2019 Week 35: Tears, Triathlons

Short version: Back to work. Jocko’s letter made me cry and that’s OK. First triathlon, went fine. Sriracha sauce as a spaceship.

Long version:

Back to work

I returned to work this week after taking nearly two weeks of holiday. I continue to find it odd that when I am busier I also get more done, but I also suspect that is the combination of routines and inspiring colleagues. The ONI band is practicing more often, and live music provides a wonderful reminder of my family home. Hearing from others about their successes both in work and outside it creates some envy, but also motivates me to strive to make more out of my time.

Something that made me cry

At the end of my holiday I took some time to reflect on the past year, including when I experienced particularly strong emotions. Often in a professional context it is appropriate to suppress emotions, and it is also common that men feel the need to project a stoic facade at the world. In the past I have taken this too far and lost awareness of my emotions, which is detrimental. I still feel generally we should act out of reason rather than emotion, but we should also be aware of our emotions and use their patterns to guide our understanding of ourselves. To this end, I wanted to share this letter written by a Navy Seal to his daughter. It left me feeling a powerful mix emotions, seeing aspects of myself in both the father and the daughter. It left me in tears.

First Triathlon

I took part in my first triathlon on Monday. It was fun. I’ve written a race report you can read here.

Instagram Art

Social media is often an echochamber, but there are opportunities to find new ideas. This week I came across spacegooose who imagines everyday items as spaceships, e.g. Sriracha sauce.

Photos from the Week

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2019 Week 30: Every Olympic sport

Short version: The Olympics is one year away. The weather is getting hotter. Sometimes scientists lie. People keep doing impossible things. I’m more active on social media.

Long version:

Olympics

One year from this Wednesday, on Friday 24th July 2020, the Tokyo Olympic games will open. The games will feature 339 events in 33 different sports, encompassing 50 disciplines. Although playing sport was compulsory in school for me (I played tennis and football (soccer) poorly), it was only while working in anti-doping alongside passionate athletes that I became motivated to try more athletic activities. Since then I have found participating in sports gives me a much greater appreciation for the strength and skill of professional athletes (though many Olympians are “amature” as not all sports have enough of a following to create professional opportunities). This creates an interesting personal challenge: to attempt to “play” each sport between now and the opening ceremony in 2020, and thereby be a much more informed spectator.

Hot Weather

Oxford had the hottest day on record this Thursday, at 37 °C. The 38.1°C in Cambridge was close to the all-time record in the UK of 38.5°C [update: it was actually the hottest day on record]. For an Australian these are not particularly remarkable temperatures, where the “Angry Summer” heat waves were 10°C warmer again, but the ABC put out a video explaining why lower temperatures in the UK feel hotter. Climate change will continue to bring hotter and more frequent heat waves.

Investigative Science

Last week I wrote about staying up to date by reading work from other scientists. Publishing papers is how academic scientists progress their careers, which creates an incentive to cheat. To sharpen my skepticism I keep an eye on papers that get taken down for false or misleading data; Retraction Watch is a blog that covers such cheating. This week I stumbled upon their collaboration Forensic Friday, which lets you practice your ability to discern real and fake data.

People do Impossible Things

A couple times this week the incredible feats humans are capable of have come up in conversation. Talking about personal strength goals, my aspirations pale in comparison to athletes like Chen Xiexia who at a bodyweight of 48 kg set the olympic record for Clean & Jerk by lifting 117 kg overhead. A number of friends are experimenting with intermittent fasting, but even a fast of a few days merely makes the record 382 day fast more impressive (an interesting article about the line between fasting and eating disorders). I remember reading (though I struggle to find the source) that it was once thought there was a limit (approx 10) to the number of marathons the human body was capable of running, but since then several athletes have run more distance than a marathon a day for several days, including Terry Fox who ran 5,373 km with one prosthetic leg and suffering from cancer. Most recently I learned that the USSR banned blindfolded chess simultaneous exhibitions because of health concerns (Morphy, Capablanca, and Alekhine reported headaches from playing blindfolded matches), but you can watch Magnus Carlsen playing a blindfolded simultaneous exhibition match.

Social Media Activity

I’ve been much more active lately on social media, particularly uploading photos from this blog to instagram. I am interested in reaching out to more people. Aside from the vain joy of having a larger audience, I hope you (the reader) find some of my content interesting, or even better comment or reach out to guide me to create better content.

Photos from the Week

2019 Week 29: Front Page News

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

Long version:

Front Page Science

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

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

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

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

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

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

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

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

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

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

Night Runs

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

Photos from the Week

2019 Week 24: Vitamins

Short version: Vitamins are important, but confusing. I am learning to row.

Long version:

Vital Amines

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.

