Category: Geek stuff

If it involves physics, math, computer science, electronics or has general geek cachet, this is the place for it.

Open thread: Antibiotic resistance

I frequently see interesting stories about antibiotic resistance, and it seems to be quite an important issue. Back in 2008, I wrote about a Canadian initiative to try to deal with the dangerous bugs.

More recently, tuberculosis has progressed from extensively drug-resistant TB (XDR-TB) to “totally drug-resistant TB” (TDR-TB).

We are going to need some new antibiotics.

2012 vernal equinox

The coming of spring is an astronomical and biological phenomenon.

The moment of the vernal equinox – the start of spring in the northern hemisphere – is the moment where the length of days is changing fastest. Biologically, spring is characterized by the re-emergence of life. In particular, it is characterized by the resumption of productive photosynthesis as leaf-bearing plants deploy their solar collectors to take advantage of longer days. This process, along with organic decay during the darker months, gives the Keeling Curve its characteristic wiggles.

In a way, each spring is a dawn for renewable energy. Aside from a few chemical-eating bugs in the ocean, pretty much all life on Earth is ultimately powered by sunlight as processed by photosynthetic organisms. Spring shows how the vast energy output of the sun can be used in the service of life.

Ubiquitous surveillance

We now live in a world where it is highly likely that various web companies, your government, and your internet service provider are tracking your web browsing. Where facial recognition software identifies you at borders, airports, and subway stations. Where your DNA may be sampled if you are arrested. Where new face tracking software gets used with old photo archives and video camera footage. Where data on what you buy and how you repay your debts is sold between companies. Where cameras track your automobile license plate to build up a database of your movements. Where drones may watch you from the sky. Where computers transcribe your speech and handwriting into searchable text. Where you can be identified at a distance by the cards in your wallet. Where your emails, phone calls, and text messages are scanned for keywords, archived forever, and used to build up webs of your known associates. Where governments and private organizations use data mining techniques against you. Where your cell phone can easily be turned into a bug that passes on what you say and type, as well as where you are. Where your Google searches may be used as evidence against you. Where anyone can listen to your cell phone calls. Where the metadata in the photos and videos you make identifies you. Where the DNA of your family members may be used to incriminate you. Where anyone on your wireless network can archive and access all your web traffic, as well as steal website sessions. Where no encryption software you can acquire does much good. Where insecure means of communication are marketed as secure. Where archives containing your sensitive personal data can be broken into (or bought) by those who wish to cause you trouble. And where anything ill-considered you did as a teenager may re-emerge to cause embarrassment or worse decades later.

The appropriate responses to this are not clear. You can simply accept that your life is an open book that anyone who cares to can pretty easily read from. You can opt out of some services (like Facebook) and employ some available countermeasures. You can move to the remote countryside and become a technology-shunning subsistence farmer (which is not to imply that all farmers shun technology, nor manage only to subsist). You can try to drive legislative, regulatory, and technological changes that address some of the issues above. What else can you do?

Index tracker three years in

Three years ago, a discussion began on this site about which investments might do the best job of growing faster than the rate of inflation. It’s a pretty important question for anyone who hopes to attain a reasonable degree of financial security. Bank accounts, government bonds, and GICs all pay well below the rate of inflation, meaning that those who are prudent enough to set money aside actually pay a penalty for doing so.

Based on the way in which equities have consistently outpaced commodities and bonds over the last few decades, my guess was that a low-fee index-tracking mutual fund was probably the best bet for ordinary investors hoping to achieve growth at a reasonable level of risk.

I bought some units of the ING Direct Streetwise Balanced Growth Fund for $8.18 each on 20 May 2009. The unit price has since risen to $9.61 – an increase of 17.5% over three years, after fees. That almost certainly beats the pace of inflation, but I am not sure how it compares to alternative investments that could have been made at the same time. Given how much the price of gold has shot up lately, I suspect it would have been a better investment for the 2009-2012 span. That said, given that gold doesn’t actually produce any return, I suspect the index tracker will dramatically outperform it over a multi-decadal timescale. Time shall tell.

P.S. I really wish there was a low-fee index tracking option that didn’t include investments in the oil, gas, and coal industries. It is particularly troubling that every major Canadian financial institution seems to invest in oil sands development.

