Jekyll2023-06-28T14:45:09+08:00https://yossadh.github.io/feed.xml[ yossadh ]personal webpageYossa Dwi HartonoLink roundup: Jan–Jun 20232023-06-30T00:00:00+08:002023-06-30T00:00:00+08:00https://yossadh.github.io/posts/2023/06/link-roundup-h1-2023<p><strong>Science</strong><br />
<a href="https://www.theatlantic.com/science/archive/2023/06/milk-mammalian-evolution-nutrition/674487/">Go Ahead, Try to Explain Milk</a><br />
<a href="https://www.bostonreview.net/articles/heat-death/">Killer Heat Waves Are Coming</a><br />
<a href="https://www.scientificamerican.com/article/science-shows-why-traditional-kimchi-making-works-so-well/">Science Shows Why Traditional Kimchi Making Works So Well</a><br />
<a href="https://www.quantamagazine.org/a-new-approach-to-computation-reimagines-artificial-intelligence-20230413/">A New Approach to Computation Reimagines Artificial Intelligence</a><br />
<a href="https://www.quantamagazine.org/cynthia-rudin-builds-ai-that-humans-can-understand-20230427/">The Computer Scientist Peering Inside AI’s Black Boxes</a></p>
<p><strong>Others</strong><br />
<a href="https://www.newyorker.com/culture/the-weekend-essay/the-case-against-travel">The Case Against Travel</a><br />
<a href="https://www.themarginalian.org/2022/07/31/simone-de-beauvoir-coming-of-age/">How to Keep Life from Becoming a Parody of Itself: Simone de Beauvoir on the Art of Growing Older</a><br />
<a href="https://asteriskmag.com/issues/1/is-wine-fake">Is Wine Fake?</a><br />
<a href="https://therumpus.net/2023/04/18/the-sound-of-home-sonorous-desert-by-kim-haines-eitzen/">The Sound of Home: Sonorous Desert by Kim Haines-Eitzen</a><br />
<a href="https://www.tabletmag.com/sections/belief/articles/meaning-life-berman-final-exam">The Meaning of Life</a><br />
<a href="https://hedgehogreview.com/web-features/thr/posts/the-dao-of-using-your-smartphone">The Dao of Using Your Smartphone</a><br />
<a href="https://culturico.com/2020/01/21/camus-atheism-and-the-virtues-of-inconsistency/">Camus’s Atheism and the Virtues of Inconsistency</a><br />
<a href="https://www.washingtonpost.com/lifestyle/magazine/fatal-distraction-forgetting-a-child-in-thebackseat-of-a-car-is-a-horrifying-mistake-is-it-a-crime/2014/06/16/8ae0fe3a-f580-11e3-a3a5-42be35962a52_story.html">Fatal Distraction: Forgetting a Child in the Backseat of a Car Is a Horrifying Mistake. Is It a Crime?</a></p>Yossa Dwi HartonoScience Go Ahead, Try to Explain Milk Killer Heat Waves Are Coming Science Shows Why Traditional Kimchi Making Works So Well A New Approach to Computation Reimagines Artificial Intelligence The Computer Scientist Peering Inside AI’s Black Boxes Others The Case Against Travel How to Keep Life from Becoming a Parody of Itself: Simone de Beauvoir on the Art of Growing Older Is Wine Fake? The Sound of Home: Sonorous Desert by Kim Haines-Eitzen The Meaning of Life The Dao of Using Your Smartphone Camus’s Atheism and the Virtues of Inconsistency Fatal Distraction: Forgetting a Child in the Backseat of a Car Is a Horrifying Mistake. Is It a Crime?Link roundup: Apr–Dec 20222022-12-31T00:00:00+08:002022-12-31T00:00:00+08:00https://yossadh.github.io/posts/2022/12/link-roundup-q2-2022<p><strong>Science</strong><br />
<a href="https://www.japantimes.co.jp/life/2022/11/28/food/japan-alcohol-wood/">Wood spirits: How Japan made the world’s first liquor from trees</a><br />
<a href="https://www.theguardian.com/lifeandstyle/2022/dec/08/artificial-sweeteners-price-of-sugar-free-are-they-as-harmless-as-we-thought">The price of ‘sugar free’: are sweeteners as harmless as we thought?</a><br />
<a href="https://www.nature.com/articles/s41587-022-01466-0">A language model beats alphafold2 on orphans</a><br />
https://github.com/FellowsFreiesWissen/computational_notebooks
<a href="https://lithub.com/why-conventional-wisdom-about-cancer-can-be-misleading/">Why Conventional Wisdom About Cancer Can Be Misleading</a><br />
<a href="https://www.science.org/content/blog-post/machine-learning-handle-proteome">Machine Learning to Handle the Proteome</a><br />
<a href="https://www.nature.com/articles/d41586-022-02083-2">‘The entire protein universe’: AI predicts shape of nearly every known protein</a><br />
<a href="https://www.nature.com/articles/d41586-022-02035-w">Could machine learning fuel a reproducibility crisis in science?</a><br />
<a href="https://www.science.org/content/article/potential-fabrication-research-images-threatens-key-theory-alzheimers-disease">Blots on a field?</a><br />
<a href="https://www.pnas.org/doi/10.1073/pnas.2112621118">PNAS | Leveraging nonstructural data to predict structures and affinities of protein–ligand complexes</a><br />
<a href="https://www.nature.com/articles/d41586-022-00858-1">Breaking into the black box of artificial intelligence</a></p>
<p><strong>Others</strong><br />
<a href="https://www.wired.com/story/nightmare-houseplant-obsession-nepenthes/">When a Houseplant Obsession Becomes a Nightmare</a><br />
<a href="https://astralcodexten.substack.com/p/book-review-what-we-owe-the-future">Book Review: What We Owe The Future</a><br />
<a href="https://www.wired.com/story/if-someone-is-typing-then-stops-can-i-ask-why/">If Someone Is Typing, Then Stops … Can I Ask Why?</a></p>
<blockquote>
<p>One can envisage several alternatives to further enhance VS predictions if experiments are not accessible/available. More than one score function might be combined to produce a consensus top-ranked list, while X-ray screening have recently identified allosteric sites that might provide a wider description of virus target. In addition, pockets are not static but prone to modifications in in vivo conditions, and a preliminary molecular dynamics (MD) stage could be implemented to produce trajectories of the targets.33 A series of representative structures (or clusters) can be subsequently used for conducting VS simulations. MD might be also used to confirm the stability of the binding pose.Finally, the simulation of a reduced number of drugs allows to use of more advanced levels of theory, e. g., ab initio or multiscale QM/MM.<br />
– <a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/cmdc.202200278">When Virtual Screening Yields Inactive Drugs: Dealing with False Theoretical Friends</a></p>
</blockquote>Yossa Dwi HartonoScience Wood spirits: How Japan made the world’s first liquor from trees The price of ‘sugar free’: are sweeteners as harmless as we thought? A language model beats alphafold2 on orphans https://github.com/FellowsFreiesWissen/computational_notebooks Why Conventional Wisdom About Cancer Can Be Misleading Machine Learning to Handle the Proteome ‘The entire protein universe’: AI predicts shape of nearly every known protein Could machine learning fuel a reproducibility crisis in science? Blots on a field? PNAS | Leveraging nonstructural data to predict structures and affinities of protein–ligand complexes Breaking into the black box of artificial intelligence Others When a Houseplant Obsession Becomes a Nightmare Book Review: What We Owe The Future If Someone Is Typing, Then Stops … Can I Ask Why?Link roundup: Jan–Mar 20222022-03-30T00:00:00+08:002022-03-30T00:00:00+08:00https://yossadh.github.io/posts/2022/03/link-roundup-q1-2022<blockquote>
<p>Since these AIs are just giant matrix multiplication machines, “intuition” now has a firm grounding in math - just much bigger, more complicated math than the usual kind that we call “logical”.<br /><br />
This would be a common pattern for sciences: much worse at everyday tasks than people who do them intuitively, until it generates some surprising and powerful new technology. Democritus figured out what matter was made of in 400 BC, and it didn’t help a single person do a single useful thing with matter for the next 2000 years of followup research, and then you got the atomic bomb (I may be skipping over all of chemistry, sorry).<br />
– <a href="https://astralcodexten.substack.com/p/what-are-we-arguing-about-when-we?s=r&token=eyJ1c2VyX2lkIjo1OTA1MjkxLCJwb3N0X2lkIjo0ODI5MTQxMCwiXyI6IlpMSmxkIiwiaWF0IjoxNjQ2MzkzMjM0LCJleHAiOjE2NDYzOTY4MzQsImlzcyI6InB1Yi04OTEyMCIsInN1YiI6InBvc3QtcmVhY3Rpb24ifQ.Eu2UCZV_OBwYPLebgWdo34SclOu2yYgTy6WagDkfDoo">What Are We Arguing About When We Argue About Rationality?</a></p>
</blockquote>
<blockquote>
<p>What he seeks to practice is, in a phrase popularized by the Marxist philosopher Antonio Gramsci, “pessimism of the intellect, optimism of the will.”<br />
– <a href="https://www.newyorker.com/magazine/2022/01/31/can-science-fiction-wake-us-up-to-our-climate-reality-kim-stanley-robinson">Can Science Fiction Wake Us Up to Our Climate Reality?</a></p>
</blockquote>
<blockquote>
