Archive for March, 2010

Lost – Episode 6.10: The Package

Posted in Lost on March 31, 2010 by Tom

My immediate thoughts, theories and reactions following Episode 6.10 of Lost – The Package. This episode was shown on 30th March in the USA and will be shown on 2nd April 2010 in the UK – don’t read on if you haven’t seen it yet, as this post contains spoilers! Continue reading

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Lost – Episode 6.9: Ab Aeterno

Posted in Lost on March 24, 2010 by Tom

My immediate thoughts, theories and reactions following Episode 6.9 of Lost – Ab Aeterno. This episode was shown on 24th March in the USA and will be shown on 27th March 2010 in the UK – don’t read on if you haven’t seen it yet, as this post contains spoilers! Continue reading

Alice In Wonderland

Posted in Film on March 23, 2010 by Tom

I’ve just seen Alice In Wonderland in 3D.

I’ve been a fan of Tim Burton and Johnny Depp for quite a while now – Sweeney Todd is one of my all-time favourite films  – so I was very much looking forward to this, and I wasn’t disappointed. I haven’t seen the 1951 Disney animated film since I was a child, and I don’t remember much of it, but this new film stirs a lot of memories, and I’m sure that people who have actually reads the books (sadly I have not) will experience that even more.

Mia Wasikowska is very good as Alice – she portrays her as an outwardly solemn but inwardly curious and imaginative 19-year old, and does so very convincingly. The decision to set the film a decade or so after Alice’s first trip to Wonderland was definitely a good move, as an older Alice fits into Tim Burton’s dark and bizarre world far better than a small child would. Johnny Depp, as expected, is utterly brilliant as the Mad Hatter, simultaneously completely insane and also very human. He’s sometimes criticised for only playing bizarre characters, and perhaps those criticisms are well-founded with roles such as Edward Scissorhands, Willy Wonka and Captain Jack Sparrow, but this is possibly his best portrayal of that kind of character. Helena Bonham Carter plays the Red Queen very well with some excellent CGI, reminiscent of Queenie in Blackadder The Second in a way that must surely be intentional. The mostly British supporting cast, including Alan Rickman, Michael Sheen, Stephen Fry and Barbara Windsor are all excellent, and their voices fit their anthropomorphic characters perfectly. Matt Lucas as Tweedledee and Tweedledum is another perfect choice – far better than the Oompa Loompas in Charlie And The Chocolate Factory, which I never particularly warmed to.

The special effects are excellent – I’ve never seen talking animals look so convincing before. I’m sure that the experience was much improved by being in 3D, although the effect isn’t quite as breathtaking as in Avatar.

This film won’t go down in history as one of the all-time greats, but it is an excellent film nonetheless and one that I strongly recommend you see as soon as possible. Don’t be late for this very important date!

Song

Confessions Of A Homeophobe

Posted in Science on March 23, 2010 by Tom

Homeopathy is something of an easy target for sceptics and comedians alike (link and link), but many people continue to spend a lot of money on homeopathic remedies, and so repeating all the reasons why these people are wasting their money could still be a worthwhile exercise.

Belief in homeopathy is a perfect example of people struggling to understand statistics, and the importance of a large sample size. This is possibly because small sample sizes – or in other words, anecdotal cases – bring with them a greater level of human interest than large sample sizes. As Stalin once said, “One death is a tragedy; a million deaths is a statistic”. Being told that homeopathy doesn’t work seems like nonsense if you know someone who took a homeopathic remedy after being told that their cancer was incurable, and then weeks later they went into remission. That seems like pretty good proof.

But it’s not. It’s really not.

If I flip a coin 1,000 times, I’d expect it to land on heads roughly 50% of the time. It might not be exactly 500, but it will be close. If I flip it 100 times, again, I’d expect around 50% to land on heads, but again it might not be exactly 50. And the percentage will probably be further away from 50% than it was with 1,000 coin tosses. If I flip it 10 times, it’s quite feasible that I could flip 10 consecutive heads. If I flip a coin just once, it will either land on heads 100% of the time or 0% of the time.

Apply this principle to miraculous recoveries from illness. For every person who defies odds of 1-in-1 million to recover, there were 999,999 who died, as expected. But because those 999,999 were fully expecting to succumb to their illness, their stories, while very sad, are unremarkable. The one person who recovered, on the other hand, will be proclaimed as a living miracle. If they happened to have tried a homeopathic remedy, that remedy will be proclaimed as a miracle cure.

