Sunday, 14 December 2008

Out of place

This was in Bath Physics Department, seems a bit out of place...

In other news there's a bug in the Ising model code which means I'm getting rather beautiful squares appearing across the system. I can't remember the last time I coded something that wasn't riddled with bugs.

Sunday, 23 November 2008

Scientists are possibly a little obsessive

I'm feeling pretty smug tonight because I finally managed to implement a new way of simulating the Ising model that I'd been thinking about off and on for years. At the same time I'm also feeling a bit sad that I've stayed up until 3am on a Saturday night doing it. I think it's the element of obsessive scientist that comes out occasionally where you have a tea/coffee fueled binge until you've solved the problem - it's probably not limited to scientists.

The reason I wanted to do this will become clear soon (as in I'll post on it). I wanted to simulate a lattice with as many sites as possible so that I can do some visualisation of renormalisation group ideas (again more on this soon). Instead of storing each site inside a byte of memory I store 8 sites in each byte and then use a bit of binary operating to get the bit I need. This means each site now only takes one bit of memory.

That was the easy bit. The hard bit was simulating this setup around the critical point. Critical points in statistical mechanics are incredibly interesting but real buggers to simulate. Fortunately there have been some very clever people who have worked out how to do this. I've not done anything that clever, but I have worked out how to implement a Wolff cluster algorithm using ~ N/4 bytes of memory which I think is good going.

I will post on this again when I've managed to run the programme on our fancy new computer (it's got 8GB of RAM) and have a nice picture to show. I will also explain what the Ising model is and what a critical point is...

Sunday, 16 November 2008

Viva and Backup update

I thought I'd return to backups briefly and say how I was getting on with some of the web based ones. Initially I was using Mozy but after some problems with the software I uninstalled it. I'm too impatient to fix problems with this sort of programme so I ditched it. Live mesh, on the other hand, just worked. I have to say I'm getting on well with it. I don't really have a lot to say about it except that it's relatively unobtrusive and I don't think it's slowing the computer down too much.

In other news I passed my viva! Hopefully this means I can start talking about statistical physics more which is sort of what I wanted to do with this blog in the first place.

Thursday, 6 November 2008


I'm pretty much backup obsessed. Of all the obessions you can have this is probably quite healthy. For example I wish I was a bit more exercise obsessed but what can you do? It's staggering how many people still don't think about backup despite the fact that they switched all their photos and music over to their PC years ago. One hard disk failure and you're buggered - and they fail depressingly often.

At work I've been using this rsync system for years. It's great, I never have to think about it but every day any new work is saved and you can track changes for as long as you like. Unfortunately I could never get this to work in Windows (through cygwin), I think it's a file system thing. Apple introduced Time Machine with their latest version of OS X. This is exactly the same system but packaged up in the neat Apple way as you'd expect. I haven't got this working on remote servers yet but I'll update if I do.

At home I'm still stuck with Windows XP (see earlier posts on why I won't switch to Linux) and I have an external hard drive. I'd really like something like Time Machine but at the moment I have to copy everything each time I backup - this is far from ideal. The simplest, and most effective, long term backup is still to post a DVD to your parents or a friend. It's cheap and it's off-site. The trouble with these last two (my current home setup) is that if my hard drive goes down I'll still lose 2-4 weeks worth of data as I can only be bothered backing up about once a month. Fortunately there is a new (new to me) solution brewing in the clouds.

It seems that storage is becoming sufficiently cheap that companies can now offer large amounts of online space for free. After reading this page I checked out a few of their recommendations. Initially Mozy looked really good but I didn't get on too well with the software so I moved to Microsoft's "Live Mesh". I have to say Microsoft appear to have knocked it out of the park with this one. I already had a hotmail account so setting it up was a breeze. Once it's installed you can just drag whatever folders you want to synchronise with the mesh. After that you just leave it in the background and it quietly makes sure you're files are synchronised. Seems to work well, I'll let you know how it goes.

This is more meant for synching files than it is backup but it obviously serves both purposes. I'm looking to use these kinds of service to fill in the month-6 month backup gap. I'll still use more traditional methods for older stuff. These systems all seem a bit early days and no doubt will improve with time, it's definitely a move in the right direction though.

