Monthly Archives: December 2009

Clive Cookson

Thanks for reading the science blog this year. Apart from a couple of days in the office between Christmas and New Year, I’m away until January 11, so the blog should start up properly again that week.

By Joseph Milton, FT science intern

Iain Darbyshire, a Kew Gardens botanist, recently identified a new plant species while walking through the garden’s glasshouses. The news of his chance discovery, and of the other new species found by Kew botanists this year, reminded me of my own plant collecting expeditions, part of a PhD in evolutionary botany, which took me across southern Africa.

After weeks tackling the bureaucracy of obtaining permits to collect plant specimens – many countries are understandably cautious about allowing foreigners to remove their flora – the slightly odd adventure that is plant collecting began.

I travelled widely in South Africa in a tiny VW Chico (picture a no-frills Polo circa 1990) taking in the three Cape Provinces and also visiting Namibia in a search for exotic groundsel species. The aim was to reclassify them based on their DNA.

Gardeners in the UK may be familiar with (and not entirely keen on) groundsels, but most will be unaware that they belong to one of the largest and most diverse plant genera, ranging from the familiar diminutive weeds to small trees. Southern Africa alone contains somewhere between 350 and 500 species, many unique to the area, and all scientifically neglected since the 19th Century.

Based in Cape Town, I drove east along the Garden Route as far as East London, and to Springbok in the terracotta-red, sun-baked north. The search found me combing beaches, scrambling up mountains and strolling through forests and heathlands – highlighting the ecological diversity both of groundsels and of South Africa. In Namibia, scouring the desert along the Skeleton Coast yielded a little known succulent species, kept alive by coastal mist.

A peculiarity of looking for plants is the need to spend a disproportionate amount of time staring at the ground just ahead, but this makes the view even more breathtaking when you do happen to look up. In Namibia, the vast barren landscapes are something to behold (left). Even in my native Scotland, I have never seen such wide, open expanses without signs of human habitation.

Concentrating on the ground also means there is a danger of stumbling into unsuspecting wild animals. A small wildcat was the worst I encountered, but it was enough to make me sing as I walked alone in the wilderness, in the hope of scaring off anything more threatening before I encountered it face to face.

Evenings were spent in cheap hostels – one an ex-apartheid era jail, another an ex-mental hospital – pressing collected specimens and cataloguing the day’s finds, followed by a well-earned beer or two with my PhD supervisor and sometime travelling companion, Professor Richard Abbott.

Southern Africa is a fascinating area to visit. Namibia, which was German South West Africa until 1915, is an odd and sometimes uncomfortable mix of traditional Africa and colonial era Germany.

In South Africa, although witnessing overt racism from the white community was not uncommon and the spectre of HIV/AIDS was ever present, there was a lingering feeling of hope for the future and a sense that things were better, and fairer, than they had ever been.

Although I successfully collected many species of interest in southern Africa, I wasn’t fortunate enough to find any that were new to science. Perhaps I should have just gone to Kew instead, but I’m glad I didn’t.

By Joseph Milton, FT science intern

Members of the public, environmentalists, scientists and businessmen will be asked for their opinions on new types of biofuels as part of a consultation launched today by an independent body that examines the ethics of biology and medicine.

Just a few years ago, biofuels were being trumpeted as a possible panacea for global warming – here was a green, renewable and sustainable source of power. And biofuels would not just help to mitigate climate change, they would offer energy security and aid agriculture and economies in the developing world. But these hopes were dashed as the darker side of the first generation of biofuels was revealed.

Land grabs and deforestation increased in some countries as the rich and powerful saw a chance to make a quick buck. Vast swathes of once biologically rich forest were replaced with palm monocultures and large numbers of people were displaced to make way for plantations.

Biofuels were also produced from food crops, contributing to the food-price spike of 2008, which in turn led to food riots in poorer countries. Mexican unrest was directly related to US maize farmers who turned from food to biofuel production, encouraged by large government subsidies.

So first generation biofuels are at best ethically dubious and, at worst, ethically atrocious, but the rehabilitation of biofuels is beginning.

The prospect of a second generation of biofuels, derived from waste materials rather than food crops or palm oil, has recently been raised. It is this new generation which the consultation by the Nuffield Council on Bioethics aims to explore.

