2019 Week 37: Bottles, Birds, Blunders, and Bumper Cars.

Short version: Plastic is everywhere, but it doesn’t make you sick. There are some familiar bird sounds at the new physics building. An honest apology keeps me involved. Oxford’s St Giles Fair returns.

Long version:

Plastic in Water

I woke up from a dream this week thinking about the amount of plastic particles humanity has introduced into the environment. The disturbing reality is that just as we have added enormous amounts of plastic to the ocean so too have we added plastic to the water we drink and the food we eat, and hence to ourselves. Plastic has been falling out of popularity, with campaigns to reduce the use of plastic in supermarkets, and bans of plastic drinking straws in the US. It is relatively rare that organic molecules become well known, but BPA (a monomer for poly-carbonate) has attracted sufficient controversy to become a household acronym (particularly when followed by the word “free”).

Ultimately, however, a reason plastic is so ubiquitous is probably also a reason it is relatively harmless: plastics are fairly inert. They don’t break down easily, and so similarly don’t get broken down or absorbed by the body easily. This study found worryingly that Chinese infants’ exposure to BPA is 10x higher than that of adults, but also found that these levels of exposure pose little risk to health.

There is a fairly comprehensive and recent report from the World Health Organisation, which similarly concludes that plastic is everywhere, but there is not evidence that it is causing harms to health. It does suggest the need for further investigation into possible health effects, and that plastic waste management needs to be improved.

Interesting to me was that while browsing this topic, I came across the website “plasticsmakeitpossible“, produced by the American Chemical Council, which in turn is made up of some pretty large companies. I’ve not delved much into how established corporations sway public opinion at arms length, and I think it would be interesting to discuss websites like “plasticsmakeitpossible” in a future blog post.

Bird Calls

This week while waiting outside the Clarendon Laboratory, I heard the strangely familiar sound of Kookaburras coming from the new physics building (the Beecroft Building). My first thought is that the birds were being kept nearby for study, but after hearing the exact same pattern of calls (recording below) I realised it was being played on a loud speaker. My guess is that it is to deter real birds from nesting/resting on the new building, but I could not find any details of this system from the architects website. The sounds do not play at regular intervals so I suspect some sort of motion sensors are involved.

Apologies

I recently received an email from a study explaining that a large amount of valuable data had been deleted. It must have been tempting to try to blame the system or a fault in the technology, but this individual took ownership of their mistake (essentially having pressed the wrong buttons), and I found myself with more trust in them as a result.

This event is also a useful reminder to implement good data management processes, including backups of irreplaceable data and some sort of delay mechanism for the permanent deletion of data.

St Giles Fair

Oxford hosts the St Giles Fair on the Monday and Tuesday following the first Sunday in September. For at least 200 years the central streets of Oxford have been closed to make way for stalls and rides, and strolling through the rides, games, and food stalls is becoming a tradition for me as well.

Photos from the Week

2019 Week 36: Flow and Food

Short version: I was thinking about how long things last. I’m looking for a good methodology for self-experimentation.

Long version:

Flow

This week I was thinking about flow, particularly through a reservoir or storage vessel, as a model for people and cities. The intuition starts with a bucket, being filled by a dripping tap and emptying from a small hole in a bottom, such that the amount of water in the bucket is fixed. Over some amount of time, all the water that was in the bucket will be replaced. If the flow in and out is very small relative to the size of the bucket, the time to replace every molecule of water in the bucket is very large (as the molecules become less concentrated, more new molecules are lost in each drop out), where the extreme case has the no flow and the original water stays in the bucket forever. In other extreme, where the hole and tap are the so large that the entire volume of the bucket is replaced with each drop, it is essentially a pipe and so the replacement rate is essentially infinite (though there is a speed with which molecules diffuse against the direction of flow in a pipe, perhaps something to look into later).

I will update this post shortly with some more thoughts, but taking as an example the question “how much of the bone in your body is made up of calcium consumed by your mother”:

1000-1300 mg/day (calcium intake) = 32.5 mmoL per day in/out. We assume some constant calcium mass in the human body e.g. 1.5% by mass calcium so for 75 kg= 975 g calcium. Probabilities give p(excretion in a day) = 1.3/975 so p(remain) = 1-(1.3/975) = 0.9986 per day = 61% remains per year = 0.61^(age in years) = amount remaining, so after 100 years 7.08e-22% remains or 10 molecules from birth. This of course is very crude. People are not born with the same weight of bone as an adult, which would make this an overestimate of calcium remaining. However not all the body’s calcium is replaced equally frequently, some may be trapped much longer deep in thick pieces of bone, meaning the flow estimate would underestimate. Suffice to say, I confidently predict we all have some calcium in our bodies originally consumed by our mothers.

Supplements and Superfoods

I’ve been hearing bits and pieces about “superfoods”, dietary supplements, and generally nutrition comes up when eating with others. There’s a lot to be skeptical about when it comes to alleged benefits of oils, powders, and pills, as the authors of Reality check: no such thing as a miracle food discuss. I’d be interested in testing the effects of some of these, being inspired by the likes of Tim Ferriss or Peter Attia, but I don’t have an obvious experiment in my head. If you have suggestions I’d love to hear from you, and will try and look more into the literature around nutrition. A good starting point on supplements is this NHS report.

Photos from the week

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 34: Paris

Short version: Here are some observations about Paris.

Long Version:

Milk and Water

Growing up in Australia and now living in the United Kingdom, when I buy milk I usually look for refrigerated shelving. As it turns out, this is not where you find milk in French supermarkets, as Ultra-high Temperature (UHT) processing removes the need for refrigeration before opening. Table of UHT milk consumption by country here.

Paris is the first city in the world I’ve found sparkling water available on tap in an outdoor public space.