If I could afford it I'd get a new mac £950 and a time capsule £200. But I can't. Damn expensive Apples. There are other network hard drive options though so that's worth keeping an eye on. Oh, and don't forget the ultimate. Despite being backed up on three computers I still emailed my thesis to my gmail account as soon as it was finished!

Wednesday, 29 October 2008


I grew up vegetarian and while I use the term a little more loosely these days it's still been years since I ate any meat at home and I mostly manage to avoid it when I'm out. You'd think it'd be easy but if you're sick of eating cheese all the time then it gets pretty hard being vegetarian.

At the weekend I wandered into a vegetarian shop just to have a look and I picked up some tartex because it's great. It occured to me while I was in there that 90% of the shop was filled with bullshit. I mean real crap. Half of it was vitamin pills and another chunk was homeopathy. I wouldn't be surprised if the guy tried to sell me an organic pencil. Is this what it is to be vegetarian? I don't eat meat because it's expensive and I love vegetables. Vegetables. Not shelf after shelf of pills.

What I want in a vegetarian shop is stuff I'd find hard to get elsewhere. And probably some sodding vegetables. Vegetables are seriously tasty and each one needs appreciating in its own right. I don't know when being veggie became about hippy crap but I think it's time to take it back. I'm a scientist, I'm not afraid of machines, I'm not totally opposed to GM (not really for it yet but that's another post), I like organic in principle but I'm not afraid of chemicals, I eat almost exclusively vegetarian food because I love it. Meat is a massive waste of resources and unless it's really good quality and cooked well then it's a total waste of time. You really miss some amazing food if you're only concentrating on meat.

If vegetarianism is still somehow linked to ludicrous things like homeopathy then it's no wonder that it instills such unprovoked hostility from our meat eating friends. It should really about all the great food. I'd actually prefer it if the veggie label wasn't there. One of my favourite places in Nottingham (Alley Café) is totally vegetarian but they don't make a fuss about it. It's just food, good food. And rather expensive beer...

So, to try and reign this rather chaotic rant in, in summary: more veg, less bullshit.

Saturday, 27 September 2008

Brain shrinkage

My mum sent me a link to a press release from the Vegetarian and Vegan Foundation. They're a bit annoyed because there's a study from Oxford University that has found a link between lack of vitamin B12 and a loss of brain volume in older people. Some, but for once not very many, newspapers have jumped to the conclusion that being vegetarian causes your brain to shrink. This really isn't what the study says. In fact I've had a look at the abstract (can't seem to get remote access to the paper) and it doesn't look like they looked at diet at all. The Oxford press release, however, does go on about diet with a disclaimer that they haven't done a clinical trial.

I'm not an expert in anything related to health and I don't want this blog be about that so hopefully I'll only make this point once: What use is this sort of press release? I can't do anything with this information. The implication is that I should eat more meat, but there was no clinical trial so this is not justified. It reminds me of the research that said a glass of red wine was good for you based on a chemical that was in it. Trouble is there are other things in it as well and the evidence actually says that this isn't true (BS about this here but I warn there are some 'orrible pictures of tumours for no apparent reason).

EDIT: Here's the Oxford press release so you don't have to click the link...

Vitamin B12, a nutrient found in meat, fish and milk, may protect against brain volume loss in older people, according to a University of Oxford study.

For the study, 107 people between the ages of 61 and 87 underwent brain scans, memory testing and physical exams. The researchers from the Oxford Project to Investigate Memory and Ageing (OPTIMA) also collected blood samples to check vitamin B12 levels. Brain scans and memory tests were also performed again five years later.

The study, published in the journal Neurology, found that people who had higher vitamin B12 levels were six times less likely to experience brain shrinkage compared with those who had lower levels of the vitamin in their blood. None of the people in the study had vitamin B12 deficiency.

