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 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 Week 18: Autonomy

This week I have had more autonomy in how I allocate my time at work. While I enjoyed the freedom, it also created expectations to perform. I might aspire to a stoic determination around ideas of “never complain, never give excuses”, but having actual excuses be removed increases the pressure I feel to deliver.

More Thoughts:

Caterpillars in Shotover

On the recommendation of a friend I ran in Shotover Country Park this weekend (see Photos from the Week below). The trails are well kept and soft under foot. There is a good variety of long steady climbs, short punchy climbs, and beautiful flat sections, great for all manner of training. There were also thousands of small (1 cm or so) caterpillars hanging from trees which I was inevitably coated in. Curious, I turned to the scientific literature and found a comprehensive description of this behaviour in the appropriately named journal Animal Behaviour. As it turns out, this is a defence mechanism to avoid predators (stink bugs and wasps). When the caterpillars detect the vibrations their predators make when hunting nearby, they dangle themselves from silk threads to escape being eaten. Interestingly they can differentiate the vibrations of wasps and stink bugs (two predators), and dangle further (30 cm) for wasps than the less adept stink bugs (only 10 cm of dangling). Not only did the study record and artificially replicate the vibrations caused by the predators to confirm this, they also measured that the extra dangling significantly increased survival in response to the wasps, but was not needed for the stink bugs. Science is awesome. Unfortunately for these caterpillars, the extra dangling also made them much more likely to become unwilling passengers on my run. Good pictures of them in this tweet.

Short Observations on Social Pressure

I remember being taught about peer pressure at school. Usually the intention was that if children are aware of what is motivating them to do something the teacher or parent thinks is negative, that they will be less likely to behave in that way. I would like to think that I’ve become more aware since I was a child, and yet peer pressure still nudges me to make bad choices. I was tagged in a run by a friend as part of a “5k for the NHS challenge”. He ran under 20 minutes and, being competitive, I wanted to beat that time. It is something that I feels possible, but would require a more intense change of pace than what seems reasonable given my current training. I really felt pressure, for about 10 days, to go out and try and run a sub 20 5k, which would have been a mistake. With other more significant pressures in my life at the moment, it is interesting to note that such a trivial (and well meaning) nudge to perform can cause such an emotional burden.

Of course the other side of this is that I was motivated to give £5 to the NHS. I have often been cynical about runners raising money for charity: the run seems so unnecessary, even costly, as the event costs could also go to the charitable cause. Fun runs do align with some causes, as exercise reduces susceptibility to cardiovascular diseases and diabetes, but in general it seems contrived to me. I must concede though, that had I not been nudged to donate via Strava, I would not have donated that £5. From this single point of data, it has been effective.

Stuff I’m reading at the moment

Measure What Matters by John Doerr, and Leading by Alex Ferguson and Michael Moritz. I am hoping to get some summarised thoughts out soon.

Photo from the Week

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 Week 13: Intensity

It has been an intense week. I am in the lab most waking hours working on COVID-19 projects. To make consecutive long days viable, I prioritise hard exercise in down time as I find it helps keep my health (physical and mental) in a good place. My efforts are only possible because the team at ONI is so supportive, be they working beside me at the bench, in the machine shop on the other side of the building, or coordinating supplies from home. It has been exhilarating to be part of a sudden surge in scientific effort, and I have found the wider scientific community to be universally selfless in their willingness to help.

Things to share this week

COVID-19
Again the media is dominated by discussion of the pandemic. I feel torn about adding to that noise, but my thoughts are now focused on that topic and primarily this blog is where I share what I am thinking about. I continue to be concerned that major media outlets, driven by the need to sell advertising clicks, are tasking journalists without the right medical literacy to create content without much consideration for how useful that content is. My suggestion remains: read from sources that specialise in the area, ignore conventional news coverage of the pandemic.
A starting point: WHO Coronavirus Homepage
Check with your local health services: US CDC, European CDC, UK NHS, Australia Department of Health.
Journals for in depth scientific content: The LancetThe New England Journal of Medicine, BMJ, and Nature.

My (uninformed) thoughts
In Week 11 I was not worried. In Week 12 I was hit by exponential whiplash. My resolve is being tested as governments take economies into lock down and hospitals become overrun. In my note on death I commented that although only 5000 had died at the time of writing, the final toll would likely be in the millions. I take no joy in that prospect and I hope I will be proven wrong. That said, I also feel that stating “millions will die” without the context of the millions who already die each year incites fear beyond the reality of the situation. I stand by the importance of seeing this crisis in the context of others happening simultaneously, e.g. climate change, tropical disease, and obesity. We humans have an incredible power to see into the future, but such a limited desire to take the actions the future tasks us with. This pandemic makes me feel that only when the danger is close in space and time are we spurred to act, and this is something I wish I could change.

