And Slaters Go Plop

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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.

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.]

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!

Consider this hypothesis:

‘Oughts’ must always be accompanied by a goal of some kind. ‘Ethical oughts’ are a subset in which the goal is in some way related to degrees of pleasure or suffering of others.

If we expand on this we can see examples of fairly straight-forward ‘oughts’ like, “you ought to pour the hot water into the tea cup” where the unspoken goal is “if you want to make a cup of tea then…”. This ‘ought’ combined with these ‘ises’ (i.e. there are ‘ises’ in that there is a cup, that there is water, that there is a creature with a goal of making a cup of tea, etc) show that it is ‘wrong’ to pour the water on the bench and ‘right’ to pour it in the cup. If the goal was to clean the dishes then the ‘ought’ would change.

Ethical ‘oughts’ like, “you ought not steal” have unspoken goals like “if you want to avoid making others unhappy then…”. This ‘ought’ is also derived from a bunch of ‘ises’ (there are other people who are unhappy when stolen from, you are a creature with the ability to steal or not steal, you are a creature who doesn’t want others to be unhappy, etc) and shows that, within this framework, there is a ‘right’ way to act and a ‘wrong’ way to act.

When you read the ethical example you are no doubt asking “well, why ‘ought’ you want others to be happy?” You could ask the same of the tea cup example; why ‘ought’ you make a cup of tea? We can step out to meta-oughts and we’ll find that the same rules apply: that even a meta-ought requires a goal of some kind and that an ethical meta-ought will involve some kind of ability to make others suffer.

We ought to make a cup of coffee because we desire it (thirst, addiction, etc). If we are to fulfil this desire then we ‘ought’ to make a cup of coffee. It is ‘right’ in this context to boil the jug.

We ought to want to make others happy (or, at least, not cause others to suffer) if we find ourselves in a society which returns favours or which punishes us when we cause harm. It is ‘right’ to not cause others to suffer in this context.

What about meta-meta-oughts? The same rules apply. Each meta-ought gradually becomes more and more empirically simple, not more and more supernaturally ethereal. They fade out into ‘ises’. We eventually end up with ‘oughts’ based on how our bodies/brains work. We ought to be thirsty because our bodies trigger a thirst response when they require water to keep working. Conversely, we ought to fight this addiction (if it is one) because our brains — through gradual understanding about how the world works — informs us that even though our bodies desire and reward us for caffeine we are suffering in other ways. We ought to avoid suffering because our bodies use suffering in order to stop us harming ourselves. Our bodies ought to provide these responses if we are to survive and spread our genes. Our genes are configured in this way because if they weren’t we wouldn’t be here. At the very foundation it’s simply a matter of patterns that survive.

At some stage our ethical oughts fade into non-ethical oughts when the ‘ought’ no longer pertains to the well being of others. Even if you believe in the existence of a God who is either a punisher and rewarder (you ought to simply because God says you ought to) or a trustworthy advisor (we ought to because God knows more about how the universe works and his advice can be trusted to bring us happiness) we eventually end up with ethical oughts based on our own personal well being which, as I have shown, fade into non-ethical oughts because they don’t involve the well being of others. If you believe in a God of some kind ask yourself “why oughtn’t I murder?” and follow those meta-oughts as far as you can. I guarantee you’ll end up dealing with a non-ethical ought based on your own well being which, in turn, will end up disappointingly as a mere surviving genetic pattern. (I personally don’t find it disappointing; I think it’s one of the most wonderful things ever. I used to though.)

It shouldn’t really surprise us that complexity arises from simplicity. We have first-hand experience of gradually arising from a single sperm and an egg. We know that the amazing diversity of life evolved from simple chemical reactions billions of years ago. We suspect that the universe itself came about from deep simplicity. When we examine oughts and meta-oughts it certainly feels as though the ought of “you ought not steal” should have come from on high but as with the case of the coffee-making we can see that even this arises from something as simple as looking after our own interests.

At their very foundation, ‘oughts’ (even ethical ‘oughts’) are ‘ises’. It’s the layers of meta-oughts that trick us into thinking otherwise. It’s also the fact that some people are happy to speak the implicit “if you want to make a cup of tea then…” in common oughts but have difficulty speaking the implicit “if you want to avoid causing suffering then…” in what we term ‘ethical oughts’.

(This was originally posted as a comment over at FruitfulFaith and it was only after seeing how monstrously huge it was that I realised it was suitable as a post in itself. I’ve had a lot of different thoughts on morality and the issues that surround it and this is a good distillation of my latest thinking. And like all my previous thoughts this will likely change too — but right now I can’t see any gaping holes and it seems a fairly robust hypothesis capable of explaining a lot.)

I little while ago I wrote a layman’s overview of mitochondrial DNA. David, over at The Atavism – who actually knows what he is talking about which it comes to all things mtDNA – has written an excellent piece on the topic where he goes into the nitty gritty of the inheritance of mutations (good, bad and neutral), discusses how these mutations provide an important piece of the puzzle showing our common ancestry with the other great apes and monkeys, and even reveals a dirty little secret he’s been keeping all these years. Go check it out.