<p>Caulfield then introduced two different ways of thinking about how we engage with ideas when we’re on the internet: The web as a garden and the web as a stream. Think of the web as an organically developing garden: a space in which there’s no predetermined order or relationship of things to one another. Caulfield writes, “Every walk through the garden creates new paths, new meanings.” What came first in the garden doesn’t matter either. Each thing in the garden is related to the other things as it exists in the moment.<br />
– <a href="https://www.cliffguren.com/articles/the-faithful-gardener">The Faithful Gardener</a></p>
</blockquote>
<p><strong>Science</strong> <br />
<a href="https://www.nature.com/articles/s42256-022-00465-9">Dual use of artificial-intelligence-powered drug discovery</a><br />
<a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009809">Twelve quick tips for software design</a><br />
<a href="https://www.quantamagazine.org/computer-scientists-prove-why-bigger-neural-networks-do-better-20220210/">Computer Scientists Prove Why Bigger Neural Networks Do Better</a><br />
<a href="https://www.science.org/content/article/this-scientist-accused-supplement-industry-of-fraud-now-his-own-work-is-under-fire">Failing the test: DNA barcoding brought botanist Steven Newmaster scientific fame and entrepreneurial success. Was it all based on fraud?</a><br />
<a href="https://thetakeout.com/foods-that-make-your-mouth-go-numb-sichuan-clove-buz-1848334167">What’s the buzz? Let’s talk about numbing ingredients</a><br />
<a href="https://www.nature.com/articles/d41586-022-00104-8">The pandemic’s true death toll: millions more than official counts</a><br />
<a href="https://www.popsci.com/health/diet-resolutions/">5 nutrition goals that are better than weight loss</a></p>
<p><strong>Others</strong><br />
https://github.com/csinva/imodels<br />
<a href="https://www.nature.com/articles/d41586-021-03748-0">Synaesthetics</a><br />
<a href="https://3quarksdaily.com/3quarksdaily/2022/02/transformative-experience-and-pascals-wager.html">Transformative Experience and Pascal’s Wager</a><br />
<a href="https://www.wired.com/story/do-good-doorbell-cams-make-good-neighbors/">Do Good Doorbell Cams Make Good Neighbors?</a><br />
<a href="https://www.theatlantic.com/magazine/archive/2022/03/why-we-are-never-satisfied-happiness/621304/">How to Want Less</a><br />
<a href="https://www.theatlantic.com/magazine/archive/2022/03/why-we-lose-friends-aging-happiness/621305/">It’s Your Friends Who Break Your Heart</a><br />
<a href="https://psyche.co/guides/how-to-wander-free-and-easy-through-life-by-being-useless">How to be useless</a><br />
<a href="https://www.vice.com/en/article/dypybk/what-we-dont-want-to-know">What We Don’t Want to Know </a><br />
<a href="https://www.laphamsquarterly.org/roundtable/its-time-some-game-theory">It’s Time for Some Game Theory</a><br />
<a href="https://thelanguagenerds.com/2019/why-does-woman-have-man-in-it-and-female-has-the-word-male-in-it/">Why does woman have ‘man’ in it and female has the word ‘male’ in it?</a></p>Yossa Dwi HartonoSince these AIs are just giant matrix multiplication machines, “intuition” now has a firm grounding in math - just much bigger, more complicated math than the usual kind that we call “logical”. This would be a common pattern for sciences: much worse at everyday tasks than people who do them intuitively, until it generates some surprising and powerful new technology. Democritus figured out what matter was made of in 400 BC, and it didn’t help a single person do a single useful thing with matter for the next 2000 years of followup research, and then you got the atomic bomb (I may be skipping over all of chemistry, sorry). – What Are We Arguing About When We Argue About Rationality? What he seeks to practice is, in a phrase popularized by the Marxist philosopher Antonio Gramsci, “pessimism of the intellect, optimism of the will.” – Can Science Fiction Wake Us Up to Our Climate Reality? Caulfield then introduced two different ways of thinking about how we engage with ideas when we’re on the internet: The web as a garden and the web as a stream. Think of the web as an organically developing garden: a space in which there’s no predetermined order or relationship of things to one another. Caulfield writes, “Every walk through the garden creates new paths, new meanings.” What came first in the garden doesn’t matter either. Each thing in the garden is related to the other things as it exists in the moment. – The Faithful Gardener Science Dual use of artificial-intelligence-powered drug discovery Twelve quick tips for software design Computer Scientists Prove Why Bigger Neural Networks Do Better Failing the test: DNA barcoding brought botanist Steven Newmaster scientific fame and entrepreneurial success. Was it all based on fraud? What’s the buzz? Let’s talk about numbing ingredients The pandemic’s true death toll: millions more than official counts 5 nutrition goals that are better than weight loss Others https://github.com/csinva/imodels Synaesthetics Transformative Experience and Pascal’s Wager Do Good Doorbell Cams Make Good Neighbors? How to Want Less It’s Your Friends Who Break Your Heart How to be useless What We Don’t Want to Know It’s Time for Some Game Theory Why does woman have ‘man’ in it and female has the word ‘male’ in it?2021 book list2022-01-05T00:00:00+08:002022-01-05T00:00:00+08:00https://yossadh.github.io/posts/2022/01/2021-books<p>Compared to 2020, I slowly regained my reading habit again. One notable book is Camus’ <em>The Plague</em> that I didn’t finish in 2020, but picked it up again.
Nothing really stood out for me, but I would recommend the starred ones.</p>
<h2 id="2021">2021</h2>
<p><strong>Cancer ward | Alexander Solzhenitsyn</strong><br />
<strong>The medusa and the snail : more notes of a biology watcher | Lewis Thomas</strong><br />
<strong>Gulp : adventures on the alimentary canal | Mary Roach</strong><br />
<strong>Lament for a Son | Nicholas Wolterstorff ⭑</strong><br />
<strong>The Long Walk: The True Story Of A Trek To Freedom | Slavomir Rawicz</strong><br />
<strong>Curiosity | Alberto Manguel</strong><br />
<strong>Vagabonds | Hao Jingfang</strong><br />
<strong>Among others | Jo Walton</strong><br />
<strong>Marriage: 6 Gospel Commitments Every Couple Needs to Make | Paul Tripp ⭑</strong><br />
<strong>The Plague | Albert Camus ⭑</strong><br />
<strong>The Ministry for the Future | Kim Stanley Robinson</strong><br />
<strong>Invisible Planets: Contemporary Chinese Science Fiction in Translation | Edited and translated by Ken Liu</strong><br />
<strong>The Art of Forgiving | Lewis Smedes ⭑</strong><br />
<strong>Letters to Malcolm: Chiefly on Prayer | CS Lewis</strong><br />
<strong>Alternative Careers in Science | Editor(s): Christopher Avery & Brian J. Walker</strong><br />
<strong>A Voice in the Wind | Francine Rivers</strong><br />
<strong>The Sacred Search: What If It’s Not about Who You Marry, But Why? | Gary Thomas ⭑</strong><br />
<strong>Why We Swim | Bonnie Tsui</strong><br />
<strong>Hands-on Scikit-Learn for Machine Learning Applications | David Paper</strong><br />
<strong>Please Look After Mom | Shin Kyung-sook</strong><br />
<strong>The City We Became | NK Jemisin</strong></p>Yossa Dwi HartonoCompared to 2020, I slowly regained my reading habit again. One notable book is Camus’ The Plague that I didn’t finish in 2020, but picked it up again. Nothing really stood out for me, but I would recommend the starred ones.Link roundup: Oct–Dec 20212021-12-31T00:00:00+08:002021-12-31T00:00:00+08:00https://yossadh.github.io/posts/2021/12/link-roundup-q4-2021<blockquote>
<p>Humility, by contrast, admits that defeat is possible. It occupies the nebulous zone between preparedness and precaution by asking a moral question: not what we can achieve with what we have, but how we should act given that we cannot know the full consequences of our actions.<br />
– <a href="https://bostonreview.net/forum/preparedness-wont-stop-the-next-pandemic/">“Preparedness” Won’t Stop the Next Pandemic</a></p>
</blockquote>
<blockquote>
<p>Rather than trying to beat the coronavirus one booster at a time, the country needs to do what it has always needed to do—build systems and enact policies that protect the health of entire communities, especially the most vulnerable ones. Individualism couldn’t beat Delta, it won’t beat Omicron, and it won’t beat the rest of the Greek alphabet to come. Self-interest is self-defeating, and as long as its hosts ignore that lesson, the virus will keep teaching it.<br />
– <a href="https://www.theatlantic.com/health/archive/2021/12/america-omicron-variant-surge-booster/621027/">Ed Yong | America Is Not Ready for Omicron</a></p>
</blockquote>
<blockquote>
