Protein Folding in a Computer Game

Creative Commons License photo: monkeyleader

Big distributed computing projects such as SETI@Home, folding@home and “the BBC Climate Change Experiment” have been around for years. They utilise extra computing power when the computer is inactive to help find aliens, fold proteins or to run climate models to predict the effects of climate change.

Computer scientists have found a new way to help them understand how proteins fold – one of the central problems in biology. From The Economist:

Proteins are the building blocks of life inside cells; they are first made as long chains of molecules and work properly only after they have folded into their final shape. But understanding the rules of protein folding remains one of biology’s central problems.

The existing program uses trial and error, and pre-programmed mathematical rules that govern folding as understood today. But users of the screensaver told David Baker, a biochemist at the University of Washington and lead scientist on Rosetta@home, they could do better.

Players use their computers to fold proteins. The more chemically stable the folded protein becomes, the more points the players are awarded. In trials of the game hundreds of players were given 40 protein puzzles to solve (for the trials, the folding solutions were already known). Many of the best players were not scientists but were able to find the correct structure faster than computers.

It’s great to know that the power of the human brain can still beat a computer! So far the experiment has only been run using proteins for which the folding solutions were already known. The next step is to give players proteins for which solutions aren’t known – the players will then be taking part in some new cutting edge research!

The Problem with Fuel Taxes and Road Pricing

8th Ave .....Midtown Manhattan
Creative Commons License photo: 708718

Congestion and pollution are two “external costs to society” which are associated with driving. When you take your car out of the garage and take a trip down to the local supermarket or pick up the kids from school, you are imposing costs on other people: exhaust fumes which others must breathe and you take up space on the road contributing to traffic jams.

To correct for social costs, governments use taxes to make sure the individual pays for the costs they impose on society or to “internalise the external costs”. There are three taxes which are used to try and discourage driving:

  • VAT on Buying a Car
  • Road Tax
  • Fuel Tax

People hate taxes. People remark that death and taxes are the only two certain things in life and I think that fuel tax is one of the most hated (in the UK, fuel tax is 64p for every litre). The government argue that this fuel tax is to correct for “external costs” but I will argue that the fuel taxes is unfair and are targeting the wrong people.

The Costs of Driving

Comings & Goings
Creative Commons License photo: Pro-Zak

Urban motorists impose greater external costs on society. City roads are full to their capacity and that means traffic jams everywhere. An extra car on the road is only going to make it worse. Congestion wastes everybody’s time. Secondly, population density is so much higher in cities meaning that the exhaust fumes produced will affect a lot more people. And not to mention noise pollution…

In contrast, rural roads are much quieter and less congested. Because there is so much spare capacity on the roads, an extra car on a rural road isn’t really going to add to congestion or effect anybody else. And although exhaust fumes are still emitted and noise pollution is still produced, it effects a lot less people: there are less people for it to affect.

So the external costs imposed by drivers in cities are greater than the external costs imposed by drivers in the country.

The effects of taxes

Beijing smog
Creative Commons License photo: kevindooley

When you buy a car, you pay value added tax on the vehicle. To keep the car on the road, you must also pay road tax. Both of these taxes will discourage people to own a car because they increase the cost of owning one. But once you own a car and it’s licensed to drive on the road, these taxes will play no part in your decision about whether to use the car to drive to work or not: whether you use it or not you’ve already paid the tax. And whether you live in the city or the country you pay the same amount of VAT and road tax.

The other tax is fuel tax. This affects people’s decision on whether to drive to work or school. If it costs £2 to drive to work you might choose to do it every day but if it cost £8 you’d probably only drive if it was raining or for some reason the trains weren’t operating.

As I’ve mentioned, the external costs of urban driving are greater. So a fair tax which “internalises external costs” should penalise urban drivers more. But the taxes on urban driving are actually lower than taxes on rural driving. Places in the city are situated much closer to each another and so less fuel is needed to drive between them. As the amount of tax paid is directly linked to the amount of petrol used, this means urban motorists are paying less tax than rural motorists. This is unfair.

Is it essential to drive?

Il terzo occhio
Creative Commons License photo: fabbio

Another factor that economists must consider is “how necessary is it to drive?”

In the city, there are a huge range of alternatives to driving. In London, there is a flat rate 90p charge on all bus journeys, where ever in London you go. Buses are also very frequent: you shouldn’t have to wait any more than 10 minutes. I’ve found that I rarely have to wait more than a few minutes.

When I’m in the country, it often costs £3 for a single bus journey and the bus only comes once an hour or sometimes even every 2 hours. And there is about a 20 minute window for the time that the bus arrives.

In the city, everything is also much closer to each another. That makes cycling or walking a much more viable option.