Also, multivitamins probably don’t do anything useful. Although, in the UK Vitamin D supplementation is useful in certain circumstances, especially winter.

Learning to Row

I am learning to row with City of Oxford Rowing Club. This was the second week of the six week beginners program, and below are photos of our second outing.

Photos from the Week

2019 Week 22: Street Art, Pride, Rowing

Short version: A colourful week, beginning with a day in Bucharest before returning from Romania to Oxford, where the streets were lively with Oxford Pride and Summer Eights.

Long version:

Street Art

Graffiti is a part of most urban environments (perhaps for as long as urban environments have existed) and continues to be seen by some as a blight and others as beautiful. When I first studied art, I remember the compulsion to learn the physical details of individual works, their historical contexts, and how they were and have since been interpreted. More recently I’ve tried more to focus on how I react to art emotionally, to try and build better awareness of my own feelings. In short, I enjoyed the street art in Bucharest.

Oxford Pride

Oxford held a pride parade. It feels like the community in Oxford is progressive on the issues of gender and sexuality, students seem pretty welcoming and rainbow flags fly throughout the year. Of course even in a progressive community it can be difficult to be in a sexual or gender minority, so demonstrations of support and solidarity serve a beneficial purpose.

Rowing

Summer eights ran again, finishing on Saturday. Bumps racing, and the ancillary traditions (such as competition between colleges over quality of Pimm’s), are strange from an outsider’s perspective, but I am inspired by the actual rowing to seek an opportunity to try it. Competition results can be seen here.

Photos from the Week

2019 Week 16: Snowdonia Way

Short version: Over the long weekend I hiked some of the Snowdonia way with a friend, it was beautiful.

Long version:

Snowdonia Way

The “Snowdonia Way” is a 156 km or 196 km walking route through Snowdonia National Park. We followed a guide book, but the route is also described on a dedicated website and by the Long Distance Walkers Association. The full route takes 6-9 stages (functionally days) depending on choices of lowland or mountain routes, but ultimately to fit comfortably into the four day Easter long weekend we only covered two slightly modified stages, focused on climbing Snowdon, the highest peak in Wales.

Trip Summary

Oxford to Beddgelert
We chose public transport over driving; our start and end points could differ without the need to collect a parked car. Being a passenger also requires less focus than driving unfamiliar (and uninspiring) highway, and intuitively public transport seems the climate conscious way to travel. A train from Oxford to Birmingham, and another from Birmingham to Bangor, was followed by a bus to Caernarfon, and finally a bus to Beddgelert.

Bedgellert to Pen-y-Pass
We started in the late afternoon, walking out of Bedgellert which was bubbling with holidaying families. A well groomed path (above) passed Sygun Copper mine and continued along the southern edge of Llyn Dinas. A brief turn on gravel road led North onto the start of the Watkin Path, near which was the first night of camping. Snowdon could be glimpsed behind nearer hills, a beautiful challenge to look up and forward to.

Taking down camp early and heading up to the ridge, it quickly warmed to an uncharacteristically warm and sunny day in Wales. Some steep hiking and a very brief scramble led to a saddle only a meter or so across, which allowed two distinct valleys to be viewed while sitting over lunch. The climb to the summit finished on a rather crowded Snowdon peak (see below), with many day walkers audibly disappointed that the cafe was closed. The Pyg Track was the chosen descent, which begins with a steep set of switchbacks but flattens out to gentle views of Llyn Llydaw and the Miner’s Track below. The heat took a toll on water supplies, but thankfully the YHA at Pen-y-Pass had drinking water available on tap.

Pen-y-Pass to Dolwyddelan
The second full day of hiking began descending through the exposed Nant Gwynant to a hydro-electric power station. A sharp climb out led onto a surprisingly wet plateau, bordered by a plantation. Passing down into the next valley the path began winding through sheep farms, and the hike ended near the the well kept Dolwyddelan Castle.

Dolwyddelan to Oxford
Due to damage to the railway line caused by Storm Gareth, Dolwyddelan was no longer connected to the Welsh railway network, and so the return trip began with a bus back to Conwy, followed by trains through Birmingham and finally back to Oxford.

Overall Thoughts
Compared to the much flatter Oxford surrounds, the steeper slopes of Wales are excitingly wild and adventurous. The thousands of years of human presence comes through, particularly with the very visible effects of mining around Snowdon. It is impressive to think how much earth was moved by human and animal labour alone, particularly when struggling under a pack. We were incredibly lucky to get four days of unbroken dry weather in a famously wet part of the world, and it certainly left us wanting to take on more hiking in the warmer months ahead.