<p>For instance, in Plato’s Euthyphro dialogue, Socrates runs into the local priest and expert on the gods, the self-same Euthyphro, who plans to do something unholy by the local standards – to press charges against his own father. Socrates asks how he, a man wise in the ways of the gods, could do something the gods would obviously condemn?<br /><br />
Euthyphro answers that, in fact, his plan passes the gods’ standards. This raises only more questions for Socrates, who presses on and asks Euthyphro to clarify what he means by holiness. If Euthyphro’s plan is so holy, surely he could explain his reasoning and spell out the nature of holiness? Under questioning, though, Euthyphro reasons himself into a corner, unable to give a clear account of holiness. The dialogue ends there, with the premier theologian of Athens excusing himself with a version of ‘I’m actually late for a thing.’<br />
– <a href="https://aeon.co/essays/what-were-doing-when-were-doing-epistemology">How do you know?</a></p>
</blockquote>
<blockquote>
<p>Researchers from Harvard and the University of Virginia brought subjects into a lab where they had to choose between two torture devices. The first option was to push a button that would deliver a safe, but still sharply unpleasant, electric shock to themselves. Two-thirds of the men in the study chose to shock themselves despite the fact that they’d 1.) all been shocked in an earlier phase of the study, and 2.) all professed that they would pay money to avoid the unpleasant experience in the future.<br />
– <a href="https://lithub.com/why-stories-are-like-taking-drugs/">Why Stories Are Like Taking Drugs </a></p>
</blockquote>
<blockquote>
<p>Sigmund Freud once stated that no one believes in their own death. In the unconscious, there is a blank space where knowledge of this one sure thing about our futures should be.<br />
– <a href="https://www.theguardian.com/society/2021/dec/07/life-after-death-pandemic-transformed-psychic-landscape-jacqueline-rose">Life after death: how the pandemic has transformed our psychic landscape</a></p>
</blockquote>
<blockquote>
<p>Inverting the old cliché, Christopher Hitchens said, ‘Everyone has a book in them and that, in most cases, is where it should stay.’<br />
– <a href="https://literaryreview.co.uk/have-you-considered-accountancy">https://literaryreview.co.uk/have-you-considered-accountancy</a></p>
</blockquote>
<blockquote>
<p>You’ve probably heard the probabilistic (aka Bayesian) side of things before. Instead of thinking “I’m sure global warming is fake!”, try to think in terms of probabilities (“I think there’s a 90% chance global warming is fake.”) Instead of thinking in terms of changing your mind (“Should I surrender my belief, and switch to my enemy’s belief that global warming is true”), think in terms of updating your probabilities (“Now I’m only 70% sure that global warming is fake”). This mindset makes it easier to remember that it’s not a question of winning or losing, but a question of being as accurate as possible. Someone who updates from 90% to 70% is no more or less wrong or embarrassing than someone who updates from 60% to 40%.<br />
– <a href="https://astralcodexten.substack.com/p/book-review-the-scout-mindset?token=eyJ1c2VyX2lkIjo1OTA1MjkxLCJwb3N0X2lkIjo0MTE2MzAwOSwiXyI6Ik5XV0dEIiwiaWF0IjoxNjMyOTE0NjQ1LCJleHAiOjE2MzI5MTgyNDUsImlzcyI6InB1Yi04OTEyMCIsInN1YiI6InBvc3QtcmVhY3Rpb24ifQ.yfJQGoOp2PSraFHRbL3VegBEdGUQWmkay-OnhpMi928">Scott Alexander</a></p>
</blockquote>
<blockquote>
<p>Pundits have urged people to “listen to the science,” as if “the science” is a tome of facts and not an amorphous, dynamic entity, born from the collective minds of thousands of individual people who argue and disagree about data that can be interpreted in a range of ways.<br />
– <a href="https://www.theatlantic.com/science/archive/2021/10/how-pandemic-changed-science-writing/620271/">Ed Yong</a></p>
</blockquote>
<blockquote>
<p>In other words, “vibes” are similar to the approximations that machine learning systems use, and the two feed off of each other synergistically. The situation is precisely encapsulated by Goodhart’s Law: “When a measure becomes a target, it ceases to be a good measure.”<br />
– <a href="https://reallifemag.com/nameless-feeling">Ludwig Yeetgenstein</a></p>
</blockquote>
<p><strong>Science</strong> <br />
<a href="https://www.nature.com/articles/d41586-021-03686-x">How COVID vaccines shaped 2021 in eight powerful charts</a><br />
<a href="https://pubs.acs.org/doi/10.1021/acs.jcim.1c00998">J Chem Inf Model | Making it Rain: Cloud-Based Molecular Simulations for Everyone</a><br />
<a href="https://www.nature.com/articles/s41586-021-04220-9">Nature | Synthon-based ligand discovery in virtual libraries of over 11 billion compounds</a><br />
<a href="https://medium.com/@anushkhabajpai/top-data-science-cheat-sheets-ml-dl-python-r-sql-maths-statistics-5239d4568225">Top DATA SCIENCE Cheatsheets (ML, DL, Python, R, SQL, Maths & Statistics)</a><br />
<a href="https://pubs.acs.org/doi/10.1021/acs.jmedchem.1c01789">J Med Chem | Explainable Machine Learning for Property Predictions in Compound Optimization</a> <br />
<a href="https://unchartedterritories.tomaspueyo.com/p/the-omicron-question?token=eyJ1c2VyX2lkIjo1OTA1MjkxLCJwb3N0X2lkIjo0NTQ1MDQ2MiwiXyI6Ik5XV0dEIiwiaWF0IjoxNjM5NDc5OTEzLCJleHAiOjE2Mzk0ODM1MTMsImlzcyI6InB1Yi0zNDc1MzMiLCJzdWIiOiJwb3N0LXJlYWN0aW9uIn0.VgqTEfJDsd6vc_kB8KB3NcAXXdfFPxDEPwKUHtGfuNk">Tomas Pueyo | The Omicron Question</a><br />
<a href="https://physics.aps.org/articles/v14/178">To Touch the Sun</a><br />
<a href="https://www.theguardian.com/society/2021/dec/07/life-after-death-pandemic-transformed-psychic-landscape-jacqueline-rose">Life after death: how the pandemic has transformed our psychic landscape</a><br />
<a href="https://www.wired.com/story/kathleen-folbigg-sudden-infant-death-mystery/">4 Dead Infants, a Convicted Mother, and a Genetic Mystery</a><br />
<a href="https://nautil.us/issue/108/change/all-the-biomass-on-earth">All the Biomass on Earth</a><br />
<a href="https://astralcodexten.substack.com/p/pascalian-medicine?token=eyJ1c2VyX2lkIjo1OTA1MjkxLCJwb3N0X2lkIjo0NDM3NTMyNCwiXyI6Ik5XV0dEIiwiaWF0IjoxNjM3ODQxNDA4LCJleHAiOjE2Mzc4NDUwMDgsImlzcyI6InB1Yi04OTEyMCIsInN1YiI6InBvc3QtcmVhY3Rpb24ifQ.fFRl73_9f6N6nAXsyV0Ix8EtvQhnnl6bh-quJDVm4G4">Pascalian Medicine</a><br />
<a href="https://www.wired.com/story/fungi-climate-change-medicine-health/">It’s Time to Fear the Fungi</a><br />
<a href="https://unchartedterritories.tomaspueyo.com/p/ocean-plastic?token=eyJ1c2VyX2lkIjo1OTA1MjkxLCJwb3N0X2lkIjo0MzI3OTI1NCwiXyI6Ik5XV0dEIiwiaWF0IjoxNjM1NzgzOTY4LCJleHAiOjE2MzU3ODc1NjgsImlzcyI6InB1Yi0zNDc1MzMiLCJzdWIiOiJwb3N0LXJlYWN0aW9uIn0.AF_NWYk9YhjH-SiDDK5S_dtVb8pRI3SJMqXR2L_Q7uo&utm_source=pocket_mylist">How to Fight Ocean Plastic</a><br />
<a href="https://github.com/Merck/DeepNeuralNet-QSAR">https://github.com/Merck/DeepNeuralNet-QSAR</a><br />
<a href="https://github.com/deepchem/deepchem">https://github.com/deepchem/deepchem</a><br />
DeepChem aims to provide a high quality open-source toolchain that democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology.<br />
<a href="https://www.bbc.com/news/science-environment-58925049">COP26: Can countries be forced to meet net zero targets? And more questions</a><br />
<a href="https://themarginaliareview.com/how-special-is-science/">How Special Is Science?</a></p>
<p><strong>Others</strong><br />
<a href="https://vimeo.com/495325925?embedded=true&source=vimeo_logo&owner=3709126">Voice above water</a><br />
<a href="https://psyche.co/guides/how-to-know-what-you-really-want-and-be-free-from-mimetic-desire">How to know what you really want</a><br />
<a href="https://en.wikipedia.org/wiki/Reactance_(psychology)">Reactance</a><br />
<a href="https://www.nytimes.com/2021/12/10/style/moderrn-love-haiti-earthquake-hold-their-hands-again.html">‘I Would Give Anything to Hold Their Hands Again’</a><br />
<a href="https://sydneyreviewofbooks.com/review/ghosh-nutmegs-curse/">Review: Delia Falconeron Amitav Ghosh | A Dazzling Synthesis</a><br />
<a href="https://www.seriouseats.com/freezer-as-cooking-tool-5212337">Freeze en Place: How to Use Your Freezer as a “Cooking” Tool</a><br />
<a href="https://existentialcomics.com/comic/423">The End of the Dinosaurs</a><br />
<a href="https://psyche.co/guides/how-to-rest-well-and-enjoy-a-more-creative-sustainable-life">How to rest well</a><br />
<a href="https://aeon.co/essays/how-we-came-to-depend-on-the-week-despite-its-artificiality">How we became weekly</a><br />
<a href="https://www.smbc-comics.com/comic/morality">SMBC | Morality</a><br />
<a href="https://www.newyorker.com/magazine/2021/11/08/energy-and-how-to-get-it">Energy, and How to Get It</a><br />
