Short version: This week I returned to studying, worked some long hours, and had my usual running routes blocked by some very wealthy children.
Taking Notes on Laptop vs Paper
I started a molecular biologyMOOC. The beginning of the course suggested note taking on paper is more effective, and cited this study. It was persuasive, but I will continue to mostly work digitally. I justify this by the ease of carrying, organising, and searching digital notes being more convenient than paper systems. This reminds me of the observation that smart-phone-toting-always-online-humans are effectively cyborgs, with tremendous capabilities for memory, problem solving, and long distance communication. That said, I do find scrap paper to sketch diagrams very helpful in the initial learning.
This week I performed some long experiments, and was complimented by colleagues on being able to sustain energy and remain positive throughout. On reflection I think maintaining good physical health (via exercise and diet) plays a significant part. Avoiding insulin spikes from binging sugar helps, even though appetite will increase during the small hours from sleep deprivation. Knowing how long you need to keep going and spacing caffeinated drinks across that time helps too. Importantly I have learned that some sleep is better than none. To prevent a heavy workload from becoming impossible; minimise unnecessary tasks and focus on completing only what is needed, then recovering (sleeping). Finally it is important to account for a diminished capacity when planning. As you tire speed of work decreases and rate of mistakes increases. Thankfully I am part of a very dedicated and supportive team, and so we are able to work together to ensure the experiments run to plan.
Flood of Children
The University of Oxford has prestige which, beyond the university itself, is used by businesses to create demand and profit. Tutoring school aged students is such a business. Summer programs run by groups unaffiliated with the university (but often using holiday vacated undergraduate accommodation) bring hundreds of teenagers to Oxford for courses costing thousands of pounds. The associated walking tours lead to pedestrian congestion as the children are shepherded around the city center (pictured below).
Short version: This week I had a couple of students in the lab for work experience, and it reminded me how much I enjoy teaching. Some thoughts.
One of the joys of my education was being repeatedly challenged to answer questions that I didn’t know the answer to. I found this an incredibly powerful way to learn both information and problem solving skills. It requires capable teachers with time to be able to explore each student’s individual thinking, as well as confident students.
Students are used to being tested on content they ought to have learned, being praised for preparing and chastised for a lack of practice. Thus it can be disquieting for them to be confronted with a question they have not prepared for. Post-education this is not very useful when working in science, where questions need to be answered that have not been answered before.
A wonderful example of taking relatively common experiences and following a path of questions and answers is “Fun to imagine“, an armchair conversation with Richard Feynman.
Science through fresh eyes
There is an XKCD comic for many situations, and one such specific situation is that there will always be many people who have yet to learn something you take for granted. In the lab, my team and I get to take for granted the understanding of many scientific concepts. However, through the eyes of inexperienced students the mundane becomes new. This is easily seen as a weakness of the students, but it is also joyful to see tools and ideas I take for granted be seen as exciting and new.
A good example of this is Pendulum Waves, which was demonstrated at the Cowley Carnival (see below).
If you play these games of asking and attempting to answer questions, often your guesses will be wrong. In order to persist and learn you must enjoy the game, and therefore you must be able to enjoy being wrong. CGP Grey summaries it well: “if you want to always be right, you have to always be prepared to change your mind”.
Short version: Vitamins are important, but confusing. I am learning to row.
The discovery of chemicals needed to sustain animals (including humans) other than minerals (e.g. salt) and the three macro-nutrients (protein, carbohydrates, and fats) is described in this paper. The term vitamins itself was coined by Casimir Funk who formed the portmanteau from Vital Amines. Particularly interesting to me was learning that the advent of the highly useful germ theory of disease led to the assumption that conditions caused by vitamin deficits (e.g. scurvy) were also caused by unknown pathogens, resulting in debates around the existence of these other nutritional compounds. The Wikipedia list of vitamins gives some chemical and medical insight into vitamins. Historically it seems that improvements in chemical extraction, purification, and structural determination led to the intermediate letter based classification we still use today, despite a more precise chemical understanding of these compounds having been achieved.
