2020 Week 24: New Normal

Tomorrow face coverings will become mandatory on public transport in England. The world is emerging from the shutdown caused by a pandemic. Harvard experimental scientists are returning to their labs. I feel remarkably unaffected: I commute by bicycle, my work continued through the pandemic, my hobbies occur at home or in nature. I have seen those around me grow more eager to return to normal, but for many that may never happen.

Hesitate less – the lesson I’m trying to implement now

I have not slept. Between the acting of a dreadful thing and the first motion, all the interim is like a phantasma or a hideous dream. The genius and the mortal instruments are then in council, and the state of man, like to a little kingdom, suffers then the nature of an insurrection.” (Julius Caesar 2.1.63-71)

I am noting when I hesitate, and attempting to hesitate less. Some decisions are better made after investing time to carefully consider the choice, particularly decisions where the costs are high, but many tasks are made more daunting by postponing them. Fear and doubt build, and the cost to act increases. To get more done, I ought to act with more urgency.

Some things to share:

Books and Blogs
How to choose what to read, or listen to, or discuss? What ideas ought I visit (and subsequently consider, and sometimes write about). It is impossible to read everything. Roughly as many books fit in a shipping container as there are days in 100 years, and content comes in many forms beyond text. In this time of ubiquitous technology and physically distanced communication, each interaction begins with a choice of what content to consume, who to connect with. In a moment I could reach out to someone new, or call a close friend, or read the words of an author long dead and buried. Dwelling too much on that choice might lead to choosing nothing at all (see hesitation above), but making the right choice seems so important.

Too often I choose randomly. Occasionally I come across an abandoned blog, such as “Where’s my backpack?” and I want to study it, fearing the hosting will expire and the content will be lost (though archives of the web exist). On one rare instance I came across a blog and found myself. Part of why I write this blog is to refine and condense my thoughts, but as I approach my 100th post it becomes difficult to recall which topics I have already visited and what I have said about them. Simply to read my own words (of varying quality) now takes significant time. If in this moment your choice was reading my words, thank you, and please share your thoughts with me (my email).

Coffee as a hobby
Manual espresso coffee making process: I don’t use a PID (proportional-integral-derivative) controller, but otherwise my process is pretty similar.

Photos from the Week:

Lady Astronaut of Mars

“And basically, the novels are: I would like The Martian Chronicles but with more women and people of color, please.”

Mary Robinette Kowal speaking at Google on her novels.

About the books

I thoroughly enjoyed reading The Fated Sky, the most recent book by Mary Robinette Kowal. It follows the multi award winning novel The Calculating Stars, and occupies the same “punchard punk” universe as the short stories Articulated Restraint, The Lady Astronaut of Mars, and We Interrupt This Broadcast. You can hear the author read an extract at the start of of this Talk at Google.

Kowal describes her use of sci-fi as “set dressing” to help “explore things that [she] is thinking about from the real world and it allows [her] to talk about them without all of the emotional baggage so [she] can approach them more as a thought experiment”. Dressed in sci-fi, Dr Elma York (main character) grapples with mental illness, patriarchy, and racism, while background elements invoke the politics of climate change.

My thoughts

I enjoyed the alternate history, the blending of the real life Mercury 13 and computers of Hidden Figures with an engaging character driven story. Kowal has done her homework, with help from Derek Benkoski (fighter pilot), Kjell Lindgren and Cady Coleman (astronauts), and Stephen Granade (rocket scientist), which gives Kowal’s depiction of space-faring such realism that it felt a little like reading astronaut Chris Hadfield’s autobiography.

It was new for me to read fiction where most of the cast, including the first person narrator, are women. As with film (I highly recommend checking out this blog post) women tend to be less represented in stories I read (e.g. The Lord of the Rings). While the main plot of The Calculating Stars centres on women fighting to be included as astronauts, The Fated Sky shifts focus to issues of race. The diversity of the cast is necessary for the story Kowal sets out to tell, and whilst she clearly has a progressive stance to share, at no point did I feel narrative was compromised to make a political point (though as far as I can tell I largely share the author’s views).

