Category: Geek stuff

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

Not applying to Oxford

In the last few days, I have told a few stories about my time with the Oxford University Walking Club: energetic mountain climbers who are very talented and excellent company. Expeditions with the club was one of the most enjoyable things during my two years in England.

In many ways, it would be appealing to go back to Oxford for my doctorate. I am sure I would appreciate it more now – after four years of work – than I did when I went in after my undergrad degree, back in 2005. There is much to appreciate: the parks, the libraries, and most wonderfully the conversations with knowledgeable and intelligent people of all disciplines.

The major reason I am not applying to Oxford is just finances. Degrees there are relatively quick (you can do an M.Phil and D.Phil in about four years), but it is usually up to students to fund themselves. Some get big scholarships like the Rhodes, but many finance it with a combination of their own savings, familial help, and debt. By contrast, the better American schools are very likely to fund you as a doctoral student.

I was looking at the statistics for Duke University, for example. They fund 95% of their doctoral students. A North American PhD can easily run for five years or more. It would be asking a lot for people to be self-funding as well, especially when the research and teaching provided by doctoral students are integral to the work of universities. The deal in the US seems to be that if you get into a decent school, they can afford to fund you. Oxford University, along with all the colleges, have an endowment of about £3.3 billion (US$5.1 billion). Yale University, by contrast, has an endowment of US$19.4 billion, while Harvard has US$32.0 billion.

Money issues aside, it should be stressed that Oxford is a charming and unique place. There is nowhere else where you can live within the history of the oldest university in the English-speaking world, now more than 900 years old. There is also a marvellous mixture of people there, and it is one of the best places anywhere for turning over new ideas. It’s unfortunate that I am unable to visit more often. Alas, avoiding flying makes that hard.

Photography in changing light

When trying to photograph a city, one basic step to avoid missing good photographic opportunities is to have your camera out and ready. Camera bags and lens caps are useful for transportation between cities, but they are not things that you should have between you and the subjects you are hoping to photograph.

In a similar vein, it is wise (and good practice) to adjust your camera settings whenever there is a major change in the light around you. When you leave your hotel, for example, you might want to switch to a low ISO setting like 200 or 100 because it is bright outside. Along with that, some suitable settings might be a medium aperture like f/8 or f/5.6, with shutter speeds set automatically via an aperture priority mode.

If you then move from the bright day outside into somewhere indoors and dark, you probably want to open up your lens to f/4 or f/2.5 (or even f/1.8 or lower if it is really dark) and bump the ISO to a level that provides acceptable shutter speeds.

Changing your settings whenever the light changes accomplishes two useful things. In the short term, it sets you up to immediately and effectively photography anything you see. In the longer term, it builds familiarity with your equipment and with photographic settings. Once you have that, you can change settings on the fly more easily when truly unexpected circumstances suddenly arise.

The serial (Oxford) comma

When writing lists, there are two different conventions for what to do before the final item:

  1. Lions, tigers and bears are charging toward us from all directions.
  2. To fend them off we will need rifles, pepper spray, and dynamite.

I strongly prefer the second approach, where the final item is set off with a comma, and not just because of where I did my M.Phil.

I have heard some people argue that the commas in a list are stand-ins for the word ‘and’. Instead of writing “life and liberty and the pursuit of happiness”, we should therefore write “life, liberty and the pursuit of happiness”. To add a comma between “liberty” and “the pursuit of happiness” while keeping the “and” is redundant.

I can see the point of this argument, but I think it takes too mechanical a view of language. The purpose of every element of language is to convey ideas and – James Joyce aside – it is usually best to do so clearly. The Oxford comma is very clear. The writer has a list of items, and each item is separated from each other item by means of a comma. In the event of a higher level list, with items separated by semicolons, the final semicolon would surely not be omitted:

His crimes were many: some related to property, like theft and burglary; some related to reputation, including many slanders; and some wanton violations of the Law of the Sea, particularly the disregard of established conventions for deciding maritime boundaries.