People who claim to have been cured of cancer by homeopathic remedies are few and far between. Occasionally one crops up in the usual storm of sensationalism (link). Most claims of homeopathy working, however, deal with more mundane problems. Headaches, backaches, sore throats and colds. Problems that aren’t really that serious. Problems that conventional medicine may well have failed to treat. Such problems tend to be very sensitive to the placebo effect. The placebo effect is in fact quite a powerful phenomenon – essentially, it is when the patient’s symptoms improve purely because they believe they are going to. Quite a lot is understood of the pathways involved in the placebo effect, and entire books are dedicated to the subject (e.g. Dylan Evans – Placebo). When homeopathy works, it is working simply as a result of the placebo effect.

A meta-analysis published in Lancet in 2005 (link) looked at the various studies into the efficacy of homeopathy, and found that, as expected, it simply does not work at any level above placebo. It really doesn’t. That is the simple and straight forward truth.

There have been some papers that claim to have found that homeopathy does work. One such paper was published in Paediatrics in 2006 by Jennifer Jacobs and colleagues (link). It concludes that homeopathic remedies successfully treat acute diarrhoea in children in Nicaragua. A victory for homeopathy?

Not quite. The next issue of Paediatrics contained a fairly damning review by Sampson and London, which concluded:

“In summary: 1) The study used an unreliable and unproved diagnostic and therapeutic scheme; 2) There was no control for product adulteration; 3)Treatment selection was arbitrary; 4) The data were placed into odd groupings without explanation, and contained errors and unexplained inconsistencies; 5) The results were not clinically significant and were probably not statistically significant; 6) There was no public health significance; 7) Selection of references was incomplete and biased to support the claims of the article, and references were quoted inaccurately; and 8 ) Editorializations were inappropriate.”

Since then, Jacobs and her team have conducted trials in various countries, with varying results. The publications have been limited to low-impact journals such as The Journal of Alternative and Complementary Medicine, which in 2007 published a study into the efficacy of homeopathic remedies In Nepal (link). Unsurprisingly, the study found that homeopathic remedies do indeed work, but the publication is barely worth the paper it was printed on. Not only does it suffer from the same problems that the Nicaragua study suffered from, but it was funded by a company from Boiron. I’ll let you Google them.

So, with the scientific literature very quickly summarised with the inescapable conclusion that homeopathy doesn’t work, I’m now going to write about two more things: Firstly, why it’s fairly obvious that it doesn’t work; And secondly, why this finding isn’t simply “what doctors want to find”.

Homeopathy is a form of alternative medicine that was first proposed by Samuel Hahnemann in 1796. The principle is that a condition can be cured by a small amount of the thing that causes it. Scientifically, this isn’t actually a completely crazy idea. Many vaccines are based on small, inactive or subtly different forms of the antigen that causes the disease. The vaccine for smallpox was cowpox, for example. However, homeopathy takes this idea and runs with it to incredible conclusions. Firstly, they don’t actually use the thing that’s causing the illness – so the cure for ‘cancer’ wouldn’t be a diluted bit of tumour. They look at the symptoms. They then take something that would cause that symptom, and dilute it. For example, if you’re suffering from insomnia, they will give you a very diluted solution of caffeine, because caffeine keeps you awake.

And by very diluted, I mean very diluted. Not the kind of diluted that shampoo is when you fill the nearly-empty bottle with water. This is dilution of astronomical proportions (I hope that the very small number of regular readers are picking up on these little references).

At some of the strongest dilutions (which means the remedy is more potent, incidentally), you would require a sample of homeopathic solution larger than the entire universe to be statistically likely to have just one molecule of the active ingredient present. In other words, it really is just water. It’s not a diluted form of the thing causing the illness – it’s just water. And this is where the real pseudoscience comes into it. Water has memory, homeopathists claim. It remembers what was once in it, and as a result of that, it works. It only remembers the active ingredient (caffeine or whatever) of course, and not all the other things that had previously been in it. This is all due to a fairly complex shaking ritual. I really don’t want to go into the detail of that, because life is too short, but James Randi explains it all very well (link).