The first novel opens to a scene involving Elma and Nathaniel’s (main characters) sex life, and their emotional, sexual, and professional relationships feature significantly in both books. Kowal states in the Google Talk that she “wanted their relationship to always be rock solid”. I am fortunate that my relationship is similar enough to find myself relating to Elma and Nathaniel. While there has been criticism that “Nathaniel York is too perfect to be realistic” (which Kowal has responded to via twitter), being able to see the familiar stresses of over-commitment to work, mental illness, and maintaining intimacy over distance, helped me invest in them both as a couple and as individuals.

Fiction and Authors

It is new for me to come to the end of a story I have enjoyed for recreational-escapist-immersion and then be able to turn to the internet to learn about the author, her process, and how to examine fiction more generally. Kowal keeps a public journal, where as I began drafting this post she shared insights into her writing process. She tweets and answers questions through Lee the Puppet and collects typewriters. By following her online presence, I learned of the existence of narrative beats and about heat welding for puppetry. Seeing an author as an actual person (with their struggles and distractions and desires) makes writing less daunting, and so encourages me to write more.

Real Astronaut CVs

Science-fiction and fantasy make for interesting psychological insights into readers. While no one has experienced contact with aliens or magic, the audience’s immersion may be first broken by a very human behaviour. In the talk Kowal discusses that her writing is criticised for her depiction of Elma’s weaknesses as it seems contradictory for Elma to be so paralysed by anxiety in a social context but utterly comfortable with near death experiences in space craft. This is in spite of the real lived experiences of those with social anxiety disorder. Another criticism of the character I have seen in a few places regards her mathematical prowess:

The least relatable thing about Elma is that she’s so smart that no one else can match her. She went to college at 14. She does math in her head. Oh, you have to solve differential equations with a piece of paper and a pencil? You’re actually a dumbass in comparison.” — librarything review by yvonnekins

I remember feeling a similar jealous sentiment towards Patrick Rothfuss’ protagonist in the Kingkiller Chronicle series. It is easy to be jealous of characters who are defined by their intelligence, particularly if you operate in a world where intelligence is worshipped. When it comes to astronauts however, Elma’s skills did not break my immersion, as I have seen astronauts tend to have pretty incredible CVs, e.g. Jonny Kim. Also child pilot and accomplished physicist Sabrina Gonzalez Pasterski is not a fictional character.

Some uncomfortable feelings when I come to write about books

Generally, despite really enjoying the story, coming to reflect on it here inspired some painful feelings. While it would be easier to ignore those feelings, that would miss an opportunity to grow past them, and fail to follow the example of sharing personal weakness set by Kowal and others who inspire me. I feel it is important to hold and express thoughts about the books I read, and I couldn’t do that if I avoided emotions that come with reflection. Emotions are difficult to untangle, but two strands I can draw out are:

1. I feel I should write about books but I don’t know why or how. I feel disappointed with myself that when I finished the first book all that made it into the blog was “I finished reading The Calculating Stars by Mary Robinette Kowal, it is excellent.”

2. I read slowly. It is also disappointing to me that it took me nearly 3 months to read The Fated Sky. I quickly convert that rate of four books a year through the relatively short human lifespan, and feel a great sense of loss that there are so many texts I will never read.

Closing Thoughts

I highly enjoyed both books (on paper), but given Kowal is a voice actor and does the narration, I would recommend listening to The Calculating Stars via audiobook. I eagerly anticipate the third book in Elma and Nathaniel’s story, due in 2022.

2020 Week 2: Acceleration

Already 12 days into 2020 and things are falling behind. I missed a Week 1 blog post, but am back with the regular Sunday blog post in a new, punchier, format. Longer posts will now be separate and linked to from the weekly posts, while topics that I return to will grow into subsections of the main website. Updates to come soon.

Things I wrote this week:

2019 Altmetric Top 100
I share my thoughts on the most shared scientific papers of 2019.

Things I read this week:

The Pac-Man rule at conferences; how to avoid excluding people by making it easier to join your conversations.

Nature: Boris asks for weirdos to hang out with him
The UK government appears to have a “cinematic” view of scientists.

Introduction to Data Science
Still working my way through this data science course, and starting to see how machine learning is an application of statistics through training some basic algorithms.

Apollo 11 (2019)
Despite being well aware of the success of the first mission to the moon, this was a compelling and immersive retelling. I found the interludes of heart rate data amusing.

