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 Today I’d think more of genomics, perhaps GWAS, while the microarray example is not entirely outdated.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

Bucket
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.

Searchlight
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 Stern Review of REF

It seems to be a distinct improvement on many counts.
One declared objective is to guard against “gaming” the system.
Many institutions will surely, nevertheless, find ways to misrepresent their research achievements. I can’t immediately see what these will be.

Apparently the rules will be published in 2017 for a REF in 2021.

BIES
The Guardian, James Wilsdon
THE, Nicholas Stern

Higher Education and Research Bill – what is it for?

This morning I attended a discussion meeting at the House of Lords concerning the Higher Education and Research Bill.

In my opinion there is an urgent need to oppose this disastrous Bill.

The Convention for Higher Education has produced a summary of the many reasons for doing so.

These include, quoting from the e-mail of invitation to today’s meeting:-

  • the proposed reorganisation of research in the UK (including abolition of the Research Councils’ royal charters);
  • the proposed introduction of a lower bar for entry into English higher education by new ‘alternative providers’;
  • the proposal to abolish Privy Council involvement in the granting of English university title, and to vest all such powers (including withdrawal of title) in a new body entirely appointed by and overseen by the Secretary of State.

The Bill seems designed to consolidate Failing management in UK universities.

In its 117 pages, the Bill contains neither definition nor description of the term university. The Bill has no declared aim. What is its purpose?

Teaching is to be overseen by an Office for Students.

The White paper’s short section “Research” is entirely about United Kingdom Research and Innovation, a superstructure for the Research Councils. Is research itself no longer a core university activity?

From the Higher Education and Research Bill:-

UK research and innovation functions
UKRI may—
(a) carry out research into science, technology, humanities and new ideas,
(b) facilitate, encourage and support research into science, technology, humanities and new ideas,
(c) facilitate, encourage and support the development and exploitation of science, technology and new ideas,
(d) collect, disseminate and advance knowledge in and in connection with science, technology, humanities and new ideas,
(e) promote awareness and understanding of science, technology, humanities and new ideas,
(f) provide advice on any matter relating to any of its functions, and
(g) promote awareness and understanding of its activities.

“…and new ideas” – listed as if these are a separate field of enquiry. I wonder what the authors imagine research to be?

A member of academic staff in a real university researches and teaches. These two activities are complementary; they support each other. Research qualifies a university teacher to take students to the boundary of existing knowledge, to try to see beyond it, and to question what they find there.

Quantum secrets of photosynthesis at Summer Science Exhibition 2016

The Royal Society’s Summer Science Exhibition is always full of interest. The 2016 exhibition had some remarkable displays and demonstrations.

Quantum secrets of photosynthesis was fascinating. I heard that energy transfer between chlorophyll molecules occurs more rapidly than can be explained by classical models, and that quantum superposition is required. I am not quite sure what that means, but need to find out. It somehow also has implications for understanding consciousness, apparently. Nicholas Allen, M.A. (Social Anthropology) was just as intrigued as I.

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My own interest in energy transfer in photosynthesis is long-standing, while I tend to think much more of great big proteins carrying chlorophyll, changing shape, and lumbering around in membranes, to break and forge alliances with different photochemical reaction centres. I’ll have something to say on this in Verviers on August 13. I wonder if there are quantum secrets hidden under the classical model I carry around and that I have, perhaps, come to take for granted?

Full marks to Dr Alexandra Olaya-Castro and her team of enthusiasts at the exhibit for an entertaining set of demonstrations, accurate in the parts I think I understand, and accessible, I know, to a much wider audience.

Failing management in UK universities

Knowledge for a Successful Society is the title of an outstanding Alternative White Paper on the future of higher education in the UK. The section on university governance is particularly perceptive and close to home. I attended the Launch Meeting in Parliament on 8th June.

The concerns addressed are very similar to those of Remedying failures of corporate management in UK universities, which colleagues and I published in 2012.

One difference is that, in 2012, the authors’ institution, Queen Mary University of London, was simply flouting the sound principles in its statutes, ordinances, and codes of practice. Today we see a government white paper that will replace these principles, to the detriment of research and teaching. The alternative white paper is a response to these. I predict that no dialogue will ensue.

It is as if the decline already in progress in 2012 has now become government policy.

What can be done to rescue UK universities?

The Right Honorable Sir Eric Pickles MP,
House of Commons,
London, SW1A 0AA

Thursday, 9 June 2016

Dear Sir Eric,

In Defence of Public Higher Education: Knowledge for a Successful Society

Please allow me to draw your attention to this Alternative White Paper. Its launch will take place on Monday 13th June, 4.30-6.00 p.m., in the Boothroyd Room, Portcullis House, Bridge St/Victoria Embankment SW1A 2LW. The document is written in response to the Government White Paper “Success as a Knowledge Economy”.

I write in a personal capacity and as a member of Council for the Defence of British Universities, one of the contributors to the Alternative White Paper.

