2019 Week 46: Patents

Short version: Patents reward innovators but limit the impact of new technologies. Also “patents” are the answer to the question “Why did Samsung build the only outdoor ice rink in Texas in a small town.”

Long version:

What I learned reading and thinking about patents

Patents are a part of the law, which is an ever changing system. As governments create and change laws, and those laws are interpreted and tested in courts, we collectively decide how the rewards of science and technology are distributed.

There is very little that is certain or obvious about patents. Their existence is both an incentive and a barrier to innovation. They can both enrich and impoverish inventors. They can both be utterly invisible and hugely controversial.

Patent trolling was used in the US to extort businesses, which seems to have peaked around 2015, and has since declined.

Some patents provide useful and specific descriptions of technology, whilst others are deliberately broad and vague.

Biotechnology has struggled to fit into the existing patent infrastructure, particularly as the line blurs between what is an invented object and what is part of nature.

Patent Trolls: Why Samsung built an ice rink in Texas

This article from Harvard Business School outlines how patent trolling, the use of frivolous patent lawsuits by businesses uninterested in innovation, led Samsung to try and win favour with potential jurors in Marhsall, Texas by building an ice rink there. Samsung also set up high school scholarships in the town, but when a supreme court decision meant that the jurisdiction where the suit was filed needed to be in the state of incorporation, the branding on the ice and the scholarships dissipated. More recently a paper was published about patent trolls last year.

Samsung, seeking favour with potential jurors, awarded scholarships to high school students in Marshall, Texas.

Patent Examples

The race to patent the Human Genome

Craig Venter’s company raced public researchers to be the first to sequence the Human Genome. You can read the story in Patrick Bradley’s paper. I found the twitter exchange below interesting, but was not able to verify or refute Venter’s claim that it was “untrue and was propaganda”. Certainly there was a race, and patents played a part, as they continue to do in biotechnology research.

BRCA1 and BRCA2

The other famous case within biotech patents is of Myriad Genetic’s patents on BRCA1 and BRCA2, two mutations related to breast cancer. Enforcing the patents meant diagnostic tests for inherited breast cancer were expensive. The debate centred on the question of whether DNA sequences could be considered a discovery or an invention, i.e. a technical question about how biotech fits within the existing patent system. Ultimately the patents were struck down. The underlying question, how much should we allow companies to profit from their research (at the expense of society, but to give incentives for more research) remains.

Intellectual Property and Piracy

Looking at patents led on to questions about copyright, trademarks, and intellectual property in general. In a world where replication of content is so trivial, and distribution technologies (i.e. the internet) are spreading so rapidly, it is unlikely legal enforcement can keep up in a meaningful way. This crash course provides some information, and I would like to return to think about the ethics of digital piracy, peer to peer sharing, and what the fairest way to regulate content could be.

A note about being connected on the internet

I find it strangely wonderful how connected the internet makes us. From a train, a coffee shop, or even my bed, I can reach out to authors and scientists, and access nearly all of the knowledge humanity has created. In researching this post, I could find out the Marshall high schools’ Samsung scholarship winners, or tweet at scientists like Craig Venter, or access patents from hundreds of years worth of inventions. It is such a powerful tool.

Other things in my life this week:

Rivers in Oxford have been rising, causing flooding around the Isis and Cherwell (see photos from the week). This excellent tracker from Anu Dudhia makes it easy to keep an eye on conditions.

I finished reading The Calculating Stars by Mary Robinette Kowal, it is excellent.

Three friends have signed up to the Edinburgh marathon, so running has gotten more social.

Photos from the Week – Flooding

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 7: Zero to One

Short version: I read Peter Thiel’s notes on startups, had a couple college formal dinners, cycled in the Cotswolds, and bought some protein powder.

Long version:

Zero to One

Peter Thiel is founder of PayPal, and an early investor in Facebook, which have made him a billionaire. In 2012 he taught a course about startups at Stanford, which via Blake Master’s notes became the book Zero to One.

I will update this post later with my thoughts on the book and other missing sections.

Photos from the Week

2019 Week 6: Happy Chinese New Year

Short version: Writing accurately about science takes time, but a few bits to push in that direction. 新年快乐!

Long version:

Writing About Science

I’ve noticed a lack of scientific content in my blog. Usually the week’s post is in the back of my mind throughout the week with a few notes in Google Keep. This week I started out early with a list of topics I’d like touch on, or even expand into, but by Sunday with relatively little progress and wanting to cover them in reasonable depth I’ve culled back significantly. At the moment my main motivation week to week in writing is to practice writing publicly, building confidence and prompting coherency in my thoughts. I would like to share insight, but presenting summaries of scientific work on interesting topics can very quickly grow into a lengthy task (e.g. Review Articles). Also, working full time in scientific research, often my weekend reading drifts into other fields, which then leads to less scientific blog writing.