Queues at the Louvre

At the Louvre tourists queue for hours to see the Mona Lisa and take a photo of it. I’ve been thinking about this behaviour. The painting is aesthetically pleasing, historically significant, and widely discussed, but so are many paintings on display in galleries around the world. Particularly odd is that most people who get to it are unable to get particularly close to it, and use that brief encounter to look at it through their phone or camera. Given high resolution images of the Mona Lisa are easily available, I would almost go so far as to call this behaviour the “wrong” way to consume art, but on reflection I can’t justify why this is so. I would suggest that the experience of the scale of enormous historic paintings such as Oath of the Horatii or The Raft of the Medusa in person provides something difficult to gain from digital copies.

Segregation

Wandering the streets of Paris it is clearly a multicultural, multiethnic city. It was notable that those different groups tended to clump, both on the larger scale of multiple city blocks, but also on public transport. Race is a sensitive issue though, and as I lack experience writing about it I’m hesitant to address it hurriedly.

Photos from the Week

2019 Week 33: Holidays

Short version: I’m on holiday.

Long version:

Holidays

Amusingly while departing Oxford I came across this piece about vacations. It is noticeable here in Paris that the city has emptied out; plenty of stores and cafes have a note in the window mentioning a reopening later in the month.

I’ve enjoyed taking the time to read, think, and jot down some of these thoughts. Alas at the moment most of these thoughts are barely comprehensible to me on rereading, and will require a little more work before sharing.

Photos from the week come from some lovely runs around Oxford and Paris.

Photos from the Week

2019 Week 32: Unsympathetic Science

Short version: Tweets spark controversy, Google studies teamwork, New Zealand takes the record for largest parrot, hire bikes pile up around China, and you can now get berglabs in your inbox.

Long version:

Guns, Germs, and Neil deGrasse Tyson

Last weekend the US experienced another mass shooting. Sadly another is the correct word, as the US averages nearly one mass shooting a day. A series of charts compiled by vox make the correlation between prevalence of guns and deaths pretty clear. Neil deGrasse Tyson in the wake of the shooting on the weekend shared some statistics (listing other preventable causes of death that occur at higher rates). This resulted in outcry on social media. That tweet and the reaction is an example of why technocracy ultimately fails; people are emotional and those emotions are real and matter.

Re: Work

Google makes a lot of money, and can afford to spend it on developing its culture and staff. Most famously this is through perks like free on site cafes and restaurants, bean-bag rooms, and video game set ups. More useful to non-googlers is the research they conduct and share on improving workplace practices. This week I was shown Project Aristotle, particularly the actions for fostering psychological safety.

Big Birds

This week in Biology Letters an article was published describing New Zealand’s giant parrot, a bird estimated to weigh 7 kg and stand about waist height. This would be similar in size to a modern albatross, as well being twice as large as the largest known parrot, however at such size it likely could not fly. It adds to New Zealand’s collection of exceptionally large and extinct birds, such as the famous Moa.

Bicycle Business Blunders

This article from the Atlantic has some incredible photos of abandoned bicycles in China. The collapse of ofo, a bike sharing company that placed millions of bright yellow bikes in cities around the world, came up discussing Matt Levine’s piece on MoviePass. Rapid growth is alluring to investors, but clearly doesn’t always lead to success.

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Photos from the Week

2019 Week 31: Taboos

Short version: In a busy week I’ve been drafting some thoughts about topics that are considered awkward, impolite, or worthy of censorship.

Long version:

There are topics that are uncomfortable to discuss, that etiquette guides suggest one avoids at a dinner party. Topics such as sex, money, politics, physical and mental illness. These are also incredibly important topics to discuss. In general I feel that all topics should be open to discussion, and that we should shake off the idea that certain things are taboo. Some thoughts:

Sex:
It is highly likely that you exist because your parents had sexual intercourse. Sex is both important, and fun, but oddly it is often a topic people feel very uncomfortable talking about. Sexual repression, particularly by Abrahamic faiths, is likely a significant contributing factor. It is interesting to note from a perspective of censorship, that film and television guidelines tend to allow much more graphic violence than graphic sexual content in a given category, despite most individuals having much more lived experience with sex than violence. I do wonder if there is a positive to this apparent contradiction: is desensitisation to violence better that desensitisation to sex?

Stereotypes and discrimination:
In Australia the series “You Can’t Ask That” puts uncomfortable questions to marginalised Australians. In attempts to avoid seeming ignorant about minority identities, individuals may not engage with them for fear of revealing that ignorance, which further entrenches that ignorance. By asking “taboo” questions this show may help break down that barrier in the general public.

Some things are better left unsaid:
There are topics of discussion that, on balance, create harm. Spreading certain types of information, regardless of truth, can have damaging effects (e.g. how to develop biological weapons, graphic descriptions of torture, anti-vaccine conspiracy theories). However it is difficult to delineate when discussing topics becomes harmful (e.g. when does skepticism become fearmongering).

Blogging Note: I would like revisit this in more depth when I have read, thought, and discussed this a little more.

Photos from the Week

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 28: Notes, Hours, Kids

Short version: This week I returned to studying, worked some long hours, and had my usual running routes blocked by some very wealthy children.

Long version:

Taking Notes on Laptop vs Paper

I started a molecular biology MOOC. 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.

Working Long Hours

There are many professions that are associated with working long hours; truck drivers, doctors, bankers, and the whole culture of Japanese salarymen. Of scientists, organic chemists seem to work particularly long hours, and anecdotally there is life in the Chemistry Research Laboratory no matter when I pass by. Working in an ambitious startup can involve challenging schedules; Elon Musk suggested in a tweet 80-100 hours are needed to “change the world”.

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).

Photos from the Week