# Blog posts

## 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 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

## 2021 book list

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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.

## 2021

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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.
“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

## Splitting a row of matplotlib subplots to columns

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Case: I have many rows of subplots and would like to divide them up in multiple columns

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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 biology

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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.

## On The Plague

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In 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 Wednesday

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The 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:
Do you still have more

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.

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Others
The project finishing mindset
The pervasive problem of ‘linguistic racism’
What friends are for Sci-fi short story
Prometheus’ Toolbox
The k-Nearest Neighbors (kNN) Algorithm in Python
The Power of Writing by Hand
Scikit-learn Crash Course - Machine Learning Library for 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

## Thaxted

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I first heard the hymnal tune Thaxted in Corrinne May’s The answer. Her lyrics is a simple psalmic consolation, and paired with the simple tune, it proves to be indelible. The Methodist church I was worshipping at had it sung in the service a number of times.

## ‘This is not a post’ post

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Magritte’s “This is not a pipe” painting is one of Douglas Hofstadter’s obsessions in Gödel, Escher, Bach: An Eternal Golden Braid. It may be a Treachery of images like the title suggests, but it is also about the treachery of language, the self-referential nature that Hofstadter calls ‘a strange loop’. For example, the famous “This sentence is not true”, a variant of liar’s paradox. If the statement is true, then it’s “not true”. If the statement is false, then it’s negated so that the falsity is “not true”. It is something that continues to endlessly boggle the mind. One might think it is a philosopher’s fancy – that, it may be – but consider that Gödel’s incompleteness theorems need that self-reference as a foundation. I concede that it is not something that may affect our daily lives, but, you know, it can make one ponder about computability, the nature of consciousness, and stuff.

Now, I have observed this self-reference in some objects, though I don’t suppose the manufacturers have the nature of consciousness in mind. Behold, the “this is not a safety barrier” safety barricade and the “this is not a lifesaving device” kickboard. You can see that these two things do not have identity crises: it’s actually the very opposite; ‘they’ are certainly sure about their functions. The safety barricade: I can function as a safety barrier, but not 100% of the time. Similarly, the kickboard: I can function as a lifesaving device, but not 100% of the time. You can almost hear the echoes of the underlying subtext (so don’t sue me), can’t you?

You can ponder this more while looking at my terrible drawing:

NB: I found it highly amusing that the safety barricade is embossed/printed/stenciled/stickered with “This is not a safety barrier”, but spray-painted with “SB”. That is one way to solve the linguistic and legalistic quandary I suppose: “It’s not a safety barrier; it is just, you know, SB”.

## Documentation episode

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Software developers know this already but when working on the latest publication recently, I was reminded that we should document obsessively.

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## 2020 book list

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Hopefully in 2020 I will read even more!

## 2020

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

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

## On efficacy

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The term efficacy is not new for the drug industry people, but of course it has now entered the public consciousness thanks to the vaccine efforts. As Carl Zimmer pointed out, our intuitive understanding of “95% effectiveness” is that 95 out of 100 people who get the vaccine will be immune.

As you might already know, it’s not exactly that. That number means that out of certain number of symptomatic, PCR-positive participants, the placebo arm has 95% more than the vaccinated arm, where vaccine:placebo population is 1:1. Taking the numbers from the NY Times article, Pfizer waited until they had 170 cases (for statistical power): 162 in placebo, 8 in vaccine. If vaccine:placebo populations are exactly 1:1, the denominators all cancel out and efficacy = (162-8)/162 = 95%. Even if it is not exactly 1:1, usually it is close to that, so this is a good shortcut for quick calculation. For exact figure, just replace the absolute numbers as fraction in that arm instead – see how the denominators cancel out when a=b :

$\Large&space;\text{Efficacy}=\frac{\frac{162}{a}-\frac{8}{b}}{\frac{162}{a}}$

So, efficacy is a proxy for the eventual effectiveness. The former is in controlled clinical trial setting, while the latter is in messy real word setting. Some points on why there will be discrepancy between the 2:

• Clinical trial population is biased – only certain kind of people would volunteer for the trial. You can expect that they usually are healthy and do not have underlying conditions. Behaviour-wise, they would tend to be more cautious as well.
• Blinding is imperfect. Some people get mild reactions from the vaccine, which sort of tell you that you are in the vaccine arm.
• Asymptomatic cases are not accounted for. The participants are not tested regularly. Instead, they are only tested when they self-report symptoms. This is the case for Moderna trials. AZ-Oxford does weekly swabs so they have data about asymptomatic cases as well.

