Science – Page 2

2020-03-152020-03-16

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 Lancet, The 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.

2020-03-01

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.

2020-02-232020-02-25

2020 Week 8: Do the living outnumber the dead?

Life is busy, I over estimated my ability to find time to read this week, and have started but not finished several texts. I (correctly) sought professional advice for some minor tendon issues, and running is feeling much more comfortable with some specific rehab exercises. I met two researchers in cyber security, and it turns out in the UK there are fairly strict laws on signals interception which make their research difficult. In other news a Russian satellite is probably stalking a US spy satellite in orbit.

Things I wrote this week

No longer posts again this week. I’m working on summarising some books I’m reading.

Things to share this week

Do the living outnumber the dead?
The short answer is no. While the global population has grown rapidly, the current 7 billion is far fewer than half the estimated 100 billion who have ever lived. This sort of population growth estimation reminded me that the sum of the n-successive powers of two is less than 2 to the power (n+1), so if the population was consistently doubling within a lifespan, then there would be more people alive than had lived previously. There is a nice intuitive explanation of this;
Consider binary
Binary 1 is Decimal 1
Binary 10 is Decimal 2
Binary 100 is Decimal 4
Generalising; binary 1 followed by “n” zeros is expressing 2 to the power n
Intuitively; the smallest four digit number is always larger than the largest 3 digit number
I.e. 1000 > 111 (or 222 for base 3, or 999 for base 10)
So the sum of 1+10+100 is 111 in binary (or any other base) which is less than 1000, and so 2^n > {2^(n-1) + 2^(n-2) + … + 2^1 + 2^0}
(I will look up how to express mathematical formulas on my own blog in future)

Science was stranger in the 1960s
NASA funded a project involving humans trying to train dolphins to speak by living with them and injecting them with LSD. Covered by The Guardian and New Scientist. Details probably in this book (but I haven’t had a chance to check it out).

The following come from my (current) three biggest sources of lost time, YouTube, Unnecessary-Fitness-Reading, and Chess.

Elon Musk reminds me of the importance of minimalism in production
Quote: “The best part is no part, the best process is no process“
Context: Musk gives MKBHD a tour of the Tesla Factory, and explains that removing unnecessary parts or processes from a product removes a risk of failure at no cost. In the case of Tesla, increasing production speed is a major issue, so eliminating unneeded steps leads to better manufacturing.

Strava makes more cool info-graphics
This time looking at motivation for running.

NBC covers boom in chess streaming
This article about e-sports sadly leaves out my favourite chess streamer, Jerry.

2020-02-16

2020 Week 7: Curfew

This week, in several situations, I ran out of time. By not setting end times for experiments, training sessions, or social occasions, I find myself realising on reflection that I regularly continue longer than would have been optimal. Of course the future is unknown, but making an estimate of how much time I ought to spend before I start, and then evaluating the situation once that time has elapsed, should help me to fit more into each day. This week’s longer post on productivity is highly relevant.

Things I wrote this week

I finished a set of thoughts on how to get more life into the fixed amount of time each day, i.e. productivity. Eventually I’ll reorganise the homepage of this website to have pages dedicated to a few significant topics, and I suspect productivity will be one of them.

Things to share this week

Atmospheric Optics collates visual phenomena that occur due to the spontaneous formation of optical systems in the sky, a common example being rainbows. Thinking about ice halos reminds me of X-ray crystallography, perhaps the most famous example being Photo 51.

Emma Stoye of Nature collated scientific photos from January, including the tracks from the head-crab like robots I shared a couple weeks ago.

The UK brought forward its ban on cars that burn hydrocarbons to 2035, some good news for the climate. I suspect unrelatedly, Telsa shares broke $1000 (and continue to be the centre of reddit shenanigans).

Artist Simon Weckert walked around with a cart full of smartphones to trick google maps into plotting non-existent traffic jams. Whilst I find google maps traffic useful on the rare occasions when I drive, I find the “performance” of having a bright red cart full of smartphones intruding into live updating maps a cute reminder of the difference between reality and abstractions.

