New Beginnings...

It may look like I have abandoned ship but nothing could be further from the truth, I have merely swapped vessels. For a long time I have been toying with the idea of trying out a new blogging platform but I resisted as I didn't fancy having to start again from scratch. Having looked at a few options though I have taken the plunge.

There are two main reasons. Firstly, this blog was never really meant to be about science and scepticism yet that is what it has become, mostly because I really don't get the chance to travel or take pictures like I used to; so for a while now I thought that I would like to separate out the two. Secondly, the Google Blogger platform really hasn't changed in 5 years; it has become increasingly outmoded and is in dire need of an update. If I'm going to start a new blog it isn't going to be on Blogger. My new blog, Skeptilogicon (forgive me the American spelling but most of my readers are from the US), was born this past Wednesday and can be found on WordPress which is, frankly, a far more comprehensive blogging platform.

I will still be posting here when circumstance permit, although it will now be a lot more infrequently; I don't travel much these days whereas I can read and write about science from the comfort of my own tube train. If I happen to take a pretty picture I'll be sure to share it. In the meantime, feel free to come on over to The Skeptilogicon and get your daily dose of science and scepticism.

Latest Pluto Pictures!

Last week NASA revealed the latest awesome images of Pluto from the New Horizons mission. Check out this amazing image of the Cthulhu Regio and Sputnik Planum below. I can see that the image has been horribly compressed when I uploaded it to the blog so it's well worth clicking on this link to the hi res original.

The dark mountainous region is Cthulhu Regio whilst Sputnik Planum is the vast, flat, icy, white expanse. The plain is another example of the puzzling lack of craters on Pluto's surface, which implies a younger age for the surface than anyone had predicted. Contrastingly, Cthulhu is the most heavily cratered, and therefore oldest, region yet seen.

According to Principal Investigator Alan Stern the most surprising thing revealed so far by the mission has been the sheer breadth of geographical features found on Pluto; it's just as varied and interesting as Mars.

The new image is a mosaic made from images downloaded since September 5th when the probe began its year long download of the data it accumulated during the flyby. We're going to need to be patient to get it all but, on the upside, it means there's lots of goodies still to come.

Badger Parade Postponed

Obscure 20 year old British comedy references aside, Governments, unfortunately, have a nasty habit of picking and choosing scientific data to fit their ideology. The latest example from our current Government concerns badgers once again. Badgers are a natural reservoir of a type of tuberculosis that also happens to infect cows. Farmers don't like having their cows infected with TB and so are generally in favour of eradicating badgers anywhere near their farms. Most farmers and other rural types tend to vote Conservative and so it is that the humble badger finds itself pitched against the might of Her Majesty's Government.

Over the past two years there has been a pilot study in two areas to see if culling badgers will reduce the incidence of TB in cattle. The pilots were based on an earlier study, The Krebs Study, that found that to achieve a 12-16% decrease in bovine TB incidence you had to kill at least 70% of the badger population every 4 years. Yes, you read that correctly. 70% of badgers have to die to achieve a very modest decrease in the numbers of cows getting TB. The Krebs Study also showed that if you failed to kill as many as that then there was a good chance that you could actually increase the spread of the TB because the badgers become a lot more mobile once they realise the apocalypse has arrived. Who could blame them?

The pilot was conducted in two English counties, Gloucestershire and Somerset, where it was necessary to kill at least 615 & 316 respectively. By the end of the allowed 6 week period of the cull (the time frame is kept short so that the blow can be dealt swiftly to the badger population before they have a chance to move elsewhere) 341 badgers had been killed in Somerset and only 274 in Gloucestershire. On top of this, an independent expert panel found that the method used to kill the badgers (trapping them and then shooting them) was inhumane; an unacceptably high percentage of them were found to suffer and for longer than was permitted.

It is difficult to see how this pilot scheme could be used to justify rolling out the culling program more widely. It's quite possible that the cull could have made the situation worse and hundreds of badgers will have suffered and died for no purpose. The pilot was broadly based on research carried out over 8 years by Professor Rosie Woodroffe. She has publicly stated that the Government's position is not backed up by the evidence. She says, 'This announcement plums new depths. In [cherry picking the data], it does a disservice to the farmers it seeks to protect, by feeding their hope of a solution to the TB problem with an approach which actually risks making the problem worse.' Indeed.