Many factors that affect brain health are thought to be out of our control, but this study suggests that simply adjusting our diets to consume more vitamin B12 through eating meat, fish, fortified cereals or milk may be something we can easily adjust to prevent brain shrinkage and so perhaps save our memory,” says Anna Vogiatzoglou of the Department of Physiology, Anatomy and Genetics at Oxford University. “Research shows that vitamin B12 deficiency is a public health problem, especially among the elderly, so more vitamin B12 intake could help reverse this problem. Without carrying out a clinical trial, we acknowledge that it is still not known whether B12 supplementation would actually make a difference in elderly persons at risk for brain shrinkage.”

Previous research on the vitamin has had mixed results and few studies have been done specifically with brain scans in elderly populations. We tested for vitamin B12 levels in a unique, more accurate way by looking at two certain markers for it in the blood,” adds Ms Vogiatzoglou.

Ms Vogiatzoglou says the study did not look at whether taking vitamin B12 supplements would have the same effect on memory.

The study was supported by the UK Alzheimer’s Research Trust, the Medical Research Council, the Charles Wolfson Charitable Trust, the Norwegian Foundation for Health and Rehabilitation through the Norwegian Health Association, Axis-Shield plc and the Johan Throne Holst Foundation for Nutrition Research.

Thesis is inches away from completion, I can smell the freedom already.

Sunday, 31 August 2008

Mac vs. PC vs. Linux

When I started my new job I was given the option of having an iMac instead of the standard issue Linux PC. They're really nice looking machines and I'd seen the impressive iSight in action so I went for it. I'm a seasoned windows user (from home), Linux user (from the PhD) and after a month getting all my work up and running on the mac I'd say I'm approaching blanket coverage of the major operating systems. Most importantly I'm now in a position to tell those people who get on their high horse about their particular OS to shut up.

Because that's what's always got on my nerves the most. Linux is a lot better than windows in many respects, but a lot worse in many others. The same goes for OS X. It depends what you're doing. Take my work for example: I'm a theoretical physicist and these days the majority of my work is numerical which means getting rather large computers to perform simulations of things rattling about, over and over and over again. All these big computers use Linux and so it's easier if your systems match. More than that though, Linux has a ton of software that is designed exactly for my needs, X-forwarding is great and its heavy use of the command line is much more efficient.

If you got into computers after Windows 95 and you don't like to fiddle under the bonnet then the chances are you won't ever use the command line. This isn't a shame in itself, it's up to you how you use your computer, but it's a shame that your choice is removed because the windows command prompt is so useless. Once you get going with a good command line interface it can make a real difference to your productivity (see for example Imagemagick).

So for work I'll (hopefully) never use Windows again. At home it's a different story. At home I use the web, edit photos and play music. Linux does all this but Windows has a better look and feel. Windows works better with my laptop's hardware (and peripharels) and there is a ton of good general software made for it. In my opinion its best bit of software is Windows Media Player. This is easily the best music player available (codec problems ruin the video playing). It's great for organising music, automatically finding artwork, creating playlists, quick search, seamless playback - the list goes on. It is infinitely better than the terrible iTunes. iTunes feels like it's actively trying to make me angry. I think it's designed to annoy you into only getting your music from the iTunes store. I'm constantly searching the net on how to get it to do this or that, WMP just does it.

Security is the top thing usually thrown at Windows. I go with the usual argument that it's just because there are more Windows PCs than anything else. Get complacent with your mac or Linux box and you'll wind up the same.

So what about the mac? Well Apple have been clever and maintained support for all things unixy (it is based on unix). This means that most of the good Linux features are supported, it does X11 so I can use most Linux programs, I can SSH into it (remote login) and so on. On top of this is has the better look and feel, it runs proprietary stuff like MS Office and it's got the best video chat facility by a mile. Apple (or maybe it's mac users themselves) always seem to be chipping away at improving the user interface. Things like exposé or Quicksilver are good examples. I'm very impressed with my iMac, it's a very neat piece of kit indeed.

Bad things about the mac are well documented. Hardware is expensive and exclusive, in many ways you're buying into a much worse monopoly than Microsoft. You won't be as compatible with everyone else (not a big deal these days), oh, and did I mention how much I hate iTunes? This shouldn't matter but Apple devotees tend to get on my nerves. I think there's a lot of fashion about owning a mac. They're always banging on the MS steal this or that. Honestly, get over yourselves. Everyone's iterating towards a better thing and Apple have reused plenty of ideas themselves (eg. spaces).