Second generation biofuel production is likely to be based on a range of technologies under development – from harvesting oils produced by seaweed to collecting ethanol produced from food waste by genetically modified bacteria.

There are plans to use waste wood and the fibrous, inedible parts of crops to produce fuel, and genetically modify fuel-specific crops to increase yields and introduce tolerance of high salinity and drought – allowing growth on land unsuitable for agriculture.

The team at Nuffield think these methods could cut greenhouse gas emissions by 80-90 per cent compared with fossil fuels, and hope biofuel production will present opportunities for income generation in developing countries, without affecting food supplies or contributing to deforestation.

They hope to gather a wide range of opinions on issues ranging from intellectual property rights for GM, which tends to be controlled by big agri-business because of the development costs, to the rights of farmers and workers in the developing world. Those wishing to participate in the consultation can do so online.

When the consultation is complete, late next year, the council will develop a set of ethical guidelines to advise government.

However, developing the new generation of biofuels will not be cheap. With the world unsure where it stands in terms of emission targets after the disappointment that was COP15, that investment may have just become harder to find.

Once again, hopes are high for biofuels. Let’s hope the investment is forthcoming, and this time the optimism is justified.

By Joseph Milton, FT science intern

The “discovery” of dark matter – the hypothetical, undetectable substance thought to make up around a quarter of the contents of the universe and the majority of the matter in it – has been covered in some newspapers and websites today.

But, while the confirmation of dark matter’s existence would certainly be big news, the media may be over-egging this discovery.

Thought to provide a kind of “gravitational scaffolding” which supports normal matter, dark matter has eluded detection since its existence was first posited by Fritz Zwicky in 1933.

Since 2003 a team of US scientists has been deep underground in the disused Soudan mine, northern Minnesota, working on the Cryogenic Dark Matter Search (CDMS).

Using a bank of 30 detectors made of germanium and silicon, cooled to temperatures very near absolute zero (−273 degrees Celsius), they have been looking for energy signatures indicative of dark matter.

A cryostat (cooled detector chamber) with detector assembly installed at Soudan Mine

A cryostat (cooled detector chamber) with detector assembly installed at Soudan Mine

Physicists think dark matter could be composed of weakly interacting massive particles, or WIMPs for short. In theory, these particles don’t absorb or emit light and have a mass similar to that of an atomic nucleus.

Scientists think WIMPs may occasionally “bounce off” atomic nuclei, leaving behind an energy trace – the signature the scientists have been looking for.

The CDMS team announced yesterday evening that they had detected two events, or energy signatures, consistent with WIMPs “bouncing off” nuclei.

But Pierre Oddone, director of the Department of Energy’s Fermi National Accelerator Lab (Fermilab) near Chicago, stressed that he could not be sure that what they had detected was the signature of dark matter.

“While this result is consistent with dark matter, it is also consistent with backgrounds,” he said, suggesting that both signatures could have been caused by natural radiation, or by cosmic rays from space.

The rationale behind placing the detectors half a mile underground under layers of shielding materials is to suppress such unwanted interference, but these background events are still periodically detected.

During a seminar at Fermilab, Dan Bauer, head of the CDMS, said there was a one in four chance that the detected signatures were background events, and a later statement from the team reiterated that “we can make no claim to have discovered WIMPs.”

What they have discovered is that the frequency of interactions between the elusive WIMPs and atomic nuclei – the “bouncing” events which leave the energy signatures and which the scientists are looking for – may be lower than was previously thought, as theoretically predicted by the mass of WIMPs. To confuse matters further, assumptions about the mass of WIMPs are also theoretical calculations.

These experiments gave the scientists a more accurate estimate of the frequency of such interactions, and the researchers said they might therefore be useful in eliminating a number of other competing theories which attempt to explain dark matter.

They went on to say that they would have to detect at least five events to be sure they were looking at dark matter signatures. To try and achieve this the team will upgrade their detectors next year and continue the search for WIMPs.

It seems the scientists have been considerably more cautious in their statements about the significance of these results than some journalists – quelle surprise.

By Joseph Milton, FT science intern

The successful mapping of two cancer genomes has enabled scientists to track the genetic evolution of skin and lung tumours for the first time, providing a catalogue of all the mutations invloved in the cancers. It has been hailed as a breakthrough which could revolutionise treatment and testing for these cancers.