So in the country there is often no choice except from to drive because everything is so far away from each another and there are no viable public transport options. In these areas, motorists must pay extortionate amount of taxes. Meanwhile urban city drivers, with the luxury of viable alternatives such as the bus, escape with lower amounts of tax. I think this is the fundamental unfairness of fuel tax.

Solving the problem

Sam Houston Tollway
Creative Commons License photo: billjacobus1

The problem is that fuel tax penalises the wrong people. The solution is to tax urban drivers more to account for the greater amount of “external costs” they impose by driving.

In London we also have the congestion charge zone (£8 to enter Central London per day) and the low emission zone (£200 per day for heavy polluting vehicles to enter London). I think this somewhat solves the issue but it’s only restricted to London.

A few years ago the Labour government floated plans for a national road charging scheme.

Motorists will receive regular bills, possibly monthly, charged at variable rates by time and geography: rural country lanes would likely be charged at the bottom of the range, around 2p a mile, with inner city rush hour roads attracting the top £1.30 rate. The government hopes motorists will change their driving habits – by staggering journeys, sharing cars or switching to public transport – to the extent that there could be a 50% cut in congestion.

From a point of view of an economist, I feel that this is the perfect solution to the problem. It would reduce congestion which would lead to time savings for everybody and stop country motorists from being unfairly penalised.

In 2007, 1.7 million people signed a petition against the national road charging scheme. The idea seems to have fallen from the agenda. Because of the inherent unfairness in fuel taxation, I hope the government will reconsider a national road charging scheme.

Yahoo! Search in Opera Speed Dial

I’ve been giving Opera a bit of a spin lately as a browser to replace Internet Explorer as my secondary browser. Anyway… Opera has a nice “Speed Dial” feature which appears when you open the browser. It features screenshots and links to 9 websites that you can preselect. By no means a killer feature and you can get a similar feature in Firefox via an extension but a nice feature none the less.

What I don’t understand is why there is Yahoo! Search functionality built into the top of the Speed Dial whilst Google Search functionality is provided in the search box in the top right corner. It makes no sense to me that a browser would offer you both a Yahoo and Google search box.

Opera Speed Dial

If somebody really wanted to use Yahoo!, they can switch to Yahoo! using the dropdown menu next to the search box.

I’d hazard a guess that this redundant, and quite frankly confusing, piece of user interface exists as Yahoo! have paid Opera to include their search box on the speed dial.

Gordon Brown wants Apprentice-style TV reality show

Gordon Brown - World Economic Forum Annual Meeting Davos 2007
Creative Commons License photo: World Economic Forum

In what must be the strangest news I’ve heard in a while, British Prime Minister Gordon Brown wants to star in his own Apprentice-style TV reality show

The email from producer Margaret McCabe pitched the show, which would feature aspiring politicians as contestants, as being targeted for the “Apprentice meets Maria/Strictly Come Dancing audience”.

The memo added that the show was “not stunt TV” and as a judge, Brown could become “more popular than Alan Sugar”.

A spokesman for Blears confirmed that a reality show was in the works: “It is a very worthy programme idea. These young people would engage and have some kind of competition, and then there would be a way of electing a young prime minister for a day.

“The idea is to get more young people interested in politics. But it hasn’t been commissioned yet. It is very early days.”

It has been documented before that Gordon Brown is a big fan of the X Factor.

I think it’s interesting how Gordon Brown is such an unpopular prime minister that he now feels like he needs to be a judge in a television reality show. There will of course be worries that this show could cheapen politics. I can’t remember whether it was just an idea which was floated or an idea which actually happened in some country, but people talked about having a reality show to determine a candidate who would stand for Member of Parliament. Of course, the problem is the winner of the show has had an unfair amount of publicity and would probably easily win election based on the fact they were once on TV, regardless of whether their politics were actually any good.

Anyway, the “Junior PM” project is still in the very early days so it’ll be interesting to see whether it gets any further.

UK Piracy Levels Falling

The BBC reports that the piracy levels in business in the UK are falling for the first time in 3 years. The piracy rate has fallen 1% to 26%.

Despite the fall in UK piracy rates and 66 other nations studied in the report, the global rate of piracy grew during 2007.

The average global rate of piracy now stands at 38% – up three points on 2006. The BSA said this was because sales of PCs grew fastest in countries where piracy was rampant.

Armenia now tops the rankings of nations with most pirated software. The BSA estimates that 93% of software used in the country is pirated. The US has the lowest rate at 20%.

Na hraně dat - On The Data Edge
Creative Commons License photo: Johny hanging…

The BSA (Business Software Association) claim the reduction in piracy is due to education.

Perhaps it’s partially due to that, but I think other factors are at play.

