14 am

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…?

12th April 2015

The Bucket or the Searchlight?

Filed under: About science,About universities — John Allen @ 7:55 pm

“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 Today I’d think more of genomics, perhaps GWAS, while the microarray example is not entirely outdated.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.

13th February 2015

In Our Time, The Photon

Filed under: About language,About science,About universities,Diary — John Allen @ 10:24 am

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.

5th November 2014

Collegiality and accountability – York University

Filed under: About universities — John Allen @ 1:27 pm

An Open Letter from York Academics to the Vice-Chancellor, Registrar and Director of Human Resources

Who has authority?

Who is accountable? And to whom?

13th August 2014

What do universities actually do? | John F. Allen’s Blog

Filed under: About universities — John Allen @ 10:19 am

What do universities actually do? | John F. Allen's Blog.

In my case, this question is no longer purely of academic interest. And what might “academic interest” actually now mean?

At the boundary of human knowledge, every new idea is a minority idea.

Academic freedom is not a luxury. It is a necessity.

Is there a contrary view?

A salute to whistleblowers | Peter Cameron’s Blog

Filed under: About universities — John Allen @ 10:12 am

A salute to whistleblowers | Peter Cameron's Blog.

26th July 2014

A comment on Academic Freedom and the Corporate University

Filed under: About universities — John Allen @ 3:34 pm

A comment on Academic Freedom and the Corporate University by John Holmwood, Jul 4, 2014.

Holmwood’s post refers to a recent blog post by David Browne, Senior Associate on the Employment Team for SGH Martineau, a legal firm whose clients include managers at the University of Warwick, famed for overseeing fair play and protecting academics’ right to dissent. To quote Holmwood, Browne “..argued that universities face the problem that ‘high performing’ academics can damage their ‘university’s brand’ by their ‘outspoken opinions or general insubordination’.” Browne’s post, “Getting your teeth stuck into High Performer Misconduct” compares foul play on a football pitch with expressing an opinion. Initially puzzled, I think I finally saw some vague similarity, and wrote the following comment on Jul 12.

If one football player bites another then the referee blows a whistle and calls “foul”. If, in consequence, the referee is disciplined, then he will find it difficult to do his job. If those who discipline him do so covertly, perhaps manipulating video evidence from which independent observers may decide on whether the bite took place, then we begin to see some sort of parallel with recent events in UK universities.

Truth is the primary and overriding concern of members of a university’s academic staff. To suspend or dismiss them on the grounds that their judgement does not find favour with administrators is to negate the reason for the university’s existence in the first place. Academic freedom is not an out-dated perk. No university worthy of the name attempts to prescribe lines of enquiry, nor conclusions reached, in research, teaching and scholarship.

To quote from one institution’s Ordinances:
“Where there is any issue as to the meaning of ‘academic freedom’ in any proceedings under these Ordinances, regard shall be had to Sections VI and VII of the Recommendation concerning the Status of Higher-Education Teaching Personnel adopted by the General Conference of the United Nations Educational, Scientific and Cultural Organisation (UNESCO) in Paris on 11 November 1997.”

I’ve recently had cause to consult the UNESCO Recommendation Concerning the Status of Higher Education Teaching Personnel of 1997.

I recommend it.

The academic, as the referee, must retain the freedom to do what he is paid for.

Otherwise, what do universities actually do?

And what is it that their managers actually manage?

19th June 2014

Research-Led Teaching

Filed under: About universities — John Allen @ 8:54 pm

Research-Led Teaching

Integrating Research and Teaching to Benefit Students and Staff

Lecture by Michael J. Proulx, with discussion of A university is… | Comments welcomed

18th March 2014

What do universities actually do?

Filed under: About universities — John Allen @ 10:18 am

Now with comments. The question remains. “How should they do it?” makes little sense without it being answered.

16th March 2014

A university is… | Comments welcomed

Filed under: About universities — John Allen @ 1:56 am

A university is a community of scholars whose purpose is to advance and disseminate knowledge. Research advances knowledge. Teaching disseminates it. Research requires freedom, supportive infrastructure, cooperation, communication, and trust. Teaching is communication and critical examination of existing knowledge within an open society where nothing is beyond question and where knowledge is thus free to advance. Research and teaching are inter-dependent.

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