Hiking in Wales vs Australia

This trip was my first hike in the United Kingdom, and my first overnight trip outside of Australia. Comparing Wales to its Newer Southern counterpart, variation in temperature and a prevalence of civilisation were the most significant differences. My pack contained many more clothing layers and a much bulkier sleeping bag to account for cold nights. This resulted in a much heavier pack than I am used to (approx 13 kg total), but with the prevalence of small towns I could have shed weight easily by purchasing food along the way. The habit of carrying provisions for the whole trip makes more sense in the more sparsely populated Australia.

(more) Photos from the Week

2019 Week 13: Tech

Short version: Technology is amazing. Cycling can be dangerous.

Long version:

Scientific Tech

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:

Consumer Tech

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.

Safe Cycling

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: Australians UK USA

Photos from the Week

2019 Week 10: Fitness in Science

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.

Long version:

Personal Observations

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 media I consumed growing 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’s High. 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’ Anatomy

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.

Links:
More statistics on half marathons and marathons. BAA Marathon and Half-Marathon results with the code shown. (I would like to be able to code informative charts like this.)

Protein Powder

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.

Importantly from an environmental perspective, looking at the World Resources Institute protein scorecard I wrote about in Week 4, dairy (from which whey protein is sourced) has the third highest impact, more than chicken and pork. Fortunately vegetable sources (i.e. pea protein) has a much lower footprint than conventional animal sources and pea protein is just as effective as whey protein in producing additional muscle growth.

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.

NASA Twin Study

I am eagerly awaiting the release of the integrated paper covering the NASA Twin Study. I suspect this will be the most intensive series of measurements made of any individual for some time. A brief summary by the Scientific American.

Photos from the Week: Solid water.

In the first photo, unusually clean ice traps dissolved gasses as they are forced out of solution. The second and third photos show Oxford’s spring weather variation.

2019 Week 9: Optimisation and Rowing

Short version: Life is full of metrics, and applying optimisation is useful, but be mindful of why not merely the how. Rowing is big in Oxford.

Long version:

Optimisation:

I can be a little obsessive about optimisation. I think it comes from doing a lot of mathematics. In the upcoming book The Metric Society, Steffen Mau describes a world where increasingly scores can be assigned to all aspects of life. I would guess the most common metrics people are concerned with are their bank balance and their weight, usually trying to maximise one and minimise the other. In everyday life I often find myself crunching numbers at the supermarket, aspiring to shave seconds off my running pace, cramming one extra experimental condition into the day. Is optimisation ultimately worth aspiring to? I’ve been reminded by friends this week that life isn’t always an optimisation problem. Optimisation can help me get faster, or spend more time at an art gallery, but it can’t tell me which one would make me happier, or is a more worthy way to spend time. I think it is important that I remember the ever growing pool of metrics are tools, rather than ends in themselves. More on this another week.

Rowing: Torpids 2019

This week the Isis in Oxford has been busy with the shouts and splashing of students rowing races. Oxford is relatively famous for its rowing. The Boat Race between Oxford and Cambridge along the Thames attracted between 250,000 and 400,000 spectators in 2017. However unlike that race, or in Olympic rowing, the boats in this week’s races (known as Torpids) do not compete in parallel, but rather line up in sequence and chase one another.

Introduction to bumps racing:
Oxford is made up of many colleges which compete in, amongst other things, rowing. Since the main river through Oxford is narrow, and the race is contested by many boats (73 men’s boats and 61 women’s boats this week), it is not possible to race side by side. Instead they compete in divisions of 12 boats (13 boats per race including the top boat of the next lower division), with each boat starting simultaneously but separated by intervals of 130 feet. The aim of the first boat is to finish the course without being “bumped” by a boat further down the sequence, whilst all other boats are aiming to catch the next boat ahead. In Torpids specifically, once you “bump” (by overtaking, making physical contact, or the boat in front conceding) you leave the race, whilst the boat that has been bumped carries on. This protects the boat that achieved a bump from then being bumped in that race, even if the boat immediately behind would have eventually (or imminently) caught it. How this plays out is that in each race a boat usually only maintains its rank (known as rowing over), moves up one position (bumping), or moves down one position (is bumped), and so only the top four seeded boats meaningfully contest the position of top ranked boat (known as “head of the river”). Getting a bump on each of the four days is nearly always the best performance a crew can hope for, and is rewarded by “blades” (oars decorated with the names of the crew) being earned. Since a boat that has been bumped carries on rowing, it is possible to be bumped multiple times, and this is reflected in some pretty significant drops (e.g. Pembroke 2nd boat falling 8 places on the last day of racing). Further complicating the results calculations is that a boat that is bumped can continue on to bump, which is the only circumstance where a boat can gain multiple places. This creates the incredibly unlikely possibility that a boat can rise from the bottom of it’s division (the 13th boat) to the top (1st) in one race: only achieved by each boat bumping the one in front in the specific sequence of reverse order; 13 bumping 12, 12 bumping 11, and so on until having been bumped by 3, 2 then bumps 1. This would result in the boats then being ordered in reverse order to their starting order. Assuming then performances consistent with that first race, all boats would then proceed to row over (finish the course without being bumped). Notably this system of racing strongly encourages starting as hard as possible to catch the boat in front as early as possible.

