DNA search, iPhone chemistry, electronic waste

Latest bookmarked science news, including my current Alchemist column on ChemWeb.com:

  • How to build a better DNA search engine – The techniques for indexing Chinese language websites could dramatically improve the speed of bioinformatic searches, according to research by SOSO, the third largest Chinese search engine
  • The chemistry of an iPhone – Steve Jobs responds to conflict minerals accusations, but might not mass spectrometry reveal the truth?
  • Two angles in that PNAS report that says climate-is-changing crowd bigger, better than nay-sayers – On which side of the climate cred camp do you sit?
  • Chemistry news on ChemWeb.com – in this week's issue of The Alchemist, resurrecting an old clotting drug could save tens of thousands of lives across the globe, a new strain of yeast can brew up second generation biofuel from agricultural and forestry waste-streams, while bringing order to polymers using metal templates might bring us organic graphite for nano-electronics applications. In bottom-up research, supramolecular chemistry proves itself under the tunneling microscope, while palm-sized magnets could give a boost to spectroscopy in the field. Finally, a Nobel chemist receives the ACS's most prestigious award.
  • Dell takes steps to tackle electronic waste in India – Dell says it is working with Indian trade association MAIT to start dealing properly with toxic technology waste in India.

10 Herbal remedies, cohosh or tosh?

Is there any significant evidence that any of the following herbal remedies actually work in treating the conditions with which they’re associated?

Aloe vera for treating minor burns, including sunburn – 2009 review concludes: “some promising results with the use of aloe vera for diverse dermatologic conditions, clinical effectiveness of oral and topical aloe vera is not sufficiently and meticulously explored as yet.”

Black cohosh for reducing menopause symptoms – UK NHS clinical knowledge database states: “There is no good evidence that phytoestrogens, black cohosh, evening primrose oil, dong quai, ginkgo biloba, or ginseng are effective for treating menopausal symptoms.”

Boswellia (frankincense) for coping with arthritis and joint pain: NHS Choices says about the study of this substance: “One trial is rarely conclusive; more data are needed.”

Cranberry for cystitis and urinary-tract infections: Science-based Pharmacy has this to say after reviewing the literature: “When it comes to alternative medicine for urinary tract infections, there’s not much use in cranberry juice.”

Echinacea for influenza and cold prevention: The British Medical Journal reports that evidence of moderate quality obtained so far would suggest that, “Compared with placebo We don’t know whether echinacea is more effective at reducing the duration of symptoms of the common cold.”

Evening primrose oil for reducing cholesterol levels: Attract Wales (a UK NHS site that answers health questions) states: “We found very few studies in humans examining the effects of evening primrose oil on lipids. Those that were found were small and contained possible confounding factors.”

Feverfew for preventing migraines: A Cochrane Review says, “There is insufficient evidence from randomised, double-blind trials to suggest an effect of feverfew over and above placebo for preventing migraine.”

Flaxseed for treating the bone condition osteoporosis:

Ginkgo for Alzheimer’s and improving mental acuity: NHS Choices reports that a recent study suggests that, “Ginkgo biloba does not improve cognitive function in people with mild—to-moderate dementia.”

Papaya for herniated spinal disks: An enzyme extracted from papaya fruit can be injected into herniated disks to dissolve the gelatinous tissue and so reduce protruberant swelling (Time magazine report), this does not imply that eating papaya will be of benefit as enzymes are proteins and are broken down by the digestive system.

UPDATE: 8th July 2010

This item has come in for some criticism from “MyQute” regarding my “attack” on “natural” “foods”. I’ve used inverted commas around those words because I disagree vehemently with their use in this discussion. Anyway, here are my responses to the attack:

First, they’re not “foods”, foods are eaten for nutritional purposes, these are meant to have medicinal effects.

Secondly, the majority are not “natural” they’re produced in manufacturing plants and sold in stores, there’s nothing natural about the processes involved.

Third, I did not simply use NHS references, check each link you’ll see.

Fourth, everything on the NHS website is vetted by medical professionals with no vested interest in the issues other than in the sense that they would rather not see people waste their money on products that may have a detrimental effect.