Chinese New Year

新年快乐!(Happy Chinese New Year!) It is the year of the pig.

Some Hopefully Useful Scientific Content

Stuff I read this week

There is an annual report into happiness. Nature celebrates women behind the periodic table. Google is developing a timber high rise in Toronto. Economic downturn improves health (particularly smoking and obesity). NHS has some simple to follow gym-free workouts particularly neck, back, and knee. Drones being used to poison rats on the Galapagos, possibly targeting Possums in New Zealand next.

A thought on Consumerism

My current context is filled with incentives to buy more stuff. One of the photos from the week is of a particularly expensive sports car that I passed on a run, and I feel that in sharing it I am participating in a culture that causes us to covet impractical luxuries. After all, given speed limits and traffic exist, it’s unclear what the purpose of owning a super car is beyond conspicuous consumption. That said, there is an aesthetic pleasure to be taken from such things.

Photos from the Week

2019 Week 4: Vegetarian

Short version: Why I don’t eat meat, some things I’m reading at the moment, and three photos from my week.

Long version:

Eating Less Meat

Since having moved to the United Kingdom, I’ve been eating less meat. The strongest motivation comes from a desire to minimise carbon impact and waste. The change has been made easy by meat substitutes being widely available and cheap (and delicious).

Evidence:
Intuitively, in order for humans to gain nutrition from an animal, that animal needs to consume either other animals or plants first. Given these processes cannot be completely efficient, there is always a lower energy cost to the environment to eat lower on the food chain. The real effect of this is described in the chart below.


High Protein Diets:
The CSIRO published a book advocating a high protein diet. It generated some controversy in part due to being funded by the meat industry. It still seems a high protein diet is healthy, but there is evidence swapping animal protein for plant protein lowers mortality overall.

More reading:
Publications from Nature and World Resources Institute about the impact of meat on climate change, which include the infographic above. Also, from a moral point of view, Consider the Lobster.

Stuff I read this week

Relevantly, restaurant reviews from the blog Vegan Eats Oxford. The Graduate Outcomes Survey was released. Matt Levine continues to write humorously about finance. Hybrid Perovskite Semiconductors are cool.

Photos: Cakes, Climbing, and Snow

Writing from home.

2019 Week 2: Habits and Goals

Short version: Building good habits makes good behaviours easier. Australians find their history confronting. Green Tea seems to be good for you. Birds have social media in Sydney.

Long version:

Habits, Mindfulness, and Technology.

At the start of 2018 I wrote “In short: learn,  improve my routine, write more.” I’ve noticed on returning to work this year that habits which felt like hard work at the start of last year are coming much more easily. Building a good routine gradually, consistently, and trying to avoid self-flagellation when I failed, has yeilded bigger benefits than I anticipated. This has been most easily observed around physical and mental health, where I’m getting up ealier, feeling more energetic through the day, and getting more exercise in.

On the other side is a reminder how powerful bad habits are. In a vlog this week John Green spoke about discovering just how often he types reddit into a browser when he quit social media. I think handling technology that is driven by so many smart people working to grab more of our attention to sell more advertising, is hard. One way I’m going to work to improve my relationship with tech this year is to make sure I have a purpose each time I interact with it. The aim is see it and use it as a tool, rather than be guided by it to burn time.

Australian History: “Slavery by Other Means”

My friend Seb wrote two articles on Pacific Islander Labour in 19th and early 20th Century Australia. My intial response to this brutal chapter of Austalian history was to attempt to trivialise it. Thoughts like “not as bad as other slavery”, “life was harsh for everyone back then”, and “life as a labourer wouldn’t have been that bad”. I would guess these are responses to shield myself from feeling, be it empathy or disgust or guilt or simply sadness. I’m not sure if an emotional engagement with history is preferable to a clinical intellectualism, but I do think the tendancy to avoid discomfort in historical interest is harmful. The extemes are feeling so strongly we are paralysed or act irresponsibly vs being callous to injustices, but the best place to sit between the extremes is not clear to me. I think both the article and the general principle are worth consideration.

Green Tea

It seems like drinking Green Tea is pretty good for you. I think all nutritional science suffers from difficulties collecting accurate data from inherently unreliable test subjects, but a quick search of google scholar seems to come up with a compelling set of results. I’m convinced enough to be swapping out some of my coffees for the world’s most popular brew.

