Monomorphic https://www.monomorphic.org/wordpress Conceptual meandering Fri, 19 Jan 2024 05:00:46 +0000 en-US hourly 1 https://wordpress.org/?v=6.4.3 Programming, simplicity and art https://www.monomorphic.org/wordpress/programming-simplicity-and-art/ https://www.monomorphic.org/wordpress/programming-simplicity-and-art/#respond Fri, 19 Jan 2024 04:38:09 +0000 https://www.monomorphic.org/wordpress/?p=1829 Programming, the writing of computer code in order to solve a specific problem, is a new intellectual discipline. It has a history going back to logic and mathematics, but it is relatively new as a human endeavour. It is constrained by hardware, by mathematics, by programming languages, and what we might call technical culture: APIs, programming interfaces, and concepts already invented by others. It is a vast canvas for thought: in the machine, imagination becomes physical reality.

For mysterious reasons I became fascinated with computers immediately when I saw one as a child in the 1990s (a friend’s Commodore 64). They seemed to be a window into a different world. As a teenager I tried to teach myself how to program. Sometimes I was self taught, sometimes formally trained, and over the course of my life it feels like I’ve touched (with varying aptitude) everything from hacky PHP and Basic to more rarefied Prolog and Haskell (today I almost exclusively use Scala). Having studied computer science academically and worked in a few fields, today I work in bioinformatics, where we study DNA and genomes – perhaps the “code” of biology and cells.

In my own estimation, my skill and creativity in programming is still increasing as I approach middle age. But over time I have come to value different things and think differently about this craft. It struck me that some of the perspective shifts I have made might apply to human creativity in general.

The biggest single such shift was a new focus on simplicity that I found only recently. In my twenties, I worked on many projects that were maybe too complex for the sake of being complex. I was probably (I’m a little ashamed to say) impressed by the difficulty of the things I myself was doing. This style of work was not pointless, as I could still produce meaningful results, and I was constantly learning. It was the free exploration of new frontiers. But it was powered by youthful arrogance: I would not easily have listened to older people telling me at the time to keep things simpler. I wouldn’t have known what they were trying to tell me. I would have insisted on covering all this ground on my own.

At some point, my designs got too big to sustain, and I was held back by my refusal to simplify things I was making. This was part a reluctance to part with work that I had put a lot of time into, and in part an indecisiveness and a desire to let my project be all things to all people. Slowly I realised that this had to change. I took the plunge and gave one of my projects a much sharper focus. The quality improved dramatically and I could keep up the work for much longer. I was wondering why I had not arrived at such a simple truth earlier.

What does such a sharp focus look like? I will try to generalise. In order to find simplicity we need a source of truth, a meaningful signal to measure against. In programming this could be the fundamental limits of algorithms (how quickly can we sort strings, how much memory do we need to represent them?) or of the domain problem (how quickly can we align DNA against a subject genome?). It could be product requirements (how fun can we make a video game that we are developing?). Once we have a source of truth, we can measure the value of any changes or additions we are making. Generally, adding code increases cognitive load, as the project becomes harder to understand and communicate. When we can measure value, we can investigate the ratio of the value gained to the cognitive price paid for it. It may not be a good return on investment. If not, we should refuse to add that code. Perhaps we make a note of the decision made and the reasons why we made it.

Simplicity often correlates with removing things, though size is not the only measure. What we should care about the most is cognitive load, the ease of understanding for a reader (and of course, ease of use for users). Code that is easy to understand is honest, and easy to return to and build on in the future. It is easy to communicate to others, so it can be a good basis for teamwork. But because this often does mean that we must mercilessly remove things that we put many hours into, the surviving code might often be just the tip of an evolutionary iceberg. Maybe in order for five branches to survive in the repository, fifty branches had to be attempted (hopefully leaving some records of what was learned). In order to find the best algorithm for a research problem, maybe ten algorithms had to be tried, and the nine unfortunate ones ripped out for the sake of simplicity. Keeping code of unclear value around (opportunistically) leads to confusion, although it can certainly be kept in some private branch in case it is needed in the future.

In general, a lot of experimental, creative processes that are trying to home in on a goal will have a lot of hidden history, in arts and crafts as well as technology. Certainly in technical and scientific research. A perfect gem can be the result of laborious experimentation that perhaps nobody remembers anymore. How much work went into discovering even the basic designs and appliances that we use in our homes every day? How many melodies did Bach never write down?

Although that may seem tragic, it brings vast benefits and is maybe the only way to reliably have a sustainable creative process in certain fields.The world might always remain complex, but we can mostly demand that productions of the mind should be simple. (I would make an exception for fields like philosophy and some of the arts, where the objective may sometimes be to undo ingrained simplicity for the sake of increased contact with reality.)