2019 Week 48: Consumption

Short version: This Black Friday weekend is a relevant time to attempt to press my thoughts on consumerism into a post. A revealing ONS data set about household spending. Also some thoughts on blogging and whales’ heart beats.

A note on structure

On top of a tangled set of thoughts about consumption, there was a lot of interesting content to read, listen to, and watch on this topic. The structure of this post suffered, and so if you’re just here to skim I suggest scroll down to the bottom and just check out Trends from the data and Whales’ Heart Beats.

Consumerism

I want stuff. Lots of people also want stuff. Often, if they can, they go out and buy stuff. This is a simple thought, but the many paths it leads down have been a tangle in my mind for some time. This post is an attempt to rectify the clash between the obvious value in markets and trade with the absurdity of waste (see the two videos below) in modern developed economies. This is highlighted by celebrations of consumerism that occur after Thanksgiving.

Chasers War on Waste

The true cost of fast fashion | The Economist

People want to be rich

I think it is reasonable to presume the overwhelming majority of people would like to have more money. Money provides security, safety, and freedom (and most of lower tiers of Maslow’s hierarchy of needs). Casey Neistat points out that for a lot of people, money will solve all problems. although people with plenty of money still have problems.

This simple desire for material wealth gets complicated by how different that desire looks at different points of time. The majority of people in the developed world have access to goods and services that were restricted to only the most wealthy only decades ago. Advances in agriculture and medicine mean even the poorest citizens have access to goods like pineapples and penicillin that would have been unimaginable to emperors and kings of centuries past. This Louis CK bit makes light of changing expectations. That desire for newer and shinier at the expense of appreciation for what we already have is, in part, created by the desire for companies to grow their sales and profits. An array of narratives are pushed through advertising. A particularly disturbing yet powerful lie is that you can change who you are simply by owning something. The idea that you can be fitter/sexier/smarter by buying something, rather than by learning or growing, sells a lot of products, despite failing their buyers.

School of Life: History of Consumerism

Black Friday

Black Friday is a day of discounted selling by retailers following Thanksgiving Day, which is observed by shops throughout much of the world. Scenes of people rushing into stores and fighting over relatively cheaper items are symbolic of a period of significant spending by consumers as the end of the year, and particularly Christmas, approaches.

A lot of people work in retail. In Australia, it is 1.3 million, nearly 10% of the labour force. This is an enormous amount of human life dedicated to the mere act of selling things (1.8 Australian lifetimes is spent per working hour by the collective in shops, life expectancy in Australia = 82.5 years). Intuitively (and so simplistically as to be utterly inaccurate) this struck me as a waste of time, given retail exists as a middle man between producers and consumers. Of course in reality at points retailers make the entire system more efficient (for example by collecting fruit and milk in bulk and distributing it to stores in lieu of each consumer visiting a farm individually), but in practice profit incentives drive this enormous work force to motivate us all to consumer more.

One way consumption is driven is through pricing. The decision to purchase an item is in part determined by the price attached to that item. Commonly items are priced at X.99 rather than X+1, because that centipoint increase is far more psychologically significant than the additional profit. A further extreme of this is quantum pricing where fewer price points mean profit margins are obfuscated. The discounts of Black Friday create the perception that shoppers are saving money by buying things at a lower price than they would otherwise, combined with a false scarcity that this is the only time to buy. In reality most consumer goods depreciate rapidly so any future time is a better time to buy. Less scrupulous stores raise prices before the sales only to mark down to pre-sale prices. One clear sign of the power of this frenzied overconsumption is the willingness for people to take on debt to purchase luxuries. Loan Sharks take advantage of Black Friday pressures to consume.

Interesting observations from some actual data

A few weeks ago I came across the BBC series “My Money“, which takes individuals and looks at their spending over a week. My fascination with how other people spend money stems from not having a good answer to “What is the appropriate/correct/optimal amount to spend on X”. There are intuitive answers to this, which is why spending £100 a week on cheese or £5 a quarter on electricity “feel” high and low, but that intuition is shaped by our relatively limited insight into other’s spending (likely dominated by our parents’ and partners’ habits) augmented by the media we consume, particularly the coercive forces of marketing.

