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Some books I read in 2021

Another year of the pandemic. I thought I’d wrap up by briefly reviewing some books I’ve read during the year.

Friedrich Nietzsche – The Birth of Tragedy. Despite this being probably Nietzsche’s earliest famous book, I somehow never managed to get a foothold in it previously. Here he formulates his early philosophy in terms of the Dionysiac and Apolline.

Friedrich Nietzsche – Human, All-too-human. (Re-read) Nietzsche’s turn to what he considered a more “scientific” viewpoint after his crisis and break with Wagner.

Seneca: Letters From a Stoic. Seneca’s letters to his protégé about life, stoic philosophy and politics are incisive and almost humorously eloquent. Every time I read something from Roman times I’m struck by how similar their society and political lives seem to have been to ours. Stoicism as a philosophy I don’t feel ready to comment on.

Leo Tolstoy – The Cossacks and Other Stories. The painterly style here is every bit as good as in War and Peace. The titular story impresses, as do the Sevastopol Sketches and the later Hadji Murat about an aging warrior.

Dino Buzzati – The Tartar Steppe. Magical realism. A meditation on organizations, ambition and time. Giovanni Drogo spends his entire life waiting for an event that might never happen. People posture, follow rules to a fault, die.

Neal Stephenson – Fall, or Dodge in Hell. This sci-fi novel explores the ultimate conclusions of the present “post-truth” algorithm-driven political landscape that we live in very well. It also explores, very elaborately, the notion of a simulated digital afterlife in ways that I found believable (assuming that we accept the notion of a simulated consciousness for the sake of the story). However, after a certain point the book becomes tedious and gets lost in its own plot. By that time readers should feel free to skip to the end.

Ernst Jünger – Storm of Steel. Jünger’s shocking, aesthetically concerned, unflinching account of WW1 is truly surreal and allows us to see the the world through the ambitious young eyes of an exposed frontline soldier at the time.

Immanuel Kant – Critique of Pure Reason. As of the end of 2021 I’ve begun on this key work in earnest, making some progress with the help of Jay Bernstein’s lecture course. If I make it through the entire book I will report back.

I will end with an admonition. I don’t have much to say about the ongoing Covid pandemic, except that if you are hesitant to get vaccinated, you may be putting other people at risk. We can and should debate the politics of how the pandemic is being managed – a topic for a different time – but getting vaccinated is common sense (it certainly is not a political stance), so please do it.

Happy 2022.

Posted 04 January 2022 † Johan § Life § Philosophy ‡ Comments (0) ° Tagged: , , , ,

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.

Posted 12 May 2021 † Johan § Bioinformatics § Computer science § Life § Philosophy § Software development ‡ Comments (0) ° Tagged: , , ,

Covid-19

It seems clear by now that Covid-19 is one of the great crises of our time, more so than the financial crisis of 2008, judging by the size of the measures announced and already taken by various countries and by the impact on human lives. In Japan I have been following live data from Toyo Keizai, the Tokyo government, and an independent source tracking hospital bed capacity.

While this will be a tragedy for many, it will also be an opportunity for societies to reset themselves and to make changes that otherwise could not have been made. New perspectives urgently come to the fore. Perhaps we discover how much of the everyday frenzied activity we were caught up in was superfluous. Certain viewpoints and positions may have to be abandoned as people come together around trust, resilience, survival, innovation.

Thus the present crisis is also a time for reflection and renewal.

Posted 13 May 2020 † Johan § Life ‡ Comments (0) ° Tagged: ,

The year and decade in review. 2020s: orderly peace?

2019 comes to a close, and with it the 2010s. Below are a few thoughts on these periods of time.

The most significant book I’ve read in 2019 is probably Hannah Arendt’s The Origins of Totalitarianism. The German title, literally “Elements and Origins of Totalitarian Rule” more closely reflects the contents of this monograph. Arendt explores antisemitism, imperialism and totalitarianism to form a grand analysis of totalitarian forms of government, which she considers to be genuinely new and unprecedented. Those who make it through the somewhat slow early chapters will be richly rewarded. It’s a very timely book – although written in the 1950’s, most of the ideas feel like they could be from last week. Elements of totalitarian rule are absolutely something we should worry about.

Another notable book from this year has been Edward Snowden’s Permanent Record. Aside from the obvious political dynamite, I found myself relating to a lot of the experiences he had growing up. Perhaps this is a generational story. In the late 90s, the Internet suddenly became relatively mainstream and for a short while, it was a very special place, seemingly full of utopian promise and all kinds of possibilities and exploration. For many born in the mid-80s this coincided with our teenage years.