Finally as I write this first blog post in a couple of years: let’s keep blogging alive! Blogs were once part of a better internet that we could still preserve to some degree, and, I think, a format that will outlast the insane social media frenzy of today. He who has eyes, let him read.

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Some books I read in 2021 https://www.monomorphic.org/wordpress/some-books-i-read-in-2021/ https://www.monomorphic.org/wordpress/some-books-i-read-in-2021/#respond Tue, 04 Jan 2022 03:24:48 +0000 http://www.monomorphic.org/wordpress/?p=1812

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.

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Covid-19 and time https://www.monomorphic.org/wordpress/covid-19-and-time/ https://www.monomorphic.org/wordpress/covid-19-and-time/#respond Wed, 12 May 2021 03:11:15 +0000 http://www.monomorphic.org/wordpress/?p=1796

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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Covid-19 https://www.monomorphic.org/wordpress/covid-19/ https://www.monomorphic.org/wordpress/covid-19/#respond Wed, 13 May 2020 04:32:14 +0000 http://www.monomorphic.org/wordpress/?p=1781 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.

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The year and decade in review. 2020s: orderly peace? https://www.monomorphic.org/wordpress/the-year-and-decade-in-review-2020s-orderly-peace/ https://www.monomorphic.org/wordpress/the-year-and-decade-in-review-2020s-orderly-peace/#comments Sun, 29 Dec 2019 23:49:58 +0000 http://www.monomorphic.org/wordpress/?p=1766

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?

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Zuboff’s Surveillance Capitalism https://www.monomorphic.org/wordpress/zuboffs-surveillance-capitalism/ https://www.monomorphic.org/wordpress/zuboffs-surveillance-capitalism/#respond Thu, 20 Jun 2019 11:34:51 +0000 http://www.monomorphic.org/wordpress/?p=1732

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?

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Enlightenment and the search for meaning https://www.monomorphic.org/wordpress/enlightenment-and-the-search-for-meaning/ https://www.monomorphic.org/wordpress/enlightenment-and-the-search-for-meaning/#respond Wed, 26 Dec 2018 08:04:05 +0000 http://www.monomorphic.org/wordpress/?p=1708

The premise of the enlightenment would be that we have finally discovered how to live rationally. Authority is located in natural science, free enterprise and free markets, and empirical knowledge. Thus we can cast aside all the superstitions of the past and finally become what we were meant to be. Can we?

Not everyone agrees. Marx, Freud and Nietzsche are commonly associated with the “school of suspicion”, throwing doubt on capitalism, on the rational mind, and on morality and religion, to take but a few examples. Freud in particular burst open the doors to the unconscious, bringing back, seemingly, the demons that the enlightenment had sought to finally bury. The bottom line of Freud’s Civilisation and its Discontents seems to be that man is doomed unhappiness, since his (sexual, violent, etc) desires will always make him clash with polite society. If true, this is truly a tragic insight.

In contrast to Freud, Jung appears to be a man of compromises. Freud’s view of the unconscious is highly centred on sexuality. The “Id” seems to be  primarily a source of threatening or disturbing impulses. Jung’s view of the unconscious is centred on the possibility of integration, of bringing separate pieces together into a harmonious whole, including the “Shadow”, broadly his equivalent of Freud’s Id. He even postulates an archetype that guides the individual towards meaningful integration of these separate parts, the Self. The self provides the individual with a sort of pattern that is repeated over and over again across a lifetime, increasingly elaborate. Eventually all the parts are, if we are lucky, integrated and even the dark or purely negative parts are given a meaning in the whole. The idea that the individual unconscious can basically provide a teleological, predefined template for an integrated personality reminds one of soul or destiny, and seems much more optimistic than Freud. But perhaps it is more accurate to call Jung a realist. He tends to insist on every phenomenon having both positive and negative aspects. Integration may fail. Life may contain excessive suffering, torment or early death. Although individuals are supposed to be naturally led towards greater integration, Jung doesn’t seem to offer any positive guarantees about mankind’s progress as a whole towards a better moral state.

Enlightenment ideas seem to be alive and well, if in a somewhat mutated form, having survived two world wars. The idea that we can design or plan a better society is perhaps questionable after the collapse of the Soviet Union (a notable exception is China, which sometimes looks as if it operates a semi-planned society, while at other times it looks more capitalist than North America). Instead, we live by the rule of market forces and rationality takes the form of scientific R&D, as well as technocratic administration, where appropriate. The rule of a number of invisible hands, the neutered “individual” as the basic unit of production and consumption. Although technological capitalism has produced immense positive effects, its dark side is also sizable.  Enlightenment has led to nihilism. Alienation is real. Although human beings can endure working as replaceable units for some time (if a man has a why, then he will endure almost any how) in general and over time, this kind of work does destroy meaning and is intolerable. What will be the long term consequences of forcibly suppressing common sense and social conscience on a mass scale?