I am consistently frustrated with the concept of normal. There are no “normal” people in the same way there is no way to roll 3.5 (the centre of the normal distribution for values) on a 6 sided die. This video featuring wrestler John Cena emphasises the difficulty in describing an “average” american. However discovering the UK’s Office of National Statistics collects and compiles data on household expenditure (among other things), and produces reports on the distribution of spending, provides data on where the distributions actually lie. I found exploring the data fascinating. I was particularly excited to find this data set breaking down typical weekly expenditure by item in pretty specific categories (e.g. “Cheese”, “Books”, and “Package Holidays – UK” are separate categories).

Here are some observations:

The big picture: income and expenditure

The distribution of incomes in the UK gives an insight into what households can actually afford.

The interactive graphic below gives insight into how the typical UK household spends (taken from this ONS report).

Trends from the data

General trends

A wealthier decile has more people per household.

Wealth increases steadily between the 2nd and 8th deciles, and sharply at both ends.

Overall spending trends

Spending in most product areas correlates with increasing disposable income on both a per person and per capita level.

Interesting specific spending trends

Food
Poultry (strongly) and beef (weakly) correlate with increasing wealth, pork and lamb are flat across groups, and bacon and ham have a weak negative correlation.

Housing
Poorer households spend proportionally much more on housing, making up 19.1 % of spending for the lower half of households, vs 11.1 % for the upper (I guess this is because of renting vs owning). This is after accounting for housing benefits to the lowest deciles.

Transport
Transport spending is correlated with income, with a sharp increase in the top decile due to the purchase of new (presumably luxury) cars.

Clothes
In the bottom three deciles women spend 2.5x more than than men on clothes, whereas that ratio is only 1.3x for the top decile.
Only the top few deciles use drycleaning services.

Alcohol and Tobacco
Spending on alcoholic drinks was correlated with income, but the trend was dominated by wine, while beer and spirits were fairly independent across the groups.
Lower income deciles spent more per person on tobacco and other narcotics.

Health and Education
Education (school fees) and sports subscriptions (gyms) correlated strongly with income.

Entertainment
There is a hump like feature in the audio-visual equipment categories in the 6th and 7th deciles.
Spending on hotels appears to have an exponential relationship with increasing disposable income.

Statistical definitions

Useful definitions from the ONS:

What is disposable income?

Disposable income is arguably the most widely used household income measure. Disposable income is the amount of money that households have available for spending and saving after direct taxes (such as Income Tax, National Insurance and Council Tax) have been accounted for. It includes earnings from employment, private pensions and investments as well as cash benefits provided by the state.

The five stages are:

1. Household members begin with income from employment, private pensions, investments and other non-government sources; this is referred to as “original income

2. Households then receive income from cash benefits. The sum of cash benefits and original income is referred to as “gross income”.

3. Households then pay direct taxes. Direct taxes, when subtracted from gross income is referred to as “disposable income”.

4. Indirect taxes are then paid via expenditure. Disposable income minus indirect taxes is referred to as “post-tax income”.

5. Households finally receive a benefit from services (benefits in kind). Benefits in kind plus post-tax income is referred to as “final income”.

Note that at no stage are deductions made for housing costs.

From Effects of taxes and benefits on UK household income: financial year ending 2017 via ONS

Amusing group names:

While looking at consumer spending in the UK, I found the following categories that the ONS uses to divide UK residents. Some of them were incredulous to the point of being amusing.

Categories:
Rural residents, Cosmopolitans, Ethnicity central, Multicultural metropolitans, Urbanites, Suburbanites, Constrained city dwellers, Hard-pressed living

Sub-categories:
Farming Communities, Rural Tenants, Ageing Rural Dwellers, Students Around Campus, Inner-City Students, Comfortable Cosmopolitans, Aspiring and Affluent, Ethnic Family Life, Endeavouring Ethnic Mix, Ethnic Dynamics, Aspirational Techies, Rented Family Living, Challenged Asian Terraces, Asian Traits, Urban Professionals and Families, Ageing Urban Living, Suburban Achievers, Semi-Detached Suburbia, Challenged Diversity, Constrained Flat Dwellers, White Communities, Ageing City Dwellers, Industrious Communities, Challenged Terraced Workers, Hard-Pressed Ageing Workers, Migration and Churn.

