Erm, does anyone have any new antibitoics?

The golden age of antibiotics is drawing gradually but definitively to an end.

Since Alexander Flemming revoloutionised the way we view diseases with his discovery of penicillin in 1928, we have stopped worryingabout ailments like whooping cough and tuberculosis. It's worth remembering though that pre-1920s these kind of bacterial infections were rife, and wiped out large numbers of people, regularly. Plague epidemics, for example, have occurred several times in the last ten thousand years, with notably widespread outbreaks in the mid 1300s, 1665 ('the great plague of London') and again just before the beginning of the 20th century. There were also localised bouts constantly happening all over the world up until Flemmings' breakthrough.

So we've seemed to have the upper hand on bacteria for the last 100 years or so - but bugs that we can't beat are coming back. For instance, MRSA [1] has been thwarting the efforts of hospital staff to disinfect-it-out-of-existence for a number of years now. Although they're not bactrial (but rather viral) in nature, the SARS [2] and swine flu epidemics are two other examples - rather more immediate and frightening ones - of why we need to sit up and start thinking about whether we are too comfortable with the ways we treat disease.

The problem is that bacteria are very quick to develop resistance to antibiotics. Drugs like penicillin, great 40 or so years ago, quickly became no good at treating a whole host of bacterial infections. So called wide-spectrum antibiotics have been a big problem; they act upon just about any bacteria they meet, so even if all the bacteria which are the source of the problem are destroyed, lots of others will inevitably remain which have had a chance to build up resistance. Up until now we've had reserve drugs, which we only use in emegencies, so bacteria don't have a chnace to develop resistence. Even these though, are beginning to become less effective. It may only be a matter of decades before we no longer have a last line of antibiotic defence. We need new drugs, and quickly.

In science, researchers often look to nature for inspiration, and for this reason it turns out that the majority of the antibiotics in clinical use today are what are called 'natural products'. These are complicated chemicals which float around in all living organisms. Especially interesting ones can be found in single-celled organisms. Typically scientists take one of these cells, (a type known as streptomyces is very popular) and extract some of its bodily fluids and try and identify the various compounds contained in them. This kind of process led to the identification of some of the most powerful antibiotics we know of, such as Vancomycin and Chloramphenicol.

Now its getting progressively more difficult to identify new, useful antibiotics. One way some scientists think we should move forward is to, again, take a quick look at nature and see what we can learn. But this time we need to look in new places.

Recently sceintists have begun to explore in depth a fact which we have known in essence for many years. That is that many species of insect actually use docile bacteria as a protection against the more vicious ones [3]. Storing the organisms in their skin or intestines, or even farming them in the open, insects appear to grow the good bacteria as a protection against the bad. The question is, what compounds are responsible for keeping the bad guys at bay?

Take for example the european Beewolf. Not a bee at all, but an insect which paralyses bees and transports them back, alive, to their sand-burrow nests. There, the imobilised bees are a welcome food source for little beewolf larvae.

The Beewolf - not a bee

The hot sandy burrows are warm and moist - perfect conditions for all types of life, including bacteria. So how is it that the beewolf larvae do so well, apparently immune to the presence of the microorganisms? Researchers have now found that the mature Beewolves smear a sticky white broth containing a previously unencountered type of Streptomyces bacteria all over the cocoons of the developing larvae [4]. The insects and the streptomyces live in a symbiant relationship - the bacteria keep the larvae safe by fighting off infections with their antibiotics, and in return they live off a diet of nice, juicy Bee. Scientists don't yet know what the active compounds the bacteria produce are, but they could prove to be potent antibacterials for human use, too.

Another symbiant partnership exists between leafcutter ants and the common fungus they feed on. The ants carefully farm the fungus, which they use as food. In many parts of the world a highly competitive fungus called Escovopsis out-competes it's fungal enemies. This never happens in ant-farmed funus patches though - why? Again, scientists have been on the trail and have found the ants have been growing bacteria alongside the fungus.

When these new-to-science bacteria were grown in a laboratory, scientists identified a new compound - dentigerumycin - and sure enough, when applied to some Escovopsis it was a potent fungicide.

There are lots more symbiotic insect-microorganism relationships out there which we haven't yet discovered. I'm not suggesting we start coating our young in sticky bacterial broths, but if we continue studying these relationships closely it is easy to imagine a whole host of potential new drugs waiting to be harvested. Then we can keep one step ahead of those pesky mutating bacteria.

Notes and references

[1] MRSA = Methicllin-resistant staphylococcus aureus
[2] SARS = Severe, acute respiratory syndrome
[3] H. B. Bode, Angew. Chem. Int. Ed., 2009, 48, 2 - 5.
[4] M. Kaltenpoth, W. Gttler, G. Herzner, E. Strohm, Curr. Biol. 2005, 15, 475 – 479

Homeopathy

Last week it was climate change, this week alternative medicines threatening developing countries. Is it me, or is benchtwentyone developing a sentimental side?

