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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

  • Oxford Canal
  • River Avon
  • Bradford upon Avon
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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

  • A beautiful run 1
  • A beautiful run 2
  • Poppy
  • River Thames
  • Flood of Children
  • Cygnets
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2019 Week 27: Socratic method

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.

Long version:

Socratic Method

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).

Confidence

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”.

Photos from the Week

  • Berries
  • Freight Train
  • Pendulum Waves
  • Joyful Street Dance
  • Crowds to the Spire
  • Drummers at Church
  • Cowley Road Carnival Car Sculpture
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2019 Week 26: 6 Month Review

Short version: After attempting (and failing) to write a blog post each week for the past 6 months, I look back on those posts and reflect.

Long version:

Identity and Expectation

A realisation occurred to me whilst thinking about the unfinished drafts for this blog. Fitness, particularly competitive fitness, is not a core part of my identity, and so it does not threaten my ego to post slow times on parkrun. By being comfortable running slowly, I run more, and in running more, I run faster. Being comfortable with being a slow runner makes me a faster runner. The ability to understand difficult concepts, and to communicate effectively, is a core part of my identity. This means being unable to understand difficult concepts, and being unable to write well, does hurt my ego. If I am insecure about these aspects, I read fewer scientific papers, I write fewer blog posts, and the result is I do not improve in these areas. The lack of progress makes me more insecure, and a cycle of procrastination begins.

The solution, therefore, is to be comfortable with not understanding, or in the case of this blog, to be comfortable writing poorly. The purpose I have identified, in attempting to write each week rather than each time I have something interesting or insightful, is a need to practice writing regularly, not a need to demonstrate the skill of writing. To be able to write more regularly, I need to stay true to that purpose, and not be swayed my the desire to be interesting, insightful, or demonstrate a level of skill I have yet to achieve.

With that in mind I post this unfinished, and hope to take time when I am up to date to examine the first 25 posts of 2019, and identify what I have done well, and what I need to improve on, as I focus my efforts on more regular content in the 26 posts to come.

Posts I liked:

The short summaries of papers from Week 8 was fun to write, but regrettably shallow. Although not a weekly blog post, I was happy with my comprehensive first race report. Writing about diet and alcohol had a real effect in my life; it made it easier to hold myself to my decision in the face of perceived social pressure. I got stuck for a while trying to write about video games, but overcoming that was useful to me in understanding my relationship with that form of entertainment. Week 15’s Minimalism felt reasonably cohesive.

Posts I did not like:

The most common mistake I see in my writing is the use of unnecessarily complex sentences. Phrases like “much of the time” instead of “often”. I would guess the reasons for this are 1) a lack of consideration and technique, 2) attempting to be precise for fear of being misunderstood and 3) an affectation in order to appear intelligent. Ultimately the goal of writing is to communicate. To be succinct first requires the ideas themselves to be coherent, and testing my ideas by attempting to write about them has helped me think more clearly. In a limited time, some ideas never become coherent, and the resulting posts are much weaker. For example, in Week 21 I didn’t understand my own conclusions about marriage or Romania, and so I feel the writing suffered. The book report in Week 7 was never written, and I cannot help but feel a tinge of shame when I think about it.

Photos from the Week

  • Pollinator by Simon Periton
  • Southern Isis
  • St Giles’
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2019 Week 25: Advice

Short version: Taking advice is not an easy skill to master. I ought to listen to the advice itself rather than assume its validity based on the person offering it.

Long version:

Advice

I have a bad habit when taking advice. I find it very difficult to listen when the advice comes from someone who does not follow that advice themselves. This is a sort of reverse authority bias, whereby I ignore good information that ought to be taken on it’s own merit. An intuitive example is the sporting one, a coach might study the tactics and strategy of a game, know their players and those of the opposition, the biomechanics of the body, and about nutrition and rehabilitation, and yet be themselves at a poor level of fitness. Thereby they might espouse accurate, useful, and ultimately critical advice, whilst being a terrible player themselves. Sport is also a good example of my bias at the group level, as often it takes skill in the activity to earn enough respect to be in a position to offer advice.

Further, I can find myself confronting the person giving me advice if I feel they are not being consistent to the underlying principle. This often comes across as confrontational, which is not how one should approach an offer of help (of which giving advice is a type). Even if it is not a direct confrontation, by challenging the person I distract myself away from considering the advice, and how it might address my own inadequacies. Seen from this perspective the motivation to react this way is obvious: it is much more comfortable to see someone elses weaknesses than our own. Conversely, once accepted and understood, it is only our own weaknesses that we are able to correct.

Confidence vs. Persistence

I am learning from the beginners rowing course, that while being confident is helpful (it prevents unnecessary hesitation, lowers stress, and makes the whole process more enjoyable), persistence (actual time practicing a skill, making it automatic) helps more.

Photos from the Week

  • Cat’s Perspective
  • Summer Sunshine on the Isis
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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

  • Rowing 1
  • Rowing 2
  • Rowing 3
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2019 Week 23: Yams

Short version: Waitrose is getting rid of some of their packaging, but didn’t stock yams.