Notable Performances of Torpids 2019:
Teddy Hall Men’s 1st boat were the highest seeded crew to get blades, gaining four places in Division 1, whilst GTC Women’s 1st boat also got blades in division 1, with an even more impressive 5 places gain. Brasenose Men’s 1st boat gained the most places on their path to blades at 7, while Hertford Men’s 2nd boat had the biggest fall of an impressive 14 places.

More details:
You can see the full results of Topids 2019 here. The full Rules of Racing are here. St Hugh’s Boat Club provide a Glossary of Rowing Terms here.

Upcoming Rowing Events:
Oxford and Cambridge compete again in London on Sunday 7th April 2019. Bumps are next being raced in Oxford on 29th May to 1st June 2019.

Other Rowing Stuff:
Australian Rowers Eat 25-30 MJ per day, British Rowing, Rowing Australia, RowingNZ,US Rowing.

Photos from the Week

2019 Week 8: 2018 Altmetric Top 100

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.

Long version:

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.

My brief thoughts on the top 21 papers ranked by Altmetrics from 2018:

1. Mortality in Puerto Rico after Hurricane Maria

The US centric nature of the metrics comes out clearly with the top ranked paper being about deaths in Puerto Rico after Hurricane Maria. President Donald Trump was not good to Puerto Rico. 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.

2. The spread of true and false news online

Fake News travels faster online than truth . Words like clickbait, chainmail, and memes matter a lot more when presidential elections and lynch mobs become an issue. I am reminded of this early Tom Scott video about flash mobs.

3. Alcohol use and burden for 195 countries and territories, 1990–2016: a systematic analysis for the Global Burden of Disease Study 2016

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.

4. Trajectories of the Earth System in the Anthropocene

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.

5. Association between physical exercise and mental health in 1·2 million individuals in the USA between 2011 and 2015: a cross-sectional study

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.

6. Dietary carbohydrate intake and mortality: a prospective cohort study and meta-analysis

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.

7. Evidence that the Great Pacific Garbage Patch is rapidly accumulating plastic

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.

8. Complementary Medicine, Refusal of Conventional Cancer Therapy, and Survival Among Patients With Curable Cancers

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.

9. Global warming transforms coral reef assemblages

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.

10. The biomass distribution on Earth

The biomass of humans is approximately 10x that of all wild mammals, and half that of livestock. Plants rule the world.

11. Radar evidence of subglacial liquid water on Mars

Reminds me that NASA has a sense of humor too. Useful to know if you believe in Terraforming Mars.

12. Comparative efficacy and acceptability of 21 antidepressant drugs for the acute treatment of adults with major depressive disorder: a systematic review and network meta-analysis

Depression can be treated medicinally, but I have an (uninformed) suspicion the diversity in response to treatments reflects a diversity in the underlying illness. This study compares antidepressants.

13. The impact of the ‘open’ workspace on human collaboration

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.

14. Structure and Distribution of an Unrecognized Interstitium in Human Tissues

Exciting to see a microscopy paper in the top 20. Highlights the importance of checking assumptions and going back to the fundamental structure, rather than abstracting.

15. Risk thresholds for alcohol consumption: combined analysis of individual-participant data for 599 912 current drinkers in 83 prospective studies

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.

16. Death or Debt? National Estimates of Financial Toxicity in Persons with Newly-Diagnosed Cancer

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.

17. Effect of Low-Fat vs Low-Carbohydrate Diet on 12-Month Weight Loss in Overweight Adults and the Association With Genotype Pattern or Insulin Secretion

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.

18. Weaponized Health Communication: Twitter Bots and Russian Trolls Amplify the Vaccine Debate

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.

19. Decreases in global beer supply due to extreme drought and heat

While climate change is bad for both natural and agricultural plants, if the previous two alcohol papers are considered perhaps less beer in the world is not a bad thing.

20. Primary care-led weight management for remission of type 2 diabetes (DiRECT): an open-label, cluster-randomised trial

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.

21. Association of Coffee Drinking With Mortality by Genetic Variation in Caffeine Metabolism

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?

Extra Thoughts

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.

Photos from the Week

It’s warming up in Oxford, and Toxic Daffodils are blooming. I managed to fit in watching a Cuppers game at the historic Sir Roger Bannister athletics track. Port Meadow is flooded, and the reflection in the sun is stunning.

Writing from home.