Curious X-shooter Antibiotics

A sneak preview of my spectroscopyNOW ezine headlines for June 1:

Bi-curious microcylinders – A team in the US has produced micrometre-wide discs and elongated rods from bi-coloured and multicoloured compartments. The composite materials could have novel applications in diagnostics, drug delivery, and a new type of display technology.

X-shooter snap the cosmos – The European Southern Observatory’s Very Large Telescope now has an X-shooter, a second-generation spectroscopic instrument that can record the entire spectrum of a celestial object in a single shot – from the ultraviolet to the near-infrared – with high sensitivity. This unique new instrument will be particularly useful for the study of distant exploding objects known as gamma-ray bursts.

Attacking antibiotics – The crystal structure of a penicillin-binding protein 1B (PBP1b) has been obtained by a team in Taiwan. The research could represent a major step forward in the development of novel antibiotics against resistant strains of bacteria.

Malaria Drug Fail

The BBC reports today that malaria has started to evolve resistance to the artemesinin family of drugs that are used as the world’s front-line defense against the most prevalent and deadly form of the disease.

Artemesinin emerged from a Chinese herbal medicine, Qinghaosu, where it was used as a fever treatment for generations. I remember writing about the earliest research in my New Scientist days and have watched the drug discovery process bring us to the point where a potent pharmaceutical could, it seemed, defeat the disease…

…no more. In Cambodia, at least, resistant strains of malaria have been spotted by two teams of scientists, working on separate clinical trials who reported disturbing evidence of reduced drug efficacy.

The BBC says researchers are blaming a weak public health system and poorly controlled drug use, as well as fake drugs, produced by international criminals, for the problem. But, the problem is not really socioeconomic at all – it’s natural selection in action. We present the disease with a changing environment and it evolves to fill the niche.

Fear of Flying

Personally, I’ve never had a problem with a fear of flying, a lot of people suffer from this often debilitating phobia though despite reassurances about road death statistics being much worse than air crashes. That said perhaps there is one aspect of flying that should be of concern – exposure to radiation from outer space, cosmic rays, in other words.

Buzzing along at high altitudes in a passenger jet exposes each passenger to a much higher dose of radiation than they would receive if they chose to travel by road, rail, or sea. Of course, the risk has to be offset with the exposure to vehicle pollution, for instance, and the much longer journey times (check-in security delays aside).

However, although we often hear about the exposure to low dose radiation air passengers receive, there is scant biomedical research looking at the effects and even then studies of the effects of cosmic rays are usually confined to before and after flight tests of aircrew, astronauts and cosmonauts.

Russian scientists at the Institute of Theoretical and Experimental Biophysics in Pushchino and the Institute of High-Energy Physics in Protvino, wanted to find out more about the chronic effects of aviation radiation and whether or not putative damage at the genetic level could be passed on to the next generation. They have now simulated the conditions of irradiation exposure during flight in mice. Their results, published this week in the aptly named International Journal of Low Radiation, make rather worrying reading.

Their simulations, which used the radiation field behind the concrete shield of the U-70 accelerator to mimic exposure during a flight at 12 or 16 km altitude, showed genetic problems in the bone marrow of offspring sired by male mice exposed to this simulated cosmic radiation. Moreover, the offspring did not have an adaptive response to the chronic, but low dose radiation.

In the last few years, new estimates of the health effects of cosmic irradiation, such as increased risk of cancer and genetic damage have shifted our perspective on radiation risks from early twentieth century hopes of a medical panacea to the idea that even low dose radiation is to be avoided at all costs.

The team points out that for someone flying 2000 hours each year, the equivalent dose of space radiation at altitude (10 to 17 km) is between 1.7 and 6 milliSieverts per day on average, amounting to a total exposure comparable to a worker in the nuclear industry or even substantially higher.

You can use this calculator to work out your likely exposure during a flight, thanks to pffli for reminding me such a tool exists on the web.