Long version:

British Supermarkets

The United Kingdom has a much more diverse supermarket landscape than the Australian duopoly I grew up with. The British landscape is tiered, with M&S and Waitrose as the expensive, Asda, Sainsbury’s and Tesco as the middle, and Aldi, Iceland, and Lidl as the cheaper options. In my shopping there is a noticeable contrast in the demographic of the customers at Waitrose compared with Aldi, both on Oxford’s Botley Road. I suspect this is a product of the price differences appealing to different socio-economic classes. The data, however, suggests the difference is small.

The photo from the week is of Waitrose’s “Unpacked” campaign around removing packaging from their stores. Reducing waste is commendable, and the campaign has been successful in encouraging me to purchase more items from Waitrose. However on visiting many of the independent grocery stores on Cowley Road I realised that “Unpacked” is actually the default way of selling goods, rather than an “innovation”.

Yams

I tried cooking yams this week, as part of a larger project to improve my cooking by working through a single cookbook (written by the team of the former London restaurant Food for Thought).

The first problem was that I didn’t actually know what a yam is. The wikipedia page offers a disambiguation. This raises the question as to why a tuber produced primarily in equatorial regions would be popular in the UK. The ready availability of carribean food in general (of which yams are a component) in the UK is partially due to the Windrush generation. Finally a pop culture note: Kendrick Lamar’s yams are “authenticity, sex, and drugs“.

粽子

This Friday was the Dragon Boat Festival ( 端午节 ). My quest for yams brought me to some Chinese supermarkets here in Oxford and the presence of banana leaf wrapped rice (粽子) reminded me of the traditional Chinese holiday, and the story of Qu Yuan (屈原).

Photo from the Week

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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

  • Street Art in Bucharest 1
  • Oxford Pride
  • Street Art in Bucharest 2
  • Boathouse Island for Summer Eights
  • Bright sun and flowers in Romania
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2019 Week 19: Balls

Short version: in a week of upper-class entertainment, I attended a Ball in Oxford, and an Opera in London.

Long version:

Balls

In the university calendar of Oxford, the warmer months of Trinity term bring with them the college balls. Students dress up in black tie to enjoy carnival rides, food trucks, open bars, and dancing. Given colleges are the term time homes of Oxford students, they are something of an extravagant house-party. The nature of the ticket pricing (a single price for entry with everything being free within the ball) encourages over consumption, particularly of alcohol. It also encourages the practice of sneaking into balls, by scaling walls or attempting unusual canal crossings.

As something of an Oxford outsider, I think I miss out on the main joy of attending a party with your peers where you live and study. They are a spectacle, and good company, music, and drink are certainly pleasant. That said, having attended a few balls last year, the novelty has worn off. I’ve written about lowering my alcohol consumption, and similarly excessive consumption of “party” foods is an unwise choice. Even the loss of sleep, as balls tend to carry on into the small hours of the morning, seems to be a price I am less willing to pay. I feel both “old” and “anti-fun” as I write this, but my priorities have shifted from this particular expression of hedonism to value each activity in a purer and more moderate form, rather than thrown together in a single event. Dancing is not particularly enhanced by heavy eating or drinking. Thrill seeking comes best in more practical clothing. Good company is better enjoyed where conversation is not drowned out by party music. Overall, while the components of a ball are very enjoyable, I find the combined experience to be less than the sum of the parts.

Opera: Billy Budd

On Friday I attended the closing performance of Billy Budd, which impressed upon me an appreciation that Britain no longer uses impressment. I feel this piece from the Financial Times has a much more informed opinion on the performance than I could form. The English language opera with an all male cast had enough elements of the Christ story to make me reflect on the oddity that the United Kingdom is technically a religious state. Also the loyalty of the titular character, despite his tragic end, is something I feel a sense of envy over. The British Navy is not a hierarchy I aspire to be a part of, but to have a clear sense of purpose, of duty, and to live up to that purpose and duty, is something that I do aspire to.

Photos from the Week

  • Students dancing into the small hours at an Oxford Ball
  • Royal Opera House in London for the last performance of Billy Budd
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2019 Week 18: Allotments

Short version: This week ONI volunteered around Oxford to celebrate 3 years since being founded, and as part of that I worked on an allotment for the first time.

Long version:

The Children’s Allotment

On the 1st of May ONI celebrated its third “Oniversary”, and with corporate social responsibility in mind we decided to volunteer our time on projects around Oxford that could use some extra hands. I was tasked with leading a team to help The Children’s Allotment clear an abandoned plant nursery on the site of Oxford’s East Ward Allotments. My first response to the exercise was sceptical, but the result was an inspiring and enjoyable day, with some satisfyingly useful results. Together we worked up a sweat, collected a few scrapes and scratches, and had our shoes filled with earth, but ultimately managed to clear the entire area of rubbish and overgrown brambles. The surprise and joy of the Children’s Allotment team, and their heartfelt thanks, left us all feeling proud at what we had achieved.

When working with a group of people every day, it becomes easy to take for granted their consistently positive qualities, and I come to take for granted the work ethic of my incredible colleagues. “ONIees” are quick to get into their work and see it through with discipline and vigour. Old and young, tall and short, experienced gardeners and those who had never kept a houseplant, all promptly donned a pair of gardening gloves and got to digging, cutting, clearing, and moving ceaselessly until the job was done.

Photos from the Week

  • Before …
  • … and after!
  • Ergs in the sun
  • Spring brings fluffy goslings