Lady Astronaut of Mars

“And basically, the novels are: I would like The Martian Chronicles but with more women and people of color, please.”

Mary Robinette Kowal speaking at Google on her novels.

About the books

I thoroughly enjoyed reading The Fated Sky, the most recent book by Mary Robinette Kowal. It follows the multi award winning novel The Calculating Stars, and occupies the same “punchard punk” universe as the short stories Articulated Restraint, The Lady Astronaut of Mars, and We Interrupt This Broadcast. You can hear the author read an extract at the start of of this Talk at Google.

Kowal describes her use of sci-fi as “set dressing” to help “explore things that [she] is thinking about from the real world and it allows [her] to talk about them without all of the emotional baggage so [she] can approach them more as a thought experiment”. Dressed in sci-fi, Dr Elma York (main character) grapples with mental illness, patriarchy, and racism, while background elements invoke the politics of climate change.

My thoughts

I enjoyed the alternate history, the blending of the real life Mercury 13 and computers of Hidden Figures with an engaging character driven story. Kowal has done her homework, with help from Derek Benkoski (fighter pilot), Kjell Lindgren and Cady Coleman (astronauts), and Stephen Granade (rocket scientist), which gives Kowal’s depiction of space-faring such realism that it felt a little like reading astronaut Chris Hadfield’s autobiography.

It was new for me to read fiction where most of the cast, including the first person narrator, are women. As with film (I highly recommend checking out this blog post) women tend to be less represented in stories I read (e.g. The Lord of the Rings). While the main plot of The Calculating Stars centres on women fighting to be included as astronauts, The Fated Sky shifts focus to issues of race. The diversity of the cast is necessary for the story Kowal sets out to tell, and whilst she clearly has a progressive stance to share, at no point did I feel narrative was compromised to make a political point (though as far as I can tell I largely share the author’s views).

The first novel opens to a scene involving Elma and Nathaniel’s (main characters) sex life, and their emotional, sexual, and professional relationships feature significantly in both books. Kowal states in the Google Talk that she “wanted their relationship to always be rock solid”. I am fortunate that my relationship is similar enough to find myself relating to Elma and Nathaniel. While there has been criticism that “Nathaniel York is too perfect to be realistic” (which Kowal has responded to via twitter), being able to see the familiar stresses of over-commitment to work, mental illness, and maintaining intimacy over distance, helped me invest in them both as a couple and as individuals.

Fiction and Authors

It is new for me to come to the end of a story I have enjoyed for recreational-escapist-immersion and then be able to turn to the internet to learn about the author, her process, and how to examine fiction more generally. Kowal keeps a public journal, where as I began drafting this post she shared insights into her writing process. She tweets and answers questions through Lee the Puppet and collects typewriters. By following her online presence, I learned of the existence of narrative beats and about heat welding for puppetry. Seeing an author as an actual person (with their struggles and distractions and desires) makes writing less daunting, and so encourages me to write more.

Real Astronaut CVs

Science-fiction and fantasy make for interesting psychological insights into readers. While no one has experienced contact with aliens or magic, the audience’s immersion may be first broken by a very human behaviour. In the talk Kowal discusses that her writing is criticised for her depiction of Elma’s weaknesses as it seems contradictory for Elma to be so paralysed by anxiety in a social context but utterly comfortable with near death experiences in space craft. This is in spite of the real lived experiences of those with social anxiety disorder. Another criticism of the character I have seen in a few places regards her mathematical prowess:

The least relatable thing about Elma is that she’s so smart that no one else can match her. She went to college at 14. She does math in her head. Oh, you have to solve differential equations with a piece of paper and a pencil? You’re actually a dumbass in comparison.” — librarything review by yvonnekins

I remember feeling a similar jealous sentiment towards Patrick Rothfuss’ protagonist in the Kingkiller Chronicle series. It is easy to be jealous of characters who are defined by their intelligence, particularly if you operate in a world where intelligence is worshipped. When it comes to astronauts however, Elma’s skills did not break my immersion, as I have seen astronauts tend to have pretty incredible CVs, e.g. Jonny Kim. Also child pilot and accomplished physicist Sabrina Gonzalez Pasterski is not a fictional character.