## Markov state models

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I’m trying to learn Markov state models for my MD analysis. I will put thoughts and notes here.

## Notes from #whisperfest 2020

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I’ve been following Inger Mewburn’s blog The Thesis Whisperer since my PhD days. She and “The Whisper Collective” is organising a conference this year and I’ve signed up for a couple of sessions. I will post some stuff that I learn in this post.

On The Reg live: podcasting with Inger Mewburn and Jason Downs
Should I have a website? (Tseen Khoo)
Soundtrap
Why podcast your research? (Lauren Gawne)
How to start your own podcast
Omnifocus
Narelle Lemon’s podcast, Teachers Supporting Teachers

Voices from the outside: Careers beyond academia
Times are bleak but don’t despair – just do stuff and meet people
mexec careers
Some tips:

• CV/Resume:
• 6 secs for recruiters to scan, and other things that we probably already know, but good to know why they do that
• Soft keywords – can be overused e.g. team player
• 3-4 pages
• Don’t use underlines, brackets
• footer with date
• save cover and CV together with filename NameLastDec2020.pdf (or .doc depending on req)

Why academia shouldn’t be a competition
No idea how to summarise this. I feel encouraged, I guess? This touches on some soft aspects of being an academic that I’m not used to evaluate for myself. I think one takeaway is the perennial metric-ising everything problem. On one hand, translating human beings into numbers is a sort of reductionism, but on the other, how else one is supposed to do evaluations and comparisons? Stuff that comes to mind and some that was brought up: IQ, uni ranking, being a good mentor, not being toxic, being a good colleague.

## Computational chemists in relation to experimental ones

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Here is a paper buried in my reading backlog, and I am pleasantly surprised that it has useful insights particularly for me.

Even though what the authors talk about is computational chemists and medicinal chemists in pharma research setting, I still learn some stuff applicable to my own role as computational chemists collaborating with experimental biologists mosts of the time. With the advent of AI, the authors then argue that the old dynamic must change.

There is a need for computational chemists to well delineate the limits of their techniques and set expectations reasonably and equally for medicinal chemists to both appreciate the bounds of what is on offer and also recognize that an equivalent evaluation of their own “hunches and predictions” might not perform any better.

## What is life, again

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I am excited to learn that Sir Paul Nurse has an upcoming book attempting to discuss this perennial question. The title is of course an homage to Schrödinger’s earlier treatise with the same title. I read that quite a while ago, and what was quite amazing was that it was written before the structure of DNA was known. I recall that I had attended a doctoral course with the same title as well. And the content was as broad as it suggests: the course coordinator invited outside speakers for talks, and often the talks were beyond mere biology, so it was a very interesting, thought-expanding, course.

The subtitle “Understanding biology in five steps” gives the central thesis: cells, genes, evolution, life as chemistry, life as information system. Information system is of course a very curious metaphor. Schrödinger was in the era of early computing – how does our understanding of life now look like when examined in parallel to modern computing?

Nurse has a 1-hour talk, which I watched with interest, so I am looking forward to read the book.

## Defining energy

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“How do you define energy?” is a question that would stump me. High school physics does not give satisfactory answer; it just gives the formula straight away. We know that it has to be of certain unit; and it fits the physics equations like such and such. Today I learned the more rigorous definition from Sabine Hossenfelder’s explainer video, but nagging me still, what is it, epistemologically?

I remember the first time I came to a similar reckoning was in chemistry lessons about electron orbitals. I was like “Huh these things are so weird how come they are like that?” and our chemistry teacher Mr A, who has philosophical penchant, just shrugged with an enigmatic smile, “That’s just what we observe them to be. These mathematical functions fit the observation.” Insert brain expansion meme here.

I have since seen many baffling things alike, especially in biology. We scientists keep pounding away at the what, what, what questions. Do we ask how and why enough? Should we? Should we not, because they are too difficult?