Social Media for Birds (and Science)

Picture of the week is an Australian white ibis or Bin Chicken. Noticable is the yellow tag, which lets you know his name is Wazza. You can help him (and research) out by posting on social media for wing tagged birds.

Writing from home.


2018 Week 8: Science Blogging

Week in Summary
I was sick this week, the international presence in Oxford is wonderful for diversity of both ideas and rhinoviruses. I continue to take (Latin) dance classes, at the novice level it still feels (and no doubt looks) a little silly, but there is fun to be had in silliness.  On Saturday I saw the Oxford Imps perform Improvised Cabaret at Modern Art Oxford. It was also a little silly, and it was certainly fun in its silliness. Life can sometimes be a little too serious, particularly in rigorous research, and they say laughter is good for the soul. On Sunday over brunch I learnt about container ships and efforts to commodify them.

Science Blogging
Further inspiration to keep on blogging came recently from Nature, and highlighted a couple of great blogs: DoctorAl (a biologist at Wilfrid Laurier University) and Scientist Sees Squirrel (an ecologist at University of New Brunswick). Another scientist to cross my news feed is the incredibly inspirational  Dr Emma Pooley.

Reading List
One of my goals for 2018 is to read 24 books. At that rate I ought to have finished four by now, however I have yet to finish even one. Instead I’ve been consuming: Instant MessagesReddit, Forums, Academic PapersWikipedia, The Economist, and occasionally The New York Times (thanks to a free subscription courtesy of the google local guides program).

Currently the books on my desk are:

  • Clark, D. (2016). Alibaba: the house that Jack Ma built. HarperCollins.
  • Sasaki, F. (2015)  Goodbye, Things: The New Japanese Minimalism Penguin
  • Thiel, P. A. & Masters, B. (2014). Zero to one: notes on startups, or how to build the future. Crown Pub.
  • Vance, A. (2017). Elon Musk. Editions Eyrolles.
  • Stone, B. (2013). The everything store: Jeff Bezos and the age of Amazon. Random House.

Delays


This post comes several weeks late. I was a little ill the actual week of this blog, and predominantly work has cascaded into time that I would otherwise allocate to writing. As such it comprises ideas that came together in Week 8 of 2018, but actually was published on Monday of Week 12 (blog catch up week).

 

Writing from the office.

2018 Week 5: Trolley Problems

There isn’t a unifying theme this week, just a mixture of things I’ve been thinking about.

Trolley Problems
Last night I attended a Raclette party and over deliciously melted cheese enjoyed conversing with American, British, Chinese, and Swiss friends. For most of the world, the prevalence of guns in the United States of America is frighteningly alien, and I recommended an episode of the podcast More Perfect about the history of the  Second Amendment which I found fascinating. Following speculation about situations where someone might use a gun, the discussion became a more abstract consideration of the trolley problem (there is also a relevant Facebook meme page).  I find it interesting that most people adopt the utilitarian perspective in the more foreign situation of pulling a lever to move a trolley, but if you reframe the decision where the actor is a doctor, the 5 are suffering failures of 5 different organs, and the 1 is an unknown backpacker come in for a check up, people find it intuitively more difficult to take the life of the stranger in the more familiar context. Perhaps this is an intuition about the risk of organ transplants making the lives of the ill less valuable than the life of this healthy traveller, or perhaps it is something about breaking the trust that the traveller imbues in the doctor. Clearly the characters tied to the tracks have no such relationship with the lever operator. One way in which this discussion is particularly timely is in considering self driving cars, who will need these decisions programmed into their code ahead of time. This MIT app lets you make judgements of such moral dilemmas, then gives you some feedback on your preferences, and you can even invent your own (the associated paper is here).

British Library
This week I visited the British Library. Each time I go I am struck by the scale of legal deposit. The system guarantees the British Library will hold a copy of every book (and some other text types) published in the United Kingdom, which some quick googling suggests is around 500 books a day, every day of the year. It can be confronting, particularly when I feel relatively poorly read, that such an unceasing torrent of new material is being created daily. Another perspective is several hundred hours of Youtube video are added every minute. In a world where there is so much information, it is a good reminder to treasure each unit of attention one has, and to invest it wisely. I hope, dear reader, you feel this is worth your time.