The genomic maps of lung cancer and melanoma, a skin cancer, produced by researchers at the Wellcome Trust Sanger Institute in Cambridgeshire and published in Nature this week, track the DNA mutations that have accumulated in diseased cells through the course of the patients’ lives, revealing the histories of the cancers as they developed in the patients.

Mike Stratton, who led the melanoma study said: ”It’s like doing archaeological excavation. You’ve got traces and imprints of all these processes that have been operative for decades before the cancer arose.”

The researchers were able to trace the replication of every error found in the genome – from a healthy, pristine cell in the embryo, through naturally occurring mutations happening in the body during growth, to cancerous cells, severely damaged by cigarette smoke and ultraviolet light.

In the melanoma patient, tumour cells exposed to sunlight showed a very high proportion of a particular type of mutation, a kind of “signature” of UV damage. But as the cancer developed inside the patient’s body, shielded from exposure to sunlight, the proportion of these UV “signatures” started to decrease.

The scientists found more than 23,000 DNA mutations in the cancerous cells of a 55 year old smoker, and more than 33,000 in cells of a malignant melanoma sampled from a 45 year old man. Most of these mutations are harmless but occassionally a damaging mutation will occur in an important gene, leading to cancer.

The teams also found evidence of DNA repair mechanisms – cells fighting back against the cancer. They could tell this was taking place becuase many more mutations were seen in non-functional areas of DNA between genes than were found in active genes, suggesting that repair mechanisms prioritise important functional areas of DNA over non-functional regions.

The project has been lauded in the press, including in this paper, as the first time cancer genomes have been sequenced in full.

But this is not the first time that cancer development has been tracked by sequencing the genome, then looking at the progression and patterns of DNA mutations. In October Canadian scientists at the BC Cancer Research Centre, Vancouver, led by Samuel Aparicio, published a paper in Nature looking at the history of mutation in breast cancer genomes.

By Joseph Milton, FT science intern

Lord Drayson, science minister, may consider restructuring one of the government’s largest science and technology funding agencies after it was forced to withdraw 25 per cent of its studentships and fellowships following budget cuts.

In 2010-11 the Science and Technology Facilities Council (STFC) will have to survive on £20m less than the current year’s budget, and it has also been hit hard by currency fluctuations.

The devaluation of the pound has meant that subscriptions to international organisations, such as the European Organization for Nuclear Research (CERN) and the European Southern Observatory (ESO), account for a much larger proportion of the STFC’s budget for next year – around 50 per cent of the total. But the council feels that membership of these organisations is worth the money spent.

The results for other areas funded by the STFC will include the 25 per cent cut in funding for researchers, and the end of a number of science projects based in the UK.

Nuclear physics was hit particularly hard, but astronomy, particle physics and space science will also have to absorb cuts. The STFC proposed “managed withdrawals” from a number of existing scientific ventures.

Scientists were dismayed by the news. Paddy Regan, a nuclear physicist at the University of Surrey, said the cuts “have the potential to kill off the UK skills base in nuclear physics…To have this at a time when the UK is discussing a nuclear new build programme… is almost comical.”

The STFC is a strangely structured beast. It was formed in 2007 through a merger of two other research councils which dealt with particle physics and astronomy, and also took responsibility for nuclear physics from a third council.

It is responsible for funding research students and fellows in these areas, as well as maintaining UK scientific facilities such as ISIS – a pulsed neutron and muon source – and the Central Laser Facility, both in Oxfordshire, and for paying subscription charges for memberships of international organisations.

Because the value of the pound is completely beyond the control of the council, and because it is understandably keen to retain membership of international organisations, devaluation will inevitably lead to the areas it can control, such as studentships, losing out disproportionately.

Lord Drayson said that he was keen to find a way round the cuts in a press release issued today in response to the STFC budget announcements, but he is very unlikely to be able to come up with any more money.

Instead he seems to be proposing a restructuring: “There are real tensions in having international science projects, large scientific facilities and UK grant giving roles within a single research council,” he says, and adds, “I will work urgently with the STFC and the wider research community to find a better solution by the end of February 2010.”