Collaboration
Nature is running a podcast “Coronapod” and the sentiments from the start of this week’s post are echoed about 15 minutes in; scientists are coming together to help each other.

Hoarding
There are reports that the UK is holding £1bn in food that was purchased as the COVID-19 situation became serious. While that is enough to leave me seeing shortages of flour and dry pasta on shelves, a quick division makes that number £15 per person, which means only a little extra spending over a week of “stocking up” can push the complex supply chain of fast moving consumer goods beyond its limits. This small change in perspective makes me feel less frustrated; an average family doubling up on their weekly shop seems foolish but understandable, compared with imagining panicked people filling their cars with pasta and toilet paper. Especially in Britain (where baking is a hobby as much as a source of nutrition) flour stocks could easily sell out as people newly working from home find the opportunity to bake. Furthermore, knowing that the system is tuned so finely to match regular demand makes me feel there is less waste than I had previously intuited. (Side note; in googling for articles on this I came across this guide to how supermarkets nudge you to spend more).

Photos from the week

2020 Week 12: Exponential Whiplash

Since I wrote last week about the pandemic, putting it in the context of other global health issues, the total fatalities due to COVID-19 have more than doubled, and major European economies have essentially halted. I had some awareness of the likely rate of spread, but was not anticipating how events have played out, and so count myself among those hit by “exponential whiplash”:

a cognitive phenomenon that sars-cov-2, the virus which causes covid-19, has been provoking around the world: exponential whiplash. Knowing in principle that something may take only a few days to double in size does little to prepare you for the experience of being continually behind the ever-steepening curve such doubling creates.The Economist

I shared on LinkedIn this week that ONI is working on research to support the fight against COVID-19 and since Wednesday my productive energy has been focused there. Like many businesses across the UK, a majority of ONI’s staff are working from home, but my skills let me keep working on new projects directly related to SARS-CoV-2. It is exciting and rewarding to be able to do so, but it is also sapping time and energy from my usual pursuits. Given that, I have only a few incomplete thoughts to share:

Things to share this week

Proximity bias
It is noticeable to me that these deaths are causing so much more economic and social pressure than the deaths by the causes I listed last week. I guess it is because these deaths are more proximate to wealthy societies, which have won huge victories against infectious diseases. Combined with the panicked behaviour I note below, I feel most people demonstrate they do not find all lives are equally valuable, even though they might espouse that value.

Pandemics vs. Climate Catastrophe
Something I’m thinking about: if society knew that these radical measures were necessary to prevent a much larger disaster much further away, would we be able to make the same cuts on air travel, entertainment, and consumption? Could we reinvent our way of life to prevent deaths from climate change, without anyone needing to die first?

Some people are panicking
I am hearing first hand accounts of stockpiling from both Australia and the UK; supermarket shelves being emptied despite no larger issues on the supply side. A friend had toilet paper snatched out of her shopping cart. There has been a spike in gun sales in the US. It saddens me to see people act out of fear, and with so much selfishness. I wonder if it is merely a lack of understanding, or a symptom of a more fundamental social focus on individuals vs. collectives.

Some people are too relaxed
I was very surprised to see stories in my twitter feed of crowds flocking to climb Mt. Snowdon and filling out beaches in Florida and Bondi. While I am feeling relaxed when it comes to my personal safety, wider compliance with public health directives such as social distancing are needed for those policies to be effective (see also vaccines).

Misleading headlines make me angry
Please take care of the media you engage with. I generally feel positive about coverage from the guardian, but headlines like Australian man, 36, diagnosed with coronavirus dies in Iceland are deceptive. It is designed to grab your curiosity (or fear) about the pandemic, and clearly implies that the Australian man was killed by COVID-19. The disease is most lethal in older people, so a younger person dying is notable. But the reality brought by the third sentence is:

“While he was found to be infected with the coronavirus, it is unlikely to have been the cause of his death,” epidemiologist Dr Thorolfur Gudnason,

I.e. an accurate headline is “Australian man, 36, dies in Iceland of unknown causes whilst infected with coronavirus”. This is a problem; in a media saturated landscape many will scroll past the headline in a feed, and it will add to anxiety needlessly.

Harvard Medical Students COVID-19 Curriculum
A friend passed on this resource, which I think provides a good balance of brevity and comprehensiveness on the disease.

