COVID-19 – BergLabs

2021-02-072021-02-08

2021 Week 5: Migration

Today I’m writing from the tarmac in Singapore, surrounded by people making the journey from Heathrow to Auckland. We are unable to leave the aircraft, isolating to protect the locals from possible transmission of the UK strain. It is strangely familiar to be flying after more than a year; the same Android based entertainment systems, the same tray portioned food, the same cacophony of mewling infants to make sleep a little more difficult. The masks are new, as are the temperature checks, but overall it’s not that different to flights past.

It’s been a particularly strange transition. In some ways, it’s a very sudden change. Yesterday I was in Oxford, tomorrow I’ll be in Auckland, almost opposite sides of the world. The UK has suffered thousands of deaths and is under tight restrictions of movement, life in New Zealand is largely as normal with virtually no cases. Despite the geographic and social change, having worked from home and living out of a suitcase the past few weeks, the coming two weeks in quarantine is likely to feel much the same as my last two weeks in lockdown.

I will deeply miss the community I shared at ONI. In my last few days I was left feeling so deeply appreciated by my friends (who happen to be colleagues) that the words that feel most true are to say I feel loved. Perhaps it has revealed an over investment, emotionally and socially, in my work. I prefer to think of it as having had the privilege to belong in a community of people who shared principles, who inspired me to be better, and who were reliably kind in the face of immense challenge.

I am excited for the adventure to come. Moving is an opportunity to set new goals, find new friends, and attempt to amplify strengths and leave weaknesses behind. It is likely changing countries in the midst of a global pandemic will be the most significant part of this year for me, but I hope that it is just the beginning of something even more meaningful.

2020-10-25

2020 Week 43: Uncertainty

In an exciting week, I’m reminded that science is less about knowing things with certainty, and much more about knowing how to deal with uncertainty. A growing debate amongst scientists regarding the best policies to fight the second wave of the pandemic draws attention to this.

Some things to share:

A scientific debate is in progress about how to deal with COVID-19: The Great Barrington Declaration (proposing less restriction on movement and meeting, particularly among the young and healthy) vs. John Snow Memorandum (favouring tighter lockdowns). A good starting point is this summary from The Economist.

The IKEA effect describes how we like things more when we have a hand in making them. (via Angela Duckworth).

Photo from the Week

A little sunshine over still waters of Oxford’s tow path.

2020-08-02

2020 Week 31: Plenty to Discover

It is joyful that, having run thousands of kilometres in Oxford, I continue to discover new routes that are fun, beautiful, challenging, and sometimes all three. This week was the first time I ran through Lye Valley Nature Reserve and Mesopotamia, Oxford.

Adrenaline

Adrenaline is not the friend of efficient work. I had some exciting events occur this week, but as thrilling as they were, they cost a lot in disrupting and distracting from the routine.

Proof reading

Things take longer to read when you have less familiarity with them. I was surprised how long it took me to read a friends manuscript this week. I suspect that there is a parabolic curve on the [amount learned] vs. [time spent] graph. There is an optimal level of novelty where ideas are able to be grasped but not already understood, and the further away from that point the faster the intellectual returns diminish.

Living in a different timezone

A friend is working in a drastically different timezone to where they are living during the pandemic. An untested suggestion I made, inspired by the excessive Casey Neistat monitor set-up, is to loop a 24-hour video of a landscape set to be in the timezone of work (and hence sleep). I suspect that the subtle cues of being able to sense the time of day from a landscape help with shifting and living on a different timezone. More trivially, if you have to do this, shift your meals, exercise, caffeine, etc. onto the desired timezone, and black-out windows to prevent being woken by the local time-zone. This is something I’ve only ever had to do for short periods to pre-acclimatise before long distance flights.

