Declan Butler, reporter This is the personal blog of Declan Butler, a senior reporter at Nature. All views expressed here are mine, and not those of Nature. Contact me at

April 22, 2011

A population density map to help provide context to my nuclear power plant proximity analysis

Filed under: Energy,Google Earth,Nuclear,Uncategorized — admin @ 9:50 pm

Following on from the population analysis I published yesterday estimating quantitatively how many people live within certain distances of each of the world’s nuclear power plants, some people have asked me for more information on population distribution itself, and whether it might provide more spatial context for the results of the analysis — for example is the plant close to urban sprawl from a major city. Or why is it that nuclear power plants in France, for example – which with 58 nuclear reactors, is second only to the United States (which has 104) in terms of numbers of nuclear reactors — tend to have fewer people living near to most of them, compared with, for example, much smaller nuclear power nations such as Germany?

So to try provide some more visual geographical context, today I’ve mashed together the results of the analysis I published yesterday in Nature — see here my 3D map of the results of that analysis — with a new very high-resolution global population density Google Earth map for 2010 created by the NASA Socioeconomic Data and Applications Center operated by Columbia University’s Center for International Earth Science Information Network (CIESIN). The underlying data is the same as we used in our previous analysis.

Mashing the two maps together certainly does provide this sort of greater context, but the result of combining them is also a bit visually overwhelming, and may be confusing at first. — so beware.

Here’s a screenshot — you can find the full 3-D interactive mashup of the two maps below the fold.


April 21, 2011

A GIS analysis of the number of people living near each of the world’s nuclear power plants

Filed under: Energy,GIS,Google Earth,Nuclear,Nuclear accidents,Uncategorized — admin @ 10:19 pm

I’ve published in Nature tonight a GIS analysis I did with the NASA Socioeconomic Data and Applications Center operated by Columbia University’s Center for International Earth Science Information Network (CIESIN), looking at how many people live within certain distances of each of the world’s nuclear power plants.

It shows, for example, that two-thirds of the world’s power plants have more people living within a 30-kilometre radius than the 172,000 people living within 30 kilometres of the Fukushima Daiichi plant. Some 21 plants have populations larger than 1 million within that radius, and six have populations larger than 3 million. One hundred and fifty-two nuclear power plants have more than 1 million people living within 75 kilometres.

I’ve published the full results in the form of a map which is best viewed using the desktop version of Google Earth — you can download my map file here. The map plots every one of the world’s nuclear plants with circle size indicating the number of people living within 75 km of each plant. Moving the mouse over any circle brings up a label, and the figure for the size of the population. Clicking on any of the plant symbols opens up an information panel showing data for population estimates at 30, 75, 150 and 300 km from the plant, as well as the total power output, and a photograph of the plant.

I did this map fairly quickly, and will add a scale etc soon. Feedback welcome. I can also be contacted at

I’ll try to publish soon the full raw dataset that we created.

Here’s a screenshot of just one of the plants on the map: Indian Point, near New York.


How population sizes were estimated

To estimate the size of populations living near nuclear power plants, Nature first created a map, based on the Power Reactor Information System database, an up-to-date database of nuclear reactors that are operational or under construction, supplied by the International Atomic Energy Agency (IAEA). The IAEA does not provide latitudes and longitudes for the reactors, so we obtained many of these by doing a database merge with the older UNEP-GRID reactor database, which contains data, including geographical coordinates, on reactors up to the year 2000. We manually geocoded remaining entries that lacked coordinate data.

To derive the population estimates, Nature teamed up with CIESIN, whose Global Rural-Urban Mapping Project (GRUMP) population database is one of the best available data sets of global population density. The team, and in particular CIESIN scientists Kytt MacManus and Liana Razafindrazay, overlaid the reactor map with GRUMP population maps for the years 2000 and 2010 in a geographic information system and computed population estimates for both years using concentric zones drawn at 30, 75, 150, 300, 600 and 1,200 kilometres from each nuclear power plant.

April 2, 2011

The world’s nuclear reactors as you’ve never seen them…

Filed under: Nuclear accidents — admin @ 8:50 pm

I haven’t been blogging here for a while, but I thought I’d crosspost this one, which I published earlier over on Nature’s blog.

The nuclear accident at the Fukushima Daichii power plant will have consequences for the future of nuclear power in Japan and elsewhere. To get a better idea of the world’s current tally of nuclear reactors, I’ve created a map of the world’s nuclear power plants and reactors using Google Earth – the maps are based on a database kindly supplied to me by staff at the International Atomic Energy Agency’s (IAEA) Power Reactor Information System (PRIS) database, so it’s reliable, and up-to-date. The database, however, lacked latitude and longitude data — I obtained many of these by doing a database merge with the older UNEP-GRID reactor database which contain data on reactors up to the year 2000, and then geocoded the remaining entries lacking coordinate data.