I sincerely hope not. None the less I think it's important people know a little bit about homeopathy and how dangerous it can be if approached from a naive standpoint. Homeopathy is a form of alternative medicine which claims to be able to treat various illness by presenting the patient with highly dilute 'preparations'. Sometimes the disease-causing item itself is used in the preparation, sometimes not. The important criterion for homeopathic preparations is that the substance used in them causes the symptoms the patient presents - whether it is the real cause or not is irrelevant. For example to treat a runny nose (caused by a virus, say) a homeopath might employ onion essence, as this induces the same symptoms.

And what do I mean by highly dilute? Well, for a patient suffering from hayfever, the homeopathic practitioner might take a grain of pollen and dilute it in 100 ml of water. He would then take a drop of this and dilute it again with a further 100 ml of water. If he repeats this action 30 times he ends up with what homeopaths call a 30C preparation, which would be administered to the patient. The general idea is that by presenting the sufferer with an extremely small amount of a substance which causes their symptoms, they will some how become acclimatised to it.

You might be thinking this seems a little rubbish. Would onion extract really cure me of my cold? Well, benchtwentyone (and many others around the globe) is here to point out that these astute individuals are 100% right. Once you have carried out dilution to that extent, you end up with essentially a jar of water. In point of fact, the chance of there being even a single molecule of the active ingredient in a 30C preparation is less than the chance of winning the lottery five weeks in a row [1].

When charged with this fact, homeopaths sometimes respond by stating that water has a 'memory' which somehow transfers an impression of the active ingredient (what little there is of it) to the body. I don't want to skirt the issue on benchtwentyone, so let's be frank - this is utterly unsubstantiated nonsense. Water doesn't have a memory, and once a substance is taken out of it there is no impression left on the water molecules. No serious scientist has ever presented a shred of evidence that anything like this is possible

So homeopathy is scientifically on very dodgy ground. If we are rating this treatment by how sure we are that it works based on pharmacological trials and scientific proof it scores a rather fat zero. In a recent report by premier medical journal The Lancet, researchers found that there is absolutely no evidence that homeopathy works at all on a biological basis [2].

It seems clear that in cases where homeopathy appears to do some good in patients (and believe it or not there are some patients who claim it does) it is merely a placebo effect. That is, the patient believes that they have been given a cure or treatment and thus something in their mentality makes them feel better even though there is no physiological change.

I was disturbed to learn this week then, that Homeopathy, while at least not life-threatening in developed countries, is now being advertised in the developing world as an alternative therapy for conditions such as HIV/AIDS, TB and diarrhoea. Homeopathic clinics offer pricey treatments for vunerable people - and are making fairly big sums of money off the back of it. This is serious stuff, as people are being given false hope in the face of life-threatening conditions. What is more there are perfectly safe and - importantly - scientifically proven treatments which can treat and help control the spread of these conditions.

A group of scientists from the VoYS (Voice of young science) wrote to the World Health Organisation last week calling for them to issue a strong statement to condemn homeopathy as the fraudulent and dangerous thing it really is. You can read the letter, which was reported on in the guardian, here. Hopefully this will signify the begining of the end for homeopathy clinics in the developing world.

References

[1] Sense about Homeopathy, a briefing document from Sense about science, published online here.

[2] A. Shang et al., The Lancet, 2005, 366, 726 - 732.

Beyond Petroleum

When I was last at my parents house in Suffolk I picked up a few DVDs to watch during my spare time in Bristol. On my way to digging out 'Withnail and I' from this pile last week I stumbled upon Al Gore's An Inconvenient truth. I'd obviously picked this up by mistake, but I must have been in the mood for science, as I quickly forgot any desire I'd had to see Richard E. Grant getting utterly drongoed for 80 minutes, and instead slipped the Gore disc into the set.

Whilst I didn't really warm to the Americanism of the whole thing, I really think you have to give credit where it's is due. Gore performs his slideshow excellently (as well he might, since, as he says repeatedly [insert American drawl here] 'I must have given this slideshow a thousand times') and certainly leaves the viewer with no doubt that climate change is real and that CO2 causes it.

It was with mixed feelings then that I strolled down a corridor in the University of Bristol this week to listen to a lecture by BPs chief Chemist, Vernon Gibson FRS [1]. Gore's film had temporarily filled me with a zeal to 'do the right thing' although I wasn't quite sure what that could be. Being British, I had some vague idea that a good way to start would be to write to my MP and tell him how exceedingly strongly I felt about the issues..