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Others
Divine Medicine

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## 2019

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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.

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## Conditional execution in bash

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Situation: You want to execute a script as soon as a particular file is created.

This is an easy one-liner:

# waiter.sh
# Usage: ./waiter.sh script_to_be_run file_to_anticipate [time_delay, def. 10 mins]
while [ ! -f $2 ]; do sleep${3-10m}; done; bash $1  The while loop keeps checking the existence of the specified file: while the file does not exist the loop will run sleep on and on. When the file exist, loop will be exited and the specified script will be run. Could it get any simpler? It seems like a waste just to continually check, but I don’t see a better option for now. (If you are wu liao run bash -x waiter.sh to see how many sleeps your waiter.sh has to go through to finally run your desired script.) One learning point – I was using this kind of thing before to make a positional argument optional: [ "$3" = "" ] && time_delay="15m" || time_delay=$3  This is a “ternary” bash construction, which you can construe as a shorthand conditional: A && B || C means “if A is true; execute B; else execute C”. Turns out the easier way is using shell parameter expansion magic: time_delay=${3-15m}  # if $3 is unset, set$3 to 15m
time_delay=${3:-15m} # if$3 is unset or null, set \$3 to 15m


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## Automated form-filling with Python

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Situation: You need to submit a lot of stuff to a website, but it only provides individual submission, not batch.

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I would make a distinction between temporary and certified assholes, because all of us under the wrong conditions can be temporary assholes. I’m talking about somebody who is consistently this way, who consistently treats other people this way. I think it’s more complicated than simply saying an asshole is someone who doesn’t care about other people. In fact, some of them really do care — they want to make you feel hurt and upset, they take pleasure in it.

… See, just get the government out of the way and everything starts to flourish! But as I’ve said many times, the FDA is not the real roadblock in this business. It’s biology. More specifically, it’s our lack of understanding of biology. Lowering standards will do nothing to help that at all.

Papers
ACS Chem Bio | Esterification Delivers a Functional Enzyme into a Human Cell
Q Rev Biophys | Frustration in Biomolecules 2014 paper, but I only read it recently. Besides providing a nice mental model of frustration in thinking about protein physics, the text is written in decidedly unacademic prose.
Nature | Complete biosynthesis of cannabinoids and their unnatural analogues in yeast
PLoS Comp Bio | Script of scripts: A pragmatic workflow system for daily computational research
This is like Makefile, but more user-friendly, you can switch languages easily, and is hosted in Jupyter notebook. If you constantly switch between bash, Python, R, and others; this is good to keep your workflow in one file. I think I don’t need it at the moment.
Others
Choosing our religion

Creation is thus seen as a relationship of radical dependence. To cite an insight deriving from St Thomas Aquinas, God’s creation of the world should not be likened to a carpenter making a chest. A better analogy would be more intimate – a singer producing a song, for instance. The difference is profound. Carpenter and chest are discrete entities. Carpenters can pass on the articles they make, never seeing them again. But a song is by definition an emanation of a singer.

A crucial difference between humans and other animals is equally plain. Genuinely fulfilled human lives involve further dimensions including dignity, which is connected with the exercise of choice; and virtue, implying the need to stretch or transcend ourselves. G. K. Chesterton wrote that it makes little sense to upbraid a lion for not being properly lion-like: lions are lions. The same is not true of human beings. People everywhere have a striking idea that they ought to behave in certain “humane” ways, but also an awareness that they do not in fact behave as they should. It is often noted that these two facts are the root of all clear thinking about ourselves and our world.

Did You Know Pandas Can Do So Much?
I find these Ruben Bolling’s illustrations amusing: 1 | 2
GQ | The Secrets of the World’s Greatest Art Thief
What We Owe a Rabbit
Regarding the Em Dash
A history of Singapore in 10 dishes

## Molecular similarity network with visualised structures

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Analogous to a Sequence Similarity Network (SSN), molecular similarity network visualises Tanimoto similarity between molecules. iwatobi shows how to construct one with molecular structures here and here using Python packages RDKit, networkx, and cyjupyter.