Some uncomfortable feelings when I come to write about books

Generally, despite really enjoying the story, coming to reflect on it here inspired some painful feelings. While it would be easier to ignore those feelings, that would miss an opportunity to grow past them, and fail to follow the example of sharing personal weakness set by Kowal and others who inspire me. I feel it is important to hold and express thoughts about the books I read, and I couldn’t do that if I avoided emotions that come with reflection. Emotions are difficult to untangle, but two strands I can draw out are:

1. I feel I should write about books but I don’t know why or how. I feel disappointed with myself that when I finished the first book all that made it into the blog was “I finished reading The Calculating Stars by Mary Robinette Kowal, it is excellent.”

2. I read slowly. It is also disappointing to me that it took me nearly 3 months to read The Fated Sky. I quickly convert that rate of four books a year through the relatively short human lifespan, and feel a great sense of loss that there are so many texts I will never read.

Closing Thoughts

I highly enjoyed both books (on paper), but given Kowal is a voice actor and does the narration, I would recommend listening to The Calculating Stars via audiobook. I eagerly anticipate the third book in Elma and Nathaniel’s story, due in 2022.

Productivity Update February 2020

Motivation

I want to get more done. I constantly have unfinished to-do lists and projects I would like to take on, if only I had more time. Rather than simply aspiring to have more time (e.g. by living longer), it is equally valuable to do more living in the time I have. I see increasing productivity as converting time I feel is wasted into time I feel is useful, by either decreasing the time useful tasks take or removing tasks that are not useful. This post is a collection of things I have found to help with this, and areas where I am seeking to improve.

Things that I think work

Prioritise health

If I am mentally or physically unwell, my productivity rapidly decreases. Keep health as a priority. Assess it regularly, and take time to eat well, exercise, and sleep. Follow good hygiene practices. When ill, make recovery the single highest priority.

Hesitate less

Increasing productivity and focus first require that you actually start doing something productive. Whatever that is, learning, training, meeting people, or something else, I often find myself hesitating to start. Fears of failure may be reasonable or unreasonable, but not starting at all makes failure a certainty. Of course some projects are more risky; the costs are higher, the harms can be bigger, but generally the first few steps don’t require such a big commitment, and having started I will be in a better place to assess what can be done. Simply put, just start.

Solve what you need to do, not what is easy to do

The blue areas (important with known solutions and unimportant with unknown solutions) take care of themselves; things that are important and easy to do get done with much satisfaction and hard things not worth doing don’t ever get started. The trick is doing the important things that don’t have solutions yet. They’re so hard! It is frustrating to try and fail, and failure is likely since the solutions are unknown. It is much more attractive just keep working in my comfort zone of known solutions, even if they are unimportant at least they are easy. The more time I shift along the yellow arrow, the more productive I am.

Focus on what is important, and do not be distracted by what is easy. I think most people are familiar with a time when, rather than write a difficult essay, or make a difficult phone call, suddenly they were inspired to reorganise their desk or tidy their house (Tim Urban goes more into procrastination in this TED talk). I’ve lately been thinking about it in terms of the diagram above; trying to focus my attention away from the easy but unproductive tasks and towards harder but more useful tasks. A related concept comes from an anecdote about Warren Buffett advising Mike Flint about goal setting.

Example – Science
Easy Productive: Setting up experiment
Hard Productive: Interpreting experimental results
Easy Unproductive: Selecting nice colours for charts and plots
Hard Unproductive: Writing new spreadsheet software

Example – Writing
Easy Productive: Choosing a topic to write about
Hard Productive: Actually writing about the topic
Easy Unproductive: Selecting fonts, organising stationary
Hard Unproductive: Writing in an unknown language

Example – Fitness
Easy Productive: Signing up for a gym membership
Hard Productive: Actually using the gym membership
Easy Unproductive: Watching YouTube videos about how to exercise
Hard Unproductive: Making YouTube videos about how to exercise