'Vern'

He's read ALL those books, you know.

Well, perhaps Vernon's lecture would provide some more concrete ideas about how we can stop killing the planet. Well, maybe. I had no idea what to expect.

In the event the talk was great. What I liked about listening to Vernon was that it was clear he wasn't making anything up - which is refreshing when the media is a minefield of outrageous environmental claims at the moment. BP has employed him to study climate change data in depth and he has a very accurate idea of what can realistically be done about it.

Bearing this in mind I felt like it might be useful to relate some of the more interesting points - the gems, if you will - that he brought up here on benchtwentyone. For once we can listen to some views on climate change policy and be sure they're scientifically sound.

The gems:

We don't need to worry about running out of fossil fuels.

This was a big surprise to me as I was always taught by my teachers at high school that we would have run out of oil by about 2015. This is decidedly not the case. BP estimates that we have enough oil left on the planet for another 42 years and enough coal for about 133 years. What we do need to worry about are issues like security of supply - the North sea is just about out of oil, and in the future we will depend on oil from the Former Soviet Union or the Middle East. This means oil will become extremely expensive within a decade or so.

Renewable energy introduction can't happen quickly.

At the moment energy production from renewable sources is growing by around 8% a year which is actually pretty quick. Unfortunately, since the demand for energy is also increasing in strides it will be impossible for us to become completely secure in these sources in the forseeable future. BP forcasts that by 2030 around 30% of our energy will come from renewables - this won't cut it. What we need instead is a decisive change in government policy to make us change and more importantly make businesses change.

Realsitically, this won't happen. In fact vernon advocates building more coal power stations. He actually stated that due to the depletion of North Sea oil and nuclear power stations like Sizewell B reaching the end of their safe working lifetimes 'the lights will go out if we don't build them'. To remedy this it is absolutely vital that we start capturing the carbon emitted from these behemoths using carbon capture and storage (CCS) technology. Companies won't invest in these systems (which cost billions of pounds) without incentives though, so governments should start legislating to put these in place.

We need new infrastructure.

At the moment we have oil pipelines which provide a relatively cheap and secure way of getting fuel to where it's needed. Any switch to different forms of fuel will entail new infrastructure. BP have calculated various different options and most come out at costing $3 trillion a year to implement.

Windfarms - a lot of hot air.

Windfarms are not ideal as a long term solution. An area the size of a football pitch can hold 2 windturbines - this may not sound too bad, but when we consider that 1 coal-fired power station produces the same amount of energy as 350 windturbines operating at full power (and they don't do this very often) we begin to see that we would need to cover Belgium in windturbines to supply all of France, say. (I'm not sure I see the problem Vernon?)

Medium and long term solutions are not the same thing.

We don't have the know-how, political will or capital to work out all of the solutions tomorrow, that much is clear. So while wind turbines aren't realsitic long-term, they are great for the time being, especially in countries where there's lots of wind and offshore. The same goes for bioethanol - ideally we'd like our vechiles to run from super-efficient batteries charged from solar power stations. We don't yet have the technology to make this happen, so it makes sense to let Bioethanol work for us in the mean time.

Solar energy seems like the most likely answer to our problems, long term.

We're begining to have the technology to utilise the sun's energy and Gibson says this is very much where he sees our future, long term. We have technologies in the making which should lead to us being able to efficiently heat our homes, produce electricity and prodcue hydrogen for use a clean fuel (figure 1). Great.

Figure 1

Energy from the sun can help us heat our homes and be captured and stored as energy. We can also generate electricity using photovoltaic cells and use this to split water split water into oxygen and hydrogen gas. Hydrogen is super high in energy and could be a clean, powerful fuel for the future.

Hope you enjoyed the gems.

Notes

[1] FRS stands for 'Fellow of the Royal Society'. The Royal Society is a prestigious club for scientists of high renown. Originally the club served as forum for an early form of peer review (see the benchtwentyone article on the subject for more information), in that scientists could meet with each other to openly discuss ideas and receive feedback. Voicing one's ideas in this elite club meant that scientists could give each other advice and share ideas without fear of being copied before they could get their theories perfected.

Ur-ine trouble if you've been eating asparagus

I was reading last week in Hugh Fearnley-Whittingstall's delightful food column that asparagus is in season again. I really enjoy this whole eating in-season produce and being eco-responsible lark (despite it being so fashionable it almost makes you cringe). It's great; you get to eat really fresh food which is also quite cheap, since there's loads of it around.

Asparagus stalks in the wild

So I've been tucking in to the zingy spears all week and have been loving it. I was surprised to learn from a friend who had been similarly glutting-out on asparagus, that he also always enjoys eating asparagus, since 'it always makes my wee smell all mental.' I was surprised by this as I had experienced no real bathroom shocks, asparagus-related or otherwise, over the past few days.

