Safely recover from a freeze in Ubuntu

July 26th, 2011

If you ever encounter a system lockup in Ubuntu here’s a little trick you can use to safely restart your computer.

Hold down the Alt and PrtScn/SysRq keys at the same time and, keeping them held down, enter the following sequence of keys: R, E, I, S, U, B. Hold each key down for a second or so and don’t rush.

What it does is it allow Linux to take control of your system, requests politely that all processes close, forces all processes to close, flushes data to disk, unmounts your filesystems and reboots.

Here’s a couple of mnemonics: ”Raising Elephants ISUtterly Boring” or “Reboot Even ISystem Utterly Broken”.

It’s extremely rare that this is necessary due to Linux’s stability but I’ve found I’ve needed this a couple of times recently (I suspect Google Chrome is the culprit) so I’m posting this here for easy future reference from my phone.


June 27th, 2011

If you think it a little eerie that the sun happens to be 400 times larger than the moon at the same time as being 400 times farther away (making it the same apparent size) then feast your pattern-recognisin’, paradolia-seekin’, Holy-Mary-in-a-pancake eyes on this:

hydrogen + zirconium + tin + oxygen + rhenium + platinum +
tellurium + terbium + nobelium + chromium + iron + cobalt +
carbon + aluminum + ruthenium + silicon + ytterbium + hafnium +
sodium + selenium + cerium + manganese + osmium + uranium +
nickel + praseodymium + erbium + vanadium + thallium + plutonium

… is an anagram of …

nitrogen + zinc + rhodium + helium + argon + neptunium +
beryllium + bromine + lutetium + boron + calcium + thorium +
niobium + lanthanum + mercury + fluorine + bismuth + actinium +
silver + cesium + neodymium + magnesium + xenon + samarium +
scandium + europium + berkelium + palladium + antimony + thulium

… and when you switch these element’s names for their numbers (their position in the periodic table) …

1 + 40 + 50 + 8 + 75 + 78 +
52 + 65 + 102 + 24 + 26 + 27 +
6 + 13 + 44 + 14 + 70 + 72 +
11 + 34 + 58 + 25 + 76 + 92 +
28 + 59 + 68 + 23 + 81 + 94

… equals 1416, as does …

7 + 30 + 45 + 2 + 18 + 93 +
4 + 35 + 71 + 5 + 20 + 90 +
41 + 57 + 80 + 9 + 83 + 89 +
47 + 55 + 60 + 12 + 54 + 62 +
21 + 63 + 97 + 46 + 51 + 69


(Thanks to David for bringing this to my attention. As he said, “I can’t decide if its scarier that such a thing exists or that someone found it”)

Change default Google localisation in Firefox in Ubuntu

May 4th, 2011

Be default in Firefox on Linux, when you use the Google search up in the address bar it defaults to a search of instead of my preferred If you want to change this, go look in /usr/lib/firefox[--version--]/searchplugins/google.xml and swap out the .com for (or whatever localised Google site you prefer).

Eternal Life

April 12th, 2011

Eternal life means there will inevitably come a time where it would take you a billion years just to type out how old you are.

Methinks it is [still] like a weasel

March 18th, 2011

Full screen version

A couple of years ago I created an online Javascript version of Dawkins’ Weasel program. I was poking around at the code today and realised that it wouldn’t be too much work to remove some of its limitations to allow it to replicate the full 28 character phrase that Dawkins used.

If you’re unfamiliar with why anyone would want to make an program like this, take a look at the original post where I explain how genetic inheritance combined with natural selection gives vastly different results to the mistaken creationist view of evolution being a ‘monkeys with typewriters’ kind of randomness. (by the way, if you change the settings so that there is only one child per generation the program will enter ‘monkeys-with-typewriters mode’).

The main differences in this version are:

  • You can now hide or show all the mutant children that were not selected
  • You can use up to 30 uppercase A-Z letter plus spaces
  • There’s a new column that shows how many letters matched (so you can see how it occasionally slips back with higher mutation rates – contrary to what William Dembski would have you believe)
  • I’ve improved the performance slightly.