In this environment, it takes a certain stubborn optimism to insist that technological and economic progress will bring about a better society (Hans Rosling, Steven Pinker). It may be too early to pass judgment on what kind of world we are building, but let us at least be keenly aware of its price.

The problem of loss of meaning is for now mainly a Western one, though it may not remain so for much longer. The same cultural forces that drove the development of Christianity – the search for the one truth – may also have driven the development of science and technology. Thus, according to Nietzsche, Christianity contained the seeds of its own destruction. Countries like India and China have perhaps not yet reached “peak enlightenment”, still absorbing Western ideas and intensifying their implementations of technological capitalism. Japan may quite possibly have reached peak enlightenment some time ago and thus shares in the Western problem, although not on a Christian basis. Thus its solutions may look different. In the near future, this problem can be expected to burden all cultures that are committed to technological capitalism.

According to Jung, God, meaning, and the divine are archetypes, which are so deeply embedded in the human psyche that they must be given a concrete form, lest they be projected and unconscious, with potentially disastrous consequences. Our best solution, temporary as it may be, could be to treat consciousness as holy, in both its social and individual forms, in both its explicit/rational and its pre-rational, implicit, potential, half-finished forms. Existentialist cinema like that of Ingmar Bergman (who would have been 100 this year) seems to locate the holy in interpersonal relationships. Tolstoy does something similar. Their views of love are realist and ambivalent: they endorse it, but it may lead one astray (Anna Karenina, Through a Glass Darkly). Yet they certainly endorse it. This region may serve as a practical locus of the holy. Is love not a form of heightened social consciousness imbued with positive possibilities? Does individual consciousness, even of a mute object, not always refer back to the social, through the meaning it contains and through its driving wish to discover and express truth?

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Photography https://www.monomorphic.org/wordpress/photography/ https://www.monomorphic.org/wordpress/photography/#respond Thu, 06 Sep 2018 06:02:40 +0000 http://www.monomorphic.org/wordpress/?p=1698 One of my recent interests has been film photography. Of course, I was interested in exploring the difference between digital and analog technology, and having taken more than my share of smartphone pictures in my life, I was ready to jump to the opposite end of the spectrum. It also helps that Japan has an excellent second-hand market for vintage cameras and lenses. Some manual focus lenses made here in the 1970s and 1980s are still considered excellent performers with today’s latest “mirrorless” digital cameras.

I have been surprised by the richness of this activity. Film photography forces a higher level of consciousness than the easy point and click photography of smartphones, which must now be almost as automatic as breathing for many. With film, it is necessary to compose the shot, consider, and then wait for the result. Of course, there will be no previews until the film has been processed. Not only am I forced to think more about the shots, I’m also forced to consider what photography is, becoming aware of myself as someone who observes and records.

Susan Sontag has argued clearly enough that photography is not objective truth. Unless some kind of scientific attitude is applied, there is too much framing, selection and cherry-picking. But photography is maybe the art form that most convincingly makes the claim to being objective truth. A phenomenology of photography, the taking of photos and their viewing, would be something rich and complex. For me as a photographer, photography is almost a pure exploration of the psyche and of my own reaction to subjects. Other people viewing my photographs would, I expect, usually discover a completely different meaning than the one I have already attached to them.

Truth and meaning-considerations aside, impressions of the physical world are on some level captured in photographs, digital as well as analog. Photography exemplifies several ways of relating to particularity through instruments and attitudes. Digital photography imposes a final alphabet and ground level of measurements, and a digital image is thus effectively a number in a very large integer space. Film photography impresses the image upon silver halide crystals, which are not homogenous, not square-shaped, and whose physical properties may or may not have been fully elucidated. In some sense the ground of film photography may be said to be open in a way that digital photography is not. For all that, of course, in 2018 digital photography may be the quickest and most practical way to get sharp and high quality images, by most people’s common sense standards. But it is hard to suppress the feeling that something must be lacking there, that we tend to make the leap too easily and quickly.

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Nietzschean toxicology https://www.monomorphic.org/wordpress/nietzschean-toxicology/ https://www.monomorphic.org/wordpress/nietzschean-toxicology/#respond Thu, 25 Jan 2018 01:40:10 +0000 http://www.monomorphic.org/wordpress/?p=1647 Although one of my main projects is software for toxicology and toxicogenomics, my background in toxicology is not as strong as in, for example, computer science, and I’m lucky to be able to rely on experienced collaborators. With that said, I’d still like to try to speculate about the field through a mildly Nietzschean lens.

Toxicology focuses in the main on identifying mechanisms of degradation. Ingesting large quantities of the painkiller acetaminophen will cause liver damage and necrosis of liver cells. This will seriously harm the organism, since the liver is such an important organ, and many essential functions that the body depends on will be degraded or perhaps vanish completely. Untreated acute liver failure is fatal. It is very clearly a degradation.