Perhaps this kind of research justifies some people’s fear of flying or more seriously maybe it gives us a reason to reduce our reliance on international air travel, which despite the possible economic costs might not be such a bad thing for the environment.

Research Blogging IconS. Zaichkina, O. Rozanova, G. Aptikaeva, A. Akhmadieva, H. Smirnova, S. Romanchenko, O. Vakhrusheva, S. Sorokina, A. Dyukina, & V. Peleshko (2009). Adaptive response and genetic instability induced in mice in vivo by low dose-rate radiation simulating high-altitude flight conditions Int. J. Low Radiation, 6 (1), 28-36

Freelance Science Writer

雷竞技官网 Science Writer – I am a freelance science writer. I’ve been plying the trade for more than a quarter of a century and have worked in most areas of science for a wide variety of outlets from daily papers, such as The Guardian and The Daily Telegraph, dozens of trade magazines in the chemical and pharmaceutical sector, countless popular science publications such as New Scientist, American Scientist, Focus, and Popular Science, and professional journals such as Science, Nature, and Proceedings of the National Academy of Sciences.

I’ve also worked for many websites, trade organisations, and various independent clients, as well as the likes of Microsoft Encarta and Dorling Kindersley, for whom I first consulted more than a decade ago and working with them as the chemistry consultant on a recent science encyclopedia with Adam Hart-Davis.

If you’re after an experienced science writer, with masses of journalistic cuttings, a portfolio stacked high with publications for a wide range of clients, and a virtual portfolio of blogs, websites, and more, stacked even higher…then please get in touch. My science writer CV can be found here, email me for a more formal resume:

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If you need to call me, email first as I am migrating from landline to 100% mobile.

My book Deceived Wisdom was published by E&T in hardback and on UK Kindle as well as other electronic formats.

Pathogen Insecurity and Bio WMD

anthraxMarc Ostfield is the Senior Advisor for Bioterrorism, Biodefense, and Health Security, US Department of State, Office of International Health and Biodefense in Washington DC and believes that the concept of biosecurity as a primary strategy to combat terrorism is nothing more than an illusion.

As a concept biosecurity, also known as pathogen security, suggests that governments can somehow assert control over terrorists who might use biological weapons, lethal pathogens, in their acts of violence against their enemies. However, virtually all pathogens exist in nature, the technology to manipulate and disseminate them is readily accessible and there are countless experts with the necessary skills to do so scattered across the globe. The anthrax attacks in the US in the wake of “9/11” are testament to this. It is odd that we have not seen further attacks of a similar nature since.

Biosecurity, says Ostfield, is essentially nothing more than a “diplomatic tool to stimulate international dialogue or scientific engagement.” It is, he adds, of only limited practical utility.

Given this state of international affairs and the enduring risk of a biological attack by a terrorist organisation, Ostfield suggests that an effective international policy strategy is needed to combat bioterrorism. Such a strategy, rather than relying on diplomatic niceties and a blinkered perspective on what is possible even with limited means, must be much wider than it has ever been.

“Foreign policy should instead emphasise enhanced biosurveillance and infectious disease early warning systems, effective and swift treatment, and strengthened preparedness and response mechanisms as the key to successful strategies to combat bioterrorism,” says Ostfield.

The fundamental flaw in assuming pathogen security can protect us from bioterrorism lies in the fact that it argues for non-proliferation of the materials and knowledge required to create a bioweapon. Unfortunately, combating biological threats is not quite as easy as tracking the whereabouts of nuclear materials, for instance, and look at how difficult that has been in the past with respect to the hunt for Weapons of Mass Destruction (WMD). Almost anyone with some life sciences training could set up a simple lab, obtain the necessary biological agents and twisted motivation, and put together a bioweapon. WMD does not have to be nuclear, bio could be just as devastating.

Foreign policy efforts must focus on greater cooperation among nations to detect outbreaks, communicate information and materials quickly and effectively, and successfully mitigate the consequences of a bioterrorism attack – with enhanced mitigation playing a crucial role in making bioterrorism a far less attractive or viable option.