But enough of this cheap toilet humour. As usual I needed to quench my insatiable thirst for scientific knowledge (or something) so I set about finding out what causes these magic odours which some people can smell and some can't.

First off, it is clear that a chemical of some sort is responsible. Scientists generally agree the one causing the grievance in this case is methyl mercaptan.

As an interesting aside though, unlike our other senses, smell is not really that well understood by scientists. We know how things like vision, touch and hearing work in quite a lot of detail, but smell remains something of an enigma.

We do know that there are various receptors in our noses, and it seems obvious that these mediate smell in some way. So far though, it has proved difficult for scientists to work out their exact structures. (Conversely, we do know the structures of lots of other proteins, for example opsin, as shown in the recent benchtwentyone article on retinal). To add to the confusion several molecules which have similar structures have wildly different scents. Conversely, molecules of vastly different sizes and shapes can sometimes smell very similar (figure 1). As a result of this confusion, there have been several not-widely-accepted theories of smelling even relatively lately [1].

Most receptors in the body are large proteins. These mediate everything from the digestion of food to the degradation of neurotransmitters and work on the theory of 'lock and key'. This means the cleft in the center of the protein has a specific shape and size which binds only a particular guest. But if this is the case for odourants, we would expect similar molecules to smell the same - which is not always the case.

Figure 1

Methyl mercaptan (the guilty party derrived from asparagus) and ethane dithiol are both sulfurous compounds which smell awful; like rotten eggs. Acetophenone has a relatively small methyl group compared to benzophenone which is much larger. They both smell similar though - people tend to describe the odour as a lot like burnt almonds.

To get back to asparagus though, it seems there are two possible explanations for the discrepancy between mine and my friend's post-asparagus wee. The first option is that one of us has a particular enzyme or bacteria in our intestinal tract which breaks down a compound present in asparagus to methyl mercaptan and the other doesn't. This might make quite good sense, as naturally occurring amino acids which contain sulfur (such as methionine) are known to be broken down in the mouth to methyl mercaptan by bacteria [2], causing bad breath. The alternative is that we both have the compound in our urine, but I don't have the correct receptors in my nose to smell it.

Stopping short of inviting my contact into a slightly too close for comfort wee smelling investigation, I consuted the British Medical Journal and found that the experiment had already been done by the professionals [3]. The researchers in question found that the chemical was present in the urine of all the 203 asparagus-fed volunteers they investigated. Also, when presented with samples of an 'unknown liquid' (the researchers obviously felt it wouldn't be proper to reveal it's true identity) the volunteers who could smell the guilty chemical in their own urine could smell it also in everyone else's.

So like it or not, if you're like me and have been chowing down on asparagus all week, you're going to have some seriously funky bathroom smells sometime soon.

[1] L. Turin, Chem. Senses., 1995, 773 - 790

[2] T. Koga etal., Infection and Immunity, 2000, 68 (12), 6912-6916.

[3] M. Lison, S. H. Blondheim and R. N. Melmed, British Medical Journal, 1980, 281, 20 - 27.

Paradigm shifts

Some scientists like to think that they pressume nothing, and have the cold pursuit of facts as their only rule. In fact this is largely nonsense. If we really stop to think about it we realise that all knowledge is based on certain assumptions and approximations. In lots of cases (most, even) these assumptions are reliable and good, but what happens when something occurs which contradicts all our percieved limitations?

A few years back a man called Thomas Kuhn demonstrated what can happen by cheekily constructing a deck of playing cards in which the suits of hearts and diamonds were coloured black and the clubs and spades were red - this of course going against the whole mind set you automatically take on as soon as you glimpse a pack of small cards with that characteristic pattern on their backs. Kuhn conducted an experiment where he quickly flashed random cards at his subjects, who he asked to try and identify them. He found most people identified the black cards as either spades or clubs automatically, even though they weren't, but displayed some degree of brow-furrowing. The second time round people were utterly confused and some even became angry. He even cited one of his subjects as crying and screaming hysterically, such was her distress at realising that somehow everything she thought she knew about cards was suddenly and inexplicably wrong with no apparent explanantion.

Kuhn conducted this experiment in order to try and illustrate his theory of 'paradigm shifts' and wrote it up in his 1962 book The Structure of Scientific Revoloutions. A historian by trade, Kuhn believed that scientists (like all of us) make a set of assumptions about their field of research. This could be based on the previous work done, where and by whom you have been taught or just on random prejudices. Generally this set of rules is shared by the majority of informed people in a field and forms what Kuhn dubbed a paradigm. A paradigm then, is like a window, the assumptions we make about things like the sills which frame the view. A paradigm shift is what happens when suddenly someone finds out something which they can't explain using the current scientifc theories - the window frame shifts to make room for new ideas.