Use technology effectively

Tim Ferris shared this article about how to use your iPhone productively. I was a little underwhelmed by the focus on apps and content to consume, rather than actual phone tweaks that help avoid distractions. Smart phones are powerful devices that can be highly detrimental for productivity. While I am certainly more productive with a suite of tools in my pocket at all times, I can also be distracted by the similarly immense collection of toys. Armies of clever people work to increase the amount of time users spend in their app or on their website, and they are often successful. Some things I have found useful:

Make your phone binary. Either it is a “toy” used for relaxation and entertainment or it is a “tool” to help you work more effectively. If it is a toy you don’t need it with you when you are working. If it is a tool then don’t install games or use it to browse content where the main purpose is to be entertained.

Put your phone in black and white. Screen technology creates images more vivid, and therefore more captivating, than reality. For the majority of useful functions, a phone doesn’t need a colour screen. Putting it in black and white makes it less attention grabbing.

Do one task at a time. Build a habit of telling yourself what task you are picking up your phone to perform, performing it, and putting the phone away again. Sending that text message doesn’t need to lead to browsing Instagram. Checking the bus timetable doesn’t need to lead to reading a news article.

Turn your phone off. When you don’t need your phone, turn it off. Notice how often you pick it up and stare at a blank screen, and put it back into your pocket. If what you need to do isn’t worth waiting a few seconds for the phone to start up, it probably isn’t worth doing at all.

Avoid vanity

Time spent checking social media is not particularly useful, but time spent looking at your own content is especially not useful. I learned that in the early days of LinkedIn, 25-35% of clicks were people looking at their own profile. The speculated reason for this, with some evidence, is vanity. I can certainly feel the urge to check posts for likes, retweets, kudos, etc. It is validating to have people consume your content and approve it. It is also not worth checking repeatedly. The few minutes many times a day adds up to a meaningful amount, the interruption disrupts flow, and the emotions (envy, insecurity, and even the validation from being “liked”) are broadly negative.

Multitask appropriately

Multitasking in some situations can boost productivity, and in others just slow things down. Learn what tasks go well together for you, and which ones shouldn’t go together. I am sure this varies significantly

An example of good multitasking:
Listening to the news while doing steady state exercising. Not every training session should be hard, often I have less intense, putting-in-the-miles work outs. This is a great time to catch up on news.

An example of bad multitasking:
Listening to music while writing. I enjoy it, but changes in songs, and particularly interesting lyrics, tend more often to disrupt my train of thought than to drown out distractions.

Define “possible” honestly

Motivation matters. Setting the bar too high for what level of productivity I want to achieve, or putting too many things on a to-do list, leads to failure, and that failure can sap away confidence and motivation to do more. Be realistic with what can be achieved, keep the ego in check, and when things become overwhelming take time to pause, cut back, and start again with a lighter load.

Things I haven’t worked out

Consume content carefully

I read slowly, and I suspect inefficiently. There is so much content being produced at such an incredible rate, I find myself “tab hoarding”, filling hard drives with PDFs, trying to skim academic papers that I forget immediately, and buying books faster than I finish them. I think the problem is needing to be selective, and to learn to not be “completionist” in my reading, but rather focus on finding things that sit comfortably in my Zone of Proximal Development, and skipping things in a text that I already know, or are well beyond my grasp.

Keep in touch

I am still not good at keeping in touch with friends. I lose time I could be using to catch up with them (via a plethora of communication platforms) fretting about how much I have failed to meet my own expectations on frequency of correspondence. I suppose this is because I am not good at selecting which relationships I ought to prioritise, and effectively let random encounters define which people I spend time with. In not wanting to leave anyone out, I leave everyone out.

Long term goals

Finally, and most challenging to me, finding a major goal to unify my interests, my work, and my hobbies, so that the whole can be greater than the sum of the parts. I lack direction, and this means that many projects I begin and abandon which might not otherwise have been wastes of time, become so.

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2019 Week 52: Retrospective Part 2

Short version: Thoughts on this year’s blog, and what is to come next year.