<a href="https://towardsdatascience.com/bamboolib-one-of-the-most-useful-python-libraries-you-have-ever-seen-6ce331685bb7">Bamboolib: One of the Most Useful Python Libraries You Have Ever Seen</a><br />
<a href="https://www.wired.com/story/sci-fi-icon-neal-stephenson-global-warming/">Sci-Fi Icon Neal Stephenson Finally Takes on Global Warming</a> <br />
<a href="https://themillions.com/2021/10/and-the-walls-came-down.html">And the Walls Came Down</a><br />
<a href="https://www.sundaypost.com/fp/composer-and-academic-solves-historical-puzzle-to-bring-the-sounds-of-ancient-rome-to-life/">Composer and academic solves historical puzzle to bring the sounds of Ancient Rome to life</a><br />
<a href="https://www.prospectmagazine.co.uk/philosophy/spinozas-religion-clare-carlisle-god-einstein-philosophy-religion-review">Spinoza’s God: Einstein believed in it, but what was it?</a><br />
<a href="https://thewalrus.ca/lucy-ellmann-air-travel/">Kill the Travel Bug: The Case for Staying Put</a></p>
<!--
**Papers**
[Production of Rainbow Colorants by Metabolically Engineered _Escherichia coli_](https://onlinelibrary.wiley.com/doi/10.1002/advs.202100743)
[How to Automate Work Using Python](https://www.freecodecamp.org/news/how-to-automate-things-using-python)
>Have you ever thought of the perfect quip or comeback after it didn’t matter—a minute, hour, or day after your conversation has ended?
Well, there’s a name for that phenomenon. It’s called l’esprit de l’escalier, or the spirit of the staircase, and refers to the perfect retort that arises at the wrong time.
-- [The Secret to Being Witty, Revealed](https://getpocket.com/explore/item/the-secret-to-being-witty-revealed)
-->Yossa Dwi HartonoHumility, by contrast, admits that defeat is possible. It occupies the nebulous zone between preparedness and precaution by asking a moral question: not what we can achieve with what we have, but how we should act given that we cannot know the full consequences of our actions. – “Preparedness” Won’t Stop the Next Pandemic Rather than trying to beat the coronavirus one booster at a time, the country needs to do what it has always needed to do—build systems and enact policies that protect the health of entire communities, especially the most vulnerable ones. Individualism couldn’t beat Delta, it won’t beat Omicron, and it won’t beat the rest of the Greek alphabet to come. Self-interest is self-defeating, and as long as its hosts ignore that lesson, the virus will keep teaching it. – Ed Yong | America Is Not Ready for Omicron For instance, in Plato’s Euthyphro dialogue, Socrates runs into the local priest and expert on the gods, the self-same Euthyphro, who plans to do something unholy by the local standards – to press charges against his own father. Socrates asks how he, a man wise in the ways of the gods, could do something the gods would obviously condemn? Euthyphro answers that, in fact, his plan passes the gods’ standards. This raises only more questions for Socrates, who presses on and asks Euthyphro to clarify what he means by holiness. If Euthyphro’s plan is so holy, surely he could explain his reasoning and spell out the nature of holiness? Under questioning, though, Euthyphro reasons himself into a corner, unable to give a clear account of holiness. The dialogue ends there, with the premier theologian of Athens excusing himself with a version of ‘I’m actually late for a thing.’ – How do you know? Researchers from Harvard and the University of Virginia brought subjects into a lab where they had to choose between two torture devices. The first option was to push a button that would deliver a safe, but still sharply unpleasant, electric shock to themselves. Two-thirds of the men in the study chose to shock themselves despite the fact that they’d 1.) all been shocked in an earlier phase of the study, and 2.) all professed that they would pay money to avoid the unpleasant experience in the future. – Why Stories Are Like Taking Drugs Sigmund Freud once stated that no one believes in their own death. In the unconscious, there is a blank space where knowledge of this one sure thing about our futures should be. – Life after death: how the pandemic has transformed our psychic landscape Inverting the old cliché, Christopher Hitchens said, ‘Everyone has a book in them and that, in most cases, is where it should stay.’ – https://literaryreview.co.uk/have-you-considered-accountancy You’ve probably heard the probabilistic (aka Bayesian) side of things before. Instead of thinking “I’m sure global warming is fake!”, try to think in terms of probabilities (“I think there’s a 90% chance global warming is fake.”) Instead of thinking in terms of changing your mind (“Should I surrender my belief, and switch to my enemy’s belief that global warming is true”), think in terms of updating your probabilities (“Now I’m only 70% sure that global warming is fake”). This mindset makes it easier to remember that it’s not a question of winning or losing, but a question of being as accurate as possible. Someone who updates from 90% to 70% is no more or less wrong or embarrassing than someone who updates from 60% to 40%. – Scott Alexander Pundits have urged people to “listen to the science,” as if “the science” is a tome of facts and not an amorphous, dynamic entity, born from the collective minds of thousands of individual people who argue and disagree about data that can be interpreted in a range of ways. – Ed Yong In other words, “vibes” are similar to the approximations that machine learning systems use, and the two feed off of each other synergistically. The situation is precisely encapsulated by Goodhart’s Law: “When a measure becomes a target, it ceases to be a good measure.” – Ludwig Yeetgenstein Science How COVID vaccines shaped 2021 in eight powerful charts J Chem Inf Model | Making it Rain: Cloud-Based Molecular Simulations for Everyone Nature | Synthon-based ligand discovery in virtual libraries of over 11 billion compounds Top DATA SCIENCE Cheatsheets (ML, DL, Python, R, SQL, Maths & Statistics) J Med Chem | Explainable Machine Learning for Property Predictions in Compound Optimization Tomas Pueyo | The Omicron Question To Touch the Sun Life after death: how the pandemic has transformed our psychic landscape 4 Dead Infants, a Convicted Mother, and a Genetic Mystery All the Biomass on Earth Pascalian Medicine It’s Time to Fear the Fungi How to Fight Ocean Plastic https://github.com/Merck/DeepNeuralNet-QSAR https://github.com/deepchem/deepchem DeepChem aims to provide a high quality open-source toolchain that democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology. COP26: Can countries be forced to meet net zero targets? And more questions How Special Is Science? Others Voice above water How to know what you really want Reactance ‘I Would Give Anything to Hold Their Hands Again’ Review: Delia Falconeron Amitav Ghosh | A Dazzling Synthesis Freeze en Place: How to Use Your Freezer as a “Cooking” Tool The End of the Dinosaurs How to rest well How we became weekly SMBC | Morality Energy, and How to Get It Bamboolib: One of the Most Useful Python Libraries You Have Ever Seen Sci-Fi Icon Neal Stephenson Finally Takes on Global Warming And the Walls Came Down Composer and academic solves historical puzzle to bring the sounds of Ancient Rome to life Spinoza’s God: Einstein believed in it, but what was it? Kill the Travel Bug: The Case for Staying PutSplitting a row of matplotlib subplots to columns2021-10-25T00:00:00+08:002021-10-25T00:00:00+08:00https://yossadh.github.io/posts/2021/10/matplotlib<p>Case: I have many rows of subplots and would like to divide them up in multiple columns</p>
<p>The solution is quite simple with modulo operator, although it took me embarassingly sometime to figure it out.<br />
First, let’s say we have a list of plot names:</p>
<div class="language-python highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="n">plots</span> <span class="o">=</span> <span class="p">[</span><span class="s">'plot1'</span><span class="p">,</span> <span class="s">'plot2'</span><span class="p">,...]</span>
</code></pre></div></div>
<p>If we plot this in one column, it would be:</p>
<div class="language-python highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="n">ncol</span><span class="o">=</span><span class="mi">1</span>
<span class="n">nrow</span><span class="o">=</span><span class="nb">len</span><span class="p">(</span><span class="n">plots</span><span class="p">)</span>
<span class="n">fig</span><span class="p">,</span> <span class="n">axes</span> <span class="o">=</span> <span class="n">plt</span><span class="p">.</span><span class="n">subplots</span><span class="p">(</span><span class="n">nrow</span><span class="p">,</span> <span class="n">ncol</span><span class="p">)</span>
