Busy Bees

The second installment of Swarm was on BBC 1 last night, I missed the first one but I highly recommend catching this before it goes off iPlayer.

The best bit was the fire ants making an ant raft to escape flooding. Ants are ridiculous.  They also had bees trying to decide where to make a new home.  The scouter bees come back with reports on possible locations, conveying the message with a dance. All the scouters sell their location and the others decide who to follow. When one of them gets enough support then they all up sticks and move - pretty smart.

On the same theme, I was at a talk recently about consensus decisions in sticklebacks. Apparently they're very reproducible in experimental terms. Again, they have to make a decision, this time about which way to swim. On their own they make the good decision the majority of the time (say 60%) but when they're in a group the almost always get it right. Each fish is pretty stupid, the group is less stupid.

I love problems like this because, while it is a biology problem, it's simple units (fish, ants, bees) that can interact with their peers in some measurable way (well, if you're really clever and patient it's measurable). From this emerges surprising a complex behaviour that didn't exist with the individual - that's what statistical mechanics is all about.

Critical-point post is still delayed, when you're debugging code at work all day it's hard to feel motivated to come home and do the same thing. It's coming though.

UPDATE: Just seen part one, those starlings are badass. They look like drops of liquid, just wait until I get my MD code working and I'm going to be simulating me some birds! (not in the weird science sense, although that would be cool as well).

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.

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...

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.

Backups

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!

Vegetarian

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.

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.