If what homeopathists are claiming is true, they should be falling over each other trying to prove it, because if they do, they will have fundamentally changed our understanding of physics. Forget what the Large Hadron Collider is doing: if homeopathy works, we can forget a lot of what we think we know about physics.

Finally, is it possible that the only reason why people ridicule homeopathy so much is that doctors and pharmaceutical companies want to carry on making money out of conventional medicine? Of course it’s not. Conventional medicine is, quite simply, medicine that works. I apologise in advance to anyone who knows anything about this, because you can probably guess what example I’m about to give. Thousands of years ago, people used to chew on willow bark to treat headaches. More recently, it was found that willow bark contains salicylic acid. A derivative of this is acetylsalicylic acid, which is more commonly known as aspirin. If alternative medicines can be shown to work, conventional medicine will gobble them up in a heart-beat and make them part of normal treatment. If homeopathy can be shown to work, the major pharmaceutical companies will rub their hands in glee at the prospect of making billions of pounds out of water. Doctors, scientists and pharmaceutical companies have nothing to gain whatsoever by disproving homeopathy. It simply does not work.

And another argument that is often heard is that even if homeopathy doesn’t work, it doesn’t do any harm for people to believe it does. It comforts them. It gives them hope. Well, that may be true. But what if those people choose homeopathy at the expense of proper medicine? In those instances, homeopathy doesn’t bring them hope – it’s assisted suicide.

And the harm doesn’t stop there. Clinical trials of homeopathy often take places in poorer countries such as Honduras and Nicaragua, and more recently have even started to be used to treat HIV/AIDS (link). Testing remedies that do not work, on children with HIV/AIDS in underdeveloped countries, is completely unethical and absolutely appalling.

In conclusion, there is absolutely no satisfactory evidence that homeopathic remedies have any efficacy whatsoever other than the placebo effect, and there is a wealth of evidence to the contrary. This is hardly surprising, given the scientific implausibility of homeopathy. Furthermore it is my opinion that not only does homeopathy do no good whatsoever, but it actually causes great harm.

But then maybe I’m just a homeophobe.

Song

The nature of free will

Posted in Science on March 20, 2010 by Tom

Our minds are full of contradictions. We like to think that we are in control of what we are doing, and that we have free will, yet many of us also believe that everything happens for a reason, that we have a destiny, and that our destiny is controlled by a higher power. Some of us are troubled by this contradiction, and manufacture all sorts of convoluted arguments in an attempt to keep both free will and fate simultaneously true. We feel trapped if we are not in control, but feel burdened by responsibility if we are. Fate is very difficult to prove, but we take free will for granted. We can prove that we have free will by being unpredictable. We know exactly what we are going to do, yet others do not. That is surely proof of free will. Or is it?

In 1948, B. F. Skinner published a paper suggesting that pigeons display a form of superstition (link). He showed that if pigeons are left in a chamber and given food at random intervals, they will make false inferences that their behaviour is causing the food to be delivered. For example, a pigeon may turn around clockwise just before food is delivered, and qill subsequently repeat that action the next time it wants food, wrongly believing that its actions caused the food to be delivered. Humans act in exactly the same way. Not only has this been shown experimentally (Wagner and Morris, 1987; Ono, 1987), but anecdotally we can all think of times when we have falsely believed that our behaviour has caused independent events to occur. For example, we might think of someone seconds before they phone, and infer some sort of psychic ability; or we might have a special ritual before a football match. Bizarrely, often when our superstitious rituals don’t work, we will think that we did them incorrectly, rather than realise that they’re completely independent and have no influence whatsoever on future events. This is the first important feature of the way we think, which I will return to later.

In 1965, Kornhuber and Deecke (link) showed that before voluntary hand movements, there is a characteristic electrical signal in the brain, which they called a readiness potential or Bereitschaftspotential. Libet showed in 1985 that that readiness potential takes place before the subject is aware of what they are about to do. This has been replicated by others, including Soon et al. who in 2008 showed that a forthcoming action can be detected in the brain up to 10 seconds before it enters the subject’s awareness. In other words, the timeline of a decision is this: The decision is made, the decision reaches our conscious awareness, the action takes place.