Paradigm shifts have occured on a global scale lots of times in history as Kuhn expertly details in his book. For example it must have been one heck of a shock when one day a bloke called Nicolaus Copernicus came along and told everyone that in fact it was not the earth which was at the centre of the universe, but the sun (of course, we now know that's not exactly the full picture either). Equally, when scientists such as Bohr, Einstein and Planck started observing that the laws of nature which work for very large objects (like footballs and planets) didn't work for very small objects (like electrons and atoms) they found they needed new laws to explain what they were seeing. We now call that quantum mechanics.

Some argue that we are currently moving from a modern to a post-modern era and this is a form of cultural paradigm shift. Modernism was characterised by the formation of large, characterless conglomerations and as a result the making of large sums of money. Post-modernism is rather the opposite: a distrust of organised bodies of all kinds (especially the government and especially the financial systems) and a search for a more personal and resonant meaning and truth.

There are paradigm shifts going on all over the place. Now you know what they are you can try and spot one and tell someone else. You'll make yourself look very intellectual. Either that or just appear wierd and alienate yourself a little.

The Hayfever Machine

Many, many, many of us in the UK suffer from hayfever and I, your intrepid science crusader, am one of them.

Hayfever (seasonal allergic rhinitis) occurs when an allergen such as pollen gets into our system and comes into contact with a white blood cell (specifically, mast cells). Usually this doesn't cause much of a problem, but in people with allergies these cells have become hypersenstised and go rather mental, releasing an awful lot of histamine.

Histamine - the cause of our collective misery

Histamine is an important chemical in our bodies. It regulates sleep to some degree (which is why when you take antihistamines the boxes always warns you not to use heavy machinery afterwards - there's a small chance you could fall asleep) and has been shown to be released during sex too. Great.

Unfortuantely for us snivellers, it has a much more obvious role which is to act as an inflammatory agent. In principle this is good as when something horrid gets into our bodies we generally need to have our noses run (so that all the bad stuff, er, flows out) and our blood vessels inflammed (so that more blood carrying bug-eating cells get to the danger zone).

It's just a shame for me and my fellow sufferers that our bodies have declared war on ice creams in the park, wimbledon, a sunday afternoon stroll by the river and genereally anything else that involes being vaguely near grass during the summer months.

Since I was a boy I have been dosed up to the eyeballs from the end of April 'til arond September with prescription antihistamine medicines. I then switched Pfizer's expensive wonder cure Benadryl (mainly captivated by the adverts involving SWAT teams in helicopters swooping to the rescue of an atishooing sufferer). I've now cottoned on that a cheap antihistamine plus some decongestants will get rid of most of my symptoms. This does still add up however.

I've now received in the post what I dub 'the hayfever machine' which claims to be able to relieve the horrors of this condition using nothing more than a red light bulb. Of course there is the slight issue that in order to use it you have to sacrifice any iota of cool you may have (in my situation as a PhD Chemist this is more or less irrelevant, but still there is a duty to report, I feel) and cram two bulb-encasing prongs into your nostrils. These two prongs have red LEDs on their ends. You sit, uncomfortably, for three minutes, up to four times a day with these fellows in your nose and the light pouring in. The manufacturers claim it's 'safe, quick and easy to use and some sufferers will notice an improvement after just a few treatments'.

I sacrifice my last iota of 'cool'

Is there any evidence that this contraption works? One study I peroused (1) stated that after following the recommended course of treatment with the machine 72% of subjects felt their symptoms had been reduced and the study coordinators even went to the lengths of conducting an endoscopy (that is, sticking a miniture camera up the patients noses) and managed to confirm pictorially that this was the case for 70% of them.

How does this treatment work? In two ways apparently and by emmitting light of two different wavelengths. One wavelength of around 635 nanometers interacts with a light-absorbing chromophore (see article on Rhodopsin) in the white blood cells which causes a complex biological cascade of reactions which have been found to stabilise the cells and reduce histamine release. The second wavelength induces a dilation of nasal blood vessels which helps bring our bodies back to their resting state (2, 3).

I'll be reporting my degree of hayfever-induced misery on benchtwentyone as I begin using the device and we'll soon see if there's any truth in these claims.

Roll on summer.

References

(1) I. Neuman and Y. Finkelstein, Narrow-band red light phototherapy in perrenial allergic rhinits and nasal polyposis, Ann. Allergy Asthma Immunol., April 1997, 78, (4), 399 - 406.

(2) E. N. Goncharenko et. al., Bull. Exp. Bio. Medicine, effect of middle wave ultra violet and red light on degranulation peritonial mast cells in rats, 2006, 129, (4), 357 - 358.