In this data-driven age, the serial comma is also in keeping with mathematical and computational conventions. The set of prime factors of my telephone number is: {2, 3, 11, 89, 709453}. Comma separated values are also a common way to store and exchange data sets.

My hope is that I have won over a waverer or two to the serial comma approach. If not, can we please at least agree to put only a single space after a period? We do not live in the age of typewriters anymore!

FileVault in Lion

While the interface changes in Mac OS X Lion are confusing, the whole-disk encryption provided by FileVault is a definite step forward.

People who have their laptops stolen and then find their confidential documents posted all over the internet really have no excuse. If it is sensitive, it should be encrypted – especially if it is on a portable device that cannot be wiped remotely.

I hope a future release of iOS includes comparable whole-disk encryption capabilities. iPhones and iPads are even easier to lose than laptops.

Fight spam! Gain life satisfaction!

Spammers are getting especially annoying these days, with targeted messages.

I have been striking back, though. My honey pot has recently caught a few of them red-handed, to be reported to such authorities as there are for such things.

If you run a web server and you want to help combat the scourge of spam, consider joining Project Honeypot.

You get a certain definite measure of satisfaction when they email you to let you know that your honeypot has helped to identify a server contributing to spam, such as by harvesting email addresses.

So far, I have contributed to the identification of a few dozen malicious IP addresses, hopefully preventing quite a lot of spam.

Biology and infinite complexity

One distinguishing feature of biology seems to be that it is always possible to examine a process in a greater level of detail, whether it is cellular respiration or blood clotting or evolution.

You can say something simple like “DNA contains genes, which are instructions for making proteins using ribosomes” but there are masses of additional complexity behind the process of protein synthesis, and there is far more that DNA does. For instance, the DNA molecule is both a store of information (base pairs) and a physical machine that does things like replication during mitosis.

A recent abstract from Science highlights some of this:

A Time and a Place for Hox Genes

Patterning of the mammalian body relies on the stepwise transcriptional activation of Hox genes. Noordermeer et al. (p. 222) show that this process involves a dynamic transition in the global architecture of Hox gene clusters, with each gene transitioning, one after the other, from a negative three-dimensional (3D) compartment to an active compartment. This bimodal configuration parallels the distribution of distinct chromatin marks, suggesting the existence of a link between the presence of chromatin domains and the formation of 3D chromosomal structures. This model for Hox gene activation would ensure the proper sequence in the transcriptional activation of Hox genes within each gene cluster.

Unless we eventually develop tools that map out every biological process down to the functioning of individual atoms (which we have basically done for processes like photosynthesis), there will always be more to learn about how living things operate.

Quiet Google

I really hate Google Instant and autocomplete – largely because I hate any user interface element that causes things on screen to change in unexpected ways. I also hate websites where little ‘preview’ windows instantly pop up when your cursor crosses over a link. When something unexpected pops up on my computer, I always think: “Waah! Something unexpected and unwelcome has surprised me unpleasantly!” and never: “How delightful! My computer did just what I wanted, without me even asking!”.

I am rather annoyed that even when you turn off Google Instant, Google turns it back on for your account after a few weeks. They really want those extra advertising revenues.

It is possible to avoid both annoying features by searching Google using this link. I call it ‘Quiet Google’ and it helps conserve a measure of calm in the universe.

Should I switch to Aperture 3?

I now have a Mac running OS X Lion and, unfortunately, it cannot run my old copy of Photoshop CS.

Buying Photoshop CS5 is awfully expensive. Even the student and teacher edition is more than $300, while the Creative Suite is more than $500.

Aperture is only $80 from the App Store. What’s more, I would be allowed to install it on any Mac I own.

From what I have read, it definitely has better native RAW support than Photoshop CS (I don’t know about CS5).

It would mean learning some new software and probably losing some capabilities, given the degree to which Photoshop is a more comprehensive and sophisticated piece of software. Still, it might be worth trying in the interim. If it turns out to be unacceptable, I can start saving my pennies and waiting for Photoshop CS6 to be released.