<span class="k">for</span> <span class="n">ind</span><span class="p">,</span> <span class="n">title</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">plots</span><span class="p">):</span>
<span class="n">ax</span> <span class="o">=</span> <span class="n">axes</span><span class="p">[</span><span class="n">ind</span><span class="p">]</span>
<span class="p">...</span><span class="n">plt</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">)</span>
</code></pre></div></div>
<p>Now if we want to split this to, say, 3 columns,</p>
<div class="language-python highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="n">ncol</span><span class="o">=</span><span class="mi">3</span>
<span class="n">nrow</span><span class="o">=</span><span class="nb">len</span><span class="p">(</span><span class="n">plots</span><span class="p">)</span><span class="o">//</span><span class="n">ncol</span><span class="o">+</span><span class="mi">1</span>
<span class="n">fig</span><span class="p">,</span> <span class="n">axes</span> <span class="o">=</span> <span class="n">plt</span><span class="p">.</span><span class="n">subplots</span><span class="p">(</span><span class="n">nrow</span><span class="p">,</span> <span class="n">ncol</span><span class="p">)</span>
<span class="k">for</span> <span class="n">ind</span><span class="p">,</span> <span class="n">title</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">plots</span><span class="p">):</span>
<span class="n">ax</span> <span class="o">=</span> <span class="n">axes</span><span class="p">[</span><span class="n">ind</span><span class="o">%</span><span class="n">nrow</span><span class="p">,</span><span class="n">ind</span><span class="o">//</span><span class="n">nrow</span><span class="p">]</span>
<span class="p">...</span><span class="n">plt</span><span class="p">(</span><span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">)</span>
</code></pre></div></div>
<p>For the row index, the modulo operator ‘resets’ <code class="language-plaintext highlighter-rouge">ind</code> for every column by modulo-ing it with <code class="language-plaintext highlighter-rouge">nrow</code>.
For the column index, simply divide <code class="language-plaintext highlighter-rouge">ind</code> with <code class="language-plaintext highlighter-rouge">nrow</code> and round down.</p>Yossa Dwi HartonoCase: I have many rows of subplots and would like to divide them up in multiple columnsLink roundup: Jul–Sep 20212021-09-30T00:00:00+08:002021-09-30T00:00:00+08:00https://yossadh.github.io/posts/2021/09/link-roundup-q3-2021<p><strong>Papers</strong><br />
<a href="https://onlinelibrary.wiley.com/doi/10.1002/advs.202100743">Production of Rainbow Colorants by Metabolically Engineered <em>Escherichia coli</em></a><br />
<a href="https://pubs.acs.org/doi/10.1021/acs.jcim.1c00341">NLDock: a Fast Nucleic Acid–Ligand Docking Algorithm for Modeling RNA/DNA–Ligand Complexes</a><br />
<a href="https://accp1.onlinelibrary.wiley.com/doi/full/10.1002/jcph.1871">Natural and Synthetic Cannabinoids: Pharmacology, Uses, Adverse Drug Events, and Drug Interactions</a><br />
<a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009207">Fifteen quick tips for success with HPC, i.e., responsibly BASHing that Linux cluster</a></p>
<p><strong>Science</strong> <br />
<a href="https://www.scientificamerican.com/article/agroecology-is-the-solution-to-world-hunger/">Agroecology Is the Solution to World Hunger</a> <br />
<a href="http://phdcomics.com/comics.php?f=2047">PHD Comics | The COVID-19 virus (SARS-CoV-2) explained</a><br />
<a href="https://www.statnews.com/2021/09/13/how-a-fatally-tragically-flawed-paradigm-has-derailed-the-science-of-obesity/">How a ‘fatally, tragically flawed’ paradigm has derailed the science of obesity</a><br />
<a href="https://www.the-scientist.com/features/mechanisms-of-long-covid-remain-unknown-but-data-are-rolling-in-69066">Mechanisms of Long COVID Remain Unknown but Data Are Rolling In</a><br />
<a href="https://www.the-scientist.com/features/sars-cov-2-s-wide-ranging-effects-on-the-body-69109">SARS-CoV-2’s Wide-Ranging Effects on the Body</a><br />
<a href="https://edition.cnn.com/interactive/2021/08/world/extreme-weather-climate-change/">Was that wild weather caused by climate change? Scientists can now say ‘yes’ with confidence</a><br />
<a href="https://www.forbes.com/sites/startswithabang/2021/08/10/sorry-skeptics-new-ipcc-report-provides-unprecedented-clarity-about-earths-climate/">Sorry, Skeptics: New IPCC Report Provides Unprecedented Clarity About Earth’s Climate</a><br />
<a href="https://www.nature.com/articles/d41586-021-02039-y">Nature | How the coronavirus infects cells — and why Delta is so dangerous</a><br />
<a href="https://theconversation.com/swimming-gives-your-brain-a-boost-but-scientists-dont-know-yet-why-its-better-than-other-aerobic-activities-164297">Swimming gives your brain a boost – but scientists don’t know yet why it’s better than other aerobic activities</a><br />
<a href="https://www.chemistryworld.com/features/the-search-for-the-grand-unification-of-aromaticity/4013915.article">The search for the grand unification of aromaticity</a><br />
<a href="https://blogs.sciencemag.org/pipeline/archives/2021/07/23/more-protein-folding-progress-whats-it-mean">In the Pipeline | More Protein Folding Progress – What’s It Mean?</a><br />
<a href="https://www.nature.com/articles/d41586-021-02034-3">Nature | Single chip tests thousands of enzyme mutations at once</a><br />
<a href="https://slate.com/technology/2021/07/covid-delta-variant-risk-vaccinated-breakthrough-cases.html">The New COVID Panic</a><br />
<a href="https://nautil.us/issue/103/healthy-communication/heres-the-right-story-for-vaccine-holdouts">Here’s the Right Story for Vaccine Holdouts</a><br />
<a href="https://vimeo.com/208145716">1st Prize Short Climate Film Winner: “Three Seconds”</a><br />
<a href="https://www.nature.com/articles/d41586-021-01836-9">Nature | Why autoimmunity is most common in women</a><br />
<a href="https://hbr.org/2021/07/writing-can-help-us-heal-from-trauma">Writing Can Help Us Heal from Trauma </a></p>
<p><strong>Others</strong><br />
<a href="https://www.freecodecamp.org/news/how-to-automate-things-using-python">How to Automate Work Using Python</a><br />
<a href="https://hedgehogreview.com/web-features/thr/posts/field-notes-of-a-sentence-watcher">Field Notes of a Sentence Watcher</a><br />
<a href="https://themillions.com/2021/09/this-isnt-the-essays-title.html">This Isn’t the Essay’s Title</a><br />
<a href="https://lithub.com/when-c-s-lewis-reviewed-his-buddys-book-the-hobbit/">When C.S. Lewis Reviewed His Buddy’s Book… <em>The Hobbit</em></a><br />
<a href="https://3quarksdaily.com/3quarksdaily/2021/09/the-rotten-tomatoes-equation.html">The Rotten Tomatoes Equation</a><br />
<a href="https://www.theatlantic.com/health/archive/2021/09/how-tell-children-truth-about-cancer/620040/">Tell Children the Truth</a><br />
<a href="https://inventwithpython.com/bigbookpython/">The Big Book of Small Python Projects</a><br />
<a href="https://realpython.com/django-diary-project-python/">Build a Personal Diary With Django and Python</a><br />
<a href="https://kontinentalist.com/stories/the-sarong-and-gender-colonialism-in-asia">A sarong’s story</a><br />
<a href="https://www.newyorker.com/culture/personal-history/forgetting-my-first-language">Forgetting My First Language</a><br />
<a href="https://www.youtube.com/watch?v=dzWRHi-Bmuk">Kim Stanley Robinson: Remembering climate change … a message from the year 2071 | TED</a><br />
<a href="https://edition.cnn.com/2021/09/06/health/love-job-you-hate-wisdom-project-wellness/">How to fix your job so that you love it, in three steps</a><br />
<a href="https://3quarksdaily.com/3quarksdaily/2021/09/kim-stanley-robinsons-global-catastrophe-epic-we-will-keep-going.html">Kim Stanley Robinson’s Global Catastrophe Epic: We Will Keep Going</a><br />
<a href="https://amp.theatlantic.com/amp/article/618219/">Growing My Faith in the Face of Death</a> <br />
<a href="https://www.ozy.com/the-new-and-the-next/the-joy-of-idle-living/440357/">The Joy Of Idle Living</a><br />
<a href="https://existentialcomics.com/comic/406">Socratic emergency</a><br />
<a href="https://www.theguardian.com/books/2021/aug/07/on-earth-4000-weeks-so-why-lose-time-online-distraction-oliver-burkeman">At best, we’re on Earth for around 4,000 weeks – so why do we lose so much time to online distraction?</a><br />
<a href="https://www.economist.com/1843/2021/08/03/why-satan-should-chair-your-meetings">Why Satan should chair your meetings</a><br />
<a href="https://www.artofmanliness.com/articles/men-without-chests/">Men Without Chests</a><br />