Fifth, the references I cite round up data from various sources, such as Cochrane Reviews and are not to single studies, they each generally weigh up all the available evidence and that points to most of these products as having little or no benefit in the claimed conditions.

Watery calendar girls draw chemical structures

A few more science stories that caught my eye this week

  • FieldView – Cresset Group – Free download release of FieldView, a new molecular viewer/editor that is designed to show molecules with their associated field patterns and physicochemical properties.
  • Watery no-man’s land – Physical chemists know water to exist in 15 distinct phases, now research by Valeria Molinero and co-workers, University of Utah, USA, shows that at 180 K ice and liquid can coexist after water crystallizes.
  • The Living Matrix: a movie promoting energy medicine beliefs – Classic bit of BS shredding. Apparently, "The heart is a functional brain. It may be the master organ for imprinting information into the holographic body field." Yeah, right
  • Two suns – Will Aderoid approach the earth to within a few dozen million miles? Of course not…
  • Over exposed calendar girl – X-rayed and X-rated, hot pin-up calendar girl is a serious case of over exposure. Eizo's calendar leaves no body part covered…
  • Novel air-conditioner cuts cost and carbon – By eradicating the mechanics common in today's air-conditioning units, the NREL believes we could cut summertime electricity bills significantly on those parts of the world where A/C is considered an essential luxury. 90% savings suggestedq

Hot science for flaming June

  • Low-temperature fraud detection – A low-temperature plasma probe can identify art fraud without damaging the artwork, which is important should the work turn out to be genuine.
  • Flat-packed particles – Graphene is a material comprising sheets of carbon just one atom thick; graphene is like a single layer of graphite. However, it was the discovery that it has some peculiar electronic properties because of the existence of massless quasiparticles that has led to an explosion of interest in this material. Some researchers suggest that ultimately it will become the material that gives us a post-silicon world in computing.
  • Yet another supernova – Just when you’d given up hope of another starburst, a third type comes along unannounced! This third class of previously unidentified supernova could help explain some anomalous observations in the night sky and even how our bodies come to contain so much calcium.
  • Skin cancer – Burning questions about malignant melanoma are more than skin deep
  • Water calculator – How much water does your household use each year, how big is the carbon footprint for that usage, what savings could you make?
  • Natural Health, Placebos and Gibberish – Great bit of skeptical vandalism in the name of science and rationalism from Dr Dean Burnett. Spot the difference!

4 tips for a healthy barbecue

The BBC weather team promise us a barbecue summer almost every year, and although we do get the occasional patch of warmth, it’s never quite as sunny and warm in the days and balmy and calm in the evenings as it is in the US or Australia where the BBQ expert is truly the culinary ruler in the summer months.

So, it’s no surprise that the American Chemical Society is offering tips on how to avoid some of the health pitfalls of barbecued food and revealing a little about the inner chemistry.

Fundamentally, there are four golden rules for a healthy and tasty barbecue, according to food chemist Sara Risch and author Shirley Corriher:

  • Don’t over-cook meat. Excessive browning or charring can produce cancer-causing chemicals, carcinogens.
  • Pre-boil fatty items such as ribs. It removes fat and reduces flaming, which will burn the meat.
  • Marinate meat before grilling for improved flavour and to cut down on flaming and burning.

There should be a fourth tip: don’t eat and drink to excess on barbecue days and don’t barbecue too often.

Related barby stuff

  • Barbecued Pork Ribs Recipe
  • Barbecue that’s good for you (yes, with the meat)
  • N.B. grillers share barbecue safety tips
  • Recipe: Barbecued Pork Tenderloin

The push and pull of third world drugs

Diseases can be classified as Type I (those that are incident in both rich and poor countries); Type II (those that are incident in both rich and poor countries but with a substantial proportion in poor countries, for example tuberculosis [and malaria]) and Type III (those that are overwhelmingly or exclusively incident in poor countries, for example, African trypanosomiasis [and leishmaniasis and Chagas’ diseases]). Type II diseases are often termed as neglected diseases and Type III as very neglected diseases.

-— Public Health Innovation and Intellectual Property Rights, Report of the Commission on Intellectual property Rights, Innovation and Public Health, World Health Organization, Geneva. CIPIH, 2006, p 25.