Non-reductive Physicalism and Conway’s Game of Life

March 15th, 2011

When you reach out to grab your cup of coffee, what is causing this action? Is there a special internal ‘you’ somewhere in there pulling the levers? If so, what is this ‘you’ made of and how does it cause these limbs of meat and bone to move? Or do you believe that you are merely a big heap of atoms, nothing more? How then do mere atoms ‘want’ to grab a cup of coffee?

These are some of the kinds of questions that rear their heads when we start to think about our ‘minds’; who ‘you’ are, what ‘you’ are made of and what our relationship is with the world around us. How is the mind different from the brain?

For a very long time a common view was held (and is still held by some people today) that ‘we’ are a non-physical essence or soul linked in some way to our physical brains — this is called ‘dualism’ because you believe in two types of ‘stuff’ — and this essence is able somehow to cause our brains and therefore our bodies to do things. But this concept is riddled with problems and I’m not going to go into them here suffice to say that very few people who’ve taken an interest in any kind of science of the mind would hold to it.

But in the absence of this non-physical explanation and in the light of the mounting evidence for the brain merely being ‘what the brain does’ we’re left in a bit of an awkward situation. How can mere atoms be emotionally moved by a song? How can bags of chemicals build a car? These kinds of questions become especially difficult when you happen to believe that the universe is such that there is a supreme being out there who has a purpose for you and yet you find dualism decidedly uncompelling. Reductive physicalism (i.e. a world which is only made of physical things that can be explained by describing the smallest parts) doesn’t really seem to have a place for a supreme, purposeful being.

A solution may be at hand however. What if we accept that, yes, atoms do clump together to form molecules and molecules clump together to form organisms that can act in their environment all in a kind of a ‘bottom-up’ path of causation. But then we will notice that things such as natural selection can themselves emerge and have a kind of a ‘top-down’ causation that, in turn, affects and improves these critters that have been produced purely by the actions of atoms. This gives us a way to view the world in the light of the best available evidence (i.e. we can have just atoms and we can include the power of natural selection and so on) at the same time as breaking away from the disconcerting concept of a world in which everything is driven by the mere mindless jiggling of atoms. This is called ‘non-reductive physicalism’ because we admit that we’re made of ordinary matter but the rules that guide atoms are not enough on their own to get us to where we currently are.

I think I spotted a flaw in this logic but in order to effectively illustrate what the error is I’m going to have to go off on a tangent and discuss a geeky bit of software called Conway’s Game of Life.

Conway’s Game of Life was created back in 1970 by mathematician John Horton Conway. In essence it’s a grid of blocks that can be either alive (black) or dead (white) in which each block conforms to four simple rules:

  1. If you’re alive and have one or less alive neighbours, you’ll die
  2. If you’re alive and have two or three alive neighbours, you’ll survive
  3. If you’re alive and have more than three alive neighbours, you’ll die
  4. If you’re dead and have three alive neighbours you’ll become alive

Using these four simple rules if you start off with a pattern of three dots selected one above the other like an ‘l’ you will find that the top and bottom dots will die (become white) because they each only have one neighbour. The middle dot will remain because it has two neighbours. The empty dots to the left and right of the middle dot will come alive because they both have exactly three alive neighbours. Once this has been calculated the grid is redrawn and you’ll notice that we now have three dots again but this time they’re side-by-side like a dash. If we apply these same rules again we’ll end up with the same configuration that we started with and so on and so on. Not really all that interesting but it’s a start.

There are many different configurations possible. Some of them remain static, some blink like the example above, some bloom out into endless randomness or collapse into a detritus of blinking and static objects. Some that have captured the imagination of many can even ‘travel’ across the screen endlessly or even generate repetitive patterns. See the image on the right for an example of one of the most common travelling objects called a ‘Glider’. See how it obeys the four rules and yet seems to have transcended them in some way. It now seems to have some additional rules like “move on a diagonal down the page and to the right”.