Short version: I travelled from Oxford to Sydney and back within a week. That is incredible, but sadly places huge costs on the environment.
Antipodes This week I needed to be in Sydney for one day. To make the round trip in a week, about half the time is spent varyingly on flights and in airports. This left plenty of time to marvel at how trivial it now is to travel around the entire planet. Sydney is close to being on the opposite side of the planet (the antipode) to Oxford, so the total journey of 16,983 km is not far off the maximum distance two points can be from each other on the surface of the earth (approximately 20,000 km). Interestingly that antipodal distance is slightly less than half the 40,075 km equatorial circumference, due to the deformations in the shape of the earth. I was unable to easily find an exact calculation of the furthest two points on earth, due to errors in the data set, and the ever changing shape of the planet.
Fuel Efficiency and Carbon Impact Passengers in a 747-400 have a fuel efficiency of about 3.1 L/100 km vs 10 L/100 km for cars. So a car with three people and a typical flight have the same carbon impact over the same distance. Thus my out and back journey consumed about 1000 L of fuel, producing 2500 kg of carbon dioxide. This is similar to the carbon emissions for a year of either eating a 75g hamburger per day, or heating a UK home.
Airborne Population (Fermi Problem)
With increasing demand and decreasing costs of air transport, at any point in time there is a proportion of the population on flights. Three ways of estimating this population:
Extrapolate from a single data point If I assume everyone flies as frequently as I do (2 days per year, and multiply by the approximately 7 billion population on earth, that gives 14 billion flying days. Dividing this by the days in a year gives about 400,000,000 airborne people at any given time. Intuitively seems very high; it reflects my financial privilege that I fly much more than the average person.
Make a set of intuitive assumptions Taking the following rough guesses: 1. all the flying is done by the wealthiest billion people 2. for every million of these people there is an airport where 3. a flight takes off every 15 minutes, 4. those flights last two hours, and 5. seat 500 people. Calculations: (flight duration = 2 hours) ÷ (flight frequency = 0.25 hours) × (airports = 1000) × (passengers per flight = 500) = 4,000,000 airborne people at any time. This result seems more realistic, and fits intuitions that very large cities of many millions tend to have multiple airports, or large airports with multiple runways. Flights might run longer, but also less frequently over the night. Some large aircraft can carry more than 500, but are fewer and travel longer routes.
Use one highly relevant fact Looking up a key fact, that there are 700,000,000,000 Revenue Passenger Kilometres flown per month, and knowing that the cruising speed for jets is about 900 km/h. Allows the simple calculations (distance travelled per month) ÷ (speed) ÷ (hours per month) gives an approximation of 1,000,000 airborne people at any time.
General Notes Time of day and season would cause the actual number to vary significantly with time. Particularly peak travel periods around regional holidays (e.g. Thanksgiving, Diwali, Chinese New Year).
Short version: Technology is amazing. Cycling can be dangerous.
Technology is amazing, and as a scientist I am very lucky to work with some of the latest, most advanced, and highest tech machines that exist. Sharing that excitement can be difficult however, as being able to measure with very high precision is not a particularly visual phenomenon. Manipulating the protein and nucleic acid building blocks of life is challenging and rewarding, but ultimately happens in drops of water that, to the naked eye, are indistinguishable to those from a mundane context.
Occasionally I have given tours of laboratories, and often I feel the equipment and materials present must be underwhelming to the visitor. The reality of science, when compared with science fiction, requires the machines we use to be simple, robust, and compatible with the rest of the lab. For example, transparent equipment with bright flashing lights is great for setting up interesting shots in a movie, but when experimental conditions need to be carefully controlled, simple refrigerator-like boxes are often the better solution.
The prevalence of powerful modern technology means that what is captivating tends to be a common phenomenon presented in an unusual context. Glowing materials can be striking (and an inaccurate representation of nuclear radiation in cinema) since most objects do not naturally emit (visible) light (at standard temperatures), but emission of light is a pretty routine phenomenon (you’re reading this on a glowing screen). In the context of the lab, a fluorescent tube or a glow stick might seem to have some high tech implication, but in an office or a disco, they are common. Similarly it is often a climactic point in a characters mastery of magical powers to lift an object with their mind, but a forklift or crane is somehow much less the substance of fantasy.