Apparently building a decent fence would be too much effort to go to. Image used with permission

Treellions and Treellions!

Good news! Thanks to combining different counting techniques we now have our most accurate ever count of the number of trees on the planet. The new figure is approximately 3.04 trillion trees. That's a lot of wood and constitutes a 7 fold increase in the previous best estimate. But don't get excited, there aren't 7 times more trees on the earth than there were last week, we've just conducted a better census.

Previously we have used just satellite imagery to count them but this isn't great at estimating density. From hundreds of miles up it isn't easy to see if a green canopy is made up of lots of smaller trees or fewer larger ones. The new technique involved amassing as many ground based surveys as possible, actually getting outside and counting the number of trees in a given area (over 400,000 hectares in total!), and then cross referencing these areas with the satellite imagery. This then allowed the researchers to know for sure what images of a particular nature translated to in reality. They then extrapolated out over the rest of the planet and Bob's your uncle.

Their results are published in this open access paper from Nature. In it they note that the number of trees has decreased by an astonishing 46% since humans came on the scene and that the number is decreasing by about 15 billion trees each year. This new data will hopefully provide more detail for climate change models and also assessments of items like soil erosion, water purification and other functions that trees perform free of charge.

I fear bonsais were not included in the survey. Image used with permission

Oldest Living Vertebrate Returns to English Rivers

Great news! One of the, frankly, most terrifying creatures I've ever laid eyes on is making a comeback in English rivers. The lamprey, asides from being some kind of monster from a Guillermo del Torro film, is actually very interesting. It is the oldest known vertebrate still alive today having been around for over 350 million years; that's over 100 million years before even the very first dinosaurs evolved. Lampreys are jawless and instead have a circular mouth with row upon row of pointed teeth, see below if you want to have nightmares. Did I mention that they can grow to be a metre long?

Anyway, although they used to be very common and successfully survived hundreds of millions of years of change and upheaval across the planet, in the last couple of hundred years their numbers dwindled over Europe and they are now endangered. However, a project by the Environment Agency has led to increased numbers across parts of northern England. The two main problems the eel-like fish had were pollution and river blockages like weirs and dams. Many UK rivers are now the cleanest they've been since the Industrial Revolution and the blockages are being overcome with the installation of lamprey tiles. These are cheap tiles that have broad based cones sticking up from them that the lampreys can curl around and use to gain purchase as they travel up river.

As unlikely as it seems they are, apparently, delicious to boot. Lamprey pie was a mainstay of royal banquets for a millennium and is still sometimes found today, for example at the Queen's jubilee celebrations in 2012. But be warned, the chronicler Henry of Huntingdon reports that Henry I was killed by consuming 'a surfeit of lampreys' in 1135, a fish that he loved but which 'disagreed with him'.

Image used with permission

The Reproducibility Problem

For some years now psychologists have been talking about the Reproducibility Problem. This is where a team of researchers publish a paper that shows some new and interesting result but when another team uses the same method to try to reproduce the result they cannot detect the effect. This is significant because one paper is never proof of anything, one paper can always be an anomaly. The ability to faithfully reproduce an effect is one of the cornerstones of the scientific method and knowing that what we see is a real effect.

An open access article in Science this week reports on a large collaborative effort to try to put some flesh on the bones of this problem. Nosek et al attempted to replicate 100 wide ranging psychological studies performed in 2008 published in three different, high quality psychological journals. They copied the methods of the original studies exactly and even used the same materials where available.

They found that 97% of the original studies had a statistically significant result but that only 36% of replications did; also, the mean effect size more than halved in the replications. This all ties in with what I was talking about in a recent post on P-Hacking, the phenomenon consciously or otherwise of massaging your results into significance. Although this study focussed on psychology I don't think it is unreasonable to assume that many fields of science suffer from a similar problem to some degree. It is a symptom of being rewarded for new and innovative research but not for reliable reproduction of existing research. To reiterate my point from my previous post, I don't think that this means science is broken, but it does mean that it is inefficient.