<a href="https://aeon.co/essays/why-is-the-english-spelling-system-so-weird-and-inconsistent">Typos, tricks and misprints</a><br />
<a href="https://jacobinmag.com/2021/07/slavoj-zizek-climate-change-global-warming-nature-ecological-crises-socialism-final-exit">Slavoj Žižek: Last Exit to Socialism</a></p>
<blockquote>
<p>the black mountain rises, a reference point<br />
to every human moment, utterly silent.<br />
No one climbs this mountain, there are no trails,<br />
because the place is holy: it does not exist to serve us,<br />
it is not meant to please us, it simply is,<br />
and in this way it is a god.<br /><br />
Mountains do not move, and that is their mountainness.<br />
– <a href="https://3quarksdaily.com/3quarksdaily/2021/09/friday-poem-268.html">Stephen Hollaway</a></p>
</blockquote>
<blockquote>
<p>It is as unscientific to blindly trust scientists as it is to dismiss them.<br />
– <a href="https://www.the-scientist.com/news-opinion/opinion-scientists-must-combat-scientific-dogmatism-69216">Opinion: Scientists Must Combat Scientific Dogmatism</a></p>
</blockquote>
<blockquote>
<p>“For it must be understood that this is a children’s book only in the sense that the first of many readings can be undertaken in the nursery. Alice is read gravely by children and with laughter by grown ups; The Hobbit, on the other hand, will be funnier to its youngest readers, and only years later, at a tenth or a twentieth reading, will they begin to realise what deft scholarship and profound reflection have gone to make everything in it so ripe, so friendly, and in its own way so true. Prediction is dangerous: but The Hobbit may well prove a classic.”<br />
– C.S. Lewis reviewing <em>The Hobbit</em>, The Times Literary Supplement, October 2, 1937</p>
</blockquote>
<blockquote>
<p>Is a flower beautiful?<br />
Is a fruit perhaps beautiful?<br />
No: they merely have color and form<br />
And existence.<br />
Beauty is the name given to something that does not exist<br />
The name I give to things in exchange for the pleasure they give me.<br />
It means nothing.<br />
So why do I say of things: “They’re beautiful”?<br />
– <a href="https://3quarksdaily.com/3quarksdaily/2021/09/friday-poem-267.html">Fernando Pessoa</a></p>
</blockquote>
<blockquote>
<p>Before 2.5 years, our brains are more fluid and plastic, enabling us to learn and adapt quickly, similar to the state of water flowing around obstacles. After 2.5 years, our brains are much more crystalline and frozen, still capable of learning and adapting but more like glaciers slowly pushing across a landscape. <br />
– <a href="https://aeon.co/essays/a-quantitative-theory-unlocks-the-mysteries-of-why-we-sleep">Why do we sleep?</a></p>
</blockquote>
<blockquote>
<p>Several supervillains have higher degrees—why don’t you?<br />
– <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1009276">PLOS Comp Biol | Ten simple rules for aspiring graduate students</a></p>
</blockquote>
<blockquote>
<p>Richard Feynman, in a lecture entitled “There’s plenty of room in the bottom: An invitation to enter a new field of physics” at the annual American Physical Society Meeting at Caltech on December 29, 1959, suggested that tiny, nanoscale machines could be constructed by manipulating individual atoms. Proteins are precisely such machines.<br />
– <a href="https://journals.aps.org/pre/abstract/10.1103/PhysRevE.104.014402">Phys Rev E | Building blocks of protein structures: Physics meets biology</a>
<!--
Have you ever thought of the perfect quip or comeback after it didn’t matter—a minute, hour, or day after your conversation has ended?
Well, there’s a name for that phenomenon. It’s called l’esprit de l’escalier, or the spirit of the staircase, and refers to the perfect retort that arises at the wrong time.
-- [The Secret to Being Witty, Revealed](https://getpocket.com/explore/item/the-secret-to-being-witty-revealed)
--></p>
</blockquote>Yossa Dwi HartonoPapers Production of Rainbow Colorants by Metabolically Engineered Escherichia coli NLDock: a Fast Nucleic Acid–Ligand Docking Algorithm for Modeling RNA/DNA–Ligand Complexes Natural and Synthetic Cannabinoids: Pharmacology, Uses, Adverse Drug Events, and Drug Interactions Fifteen quick tips for success with HPC, i.e., responsibly BASHing that Linux cluster Science Agroecology Is the Solution to World Hunger PHD Comics | The COVID-19 virus (SARS-CoV-2) explained How a ‘fatally, tragically flawed’ paradigm has derailed the science of obesity Mechanisms of Long COVID Remain Unknown but Data Are Rolling In SARS-CoV-2’s Wide-Ranging Effects on the Body Was that wild weather caused by climate change? Scientists can now say ‘yes’ with confidence Sorry, Skeptics: New IPCC Report Provides Unprecedented Clarity About Earth’s Climate Nature | How the coronavirus infects cells — and why Delta is so dangerous Swimming gives your brain a boost – but scientists don’t know yet why it’s better than other aerobic activities The search for the grand unification of aromaticity In the Pipeline | More Protein Folding Progress – What’s It Mean? Nature | Single chip tests thousands of enzyme mutations at once The New COVID Panic Here’s the Right Story for Vaccine Holdouts 1st Prize Short Climate Film Winner: “Three Seconds” Nature | Why autoimmunity is most common in women Writing Can Help Us Heal from Trauma Others How to Automate Work Using Python Field Notes of a Sentence Watcher This Isn’t the Essay’s Title When C.S. Lewis Reviewed His Buddy’s Book… The Hobbit The Rotten Tomatoes Equation Tell Children the Truth The Big Book of Small Python Projects Build a Personal Diary With Django and Python A sarong’s story Forgetting My First Language Kim Stanley Robinson: Remembering climate change … a message from the year 2071 | TED How to fix your job so that you love it, in three steps Kim Stanley Robinson’s Global Catastrophe Epic: We Will Keep Going Growing My Faith in the Face of Death The Joy Of Idle Living Socratic emergency At best, we’re on Earth for around 4,000 weeks – so why do we lose so much time to online distraction? Why Satan should chair your meetings Men Without Chests Typos, tricks and misprints Slavoj Žižek: Last Exit to Socialism the black mountain rises, a reference point to every human moment, utterly silent. No one climbs this mountain, there are no trails, because the place is holy: it does not exist to serve us, it is not meant to please us, it simply is, and in this way it is a god. Mountains do not move, and that is their mountainness. – Stephen Hollaway It is as unscientific to blindly trust scientists as it is to dismiss them. – Opinion: Scientists Must Combat Scientific Dogmatism “For it must be understood that this is a children’s book only in the sense that the first of many readings can be undertaken in the nursery. Alice is read gravely by children and with laughter by grown ups; The Hobbit, on the other hand, will be funnier to its youngest readers, and only years later, at a tenth or a twentieth reading, will they begin to realise what deft scholarship and profound reflection have gone to make everything in it so ripe, so friendly, and in its own way so true. Prediction is dangerous: but The Hobbit may well prove a classic.” – C.S. Lewis reviewing The Hobbit, The Times Literary Supplement, October 2, 1937 Is a flower beautiful? Is a fruit perhaps beautiful? No: they merely have color and form And existence. Beauty is the name given to something that does not exist The name I give to things in exchange for the pleasure they give me. It means nothing. So why do I say of things: “They’re beautiful”? – Fernando Pessoa Before 2.5 years, our brains are more fluid and plastic, enabling us to learn and adapt quickly, similar to the state of water flowing around obstacles. After 2.5 years, our brains are much more crystalline and frozen, still capable of learning and adapting but more like glaciers slowly pushing across a landscape. – Why do we sleep? Several supervillains have higher degrees—why don’t you? – PLOS Comp Biol | Ten simple rules for aspiring graduate students Richard Feynman, in a lecture entitled “There’s plenty of room in the bottom: An invitation to enter a new field of physics” at the annual American Physical Society Meeting at Caltech on December 29, 1959, suggested that tiny, nanoscale machines could be constructed by manipulating individual atoms. Proteins are precisely such machines. – Phys Rev E | Building blocks of protein structures: Physics meets biologySemi-automating Mailchimp daily newsletter2021-08-25T00:00:00+08:002021-08-25T00:00:00+08:00https://yossadh.github.io/posts/2021/08/mailchimp<p>I am in charge of uploading a Mailchimp daily email newsletter. Here is some code to pre-fill everything except the content utilising Mailchimp API.