Photos from the week

Marathons have been cancelled which takes the pressure off. I can take my time to get back into higher mileage running. It also means I enjoy the scenery a little more.

2020 Week 11: Epidemiology

It was another exciting (but confidential) week at ONI. Evenings included a little live music, training, reading, and trying out the game Terraforming Mars. The increase in daylight going into spring is improving my mood, and conversation continues to be dominated by COVID-19.

Things I wrote this week

People are dying from a new strain of coronavirus, but I am not worried. I try to explain why in this note.

Things to share this week

There has been good news on viruses: the last patient being treated for Ebola was discharged, starting the final count down until the outbreak can be declared over.

Honeywell, as a google image search will suggest, are mostly known for making safety equipment and thermostats. As a chemist, I also am familiar with buying Honeywell research chemicals. In this paper they have revealed that they are also developing quantum computing. While a huge conglomerate like Honeywell doesn’t need its various business units to be aligned, there is a (tenuous) link between thermostats and quantum computing. The delicate states of the ytterbium ions that hold the quantum information require ultra low temperatures, in this case -260.5°C at the trap.

Political news about the democratic primaries quietens down as Biden seems to have secured the nomination. Meanwhile the internet continues to create conditions for fierce political conflict, the latest battleground being the knitting world.

New Zealand has a unique wildlife, including a historic lack of mammals, and subsequent flourishing of bird life. On the arrival of mammals (including us humans) bird life that had existed without predators suffered, but this recent paper shows that is not entirely due to lack of intelligence in birds.

Rockets are expensive, and not just the kind that will get us to Mars. “Israel, for example, routinely expends $50,000 interceptors on home-made rockets that cost about $1,000“. The solution to this? Lasers.

Photos from the week

A note on fear and death under the current pandemic

Short version:

Since I posted last week, coronavirus continues to dominate media and conversation. First, my advice is unqualified, go to the NHS and CDC instead. If you’re here for my thoughts they are:

1. Don’t panic. It doesn’t help, and this is relatively normal.
2. Journalists know less than clinicians and epidemiologists. Avoid media, instead use the NHS and CDC. For scientific updates, the WHO and journals (The LancetThe New England Journal of Medicine, and Nature). Engaging more than once per day is not helping you stay healthy. Stress weakens the immune system.
3. If you’re healthy and under 50, your personal risk is very low (but the elderly should isolate).
4. If this pushes you to take care of your hygiene and health as you should have been doing already, that’s great.

Long version:

Death

Currently, my media (and conversation) are saturated by the coronavirus pandemic. People seem generally frightened. As I write this, there have been just over 5000 deaths, the first being on January 11th in China. Of course as you read this that number will be higher, and if you are reading it relatively soon it will likely climbing at a faster rate. The final death toll will likely be in the millions. That is, of course, terrible, but it is only terrifying if these numbers are the first point of engagement with public health statistics. This paper from the Journal of Emergency Management points out that the flu outbreaks in 1957 and 1968 both had death tolls over a million, and while the flu of 1918 is being cited as analogous, it hit a population exhausted by 4 years of world war, and when life expectancy was under 50 due to bacterial infections (penicillin being discovered in 1928). People are dying constantly, for example in our modern context:

About 150,000 people die every day
42,000 die from heart attacks and strokes
11,000 die daily due to air pollution
8,000 die from lower respiratory infections (like COVID-19, but this data is from 2016)
4,300 die from diabetes
4,000 die from tuberculosis, every day
4,000 die from malaria, every day
3,800 die from motor vehicle accidents

So, in context, the total deaths we have seen over two months are on a similar order of magnitude to the deaths associated with car accidents or diabetes that happen every day. That said, the death rate will climb, and public health interventions can flatten the curve (worth the click through) to help save lives, but I feel that a significant part of the fear of death is the relative unfamiliarity of most people with it, when it is a very common occurrence.

A note where I hedge: As discussed in 2019 Week 32: Unsympathetic Science, mass shootings draw attention (and therefore public fear) to gun deaths despite being a regular occurrence in the US. I feel the situation here is similar in that the initial fear creates media interest which in turn creates more fear and the feedback drives a frenzy. Unlike the diseases we are familiar with, there are many unknowns to coronavirus, and there is a possibility that it overtakes the causes of death described above.

Reactions

So the psychological behaviours of this pandemic is also interesting.