I believe that the quality of higher education in England and Wales will be affected adversely and irrevocably by the changes to University governance proposed in the White Paper. The aim of the Alternative White Paper is to describe policies that will, instead, protect the advancement and dissemination of knowledge and understanding, the twin primary purposes of any university in an open and prosperous society.

Please, if you can, attend the meeting on Monday next. The future of Higher Education is at stake.

Yours sincerely,

John F. Allen

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30 May | Institute of Cell Biology, University of Bern

Mitochondria, ageing and separate sexes

This seminar was given at the kind invitation of Prof. Dr. Mariusz Nowacki.

I received excellent questions and comments from members of an expert audience. There seemed to be agreement on my view of the experiment we should do next.

It was a pleasure to meet Mariusz’s lab members, including Dr. Estienne Swart and a special host, Dr. Sarah Allen.

I also appreciated the introduction to colleagues. Prof. Dr. André Schneider in particular had fascinating research to report on protein import into mitochondria, with, he believes and I agree, so much to tell us about the origin and evolution of eukaryotes. André thanked me for acknowledging past discussion with Jeff Schatz, whom he knew as his postdoctoral advisor and mentor, and who had provided the first compelling evidence for mitochondrial DNA. In about 1996, in Lund, Sweden, Jeff had recommended not wasting time on Xenopus oocyte mitochondria since they were “really boring; no cytochromes, no ox-phos”. I tried but failed to explain why I thought this was an interesting comment.

André’s comment in Bern was prompted by an acknowledgement slide I’d prepared, and worried about, thanking Jeff and also Lars Ernster for early encouragement. I can’t be sure about Jeff’s view, but Lars definitely liked the mitochondrial theory of ageing, and even showed a summary graphic, Figure 1 from my 1996 Journal of Theoretical Biology paper, in a seminar he later gave in Lund. I recalled apologising to Ernster, an outstanding biochemist and experimentalist, Nobel Chemistry Committee member and spokesman, for proposing “just an hypothesis”.

His reply? – “This is what we do!

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Sarah outside the former home of Bern's most famous resident.
Sarah outside the former home of Bern’s most famous resident.
Two members of the Allen family.  Bern, Switzerland, 30th May 2016.
Two members of the Allen family. Bern, Switzerland, 30th May 2016. Photo taken by Estienne Swart.

4 May | Instituto de Neurobiología UNAM

Energy, ageing, fidelity and sex. Oocyte mitochondrial DNA as a protected genetic template

A lively audience packed into a small lecture theatre in the beautiful UNAM Campus Juriquilla.

Good questions introduced many ideas new to me. I thank Dr Alfredo Varela, the newly-appointed director of the Institute of Neurobiology, for generous hospitality. This included an afternoon of presentations and discussion of current research in Alfredo’s laboratory.

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Mexico Lectures April–May 2016

Mitochondria, ageing, separate sexes

3 May | Departamento de Bioquímica, CINVESTAV

Regulation of photosynthesis. Control of chloroplast DNA transcription and membrane protein phosphorylation

I felt at home in the research laboratory of Dr. Carlos Gómez of the Department of Biochemistry. I saw a French Press, spectrophotometers and fluorimeters, SDS-PAGE, sucrose gradient centrifugation, and cultures of fascinating cyanobacteria. I learned that Spirulina, once a Mexican speciality and export, is now called Arthrospira. Krisha Rao in King’s College London once gave me a brick-red Spirulina ferredoxin preparation, I seem to recall at 10 mM. I now know Krishna had purified it from Sprulina obtained in Mexico when Krishna worked as a visitor in Carlos’s lab.

Unfortunately I overran again. This seminar was a daunting task, the title requiring me to reach back to a time before most of the audience had been born. It was not all history. The research included Iskander Ibrahim‘s results, published in February this year, on phosphoryl group transfer from cyanobacterial Histidine Kinase 2. So this lecture presented both older and newer work than any lecture in my Mexico tour. An attentive audience again came up with fine questions.

s- dr john f allen

Carlos Gómez and Fanis Missirlis
Carlós Gomez and Fanis Missirlis

Mexico Lectures April–May 2016

Regulation of photosynthesis

29 April | Instituto de Fisiología Celular, Universidad Nacional Autónoma de México

A formidably well-informed audience volunteered numerous good questions during and after my presentation Energy, ageing, fidelity and sex. Oocyte mitochondrial DNA as a protected genetic template. I sensed a degree of polite scepticism. Good. There is no point in explaining things to people who already agree. Such an appreciative and critical audience is definitely good for morale. What a contrast with the department in which Fanis and I were once colleagues.

Lunch was followed by a guided walking tour of the spectacular UNAM campus. Warmly recommended. It’s not my place to comment, but the “Autonomous National University of Mexico” (which it is) should surely be better known internationally. Go there if you ever get the chance. It’s a great place. We’d seen that already on 27 April.

I am most grateful to my host in IFC-UNAM, Xochitl Pérez Martínez, pictured here with Fanis Missirlis.

UNAM lecture 29 April 2016

Mexico Lectures April–May 2016

Mitochondria, ageing, separate sexes