It is these demarcation lines drawn between the three “types” of diseases that has, in many ways, led to disease in what we used to call the Third World to be all-but ignored except in terms of media lamentation. One might suggest that the phrase “developing world” paints too rosy politically correct a picture despite serious poverty, malnutrition, and disease. Indeed, it’s almost as if labelling diseases in this way resurrects the old First, Second, and Third World ethos, although some observers point out that people in the pharma industry don’t actually use the terms Type I, II, and III.

Despite the introduction of stronger patent protection in India in the wake of the World Trade Organization’s TRIPS (Trade Related Aspect of Intellectual Property Rights) agreement, the pharma multinationals are not addressing Type III diseases. Even so-called compulsory licensing (a euphemism that gives “authorisation to a government or company to make and sell a pharmaceutical drug without the permission of the patent holder”, has not seen disease in India, China, Brazil and elsewhere challenged in any serious way.

Writing in IJTG, Sudip Chaudhuri of the Indian Institute of Management Calcutta, in Kolkata, West Bengal, India, suggests that a policy shift that more openly encourages partnerships between public and private sector is now needed, and the same approach might be adopted in Brazil and China, too.

In general, multinational corporations do not find diseases in poor nations attractive enough for research and development (R&D) investment. The markets are enormous, but there is not enough hard cash circulating to provide a big enough return on investment to keep shareholders happy. Some companies, AstraZeneca and GlaxoSmithKline, among them, have realised that drugs must be developed for neglected diseases regardless, while there has definitely been a perceptible increase in R&D driven by not-for-profit organisations and foundations such as the Drugs for Neglected Diseases Initiative, Medicines for Malaria Venture (MMV). Regarding India in particular, GSK’s donation program for lymphatic filariasis is having a great impact. And also in India, Merck announced a new partnership (The MSD Wellcome Trust Hilleman Laboratories) that is not only based in India, but will address developing world needs from there.

Nevertheless, it’s a never-ending battle and more needs to be done. The G-FINDER survey, funded by the Bill and Melinda Gates Foundation, highlights how much various people and organisations are investing in neglected tropical diseases.

The motives for pharmaceutical R&D can be twofold: Push incentives include public support (underpinned by direct public spending on R&D grants or tax credits). According to Chaudhuri, an National Institute for Health Care Management (NIHCM) foundation study revealed that 48 of the 50 of the best-selling drugs approved by the US Food & Drug Administration (FDA) during the 1990s were developed with some government funding during the product cycle. The major pull incentive is the likelihood of profit guaranteed by the patent system.

Unfortunately, in India, and presumably the other Type III countries, much of the pull incentive is irrelevant. “Pull mechanisms offer a better return for the output of R&D,” explains Chaudhuri, “It presupposes that the companies have the capacity and capability to undertake R&D. If they do not have this, if they cannot generate an output in the first place, obviously the question of benefiting from the higher value of the output promised does not arise.”

“In the developing countries, even if drugs were to be developed for neglected diseases, the return despite market exclusivity would be very low because of the low purchasing power and virtual absence of any health insurance,” he adds. Without an incentive to innovate companies in these regions of the world will either ignore Type III diseases or else produce illicit generic versions of patented drugs.

But, is it possible through government intervention and public sector collaboration to develop the infrastructure and funding for new drug R&D? In promoting new drugs for neglected diseases, governments of developing nations could provide both the push and the pull.

Efforts towards this goal have already been made in recent years, explains Chaudhuri. Indeed, all the major national laboratories in the drugs field (including CDRI, IICT, NCL, CCMB and IICB), academic institutes (including Indian Institute of Science, Bangalore, All India Institute of Medical Sciences, New Delhi, National Institute of Pharmaceutical Education and Research, Chandigarh) and about 50 pharma companies (Dr. Reddys, Ranbaxy, Dabur, Glenmark, Lupin, Cadila Pharmaceuticals and Alembic) are working towards this goal.