Fantasy choices

I watched Howl’s Moving Castle on the weekend, finding myself repeatedly muttering under my breath “that’s beautiful” at the imagery. One piece of magic featured in the film is a door which, at the turn of a dial, opens onto four different locations. A discussion of the film that followed asked “if you could have a magic door connecting you to four places, where would you choose?”. A cynical answer would be to place doors in two cities with significant air traffic and charge for the teleportation service, e.g. near instant transport from London to Los Angeles. People have gamed real systems in this way. Perhaps the question is really asking “what are your four most important places”, e.g. a family home, your best friends house, your favourite holiday spot, and your place of work. Assuming the freedom to choose where to live, the playful question can have a very serious implication; where is the best place for someone to be?

Photos of the week

2020-07-18

2020 Week 29: Holidays

I’m taking some holiday at the end of this week, and the change in routine is a moment for reflection. I have been thinking about the past years, the progress I’ve made and the things I still need to work on. A goal of this blog is to create posts that are interesting and useful to others, but also to maintain a routine of writing regularly. Moving forward I’ll (try again to) keep these weekly posts brief, and put more time into longer, higher quality posts.

Things that keep me happy

I am happy with my life, and part of that is having developed habits that cultivate happiness.

Physical Exercise
Regular physical exercise. Days that start with sustained high-heart-rate exertion go better than days that do not.

Meditation and Mindfulness
I’m learning to be more present, more focused, and more aware of my own thoughts. Practising meditation develops these skills.

Personal Reflection
Knowing what actually happened in the past through written reflection helps me get a better perspective on my own life. I can keep myself accountable, and see a bigger picture to better plan and act.

Taking time to appreciate
When things go well, or are pleasant, taking a little extra time to appreciate having those things in my life makes my usual focus on problems less of an emotional burden.

Good Relationships
I am most appreciative to be able to call so many good people my friends.

Things to Share

Zwift runs a virtual Tour de France
The virtual cycling platform that is increasingly filling my strava feed bridges e-sports and traditional sport.

COVID-19 Vaccine News
Initial trial results from the mRNA vaccine against SARS-CoV-2 from NIAID and Moderna.

PhD Students in Australia are suffering:
A survey of students at the University of Sydney shows that already precariously placed PhD students have been pushed off the financial edge by the pandemic.

Photo from the Week:

Exploring new parts of Oxford on staycation

2020-07-05

2020 Week 27: Warning Label

Brief update; I am content. I have been feeling more confident generally about life this week. I am learning to perform my new role, from both success and failure. I am taking my time to appreciate good emotions, and not dwelling on bad ones. Physical training continues to plan. I have enjoyed several good conversations. Having identified my passion for engaging with talented and motivated people, I am fortunate that I get to do that so frequently at ONI.

Choosing a Perspective

Philosophy ought to come with a warning label. Dwelling too deeply into difficult, unanswered, and perhaps impossible questions carries the risk of becoming seriously lost in one’s own mind. A recent conversation ended with the question: If we can change how we feel about our experiences, thereby potentially enjoying any experience, which experiences should we choose (and choose to enjoy)? Intuitively we should choose to be happy and to do good in the world, but how do we pin down what is good in the world aside from what makes us and others happy?

I have been thinking about this David Foster Wallace speech (transcript). it focuses on choosing how you relate to people and describes a routine visit to a supermarket. Wallace asks the audience to consider hidden acts of compassion and kindness behind the people making up the frustrating queues and parking lots and highway traffic. Another, perhaps more simple, choice of perspective is to appreciate the supermarket itself. If the abundance and affordability of vegetables is celebrated, then a squeaky trolley wheel or a long queue pales compared to the miracle that the world has provided you food. For much of human history, much of human labour was spent securing a supply of food. Today for most that supply is trivial, and in my mind, worthy of appreciation.

Yesterday while drafting this I shared a quote from that speech: “The really important kind of freedom involves attention and awareness and discipline, and being able truly to care about other people and to sacrifice for them over and over in myriad petty, unsexy ways every day.” Focusing on the shopping and not the shoppers can bring happiness through attention and awareness and discipline, but it does seem a trivial exercise compared with caring and sacrificing for others.

Vaccine Updates

While the UK is getting closer to normal with the reopening of the central cultural venue, the pub, I suspect until the deployment of a vaccine for COVID-19 social and professional interactions will continue to be shaped by the disease. On Tuesday Chemistry World published this helpful update on the development of a vaccine for COVID-19. On Thursday The Economist declared Oxford the current leader.