## Extracting sequence from PDB file

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There are times that you need the sequence of only the resolved amino acids in an X-ray crystal structure, not the full sequence of the construct. If you download the FASTA sequence or check the SEQRES record in the PDB file, you would only find the full sequence.

## How to persistently run your script with Bash

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This is a simple script that saves a lot of headaches for me. The situation: I’m running a proprietary software and it seems that there is a problem with the way our license server is setup, because from time to time the process will stop due to “not enough license” even though we have enough. Then we have to rerun, which is ok because there are checkpoint files, but it is a pain to constantly check whether my run has crashed or not.

## Swedish loanwords and pronunciation woes

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I’m reading Oliver Sacks’ Uncle Tungsten and was delighted to find out that tungsten is a Swedish loanword (lit. heavy stone). That got me revisited my list of Swedish loanwords we have in English, as well as some names that have become scientific terms.

## Automated area under the curve (AUC) calculation with Grace

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I wish I have an elegant solution for this like automated linear regression, but I don’t. This solution that I came up with is hacky, but it works.

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Our double task is now to preserve and foster both biological evolution as Nature designed it and cultural evolution as we invented it, trying to achieve the benefits of both, and exercising a wise restraint to limit the damage when they come into conflict. With biological evolution, we should continue playing the risky game that nature taught us to play. With cultural evolution, we should use our unique gifts of language and art and science to understand each other, and finally achieve a human society that is manageable if not always peaceful, with wildlife that is endlessly creative if not always permanent.

Nature | The ten commandments for learning how to code
The Atlantic | Scientists Are Totally Rethinking Animal Cognition
Nautilus | How the Biggest Fabricator in Science Got Caught
On one hand, it is good to pre-screen data with a statistical tool, but on the other, is it that hard to generate data that appears to be experimentally derived? I can imagine, instead of coming up with the numbers oneself, one could sample from a random number generator with specified distribution. How would one detect this sort of fraud?
Nautius | Why Misinformation Is About Who You Trust, Not What You Think
NY Times | Why Do South Asians Have Such High Rates of Heart Disease?

Studies show that at a normal body weight — generally considered a body mass index, or B.M.I., below 25 — people of any Asian ancestry, including those who are Chinese, Filipino and Japanese, have a greater likelihood of carrying this dangerous type of fat.

Eat Meat. Not Too Much. Mostly Monogastrics.

…a diet including chicken and pork, but no dairy or beef, has lower greenhouse gas emissions than a vegetarian diet that includes milk and cheese, and almost gets within spitting distance of a vegan diet.

All LSTABs face a dilemma. Politicians generally prefer direct answers to their questions. In other words, they want policy recommendations. They have been known to ask for ‘one-handed scientists’, so that they don’t have to hear ‘on the other hand’.

Borgwardt says the Korean study shows that tea has “a relatively strong effect”, on a par with that of 2.5 hours of exercise per week. Epidemiological studies suggest that long-term habitual consumption of green tea might reduce the risk of dementia. One study of people aged over 55 in Singapore, for example, found that those who drank as little as one cup of tea per week performed better at memory and information-processing tasks than did non-tea-drinkers2.

However, nearly two decades after the first predictions of dramatic success, we find no impact of the human genome project on the population’s life expectancy or any other public health measure, notwithstanding the vast resources that have been directed at genomics. Exaggerated expectations of how large an impact on disease would be found for genes have been paralleled by unrealistic timelines for success, yet the promotion of precision medicine continues unabated

“Twelve years until we all die” is catchier than “under some reasonable but debatable assumptions about economic growth, policy choices, and the physical climate sensitivity, the carbon budget to stay below the arbitrary threshold of a 1.5 degree C temperature increase relative to pre-industrial conditions appears to be exceeded by 2030”.

## Doing t-test in batch

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Situation: I want to do t-test between two sets of experiment A and B. Each A and B were run in triplicates, so we have:

data_A_1.dat
data_A_2.dat
data_A_3.dat
data_B_1.dat
data_B_2.dat
data_B_3.dat


How to run t-test between every combination of A and B, as well as all A combined vs all B combined?

## Plotting business: Automated linear regression with Grace

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What software do you use to plot?