I’ve lived in Japan throughout the 2010s, the final part of the Heisei (平成) era. In 2019 this era came to a close and we are now officially in Reiwa (令和). I can’t easily summarise the 2010s. Both my personal life and Japan seem to have undergone great change during this time, and sometimes it’s hard to separate one from the other. The Fukushima incident in 2011 was perhaps a watershed moment that Japan is still grappling with. Although the future of nuclear power has not yet been resolved, the country’s response to such a tense incident has in many ways been admirable, and the famous Japanese virtue (sometimes a double-edge sword) of stability certainly came through. The surrounding world is also changing, and Japan, though still a relatively separate culture, is becoming considerably more open and mixed as a society, perhaps out of necessity. Tourism and labour imports have both increased significantly. This raises interesting questions about what kind of society Japan might be in 10 – 20 years.

During the decade I have had diverse personal and professional experiences. I lived in Tokyo, Osaka, then Tokyo again. I was able to complete a PhD thesis. I visited many countries for the first time, and became interested in bioinformatics (mainly as a field in which to apply fundamental computer science and software engineering). I took up several new hobbies, obtained permanent residency in Japan, and was able to improve my Japanese to the point of reading novels, although I’m still not quite where I’d like to be with the language. I’ve been reading a lot of philosophy and general literature and tried to systematically develop a worldview (fragments of which sometimes appear on this blog). Not everything I tried to do worked out the way I expected, but the learning has felt very valuable, and I do feel much wiser and more capable about my approach to many things. I expect to be sincerely expressing the same sentiment in the year 2029, though.

One technical focus this year was improving my Spark (and Scala) skills and developing an algorithm for De Bruijn graph compaction (similar to what Bcalm does). I was pleased with the efficient research process I was able to achieve, probably my best ever on this kind of project. In terms of my professional path, the overall trend for me seems to be towards smaller firms and greater independence. (Although I remain with Lifematics, I will now also be available for consulting and contracting opportunities in bioinformatics as well as general software development. If you are reading this and think you would like to work with me, do get in touch.)

Thus ends a politically very strange decade, from a global perspective, and we enter the brave new world of the 2020s. Will it be a time of “orderly peace”, as the name 令和 suggests?

Posted 30 December 2019 † Johan § Bioinformatics § Computer science § Life § Philosophy ‡ Comments (1) ° Tagged: , , , , , , ,

Zuboff’s Surveillance Capitalism

Earlier this year I read Shoshana Zuboff’s The Age of Surveillance Capitalism and was strongly affected by it. It’s always hard to judge how new works will age, but I found her narrative a poignant comment on the last few decades of the information society: a society that evolved quite differently from what many expected from the early days of the Internet. I’m willing to guess that this book will remain relevant for a long time as a snapshot of the direction that society has taken in our present time. Morozov has analysed the book in more detail than I am capable of. Here I will try to relate some of Zuboff’s points to the ideas I have developed on this blog. Unlike Fleischer (Swedish) I feel that the length of this book is justified.

I’m not categorically against capitalism (yet), but I do believe that capitalism can take problematic forms and sustain negative processes in society. Zuboff argues that what our contemporary social/behavioural data-driven internet giants represent is nothing less than a genuinely new form of capitalism that is essentially dependent on the need to observe and predict (ultimately, influence) increasingly minute forms of human behaviour. All those accidental data leaks from mobile apps, etc., are not accidental. She draws liberally on Arendt (The Origins of Totalitarianism) to make her case. There’s ample room to draw on Heidegger (enframing/gestellung), but for some reason, Zuboff chooses not to go there.

Humans wish to live in freedom (we usually agree) and perhaps do live in freedom. But what is this freedom? One definition would be that free actions do not have a calculable cause, need not be rational. In a certain way, freedom is the freedom to be arbitrary, to be irrational. This might not mean that causes do not exist, but it may mean that the right to conceal causes is important.

But from a systems point of view, entirely free, as in unconstrained, humans (in a vacuum, or a blank space devoid of meaningful relations or objects, etc) are not free. Probably, we feel most free when we are constrained to the appropriate degree: we need a floor to stand on, momentum to move with, fixed points to brace against… if the constraints are appropriate and partial in this way, then we develop a style of behaviour. In theory, we can imagine a situation where humans are so constrained that they can hardly make any choices from one moment to the next. Exploiting the gap between on one hand totally constrained and specified behaviour, and on the other hand the moderate constraints of an “appropriate” situation in the above sense, a situation with slack, we are free to play, to endow our actions with style, to perform. Perhaps this is one useful notion of freedom. Behavioural markets, then, purchase the right to choose our behavioural styles for us, to invisibly constrain us and introduce more friction. Perhaps they convert the slack into profit, perhaps they transfer it to other actors using money as a conduit. (Of course, we may think of the ability to endow one’s own actions with style in such a constraint gap as the flow of particularity.)

Why is human freedom still a scary notion to us, individually and collectively? Many consumers and techno-optimists would happily trust the voice of the algorithms rather than personally make choices. Many rush to record and give away vast quantities of data. Various forms of private and governmental surveillance combine in ways probably unimaginable to most who participate in it. Which unconscious drives are at work here? What do we hope to gain as a society? Can the internet, software, and modern electronics not be applied to nobler ends?

Posted 20 June 2019 † Johan § Philosophy § Uncategorized ‡ Comments (0) ° Tagged: , , , , ,