(3) http://www.lazrpulsr.com/files/How_does_light_therapy_work.htm

Josh goes to Parliament

This week I strode off to the houses of parliament to attend the grandly named 'voice of the future, 2009'. This was essentially a bundle of Chemists and a smattering of Engineers and Biologists firing Question time-style questions at some of the people in and around government.

To my disappointment, it turns out that a third of the MPs are now housed in Portcullis house (referring to the portcullis on the house of commons logo) which is not the beatiful gothic structure tagged onto the side of Big Ben I had hoped for. A child-like excitement had filled me at the thought of getting in there. Emerging from Westminster tube station into the drizzle though, I wandered over to a police officer outside the commons and asked if he could 'point this portcullis place out to me'. He did so, towards a grey, dark building. I was a little disappointed. Admittedly, the place is extremely swish once you get inside, and indeed, is reputedly the most expensive office building in the world today. I especially loved the life-size picture of David Cameron I spotted hanging in one of the balconies.

Portcullis house - the one on the left that looks like a prison.

After 45 minutes of queuing I was scanned and frisked. I then entered the fray, heading to the Attlee suite.

The morning was taken up by a pleasing display of confidence from Lord Paul Drayson, a self-made bio-tech guru and current Science minister. Drayson spoke passionately of our need to 'play to our strengths during this time of economic difficulty' and 'get specific' on our plans do that this year. He also suggested our natural advantages in terms of tidal energy generation (we have a lot of coatline) could be coupled with our engineering experience in building off-shore rigs to fuel world-leading research into this type of tidal energy generation. I guess this is one way he wants us to 'get specific'. It does leave one wondering though, if one happens to work in an industry which the UK does not lead, will Drayson consider you a priority?

I also managed to glean an quick chat with Stephen Williams, MP for Bristol West and coincidentally shadow (Lib. Dem., if you want to know) minister for Universities, Innovation and Skills.I asked his opinion on the REF as a replacement for the RAE as a method of deciding on how much government funding an institution receives. Afficiandos of joshua-howgego.com will know some of my thoughts on this matter from my previous post on the subject of peer review. Stephen agreed the new proposals 'do seem to give poeple the chance to fiddle [the statistics]' and on the whole didn't seem too impressed with the scheme. In truth Stephen spent much of our 'interview' trying to work out who I actually was, at one stage plucking out a copy of my previous weeks email from his portfolio and studying it with brow furrowed, as if my explanation that I was a PhD Chemist who was interested in politics didn't quite convince him. Well fair enough I suppose.

You can find out more about the REF, if you're so inclined, here: http://www.hefce.ac.uk/Research/ref/

JH and Stephen Williams, MP for Bristol West

Lord Drayson, Science minister, speaks of his commitment to our scientific strengths

A post doctoral researcher grills the pannel

Shadow Science minister Adam Afriyie is an advocate of a 'scientific approach to policy making' - that is weighing up all the evidence before drawing conlusions in line with our current understanding. He has recently introduced a 'science induction' for all new MPs. Good work, Adam.

Peer Review



It was this time in 2006 when Gordon brown announced his plans to overhaul the Research Assessment Exercise (RAE); the way in which the government decides on funding for science and technology research in the UK. There have been loud cries of alarm from all sides of the scientific community since then, ‘what’s wrong with the way we do things now,’ they ask?

The RAE is based on the system of Peer Review. It’s a ludicrous idea when one first hears about it – in what other subject would competing experts in a field, be allowed to critically review each others work, and advise the politicians how good it is? Some conflict of interest you would think, no? Yet this is the system the government has used for a hundred years and it’s also the way the editors of scientific journals decide which work they print - and which they bin.

It has been said of Peer Review that it is to Scientists like democracy was to Winston Churchill, that is, ‘the worst type of government, except all those other types that have been tried.’ So maybe the time has come to take a fresh look at Peer Review, and see if we can do any better.



The faults of Peer Review

We scientists can admit that the failings of Peer Review are not inconsiderable. The main objection (on the part of the government at least, who must foot the bill) is that task of coordinating the independent reviews is bureaucratic and costly. Journals have to pay the expenses this brings too, and they account for them by charging scientists large sums to read the intellectually valuable scientific goodies they contain. This seems somewhat unfair for hard-up developing countries and isn’t all that much fun for UK Universities struggling in the wake of the credit crunch either.

More fundamentally, Peer Review has been accused of slowing down the development of science – which is just not cricket. This is because well-known and well-respected experts (the people best placed to review a journal) can be old fashioned and loathe to accept radical new ideas which contradict with their accepted hypothesis. This means bright, radical, young 21st century Darwins (i.e. people with brilliant ideas which unfortunately go completely against the grain of the current accepted opinion) can go disappointingly unpublished.

