And Slaters Go Plop

From the new They Might Be Giants kids’ album, Here Comes Science.

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.

Neil deGrasse Tyson succinctly sums up the scientific method:

Do whatever it takes to not fool yourself when trying to understand the world around you.

(Thank you Ken!)

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.

No one believes that they are dogmatic. We’re all far too reasonable for that carry on. But we can all point to a number of other people who we would term as dogmatic and, with a little imagination, we should be able to understand that they probably don’t think they are dogmatic. This leaves us with a dilemma; how do we know that we are not being dogmatic ourselves? If we can see others acting dogmatically who are unaware of it then, chances are, we could be too.

By ‘dogmatic’ I am describing an absolutist kind of belief that, if I could summarise in my own words, boils down to the fact that you would really rather hold to what you believe than accept an alternative even if the alternative is true. Dogma is the belief you refuse to interrogate.

Dogmatism can get in the way of new truths. The reason for this is that if you are unwilling to honestly put a belief to the test then you will never find out if that belief happens to be false. A valid argument can be made that perhaps there are some beliefs that we’d be better off clinging to rather than risking finding out a truth that would cause you great unhappiness. Would you like to find out that your partner cheated on you all those years ago? What if we discover that we are really just a brain in a jar somewhere living a simulation? What if God really is imaginary? What if God really is real? Whether we dare to search for the truth of a particular matter is a personal decision. But if we refuse to honestly put our beliefs to the test then we ought to show a little more humility when telling others what we ‘know‘ to be true.

So, assuming we do want truth, how do we avoid dogmatism? The best way I can think of is to actually value truth over any existing belief. This can be excruciating, especially when a belief is foundational to any meaning you get out of life. I found it very difficult many years ago to say to myself in all honesty that I would hold truth higher than my belief in the existence of God. If you’ve never believed in God you’ll probably struggle to understand the significance of this but, to a believer, God is truth and so it can seem a kind of fundamental blasphemy to say that you would even challenge the idea. If you do believe in God, fear not, many respectable people have done what I did and kept their belief afterwards and I greatly respect them for it.

Other than valuing truth over existing beliefs I’ve come across another technique that can help to break the emotional attachment we often develop with our dearly-held beliefs. That is to regularly switch perspectives or, “state the opposite”. An example of this is to first say what you believe i.e. “Labour has the best health policies” and then say the opposite i.e. “National has the best health policies” or, “Act has the best health policies” and try to mean it. You can do this with just about any belief in which you are tempted to take sides and it really can help to make you more objective because it can lessen the effects of the ‘in-group/out-group’ factor.

Does anyone have any other good tips or tricks for finding truth that can be used by anyone regardless of their starting assumptions?

In a perfect world, when faced with a contentious issue, we would assimilate the facts, weigh them against each other and come to a reasonable consensus (pending further information, of course). We don’t live in a perfect world however and I’ve observed in myself and in others that we often tend to treat our existing beliefs about the way the world works as if it were our favourite football team; we’ll stand behind them through good times and bad, through confirmatory and contradictory evidence.

This is a fairly natural thing to do and if we are aware of our own confirmation bias we can do a lot to gradually eliminate those ideas we previously held to be true but which were, in fact, false.

However, I’ve noticed that when two people attempt to discuss a contentious issue from two very different starting assumptions, instead of fostering a willingness to seek the truth regardless of the impact to our existing beliefs, we are driven further toward defending them against this new ‘enemy’.

I think that if our goal is truth then we ought to spend most of our time challenging our existing beliefs in dialogue with people with whom we have much in common. That way we’ll be less inclined to go into defensive mode and more likely to gracefully discard what was previously an incorrect belief.

This would mean that in many cases there would have to be a certain level of exclusivity to discussions but I think it would go a long way toward self-improvement even though it may take a very long time to unravel long-held presuppositions.

I want to be able to thrash out what I see as difficulties to do with consciousness or first causes without having to deal with the distraction of religious dogma or new age pseudo-science and, more importantly, I’d imagine that there are many conversations that other people would like to have without me jumping in and blurting out what I know must be true.

So, for those of you who have found me an irritation in the past, I hope to be less in your face with what I perceive to be the absolute truth. If you think I’ve got something wrong and you hold very similar starting assumptions to me then please feel free to rigorously discuss your ideas with me. If you hold very different starting assumptions please try to allow for the fact that you may be wrong and I will try my best to do likewise. We may, after all, both be wrong.

In a perfect world we should be happier to learn that we have been wrong than that we have ‘won’ an argument.

The lecture lasts around 40 minutes and the rest is questions and answers.

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.

Back in August 2006 a company called Steorn took out a full-page advert in The Economist claiming they had developed a free energy device – charmingly called an Orbo – and were looking for qualified scientists to be a part of their validation process. Steorn is based in Dublin, Ireland and is headed up by a guy called Seán McCarthy.

The claim of free energy is a big one. Many people have attempted it – even Da Vinci tried his hand at it – but so far no one has succeeded. Free energy isn’t the same as solar energy or wind energy, it’s an entirely different beast. There is a law in physics called The Conservation of Energy which says that the energy contained within a closed system will remain constant. This is not a law to be trifled with as it has an enormous amount of strong scientific evidence to support it and, so far, not a shred of evidence against it. Some physicists have even said that a violation of this law “would undermine not just little bits of science – the whole edifice would be no more”.

What Steorn are claiming is that they have a device which, isolated from any external energy source, will produce more energy than it requires to run. This is huge. This would solve all of the world’s energy problems. Imagine it; hook this thing up to a 9 volt battery and it will produce more than 9 volts which you will be hook up to another Orbo (or even back into itself, thus removing the need for a battery in the first place) and so on, giving you potentially infinite energy.

So, should we believe them? After all, scientific knowledge is continually being added to and there have been plenty of times in the past where the ‘scientists’ of the day have scoffed at a new idea. Could this be the next major development in our understanding of the universe? A whole new paradigm? They seem like really genuine people and qualified engineers have been singing their praises. There doesn’t seem to be any overt financial scam going on either.

What we should do is be sceptical (or, ‘skeptical’ if you live in the US). This simply means that we should demand good evidence before believing the claim. And there are some strong warning signs that we should heed as well:

1. So far there have been thousands of claims of free energy but none have succeeded
2. The most alluring of these claims have involved magnets, the Orbo does too
3. We have not heard back from their panel of science validators
4. Good science is usually done in the public domain where peer review is encouraged rather than by going directly to the media
5. They attempted a demonstration in July 2007 but it was a complete failure
6. They have provided no explanation for how they have been able to achieve free energy
7. So far all we have is anecdotal evidence
8. It goes against some of the best-established science

My thoughts are that they probably genuinely believe in what they are doing (I like to look for the good in people) but that they are either accessing an external source of energy they hadn’t considered or that they are subconsciously allowing themselves to overlook another critical issue in their excitement. I’m deeply suspicious given their reluctance to demonstrate the technology and their unconventional approach of avoiding the public rigour of the scientific community and instead choosing to talk to the media (who are much more gullible).

I would love for them to have broken a strongly-held law of physics, especially given the potential benefit our world could gain. But I’m going to need some very strong evidence before I’m convinced.

I’ll leave you with Robert Park’s Seven Warning Signs of Bogus Science:

1. The discoverer pitches the claim directly to the media
2. The discoverer says that a powerful establishment is trying to suppress his or her work
3. The scientific effect involved is always at the very limit of detection
4. Evidence for a discovery is anecdotal
5. The discoverer says a belief is credible because it has endured for centuries
6. The discoverer has worked in isolation
7. The discoverer must propose new laws of nature to explain an observation