If I was buying a new laptop tomorrow I'd go for a mac. For me it covers the maximum amount of my daily stuff and I do like the interface. In general I would only recommend it if you know why you want to spend that bit more. I don't think Linux is ready to be my only OS just yet but I'll always run it on the side. The bottom line is they all do the job, they all crash (despite what people say), but most importantly of all they all run firefox so you won't really notice the difference most of the time.

Wednesday, 30 July 2008

Glass in the New York Times

When people think of physics they tend to think of particle accelerators, string theory, E=mc² and so on, so when I tell them I'm studying glass they always look a little disappointed. Anyway, a couple of weeks ago we got a New York Times article from a guy called Kenneth Chang so we're all quite pleased about it. I had written a long post about it but I ended up just repeating what's in the article, so I've decided to list some main points and provide a few extra links.

He managed to give a good sense as to how much debate there is in the field. One thing everyone agrees on however, and where the article begins, is that cathedral windows do not sag because the glass has flowed.
"Medieval stained glass makers were simply unable to make perfectly flat panes, and the windows were just as unevenly thick when new."
If you want something that does do that then let me point you in the direction of pitch, which drips about once a decade but shatters when hit with a hammer. So what is glass then? Is it a liquid or what?

Glass has the same structure as a liquid. If you take a photo you couldn't really tell the difference. A liquid that's on its way to being a glass, a supercool liquid, is the same as well. If instead of a photo you look at a video you'll see that it's actually really different. Weeks and company have actually done this and you can see regions really close to one another, some with lots of motion, some hardly moving at all. This is the dynamic heterogeneity, mentioned in the article, that goes along with the hugely increasing viscosity. Their website has loads of great stuff, including movies and a link to a freely available version of the Science paper, I recommend taking a look.

The region that I'm roughly poking about in at the moment is to do with vibrations and rigidity. This is touched on in the article a couple of times. Matthieu Wyart and others have spent a lot of time developing the idea of a glass as a marginally rigid solid (the introduction to Wyart's thesis is actually quite readable and freely accessible). It's looking at how the random liquid structure affects things at low temperatures.

Anyway, I'll leave it there. If I've missed any important links just stick them in a comment. Been a bit too busy writing my thesis to do this properly. Dear God let it end soon!

Wednesday, 23 July 2008

Moving adverts

A couple of weeks ago I was in London and passing through Liverpool Street tube station. Something that I've been dreading for years has finally started; they're now projecting moving adverts on to the wall. They've had the LCD screens on the escalators for ages now, they're not great but they only fill a small part of your peripheral vision - they're after the rest.

TFL try and sell this as something great for the commuters
We believe that this technology will enhance passengers' journeys
Really? Are you sure it won't get on their nerves? Would you stop it if it did? The eventual aim is to have every pixel of your periphery flashing and shouting so that your brain is so confused with the unmanageable amount of information that you'll do anything they tell you. Or stumble in front of a train.

It's an inevitability, an arms race. If you cover every square inch in posters then, per square inch, they're all worth less. So to make your milliacre more valuable it must now move. Soon they will all move. Then they'll start shouting at you, then they'll get linked to your oyster card so they'll be calling your name. Worse, linked to your nectar card so they can chase you down the street offering you carefully selected products you might like.

Not everyone agrees with me: this advertising blogger thinks it's great and shows how hi-tech we are. TFL clearly like it. Anyone else? I'd really like to know.

I have the attention span of a pea. It takes nothing for me to lose track of what the hell I was thinking, what someone just said or even why I got on this train in the first place. Please, I'm begging, leave my poor brain alone!

Saturday, 19 July 2008

Plausible theories from experts

This posting, from the rather excellent Mind Hacks, got me all worked up again (this is quite easy to do). It just struck me how easy it is to say something plausible, for example "increasing violence is caused by computer games", and then make no attempt to check whether it's true.