First of all, Microsoft has essentially been giving away it’s flagship products for free or a very low prices to students. Certainly students and teenagers used to use a lot of pirated software because they have no income of their own, no credit card or way to buy software and also have greater knowledge of how to use programmes such as P2P. I believe quite a few people have been taking up the offer of discounted software from Microsoft so I think this has helped in reducing piracy.

Secondly, with so much good quality open source software out there these days there is no good reason to buy pirated software. Open source software is usually at least as good as their commercial counterparts and are much easier to obtain than their commercial counterparts.

I’ve been thinking about the economics of open source software. It’s surprising that software which costs absolutely nothing could be economically sustainable especially when so much of economic theory says that software which is developed by commercial companies should be much more innovative and of a higher quality.

I really don’t agree with software piracy but I think with the wide availability of decent open source software, I don’t think there are any good reasons for it either.

Atari Family Trainer: Outdoor "Wii Fit"

Atari have announced Family Trainer for the Wii which will be in competition with Nintendo’s own Wii Fit.

Family Trainer lets all the family and friends get physical by engaging the whole body in a variety of easy-to-understand, fast-paced and wildly entertaining activities. Family Trainer is scheduled for European release in September 2008.

Wii Fit Stand
Creative Commons License photo: włodi

The game includes the specially designed Family Trainer mat controller which, when combined with the Wii Remote, lets players get totally physical in a series of crazed challenges.

There are over a dozen frantic single and multiplayer challenges to choose from all based on outdoor challenges amusingly interpreted for the world of Family Trainer, such as river rafting, mine karting, log jumping, rope skipping and much more. The activities take place in a variety of colourful locations including jungle forests full of ancient ruins, a haunted mansion complete with hordes of zombies, and a fairytale world where riding on toys and floating amongst the clouds is the order of the day.

I think it’s great how Nintendo seem to have carved out a niche in the games console market for family and exercise based games. Wii Fit has taken off really successfully and perhaps by the time Family Trainer is released, people might have got sufficiently bored by Wii Fit to want a change.

Unlike Wii Fit, this sounds like a much more multiplayer game so it’d be interesting to see what it’s like when it comes out.

Data Visualisation in Javascript

Processing.js is quite something. Its a port of the Processing data visualisation programming language into Javascript. A great use of the <canvas> functionality in recent browsers. Because it pushes the browser to it’s maximum, it is recommended you use it only with the latest beta browsers: Firefox 3, WebKit nightlies and Opera 9.5.

If this doesn’t sound impressive to you, check out some of the demos:

There really are all kinds of things from physics to fractals, from clocks to modern art.

What can I say apart from that it’s left me speechless and quite how processing.js can weigh in at over 5000 lines and compresses to under 10kb.

I suppose the sluggish performance in the browsers is the main downside of this but I guess that this will get better in time as I haven’t seen enough intensive <canvas> applications lying about which would warrant browser makers putting time into improving performance.

Appearing Offline on MSN/Windows Live Messenger: Game Theory Analysis

Creative Commons License photo: jenn_jenn

A few years ago, Microsoft introduced the ability to “hide” on Appear Offline on MSN Messenger and to keep talking to people. This is quite a useful feature for the anti-social types who really don’t want anybody to talk to them!

I’ve noticed some interesting trends since this feature has been introduced. The people who used to have their status stuck on “away” now use appear offline. This is perhaps frustrating when you then end up calling or texting at extortionate rates your friend instead whilst you’re actually both sitting at your computer!

The reason why people use “appear offline” is so they can be selective about who they talk to. Fair enough. But when other people also use “appear offline”, it doesn’t work. This could be illustrated using a bit of game theory.

Appear Offline

Initially, lets say that both persons A and B gain 2 units of utility from being online in MSN Messenger. This utility could be in many forms: pleasure gained from sharing gossip, money saved in not having to text or time saved. The exact form of the utility isn’t important.

Let’s go into hiding… 

grandmaster FLAX ~ II
Creative Commons License photo: striatic

Now lets say Person A decides to “Appear Offline” but Person B is still “Online”. Person A will only talk to Person B when it is beneficial to him. Person A will still gossip with Person B but only in times convenient to himself and when he’s stuck on his particle physics essay, he can still see when Person B is online and get help from him. For this reason, Person A’s utility increases from 2 to 3.

But Person B won’t derive any utility. When he needs somebody to talk to, or has run into a brick wall upgrading to Service Pack 3, he won’t be able to get through to Person A on MSN Messenger. Instead, he might end up calling or find a more sociable person to talk to! Hence Person B derives no utility from this arrangement.

Notice that the payoffs are symmetrical. If Person B decides to “Appear Offline” but Person A doesn’t, Person B will gain 3 units of utility whilst Person A will gain nil.