1. Hoarding toilet paper seems extremely odd to me, and I made the observation that no one has ever died from a lack of toilet paper. Large parts of the world don’t use toilet paper at all. I assume people, being afraid, want to take action to attempt to feel prepared. Panic buying is a self fulfilling prophecy: since stores stock shelves based on what they usually sell, when a sufficiently large minority feels they need to stockpile, they create the shortage they are attempting to prepare for.
2. This virus seems to sit at some optimal point for generating a media frenzy. Health issues like obesity or opiates have not been able to capture the public consciousness to the same extent. Even the return of previously eradicated diseases like measles has not fully captured the public consciousness. Perhaps the authoritarian lock down by the Chinese government creates a setting that lends itself to the public imagination.

A thought experiment I have been playing with:

If you are afraid of the current coronavirus pandemic, how much would you pay to avoid it. £10? £100? £1000? Much more? I would guess you are more afraid of (and therefore willing to pay much more to avoid) coronavirus than you would be of a regular flu, but the flu kills many tens of thousands each year and many people don’t feel the need to buy the annual vaccine. Presumably you are more concerned with death than with suffering the fever or cough, and so whatever the amount you price avoiding coronavirus, I would expect you would also pay to avoid a heart attack, stroke, cancer, or lethal car accident. Given that, here are some things you can do to decrease your chance of death by a much more significant amount!

Stop smoking

Smoking statistics are intense. Smoking kills more than 0.1% of the US population each year (a likely estimate for the total coronavirus deaths), but 5% of the US population has a smoking related disease right now. With 300 under 18s becoming daily cigarette smokers every day, this is not a problem that comes from “before people knew it was bad for them”.

Drive safely

You probably know of someone who died in a car accident. Driving under the influence of drugs or alcohol and speeding are known to be dangerous, but in the US alone 9 people die each day from distracted-(using a smart phone while)-driving.

Maintain a healthy weight

Costing obese UK citizens 9 years of life expectancy, poor diet is catching up to smoking as the single worst health decision a person can make. Cutting back on high calorie low nutrition food (e.g. sugary drinks and snacks) and finding time to exercise regularly makes you less susceptible to a wide range of diseases (including coronavirus).

Prepare to get help for mental health

Addiction kills slowly. Suicide kills quickly. Both are preventable if people can get help, but when help is needed most it is hardest to navigate towards it. Start talking to friends, loved ones, and your health services about mental health and drug use, so that if things do go bad one day, you’re familiar with the system when you actually need it.

Note, I did not have time to convert DALYs into expected years of life saved for each of the above decisions, but this paper has a very useful table if you want the numbers.

Other things that didn’t fit above but I wanted to share:

A disease burden of influenza special issue from 2018

Netherlands infectous disease burden

Highly shared summary on slowing the disease progression from Tomas Pueyo

How long the virus survives on stuff

Economist explains the structure of the virus and how it relates to possible drug targets.

2020 Week 10: Coronavirus

My physical and mental health are good. Life is satisfyingly busy. Lots of time this week eaten by logistics, so a brief post on the topic of many conversations this week.

Things to share this week

Coronavirus

The new strain of coronavirus is being covered widely in the media. The latest scientific information can be found at The Lancet, The New England Journal of Medicine, and Nature. This virus has drawn huge attention, particularly compared with other common transmissible diseases. It is good that people are learning to take hygiene and self imposed quarantine seriously, since the common flu strains cause tens of thousands of deaths each year. It is not good if people panic, and I echo the sentiments of Dr Abdu Shrarkawy, particularly: “Temper fear with reason, panic with patience and uncertainty with education. We have an opportunity to learn a great deal about health hygiene and limiting the spread of innumerable transmissible diseases in our society.”

Side point: perhaps the most striking example of the gap in public understanding of epidemiology is the hits to Constellation Brands‘ “Corona” beer. An example of fearful lack of patience comes form the brief Australian toilet paper shortage.

Photos from the week

2020 Week 9: Book thoughts

Some exciting breakthroughs at work leave less time for extracurriculars. Life is generally good.

Things I wrote this week

I finished writing some thoughts about The Lady Astronaut of Mars series by Mary Robinette Kowal.

Things to share this week

Twitter backlash can change a person’s life. In this 2015 New York Times Magazine article a person making jokes (in poor taste) to her 170 followers went viral and triggered an outpouring of public shaming. The internet makes the spread of information so fast and irreversible that I am fearful of making a mistake that lands me in infamy.

I learned about this glider that you can launch by running and I want one. (Video of it in action). Much of my excitement is driven by the possibilities of carbon neutral air travel. Related; this scientist has turned to tree planting to offset the emissions from his air travel.

Earth temporarily has two moons! (Technically a temporary satellite).

Bill Gates writes some sensible thoughts on COVID-19, he has been advocating better pandemic preparation for some time. I hope to write a longer piece on the virus soon.