Technically you can automate the content upload, too, but it requires more html-fu than I have.</p>
<p>First, a setup:</p>
<div class="language-python highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="kn">from</span> <span class="nn">mailchimp_marketing</span> <span class="kn">import</span> <span class="n">Client</span>
<span class="kn">import</span> <span class="nn">mailchimp_marketing</span> <span class="k">as</span> <span class="n">MailchimpMarketing</span>
<span class="kn">from</span> <span class="nn">mailchimp_marketing.api_client</span> <span class="kn">import</span> <span class="n">ApiClientError</span>
<span class="kn">import</span> <span class="nn">pprint</span>
<span class="n">pp</span> <span class="o">=</span> <span class="n">pprint</span><span class="p">.</span><span class="n">PrettyPrinter</span><span class="p">(</span><span class="n">indent</span><span class="o">=</span><span class="mi">4</span><span class="p">)</span>
<span class="kn">from</span> <span class="nn">datetime</span> <span class="kn">import</span> <span class="n">datetime</span>
<span class="kn">from</span> <span class="nn">datetime</span> <span class="kn">import</span> <span class="n">timedelta</span>
<span class="kn">import</span> <span class="nn">dateutil.parser</span>
<span class="k">def</span> <span class="nf">convert_list_of_campaigns_to_id_title_dict</span><span class="p">(</span><span class="n">r</span><span class="p">):</span>
<span class="n">id_title_dict</span> <span class="o">=</span> <span class="p">{}</span>
<span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">r</span><span class="p">[</span><span class="s">'campaigns'</span><span class="p">]:</span>
<span class="n">id_title_dict</span><span class="p">[</span><span class="n">i</span><span class="p">[</span><span class="s">'id'</span><span class="p">]]</span> <span class="o">=</span> <span class="n">i</span><span class="p">[</span><span class="s">'settings'</span><span class="p">][</span><span class="s">'title'</span><span class="p">]</span>
<span class="k">return</span> <span class="nb">dict</span><span class="p">(</span><span class="nb">sorted</span><span class="p">(</span><span class="n">id_title_dict</span><span class="p">.</span><span class="n">items</span><span class="p">(),</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">item</span><span class="p">:</span> <span class="n">item</span><span class="p">[</span><span class="mi">1</span><span class="p">]))</span>
<span class="n">api_key</span> <span class="o">=</span> <span class="s">"YOUR_API_KEY"</span>
<span class="n">server_prefix</span> <span class="o">=</span> <span class="s">"YOUR_SERVER_PREFIX"</span>
<span class="n">client</span> <span class="o">=</span> <span class="n">MailchimpMarketing</span><span class="p">.</span><span class="n">Client</span><span class="p">()</span>
<span class="n">client</span><span class="p">.</span><span class="n">set_config</span><span class="p">({</span>
<span class="s">"api_key"</span><span class="p">:</span> <span class="n">api_key</span><span class="p">,</span>
<span class="s">"server"</span><span class="p">:</span> <span class="n">server_prefix</span>
<span class="p">})</span>
</code></pre></div></div>
<p>Extract some info from an existing campaign that has the same parameters as the ones you are automating.
Use pretty print to save your eyes. For my newsletter, I look for:</p>
<ul>
<li><code class="language-plaintext highlighter-rouge">list_id</code></li>
<li><code class="language-plaintext highlighter-rouge">list_name</code></li>
<li><code class="language-plaintext highlighter-rouge">template_id</code></li>
</ul>
<div class="language-python highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="c1"># Count is the number of campaigns returned
</span><span class="n">r</span> <span class="o">=</span> <span class="n">client</span><span class="p">.</span><span class="n">campaigns</span><span class="p">.</span><span class="nb">list</span><span class="p">(</span><span class="n">count</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
<span class="n">pp</span><span class="p">.</span><span class="n">pprint</span><span class="p">(</span><span class="n">r</span><span class="p">)</span>
</code></pre></div></div>
<p>Then we are ready to create the campaigns.
Create a date:title dict first. My campaign title is just YYYYMMDD date, so my dict looks like this:</p>
<div class="language-python highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="n">titles</span> <span class="o">=</span><span class="p">{</span>
<span class="s">'0901'</span><span class="p">:</span><span class="s">'lorem'</span><span class="p">,</span>
<span class="s">'0902'</span><span class="p">:</span><span class="s">'ipsum'</span><span class="p">,</span>
<span class="s">'0903'</span><span class="p">:</span><span class="s">'dolor'</span><span class="p">,</span>
<span class="p">}</span>
<span class="c1"># create campaigns
</span><span class="k">for</span> <span class="n">date</span> <span class="ow">in</span> <span class="n">titles</span><span class="p">:</span>
<span class="n">client</span><span class="p">.</span><span class="n">campaigns</span><span class="p">.</span><span class="n">create</span><span class="p">({</span>
<span class="s">"type"</span><span class="p">:</span> <span class="s">"regular"</span><span class="p">,</span>
<span class="s">'recipients'</span><span class="p">:</span> <span class="p">{</span><span class="s">'list_id'</span><span class="p">:</span> <span class="s">'YOUR_LIST_ID'</span><span class="p">,</span>
<span class="s">'list_is_active'</span><span class="p">:</span> <span class="bp">True</span><span class="p">,</span>
<span class="s">'list_name'</span><span class="p">:</span> <span class="s">'YOUR_RECIPIENT_LIST'</span><span class="p">,</span>
<span class="s">'segment_text'</span><span class="p">:</span> <span class="s">''</span><span class="p">,</span>
<span class="p">},</span>
<span class="s">'settings'</span><span class="p">:</span> <span class="p">{</span><span class="s">'subject_line'</span><span class="p">:</span> <span class="s">"MY DAILY NEWSLETTER – "</span><span class="o">+</span><span class="n">titles</span><span class="p">[</span><span class="n">date</span><span class="p">],</span>
<span class="s">'title'</span><span class="p">:</span> <span class="s">"2021"</span><span class="o">+</span><span class="n">date</span><span class="p">,</span> <span class="s">'from_name'</span><span class="p">:</span> <span class="s">'YOUR_NAME'</span><span class="p">,</span>
<span class="s">'reply_to'</span><span class="p">:</span> <span class="s">'YOUR_EMAIL'</span><span class="p">,</span>
<span class="s">'to_name'</span><span class="p">:</span> <span class="s">'*|FNAME|* *|LNAME|*'</span><span class="p">,</span>
<span class="s">'template_id'</span><span class="p">:</span> <span class="n">YOUR_TEMPLATE_ID</span><span class="p">,},</span>
<span class="p">})</span>
</code></pre></div></div>
<p>Now let’s schedule the campaigns. Create a campaign_id:title dict, then just loop over it:</p>
<div class="language-python highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="c1"># fetch all unscheduled campaigns (status='save')
</span><span class="n">r</span> <span class="o">=</span> <span class="n">client</span><span class="p">.</span><span class="n">campaigns</span><span class="p">.</span><span class="nb">list</span><span class="p">(</span><span class="n">fields</span><span class="o">=</span><span class="p">[</span><span class="s">'campaigns.id'</span><span class="p">,</span><span class="s">'campaigns.settings.title'</span><span class="p">],</span><span class="n">status</span><span class="o">=</span><span class="s">'save'</span><span class="p">,</span><span class="n">count</span><span class="o">=</span><span class="mi">50</span><span class="p">)</span>
<span class="c1"># check that output is only your campaigns (there might be other saved drafts from the past)
</span><span class="n">pp</span><span class="p">.</span><span class="n">pprint</span><span class="p">(</span><span class="n">r</span><span class="p">)</span>
</code></pre></div></div>
<div class="language-python highlighter-rouge"><div class="highlight"><pre class="highlight"><code><span class="c1"># convert output to dict
</span><span class="n">to_schedule</span> <span class="o">=</span> <span class="n">convert_list_of_campaigns_to_id_title_dict</span><span class="p">(</span><span class="n">r</span><span class="p">)</span>