The fourth possible situation is when both Persons A and B decide to “Appear Offline”. Neither persons derives any utility from this arrangement as they’ll never talk to each another. They might as well actually be offline.

The best arrangement 

Holy Rollers
Creative Commons License photo: J. Random

As we can see, in this analysis the best possible outcome is that both persons A and B are online. They both derive 2 units of utility from this arrangement and 4 units of utility are gained in total.

Person A or person B could seek to increase the utility they gain by appearing offline. This increases their own utility to 3 units. Would they do this in reality? Rationally, probably yes.

If person A decided to stay “online”, person B would gain 2 units of utility from staying online and 3 units from appearing offline. So in this situation, person B should appear offline to maximise their own payoff.

If person A decided to “appear offline”, person B gains no utility either way. So it really doesn’t matter whether person B stays online or appears offline. But they don’t lose any utility by appearing offline.

By considering all the possible outcomes, person B will rationally choose to appear offline to maximise their payoff. As the situation is symmetrical, person A should also rationally choose to appear offline. The outcome? Both persons A and B “appear offline” and nobody gains any utility.

Back to the real world…

In this discussion and game theory model, I’ve abstracted from reality. Of course, it isn’t true that everybody on MSN Messenger appears offline these days. But I will say that amongst my contact list, I know quite a few people do and it has lead to some annoying situations. I’m even guilty of “appearing offline” on many occasions without realising the person I want to talk to is also appearing offline and waiting for me to come online.

Spicing up your blog posts with photos

Creative Commons License photo: pietroizzo

One problem with many of my blog posts in the past has been that they aren’t particularly interesting to look at! In the many designs which have been used in the site, I’ve played around with different fonts, text and line spacing and different text sizes to try to make text as palatable as possible. However you style your text though, I still believe your pages will look bland when you have a lot of it!

I’ve recently been experimenting with using some images to spice up the look of the blog.

This posed a problem. Where do the photos come from?

My Own Photos
I do love photography but I’m by no means a good photographer! My photograph collection is also fairly small (by a small collection I mean 8,000 photos totally 9GB) and un-indexed! And I’m fairly sure some obscure and badly lit shots from many months ago wouldn’t add that much to the post…

Google Images
Every student in the world types terms into Google Images and plagiarises images to spice up their homework or class Powerpoint presentations! However, it’s slightly illegal and constitutes copyright infringement unless the image is public domain. And it’s not exactly easy to find public domain imagery on Google Images…

Creative Commons License photo: chotda

This is the third and the best option. I’ve used Flickr for quite a while but my photography is pretty lame. The best thing about Flickr though is being able to see photos taken by others. On Flickr you can search for Creative Commons licensed photos. Essentially, the Creative Commons license allows you to use the image on your webpage providing you credit the author and link back to the original.

I’m hoping that this will add a bit of colour to the blog and more pleasant reading. I’m discovering some fantastic new photos whilst searching for and adding photos to my blog posts and I hope you’ll see some photos you’ll love too!

As a bit of advice to anybody who wants to do the same thing on their blog… it’s often better to sort photos by “Most interesting” rather than “Most relevant”. That’ll mean the photos are sometimes less relevant but they’re often of a much higher quality!

Choosing a strong and memorable password

Creative Commons License photo: Thomas Hawk

I don’t think I’m alone in having difficulties inventing strong and secure but unique and memorable passwords for every website. The problem has really exploded recently as I’ve started to do more online shopping making it even more important to keep all my accounts secure.

I found out about the following technique to choose strong and memorable passwords today and I think it’s really good.

A good technique for choosing a password is to:
Choose a phrase between 8 and 16 words long that will be easy to remember. You can include names and numbers too.

Take the first letter of each word in order, including any numbers, capital letters or punctuation. This then becomes your new password.

For example:

Choosing the phrase: ‘My pet dog’s first name is Rex!’ would result in the password: MpdfniR!

or the phrase: ‘My sister Peg is 24 years old’ would give the password: MsPi24yo

Choosing a password in this way produces a password which should be easy to remember, but cannot easily be guessed. With practice, you should be able to choose phrases which provide the required number of different character types.

You can choose words and associations which are relevant to the site you may be visiting. Say – you might associate that with the environment and therefore one of Gandhi’s sayings: “Earth provides enough to satisfy every man’s need, but not every man’s greed.” By taking the first part of his quote and applying the quoted method, you might have a password like “Epe2semn,“.

I think by more or less any measure, this password is pretty secure. It contains a mixture of uppercase and lowercase characters, numerical characters as well as punctuation.

Some scientific research on this method is detailed in a Cambridge University paper “The memorability and security of passwords – some empirical results” (2000).