Google Earth, with its unparalleled pan and zoom functionality and the relative ease with which it can be interfaced with databases, is my preferred tool for mapping and visualizing geographical data. Here’s the link to my beta map – remember that to view the file you must first download Google Earth (I’ve also done these maps in my spare time, so please be forgiving of any rough edges)

Here’s a quick summary of what the map shows:

1. All the world’s nuclear power plants are depicted on the map as circles. Their names appear in yellow on browseover, with the size of the circle proportional to their total MW electricity output. I calculated the MW output by summing that of the plant’s operational reactors, plus that of those already under construction.

2. Where it gets more interesting is that if you zoom in and then click on a power plant, its circular symbol will open up to show each individual reactor at the plant, with the colour of the circle of each reactor depicting its design (for example, “boiling water reactor”). Then clicking on any reactor will bring up an information panel, giving the reactor’s basic technical details, and where available a photograph of the plant, as well as links to recent news stories about the plant.

A major advantage of Google Earth is that it is also easy to overlay other layers of data on top of this base map of nuclear power plants and reactors, so (time permitting) I could envisage, for example, adding such relevant geographical layers as datasets on population density, past significant earthquakes and tsunamis, as well as seismic risk. Let me know what sort of data you would like to see added as supplementary layers. But for now, I thought I’d just get the base map out the door.

For full coverage of the Fukushima disaster, go to Nature’s news special.

July 8, 2009

Iran 2005 presidential candidate says protests mark ‘turning point’ — change ‘inevitable’

Filed under: Iran,Justice — admin @ 5:21 pm

Mostafa Moin, a candidate in Iran’s 2005 presidential elections speaks out on the current situation
Photo credit

I’ve an interview in this week’s Nature with Mostafa Moinpdf here — who was the reformist candidate in Iran’s 2005 presidential elections, following which Mahmoud Ahmadinejad became president. Moin, a medical researcher, and former minister for higher education and for science, has long argued – see my 2006 interview here — that building a stronger civil and democratic society in Iran is key to the country’s scientific development and it becoming a knowledge-based society. He says that events since the disputed 12 June election mark a turning point in the relationship between the people of Iran and its government.

Young Iranians and women are increasingly attached to such principles, he says. They have become the driving force in the grassroots post-election movement in Iran that has moved beyond allegations of vote-rigging, he says, to become a broader civil rights movement, echoing the initial aspirations of the 1979 Islamic Revolution — for civil rights, including greater justice, freedom, democracy, and equality.

In the article, Moin also slams Ahmadinejad’s track record on science, academic freedom and social reforms. He calls on the international community, and academics and scientists in particular, to denounce abuses of academic freedom and human rights, such as the Iranian government forces’ crackdown on students, academics, scientists and other protesters since the contested election, and its violations of the people’s constitutional rights, for example the right to demonstrate peacefully.

“I would like to say to my scientific colleagues, wherever they are, that while Iran, an ancient civilization, has its own cultural background and national interests, the nation and its academics wish to be productive and constructive members of the international community. They reject government adventurism and the creation of a climate of tension internationally,” says Moin.

To read the full print version of the Q&A click here. I’ve also three answers which we didn’t have space for in the print version. I’ve appended some excerpts at end of post.

On 2 July, Nature also published a strong editorial, “We are all Iranians” Mir Hossein Mousavi, the reformist candidate, has cited the Editorial on his Facebook page, here.

Nature also published a news article 24 June, “Iran diaspora responds to protests

Some excerpts from tonight’s article

In our last interview, you said that support by Iranian young people and women for the principles of a civil and democratic society were what would “shape Iran’s future”. Has that shaping moment come?

Yes. The recent growth in Iranian women’s and young people’s political and social awareness has set the stage for their current demands for greater civil liberties, and structural and democratic reforms. The outcome of the 2005 presidential election, combined with the subsequent mismanagement of the government, has catalysed this process — and explains the 85% voter turnout in last month’s presidential election, and the demand for change. The youth, and in particular the supporters of the reformist candidate Mir Hossein Mousavi, played a major role in creating the extraordinary enthusiasm and motivation surrounding the elections. I remain optimistic as to the role, and the movement, of Iran’s youth.

What is your assessment of Mahmoud Ahmadinejad’s track record on science, and on academic freedom and social reform?

Scientific activity has stagnated. Students and young scientists have been discouraged. Pressure has been exerted on scientific forums and centres, and academic freedom restricted. The brain drain of elites has worsened. Administrations have been massively populated with people from the military and the security forces. We have an economic recession; destruction of ethical norms and public culture; and the scientific, political and cultural isolation of Iran in the international community. These are among the achievements of Ahmadinejad.