Forms of address

One of the trickier aspects of corresponding with lots of relative strangers is never knowing quite what to call people.

This is all in relation to written communication. In one-on-one speech, I go out of my way not to call people anything at all.

Academic titles

To start with, there is the eternal question of how to refer to an academic who you don’t know. They probably have a title, which might be ‘Associate Professor’ or ‘Assistant Professor’ or just ‘Professor’. Do you call everyone ‘Professor X’? Or do you use the title on their website? What about people who are excessively quick to call themselves ‘professor’? I have seen it on the business card of a doctoral student.

My solution – call everybody with a doctorate ‘Dr. X’. It doesn’t matter if they just got their doctorate yesterday or whether they have won an armload of Nobel Prizes. ‘Dr. X’ is a perfectly polite form of address between strangers.

Exception: close friends and fellow former students. You may have worked half a decade to get that post-nominal P.H.D., but if we were in first year together I reserve the right to call you by your first name indefinitely.

Other titles

I basically ignore them. ‘Reverend X’ and ‘Lieutenant X’ and ‘Engineer X‘ and ‘Mayor X’ and ‘Prime Minister X’ are all liable to be referred to simply as “Mr. / Ms. X”.

Women

It’s a bit embarrassing that there even has to be a space for this, but such are the sexual double standards of our society. There is nothing as neutral as ‘Mr. Smith’ that you can call a woman. Every option carries a political message. Using ‘Miss Smith’ or ‘Mrs. Smith’ means buying into the somewhat absurd notion that a woman’s whole identity changes when she gets married (and when a man’s does not). I use ‘Ms. X’ anytime I can’t call someone ‘Dr. X’. That goes for any stranger, usually until they specifically tell me to call them something else.

Someone who you know nothing about

Say you discover that www.websitename.com has been horribly defaced. You want to contact ‘webmaster@websitename.com’ but you don’t know any part of their name, or whether they are male or female.

In this circumstance, I usually go with ‘Good [time of the day]’ if I am being less formal and ‘Sir or Madam’ if I am being more formal.

Referring to me

I am perfectly happy to have everybody call me ‘Milan’.

Whenever I see a letter for ‘Milan Ilnyckyj, BA’ I know it is UBC writing to ask for alumni donations.

Timex Expedition

Recently, the Mondaine watch I got at the Museum of Modern Art in New York stopped working. It was under warranty, so I sent it to the address listed on the warranty card as an expedited parcel. It was returned to me as undeliverable.

While I am figuring out how to convey it to them, I got an inexpensive Timex Expedition watch as a replacement. I used very similar watches back in elementary school. I remember getting a new one every time the battery on one died, for about $40 apiece. They are about the same price now and – after a couple of days of using it – I can say that it is the best watch I have used in a while.

It has three alarms, and it very easily lets you set one for weekdays and one for weekends. It has an accurate chronometer and countdown timer. The controls are intuitive (or perhaps I remember from elementary school). You can press one button to display an alternate timezone (I have mine on GMT / UTC.). It has a big button on the front that makes it light up in an effective but unobtrusive way (much less annoying than checking your cell phone). And it’s good to 100m underwater – a position that if I ever reach, I will probably have already died reaching. It shows the time, day, date, and day of the week at a glance, and I think it takes less thought to comprehend the time expressed digitally. Analog watches always make me pause a moment to interpret them.

The watch is small and light and comes with a comfortable and reasonably attractive-looking strap. It definitely isn’t dressy, but it is highly functional and attractively priced.

We’re made of cheap stuff

As a child, I visited Vancouver’s Science World on what was probably a monthly basis. I knew most of the stage shows by heart (‘Arcs and sparks’ was the most energetic, complete with exploding pickle), along with the dramatic vocal introduction at the OMNIMAX theatre.

One display I remember well was located in the main atrium area. It was a scale that weighed you and then told you in a robot voice how much it would cost to buy lab-grade versions of all the chemicals that comprise you. It would say: “You contain $1.24 worth of carbon” or “You contain $0.03 worth of iron”. At the end, it said that you had a monetary value of X amount “give or take a few cents”.