Moreover, the Open Source Drug Discovery (OSDD) initiative led by the Council of Scientific and Industrial Research (CSIR) is pushing R&D for new drugs for neglected tropical diseases such as malaria, tuberculosis and leishmaniasis by providing a collaborative platform for scientists, doctors, software professionals, students and others to facilitate drug discovery. Medicines themselves are only part of the problem and various pharma company initiatives are in place: http://www.globalhealthprogress.org

Unfortunately, regulatory approval and the obligatory clinical trials carried out in developed countries are a current stumbling block for all efforts. Chaudhuri and colleagues are now campaigning to expand the public-provate partnerships to include organisations from other innovative developing countries such as Brazil and China. They are also looking to make it possible for clinical trials for drugs against Type III diseases to be considered valid in India, Brazil, and China, where they are much cheaper to run than in the developed world.

At the time of writing, The Global Network for Neglected Tropical Diseases, an initiative of the Sabin Vaccine Institute, was set to host a briefing in conjunction with the Congressional Malaria and Neglected Tropical Diseases (NTD) Caucus on current and future efforts to control and eliminate NTDs. Merck’s Ken Gustavsen told me that, “As with any problem, more can be done – pushes and pulls – to address this. And with continued attention by all partners (companies, NGOs, governments, etc.), progress will continue to be made.”

If we are to have demarcation lines on types of diseases, then surely the same lines should be applied to testing the drugs to treat them. It’s not a matter of push and pull, but give and take for pharmaceutical R&D.

Research Blogging Icon Sudip Chaudhuri (2010). R&D for development of new drugs for neglected diseases in India Int. J. Technology and Globalisation, 5 (1/2), 61-75

Enzymes, chemicals, and metal vapours

Latest science news from yours truly on SpectroscopyNOW.com

  • Don’t get your kinases in a twist – New drugs that block kinase enzymes irreversibly could be used in cancer therapy as well as in studying how this class of enzymes functions. An informatics analysied has allowed molecular editing to produce novel leads.
  • X-rays spot left and right handed chemicals – US scientists have made a catalyst that triggers the creation of chemical structures exhibiting a difficult-to-make form of chirality, or handedness, known as atropisomerism, they report in the journal Science. Single-crystal, heavy-atom X-ray analysis of the major product allowed the team to assign an absolute configuration and so demonstrate efficacy.
  • Palm-sized magnet – German researchers have developed a light, permanent magnet that is suitable for NMR and fits in the palm of your hand. They say it could be used for portable, high-resolution NMR instruments for field studies of important chemicals.
  • Nano cell for laser science – An international team of scientists have developed a new nano-cell for laser spectroscopy that opens up new ways to study absorption and fluorescence of metal vapours
  • Six new planets discovered – A veritable menagerie of new planets discovered from ‘shrunken-Saturns’ to ‘bloated hot Jupiters’, as well a rare brown dwarf with 60 times the mass of Jupiter.
  • First flaming June Alchemist – An old marine alkaloid may find new use in metastatic pancreatic cancer, bitter blockers could be just the thing for nasty-tasting Brussels sprouts, and lotus seed skins offer hope for a food waste product. Also in this week's Alchemist, screening crops for cyanide, gas reactions in crystal lattices, and an award for cellular insights.

Three decades of major oil spills

How does the ongoing saga of the BP oil leak in the Gulf of Mexico following the Deepwater Horizon disaster compare with three decades of major oil spills. An infographic from the oil spill timeline page of Iglu Cruises provides a visual comparison using data apparently sourced from the BBC.

Click for full-size image

Unfortunately, the Iglu graphic somewhat distorts the relative size of the figures. Those oily blobs are scaled by diameter rather than area, so what looks like a huge difference between the recent Gulf leak and Saddam’s deliberate spillage is not quite as enormous as it appears if you assume the relationship is about area of the oily blobs. My apologies for republishing this without making this clear in the initial blog post. I’ve now add red circles that show the actual relative size of each oil spill based on the area of the circles rather than their diameter, which is the more usual way of representing such statistics.

The complete infographic also shows some aspects of the human and environmental impact as well as the variance in the flow rate of oil from the well according to BP and independent observers. I’m disinclined to critique the rest of it given the dubious oily blobs.

Cosmic Variance mentioned this.