Photos from the week

2020-02-09

2020 Week 6: Fragile

A satisfying week of ratcheting up my output. Some long but interesting experiments at ONI, catching up on reading, a couple of social evenings, and the most intense week of training since September 2019. That said, I’ve been feeling a little fragile. My physical and mental health are both good. I’m happy with what I’m getting done each day but have caught myself with muddled thoughts here and there. Particularly, I am worrying about illness and injury a little more this week. A couple observations on this:
1. The news of coronavirus outbreak in Wuhan is causing alarm, but people are generally much less concerned about familiar diseases such as influenza. In the case of a far away outbreak, I can follow the advice that after taking reasonable precautions (e.g. washing hands before eating) it is foolish to worry about the possibility of getting sick (there is no need to suffer before the actual illness starts). I was not able to follow this advice when a different viral outbreak occurred in my social circle. I am vaccinated, and so very likely immune, but knowing I have been exposed directly it is difficult to silence my paranoia.
2. I have been recovering from a running injury, relatively minor but still the most significant injury I have had to date. I am left feeling much more vulnerable than I did before my injury, even though I ought to have been following the same injury preventing exercises either way. I let the idea of being particularly resilient become entwined with my identity, and having that misplaced belief confronted is emotionally challenging.

Things I wrote this week

The irony is not lost that I continue to delay a piece on productivity. I’m also writing about The Fated Sky (link to publisher and extract) which I finished reading this weekend.

Things to share this week

Donald Knuth and getting to the bottom of things
Knuth is a legendary computer scientist, and as well as writing The Art of Computer Programming, he also wrote the dialogue Surreal Numbers, or Surreal numbers: how two ex-students turned on to pure mathematics and found total happiness: a mathematical novelette. I recently learned that he does not use email, as he explains here:
“Email is a wonderful thing for people whose role in life is to be on top of things. But not for me; my role is to be on the bottom of things. What I do takes long hours of studying and uninterruptible concentration. I try to learn certain areas of computer science exhaustively; then I try to digest that knowledge into a form that is accessible to people who don’t have time for such study. “
I find this inspirational in several ways: I aspire to find a passion that allows me to focus so clearly on the one goal. I would love to have the opportunity to pursue that passion so single mindedly as to not need the convenience of email to “stay on top of things”. I would love to reach expertise where others go out of their way to reach me despite not using email.

The Dalek Game
While opening too many tabs writing about The Fated Sky, I came across Kathleen Jennings illustrations of Daleks, based on a game played by replacing words in titles with the iconic Dr Who villains. Related; I look forward to trying Blurb Wars next time I’m with some creative people.

Functional Threshold Power
FTP is the maximum power output that a person can transfer (e.g. to a bike or rowing machine) continuously for an hour, and is a common measure of cardiovascular endurance amongst cyclists. I’ve been looking at this set of charts about FTP, and it is humbling to see myself on the left tail of the distribution. Some relevant literature from Nature.

Photos from the week

Rare winter sunshine on the river Thames

2020-01-26

2020 Week 4: Xīn Nián Kuài Lè! 新年快乐!

Saturday was Chinese New Year, and I was fortunate to celebrate in traditional style by making dumplings and watching the CCTV New Year’s Gala. 2020 is the year of the rat, and the first year in a new cycle of 12 years. The ordering of the animals is explained in this amusing story.

Things I wrote this week

No longer posts to share just yet, I’ve been working on sharing some thoughts about productivity, and am hoping to finish it off in the coming week. I’ve also started writing some fiction, for the first time since school, inspired by a writing club which has started at work.

Things to share this week

Chinese news wasn’t all song and dance, the Wuhan virus caused the lock down of two cities, Wuhan and Huanggang.

Davos hosts the World Economic Forum where Russia continues its cold war antics.

This paper caused some controversy; it is unclear if algorithms or people are driving more extreme content since we don’t know how the algorithms work.

Photo from the week

2020-01-19

2020 Week 3: Acceptance

This week I celebrated both two years with ONI and twenty seven years of life in general. I felt particularly cared for by the people around me, and appreciated both that this is the case, and that I am aware and able to enjoy the feeling. It is one thing to accept someone into a community, but it is even more difficult to make them feel accepted.

Things I wrote this week:

Training Fasted, a spontaneous experiment I conducted, noting how my physical performance shifted in response to not eating over a 30 hour period.