Here, have a play with this one online but please come back to see how this all relates to the seeming conundrum of minds, bodies and non-reductive physicalism.

Even more complex, see the example on the right of a ‘Gun’ which produces an endless stream of gliders. Now we can’t help but lose track of our four simple rules and we’re now seeing actual entities interacting with each other in a seeming causal manner. The gun has got two stopping/absorbing blocks with a couple of arrow-things that fly back and forward between them producing a stream of gliders which move diagonally away from the gun.

Can you see where this is going yet?

What we’re doing — albeit at a simplified level — is we’ve acknowledged that four simple rules can create some interesting patterns and then we’ve started thinking about the movements of the patterns themselves in a way that doesn’t seem to need to account for the four rules any more and, if we aren’t too careful, we might be tempted to think that the four rules weren’t sufficient to describe a ‘Gun’ that ‘produces’ ‘Gliders’.

This is exactly what I see happening when people posit non-reductive physicalism. As with Conway’s Game of Life where I can show you just enough yet be able to drag you back to admitting that, yes, these four simple rules are up to the task of producing what we perceive as guns and gliders so it is with the power of atoms to use a very simple set of rules (i.e. varying degrees of attraction/repulsion/jiggliness and so on) to produce molecules, chemicals and organisms which interact with each other. And to even provide us with brains in which to build mental constructs — which are themselves purely physical — of things such as glider factories and natural selection).

Non-reductive physicalism can be fairly described as “the idea that while mental states are caused by physical states they are not reducible to physical properties”. But what I think they are really saying is “In order for us to understand mental states, we can’t do it just by looking at the atoms that make them up”. Which, to me is exactly the same as saying “while glider guns are caused by the four rules they are not reducible to those rules” or, “In order for us to understand the behaviour of glider guns, we can’t do it just by looking at the the four rules”. But this speaks more to how our limited physical minds operate and how we require the use of analogies within analogies in order to form predictions and descriptions about the world. Not to how the world really is.

[The three images above are all sourced from the Wikipedia page on Conway's Game of Life. The Glider Gun image was created by Kieff.]

Spider with babies

February 27th, 2011

We have spiders that we accommodate in the ceiling corners of our house because we hope they deal to rogue mosquitoes and the like. Here’s one who looks like she’s in the process of perhaps eating the remainders of the hatchery. Cute!

Plastic vs Glass Carboy

February 24th, 2011

Over the last year or two I’ve been using a couple of 30L plastic fermenters while brewing. One of them, the second one I bought, has developed odd white ‘scratch’ lines and I’m not sure what’s caused them. I’ve never used anything harsher than a nylon scrubbing brush to clean it and I’m tempted to think that these are actually artefacts of a kind of blistering of the plastic rather than actual scratches. Perhaps something to do with a fault in the manufacturing process as my other fermenter shows no signs of these.

Difficult to see, but here are the odd chalky-looking scratches.

Any form of surface damage worries me because I can’t be as sure I’ve been able to remove any embedded bacteria or other unwanted organisms and so I decided to splash out and pay twice the amount for a 23L glass carboy.

I’ve never used glass before and am aware that there is a danger involved when lifting and that transferring liquids can be tricky due to the lack of a tap at the bottom. I am, however, looking forward to being able to watch vigorous fermentations through the glass!


I’ve just taken a much closer look and it appears that these aren’t scratches at all. Some kind of crystallisation or chemical build-up which came away when I used my fingernail. Any ideas? (Oh well, still looking forward to using the glass carboy even if it was money unnecessarily spent).

Ben Goldacre on the placebo effect

January 24th, 2011

My wife bought me Goldacre’s Bad Science recently and I came across this talk of his on the placebo effect (which I found fascinating):

HT Pharyngula

Apologia podcast discussion on Sam Harris’ Moral Landscape

January 10th, 2011

I came across an interesting (to me) and civil discussion on Sam Harris’ new book, The Moral Landscape.

Part 1 (41MB), Part 2 (43MB), Part 3 (75MB)