Long version:

Climate Catastrophe

Sydney, Australia, has a world famous fireworks display to mark the new year. This year, due to raging bush fires, there has been a call to cancel the display. This could only be symbolic, given that the contracts had been signed and the money paid. The fireworks went ahead. I think about the framing a former PM used, that climate change is “the greatest moral challenge of our generation”. That was 12 years ago. While a lack of economic literacy leads to the idea that the costs of the fireworks show could somehow be redirected to fight the fires, it is a deeper problem in human nature that allows the cost of dealing with climate change to grow impossibly in the future, rather than taking less painful action today. I feel another man made disaster gripping Australia, the obesity epidemic, to have similar roots.

It is difficult to think about the end of a year and the start of a new one without thinking about the scale of the challenges ahead. This briefing highlights how quickly time is running out to cut emissions. With governments in power across the English speaking world that so effectively wield tools of misinformation, I fear for our collective ability to make the right decisions. They are uncomfortable choices to make, but the consequences of ignoring them are going to be so much worse.

Reflection on 2019 Blog Posts

At the start of 2019 I wrote that “Last year I managed 11 posts out of 52 weeks for a 21% success rate.” It makes me proud to have hit “publish” for each week of 2019, though many came late. In total the posts came to a little over 30,000 words. They lack the quality and coherency of a novel or a thesis, but it has been a learning process, and reflects many of the topics I thought about in the last year.

Some favourites included:
In Week 38 I looked at the carbon costs in consuming New Zealand apples in the UK, which alongside Week 4 (on plant vs animal protein) are the two posts I’ve most often shared over a meal. Scientific content peaked when I focused on sharing papers, such as Altmetric in Week 8 and cover pages in Week 29. In Week 39 when explaining microwave ovens, I painfully came across the perfect article only after I had written most of the content. The data set I used writing about consumption in Week 48 was the most fun to explore.

Goals for 2020 Blog

The amount of content on berglabs as a whole has increased at least 5-fold in the last year. A reorganisation is due. It’s not easy to find content on the blog. Certain themes, like nutrition, or summaries of academic work, could be better grouped. I hope to reorganise the tags to make things a little easier to find. I aspire to write longer more coherent pieces, but cannot sustain that weekly, and so perhaps a monthly or quarterly essay to give more time to go deeper into a topic. A projects page may help me find collaborators, or pitch ideas that I would like to see in the world (inspired by Kevin Lynagh). I’ve also been toying with a page dedicated to people I think should be on pedestals, and a page announcing my values, the few things I believe to be clearly “good” or “bad”.

Photos of the Year

(click to expand)

2019 Week 51: Retrospective Part 1

Short version: In the last two weeks of 2019 I take a look back at 2019.

Long version:

Hello and Happy Holidays

As the days remaining in 2019 enter the single digits, there is a general sense that now is the time to look back at year gone past, and to reach out to friends and family who are missed. However and whenever you come to these posts, I hope that you are well, and the year past has held many joyful moments. I hope, too, that you have been challenged, put under pressure, and even suffered a little, and that you have come through that stronger and better for it. I feel fortunate that the past year has been just that for me. Here are some thoughts:

Health

Physical and mental health were consistently good, with a couple dips towards the end. Living in Oxford I have good access to health services, particularly a work environment that understands the importance of mental health. I lost approximately 4 days to physical or mental illness, and required no significant interventions.

Science

At ONI I continue to have the privilege of working in an exceptional research and development team. Much of that work is confidential, but avoiding specifics I am proud to have helped make some significant breakthroughs alongside some incredible scientists. I am confident super resolution will play a significant role as bio-technology advances, and it is incredibly exciting to have a job where I work at the cutting edge of that advance.

Learning

Aside from what I learn at the lab bench, I’ve also been taking the opportunity to learn from articles, podcasts, text books, and online courses. I’ve been enjoying Rafael Irizarry‘s textbook and courses on data science, the economist‘s coverage of current affairs. I feel fortunate to live in a time where I can communicate with other researchers from nearly anywhere in the world, either through their publications or via social media.

Writing

Combining work, this blog, and other personal projects, I have written more in 2019 than any year prior. Next week I intend to look back through this year’s blog posts, picking up corrections, and outlining some goals and challenges for myself in the coming year. It has been an emotional and intellectual challenge, grappling with my insecurities and ignorance alike, but I feel it has been immensely rewarding and I am excited to develop my writing in the years to come.