Personal conflict: running tech

I like running, and improving my fitness more generally, I suppose because it helps me to self actualise. One of my personal weaknesses in fighting back against the commercial marketing machine has been in running tech. As such, I found this video from the New York Times both entertaining and helpful in realising the main thing I need to run faster is not a piece of equipment, but to simply run more and faster.

December blogging reflection

Lately I’ve been posting each week on Sunday come what may. There’s a pretty wide variance in how much time goes into each post, which is not always related to the quality of each post. Some topics I have a better understanding of before I start to write. Some observations are not insightful. Some posts go out unfinished.

Ideas vary in quality. Some ideas were probably not worth writing about at all, while others are so huge they could easily fill hundreds of pages. Not every idea is a good idea, and even a good idea poorly executed is not a good result.

Some topics deserve to be revisited, edited, improved, expanded etc. But writing in this weekly format is useful. Sometimes quantity results in quality. If I maintained a high expectation for each blog post I would write less, and my writing would not improve. Moreover in trying to write each week I am motivating myself to learn. I do hope to better organise myself in the next block of blogging (i.e. next year’s posts) to segregate space for tackling bigger topics less frequently, with a less structured more regular section.

As I was writing this post I received Peter Attia’s weekly email, describing his struggles with writing. It was extremely motivating to read words that felt so familiar they could have been my own. I would not wish insecurities on anyone, but it is deeply reassuring to be reminded those feelings are normal.

While on the topic of other writers; blogs I’d like to share:
Econometrics By Simulation: interesting applications of statistical software.
Beau Miles: Came across some of his films, the first content in a while to make me really miss Australia. Describes himself as “Award winning filmmaker, poly-jobist, speaker, writer, odd.”

Whales’ heart beats

A wonderful aspect of having scientists as friends is that they share exciting science with you that you would otherwise miss. One example is this paper about how the heart rate of blue whales changes as they dive for food. Their enormous hearts beat as slowly as two times per minute and as quickly as 37, which is about as fast as is physically possible. It also contains this informative figure, which I feel tells the story clearly and succinctly.

Photos from the Week

2019 Week 46: Patents

Short version: Patents reward innovators but limit the impact of new technologies. Also “patents” are the answer to the question “Why did Samsung build the only outdoor ice rink in Texas in a small town.”

Long version:

What I learned reading and thinking about patents

Patents are a part of the law, which is an ever changing system. As governments create and change laws, and those laws are interpreted and tested in courts, we collectively decide how the rewards of science and technology are distributed.

There is very little that is certain or obvious about patents. Their existence is both an incentive and a barrier to innovation. They can both enrich and impoverish inventors. They can both be utterly invisible and hugely controversial.

Patent trolling was used in the US to extort businesses, which seems to have peaked around 2015, and has since declined.

Some patents provide useful and specific descriptions of technology, whilst others are deliberately broad and vague.

Biotechnology has struggled to fit into the existing patent infrastructure, particularly as the line blurs between what is an invented object and what is part of nature.

Patent Trolls: Why Samsung built an ice rink in Texas

This article from Harvard Business School outlines how patent trolling, the use of frivolous patent lawsuits by businesses uninterested in innovation, led Samsung to try and win favour with potential jurors in Marhsall, Texas by building an ice rink there. Samsung also set up high school scholarships in the town, but when a supreme court decision meant that the jurisdiction where the suit was filed needed to be in the state of incorporation, the branding on the ice and the scholarships dissipated. More recently a paper was published about patent trolls last year.

Samsung, seeking favour with potential jurors, awarded scholarships to high school students in Marshall, Texas.

Patent Examples

The race to patent the Human Genome

Craig Venter’s company raced public researchers to be the first to sequence the Human Genome. You can read the story in Patrick Bradley’s paper. I found the twitter exchange below interesting, but was not able to verify or refute Venter’s claim that it was “untrue and was propaganda”. Certainly there was a race, and patents played a part, as they continue to do in biotechnology research.