Against Peer review is also the fact that it is no use whatsoever at detecting major fraud. If a researcher simply makes his graphs up, realistically, a reviewer (who could be on the other side of the world) can have no idea. This was exactly what happened in the memorable of case of Hwang Woo-Suk, the (ahem) celebrated Korean researcher and his work on the cloning of human embryonic stem cells. He published his work in the high impact journal Science in two ‘landmark’ papers in 2004 and 2005. His written experimental section, conclusions and experiments appeared totally sound; it was just a shame he never actually carried any of these out.

The fact is though, Peer Review does work well in 99% of cases – believe it or not. It is an excellent way of professionalizing and shaping up a paper; stopping the authors drawing rash conclusions, or over hyping their results. Reviewers can even offer input on a particular experiment which might prove the results more conclusively and make the research more convincing. Most importantly, scientists trust Peer Review (and indeed it is this mutual trust which allows the system to work at all) – changing the system will always be met with healthy scepticism.

Finally, we should remember that as Irene Hames, editor of The Plant Journal put it recently, ‘Peer Reviewed journals are not records of absolute truth, merely records of work carried out,’ and that in science you can only ever be right until someone proves you wrong.



The solutions

Browns new framework for dishing out cash to scientists, the research excellence framework (REF) will do away with all that filthy bureaucracy in one swipe, to replace it with a statistical system. Instead of using Peer review directly, the REF will generate a bibliometric evaluation of how good each research application is using figures such as the amount of publications a researcher has achieved in the past year say, or the amount of private funding they have acquired.

Many researchers argue this statistical approach is unfair; probably much worse than Peer Review ever has been. The thinking behind this objection being that great scientists could be given a poor rating if they have taken a career break (to have children or get over an illness say) and thus haven’t published enough work that year. Early-career researchers could loose out too, if they don’t make the breakthrough they need to get published before the REF comes around.

In my opinion, we clearly need to opt for including some form of Peer Review in the new procedure - it is vital in deciding scientific merit, and avoiding unfair prejudices.

How could we make Peer Review even better, though? To stop the those radical young scientists with great ideas getting sidelined from reputable journals, some have called for the introduction of so-called double blind reviewing, in which neither the reviewer nor the author of papers know the identity of the other. This might mean prejudice against radical newcomers is minimised.

What about the price of the journals? Could we open up science to the developing world and make the whole process more transparent to boot if we adopted an open access system? This would mean all journals were freely available to view (on the internet for example), and authors themselves would have to pay to have them published. This would be a radical reform indeed, and forcing scientists to pay to be published might lead to authors simply creating blogs of their work online, which would be equally free to view, but somehow less trustworthy.

In conclusion, it appears that Churchill was right. Peer Review might not be perfect, but it is the best idea we have. Perhaps we can eventually learn to see it as what it really is; the (ever so slightly flawed) arbiter of scientific quality.

To read more about Peer Review, find out how it works and join the debate try visiting:

//www.senseaboutscience.org.uk/index.php/site/project/29/

Awful Organic?

This is an article I wrote around a year or so ago, which I sent off to 'Spark*', the University of Reading student newspaper (fortunately for me they'll publish just about anything!) I was really embarrassed with how arrogant my first draft sounded (can't believe I sent it off sounding like that...) but I've now given it a few tweaks so hopefully it sounds a lot less preachy this time around!



Awful Organic?


It seems like these days we can’t so much as walk down the street without some kind of advertisement presuming to tell us what we should and shouldn’t eat. The British public seem to be obsessed with food and as symptom of this it appears new, weird and wonderful eating disorders are appearing on an almost daily basis. My new favourite amusing, food-related condition is orthorexia; a state where sufferers are obsessed with eating only foods which they see as ‘pure’.

But what do we mean by pure? I guess different people have different definitions: Foods with a low GI, low saturated fat content, foods which include whole grains and food which is certified organic – and there are others. It’s organic food that I want to talk about in this article however because – I’m going to go ahead and say it - I think it’s (at the very best) extremely over-hyped.

Firstly, organic food is only ever organic if an accredited body, the best known being the SA (Soil Association), say it is. The SA was set up by Defra (the government department for rural affairs) and is generally well respected. One of their more recent items certified as a faux pas for organic foods though are scientifically trendy nanoparticles. Their view however is that any synthetic nanoparticles are banned whereas natural nanoparticles (such as soot, for example present in foods grown next to a power station) are deemed fine. Is it me or does this just not conjure up a picture of purity and wholesomeness? The trouble is they can pretty much create whatever list of acceptable chemicals they like and these may then be used on organic crops. The key word is always natural – as long as something is natural is can pretty much go onto organic food.