Photo from the Week

2020-06-28

2020 Week 26: Find what you look for

The first half of 2020 is coming to an end, a time to assess progress on personal goals (or KPIs or OKRs). One personal goal was to write shorter weekly posts in favour of longer irregular posts. The 3 times I’ve succeeded in writing longer posts so far are A note on fear and death under the current pandemic, Lady Astronaut of Mars, and Productivity Update February 2020. I’ve been learning a little about funnels, and think that this might be a useful model for planning such posts in the future.

A side effect of science

As scientific research on SARS-CoV-2 is published, the general public is becoming more aware of preprint servers, redaction, and the messy side of science. I have not kept up with the deluge of publications, but a few friends have been asking for my opinion on some headlines. I shared the following observation:

As universities shut down, scientists saw the opportunity to return to doing research (which they enjoy) by studying SARS-CoV-2 in their field. Hypothetically, a group that studies kidney disease, might look into the effect of COVID-19 on the kidney. It’s improbable that a respiratory disease improves kidney function, so if an effect is observed it is probably detrimental. The likely result will be a publication linking SARS-CoV-2 and kidney deterioration. It may well be the case that common strains of corona-virus or influenza (or any illness) have a similar negative effect on the kidney that, under normal circumstances, would not be of a sufficient magnitude or interest to investigate. In this way, scientific publications and the resulting mainstream media headlines might cause undue alarm simply due to the unusual focus of the entire scientific community on a single disease.

By a similar mechanism to over-policing, intensive research focus can make a disease seem worse than similar, less investigated diseases. Be careful what you look for, you might actually find it.

Quote I’m Pondering

You cannot hope to build a better world without improving the individuals. To that end each of us must work for his own improvement, and at the same time share a general responsibility for all humanity, our particular duty being to aid those to whom we think we can be most useful.
Marie Curie

As a People Growth Engineer, my personal interest in self improvement is now linked to my professional responsibilities. ONI, through democratising life science research, is building a better world, but for us to achieve this we need to improve as a company, and therefore as individuals. Personal development and self improvement can feel selfish, but along with observing Curie’s duty “to aid those to whom we think we can be most useful”, individual improvements do lead to a better world for all.

Photo of the Week

2020-06-142020-06-14

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:

2020-06-07

2020 Week 23: Protests, Poisons, and Pasta

Following the Killing of George Floyd in Minnesota, protests against racism have spread across the US and the world, including here in Oxford. The police should not kill people. People should not fear violence or death from the police. Black lives matter. Going beyond these general, and hopefully obvious, statements requires looking into an incredibly complex set of historical, socio-economic, and policy questions. I tried to read and synthesise a meaningful comment this weekend, and was overwhelmed. I fear that the outpouring of emotion in these protests becomes twisted into a force for further political polarisation. In 2014 Police Chief Edward Flynn made comments that have stuck with me since; it is worth remembering that the ugliness of the world is faced and fought daily by good people, and we ought not forget their courage and sacrifice when people who look like them do terrible things.

Chemistry and Cleaning

When people are frightened, and poorly informed, they tend to act against their own interests. The US president speculated at a press conference if something like disinfectant could be used by injection to treat COVID-19. If a student posed this question to me I would attempt to guide them via the Socratic method to the nature of Denaturation. If the leader of the Free World poses it, a non-trivial minority poisons themselves.

Photos from the Week: Pasta

There have been many surprises in 2020; I would not have expected The Economist to print a recipe for making pasta from scratch in response to a global pandemic. Photos from my attempt:

2020-04-19

2020 Week 16: Decision Fatigue

Priorities become clear in a crisis. The pandemic continues to dominate life, news, and my research. I continue to cope well despite long hours most days, largely (as I’ve discussed in the last couple weeks) due to a community of supportive people around me along with a good diet and regular exercise. Another reason I’ve noticed is “crisis mode” narrows my focus onto a few specific tasks, removing choices, and thus I avoid decision fatigue. I am lucky that there are so many possibilities in my regular life, but invariably I end up feeling torn between possible commitments. In lock-down I can only be at home or in the lab, so I am not choosing between interesting lectures in Oxford, or potential hiking trips, or social events. There is much less fear of missing out, when there is less to miss out on.