UPDATE: Kevin Zelnio has written a critique of the state of oil spills and published a bar chart covering the last fifty years.

Materials, nanotechnology, iPhone app

Science news links for June 3rd through June 8th, including my latest contributions to Materials Today magazine:

  • Nanotechnology fights cancer – Functionalised single-walled carbon nanotubes, rather than being a health risk, cause T cell antigens to cluster in the blood and stimulate the body's natural immune response.
  • Flat-packed carbon – Synthesising and isolating new forms of pure carbon allotropes, has been the focus of much research during the last two to three decades not least because of the discovery of the fullerenes, carbon nanotubes, and more recently graphene. It is the possibility of synthesizing thin films akin to graphene, but with novel connectivity that piqued the interest of researchers in China who have now produced a novel allotrope called graphdiyne.
  • Dipping into nanotechnology – An ability to answer questions at the boundaries of nanotechnology, materials and biology sets apart Steven Lenhert, the newest faculty face of nanoscience at The Florida State University. His research melds metals and semiconductors with biological materials and could lead to a range of new products in medicine and manufacturing for tissue engineering, drug discovery, and computer chip fabrication.
  • Lie detection: Part 2 – Brain scans and lie detectors
  • The Evolution of Computer Science – Computing the energy levels of a helium atom in 1958 was significantly harder than it is today. But a comparison of then and now methods reveals some counterintuitive anomalies about the impact of computer science.
  • Magnetic stent therapy – Magnetic nanoparticles carrying a pharmaceutical payload can be pulled towards blood vessel blockages to help clear them, according to research published earlier this year.
  • Waterfall iPhone app – Like Tetris but with water molecules and ice crystals. The ice caps are melting, you have to rebuild them one water molecule at a time!

Testing tests

Teaching is meant to help students learn, usually about a specific subject, but more broadly about social interactions, working in a team, under duress, about life in general. They say that your schooldays are the best days of your lives, but perish the thought I’ve never been one for clichés and that one smacks of sentimental notions about the good-ole-days, as far as I’m concerned. One aspect of institutional learning, the kind to which the vast majority of us have succumbed at some point in our lives is assessment, tests, exams, SATs, O-levels, highers, GCSEs, CSEs, K12 , degrees, vivas etc. Those are not part of the “best days” ethos, as far as most people are concerned.

But, what do we mean by “assessment”. According to Ana Paula Alturas of the Lisbon Business School and Bráulio Alturas of the Department of Information Science and Technology, ISCTE — Lisbon University Institute, writing in IJIOME, “Despite the good intentions of teachers, assessments always end up transmitting, essentially, information about the position of some students in relation to others, or identifying the ‘good’ and the ‘bad’ students.” So, not necessarily a good thing.

Pressure groups are constantly applying, well…pressure…to the educational authorities either to increase the power of tests, to eradicate tests, to dumb them down and ease off student workload, or to un-dumb them up in order to raise standards to what they were “when we were at school”.

The Alturas team has examined the results when the same test is applied to assess two different groups of students (a group of graduate students in a post-graduate program and a group of non-graduate students in a post-secondary program) who were taught exactly the same content. The tests were designed so that neither group required prior knowledge of skills.

The team found that the average grade in the test among graduate students was almost 16, whereas it was just over 11 for non-graduate students. Female students averaged a smidgeon over 12, whereas males scored over 14 on average. In addition, the average grade of students over the age of 25 years old was almost 15, whereas it was two points lower for those under 25. Age and experience seem to be very important in how well a student does in a test, given that all volunteers had the exact same training for the tests.

The researchers suggest that this finding, which is corroborated by other studies highlights a fatal flaw in testing students and current teaching methods. “Considering that compulsory school should prepare students to continue their self- learning, the current form of assessment seems to us incompatible with this objective,” they explain. “It is in school that all favourable conditions for a prudent choice can be found: information about the world of work, information about themselves, about their possibilities, interests and values.”

Research Blogging IconAna Paula Alturas, & Bráulio Alturas (2010). Differentiation in the assessment between different groups of students: are experience and maturity more important than learning time Int. J. Information and Operations Management Education, 3 (3), 256-271 DOI: 10.1504/IJIOME.2010.033549