Fitness

Although the last two races have been disappointing, I have continued to build on the fitness progress of 2018, with highlights being a 10k PB, a marathon PB, my first triathlon, and learning to row.

Fun and Games

Although it was a busy year, making good use of recreation time led to some wonderful experiences. Camping and climbing Snowdon, making new friends over board games, improving my cooking, and listening to live music performances were the highlights.

Goals for 2020

The year was not without mistakes. Time was wasted, I was silent when I should have spoken, I acted when I should have waited. At the moment, here are some of my ideas on how to do better next year:

  1. Consume good media, mindfully.
  2. Have deeper conversations
  3. Act with courage, always
  4. Consistency over intensity

2019 Week 43: Big Things

Short version: A few big things to talk about; nuclear war, bribes, engineered environments, mistakes, and courses.

Long version:

Big Problems

In Oxford I enjoy meeting people passionate about studies I might not have otherwise ever considered. This week I was introduced to ALLFED, a group who spend their time working out how to feed the population who survive a nuclear war. In the current political climate it can be both frightening and paralysing to think the fate of billions rests on the whim of a few individuals. Knowing some out there are trying to be prepared give me confidence that humanity can survive its own incredible destructive power. This work fits under the umbrella of Effective Altruism, which is persuasive (I have a few friends who are strong proponents) but also complex.

Big Presents

There is a common understanding that bribery is wrong, but it is not immediately obvious why. The answer I seem to find is that the central issue of bribery is when a person is able to take an advantage for themselves (the bribe) in exchange for acting against the external interests they represent (e.g. the university in the case of a college admissions administrator). Some examples:

This year a scandal broke regarding admissions to US colleges, where coaches were bribed to select students without athletic ability on an athletic basis. At face value the harm here appears to be a violation of meritocratic principles; students ought be selected on their talent rather than the wealth of their parents. In fact generally wealthy parents are able to have their students attend top universities despite their academic or sporting ability, via large donations to universities. The wrong here comes from the coaches personally profiting from the student’s admission, rather than the university itself.

In China large gifts were given by banks to politicians, and in Australia political donations by banks have been scrutinised, while the volumes of donations in the US are much higher. Cash donations, crystal tigers, coffee; for politicians these rarely come without strings attached. A journalist buying coffee or even a meal in exchange for an interview seems natural, a company paying a politician to be awarded a contract is graft. In between these, it is difficult to work out where courts or courts of public opinion ought to draw the line.

Big Artificial Environments

People have managed to make some incredible changes to their environment. This week The Wave opened in England, an artificial lake that generates artificial waves so that people can surf. There is also warm weather skiing on plastic and the more extreme indoor ski slope cooled to negative temperatures in hot Dubai. The football world cup will required air conditioned stadiums. All this gives hope that technology can repair the damage we are doing from burning fossil fuels, but also these feats of engineering require enormous amounts of energy themselves.

Big Mistakes

In my reading about health, smoking seems to be the worst decision a person can make. This week I saw some calculations about how smoking is a terrible financial mistake, in addition to the health costs.

Big Classes

This week I finished a Massive open online course (MOOC) on statistics, making it the first online course I’ve completed. Previous attempts, such as the biology course I started in Week 28, have been derailed by lack of interest or energy. I was particularly reminded of the importance of working in your Zone of Proximal Development by this line of mathematics.

Depending on your familiarity with logarithms, this may either appear indecipherable or trivial. I particularly remember encountering logs around the age of 15, and it being the point in my mathematical learning where maths stopped being intuitive. It was confronting to not find the subject easy. Unfortunately I couldn’t see or be shown how pushing past that initial discomfort would lead to valuable personal growth, and I moved away from mathematics to subjects I “felt I was better at”. I think the feeling of being overwhelmed, of being stuck, drives many people away from opportunities to grow and empower themselves, and it is a feeling I am still striving to become more comfortable with.