BRCA1 and BRCA2

The other famous case within biotech patents is of Myriad Genetic’s patents on BRCA1 and BRCA2, two mutations related to breast cancer. Enforcing the patents meant diagnostic tests for inherited breast cancer were expensive. The debate centred on the question of whether DNA sequences could be considered a discovery or an invention, i.e. a technical question about how biotech fits within the existing patent system. Ultimately the patents were struck down. The underlying question, how much should we allow companies to profit from their research (at the expense of society, but to give incentives for more research) remains.

Intellectual Property and Piracy

Looking at patents led on to questions about copyright, trademarks, and intellectual property in general. In a world where replication of content is so trivial, and distribution technologies (i.e. the internet) are spreading so rapidly, it is unlikely legal enforcement can keep up in a meaningful way. This crash course provides some information, and I would like to return to think about the ethics of digital piracy, peer to peer sharing, and what the fairest way to regulate content could be.

A note about being connected on the internet

I find it strangely wonderful how connected the internet makes us. From a train, a coffee shop, or even my bed, I can reach out to authors and scientists, and access nearly all of the knowledge humanity has created. In researching this post, I could find out the Marshall high schools’ Samsung scholarship winners, or tweet at scientists like Craig Venter, or access patents from hundreds of years worth of inventions. It is such a powerful tool.

Other things in my life this week:

Rivers in Oxford have been rising, causing flooding around the Isis and Cherwell (see photos from the week). This excellent tracker from Anu Dudhia makes it easy to keep an eye on conditions.

I finished reading The Calculating Stars by Mary Robinette Kowal, it is excellent.

Three friends have signed up to the Edinburgh marathon, so running has gotten more social.

Photos from the Week – Flooding

2019 Week 29: Front Page News

Short version: I summarise and share thoughts on articles from the covers of current editions of high impact journals. I ran late at night and it was serene.

Long version:

Front Page Science

Human knowledge is vast, and discovering is more difficult than learning from others what was discovered before. This explanation of what a PhD is visualises that point. Scientists need to communicate with each other about their results, and do so by publishing articles collected and edited by journals. Today with journals available online it is rare to open a physical periodical rather than read individual articles digitally (or printed one by one). Those hard copy collections still exist, and necessarily they have a front cover. This week I looked up the covers of some high impact journals (see below), read the related article, and wrote down my thoughts.

Snooze Report
On the cover of Nature.
This paper studies sleep in Zebrafish. While we all sleep, it is a complicated process with many aspects still not understood. Zebrafish are a model organism, that is they can be used as a substitute for understanding processes in humans, and have been studied extensively. Zebrafish are known to sleep based on behavioural criteria (essentially they stop moving for a while for regular periods), but it is hard to compare Zebrafish sleep to humans (or mammals in general) in a more detailed way. This is because sleep is studied in humans by looking at electrical signals from the brain (via electroencephalograms or EEG), but fish do not have a similar part of the brain (the neocortex) where human sleep signals are recorded. The team behind this paper, mostly from Stanford, used a light microscope based method to look at Zebrafish brains while they slept, and discovered two sleep signatures that they call “slow bursting sleep” and “propagating wave sleep” that they claim to be similar to our “slow-wave sleep” and “rapid eye movement sleep“.

Artificial Muscles
On the cover of Science
Much of science and engineering aims to replicate nature, be it materials (the first plastics replaced natural materials like silk and ivory), phenomena (electric lighting replacing flames), or biological feats (aircraft allowing human flight). Being able to artificially produce the mechanical properties of muscle (fibres that can contract) is important for robotics and prosthetics that more accurately mimic what natural creatures can do. This group, mostly from MIT, have created fibres that can lift 650 times their weight, and withstand thousands of cycles.

African Killifishes
On the cover of Cell
The advances made in DNA sequencing accelerated rapidly, and whole genome sequencing is now routinely available to researchers. This research team studied the genetic code of 45 killifish species to better understand the relationship between genes and life span. Killifishes have a range of life spans due to species diversifying and adapting to different environments. Killifish with shorter lives tended to have more genetic code, including both more redundant code and more detrimental mutations.

Controlled patterning of stem cell cultures
On the cover of Nature Methods
Three key concepts underpin this paper: Stem cells are cells that can become other types of cells. Morphogens are chemicals that, through their distribution, influence how cells develop, and eventually leads to the organisation of different types of cells in complex organisms. Microfluidics is the process of handling very small amounts of liquid. Those three come together in this method that explains how using a microfluidic device to introduce morphogens in a gradient over stem cells alters the patterns that they develop.

Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation
On the cover of ACS Chemical Reviews
Reviews are an intermediate type of publication between cutting edge research and established science found in textbooks. This paper covers computer simulations of membrane ion channels, and is a comprehensive 72 pages (excluding the 923 references). Membrane ion channels are important for electrical activity in biological systems, i.e. the nervous system. Computer simulations have become increasingly important in chemistry, made particularly famous in 2013.

A one-dimensional individual-based mechanical model of cell movement in heterogeneous tissues and its coarse-grained approximation
On the cover of Proceedings of the Royal Society A
My mathematical understanding is far from the frontiers of mathematical research, and so I don’t often read papers from mathematicians. This paper presents a model, that is a mathematical representation, for cell movement in tissue. The power of mathematics, and of models, is to be able to generalise from limited information. In this case the hope is a generalised model might inform a better understanding of disease.

Guiding spin waves in artificial antiferromagnets
On the cover of Nature nanotechnology
Spin is a fundamental property of subatomic particles, such as electrons. Magnetism is a directly observable consequence of spin, in a similar way to static electricity being a directly observable consequence of charge. We manipulate charge in conventional electronic devices, and spintronics aims to manipulate spin in a similar way. This paper describes spin-waves being controlled, and is a step towards more complex applications of spin.

Rapid Plant DNA Extraction
On the cover of ACS Nano
The paper describes a method for extracting the DNA from plants using a patch covered in hundreds of sub-millimeter needles. This reduces a multi hour chemical extraction to a few minutes work.

Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection
On the cover of Nature biotechnology
Oxford Nanopore, like ONI, is a spin out of Oxford University. They develop a device for rapid and portable DNA sequencing. In this paper they apply that technology to diagnosing bacteria in respiratory infections. Conventional identification by growing the bacteria taken from a patient sample takes 2-3 days, whereas the Nanopore method could give results in a few hours.

Night Runs

Early this week I wanted a long run, but only had time to start at midnight. I decided to go for it, and found I really enjoyed the quiet streets. Particularly the lack of vehicle traffic meant I could run on the road. Even having the whole footpath to myself the alternating sloping driveways and flat footpath required attention, while the smooth asphalt gave me space to get lost in my thoughts. I had decided to run unplugged, without music or a podcast, and even turned off the backlight on my watch, setting the pace purely on feel. After the first few kilometres I found a rhythm and just listened to my foot fall, soaking in the serenity. An additional fun moment was running through some road works barricades, which gave me the impression of being on the course of a race.

Photos from the Week

2019 Week 7: Zero to One

Short version: I read Peter Thiel’s notes on startups, had a couple college formal dinners, cycled in the Cotswolds, and bought some protein powder.

Long version:

Zero to One

Peter Thiel is founder of PayPal, and an early investor in Facebook, which have made him a billionaire. In 2012 he taught a course about startups at Stanford, which via Blake Master’s notes became the book Zero to One.

I will update this post later with my thoughts on the book and other missing sections.

Photos from the Week

2019 Week 6: Happy Chinese New Year

Short version: Writing accurately about science takes time, but a few bits to push in that direction. 新年快乐!

Long version:

Writing About Science

I’ve noticed a lack of scientific content in my blog. Usually the week’s post is in the back of my mind throughout the week with a few notes in Google Keep. This week I started out early with a list of topics I’d like touch on, or even expand into, but by Sunday with relatively little progress and wanting to cover them in reasonable depth I’ve culled back significantly. At the moment my main motivation week to week in writing is to practice writing publicly, building confidence and prompting coherency in my thoughts. I would like to share insight, but presenting summaries of scientific work on interesting topics can very quickly grow into a lengthy task (e.g. Review Articles). Also, working full time in scientific research, often my weekend reading drifts into other fields, which then leads to less scientific blog writing.

Chinese New Year

新年快乐!(Happy Chinese New Year!) It is the year of the pig.

Some Hopefully Useful Scientific Content

Stuff I read this week

There is an annual report into happiness. Nature celebrates women behind the periodic table. Google is developing a timber high rise in Toronto. Economic downturn improves health (particularly smoking and obesity). NHS has some simple to follow gym-free workouts particularly neck, back, and knee. Drones being used to poison rats on the Galapagos, possibly targeting Possums in New Zealand next.

