The Bucket or the Searchlight?

“The Bucket and the Searchlight: Two Theories of Knowledge” from 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 fallacy underlies many mistakes. Notably in universities.

I raised Popper’s question 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, was 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 Today I’d think more of genomics, perhaps GWAS, while the microarray example is not entirely outdated.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. Data are scooped up, at random.
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.

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. Data are examined to see how they compare with the prediction of an hypothesis. The 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 Building Blocks of Microbial Evolution

It was an honour and a pleasure to participate last week in the Society for General Microbiology Annual Conference in Birmingham.

Two sessions were of special interest, and did not overlap. These were The building blocks of microbial evolution and Mitochondria and related organelles in microbial eukaryotes. The conference also had fascinating plenary and prize lectures.

Good to meet old friends and colleagues, and make new ones. Good, too, to see such progress in understanding fundamental problems.

My presentation in Birmingham, on 30 March, was entitled Anoxygenic photosynthesis and the archaean world. In it, I presented my hypothesis for the events that caused the transition from anoxygenic to oxygenic photosynthesis, and from the Archaean to the Proterozoic aeon. This was also the subject of A redox switch hypothesis for the evolutionary origin of oxygenic photosynthesis, which I gave on 24 March to the 2015 Iron–Sulfur Proteins Meeting at the MRC National Institute for Medical Research, Mill Hill.

I am optimistic that I can see a means by which to test this hypothesis, as it is outlined in The origin of atmospheric oxygen on my research web page.

International Convention Centre, Birmingham
International Convention Centre, Birmingham

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.