Photos from the week

Dry Ice Fog for Halloween

2019 Week 41: Changing your mind

Short version: An interesting question to reflect on, a mantra I find useful, another reason to avoid diabetes, the Nobel Prize rejection, and making my phone less distracting.

What would it take to change your mind?

I’ve been thinking about this question recently. In many ways our beliefs about the world, what we hold “in mind”, is intertwined with our identity. How those ideas form, and how they can be changed, informs who we are and how we act. I have not spent much time thinking about what specific influences would be required to change my beliefs. I would like to think that, as a scientist, I am willing to “turn on a dime” in response to strong evidence, but what specifically constitutes strong evidence?

On a population level changing minds is critical to governance. Journalist Carole Cadwalladr gave a TED talk with some fascinating images; advertisements run on Facebook that she suggests influenced Welsh citizens to vote against their own interests on the Brexit referendum. I wonder if those citizens would be able to identify what caused them to be so fearful of hypothetical Turkish migrants (specifically) or the EU (generally), and what evidence or experiences they would now require to lose those fears.

I would suggest you try the thought experiment (and would love to hear your thoughts!). Consider what might cause you to change your mind on beliefs that you hold at different strengths. What might make you change the political party you feel aligned with? Your religious views? Views on climate change? On who you are? At the moment my own thoughts are quite confused, but I find the exercise interesting.

A useful mantra

When trying to understand why someone has acted to cause you harm, I find it useful to remember the order of these three causes:
Apathy. Incompetence. Malevolence.

I realised that it is very rare that a negative occurrence is the result of malicious intent, but often we suspect that cause. I’ve explained my thoughts (and the three word reminder above) a couple times in person in recent weeks.

First for something malicious to occur someone needs to care enough to do consider a malicious act and then act on that thought. Most people just do not give significant thought to others, and generally people err on the side of inaction. Even when a relationship is positive and significant, the frequency of thinking of doing something good translating into actually doing it is relatively low, and most people only have a small number of such intense relationships. Consider how many such strong relationships you have, compared with how many people you cross paths with regularly, and this can likely be extrapolated to others. Just as apathy may cause you to thoughtlessly inconvenience one of these people, so too might their apathy inconvenience you. (There is a related punchline in a joke about gun ownership I rather enjoy: if you are buying a gun for personal defence you must (absurdly) have a high opinion of yourself that anyone cares enough about you to try and attack you).

Second, much of the time when we try to influence the world we make mistakes and influence it in an unintentional way. Just as a good intention can produce a bad outcome, so too does an attempt to manifest a bad intention have a chance of producing a good outcome, or no outcome at all. Since most people tend not to practice malicious acts regularly (I hope), then most people even if attempting to cause harm will do so poorly. More often people trying to be good may fail, and therefore accidentally cause harm. The harm is caused by incompetence rather than malice.

Finally, only if apathy and incompetence are considered and ruled out should we consider ill will. Our mind rushes to this conclusion first, stories we learn from an early age arrange themselves around characters acting in opposition, “good” vs “bad”. It is more comfortable to consider a simple and ordered narrative where people are competent and their actions match their intentions, rather than the complex disordered reality where the two are often not coupled. We are at the centre of our own misfortune, and so assume people can see what we do and must therefore notice and care about our strong emotion. Ultimately these are misguided assumptions.

Remember, when next bitterly considering why you were wronged, the likely reason is Apathy, then Incompetence, and only then, Malevolence.

Diabetes and Alzheimer’s

Diabetes is a prevalent disease in the developed world, and can partially be addressed through lifestyle interventions, like maintaining a healthy diet (and hence weight) and exercising. If there weren’t already enough reasons to avoid diabetes, I’ve recently come across the term “type-3” diabetes, an alternate name for Alzheimer’s disease, due to similarities between the diseases and correlation between Alzheimer’s disease and type-2 diabetes.

Nobel Prize Winner’s Nature Rejection Letters

This week the Nobel Prizes were announced, including one for Peter J Ratcliffe, for his work on hypoxia. I’ve seen some tweets sharing a letter to Ratcliffe declining to publish a paper from him. The message is often one of encouragement to persevere in the face of criticism, or that Nature has made a serious blunder by not publishing the work.

