Yossa Dwi Hartono

Yossa Dwi Hartono

Computational Biologist / Structural Bioinformatician

Link roundup: Dec 2018

1 minute read

Published:

Science
TED talk | Hans and Ola Rosling: How not to be ignorant about the world Classic Hans Rosling TED talk [via 3 Quarks Daily]
Nautilus | Iron Is the New Cholesterol Donate blood, people!
In the Pipeline | We Have Given People Amyloid Disease
Kurt Gödel and the romance of logic
Nature | Enzymes engineered to trap reaction intermediates with link to the paper therein
The Scientist | Scientists Don’t Stay for Long in Their Jobs Anymore: Study
What’s the Most Dangerous Food of All Time?
Synthetic biology: A call for a new culture of responsibility
Science | Chess, a Drosophila of reasoning
The Scientist | Book Excerpt from Gene Machine “…author Venki Ramakrishnan relays the moment when he and collaborators finally solved the structure of a ribosomal subunit.”
The Atlantic | The CRISPR Baby Scandal Gets Worse by the Day
Popular Science | Cannabis gets its high-inducing power from ancient viruses
Paper
BMJ | Key opinion leaders’ guide to spinning a disappointing clinical trial result [via In the Pipeline]
Science | Molecular to organismal chirality is induced by the conserved myosin 1D [via In the Pipeline]
Proc. R. Soc. London, Ser. A | The origins of quantum biology A nice historical review
J Med Chem | qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps
Nature | Mannose impairs tumour growth and enhances chemotherapy [via In the Pipeline]
J Med Chem | Two Decades under the Influence of the Rule of Five and the Changing Properties of Approved Oral Drugs
Others
Aeon | Who decides what words mean [via Language Log]
Graphical vi-vim Cheat Sheet and Tutorial
The Atlantic | The World’s Most Efficient Languages

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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

Published:

Science
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

1 minute read

Published:

Science
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

2 minute read

Published:

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

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?