When the H1N1 swine flu outbreak happened, there were huge numbers of conspiracy theorists who crawled out of the woodwork. Vast numbers of them attempted to post their nonsense on Sciencebase, but thankfully the moderators and spam filters trapped it. The most obvious reason that swine flu is not the result of a deliberate bioweapon release is that it’s not very good. A bioterrorist could create a much worse pathogen and release it into the population from within the US itself. Should that ever happen, no amount of airport screening simulations are going to preserve homeland security.

Research Blogging Icon Marc L. Ostfield (2009). Pathogen security: the illusion of security in foreign policy and biodefence Int. J. Risk Assessment and Management, 12 (2/3/4), 204-221

Light, Trials, Balls

hollow-ballIn my SpecNOW science news column this week:

C60, C80, C0, Go! – X-ray crystallography, nuclear magnetic resonance spectroscopy, and other techniques have allowed German chemists to demonstrate their synthesis of the first non-carbon analogue of the C80 fullerene molecule. And yes, the title is an allusion to the Malcolm McClaren fashion vehicle of the post-punk era, Bow Wow Wow.

雷竞技炉石传说 ynthetic disorder – An international team has used solid state NMR spectroscopy to determine the structure of the chlorophyll molecules in green bacteria that are responsible for harvesting light energy. The discovery might ultimately lead to artificial photosynthetic systems.

Clinical reflections – Clinical research studies into drug efficacy and side effects have often been laborious and time consuming, new software that analyses “anonymised” patient electronic medical records could reduce investigation times from months to minutes.

This week, The Alchemist observes evolution in the test tube in this week’s issue and ponders the notion of a plastic pancreas. The vomeronasal organ of mice reveals new chemical secrets about rotten food and sickly individuals while high-power lasers go down the tubes. Microscopic molecular balls also caught the Alchemists eye while kudos goes to soft matter pioneer George Whitesides for his winning the inaugural Dreyfus Prize in the Chemical Sciences.

Backyard Archaeology

UPDATE: While scanning the web for something wholly unrelated to this post, although connected to Cottenham, I spotted the report from the University on our test pit here. This is what they said at the time about the findings in our garden:

“A single sherd of Romano-British pottery occurred here, and is in good condition. It is the only pottery from that context, and may represent evidence of occupation during that period. The small quantities of medieval pottery show that there was activity on the site in the 12th and 13th centuries, but then it appears to have been abandoned until the 16th century. There appears to have been low-level activity there since then.”

archaeology-mini-digThis weekend we, and a dozen other properties in our village, hosted a team of archaeologists from the University of Cambridge. The team, led by Dr Carenza Lewis (well known to Time Team viewers), were intent on unearthing the secrets of the centuries locked in our gardens. So, armed with mattocks and buckets, we mucked in and set about digging out layer by layer a one cubic metre chunk of earth from various sites including our front garden.

Turf was first taken up, I say turf, our weed and moss-infested lawn is nothing to write home about. Then the first layer of top soil was hacked out and sieved through a 10mm mesh and any “finds” inspected and added to the first “context” tray. Given that our house was built in 1967 on old orchard land it was fairly unlikely that anything of particular interest would be found in that layer, our tame archaeologist and digger, Gary told us.

sherdsA small sample of soil from the first 100 mm context layer was stored in a carefully labelled plastic bag and then the next layer scooped out. Marginally more interesting fragments began to emerge as layers were peeled away under the shade of our mountain ash: obvious fragments of red brick, tiny chunks of crumbly mortar, and a few sherds of pottery, lengths of clay pipe, one or two old nail heads were found in between the tiny chunks of napped, or worked, flint. Not huge quantities but enough from the time of the founding of Cambridge University 800 years ago, the mediaeval period and before, to pique the interest and to inspire further digging.