The assumptions here are interesting. Ratcliffe’s Nobel Prize indicates a significant contribution, but it does not mean that every paper he wrote warranted publication at all, let alone publication in any specific journal. Perseverance is naturally a requirement for success in a field (trivially if you quit before you succeed you cannot succeed), but that perseverance needs to include a willingness to adapt to both criticism and praise from peers, not blindness to it (though that adaptation can also be bolstering evidence and pushing back against the criticism, rather than conceding to it). Finally the publisher here (Nature) is responding to the comments of the reviewers who would be other researchers in the field (peers), rather than merely dismissing the work, which I feel can be lost in the suggestion that Nature made a mistake not publishing the work: they were following the procedures which fundamentally led to their success and prestige as a journal.

As an aside: Ratcliffe ended up having 28 papers (to date) in Nature family journals, of which 3 are in nature itself, so I doubt anyone is holding a grudge.

Phone Distractions

I wrote about changing my search engine, and while some tasks now take longer I have adapted and think there is some improvement to the content I consume. This week, at a friend’s suggestion, I switched my phone to monochrome (greyscale), in an attempt to make it less visually alluring. I am surprised how effective such a small change is, the content is the same, but the stimulus is reduced, and it makes it easier to moderate my time mindlessly scrolling.

Oxford Half Marathon

This week I ran the Oxford half marathon, and while at the moment I am still overdue on the Blenheim Palace half race report, I’m hoping to write both and update the respective blog posts soon.

Photos from the week

2019 Week 40: Charts and Code

Short version: Intuitions about how we look at data. Taking small steps with code. Art at the Tate Modern.

Long version:

Sneaky Spreadsheets

This week I have been processing some experimental data and realised how the same data can be plotted in seemingly different ways. Often looking at the numbers themselves can be challenging, particularly if there are hundreds of points with multiple values at each point. For this example we take some simple data about income distribution in the UK. The numbers alone are accurate but making inferences takes consideration and a little mental arithmetic.

A linear column chart is the simplest and fastest way to visualise the data in a spreadsheet program (excel, google sheets, open office calc). It shows the 99th percentile as much larger than the other values, and the increases seem bigger between the higher percentiles.

Taking a logarithmic plot makes each step along the distribution seem more even, but the 99th percentile still seems noticeably larger.

But by changing the minimum axis value on a logarithmic plot the distribution seems much flatter overall.

And we can go to the opposite extreme, by plotting a pie chart the high income earners (top 1%) seem to take a massive share of the pie.

Code

I am not proficient in code, and find that embarrassing. That is an odd statement, I’m not proficient at many things (skateboarding, Portuguese speaking, cello playing) but few of those things cause me to feel embarrassment. Technological proficiency, unlike skating or playing a string instrument, is a part of my identity, and I feel that being able to code (or at least write basic scripts) is a part of being good with tech. When I go to write code, I am confronted by the gap between what I feel my skill should be and where my skills actually are, which is uncomfortable. Moreover it causes me to hide, refraining from asking for help, and I end up doing things in a slow and repetitive way. To push back against that urge, here is an attempt to write a simple python script to extract folder information from a directory tree.

import os
import re
print "This removes files from saved directory trees"
path = "./"
print "I will run in the local folder"
linecount = 0
for filename in os.listdir(path):
        if filename[len(filename)-4:]==".txt":
            with open(os.path.join(path, filename), "r") as file:
                output= open(filename[0:len(filename)-4]+"_folders.txt","w+")
                for line in  file:
                    if len(line) > 6:
                        if line[len(line)-6]!=".":
                            if line[len(line)-5]!=".":
                                if line[len(line)-6:]!="Cloud\n":
                                    output.write(line)
                                    linecount = linecount +1
            print("I found "+str(linecount)+" lines and put them into "+filename[0:len(filename)-4]+"_folders.txt")
            linecount = 0
        else:
            print("I did not process "+filename)
            linecount = 0

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Photos from the week

From the Tate Modern exhibition by Olafur Eliasson

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 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

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