A large part of the blame lies with journal editors who aren't interested in publishing replications, but also with those in charge of allocating grant money and in Principal Investigators who want to up their research impact. I'm afraid that, at the end of the day, a lot of science is simply not new and sexy, it is about meticulous, hard graft that won't set the world afire but will, slowly, push back the boundaries of our knowledge. Nosek sums up the situation well in his paper:

Reproducibility is not well understood because the incentives for individual scientists prioritize novelty over replication. Innovation is the engine of discovery and is vital for a productive, effective scientific enterprise. However, innovative ideas become old news fast. Journal reviewers and editors may dismiss a new test of a published idea as unoriginal. The claim that “we already know this” belies the uncertainty of scientific evidence. Innovation points out paths that are possible; replication points out paths that are likely; progress relies on both. Replication can increase certainty when findings are reproduced and promote innovation when they are not. This project provides accumulating evidence for many findings in psychological research and suggests that there is still more work to do to verify whether we know what we think we know.

Image used with permission from here

Universal Flu Vaccine: A Step Forward

Great news! We have made another step in the direction of creating a universal flu vaccine. This has always been a goal but an elusive one. For many years now we have had to make an educated guess each year as to what the most prevalent strain of flu will be in the upcoming season, production of a vaccine for that one strain is then ramped up through the summer to try to ensure a good supply for the winter. Remember, each single dose of flu vaccine is created inside a chicken egg. Think how many millions of eggs must be needed each year just to help us stop getting flu!

Anyway, sometimes our best guess isn't as good as it could have been, plus there is no protection from the many other strains of flu that may or may not be doing the rounds at any given time; so it's an imperfect system. Then why haven't we made a universal vaccine before? Well, let's picture an influenza virus. Imagine a ball with lots of lollypops sticking out of it. The sweet, delicious head of the lollipop is the part that can change and vary and evolve and is what makes them so darned hard for our immune systems to recognise and adapt to. If you've heard terms like H5N1 and H3N2 then these refer to this part. The stick part of the lollipop (the haemagglutinin stem) is unchanging and seems to be the same in every strain of flu so far studied. It would seem sensible to create a vaccine that targets this unchanging stalk component rather than the ever evolving blobby head, but this has never been possible because the stalk is physically difficult to access. Imagine flying over a dense forest canopy and trying to find a way to hack at a tree trunk.

In the past some clever people have found a way to decapitate the stalk and so free it up for attack, but it turned out that the stalk then sort of just fell apart leaving nothing for our immune systems to attack. In a new paper in Science a team from Leiden, Germany, detailed how they were able to decapitate the stalk but then modify it so that it was stable thereby leaving a target. Then they created an antibody that is able to recognise the stem and provoke an immune response and protection from the virus.

Mice infected with the lethal H5N1 strain of influenza were fully protected. Macaques still had a bout of the flu but the symptoms were much less severe than normal. The concept, then, has been proved. The next stage will be human trials, but these typically take several years to perform so we are still someway from a universal vaccine for ourselves. It's a prize worth waiting for, though; half a million people generally die from flu each year, and that's in a good year. Last year a mutation in the H3N2 strain, which the vaccine was targeted against, resulted in a vaccine that provided little protection and a commensurate spike in deaths. Perhaps in a decade the flu vaccine will be a part of the childhood vaccination program and that will be all we need for the rest of our lives, that would be a truly wonderful achievement.

Three dimensional influenza structure; image used with permission

3D Hologram Could Map Black Hole Contents says Stephen Hawking

Stephen Hawking has been at it again, being all controversial and awesome. At a meeting of the Royal Institute of Technology in Stockholm he has given a talk that may go someway to explaining the Information Paradox of black holes.

In the 1960s Hawking became famous for proving the existence of black holes and that nothing, not even light, is capable of escaping their vast gravitational pull. In the 1970s he became even more famous for disproving his earlier proof. He then contended that something could indeed escape a black hole, a type of radiation that went on to bear his own name. The idea that black holes can evaporate away via Hawking radiation is one of the concepts behind the Heat Death of the universe, the theory that the universe will 'end' by merely ceasing to contain a single atom of anything several trillion years from now becoming a vast expanse of uniform, cold nothingness.

There is a problem, though; if black holes irrevocably swallow up matter and energy then the information, or properties, of that matter and energy are lost and this violates key tenets of quantum theory which says that information must be preserved. Physicists and mathematicians studying black holes have spent the last several decades trying to find a way around this conundrum.