In a way, the display illustrates that is remarkable about biology. You can take utterly mundane stuff – air and soil – and turn it into astonishingly complicated chemicals and structures, everything from the complex fragrances of flowers to DNA to the core of an oak tree to a human brain. Botany and plant cultivation are a kind of alchemy precisely because of how they allow the transformation of garden-variety raw materials into complex products. You can have all the materials necessary to make a wombat, but there is really no way to put them together in the right way unless you have a couple of fertile wombats on hand as well.

The same reality intersects with the practice of organ donation. Right now, a mass of a few kilograms located inside my thoracic cavity might be a highly-valuable liver or kidney. Without the benefit of a functioning circulatory and immune system – or, failing that, proper care and refrigeration – it becomes a near-worthless lump of meat in just a few hours. We’re made of cheap stuff; the added value is in the organization.

Lark sleep monitor

For the past couple of months, I have been using a Lark sleep monitor. It’s an accelerometer that you wear on your wrist at night that interfaces with your iPhone. It both works as an alarm clock and as a measuring device that provides data on the length and quality of your sleep. You set when you want to wake up and it wakes you at that time with nearly silent vibration (and a backup sound alarm from the phone).

The device has a few obvious uses. If two people sleep in the same bed but normally wake at different times, the Lark would allow one to more easily wake on time without waking the other. The Lark also lets you collect statistics about yourself, and evaluate how well you sleep in different environments and conditions.

For instance, I slept for an average of 8:41 per night when on vacation at my aunt and uncle’s very quiet house in Bennington, Vermont (with one early morning on December 25th). That compares with an overall average sleep time of 7:45 over the past couple of months.

So far, I have collected data for 86 days. More accurately, I have data for 81 of those days and null values for the five days when I wasn’t able to use the Lark – for instance, because I was taking an overnight Greyhound.

My recent sleep stats

This table shows some simple summary statistics:

Mean Median Standard deviation
Time asleep 7:45 7:56 2:00
Sleep quality 8.5 8.7 0.84
Fell asleep in 0:37 0:30 0:34
Woke up (# of times) 18.9 18 6.39

 

In blue, this time series shows time spent asleep. In pink, it shows how much time was spent falling asleep:

This is a histogram of time spent asleep:

And this shows the frequency of the different qualitative sleep ratings assigned by the Lark software:

The Lark software informs me that the amount of time it takes me to fall asleep “needs work”, as does the number of times I wake per night. My overall length of sleep and sleep quality it deems “OK”.

The biggest thing that jumps out at me from my own data is the sawtooth pattern of sleep. I tend to alternate between a night with relatively little sleep (about six hours) and a night with relatively much (about nine hours). Given that I usually need to wake up at 6:30am or 6:45am, these correspond to nights when I go to sleep around midnight and others where I collapse around 9:00pm or 10:00pm.

Remember, the Lark distinguishes between time spent falling asleep (the period before the first time of prolonged stillness detected by the Lark) and time spent actually asleep. A night recorded as eight hours of sleep is therefore a night with eight hours of stillness comparable to that of sleep, rather than a night when you spend eight hours in bed. Being able to distinguish those two things may be the most valuable thing about the Lark.

Evaluation of the Lark

Overall, I think the Lark works very well. It has never failed to wake me up, and the iPhone software works well.

One suggestion to all iPhone owners is to put your phone in ‘Airplane mode’ at night. That way, it doesn’t beep or buzz when you get late-night texts and emails. You can still use the Lark in this mode, but you do need to follow a simple procedure:

  1. Set the iPhone to ‘Airplane mode’
  2. Manually turn Bluetooth back on
  3. Connect to the Lark
  4. Set your alarm time in the Lark software
  5. Sleep, and be woken

One useful feature the makers of the Lark could add would be the ability to set pre-programmed alarms for different days of the week. For example, you might set your default Monday-Friday alarm for 6:30am or 7:00am, but your weekend alarm for a more reasonable 9:00am or 10:00am.

One side note: it is easy to transfer the basic sleep data from the Lark into your preferred statistical analysis software. For people who don’t want to do that, the company sells an absurdly overpriced (US$$159!) subscription service that keeps track of your data for you online and provides ‘coaching’.