In this case the plausible statement is on the use of facebook, the internet, other such things. It even managed to be press released by the Royal College of Psychiatrists. This starts off
A generation of Internet users who have never known a world where you can't surf on-line may be growing up with a different and potentially dangerous view of the world and their own identity, according to a warning delivered to the Annual Meeting of the Royal College of Psychiatrists.
Could be true. I wouldn't like to say. Things start to smell a little funny when they say
This is the age group involved with the Bridgend suicides and what many of these young people had in common was their use of Internet to communicate.
OK stop there. Now I'm suspicious, don't all young people use the internet? By the way, the Bridgend suicides are also being blamed on mobile phone masts and, for all I know, computer games. In fact it feels like there is a rather sinister trend for untested/untestable claims to be applied to these tragic events, and why? Because it will get press attention. Without a doubt.

It seems that a horrible statistical fluctuation in the all-too-large distribution of teenage suicides is not a satisfying reason for the media or the public. And this leaves the door wide open for "experts" to fill the gap.

It's just too easy to say you think something is true and then press release to an unquestioning media. A classic example is the evolutionary psychology stuff (badscience has lots on this). These are the claims that we will split in to two distinct races or that we will evolve big willies. The papers just say that "Experts say..." washing themselves of responsibility. But who are these experts? Many of the proposals are plausible but that's not enough.

I could spend all day coming up with things that could be true. Unless it is testable then what use is it? Physicists come up with plausible theories all the time, but no one will get the nobel prize until it can be tested. The famous Feynman quote goes
"It doesn't matter how beautiful your theory is, it doesn't matter how smart you are. If it doesn't agree with experiment, it's wrong."
I appreciate that physics experiments are much easier (and by that I mean controlled) than social experiments, but that's no excuse for claiming you have the answer when all you have is a plausible explanation. It's a massively important distinction.

To anyone claiming to know the cause of the Bridgend suicides I beg you to think carefully; teenage suicide is a serious problem and they deserve much much better.

Edit: Here's the BBC coverage

Saturday, 5 July 2008


Ok, a bit of proper science to try and establish some balance. This is a bit of a lazy post but I did mention I'm busy writing my thesis. On supercooled liquids...

Supercooled water is just water that is below its freezing point but for one reason or another didn't crystalise. It's a form of metastable equilibrium. If you give it a big enough kick then it can escape and this happens

And you can do it with beer

If you keep cooling it further then you eventually get glass, and that's all glass is. Now my stuff is more interested on the supercooled goes to glass bit rather than freezing beer but you get the idea.

Friday, 27 June 2008

Jeremy Clarkson and the prius

Jeremy Clarkson was just on top gear reproducing the old myths about the toyota prius. There were two strong statements in the program, one I can get on board with, and one where Jeremy Clarkson gave in to lazy temptation of quoting something because you want it to be true, rather than checking it actually is.

Firstly they did a track test comparing the prius against a BMW and found the BMW did better for mpg. This is something I've seen around and I'm certainly open to the fact that hybrids are beatable. They are, after all, just an attempt to make a petrol powered vehicle more efficient. I can't vouch for these tests though, from what I can gather they mostly seem to rely on motorway travel to beat the prius (which is best in the city).

The second thing though is completely contemptible of Clarkson. It's an old piece of bullshit that has been blogged about loads (badscience usually a good place to start) that the Prius is worse over its lifetime than a land rover (last time it was a hummer). I can't do a better job than has been done already, but it comes down to a dodgy report done by a marketing group. Now it's been broadcast on such a huge platform I doubt we'll ever here the end of it.

UPDATE: I think the dodge claim is about 45s in.

Tuesday, 24 June 2008

First Post

Welcome to my new blog. I haven't quite worked out what to do with it yet but I think it's good to have a blog, the internet's already full of useless crap so this isn't going to make it any worse.

Right now I'm writing my thesis so I doubt I'll be putting much on here but when I do I suspect it'll mainly be based on the two things: physicsy stuff and statistics stuff. The former should be mainly positive (things I think are really interesting) and the latter will be mostly negative (ranting about stats-abuse). I guess we'll see how it goes.