A thought on Consumerism

My current context is filled with incentives to buy more stuff. One of the photos from the week is of a particularly expensive sports car that I passed on a run, and I feel that in sharing it I am participating in a culture that causes us to covet impractical luxuries. After all, given speed limits and traffic exist, it’s unclear what the purpose of owning a super car is beyond conspicuous consumption. That said, there is an aesthetic pleasure to be taken from such things.

Photos from the Week

2019 Week 4: Vegetarian

Short version: Why I don’t eat meat, some things I’m reading at the moment, and three photos from my week.

Long version:

Eating Less Meat

Since having moved to the United Kingdom, I’ve been eating less meat. The strongest motivation comes from a desire to minimise carbon impact and waste. The change has been made easy by meat substitutes being widely available and cheap (and delicious).

Evidence:
Intuitively, in order for humans to gain nutrition from an animal, that animal needs to consume either other animals or plants first. Given these processes cannot be completely efficient, there is always a lower energy cost to the environment to eat lower on the food chain. The real effect of this is described in the chart below.


High Protein Diets:
The CSIRO published a book advocating a high protein diet. It generated some controversy in part due to being funded by the meat industry. It still seems a high protein diet is healthy, but there is evidence swapping animal protein for plant protein lowers mortality overall.

More reading:
Publications from Nature and World Resources Institute about the impact of meat on climate change, which include the infographic above. Also, from a moral point of view, Consider the Lobster.

Stuff I read this week

Relevantly, restaurant reviews from the blog Vegan Eats Oxford. The Graduate Outcomes Survey was released. Matt Levine continues to write humorously about finance. Hybrid Perovskite Semiconductors are cool.

Photos: Cakes, Climbing, and Snow

Writing from home.

2019 Week 2: Habits and Goals

Short version: Building good habits makes good behaviours easier. Australians find their history confronting. Green Tea seems to be good for you. Birds have social media in Sydney.

Long version:

Habits, Mindfulness, and Technology.

At the start of 2018 I wrote “In short: learn,  improve my routine, write more.” I’ve noticed on returning to work this year that habits which felt like hard work at the start of last year are coming much more easily. Building a good routine gradually, consistently, and trying to avoid self-flagellation when I failed, has yeilded bigger benefits than I anticipated. This has been most easily observed around physical and mental health, where I’m getting up ealier, feeling more energetic through the day, and getting more exercise in.

On the other side is a reminder how powerful bad habits are. In a vlog this week John Green spoke about discovering just how often he types reddit into a browser when he quit social media. I think handling technology that is driven by so many smart people working to grab more of our attention to sell more advertising, is hard. One way I’m going to work to improve my relationship with tech this year is to make sure I have a purpose each time I interact with it. The aim is see it and use it as a tool, rather than be guided by it to burn time.

Australian History: “Slavery by Other Means”

My friend Seb wrote two articles on Pacific Islander Labour in 19th and early 20th Century Australia. My intial response to this brutal chapter of Austalian history was to attempt to trivialise it. Thoughts like “not as bad as other slavery”, “life was harsh for everyone back then”, and “life as a labourer wouldn’t have been that bad”. I would guess these are responses to shield myself from feeling, be it empathy or disgust or guilt or simply sadness. I’m not sure if an emotional engagement with history is preferable to a clinical intellectualism, but I do think the tendancy to avoid discomfort in historical interest is harmful. The extemes are feeling so strongly we are paralysed or act irresponsibly vs being callous to injustices, but the best place to sit between the extremes is not clear to me. I think both the article and the general principle are worth consideration.

Green Tea

It seems like drinking Green Tea is pretty good for you. I think all nutritional science suffers from difficulties collecting accurate data from inherently unreliable test subjects, but a quick search of google scholar seems to come up with a compelling set of results. I’m convinced enough to be swapping out some of my coffees for the world’s most popular brew.

Social Media for Birds (and Science)

Picture of the week is an Australian white ibis or Bin Chicken. Noticable is the yellow tag, which lets you know his name is Wazza. You can help him (and research) out by posting on social media for wing tagged birds.

Writing from home.