A few particularly exciting instruments I’ve had the privilege to work with:
I enjoy consumer technology, and fondly recall walking the cavernous trade show floor at CES. The sheer volume of sales of consumer devices helps to dilute the cost of design work, both in physical hardware and in virtual interfaces. The result is that the aesthetic experience of using a consumer device is often significantly better than that of a technologically more advanced scientific device. Youtubers like Lisa Gade, Marques Brownlee, and Dave Lee share the experience of the latest consumer devices, but I often feel conflicted watching such video. While fun, such content feeds into unnecessary marketing driven consumption that I is a social and environmental blight. I also find sports gadgetry a compelling source of procrastination, e.g. DcRainmaker‘s blog.
In March while cycling I was involved in a collision on the way to work. Luckily I came away with only very minor injuries. It is a useful reminder that there are risks to using the roads, and that those risks can be minimised. Three thoughts:
Have your kit in order: Wear a helmet. Large meta-studies say they help. Doctors in emergency departments have told me they help. Bicycle helmets have saved me from major head injuries at least three times. Making sure they fit is important. After damage replace them. Check that your brakes are working and work well, and practise stopping hard, especially in difficult conditions like downhill or in the wet. Wear visible clothing. You need to be seen.
Ride like you are invisible: Even when wearing high visibility clothing and using lights, it should be assumed that cars cannot see you. Even in cities where cycling is less common, drivers might only be looking out for cars and miss cyclists, something that’s particularly common when waiting to turn across traffic. Cars have a physical structure that can create blind spots. Many drivers are distracted by phones or passengers, especially when travelling at lower speeds or through slow moving traffic. Ultimately, the risks you take by assuming you will be seen by other cars can be minimised, even if it ought to be the responsibility of the drivers.
Organ Donation: If you lost your life in an accident today, I would be devastated. But a sad day is worse if someone else misses their chance to live because we didn’t submit a trivial form. Please sign up to be an organ donor: AustraliansUKUSA
Short version: I grew up thinking science-y people weren’t fit, but there is plenty of fitness in science, and scientific reasons to keep fit. I share some thoughts on anatomy, metrics, protein powder, and astronauts.
I remember thinking of exercise as inherently a waste of time; why would you ever want to run in circles and just end up at the same place? I’m sure this was in part informed by the mediaI consumedgrowing up; portraying the stereotypical nerd as being interested in mathematics, science, technology, along with a lack of physical fitness (also, in retrospect, portraying very fit people as not particularly bright). I identified with those archetypes and spurned exercise through much of school, as did many of my peers. It was later in life that I realised improving cardiovascular endurance was important to health. Starting to run I discovered the joy of Runner’sHigh. A competitive mindset and an internship in an anti-doping laboratory led me to build regular exercise into my routine, something I’ve enjoyed maintaining for the past few years.
Athletes setting world records are obviously different from the norm. Skill, dedication, talent, training, and genetics all contribute. I find conversations about athletes success tend to drift towards the genetic element, perhaps the intrigue is due to the allure of quantifying potential, or perhaps it provides a comforting fatalism for the undertrained. Most likely it is interesting simply because it is poorly understood compared with the simplicity of regular training or perceptible skill.
David Epstein gave a TED talk in 2014 where he shared a number of facts about the nature of athletes’ physicality. It particularly stood out to me that a transition in sport occurred (in parallel with the rise of broadcast media) from favouring a generalist body type of average proportions, to a plurality of extremes. One of the most memorable statistics is that Hicham El Guerrouj and Michael Phelps, who differ in height by 17 cm, have the same length legs (running advantages longer legs proportional to height, whereas swimming is the opposite). These characteristics are difficult to change: no amount of training will allow these two to exchange their body type. Training can however alter different aspects of the body to similar extremes.