So, combining the last two paragraphs: If humans are able to form false beliefs about causation so easily, it is not difficult to believe that by knowing what we are about to do before we do it, that could be misinterpreted as some form as control, or volition. Every time a decision reaches our consciousness before it its end result, we will believe that our consciousness has in fact produced that decision. In is important to note that many actions do not reach our consciousness until after their end result, or sometimes not at all. Reflex reactions like moving our hand away from a hot surface, or even something complicated like playing the piano can take place without any real conscious awareness. In my research degree last year, I investigated the possibility that even movements that we consider to be ‘conscious movements’ start to take place before we are aware of them.

So is free will and indeed consciousness itself just an illusion? I can’t put this argument into better words than my supervisor, Roger Carpenter, did in his book, Neurophysiology, so instead I will simply post a link to it (link).

But even if free will is an illusion, and what we call our ‘consciousness’ is just a spectator, does it really matter? We are our brain, and just because our decision-making incorporates randomisation, that does not mean that the decisions it reaches are arbitrary. Our brain contains our memories, experiences and desires, and therefore even if all our decisions are simply a product of a stimulus-response mechanism, it is still essentially free will.

I’d like to return to this subject and write about it in more depth at a later date. As I said earlier, I did some work on this subject last year. I’m hoping to get it published at some stage, so I can’t go into too much detail about it, but hopefully one day I will be able to post a link to it!

For references, Continue reading

Statistically significant science

Posted in Links, Science on March 20, 2010 by Tom

If you find anything in this blog interesting, I recommend another new science blog:

http://statisticallysignificantscience.wordpress.com/

Lots of interesting science stuff there – the case of Phineas Gage is a classic which sadly far too few people know about.

Exogenesis

Posted in Science on March 19, 2010 by Tom

“And God said, Let the earth bring forth the living creature after his kind, cattle, and creeping thing, and beast of the earth after his kind: and it was so.”

Nowadays, there are very few mainstream scientists who regard Genesis as an accurate description of the origins of life on Earth. Not only is there a huge wealth of evidence that the earth is considerably more than 10,000 years old, but Darwin’s Theory of Evolution provides a beautifully simple model, describing how random mutations and natural selection have produced the vast diversity of life that inhabits our planet. However, evolution does not explain how life begun.

The first thing to note is that there is still some debate over the precise meaning of ‘life’. There is no unanimous agreement over whether or not viruses can be described as ‘living’, for example. However, viruses certainly require other living organisms to reproduce.

One theory is that life spontaneously generated from non-living matter (abiogenesis). Aristotle claimed that, for example, aphids spontaneously arise from dew. However, Francesco Redi showed in seventeenth century that maggots do not appear in meat when flies are prevented from laying eggs. Two centuries later, Louis Pasteur showed that bacteria and fungi do not spontaneously generate in nutrient-rich, sterile environments. This is evidence that life does not spontaneously generate from non-living matter. However, although now life generates from other life, there must have been a point in time when life did indeed spontaneously generate from non-living matter, and it probably had to be happening quite regularly. Darwin speculated that a life spontaneously generated in a “warm little pond, with all sorts of ammonia and phosphoric salts, lights, heat, electricity, etc. present, so that a protein compound was chemically formed ready to undergo still more complex changes“. The reason why we do not observe this happening now is because the necessary ingredients would never be able to exist in the necessary conditions, because they would be instantly devoured or absorbed by nearby organisms. Think of planting a small flower. This is easy to do in a small plot of soil, and the flower will thrive. But plant it in a forest, and it is likely that the flower will die, because its light is blocked by the trees above it. Essentially, existing life stops new life from spontaneously generating.

Furthermore, Alexander Oparin suggested in the early twentieth century that atmospheric oxygen prevents the synthesis of crucial organic compounds. Our atmosphere currently contains around 21% oxygen, and oxygen is of course essential to all aerobic organisms. This is an example of the great beauty of evolution: life cannot spontaneously generate in an atmosphere containing oxygen, yet through random mutations and natural selection, some of the properties of oxygen which make it lethal to simple organisms can be exploited by more complex organisms, giving rise structures as complex as the human brain. The earth containing the earliest life forms has been termed an RNA world, with organisms based on RNA instead of DNA and capable of self-replication. It is unknown when this may have happened, but the oceans and atmosphere of the Earth did not develop until around 4.1 billion years ago.