This week saw the launch of the new Sign On campaign. The essence of it is that world leaders are meeting in Copenhagen later this year and by signing up to Sign On we are letting John Key know that we want New Zealand to agree to set a target 40% reduction of emissions by 2020.

The reasons I support this campaign are threefold:

Firstly, the science behind the need for a 40% reduction is clear and strong; anything less is not going to be enough.

Secondly, I don’t have the willpower myself to achieve a 40% reduction and I believe this is one of the roles governments perform; to constrain some of our harmful and selfish urges and to reward behaviour that is mutually beneficial.

And, finally, I see great technological opportunities for our civilisation should we find the motivation to innovate. I’m confident we’ll come up with energy, transport, agriculture and production technologies far superior to what we have now. We just need the will to do so. As I heard someone say, the bronze age didn’t come about because stones became scarce; bronze was a better technology. I think that there is another age waiting for us beyond the oil-and-deforestation age.

I also like the fact that the campaign is saying nothing about how we ought to go about achieving a 40% reduction. That can wait. First we need the will to make a commitment and then we can act on the best advice from our scientists, politicians and economists to see how we will best achieve this target.

So, if you share my opinions on this, head on over to the Sign Up website and add your name to their list of participants. And perhaps let your local MP know where you stand on the issue too. Hopefully enough people will step forward to let our prime minister know that we taking this seriously.

Hamlet: Do you see yonder cloud that’s almost in shape of a camel?
Polonius: By the mass, and ’tis like a camel, indeed.
Hamlet: Methinks it is like a weasel.

In attempting to discredit evolution by natural selection, creationists have often described the impossibility of random mutations in DNA being capable of anything beneficial as the equivalent of a tornado in a junkyard accidentally building a 747 or a group of monkeys bashing the keys of a typewriter to successfully write the works of Shakespeare.

And they’re right. If evolution was merely random mutations then it would be unfathomably impossible for life to evolve as it does. But here’s the rub: no evolutionary biologists claim that random mutations alone cause the diversity of life we observe. This is where the crucial natural selection part comes in. Evolution occurs by random mutations, most of them neutral, where any beneficial mutations are selected for by the environment and those successful mutations go on to have more children who will likely inherit those beneficial mutations. And so on and so on.

To illustrate the point, back in 1986 Richard Dawkins in his book, The Blind Watchmaker demonstrated a simple program which he named ‘Weasel‘ as a reference to the concept of monkeys and typewriters and the above quote from Shakespeare. ‘Weasel’ starts with a jumble of letters, spawns ‘children’ from them (i.e. multiple copies), each with slight mutations and selects whichever ‘child’ is the most similar to a target phrase to spawn a new generation of children.

The point of the program was not to demonstrate every aspect of evolution by natural selection (that’s rather too much to ask of a small page of code), just the power of mutation when combined with a selection process as opposed to brute-force random chance.

Below I’ve created a simple version of Dawkins’ program that is limited to a single word and which will, due to the limitations of Javascript and browsers, only attempt a maximum of 500 generations. Have a play around to get a feel for how random mutations can result in very non-random outcomes when there is a selection criteria combined with heritability.

(Note: an updated version is available in a new post, Methinks it is [still] like a weasel)

Full screen version

If you know how to run Python and want to check out a version closer to that of the original ‘Weasel’, take a look at the one created by fellow blogger and PhD student in evolutionary genetics, David, over at The Ativism. His is not limited to 500 generations like mine and he includes the newer concept of the option of ‘locking’ successful mutations.

The Golden Rule. Treat others how you’d like to be treated. Almost every culture in the world has a version similar to this and the only real variation is in the definition of who the ‘others’ are. In most primitive cultures, ‘others’ didn’t include the tribe over the mountain but, as we have formed larger and more inclusive societies, we are extending the boundaries of who qualifies as an ‘other’.

Most people reading this will likely have a boundary that now includes all humans. Some may extend this boundary to other animals capable of suffering to various degrees. Everyone I’ve met agrees that The Golden Rule is a good rule to live by but there are a large range of interpretations as to who the ‘others’ are.

A question I have is, should chimps and orangutans belong to this group we call ‘others’? What about other animals such as cows and sheep? Should we treat them as we would like to be treated? If not, why not?

This is a touchy topic and one I’ve given a bit of thought to over the last few years in examining whether I ought to become a vegetarian. In short, I still eat meat. I’ve decided that my boundary for ‘others’ is largely dependent on the issue of suffering. This is a fuzzy line however and roughly translates to an unwillingness to eat the meat of animals who, in killing them, has caused unnecessary suffering to either them or to others. I’ve found that there is no easy answer and that much of this is because we expect to be able to draw nice, clear-cut lines in what is (as is usually the case in matters like this) essentially a gradient. And I’ve found that it’s a good idea not to even try to draw too distinct a line and to be prepared to shift it regularly depending on the many factors that can apply (i.e. I would kill and eat a chimp if I were starving to death and had no other option but wouldn’t dream of it in my current status.)

