Yossa Dwi Hartono

Yossa Dwi Hartono

Computational Biologist / Structural Bioinformatician

Link roundup: Jun 2019

1 minute read

Published:

Science
Inside the ‘secret underground lair’ where scientists are searching the galaxies
23 ‘facts’ you learned about healthy eating and nutrition as a kid that are no longer true
Pop Sci | The 10 worst insect stings in the wild
The Scientist | Could Tolerating Disease Be Better than Fighting It?
In the Pipeline | A New Way For the Machines To Handle Reagents

For those in the crowd who aren’t synthetic chemists, it cannot be emphasized enough that there is no way that you could have known about either of these choices beforehand – and that if you change the reaction to another bromo-heterocyclic system, the optimal base and solvent are likely to switch again to something else entirely. It’s as bad as cell culture or X-ray crystal growing, two other areas that are famously infested with evil spirits and voodoo rituals. You run into these systems that are just intrinsically very sensitive to initial conditions, with variables that are sometimes too small or obscure for you to even realize that they’re variables.

Potassium hunting on protein factories
Biotech Cockaigne of the Vegan Hopeful
Quanta | Neuroscience Readies for a Showdown Over Consciousness Ideas
Physics Today | The mysterious crystal that melts at two different temperatures
TLS | Weighty matters
Nature | Reproducibility trial publishes two conclusions for one paper

Papers
PLoS Comp Bio | Open collaborative writing with Manubot

Others
The New Yorker | Liu Cixin’s War of the Worlds
How to Pick a Career (That Actually Fits You)
Book Review: The Secret Of Our Success
The Pu-erh Brokers of Yunnan Province
Aeon | A Revolution in Time

Leave a Comment

Your email address will not be published. Required fields are marked *

Markdown is supported.

You May Also Enjoy

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?

2021 book list

1 minute read

Published:

Compared 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.