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 Today I’d think more of genomics, perhaps GWAS, while the microarray example is not entirely outdated.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

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 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