Reformists have in the past criticized US funding and support for regime change as being counterproductive, and playing into the hands of opponents of reform. What do you think of US President Barack Obama’s handling of the current crisis, and his overtures towards Iran?

During its long history, the Iranian nation’s self-esteem and generosity means it has not needed or sought outside help. Moreover, history has taught the Iranian people to be suspicious of foreign interference — by the major powers in particular — in its internal affairs. So far, the positions and approach taken by Obama, a politician and academic, have been much more realistic and sober than those of his predecessor, and can be considered as a start towards bigger practical steps.

The demands of the people now seem to have moved beyond allegations of vote-rigging to now echo the initial aspirations of the 1979 Islamic Revolution — for civil rights, including greater justice, freedom, democracy and equality. Is that the case?

Exactly. The typical slogans chanted by the protesters were calls for a return to the freedom-loving, justice seeking and ethical and spiritual ideals of the 1979 revolution. The manner in which the recent elections were held, and its serious social and political consequences, mark a turning point in the relationship between the people of Iran and its government. People, and the young generation in particular, feel that their intelligence and personality have been insulted, and that their votes have been subject to treason by means of lies and deceit. The consequences of this will become apparent in the relatively near future.

Progressives, including academics, were purged in the aftermath of the 1979 revolution, and to a lesser extent again under Ahmadinejad. Have they reasserted themselves during the current crisis, and played any significant role?

Students, young academics and the educated strata of Iranian society have played a major role. Alongside their protests against political constraints and election violations, students also protested against this purge of their professors. All Ahmadinejad’s rivals in the presidential elections have also denounced the massive and illogical purge of the country’s scientific and managerial elites.

April 15, 2009

“John Maddox 1925-2009. In memory of a transformative editor of Nature.”

Filed under: Uncategorized — admin @ 8:43 pm

Nature tonight carries a special section dedicated to the sad news of the death on 12 April of Sir John Maddox, who was editor of Nature for many years. In an Editorial — In memory of a transformative editor of Nature.– Philip Campbell, the present editor of Nature, pays tribute to John, capturing much of the essential of an extraordinary character, a giant, who forged much of what Nature has become since — the New York Times, and other media outlets also have obituaries.

Excerpt from the Nature editorial:

“It was with great sadness that I and my colleagues at Nature learned of the death on Sunday of Sir John Maddox — or ‘JM’, as his colleagues always referred to him.

There was puzzlement, too. Yes, John had been looking frail recently, but, well, this was JM — the perpetually restless, irresistible, unstoppable force. The editor who conducted some gatherings with ‘shock and awe’ as some recall. The ‘man with a whim of iron’ as others used to call him. And the man who survived countless cigarettes and glasses of red wine, many consumed late into the night as he wrote the week’s Editorials at the last possible moment.”

The Editorial also highlights that John founded science journalism at Nature — he saw journalism as on a par with science, as being about uncovering truth — at a time when science journalism barely existed.

“He also established a strong tradition of journalism in Nature. John was a man of many parts but above all he was a journalist, and took pride both in the label and in the craft. He had trained and researched as a physicist, he had an all-consuming intellect, he absorbed research as fast as he could read it — and he was a virtuoso science writer, coming to Nature with substantial experience as a newspaper science correspondent. Many leading writers and editors in today’s science media passed through Nature during his time, and learned above all how to recognize and seize moments of editorial opportunity even if, many a time, flying by the seat of one’s pants. He established the ‘voice of Nature’ in unsigned Editorials (although the voice was often unmistakably his own). And he led the way in developing extensive supplements in which he reported and opined over many pages, often compelling in their narrative, his penetrating perceptions of the state of science and its leadership in this country or that.”

John hired me in 1993, during a long and stimulating breakfast job interview in the Lutetia hotel in Paris, and I’ve fond memories from my early years at Nature of his formidable character and intellect: — he taught me a lot. As Nature’s Editorial tonight ends on: “JM was unique, and those of us who knew him and learned from him will feel the world to be a smaller place in his absence. But his was a powerful spirit, and we continue to thrive on it.”

January 28, 2009

An appeal to President Ahmadinejad

Filed under: Uncategorized — admin @ 7:57 pm

An appeal to President Ahmadinejad; that’s the title of the lead Editorial in tomorrow’s Nature. I’ve appended some excerpts from the Editorial below. I’ve also an accompanying news story here — note all Nature news stories are free to access for one week — which describes the facts of the case, which I blogged about earlier here.