It is estimated that the Earth is around 4.55 billion years old. The oldest evidence of life is 3.5 billion years old, and comes from fossilized stromalites. These are formed by cyanobacteria, a photosynthetic bacteria. This means that photosynthetic bacteria must have evolved no later than 3.5 billion years ago. This means that between 4.1 billion years ago and 3.5 billion years ago, life must have spontaneously generated from various chemicals, and evolved into photosynthetic bacteria. That gives the evolution around 0.6 billion years.

A further complication is that in the period of time between 4.1 billion and 3.8 billion years ago, the Late Heavy Bombardment occurred: a period of time in which the entire Solar System was bombarded with very large asteroids. Evidence for this is provided by craters on the Moon. This bombardment is likely to have obliterated any life that had managed to generate on Earth, which reduces the time between spontaneous generation and evolution to photosynthetic bacteria to a maximum of 0.3 billion years.

In contrast, the universe is around 13.7 billion years old (or 12 billion years old according to Katie Melua – link). At least one cycle of star birth and death is required for the synthesis of carbon, nitrogen and oxygen, all of which are essential to life. This would take several billion years. However, it is very likely that the universe has been theoretically capable of supporting life for upwards of 10 billion years, and that by the time photosynthetic bacteria were present on Earth, life could have existed elsewhere in the universe for over 6.5 billion years. The rather tempting question is obvious: if humans were able to evolve on Earth within 4.55 billion years of its formation, what kind of life could have evolved elsewhere in the universe in over double that time?

There is currently no evidence of any life outside Earth. There are around 400 billion stars in the Milky Way, our galaxy, and there are around 170 billion galaxies in the universe (the size of galaxies ranges from as little as 10 million stars to as many as 1 trillion). If there is nothing particularly special about our Solar System, then any number of the other 70,000,000,000,000,000,000,000 solar systems could contain life. Even if our Solar System is exceptional, perhaps as rare as 1-in-a-billion, there are still 70,000,000,000,000 others like it. These are numbers of homeopathic proportions, which make the possibility of life – intelligent life – on other planets seem not just likely, but almost certain. But yet we have no evidence whatsoever of any extraterrestrial life. The contradiction between the high likelihood of alien life, and the complete lack of evidence for any is known as the Fermi paradox.

There are all sorts of theoretical explanations for this paradox. Perhaps intelligent life always ends up destroying itself before it is able to communicate with other planets; perhaps the Earth is in fact unique and no other planets can support life; perhaps once life becomes intelligent enough to communicate with other planets, it reaches a point in philosophical enlightenment where it decides it doesn’t want to; perhaps the evidence is there, but we can’t see it; perhaps no planet has the resources to support interstellar travel; perhaps interstellar travel is technologically impossible; perhaps Earth is being observed by others who do not wish to interfere; or perhaps they are already amongst us. All we can do is speculate.

So, if life can develop on other planets, can it travel between planets? This concept is known as exogenesis or panspermia.

We know that material can be transferred between planets – we regularly receive meteorites from Mars. It is unlikely that life would be able to survive travel across space: radiation, cosmic rays and stellar winds are all very damaging to life. Although DNA can survive for a few million years in extremely harsh conditions, as found in Antarctic glaciers, this is probably not sufficient time for interstellar movement.

One intriguing theory proposed by Francis Crick, the co-discoverer of the structure of DNA, is that of Directed Panspermia (link). The theory is that planets that may be able to support life may have been chosen by intelligent life on another planet, who then sent life on spaceships containing organisms to these planets. Crick’s conclusion is that Directed Panspermia cannot be completely dismissed, although it is very difficult to estimate its likelihood as many of the necessary parameters are completely unknown.

Of course, even if exogenesis is possible and has happened, life still had to start by abiogenesis somewhere. Occam’s Razor would probably prefer the theory that abiogenesis took place on Earth, and perhaps takes place on other planets, with no transferrals between planets, but again, it is very difficult to estimate the relative probabilities when so many of the variables are unknown.

Finally, if Directed Panspermia is possible, then regardless of whether or not it has happened before or was responsible for the start of life on Earth, one intriguing question is whether or not it will happen in the future. It seems likely that when we finally run out of resources on Earth, we will either have to harness the resources of outside our planet, or become extinct. It could be that in the distant future, we may feel that our only hope of survival is to move to a different planet.

If that ever happens, it’s just possible that it may not be for the first time.

Song (three parts)