That suggests that the STFC’s days, at least in its current form, may be numbered.

By Joseph Milton, FT science intern

Simulations run by a team at the University of Bristol suggest that the melting of the Greenland ice sheet could be prevented by reflecting sunlight from the earth’s surface, a geoengineering technique.

Geoengineering offers radical solutions to climate change, involving large-scale alterations to the environment, directly affecting the climate. Discussion of these potentially risky procedures is increasingly common as many scientists reach the conclusion that CO2 emission reduction targets are not being met, and are unlikely to be. The Royal Society recently invited a panel of scientists to look into the subject and produce a report: Geoengineering the climate: science, governance and uncertainty.

The research at Bristol, led by Peter Irvine and published today in Environmental Research Letters, found that the temperature of the planet could be reduced to pre-industrial levels, saving the ice sheet, by reflecting 4.2 per cent of incident sunlight back into space.

But reflecting such a high percentage of sunlight, while doing nothing to reduce atmospheric CO2 levels, could reduce rainfall and change weather patterns, so the team also investigated reflecting 2.5 per cent of sunlight. They found this reduced the undesired side effects, but still cooled the planet enough to avoid the collapse of the ice sheet.

The Bristol team suggest sunlight could be deflected using geoengineering techniques known as solar radiation management. One option is the use of space reflectors – trillions of tiny reflective particles at the Lagrange point, the point in space at which the Earth and the Sun’s gravitational fields cancel each other out.

Professor Peter Cox at the University of Reading, who worked on the Royal Society report, says it might work: “It would be like just turning the sun down a bit.” But obviously there are technical considerations. As Professor Joanna Haigh of Imperial College, another of the report’s authors, points out: “The costs and the timescales involved would be absolutely enormous.” Neither thinks this technique is feasible in the near future.

Another option suggested by the Bristol team involves the addition of sulphate particles to the atmosphere, where they would reflect solar radiation. Prof. Cox says this is more difficult to rule out than he had imagined before the report was written, but Prof. Haigh is less convinced: “Who knows what the knock-on effects would be?” she says.

Solar radiation management is one of two broad categories of geoengineering techniques. The second is carbon dioxide removal, recently suggested as a possible complement to mitigation actions by Rajendra Pachauri, head of the Intergovernmental Panel on Climate Change.

Removing CO2 from the atmosphere would be a better long-term solution to global warming, as it would tackle not just global temperatures but other problems associated with high levels of greenhouse gases too, such as ocean acidification. But it would be very slow to affect the climate. On the other hand, the effects of reflecting sunlight could be seen within a few years.

Peter Irvine stressed that geoengineering should only be regarded as an emergency response: “It is no substitute for reductions in the emission of CO2,” he said.

Clive Cookson

I did my bit for biomedical research last night, spending a couple of hours as a participant in the UK Biobank project.

I was one of 400,000 middle-aged people who have undergone a long battery of mental, psychological and physical tests – and given blood, urine and saliva samples – in the cause of helping scientists to disentangle the links between genes, lifestyle, health and disease.

Biobank, with £60m funding from the UK government and Wellcome Trust, is building one of the world’s most ambitious medical/genetic databases.

Several weeks ago I was offered and accepted an appointment at 5.20pm on Saturday at Biobank’s Hounslow assessment centre (about half an hour’s drive from home). I received a well-written information leaflet, which emphasised the voluntary nature of the project and the participant’s right to withdraw at any point, followed by reminders of the appointment by post, email and text message.

So I arrived promptly for the assessment on the third floor of a modern suburban office block – a large open space with colour-coded booths round the edge.

After I’d checked in and confirmed again that I was happy to take part, the receptionist took me to a computer terminal where I completed a very detailed questionnaire about my lifestyle, from the number of pieces of dried fruit I ate per week to my consumption of various drinks, from my exercise habits to sex partners of the same and opposite gender. How long had I used a mobile phone and against which ear did I normally hold it? There was lots too about my mood, social and family contacts, and so on.

Then came computer tests of my reactions (how quickly could a press the button when two identical cards flashed on the screen?) and memory (could I remember patterns?). My hearing in each ear was probed at length, as I had to make out digits spoken at different volumes and against various background noises.