In short,

Iran has sentenced two of the country’s HIV researchers to prison for communicating with an “enemy government” and plotting to overthrow the state. Arash and Kamiar Alaei, who are brothers, underwent a half-day trial on 31 December in Tehran’s Revolutionary Court. Kamiar was sentenced to three years in prison, and Arash to six.

The Iranian authorities notified the physicians’ lawyer, Masoud Shafie, of the verdicts on 20 January. He has 20 days to appeal and intends to do so; the brothers say they are innocent.

The Alaeis were arrested last June, and their detention and trial were “unfair even by the draconian standards of Iran’s penal code”, says Jonathan Hutson, a spokesman for Physicians for Human Rights, based in Cambridge, Massachusetts.

For more information see Physicians for Human Rights’ special website on the case which includes action steps that you can take, including a petition.

Excerpts from the Editorial

Iran now has one of the best prison programmes for HIV in not just the region, but in the world,” exclaimed Hamid Setayesh, the UNAIDS coordinator for the country, in 2006. “They’re passing out condoms and syringes in prisons. This is unbelievable. In the whole world, there aren’t more than six or seven countries doing that.”

Human-rights organizations who have examined the brothers’ cases say that their detention, which began in June last year, and their convictions on 31 December in a closed trial lasting barely half a day, both fell far short of the minimum international legal norms for a fair and equitable procedure.

An especially puzzling aspect of the case is that Iran’s president, Mahmoud Ahmadinejad, has publicly supported international collaboration in science. Speaking at Columbia University in New York in September 2007, he invited Columbia faculty members and students to work with their counterparts in Iran. “You’re officially invited,” he said.

Such dialogue — ‘smart power’ — should be encouraged by all sides, because cooperation in the relatively apolitical areas of medicine and science keeps open rare avenues of back-channel diplomacy. Unfortunately, ‘dumb power’ is currently prevailing. The action of the Iranian judiciary in this case can have only a chilling effect on such activities, and there have been ill-considered moves elsewhere. Prime examples are the shortsighted visa policies being pursued by nations such as France, which unjustly discriminate against Iranian researchers (see Nature 456, 680–681; 2008), and the Bush administration’s declaration that the United States is seeking regime change in Iran by supporting ‘pro-democracy’ elements there. Academics in Iran who desire reform, but by self-determination, say that such covert US policies have left them vulnerable to the same charges faced by the Alaei brothers. More smart power is needed all round.

President Ahmadinejad. Your country’s HIV-prevention programme has won respect in the Muslim world and beyond. As you said at Columbia University, the open scientific and medical dialogue needed to progress in issues such as the fight against AIDS must be above the contemporary realpolitik of broader political issues. We urge you today to request the appropriate authorities to review the cases of Arash and Kamiar Alaei so that the truth may prevail.

November 17, 2008

What impact will the financial crisis have on science & innovation?

Filed under: Uncategorized — admin @ 9:25 pm


Nature has launched a special on what the financial crisis might mean for science and innovation. It already includes more than a dozen articles and will be continually updated. It’s all on free access.
If you want a great easy-to-understand 4-page overview, your first stop should be this feature — Science in the meltdown by lead writer, Mitch Waldrop, my colleague in DC — and an accompanying editorial — Danger and opportunity — both of which I’d a hand in.
To see a complete list of the articles, go to Special: Financial Crisis.

November 5, 2008

How America really voted yesterday + maps going back to the 1960’s

Filed under: Uncategorized — admin @ 6:39 pm

This morning the 8-year old son of a friend of mine looked at a map of the electoral results online and said: “I don’t understand; Obama won, but the map is all red.”

Too right. Maps of the results of the US presidential election usually show up as a patchwork of red and blue states across the country. But visualizing votes by the geographical area of states distorts the true picture — a state with a large area but relatively small population will dominate, whereas small states with large populations vanish from view. Indeed, despite this election’s convincing Democrat victory, conventional maps depicting the election results again show a nation awash with red.

Here, I map the results as a cartogram, which adjusts the area of the states on the basis of the number of electoral college votes [number given in brackets in map] they represent. This — as can be seen from the dominance of blue — gives a more accurate picture of how the United States voted in 2008.

In passing, to see Nature’s complete coverage of the election, click here.
Nature, for the first time since its creation in 1869, this year endorsed a US presidential candidate — see here:
Quote: “This journal does not have a vote, and does not claim any particular standing from which to instruct those who do. But if it did, it would cast its vote for Barack Obama.”

