Covid-19 and time

I can now conclusively answer the question raised at the end of my blog post from December 2019: the 2020s are not a decade of orderly peace. What a strange year. But weren’t years always strange?

Time passes not only quantitatively but also qualitatively. A year spent with Covid-19 seems to have passed differently from a year without it. Maybe boredom has increased (possibly for the better), maybe focus has increased. For many there has been, and continues to be, untold suffering. The mRNA vaccine, based on a technique that was overlooked by academia for a long time, at this moment looks to become one of the great success stories of science. Possibly and hopefully. Many countries have aggressively and successfully vaccinated large swathes of their populations; Japan is unfortunately still in the early stages of this process. The pandemic year almost seems to have removed us physically from the world before, opening up a widening chasm that we may or may not be able to cross again. Looking across that chasm from 2021, both the present time and that time before the pandemic seem alien and strange.

Around this time last year, when lockdowns were starting to happen in some countries, the prospect of a two week lockdown seemed to me an unbearable burden. (To date Japan has not had a hard lockdown.) Today, of course, that seems like it would have been a small price to pay, given what some other countries, like Taiwan, have achieved. I must not be as good at deferring present benefits for future rewards as I thought.

On a different note, for the technically-minded: During the past year I was able to channel a lot of energy into research on k-mer counting, a genomic data problem. A medium post (in the early stages of this work) and eventually a paper were published. The main achievement was to find a novel way of grouping k-mers — short genomic subsequences — into evenly sized bins, which greatly speeds up many kinds of processing. This would not have been possible without previous work on FastKmer (Ferraro Petrillo et al) and the new randomized algorithm PASHA for generating compact universal hitting sets (Ekim et al). This work may also be an interesting case study on the low hanging fruit available when aggressive engineering, specifically for the purpose of improving parallelism, is applied to existing algorithms.

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