Yossa Dwi Hartono

Yossa Dwi Hartono

Computational Biologist / Structural Bioinformatician

Link roundup: Oct–Dec 2020

4 minute read

Published:

The world came into a standstill in March, including this blog. Here’s to a restart.

Papers
Science | Genetic interaction mapping informs integrative structure determination of protein complexes
Chem Sci | Ligand design by targeting a binding site water
Sci. Rep | Statistics for the analysis of molecular dynamics simulations: providing P values for agonist-dependent GPCR activation
Science | Protein storytelling through physics Nice general MD review
J Med Chem | Chemists: AI Is Here; Unite To Get the Benefits
Sci. Rep | Moving targets in drug discovery

Science
In the Pipeline | The New Mutations
It occurred to me that I’m trying to introduce mutations to my enzyme and here is the virus doing just that using the world as its test tube…What do you call this? Poignant? Amusing? Ironic?
The Atlantic | How COVID-19 Changes Our Sleep
The Atlantic | How Science Beat the Virus
Nature | The peanut snack that triggered a fresh approach to allergy prevention
How the novel coronavirus has evolved
Nature | Oxford COVID vaccine paper highlights lingering unknowns about results
PyCaret: Useful ML tool for chemoinformatics #chemoinformatics #RDKit #Machine learning
Nature | How to write a superb literature review
In the Pipeline | Get Ready for False Side Effects
Sci Am | The COVID Science Wars
Helen Berman: the crystallographer who pioneered the Protein Data Bank
Nautilus | Kim Stanley Robinson Holds Out Hope
Nature | Postdoc survey reveals disenchantment with working life
‘disenchantment’ is a curious diction… I suppose many of us have been charmed by the wizards of the ivory tower.
Life with purpose
Nature | Why your scientific presentation should not be adapted from a journal article
COVID-19 Molecular Structure and Therapeutics Hub
In the Pipeline | Vaccine Possibilities
SciAm | Mysteries of COVID Smell Loss Finally Yield Some Answers
Nature | Five rules for evidence communication
meta, biomedical research search engine
Nature | Science search engine links papers to grants and patents
C&EN | Covalent drugs go from fringe field to fashionable endeavor
In the Pipeline | Vaccine Efficacy Data!
How can climate be predictable if weather is chaotic?
brainpickings | Tenacity, the Art of Integration, and the Key to a Flexible Mind: Wisdom from the Life of Mary Somerville, for Whom the Word “Scientist” Was Coined
The New Yorker | How the Coronavirus Hacks the Immune System

Others
Educated Fools: Why Democratic leaders still misunderstand the politics of social class
Beyond Tokyo and Jerusalem Shusaku Endo’s Silence review
Yo-Yo Ma, Kathryn Stott - Over the Rainbow (Official Video)
LARB | Of Course They Would: On Kim Stanley Robinson’s “The Ministry for the Future”
Thesis Whisperer | While you scream inside your heart, please keep working.
Do Elephants Have Souls?
Huawei, 5G, and the Man Who Conquered Noise
Wired | Remembrance
How to have a difficult conversation
Twitter magic realism bot
See a Stunningly Surreal Bookstore in China

Python
Top 11 Github Repositories to Learn Python
github.com/TomNicholas/Python-for-Scientists
github.com/garrettj403/SciencePlots
github.com/rasbt/python_reference
github.com/matplotlib/AnatomyOfMatplotlib
github.com/jerry-git/learn-python3

Do you need a little darkness to get you going? –Mary Oliver

He adopted the following strategy: say what you know; what you don’t know; what you are doing to find out; what people can do in the meantime to be on the safe side; and that advice will change –Nature article

In my work as a mediator, I’ve learnt that successful conversations always involve what I call a ‘gem statement’. When two parties have listened long and hard to each other – have made the heroic effort to listen curiously and empathically even when they disagree strenuously – someone eventually unearths a glowing, priceless gem. It usually takes the form of a short, powerful statement –How to have a difficult conversation

aside from faith,
as far as you know,
you will never have another heart.
better to grow the one you were born with.
–Anahata, by Lenelle Moïse

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Link roundup: 2024

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Chaos and cause

To fully appreciate what this means, heed a lesson from Fyodor Dostoyevsky’s great novel, The Brothers Karamazov (1880), which asks how a benevolent God could allow suffering. There is just one virtuous character in the novel, the monk Father Zosima, whose simple teaching, dictated through the genius of Dostoyevsky, sheds light on chaos, causation and difference-making:

See, here you have passed by a small child, passed by in anger, with a foul word, with a wrathful soul; you perhaps did not notice the child, but he saw you, and your unsightly and impious image has remained in his defenceless heart. You did not know it, but you may thereby have planted a bad seed in him, and it may grow, and all because you did not restrain yourself before the child, because you did not nurture in yourself a heedful, active love … for one ought to love not for a chance moment but for all time. Anyone, even a wicked man, can love by chance. My young brother asked forgiveness of the birds: it seems senseless, yet it is right, for all is like an ocean, all flows and connects; touch it in one place and it echoes at the other end of the world.

Link roundup: Jan–Jun 2023

less than 1 minute read

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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 2022

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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 2022

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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”.

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

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Dual use of artificial-intelligence-powered drug discovery
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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
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https://github.com/csinva/imodels
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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?