Election: 2008
President: Barack Obama [D]
Main Opponent: John McCain [R]
Electoral Vote: Winner: 349 (as of 4/11/2008 with NC & MO still to be called)
Vice President: Joe Biden
V.P. Opponent: Sarah Palin

Technical note: the cartograms were generated using the ScapeToad software implementation of the Newman–Gastner algorithm. This algorithm was developed by Mark Newman of the University of Michigan in Ann Arbor and Michael Gastner at the Santa Fe Institute in New Mexico, and was first used in the US 2004 presidential elections (M. T. Gastner and M. E. J. Newman Proc. Natl Acad. Sci. USA 101, 7499–7540; 2004)
Mark Newman tells me that has posted his cartograms of yesterday’s elections here, which go into even great detail. Well worth a look.

Here are cartograms of some past presidential elections, going back to the 1960’s, with area adjusted for the electoral college votes attributed to each state for that election — they have changed over the past 40 years. The map below is of the 2004 election; click “Continue reading” to see the rest. Note: I’ve generated these quickly from a database, so let me know if you spot any errors
Data and notes extracted from US national archives.

Here’s the rest:

Election: 2004
President: George W. Bush [R]
Main Opponent: John F. Kerry [D]
Electoral Vote: Winner: 286
Popular Vote: Winner: 60,693,281
Votes for Others John Edwards (1)
Vice President: Richard B. Cheney (286)
V.P. Opponent: John Edwards (252)
Notes: One Minnesota elector voted for John Edwards for both President: and Vice President:. During the counting of the vote in Congress, Rep. Stephanie Tubbs Jones (D-Ohio) and Sen. Barabara Boxer (D-Calif.) raised objections to the Ohio Certificate of Vote alleging that the votes were not regularly given. Both houses voted to override the objection, 74 to 1 in the Senate and 267 to 31 in the House of Representatives.


September 17, 2008

Some cartograms of US science & technology

Filed under: GIS,Open data,Uncategorized,Venture capital — admin @ 7:38 pm

As anyone who has visited WorldMapper knows, cartograms are an interesting way of visualizing date on geographical areas. I’ve an article in Nature tonight where I’ve generated cartograms for some indicators on US science and technology.
Some excerpts at end below, and also a Picasa slideshow of some of the cartograms — it’s the first time I’ve used the Picasa embed, and its too subliminally speedy. You can press the stop button, and then click back and forward on the below, and there is allso a static version where you can just click through the slides at a normal human pace ;-> — click this link to the Picasa album.

The cartograms reveal the United States distorted in proportion to a variable other than area — such as state spending on R&D. The maps here were made using data from the State Indicators chapter of the 2008 edition of the US National Science Foundation’s (NSF’s) Science and Technology Indicators. For simplicity, the cartograms use a base map of the 48 contiguous mainland states and the District of Columbia.
I haven’t included a detailed description of the indicators – -see the NSF chapter for that.

The Gastner & Newman 2004 PNAS paper introduced an improved algorithm for generating cartograms, which was the one used here. The software implementation is the open-source ScapeToad, released in May by the Chôros Laboratory at the Swiss Federal Institute of Technology (EPFL) in Lausanne, which researches the concept of space in society, from urban planning to territorial development.

Note that per-capita and other cartograms that use normalized data can be confusing, cautions Michael Goodchild, a geographer at the University of California, Santa Barbara – in theory a state with just a few researchers and a tiny research budget, for example, might nonetheless appear huge on such a map. Where possible it might be better to use raw non-normalized data, such as total population to scale state sizes in cartograms, and then layer on data on other related information on top. There are examples of both types of data in the slideshow above.

PS Nature also has a short editorial on visualization this week, and just last week a fab special on “Big Data.”

August 20, 2008

Anthrax case not closed, says Nature

Filed under: Uncategorized — admin @ 6:36 pm

Nature has a strong editorial out tonight (pdf here) on the FBI’s accusation that Bruce Ivins was behind the 2001 Anthrax attacks in the US. It asks “Was Bruce Ivins a scientist-gone-wrong who single-handedly orchestrated the 2001 anthrax attacks in the United States? Or was the 62-year-old anthrax-vaccine researcher at Fort Detrick, Maryland, an emotionally unstable innocent whose profile made him a convenient fall guy for the FBI?” and calls for a full enquiry.

Some excerpts below:

April 30, 2008

Science data needs to be more spatially-enabled, says Nature

Filed under: GIS — admin @ 9:55 pm

Here’s an Editorial from tomorrow’s Nature — link here — on the need for scientists to routinely record spatial data with samples, viral sequences, field observations, and other entities. It proposes a major change in the policies of journals and databases to mandate recording of such data as a prerequisite for having a scientific paper accepted. Feel free to use this blog’s comment facility to express your opinion on this, or email me at

During the research for this Editorial, Nature picked up considerable frustration from spatial scientists in many fields about the fact lack of spatial data in otherwise valuable datasets made them all but useless for more quantitative spatial analysis. For the sake of brevity and readability in this short article, we reduced the concept of spatial data to latitude and longitude, but clearly any working system would require more detailed spatial standards, depending on fields.