Hawking, in collaboration with University of Cambridge physicist Malcolm Perry and Harvard theorist Andrew Strominger, have proposed a potential mechanism. Like many things on the cutting edge of physics it sounds a bit abstract and difficult to follow but, who knows, maybe this will be high school level knowledge a decade from now. As far as I understand it, which is by no means fully, they are suggesting that as an object, let's say Iain Duncan Smith, passes the event horizon of a back hole, a record of his black heart and other wretched components will be forever preserved in the form of a three dimensional hologram. The hologram consists of two space dimensions and one time dimension and would need to be capable of storing enough information to theoretically map out the innards of the black hole and everything it has consumed.

They go on to claim that as Hawking radiation leaves the black hole it would somehow pick up a bit of the hologram data and that way information would be preserved and the laws of physics remain intact. However, the data would come out in a random, unreadable format thereby also preserving the idea that nothing useful can escape a black hole. An analogy was made to burning an encyclopedia; if you were to take an encyclopedia, you know, a paper one, and set fire to it and then keep all the ashes then technically you could say you still have all of the information it once contained, but practically speaking there's no way you could actually retrieve it.

I know, it sounds like an imaginative fudge to try and escape a tight spot, only time will tell. Indeed, it's difficult to say anything a this point as we only have a speech to go on, it will likely be some months before an actual paper is published for proper analysis. Once that is released it will no doubt get the proper scrutiny that such an idea warrants. Give it another decade or two and we might have it figured out, but we'll get there in the end.

Image used with permission

Another Nail In The Coffin of Homeopathy

Great news! A recently published judicial review of the decision by the Lothian Health Board to defund homeopathy has given a sound slap in the face to anyone still left out there that thinks homeopathy has a shred of credibility left.

To give a little background; in January 2012 the Lothian Health Board conducted a review of the homeopathy service it was providing and concluded that the service was not worth funding any further. Any sensible person would immediately realise that this was because it would be unethical to provide public money to fund a 'treatment' based solely on pre-Victorian era magic. However, an idiot by the name of Honor Watt decided to challenge the decision by instigating a judicial review. She was aided by an undisclosed charity, the word on the street is that it was the British Homeopathic Association (BHA).

Even hardcore homeopaths know that they can't win an argument on the science, witchcraft doesn't stand up well to logical arguments, so the tactic used was to say that the decision made by the health board was discriminatory. They didn't say which particular characteristic had been discriminated against so I'm going to go right ahead and assume it's stupidity. Now, whenever an NHS body makes any kind of decision like this it is obliged to carry out an impact assessment with regard to potential discrimination. They had tried to gather as much demographic information as possible before the decision was taken but this was somewhat hampered by the fact that the homeopathy clinics didn't bother collecting even the most basic information about their patients, a highly unusual practice when one is supposedly performing a medical intervention. Anyhoo, on the information available they concluded that no one group of people would be unduly affected.

The killer blow came at the end of the judgement (paragraph 32). The judge, Lord Uist, said:

In any event, even if I had concluded that the Board had failed to comply with its PSED, I would have refused to reduce the decision under review.  It is plain that the Board, as it was entitled to do, accepted the view that there was no scientific evidence for the efficacy of homeopathy and that funding for it was a waste of the limited funds at its disposal.  In these circumstances the countervailing factor in this case was so powerful, indeed overwhelming, that no decision other than the one taken by the Board was conceivable.  A different decision, namely, to continue spending money on a service whose efficacy was not established, would have been unreasonable.

This basically means that, even if the decision had been discriminatory, he would not have overturned it as homeopathy has no basis in medical science and it would be unreasonable to fund it under any circumstance. These are strong and unequivocal statements. There are very few boards in the UK that still provide any funding for homeopathy, I think we're in to single digits now, but even one is too many. Hopefully this judgement will provide the impetus required to finally eradicate this wasteful and potentially harmful practice from public healthcare settings.

Samuel Hahnemann, the originator of the nonsense that is homeopathy

ISS to Destroy Planet

Is it me, or is the International Space Station about to throw its javelin of destruction at the earth?

Watch out!