In my current status I don’t like animal experimentation that causes suffering. I prefer to eat chickens that have had freedom to roam. I don’t mind eating sheep and cows so long as they are treated well. I don’t want to encourage cramped pig pens so avoid pork unless it’s free range. Chimps, orangutans, elephants, whales and dolphins (to name but a few) are very much in my group of ‘others’ and I would see the hunting and killing of one as causing similar suffering to killing a human.

Roughly, where is your boundary and why?

The Otago Bike Trail takes advantage of a decommissioned rail track that used to run from Middlemarch up through Wedderburn and down into Clyde from 1879 until 1990. The rails and cycle-unfriendly rocks have been removed and it now provides the perfect gradient and stunning scenery for leisurely cycling.

It’s relatively inexpensive, relaxing, safe and the perfect way to see some of the most beautiful countryside New Zealand has to offer.

Sal and I did the trail a couple of weeks ago. Read on if you’d like to know what we thought were the highlights, lowlights and, most importantly, how not to win at curling.

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In our bodies we contain two different types of DNA. There is the bog-standard (or, nuclear, because it’s in the nucleus) DNA which is a combination of half of your mother’s and half of your father’s DNA which you inherited when one of your father’s sperm fused with one of your mother’s eggs. And then there is Mitochondrial DNA which is different to nuclear DNA in that we inherit it directly from our mother alone as a part of the egg which is swarming with hundreds of thousands of mitochondria . Nuclear DNA fulfils the role of building our bodies and mitochondrial DNA provides the means for mitochondria to generate the energy a cell needs to do the things it does (i.e. dividing or making stuff). When cells divide they make a duplicate of your DNA and, inevitably, the mitochondria end up dividing themselves up between the newly-formed cells where they will recombine with each other to keep the numbers up.

If you are a mushroom, a plant, or an animal (from jellyfish to wetas to elephants) you will have mitochondrial DNA and if your species uses sex for reproduction you will likely have inherited it from your mother.

Every time nuclear DNA is recombined during procreation and every time mitochondrial DNA is recombined within the cells of your body little mutations can occur. Most of these mutations are neutral in that they don’t inhibit or enhance the functioning of the DNA.

What this means is that, while our nuclear DNA will pick up on average 128 mutations (out of ~3,000,000,000 base pairs) during sexual reproduction, mitochondrial DNA have more mutations (out of only ~17,000 base pairs in mammals) without the added complication of sexual recombination and this makes it much easier to compare mitochondrial DNA between people and, therefore, make reasonably accurate predictions for just how closely maternally related they are by comparison of their mitochondrial DNA alone.

Let’s say we take your mitochondrial DNA and compare it with your sibling’s. We will find that the two samples are almost, but not quite, identical. This is because there have been a handful of mutations in the time that you’ve had your mitochondrial DNA to yourselves. Now if we take your sample and compare it to a maternal cousin (i.e. you mother’s sister’s children) you will find that, while still almost identical, a few more changes will have crept in. You will notice a pattern of increasing change occurring as you compare the mutations of maternal second cousins, third cousins, fourth cousins and so on and so on.

Now, once you have established what rate of change you can expect between maternal relatives you can go ahead and test your neighbour. If you find that your neighbour’s difference in mutations are only about those of, say, your maternal second cousin then you will be able to fairly confidently predict that you have just met a previously unknown second cousin. If, however, you compare you neighbour’s mutations and they are larger than what you would expect from a close relative you should be able to make a prediction for how many generations ago it was that you shared a common grandmother based on the rate of change.

You may have heard before of a ‘mitochondrial Eve’ that was talked about a few years back. They got to this conclusion by testing as many diverse people in the world as they could think of and compared their mitochondrial DNA to see what was the greatest difference they could find. It turns out that the most remote common maternal ancestor they could identify lived around 8000 generations and perhaps 170,000 years ago. The exact numbers are, understandably, still hotly disputed but the fact of the genetic relationship is sound.

Some people have taken this to mean that this ‘Eve’ was actually the first human but they’ve missed the point. We could have done a ‘mitochondrial Eve’ analysis for just the people of a particular village in South America and found that their mitochondrial Eve was only 50 generations ago. Conversely, we could have done a mitochondrial Eve analysis of humans and chimpanzees and discovered that they are around 250,000 generations and 7 million years ago (as, indeed, they have found).

There are many other ways to measure the relatedness between animals including the Y chromosome (which is passed exclusively from father to son) and a plethoria of nuclear DNA comparisons. But I’ll leave those explanations to people who actually know what they are talking about. If this kind of stuff interests you like it does me, I wholeheartedly recommend The Ancestor’s Tale by Richard Dawkins.