Toxicology wishes to understand the mechanisms that lead to such degradation. If we understand the sequence of molecular events that eventually leads to the degradation, perhaps we can either make some drug or compound safer, by blocking those events, or we can distinguish between safe and unsafe compounds or stimuli.

Safety testing of a new drug, however, is done in aggregate, on a population of cells (or, in a clinical trial for example, on a group of animals or even humans, after a high degree of confidence has been established). If only a few individuals develop symptoms out of a large population, the drug is considered unsafe. But in practice, different individuals have different metabolism, different versions of molecular pathways, different variants of genes and proteins, and so on. Accordingly, personalised medicine holds the promise of – when we have sufficient insight into individual metabolism – being able to prescribe unsafe drugs (for the general population) to only those individuals that can safely metabolise them.

It is easy to take a mechanism apart and stop its functioning. However, while a child can take a radio apart, often he or she cannot put it back together again, and only very rarely can a child improve a radio. And in which way should it be improved? Should it be more tolerant to noise, play sound more loudly, receive more frequencies, perhaps emit a pleasant scent when receiving a good signal? Some of these improvements are as hard to identify, once achieved, as they might be to effect. Severe degradation of function is trivial both to effect and to identify, but improvement is manifold, subtle, may be genuinely novel, and may be hard to spot.

An ideal toxicology of the future should, then, be personalised, taking into account not only what harms people in the average case, but what harms a given individual. In the best case (a sophisticated science of nutrition) it should also take into account how that person might wish to improve themselves, a problem that is psychological and ethical as much as it is biological, especially when such improvement involves further specialisation or a trade-off between different possibilities of life. Here the need for consent is even more imperative than with more basic medical procedures that simply aim to preserve or restore functioning.

In fact, the above issues are relevant not only for toxicology but also for medicine as a whole. Doctors can only address diseases and problems after viewing them as a form of ailment. Such a viewpoint is based on a training that has as its topic the average human being. But species and individuals tend towards specialisation, and perhaps the greatest problems are never merely average problems. Personalised medicine as a field may eventually turn out to be much more complex than we can now imagine, and place entirely new demands on physicians.

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Action, traces and perception https://www.monomorphic.org/wordpress/action-traces-and-perception/ https://www.monomorphic.org/wordpress/action-traces-and-perception/#respond Fri, 25 Aug 2017 02:21:43 +0000 http://www.monomorphic.org/wordpress/?p=1638 A sketch of the ways that concepts allow us to make sense of traces of action in the world (or simply of processes, if we do not wish to posit an actor).

Actions (or processes) leave traces. Traces of such processes include beings, such as houses, roads, animals and plants, and also non-beings, some of which may be potential beings, for example new species or scientific phenomena to be named in the future.

The intelligibility of traces depends on having access to meaningful concepts, such as the concept of an oak or an owl. Not only must we have developed the relevant concept in ourselves and become sufficiently familiar with it, but it must also present itself at the right time when we encounter pre-conceptual oak-indications or owl-indications (or traces of an oak-making process). Some doubt as to whether the traces are of an oak or of a different tree is allowed at first, but not later as the learner becomes more experienced in the world of trees.

What presents itself is not merely an instance of the concept “oak” but also qualities of the oak. It may be towering, withered, majestic or small. Weather conditions and parasites may have left all kinds of marks that interleave themselves with the basic impression. The oak’s particularity is inexhaustible. “I saw an oak” is in no way a complete account of what was seen. Indeed the task of seeing the oak itself may be time-consuming and difficult if taken seriously. A world where all oaks were merely pure instances of the oak concept would be a completely meaningless one.

If what is perceived is man-made, then it will be the perception of a process that contains in part a sequence of actions carried out by humans (but necessarily has its ultimate origin in a non-human process). Here the additional dimension of intent may be added to the act of perception. Through our understanding of ourselves and of our culture, we may be able to work out what was created and why, and for what purpose. The case of a neighbour redecorating their garden is comparable in quality to that of encountering a foreign culture and trying to understand its religious ceremonies and objects. In a time of conflict, we may look at the object as a source of potential hostility or friendliness.

Man-made objects will be the easiest ones to imitate since intent and human actions may be extracted from the traces. Seeing a man-made object will in many cases allow someone with sufficient pre-existing skill to create a similar object. Natural processes are considerably harder. We are as yet unable to manufacture oaks or owls from scratch (not the same as sowing an acorn or hatching an egg). Laboratories, biomedical and otherwise, are constantly at work translating the processes of nature into sequences of human actions (e.g. molecular cloning protocols). Thus science works by expanding the space of what is, or can be, man-made.

 

 

 

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