Physiological adaptations from training can be as radical as the size difference between NBA basketball players and Olympic gymnasts. Specifically, athletes’ hearts really are significantly bigger than those of the untrained population (particularly endurance athletes). The body responds to stress, and the process of repeated exertion to influence adaptations that increase performance for a given activity is the basis of all training. When I worked in anti-doping an office legend described a cycling team that, in the days before blood doping was banned or effectively enforced, would need to sleep with heart rate monitors that would wake them if their heart rate got too low for fear of their hearts stopping altogether.
Marathon Times and Personal Metrics
I’m pretty motivated by quantifiable goals. Either arbitrary times (usually round numbers) or achieving a certain relative performance (e.g. placing in the top 1%). This paper examining marathon finishing times suggests I’m not alone. Times tend to bunch below “whole numbers” such as 3 hours and 4 hours, as well as smaller bunching observed across 5 minute increments, as people dig a little deeper to get below their goal times.
The literature suggests that, when combined with training, protein supplementation increases gains in strength. I find that protein powder is a convenient way to add protein to my diet, particularly as a vegetarian. The NHS points out that the same benefits of protein powder can be achieved from other protein-rich foods, and that the lack of vitamins and nutrients of protein powder compare to a balanced meal make it a poor replacement for meals. It also recommends not exceeding intakes of 111 g per day for men or 90 g for women, which more or less concurs with the BMJ’s study suggesting the benefits of protein supplementation cease after 1.62 g/kg/day i.e. 120 g for a 75 kg person.
That all said, there are good reasons to be skeptical of any benefit of supplementation at all beyond a healthy balanced diet. Trying to define a healthy balanced diet though could easily be several papers (or blog posts) by itself.
Short version: I write about the top 21 highest impact papers of 2018 according to Altmetric, a rank based on mentions in academic publications, news media, and social media. They mostly relate to health or the environment.
Metrics and Rankings
It is interesting and useful, but difficult, to be able to compare the quality and impact of publications. There are many methods to quantify this, one of which is Altmetrics. This scores publications based on mentions in the news, on Facebook, in patents, and other sources which are tallied and weighted. Since it takes less time to write a tweet than a citing publication, Altmetrics respond much more quickly and reflect a much wider potential audience than more conventional measures, but for the same reasons are less accurate measures of quality.
The US centric nature of the metrics comes out clearly with the top ranked paper being about deaths in Puerto Rico after Hurricane Maria. PresidentDonald TrumpwasnotgoodtoPuertoRico. The study measured 4645 excess deaths from 20th September 2017 to 31st December 2017, 70 times higher than the official toll of 64. Deeply disturbing.
I am disappointed to have missed this paper in Week 5. This article from The Lancet recommends the best level of alcohol to consume is none, finding alcohol causes deaths through tuberculosis, road injuries, self harm, and cancer. There are some clever methods used to look at measuring actual consumption by individuals, presented in maps on the third and fourth pages.
This is pretty grim. Describes the “Hothouse Earth” as “…a pathway that could not be reversed, steered, or substantially slowed”. Talk to people about climate change. Work out what you can do to minimise your impact. Katharine Hayhoe has a great facebook page that can help bridge the gap for climate change skeptics.
Exercise usually makes people feel better, and the biggest rewards occur going from none to some. While your brain does use a significant proportion of your daily energy expenditure, the rest of your body needs movement to function properly. This study quantifies that relationship with mental health, finding optimal benefits from sessions of about 45 minutes and 12 to 20 sessions per month.
Studying nutrition is made difficult because the timescale of the effects you are trying to measure (over lifetimes) means that experiments are difficult to control. That said this study finds that ideally 50% of your energy intake should come from carbohydrates, and if you cut carbs, you should not supplement them with animal fats and protein, but go for plant based options.
Just because information is painful or disappointing, doesn’t mean it should be ignored. This paper described the exponential growth of plastic in the Great Pacific Garbage Patch. This SMBC comic is highly relevant.
The death of Steve Jobs is a famous case of “Complementary and Alternative Medicine” demonstrating that brilliance in one area is not mutually exclusive with stupidity in another. This paper points out that cancer patients who opt into these unsubstantiated treatments are more likely to refuse more established medicine, and therefore are twice as likely to die. Relevant Tim Minchin beat poem.