Things to share this week:

A team from the University of Vermont, Tufts, and Harvard published the dryly titled paper A scalable pipeline for designing reconfigurable organisms. As the video from the Supplementary Information shows, the team have actually grown (or built) working biological machines based on computer aided designs. The resemblance to headcrabs is eerie, but the work is very impressive.

I came across this Zombie Simulation coded in R, while looking for help with my own R code. It reminds me of people who hack Doom onto TI-83 calculators.

I played two games of Captain Sonar, a chaotic submarine-warfare themed board game between two teams who must work cooperatively to out maneuver their opponents. Not an easy game to learn, but a lot of fun.

2020-01-09

2019 Altmetric Top 100

Fires in the Amazon and Australia, a case of HIV cured, and the 50th anniversary of the moon landing, were all big headlines for science in 2019. This summary of the science that shaped 2019 from Nature covers a few more stories. There is not one clear metric to quantify the “biggest” story in science, but Altmetric creates a ranking based on the media (social and conventional) impact of scientific papers. I previously wrote about 2018’s Altmetric Top 100, and this year I take a look at the themes.

AI and Fake News

The top paper of 2019 was this description of a system developed at Samsung to create realistic video of talking heads from single images. The authors provided a video summary of the work, and the result is impressive and unsettling. AI image generation also took out the 5th slot with image generation.

While crossing the uncanny valley remains a challenge for visual effects artists, the strong emotional reaction to this paper is driven by a fear. As it becomes easier to fabricate content, it becomes harder to trust the media we consume. There is also the fear that we could become victims of these “deepfake” techniques. Fake news was the subject of the 51st ranked paper “Less than you think: Prevalence and predictors of fake news dissemination on Facebook” and the 58th ranked paper “Fake news on Twitter during the 2016 U.S. presidential election“. On fake stories making real news; the 44th ranked paper about the 44th President’s birth was pushed up the altmetric rankings as “The researchers avoided calling the subjects’ views ‘racist’, earning them a high-scoring Twitter roasting.”, highlighting how issues of race can drive a flurry of discussion on social media.

The world is on fire

Bill Nye demonstrates the point on Last Week Tonight

As Climate change continues to worsen so do its effects. If you’re not familiar with the scale of the problem I recommend this briefing; Global warming 101. About 1 in 6 papers in the top 100 were on or about climate change, with 3 of the top 10. World Scientists’ Warning of a Climate Emergency has an authorship exceeding 10,000, stating that “Earth is facing a climate emergency”, and highlighting the disturbing gap between the scientific and political consensuses.

Human Health

Just as health research makes up a huge share of scientific research projects, so too did papers on health make up a big share of the altmetric 100. Many of the papers featured are only surprising in the unwillingness of the public to conform to the recommendations. Vaccines work (and do not cause autism), exercise is good for you and most people need to do more, highly processed food and sugary drinks are bad for you, and eating only junk can lead to terrible health (including blindness).

In a moment of doctors showing that publications don’t have to be more complex than “check out what this guy just coughed up”, this cast of the right bronchial tree was coughed up and became this publication, ranking at 19th.

This highly discussed paper (74th) was retracted, demonstrating both that scientific papers (even in top journals) should be questioned, and that scientists are actively doing that questioning. The article relates to the He Jiankui affair that made headlines for the gene editing of human beings, however that work itself has not been formally published, and the scientist himself was sentenced to prison.

Scientists have fun too

“Joke” papers such as 8th ranked “Parachute use to prevent death and major trauma when jumping from aircraft: randomized controlled trial” and 61st ‘”Death is certain, the time is not”: mortality and survival in Game of Thrones‘ show that scientists (and critically, publishers) can have a sense of humour too.

Take Home Points

With tools like google scholar and increasingly open access publishing, the scientific literature is becoming ever easier to consume.
AI is becoming more powerful at image generation and manipulation, and will threaten the reliability of video footage as evidence.
The climate has changed and the consequences are already being felt. Urgent action is necessary.
Whilst advances in medicine are lessening the burden of diseases, educating the public to make good choices on vaccines, drug consumption, and nutrition would have an enormous impact on health.
Publishers and reviewers have a sense of humour (requires further verification).