Some oddities emerged such as “clinker” like layers of seemingly charred material that had a sooty smell and were leathery with surface markings. Dr Lewis was hard-pushed to identify these at the time. To our inexpert eyes they looked like pieces of charred leather. However, they had been sieved from around context 4 which was probably too old and deep for leather to have survived.

roman-potAs we reached towards the final green-sand, natural layer (context 7) at just over a metre deep the last sieving I did revealed a sherd that was unlikely to be mediaeval, it was turned pottery, unglazed and smooth, hinting at mass production…and perhaps dating back to the Roman Empire.

“There were some interesting finds to help identify in which parts of the village there was probably occupation in Roman, Saxon, pre- and post-black death mediaeval, and later times,” Stanford told me. “One likely conclusion on the evidence so far is that Cottenham was hit hard by the black death and then revived in the early-mid 16th century,” he added, “but not as a wealthy community. We hope that future digs will continue to help us fill out the picture.” There will be a new dig during the village’s biennial midsummer Fen Edge Family Festival.

One exciting find in a site off the High Street near the church was a piece of Saxon pottery of the kind used for funerary urns, It is extremely rare, according to pottery expert Paul Blinkhorn.

Our finds, and those from the other sites in Cottenham carrying out a mini dig (all organised by John Stanford of the Fen Edge Archaeology Group) are now with the experts back at Cambridge, and we’re hoping to hear great things as they dig out nuggets of information about the distant past of this small settlement on the edge of the Cambridgeshire fens.

“A single sherd of Romano-British pottery occurred here (our test pit, TP14), and is in good condition,” says Paul Blinkhorn in his report on the mini dig, “It is the only pottery from that context, and may represent evidence of occupation during that period. The small quantities of medieval pottery show that there was activity on the site in the 12th and 13th centuries, but then it appears to have been abandoned until the 16th century. There appears to have been low-level activity there since then.”

Heavy Metal Packaging

Researchers in Argentina have developed a new approach to testing food packaging for trace amounts of the toxic heavy metal cadmium.

Cadmium is one of several additives used extensively in the manufacture of plastics. Regulations limit the concentration of cadmium allowable, of course. In the European Union that limit is 100 milligrams per kilogram. But, the toxic metal has a long biological half-life (10 to 30 years) and so essentially accumulates in your body on repeated exposure.

Analytical advances aside, I asked Rodolfo Wuilloud of LISAMEN, how big a problem is cadmium in food packaging? Should the public be concerned?

“The presence of heavy metals in plastic food packaging is an important problem considering the extended use of this type of packaging,” he told me, “Concentration of heavy metals should be limited in order to reduce their potential health impact resulting from their possible migration from the packaging material into food and also to ensure that such substances are not released into the environment, for example in emissions or ash when packaging is incinerated, or in leachate when packaging is landfilled.”

He adds, that it is important that the public should be aware of this problem. Concern is the first step towards getting governments to change environmental policies. “It is necessary to introduce national measures to ensure that packaging is allowed on the market only if it complies with certain requirements in their composition so as to prevent the addition of noxious heavy metals to packaging and to reduce the impacts on the environment and human health,” Wuilloud’s colleague Estefania Martinis says.

The team used room temperature ionic liquids (RTILs) as an online pre-concentration medium for flame atomic absorption spectrometry analysis of trace cadmium in plastic food packaging materials. Critically, the use of non-volatile, non-flammable RTILs instead of volatile and flammable organic solvents is helping in this regard by allowing analytical scientists to breathe new life into powerful techniques, such as atomic absorption spectroscopy, that have been labelled “old fashioned” in recent years as other methods emerged.

Research Blogging IconMartinis, E., Olsina, R., Altamirano, J., & Wuilloud, R. (2009). On-line ionic liquid-based preconcentration system coupled to flame atomic absorption spectrometry for trace cadmium determination in plastic food packaging materials Talanta, 78 (3), 857-862 DOI: 10.1016/j.talanta.2008.12.051

Mercury, Climate Change, Cosmos

Fire and Ice, Global Warming
Mercury seals, ancient climate change, and even older microwaves, all feature in my Spotlight column over on Intute, this month.