GMOs: Why the Disconnect?

A couple of weeks ago I wrote a post bemoaning the reluctance of the general public to catch up with the science of GMOs; it puzzled me as to why a technology that is so clearly a force for good in the world should be reviled as a kind of dirty, leprous freak. I have every confidence that in the fullness of time the public will get onboard and we will begin to reap the multifarious benefits such as increased crop yield, decreased pesticide use, increased drought resistance and increased nutritional content; in the meantime, though, we need to think of ways to push understanding forwards. A good place to start would probably be to try to understand what is at the heart of the distrust aimed at GMOs.

A paper published last month in Trends in Plant Science by a group of Belgian philosophers and biotechnologists may begin to do just that. They attempted to explain why there is such a wide gap between public opinion and the scientific evidence and why it is so persistent. The initial premise is that most people have no clue how GMOs are produced or what they even are. If you have no actual knowledge on a subject then you are far more likely to rely on intuition, folk biology and emotions. These can feel very compelling inside us and are easy notions to communicate to others.

One concept they proffer is that of psychological essentialism. This can make people think of DNA as an essential, primal, inviolable part of an organism, something intrinsic to it that makes it what it is, sort of the physical counterpart to a soul. If you take some of this essence from one organism and add it to another it can provoke a feeling of disgust. People also believe that the second organism will have some of the traits of the first. For example, an opinion poll in the US found that more than a half of recipients believed that a tomato that had fish genes incorporated into it would taste of fish. Which it wouldn't, by the way. This doesn't stop anti-GMO organisations playing up to such fears, however.

The paper looks at the disgust angle in some detail. It appears that many people think of the addition of genetic material more of as a contamination. Given that one of the main reasons our sense of disgust evolved was to stop us eating potentially harmful foodstuffs, this would be a compelling feeling in the absence of hard knowledge to counteract it. Once you feel that something is disgusting or amoral then it is very easy to believe almost anything else negative about it. I think this is very much a part of the strategy on immigrants today; first you make them seem sub-human, then you can treat them any way you like. Because the feeling of disgust is a subconscious one we will tend to look for a reason to justify it, and so we will grab on to any reason at hand, even a false one, as we all like to believe we're rational, sensible people.

These kind of primal intuitions about a topic are the most difficult to fight against. You can't use logic and reason to argue someone out of a position that they didn't arrive at through logic and reason. In terms of changing attitudes the authors best suggestion is that we just have to do our best to educate people as to the facts, starting with children of course. The problem with that is that the science of the classroom normally lags a decade or two behind the science of the laboratory and there are a lot of hungry people around the world that won't be able to wait that long.

Image used with permission

US Chimp Unemployment to Surge

Invasive scientific research on chimpanzees (Pan troglodytes) appears to be on the verge of completely stopping in the United States. It comes as a result of a new rule introduced by the US Fish and Wildlife Service requiring all projects to apply for a new license. In this context, invasive research is defined as any that would harm, stress, harass or change the behaviour of an animal and would require a new permit. Even something as innocuous as drawing blood or taking a hair sample would need the new permit. And no one has applied for one. Not a single facility in the US has applied to continue with their research projects. This means that all work will have to have ceased by the September 14th deadline forcing chimpanzees across the country to down their rudimentary tools.

Public opinion in the US has been steadily but strongly turning against the concept of primate research in recent years and it would appear that none of the labs want to stick their neck out and risk the wrath of the populous. Behavioural research, which basically just involves watching the chimps, can continue.

I'm not entirely sure how I feel about this. Whilst I'm very against the unnecessary suffering of any animal I think there are situations where it is necessary that they suffer. Put in slightly less jarring language, I am in favour of animal research when it is appropriate and properly managed. In the UK there is a law that requires anyone planning an animal experiment to apply the three Rs when doing so; wherever necessary they must Replace the use of animals; Reduce the number of animals; and Refine procedures to limit suffering. I'm very much in favour of these guiding principals.

My concern would be in the potential limits now placed on certain types of research. How much will this hold back progress? Will there be a commensurate increase in research in other animals to make up for the reprieve of the chimps? Perhaps more macaques will now be studied and the overall amount of suffering will remain the same?  I certainly don't know the answers but I will be watching developments in the US with interest.