<span class="c1"># schedule. Here the timing that I want is actually 1 day before the date in the title
</span><span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">to_schedule</span><span class="p">:</span>
<span class="c1"># send_date = title_date minus 24hr
</span> <span class="n">a</span> <span class="o">=</span> <span class="n">dateutil</span><span class="p">.</span><span class="n">parser</span><span class="p">.</span><span class="n">isoparse</span><span class="p">(</span><span class="s">'2021-09-'</span><span class="o">+</span><span class="n">schedule</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="o">-</span><span class="mi">2</span><span class="p">:]</span><span class="o">+</span><span class="s">'T16:15:00+00:00'</span><span class="p">)</span>
<span class="n">send_date</span> <span class="o">=</span> <span class="n">a</span> <span class="o">+</span> <span class="n">timedelta</span><span class="p">(</span><span class="n">days</span><span class="o">=-</span><span class="mi">1</span><span class="p">)</span>
<span class="n">client</span><span class="p">.</span><span class="n">campaigns</span><span class="p">.</span><span class="n">schedule</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="p">{</span><span class="s">"schedule_time"</span><span class="p">:</span> <span class="n">send_date</span><span class="p">.</span><span class="n">isoformat</span><span class="p">()})</span>
<span class="c1"># client.campaigns.unschedule(i) # unschedule with this if you made a mistake
</span></code></pre></div></div>Yossa Dwi HartonoI am in charge of uploading a Mailchimp daily email newsletter. Here is some code to pre-fill everything except the content utilising Mailchimp API. Technically you can automate the content upload, too, but it requires more html-fu than I have.On _The Plague_2021-07-27T00:00:00+08:002021-07-27T00:00:00+08:00https://yossadh.github.io/posts/2021/07/plague<p>In the beginning of the pandemic, commentaries on Albert Camus’ <em>The Plague</em> (1947) mushroomed and the book sale went up, for obvious reasons. I, too, joined this train, reserving the book from the library. In a somewhat ironic meta-allegory of the pandemic though, I read it halfway, and due to no loan extension because somebody else reserved it, gave up on it. Don’t my languid lockdown reading pace, and the helplessness of it, reflect the general gloomy pandemic mood, a little bit?</p>
<p>This year, somewhat reinvigorated, I obtained the book again and restarted and finished it.</p>
<p>One thing that I noticed is the uncanny parallel of the lockdown of the city of Oran due to the plague, and our own restrictions. Oh, there is nothing new under the sun, like the Preacher said. People’s denial in the beginning; lockdown fatigue; obsessions with the numbers of cases and death, then getting numbed by it; “….the only certitude they have in common–love, exile, suffering”.</p>
<blockquote>
<p>…in a sense, disease is the only real actor here.<br />
<a href="https://www.latimes.com/entertainment-arts/books/story/2020-03-23/reading-camu-the-plague-amid-coronavirus">– LA Times article</a></p>
</blockquote>
<p>The other thing that was striking in the book was the plague just… happens? What I mean is, it just strikes like the force of nature it is, strangely in absence of malice. The LA times puts it like this: “There is no anger or bitterness in this book, only an immense spirit of forbearance and pity.” Now that I am inside the story of current pandemic reality, I feel that way towards SARS-CoV-2 to some extent. It is just a nanomachine; it has no animosity. Yet, yet: It gives us the trolley problem of either killing the economy or killing by infection. But, but: it has no agency.</p>
<blockquote>
<p>This god loves the virus as much as the child.<br />
<a href="https://www.thesunmagazine.org/issues/400/ode-to-the-god-of-atheists">– <em>Ode To The God Of Atheists</em></a></p>
</blockquote>
<p>I think, a point that is always in the air in these commentaries, but is never really brought to the forefront, is the message of hope. Of humanity surely – the narrator: “there are more things to admire in men than to despise” – but I’m talking about beyond. It is understandable though: Camus himself was a non-believer. But I cannot help but think, when I reached the end of the book, that, ah, I’m lucky I’m outside this book, with this, if you like, God-like view, and I know in the end the plague dissipates.</p>
<p>Even if you don’t believe in God, I would think you will draw a little consolation from the fictive distance. When I started reading, I did not know that the ending would be hopeful, but I carried on reading anyway, because I know I am not inside the story: I can think, feel, empathise safely; the plague has no power on me. But, since I am a believer, I take consolation one step further. Like the reader me, I believe that God is standing in eternity, outside the book of time, and He knows the ending.</p>Yossa Dwi HartonoIn the beginning of the pandemic, commentaries on Albert Camus’ The Plague (1947) mushroomed and the book sale went up, for obvious reasons. I, too, joined this train, reserving the book from the library. In a somewhat ironic meta-allegory of the pandemic though, I read it halfway, and due to no loan extension because somebody else reserved it, gave up on it. Don’t my languid lockdown reading pace, and the helplessness of it, reflect the general gloomy pandemic mood, a little bit?It is Wednesday2021-07-14T00:00:00+08:002021-07-14T00:00:00+08:00https://yossadh.github.io/posts/2021/07/wed<p>The sky cried her heart out<br />
tempestuously on Monday<br />
On Tuesday morning <br />
the tears kept falling<br />
percolating the slumbered<br />
It has slowed to rare droplets now<br />
But I wonder: <br />
with your grey countenance<br />
Do you still have more <br />
sadness to pour out?<br /></p>
<p>It is a gloomy day. The new COVID-19 cases today in the world is 208k, more than 1/4 of which are from Indonesia.
Singapore experienced a steep surge after a lull as well.</p>
<p>Here is another verse of consolation (<a href="https://en.wikipedia.org/wiki/Do_Not_Stand_at_My_Grave_and_Weep">source</a>):</p>
<p>Do not stand<br />
By my grave, and weep.<br />
I am not there,<br />
I do not sleep—<br />
I am the thousand winds that blow<br />
I am the diamond glints in snow<br />
I am the sunlight on ripened grain,<br />
I am the gentle, autumn rain.<br />
As you awake with morning’s hush,<br />
I am the swift, up-flinging rush<br />
Of quiet birds in circling flight,<br />
I am the day transcending night.<br />
Do not stand<br />
By my grave, and cry—<br />
I am not there,<br />
I did not die.<br /></p>
<p>Man Arai, a Japanese composer, <a href="https://music.apple.com/us/album/%E5%8D%83%E3%81%AE%E9%A2%A8%E3%81%AB%E3%81%AA%E3%81%A3%E3%81%A6-a-thousand-winds-ep/279130943">set a melody to this verse</a>, and here are some other sung versions:<br />
<a href="https://www.youtube.com/watch?v=t7ybl0aHo6I">By Hayley Westenra in English</a><br />
<a href="https://www.youtube.com/watch?v=U6oKoT_Zwwg">By Paul Kim in Korean</a>. The Korean version was also often sung as a tribute of the 2014 Sewol ferry accident.</p>Yossa Dwi HartonoThe sky cried her heart out tempestuously on Monday On Tuesday morning the tears kept falling percolating the slumbered It has slowed to rare droplets now But I wonder: with your grey countenance Do you still have more sadness to pour out? It is a gloomy day. The new COVID-19 cases today in the world is 208k, more than 1/4 of which are from Indonesia. Singapore experienced a steep surge after a lull as well. Here is another verse of consolation (source): Do not stand By my grave, and weep. I am not there, I do not sleep— I am the thousand winds that blow I am the diamond glints in snow I am the sunlight on ripened grain, I am the gentle, autumn rain. As you awake with morning’s hush, I am the swift, up-flinging rush Of quiet birds in circling flight, I am the day transcending night. Do not stand By my grave, and cry— I am not there, I did not die. Man Arai, a Japanese composer, set a melody to this verse, and here are some other sung versions: By Hayley Westenra in English By Paul Kim in Korean. The Korean version was also often sung as a tribute of the 2014 Sewol ferry accident.