Mercury seals – The Polar Bear has often been given the role of proverbial environmental canary, coming to prominence in the movie An Inconvenient Truth by former US Vice President Al Gore. But, researchers in Canada have now reported for the first time how high levels of the toxic metal mercury present in certain Arctic seals could also be an indicator of the effects of climate change, hinting at how vanishing sea ice caused by rising temperatures may be to blame. The study provides new insights into the impact of climate change on Arctic marine life.

Global thermostat – Could increased chemical weathering of rocks by rivers increase the absorption of carbon dioxide from the atmosphere and so regulate the planet’s temperature? Ocean chemistry is affected by the chemical breakdown of continental rocks by rain and ground water, according to UK scientists. Their research published in Nature points to how climate change affects this breakdown and could have important implications for understanding Earth’s history.

13.73 Billion years BCE – Science doesn’t have a lot to say about what happened before the Big Bang, but researchers have now developed microwave detectors that will let them take a look at the first trillionth of a trillionth of a trillionth of a second after that primordial cosmic event.

Slumdog Engineer

Having discussed the possible environmental risks of charitable aid in the form of obsolete electronic goods to the developing world, it seemed to timely to mention other research looking into strong solutions to some of the critical problems facing people in many parts of the world.

Researchers, Priti Parikh and Allan McRobie, in Cambridge, England, suggest that the current cocktail of approaches used to address poverty in the slums often stretches scarce resource too far. Interventions in health, education, physical improvements, and governance often cement in place the “poverty” mindset and set the slums apart from the urban infrastructure by using minimal paving, having public water posts and community latrines.

These two engineers have researched an alternative approach known as Slum Networking, which was pioneered by Himanshu Parikh. This approach is holistic and proposes comprehensive water and environmental sanitation infrastructure as being central to improving the slums not by locking them into disadvantaged islands of deprivation but by assimilating them into a city’s high-quality urban infrastructure.

Slum networking avoids the resource bottleneck and gets over the significant barriers people face when they are given the label “poor” and simply offered “aid”. Some facts about people:

  • More than a billion people worldwide have no access to an improved water source
  • 2.5 billion do not have access to improved sanitation
  • Almost 2.5 billion of the people without improved sanitation are among those hardest to reach: families living in remote rural areas and urban slums, refugees and those trapped by poverty and disease.
  • Of the 1.1 billion people with no access to an improved water source, 42% live in Sub-Saharan Africa
  • In South Asia, fewer than four out of every ten people has access to improved sanitation.
  • UNICEF/WHO in their 2004 report explain that without rapid improvements half a billion people will never see improved sanitation.

The researchers have examined how slum networking was implemented in Sanjaynagar in Ahmedabad, India, and compared it with a similar settlement that had none of these interventions in another part of the city. The success of slum networking suggests that it might be used more widely and in other parts of the world.

Moreover, the paradigm shift in thinking about poverty that it suggests, which in essence recognises people as people regardless of their wealth, or lack of it, could serve as model to improving the lot of millions of people across the globe regardless of whether or not their domicile has been given the tag of “slum”.

The team describes how their study validates the technical approach of slum networking and shows enormous community benefits. “Our study proves that physical infrastructure rapidly alleviates poverty with tangible improvements in health, education, disposable incomes and quality of life,” the researchers explain. “It shows that huge investment multipliers have been achieved as a result of infrastructure development and the partnerships. The key reported reason for community investments is the provision of individual facilities at low costs.”

Parikh studied engineering in India and worked there as a development engineer on slum improvement projects and as a volunteer after the 2001 Gujarat earthquake. She has now completed her PhD focusing on water and environmental sanitation in slums in India and South Africa under McRobie’s supervision in the Department of Engineering at Cambridge.

Research Blogging IconParikh, P., & McRobie, A. (2009). Engineering as a tool for improving human habitat International Journal of Management and Decision Making, 10 (3/4) DOI: 10.1504/IJMDM.2009.024993