My view is that this rule of thumb seems a bit dodgy to say the least. This may make me sound like a bit of a heretic, but let me explain using an analogy! We use synthetic medicines to keep human bodies healthy and in the vast majority of cases these days we have sufficient scientific knowledge to make these medicines safe. If we were to use natural remedies to cure our ailments they would be in general not as effective. This is they key, because the same is true of plants. In general natural pesticides and fertilisers are much, much less effective than synthetic types. Don’t forget, this is not the 50s and we don’t use DDT anymore; agrochemical companies spend literally millions each year testing their products and ensuring they will do us no harm and that they are so effective that the amount needed for several hectares of lands can be quoted in grams.

With the global credit crunch and the fact that in lots of regions of the world there are clearly not enough crops to feed the population, is such a wasteful method of farming as organic really ethical? The only advantage it appears to yield is a vague warm feeling that when we pay that extra 50p for our carrots we are somehow doing the environment good and getting healthier produce. Is it worth it?

Ok, so I’ve given a pretty negative view of organic farming, and it’s true that conventional methods aren’t exactly perfect either. The fact that they create monocultures which reduce biodiversity is clearly not their most redeeming feature. And of course it takes many a long year, and lot of money and a lot of energy to take a pesticide or herbicide from conception to market, so in the process of making farming more efficient in this way we are also stamping down with a large to, frankly, enormous sized carbon footprint.

Read more about organic food and see what the Soil Association have to say for themselves at http://www.soilassociation.org/

Time for Richard Dawkins

Richard dawkins is this week, retiring from his post as Charles Simonyi (in case you're wondering, a very rich man who used to work for Microsoft) chair for the Public Understnding of Science at Oxford. What follows is therefore quite an apt article, which I wrote earlier this autmn.


Time for Richard Dawkins

Eminent and prolific, Professor Richard Dawkins has been a symbol for all that is scientific, intelligent and English for many a year now. The scientific community will wish him well this year, as he reaches the age for mandatory retirement from his post as Simonyi chair for public understanding of science at the University of Oxford.

In the aftermarth of his most recent and controversial (to say the least) book, ‘The God Delusion’ how can us lesser intellectual mortals engage with what has become known as the Oxford God debate? As I have considered this question I have begun to ask, are there some things which science - and even Richard Dawkins - will simply never be able to explain?

Firstly, it is imperative that we have a sound grasp of what it means to a scientist to explain something. For example, it is apparent that we exist in a universe with extremely complex laws of nature, intelligent life and beauty in many places. How do we explain the fact that it exists at all? What this boils down to in a scientific sense is that the existence of our universe is improbable without a cause. So any explaining theory which makes the existence more probable is initially a reasonable one. The best thing science has got at the moment is the Darwinian theory of evolution, as propounded by Dawkins in books like ‘The Blind Watchmaker’ .

The Watchmaker analogy says that something with complex inner workings such as a watch (or a human person) is so complex that it necessitates a designer; a watchmaker (or a God). The Blind Watchmaker theory, as explained so eloquently by Richard Dawkins, postulates that if the watchmaker was blind (i.e. not an intelligent being) a watch might still eventually get finished if the watchmaker (evolution) was allowed enough time to try lots of different combinations. This makes life on earth seem much more probable – in fact, given that the time period is something like one billion years I makes it almost certain – and so is a very good scientific theory.

Theologians, for the most part, accept this as good science, and most likely the truth. Where some experts disagree with Dawkins is where the universe came from in the first place. Professor Dawkins believes that something as complicated as our universe must require a cause which is at least as complicated as the universe. It can never, in his view, therefore be an explanation because it in turn requires an even more complex explanation. Was God created by a super-God and he in turn by a hyper-God?

Ex-Regius professor of Divinity at Oxford University, Keith Ward, points out in his recent work that this paradox does not really exist. Since physicists agree the Universe is composed of not merely space, but Steven Hawkin-esque ‘space-time’ then this, surely, is what God (if we suppose for a minute that there is one) must have created. If God created time, then it is clear he can not have a cause – the question, ‘what came before God then?’ has no meaning when we take time out of the equation.

The more we discover about the laws which govern our Universe the harder it becomes for us to conduct experiments to test our theories and make our observations – the switching on of the Large Hadron Collider in Geneva has had to be delayed over until after winter; unfortunately if they switched it the super conducting magnets on now they would suck enough power out of the French national grid that the French would have nothing left to heat their homes!

Realistically speaking we are beginning to reach the boundary of testable science when we deal with Bosons and quarks.

Are these the lengths we have to go to in order to get answers about cutting edge science? Let us not give up the search for understanding, but let us also be humble enough to admit that we may simply not have the capacity to make the measurements necessary to uncover the innermost secrets of the cosmos.