After the computer I was moved successively from one booth to another, where Biobank staff undertook various physical investigations, including size and shape, strength, bone density, lung function and eyesight. Finally after a phlebotomist had extracted seven tubes of my blood, I was sent to the gents to give a urine and a saliva sample, which I deposited in the centre’s fridge.

Participants leave with a basic one-page print-out of a few of their results. I was not surprised to find that my body-mass index was too high or my waise circumference “borderline”, though it was reassuring that my lung function was good and my bone normal.

But of course the individual’s assessment is not the point of the exercise. It is to play a tiny part in a vast research exercise that should benefit future generations.

By Joseph Milton, FT science intern

Some spectacular images have been captured by a new British-built telescope at the European Southern Observatory‘s (ESO) Paranal Observatory in the Atacama Desert, Chile.

They are the first pictures from the Visible and Infrared Survey Telescope for Astronomy (VISTA), the world’s largest survey telescope, which detects infrared wavelengths, revealing a novel view of the southern sky. VISTA should add to our understanding of the nature, distribution and origin of stars and galaxies, and may help determine the nature of Dark Matter and Dark Energy.

The £37m telescope was conceived, designed and built by a consortium of 18 UK universities, project-managed by the Science and Technology Facilities Council’s UK Astronomy Technology Centre (STFC UKATC), then given to the ESO. Britain joined the organisation in 2002, and was not a member at its 1962 inception. Now we pay a subscription and have given them VISTA as part of an accession agreement, strengthening links between the UK and the ESO.

It is certainly an impressive piece of kit – the main mirror is 4.1 metres in diameter and deviates from a perfect surface by no more than a few thousandths of the thickness of a human hair. It is the most highly curved mirror of this size and quality ever made.

At the heart of VISTA is a 3-tonne infrared camera with 16 sensors, totalling 67 million pixels, allowing VISTA to view objects too cool to be viewed by visible light, hidden behind dust clouds or so far away that the expansion of the Universe has stretched their light beyond the visible range. Because infrared radiation coming from space is very faint, the camera must be kept at a temperature of -200 degrees Celsius and is sealed with the largest infrared-transparent window ever made.

VISTA can detect faint sources and also cover wide areas of sky quickly, so it will be able to detect and catalogue objects over the whole southern sky with unprecedented sensitivity. The jump in observational power it represents is equivalent to changing from the naked eye to Galileo’s first telescope.

The Flame Nebula (NGC 2024), a spectacular star-forming cloud of gas and dust in the constellation of Orion.

The Flame Nebula (NGC 2024), a spectacular star-forming cloud of gas and dust in the constellation of Orion. Without VISTA’s infrared sensors, this image would be obscured by thick dust clouds.

Clive Cookson

Lord Drayson, UK science minister, has announced another step toward giving Britain its much needed national space agency.

He says the “bureaucracy busting” body will replace the existing British National Space Centre, which coordinates the activities of nine government departments and agencies but has no power of its own.

Government spending on space – around £270m a year, much less per capita than other advanced industrial nations – will not increase.

But Drayson says the unified agency will increase Britain’s clout in international negotiations. “I and my predecessors have had to negotiate with our hands tied behind our back,” he told me.

It will also support the country’s growing space and satellite industry, which contributes £6.5bn a year to the UK economy and supports 68,000 jobs

The location and name of the new agency will be decided in the new year. Candidate names include British Aeronautics and Space Agency (Basa) and Her Majesty’s Space Agency.

Another significant event for the sector is the publication today of a government-commissioned review of Britain’s future options for space exploration.

The review concludes that the best option would be for Britain to end its long refusal to engage with manned space projects. By spending just £100m a year more than it does today, the government could take part in international projects to send people back to the moon and, possibly, on to Mars.

The returns for both science and innovation would greatly outweigh the additional public expenditure, according to the review panel.

Sadly, however, Drayson says “the broader economic climate means we’re not in a position to change our current approach to investment in space exploration.” But there is hope for the future…

The world of research

The science blog is no longer updated but it remains open as an archive.

Clive Cookson, the FT's science editor, picks out the research that everyone should know about, in fields from astronomy to zoology. He also discusses key policy issues, from R&D funding to science education. He'll cover the weird and wonderful, as well as the serious side of science.

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