## Formatting list of SMILES with bash scripting

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Here is a fun text manipulation exercise using bash you can do in less than an hour. Given that I have this text file, file.smi:

smiles1 some_id_abc
smiles2 some_id_xyz
...


I want to have it like this:

smiles1 C00000001
smiles2 C00000002
...


This was my real-world need of converting a list of SMILES to a format that is accepted by a conversion programme. Looks easy right?

## Book notes: On not speaking Chinese

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This book is quite different from my usual reading, which is mostly fiction, science-fiction, and popular science. This book is categorically a humanities book. In fact, some chapters were previously published in humanities journal. Nevertheless, I persevered through, since the subject is close to my heart (and my identity). Also, Ien Ang’s writing is not boring academic prose. It is certainly not easy reading, but it is very readable and her personal stake in the subject also helps. The book is an academic, yet also personal, essay.

## Simple web scraping with Python

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The situation: I wanted to extract chemical identifiers of a set of ~350 chemicals offered by a vendor to compare it to another list. Unfortunately, there is no catalog that neatly tabulates this information, but there is a product catalog pdf that has the list of product numbers. The detailed information of each product (including the chemical identifier) can be found in the vendor’s website like this: vendor.com/product/[product_no]. Let me show you how to solve this problem with bash and Python.

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Science
Nature | Can quantum ideas explain chemistry’s greatest icon?
Quizzes from Harvard’s The Music Lab If you have always suspected that you are tone deaf, have I got a quiz for you.
Nature | Extreme chemistry: experiments at the edge of the periodic table

This is somewhat as expected: the strength of chemical bonding tends to decrease down a periodic group, as atoms get larger. But to fully explain superheavies’ chemistry, Pershina’s calculations must also take into account relativistic effects. In very heavy atoms, which have super-strong interactions between the innermost electrons and the highly charged nuclei, the electrons are travelling so fast (potentially at more than 80% of the speed of light) that their mass increases, as special relativity predicts. This pulls them farther in towards the nucleus, which can mean that they screen the outer electrons from the nuclear charge more effectively. That alters the outer electrons’ energies and, consequently, their chemical reactivity.

Nature | Flying squirrels are secretly pink
Harvard Business Review | Time for Happiness
In the Pipeline | Exercise And Its Signaling
In the Pipeline | Quinine’s Target Quinine’s target has been identified. This is significant step in malaria research.
BBC | A bit of meat, a lot of veg - the flexitarian diet to feed 10bn
The Smithsonian | The Statistician Who Debunked Sexist Myths About Skull Size and Intelligence
PopSci | Saturn is ancient, but its rings are only as old as the dinosaurs
Nature | Watch: Robot reveals how ancient reptile ancestor moved It’s cool that they even make interactive demo
Nature | Cryptic DNA sequences may help cells survive starvation
In the Pipeline | Nivien’s Shot Drug research is hard
In the Pipeline | Come One, Come All to These Kinases.
Is Sunscreen the New Margarine?
Nature | Designer protein delivers signal of choice Layman summary of a new paper
The Conversation | The periodic table is 150 – but it could have looked very different
Science | Four lessons about transitioning from academia to the ‘real world’
Brain Pickings | Love After Life: Nobel-Winning Physicist Richard Feynman’s Extraordinary Letter to His Departed Wife
The Guardian | Why exercise alone won’t save us
The Scientist | Can Viruses in the Genome Cause Disease?
The Atlantic | Why Exaggeration Jokes Work
Wired | How a Reclusive Lizard Became a Prize Find for Wildlife Smugglers
3 Quarks Daily | The vast and mysterious real numbers
Paper
PLOS Comp Bio | Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures
Science | An enantioconvergent halogenophilic nucleophilic substitution (SN2X) reaction
Science | Porphyromonas gingivalis in Alzheimer’s disease brains: Evidence for disease causation and treatment with small-molecule inhibitors
PLOS Comp Biol | Ten simple rules on how to create open access and reproducible molecular simulations of biological systems
ACS Catalysis | Structure-Guided Triple-Code Saturation Mutagenesis: Efficient Tuning of the Stereoselectivity of an Epoxide Hydrolase
Cell Chem Bio | What Makes a Kinase Promiscuous for Inhibitors?
Nature | Enzymatic assembly of carbon–carbon bonds via iron-catalysed sp3 C–H functionalization
It’s nice to see that even though Frances Arnold just received the Nobel Prize, she is still actively publishing papers. Or maybe I notice just because I am on the lookout for publications on protein design ¯\_(ツ)_/¯
PNAS | Dietary sugar silences a colonization factor in a mammalian gut symbiont [via Scientific American]
Others
What Was It About Animorphs? I never finished reading Animorphs when I was a teenager because the library didn’t have the complete collection. Reread everything last year and glad that I did.
Language Log | Slavs and slaves
NYT | Virginia Woolf? Snob! Richard Wright? Sexist! Dostoyevsky? Anti-Semite!