Other thoughts from the week:

Will ending lock-down lead to a sudden increase in injuries?

I suspect when lock-down ends and gyms reopen, some proportion of people returning to their workouts after several weeks off will injure themselves. There have been several unexpected effects of the pandemic, such as a decline in accident and emergency admissions (perhaps because increases in hand-washing have led to fewer incidents of food poisoning, or perhaps because people are afraid of contracting COVID-19 by going to hospital). Gyms are closed to prevent transmission of the disease, and so people are not training and their strength and technique are diminishing. Though I hope everyone will return to training accounting for the break when gyms eventually reopen, I suspect there will be a measurable minority who attempt to resume at their pre-lock-down fitness and overexert themselves, resulting in injury and increased demand on rehabilitation services.

Things that seem special may not be

SARS-CoV-2 likely originated in animals (probably bats), making it a zoonotic disease. Bats have been known to carry diseases that can be transmitted to humans including marburg, the previous SARS, and Ebola. Naturally this raises questions about some special attribute of bats that make them more likely to spawn pandemic generating viruses. This paper from the University of Glasgow suggests that the only thing “special” about bats is their diversity. Together with the commonly disease associated Rodentia (rodents), Chiroptera (bats) account for 3938 species, or 60% of all mammal species. If viruses are randomly distributed amongst mammals, and the ability of those viruses to then infect humans is similarly random, then the observed frequency of diseases like COVID-19 coming from bats is explained without any special attribute of bats themselves.

This is a good reminder of a general principle, that because what we observe is so small relative to totality of existence, we are much more likely to attribute “special” meaning to general phenomena. I think this is most useful to remember when it comes to relationship and personal problems, as we assume our uniqueness implies a uniqueness of our problems. An example from this TED talk on depression describes a couple who are both hiding their prescription for antidepressants from each other because they both feel the other could not possibly understand.

Photos from the Week

2020-04-05

2020 Week 14: Quieter Paths

Oxford has grown quieter under the current lock-down. Government guidelines still allow for outdoor exercise, and so I have continued to run to and from the lab. The photos from the week capture some beautiful moments from these runs.

Things to share this week

Places you can visit from self isolation
Take a look around the American Museum of Natural history via google street view.
Enjoy the paintings of The National Gallery via google street view.
NASA has virtual tours of the Glenn Research Center and the Langley Research Center.
The Guardian published a guide to virtual tours of landmarks.
There are also entirely virtual worlds with real people to explore in massively multiplayer online games.

Children’s COVID-19 E-book
A friend has written a children’s book on COVID-19, which you can download here. The link is also soliciting donations which will go to support medical charities fighting the pandemic.

Theory of Everything (2014)
I’ve had this on my “to watch” list for a couple years. It focuses on the relationship between cosmologist Stephen Hawking and his first wife Jane through his scientific ascension and physical decline. I enjoyed the theatrical sets; the narrow blackboard-walled room where Penrose introduces black holes, the cold hospital where Hawking is diagnosed with ALS, and the sandstone quads and bridges of Cambridge. The relationship between Stephen and Jane is complicated by two love triangles involving Jonathan (who joins the family as friend and carer) and Elaine (a nurse to Stephen who became his second wife). However, when the real Jane says “There were four of us in our marriage“, rather than four people she is referring to Physics and ALS as the other two partners. I felt that the film prioritised the romantic tension between the characters over the more difficult to portray relationship vs career tension created by extreme devotion to physics, resulting in a compelling but less accurate story. The portrayal of scientists relies on Oxbridge archetypes and falls short of the political nuance of Contact (1997), one of my favourite films. For example, in a letter to Astronomy & Geophysics Adrian L Melott points out the missed opportunity to depict Dennis Sciama as a skilled mentor. You can watch the trailer via YouTube.