April 16, 2008

Agent Orange studies stalled

Filed under: Uncategorized — admin @ 6:07 pm

I’ve the lead news article tonight in Nature with an exclusive — Further delays to full Agent Orange study — on a complex story behind efforts to get done a large-scale epidemiological study of the health effects, and other combat factors — on Vietnam veterans, almost 30 years after it was first mandated. Nature has an accompanying Editorial — A ghost of battles past.

NOTE: All Nature news stories are free online for at least a week to registered users — and registration is FREE.

A few excerpts from the long news article, and the Editorial, below:

A study to investigate the health effects of Agent Orange on Vietnam War veterans is being obstructed by the US Department of Veterans Affairs (VA), claim scientists and veterans’ organizations.


April 2, 2008

Fighting climate change by architectural design

Filed under: Uncategorized — admin @ 6:55 pm

Ultra-low energy homes are not necessarily architectural boutique projects: above are low-income “passive” terrace houses in Lindas, Sweden

I’ve a 4-page feature in Nature tonight on the huge potential of green architecture for mitigating climate change (pdf file here).

It’s been one of the most challenging articles I’ve had to write, as I had to leave out so much, but at the same time one of the most satisfying. This is a hugely important topic. Buildings account for up to half of all energy consumption, and are the biggest single contributor to greenhouse gas emissions. Much attention is given to exotic future remedies, such as carbon sequestration and clean coal. But a way to slash emissions using existing technologies is sitting under our noses: simply rethinking how we design the buildings we live and work in, to use much less energy.

The arguments for building with energy needs met largely by marrying with the local environment and passive strategies are so compelling that the research for this article is persuading me to switch my own plans to buy a place in French Touraine, where I live, to instead build a zero-energy home — no small challenge though, given that French builders are far behind their German, Swiss, and Austrian neighbours here.

I’ve posted just a few of the links I collected during the research to here on Connotea, and hope to add more.

It’s impossible to excerpt from an article of this length in any sensible way, but just to give you a flavour, here below are a few:


February 22, 2008

Iran’s nuclear programme

Filed under: Iran,Non-proliferation,NPT,Nuclear — admin @ 7:43 pm

On 12 February, I wrote a detailed and neutral analysis of Iran’s nuclear programme and its potential capacity to produce weapons. The article was in anticipation of the report by IAEA on Iran sent to its board today, that was intended to wrap up the IAEA’s investigation of Iran’s past and present nuclear activities. The report is classified until 3 March, but has been leaked, and I append a full copy below fyi — as with WHO, other intergovernmental, and government, reports you need to understand diplomatic speak fluently to understand the nuances.

My earlier article also included 2 short boxes — one on the main outstanding issues that IAEA still had to obtain satisfactory answers to, and another on potential weapons break-out scenarios.

Today’s report by the IAEA reveals a disappointing lack of progress, far short of the agency’s expectations. But there is nonetheless reason to believe that reason may yet prevail in this charged dossier, where excessive belligerence on all sides has stalled an acceptable resolution.

I’ve appended below some excerpts from my earlier articles, which may help interpret the new IAEA report. For more detailed analyses of the technical issues in the Iran case, I’d recommend the site of the Institute for Science and International Security, and a January article in the Bulletin of the Atomic Scientist by Richard Garwin, a former nuclear weapons designer who is now a major force for disarmament. Another good source of information is the Nuclear Threat Initiative. The IAEA page on Iran is here.

Abridged excerpts from my earlier articles, and the full text of the new IAEA report appended below:

January 23, 2008

Nuclear proliferation — a wake-up call

Filed under: Uncategorized — admin @ 8:21 pm

After the success of the international mobilization in the Libya hostage crisis, I’ve been informing myself, through discussions with many people, as to what are the most pressing issues, where change could be made, and influence and impact exercised, by similarly raising awareness among both the public and those well-placed to create change. With US elections this year, and the review conference of the nuclear non-proliferation treaty (NPT) coming up in 2010 — which in intergovernmental terms is tomorrow — I’ve no doubt as to what is one of the most pressing issues of our time. It is nuclear proliferation, and it is a way more complex issue than just Iran or rogue states. And we have a window of opportunity to make progress on it now. The first step is becoming informed; it’s not an easy topic to grasp in all its complexity, but it is well worth it.

I’ve been happy that in this month of January 2008 alone, Nature has dedicated 2 editorials to the topic, and 3 news analyses — it is going to be a topic that you will hear much more about on this blog throughout this year.