The Great Barrier Reef is undergoing a series of bleaching events. While bleaching does not guarantee death, the longer the bleaching the harder it is for corals to recover. This study quantifies that relationship, and finds a nonlinear relationship where prolonged or intense heat results in rapidly increasing losses. More recently a million tonnes of sludge is to be dumped on the reef. The SMBC comic is still highly relevant.
Discussed in The Economist, this paper from Harvard Business School finds open plan offices seem to counterintuitively decrease face to face interactions and increase online communication. Having worked in a few different office layouts, I would suggest that the staff themselves make a bigger difference to communication than the layout. Also sociometric badges are a thing.
Although being slightly more positive on drinking than the alcohol study above, particularly noting “increased alcohol consumption was log-linearly associated with a lower risk of myocardial infarction”, overall the study found a decreased life expectancy overall for alcohol consumers. It goes on to suggest lowering the recommended limits for alcohol consumption to less than 100 g per week.
The US continues to confuse the rest of the world with its views on health care. Specifically this study reveals that of US cancer patients, 42.4 % will have used up their entire life savings within 2 years.
It doesn’t seem to matter if you cut down on calories via lowering fat or lowering carbohydrate consumption, so long as you’re consuming less you will lose weight. Particularly interesting is the undermining of genotype evidence.
It’s interesting to question the causation here: are Russian Trolls trying to lower vaccine acceptance to weaken health in the US, or are they trying to build rapport with people prone to unfounded conspiracy theories, such as being anti-vaccine, to then promote other (political) falsehoods. Also: how vaccines work.
I’ve had several friends in medicine mention their direct observations of this in individual patients, but here it is presented as the aggregated results of 306 individuals. Weight loss results in remission of type 2 diabetes.
Coffee (maybe) is good for you! But the study suffers from “a ‘healthy volunteer’ selection bias”. Interestingly “Participants drinking 4 or more cups per day … were more likely to drink instant coffee and be current smokers, whereas participants drinking 1 to 3 cups per day were older, more likely to have a university degree, and more likely to report “excellent” health.” So the causation question remains: does coffee make you healthy, or do healthy well educated people drink coffee?
It’s a little unsatisfying to be able to spend so little time on such interesting questions, but the nature of inquiry is a trade off between breadth and depth. This week I opted for breadth, and it serves as a reminder for how much interesting content there is being generated in the world.
Short version: Writing accurately about science takes time, but a few bits to push in that direction. 新年快乐!
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.
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.
Short version: I’m drinking a bit less, the media still likes skewing science to get page views, live music is wonderful, it snowed more in Oxford.
Personal Experience: Last week I wrote about having made the change to not eat meat. More recently I’ve been toying with cutting back on alcohol. Throughout January I observed a one drink per day maximum. This was most difficult socially, as I don’t have a single reason for cutting back, and there are many contexts where accepting drinks is the polite behaviour. Moreover it often felt more difficult to explain setting a threshold of one, than simply saying I didn’t drink, or was undertaking Dry January. I think in general this comes from a desire for principled consistency. While consuming alcohol is fun, I felt overall I was able to have just as good a time while consuming less, with benefits felt in sleep and recovery from training.
Guidelines: The Australian Government Department of Health recommends no more than two standard drinks per day long term and no more than four standard drinks per day (where a standard drink is 10 g or 13 mL of ethanol). The British NHS has a similar 14 units per week, to be spread over 3 or more days , but using smaller units (8 g or 10 mL of ethanol). Of course the US is a little trickier to compare due to the lack of the metric system but the CDC recommends one drink for women and two for men, with much larger units (14 g being 0.6 ounces, or 18 mL).
I listened to the City of Birmingham Symphony Orchestra perform Prokofiev’s The Love for Three Oranges: Suite, Beethoven’s Violin Concerto, and Vaughan Williams’ Symphony No. 4. I particularly enjoyed the drama of the final piece, and the incredible energy of the orchestra. The soloist Augustin Hadelich has a pretty incredible life story, and incredibly clean sound.
Short version: Why I don’t eat meat, some things I’m reading at the moment, and three photos from my week.
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.