Motivation and Mental Health
This week I felt the first few cracks of trying to squeeze as many productive hours into a week as possible. On reflecting, I am reminded that positive feedback is important, and low motivation can be the result of too much focus on the negative. Setting up for “easy wins”, where you are able to make progress without much difficulty or excitement, can help build momentum to tackle more difficult tasks. I also need to improve sleep hygiene, checking the bright light of a smartphone in the middle of the night is not aiding rest and recovery.

Writing from the Radcliffe Camera

2018 Week 2: What is your biggest failure?

Career
This was my first week at ONI and it was great. The team is brilliant, and represents almost as many countries as it has people. In my previous job, as in this one, a personal blog is not the place to discuss the specifics of work (that might be commercially sensitive), but it is an exciting and satisfying environment to be in.

Languages
I’m on a 14 day streak for Chinese on duolingo. I first heard about duolingo from the TED talk of Luis von Ahn, which is probably a little dated, but certainly interesting from a “history of crowd sourcing” perspective. Notably it seems to have grown to be much more about learning languages than translating the entire internet, which is not to say crowd-sourcing has been unsuccessful (see Niantic and PokemonGO). Freakonomics did a podcast about how (financially) valuable it is to learn a second language,  talking with Albert Saiz who wrote a paper. In short, it’s not particularly valuable, unless the second language you’re learning is English.

Reading
Before we get serious I’ve discovered a guy here called Chris McIntyre writes a weekly email called “Interesting Things I Come Across” and it lives up to its name.

Failing
There are some questions that seem to come up in interviews no matter the position or experience. Having a concise answer to “Tell us about yourself” or “why do want the position”.  One I found difficult is “What is your biggest failure”, and in answering it over and over I’ve started to make sense of it. My failure is quite literal. I failed a number of subjects during my studies at University. Specifically 8 discontinues, 6 absent fails, and 3 fails, from 2014 to 2016. It still stings to look that up, and look at a rather large hole in an otherwise reasonably good transcript. I’m still afraid to admit it.

For most of my life I held the foolish belief that it was impossible for me to burn out. I thought that I was intelligent, but lazy. I relied on the “Panic Monster” to push through days without sleep so I could start a term’s project a couple days before the deadline. I remember explaining the reason I had so overwhelmingly over-committed myself was that “I could never have the discipline to do things gradually over time, but I always managed to scrape through, so the best way to be efficient  was to do lots and lots of things”. These beliefs were so core to how I saw myself that eventually when I did burn out, it was took me 3 years to finally accept and change these unhealthy views.

Thankfully I’ve since learned that I, like most, do not have an unlimited capacity for pressure. That I do need rest. That being smart is not all that matters. That talent is important, but consistent application of effort over time counts twice as much. Perhaps most important of all, that it is OK to ask for help.

That’s an imperfect summary, but it is certainly a good place to start.

Written (mostly) from the Oxford Hackerspace.

July 2017: Job Hunting and Rock Climbing

I left Sydney for Oxford in early July, so a month having elapsed, this is what I’ve been up to:

Job Hunting
My primary goal has been finding work. So far that looks like:

   Positions Considered             81
   Applications             16
   Rejections               6
   Recruiter Calls               4
   Interviews               3
   Offers               0

Unfortunately no offers. I’ve focused on jobs in Oxford, so have applied to positions from the university. In a wider search, reed has seemed more relevant to me than indeed,  and making a profile there has been the main source of calls from recruiters, which seems promising. It’s probably time to extend the search to include London, though I’m still hoping to find something here in Oxford.

Reading
Aside from many job descriptions, I’ve been reading Huffington’s The Sleep RevolutionThe Economist, and reddit.

Hackerspace
Having become a member of the Oxford hackerspace, I’ve been helping out a little with the 3D printing service. Producing tangible objects is very satisfying in contrast to job hunting.

Fitness
I’ve tried two new activities: squash and rock-climbing/bouldering. My staples of running/cycling and weightlifting leave a gap over hand-eye coordination, which squash fills in well. After about 8 hours I think I’m starting to develop muscle memory for basic play. I was surprised to find climbing has a huge mental component; planning and executing the correct strategy seems just as important as strength. It’s certainly fun, and much more mentally involved than lifting weights or running, but for pure fitness training not as effective.

Chess
I’ve played 207 games of chess. I haven’t improved much, so should add structured training rather than just blundering repetitively through similar openings. It’s probably also been more procrastination than relaxation this month.

Berglabs
And, of course, I’ve resuscitated this domain and updated it with a WordPress theme.

Travel
Life has taken me to London (by train) and Eyam (by car).

Writing from the Clarendon Laboratory, Oxford.