Here are the links to the Nature articles from this month:
1. Resurgent nuclear threats
2. Nuclear war: the threat that never went away
3. Nuclear war: the safety paradox
4. Fuel’s paradise
5. Nuclear fuel: keeping it civil

Excerpt of one editorial: (more…)

Q&A with Larry Brilliant, executive director of

Filed under: Uncategorized — admin @ 7:34 pm

I had a chat last week with Larry Brilliant, executive director of, Google’s philanthropic arm, which plans to tackle emerging diseases, climate change and poverty. I’ve tried to distill this into what’s known in journalism jargon as a Q&A format in this article in Nature tonight.

Brilliant has had a fascinating career; for a quick summary see the Wikipedia entry on him, including being involved in the eradication of smallpox. His TED talk can be found here, and while we are at TED, here are two must-watch TED talks on bringing health and poverty data to life by Hans Rosling from the Karolinska Institute — who is at at the moment. We gave Hans’s work a nod in a recent Nature editorial

Brilliant faces a major challenge in mapping out a coherent and effective strategy, but with Google’s resources and networks behind it, could be a real force for change; I for one will be watching the development of this young organization, which is still naturally finding its feet, with great interest.

Here are some excerpts from the Q&A with Larry Brilliant:

The grants announced last week were small compared with those made by the Gates Foundation’s Global Health Program.

It’s too early for substantial funding but Google has set aside a generous amount for philanthropy — 1% of equity and 1% of profit. We’ve invested a total of US$75 million so far, but I consider these mostly exploratory grants. It is the beginning of a long process and we will be ramping up giving in the future.

How will the organization work to anticipate new pandemics?

With our ‘Predict and Prevent’ initiative we hope to develop an entire new science of epidemiology and surveillance, both for existing diseases and to spot emerging ones early on. One way is to strengthen national health services — look at the polio surveillance system in India, for example, which is the finest for any disease. We are now funding the Global Health and Security Initiative’s work on the Mekong Basin Disease Surveillance network, to boost diagnostic capacities, train people and help create a regional surveillance network for this hotspot, which covers Cambodia, China, Laos, Myanmar, Thailand and Vietnam. It is also using tabletop planning exercises with modern war-gaming techniques to better prepare a pandemic response. The Mekong project is about creating best practices that can then be transposed elsewhere. It’s all about sharing data, visualizing data and creating the IT tools that people would like these countries to have to mount fast and effective responses.

I see Google is also involved in biology.

We want to detect emerging pandemic agents. Humans are increasingly coming into closer contact with animals in many places, creating hotspots where new diseases emerge by jumping the species barrier. So we plan to support work that takes paired blood samples from animals eaten for bushmeat in Africa, and from their hunters. This will create genomic maps of the viruses present, and reveal how these agents change over time. It’s part of an entirely new chain of information gathering, which at some point will need to be centralized by the World Health Organization, the World Organisation for Animal Health or a non-governmental organization.

How are your relations with the Bill & Melinda Gates Foundation?

I love the Gates Foundation, they are wonderful people, and we will work with them. They have been so kind to me and They invited us round to help us understand philanthropy and how it can best be used. When I heard Bill and Melinda speaking recently on their commitment to malaria, I had tears in my eyes.

And here’s one important question that got cut because of space:

Have you a message for Nature’s scientist and other readers?
Look at’s goals, and if convergent, they should articulate a way that they think they can help, and write to the relevant groups leader. We are looking for partners everywhere.

A very mysterious foundation

Filed under: Uncategorized — admin @ 6:56 pm

That’s the title of an article I’ve in Nature tonight on the World Innovation Foundation, a Bern-based charity, which I found operates in fact largely out of a one-man building consultancy in Huddersfield, a town in Northern England.

Some excerpts

Some 3,000 scientists, including more than 100 Nobel laureates, have apparently accepted membership of a body called the World Innovation Foundation (WIF), which claims to be a powerful world-changing network to provide “the technological tools and miracle technologies that we shall all need to solve the world’s impending global problems”.

No fewer than four Nobel laureates hold executive positions in the WIF’s governance, according to its website: Jerome Karle, William Knowles, Robert Huber, and Yuan Lee. Huber, described as vice-president, claims that he has no recollection of joining the organization. “I am not aware what this organization is,” he says.

Yuan Lee, a 1986 Nobel laureate in chemistry, says he has had “very limited” involvement with the foundation that amounted to accepting a 2002 invitation to join, signing a WIF letter opposing the Iraq war, and accepting in 2004 the position of the WIF ‘national representative’ in Taiwan. Since accepting this position he has had no dealings with the WIF, he says.

Nature polled several WIF fellows who advertise their fellowships on their websites. What emerges is a pattern whereby scientists join on the strength of the list of existing members, but know little about the foundation or its activities.

December 5, 2007

“Don’t make the mistake of looking for the future in your rear-view mirror.”