I think we’d all be better readers if we realized that it isn’t the writer who’s the time traveler. It’s the reader. When we pick up an old novel, we’re not bringing the novelist into our world and deciding whether he or she is enlightened enough to belong here; we’re journeying into the novelist’s world and taking a look around.

As Tintin turns 90, the comic book hero is still teaching children about the world
I have a similar anecdote with the author about the informativity of comic books. Though it was with Doraemon, of all things.
Language Log | Sinographs for “tea” Fascinating. Adding The True History of Tea to my to-read.
Buzzfeed News | How Millennials Became The Burnout Generation
The Next Level of Data Visualization in Python

Published:

## The Two Cultures | CP Snow

The stuff Snow was talking about in this lecture feels antiquated now. Probably it was the peculiar time and place that polarised the “two cultures”. Or perhaps it was Snow’s caricaturisation. (Snow himself looked retrospectively at his 1959 lecture in Part II.)

Nevertheless we can always learn something – some of the points are interesting and and applicable. The divide of the current age though is between scientists and non-scientists – hopefully it is something we will overcome. The introduction by Stefan Collini also proves to be a commentary that is also worth reading.

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Structure leads to function is a fundamental tenet of structural biology. It may sound obvious (or not), but the implications are profound.

## Job title

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What science field label do you give yourself?

## Muscle memory

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I have been teaching swimming to a friend who is relatively a beginner. I often found myself having no words to describe a certain motion or posture and go “you just have to experience it with your body”. While I do attribute this partly to my lack of training as a swimming instructor, I still think there are things that cannot be conveyed in words, especially when it comes to motoric stuff, don’t you think?

Martial art: Definitely a motoric stuff
Image credit: SMBC Comics

Anyway, thinking about this my mind wandered to the talk about failures in science. It’s like this – before I did my PhD I have of course heard things about the inevitable stress and failures (and I find myself saying the same thing to pre- and current PhD students too) but knowing it cognitively is different from experiencing it oneself, isn’t it?

Here is a recent Nature article on the subject: <Scientific progress is built on failure>. Reading this, on one hand I hope that a PhD student or a prospective one takes note and does the necessary mental preparation; but on the other hand, I cannot help but go “My son, I know these things would fall on deaf ears. You just have to experience it for yourself”.

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## Why do simulation?

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Why do we do what we do? — is a question that should be asked by practitioners of any vocation

## Tomas Tranströmer and many-worlds interpretation

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Finding science in literature

## Good practice for bash scripting

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I will illustrate some good practices of writing bash scripts by showing you how I write and refactor my bash script dock.sh that does some preparation for docking and then launch docking.

## Revisiting Gödel

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For years after I first encountered Gödel’s incompleteness theorems, they had utterly baffled me (just look at the Wikipedia page and tell me if it is comprehensible). So I dismissed it as one of those inexplicable-to-non-mathematicians things.

## Rainbow connection

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My most impressionable memory of seeing a rainbow happened in a tourist bus in Iceland. It was faint, like a watercolour painting on the canvas that was the pale blue sky and the treeless Icelandic landscape. I noticed it first, and a few minutes later the whole bus was teetering at one side of the bus, peering spellbound out of the window (except for the bus driver, I hope).

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## Regarding that lab notebook… (Part 2: Is there a better way?)

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Searching, searching, for a better receptacle.

## Regarding that lab notebook… (Part 1: Lab notebooking and me)

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‘Tis the receptacle of our tinkering of the world, out of which we distill and crystallise knowledge.