Filed under: Energy,Venture capital — admin @ 9:35 pm

I love this quote; it’s the sort of inspirational one that you’re tempted to stick above your computer screen. It’s from Vinod Khosla, a veteran entrepreneur who co-founded Sun Microsystems, was a partner in Kleiner Perkins Caufield & Byers in Menlo Park, California — the company that nurtured the likes of Amazon, Google and Genentech — and who now heads Khosla Ventures, also in Menlo Park, one of the most prominent clean-energy venture-capital firms

It’s from a two-page article I published tonight in Nature, which details what is probably one of the most significant trends in energy research for over 40 years: the current huge interest of venture capitalists in green energy. As the article makes clear, this is more than a fad, but a potentially world changing development.


Silicon Valley is greening. Investors are flocking to low-carbon (clean) energy technologies, fuelling a boom in the sector, with investments set to overtake those in Internet start-ups. But does this venture-capital explosion herald another dotcom bubble?

Earth monitoring special in Nature

Filed under: GIS,Google Earth,Open data,Semantic web,Web services — admin @ 9:25 pm

Nature has a special issue on Earth monitoring out tonight.


Nearly fifty years ago —things were up and running by March 1958 — Charles Keeling and colleagues began a series of measurements of atmospheric CO2 on Mauna Loa in Hawaii. The results, made graphic in the jagged ‘Keeling curve’ running across this week’s cover, made the world take notice — eventually. The Mauna Loa measurements constitute the longest continuous record of atmospheric CO2 in the world. The steady rise in CO2 that they record now forms the accepted backdrop to today’s climate science and economic and political decision making. As well as being an important resource in itself, the Mauna Loa record highlights the vital importance of Earth monitoring programmes. The fiftieth anniversary of the start of this work is marked in this issue by News Features and other pieces on the Earth monitoring being done today, historical pieces on the Mauna Loa data and more.

I’ve a long futuristic article in the special looking at how close we might be to a totally monitored Earth by 2025: Earth Monitoring: The planetary panopticon

Nature itself has an great editorial — Patching together a world view — which provides a great big picture view, that I’d have struggled to write, so kudos to my colleagues who did such a good job of capturing succintly such a vast topic.

Alex Witze then contrasts my upbeat forecast with the lack of leadership of, and the disarray in, the US’s current Earth monitoring programmes — Earth Observation: Not enough eyes on the prize.

And the journalistic content doesn’t stop there: there are also features on:
Earth Monitoring: Observing the ocean from within

Earth Monitoring: The crucial measurement

And to finish it all off there are two Commentaries by scientists
Earth monitoring: Cinderella science
Earth monitoring: Vigilance is not enough

And an online version of all is here, including a timeline of Earth monitoring.

The Freeing of the Tripoli Six: The inside story of how scientists saved medical workers from the firing squad.

Filed under: HIV,Justice,Libya — admin @ 9:06 pm

I haven’t been blogging for a while; been taking some time out for other projects, and the blog had become almost entirely devoted to original posts on the Libya death penalty case, a hard act to follow. An article in the November issue of Discover magazine, now free online, provides an opportunity to close that chapter, and start blogging on more mundane matters. The long article, by John Bohannon, a journalist colleague who writes for several science publications including Science, tells the story of scientists’ actions in the Libya case. It covers many of the events blogged here as they happened — see summary here — but as a gripping detective story — it makes a good read.


Late in September 2006, Nobel Prize–winning molecular biologist Richard Roberts was thumbing through the journal Nature when he read an article by one of their senior reporters, Declan Butler, about a group of foreign medics on death row in Libya. Butler’s article, along with an anonymous editorial entitled “Libya’s Travesty,” described how the medics’ appeals were nearly exhausted. “I had been aware of the situation through the media,” says Roberts, the chief scientific officer at New England Biolabs in Ipswich, Massachusetts. “But the case seemed so open-and-shut, I’d assumed that diplomacy would sort the situation out.” But as the editorial warned, “Diplomacy has lamentably failed to deliver,” and “scientific leaders need to use all their influence” to persuade their governments to take action.

“It was a call to arms,” says Roberts. So he picked up the phone and contacted Butler, who painted a grim picture of the situation. Ever since the death sentence was handed down in 2004, the absurd case had been bouncing between Libya’s courts as the medics languished in jail; there had been at least one suicide attempt among them. Butler was glad Roberts wanted to help. After watching the Libyan affair from a journalist’s vantage point, says Butler, “I found myself in a position to be useful. What was needed was for someone to work behind the scenes, connecting influential scientists with each other and with diplomats involved with the case.”

August 1, 2007

Nature calls for exoneration of medics in Libyan case

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 9:14 pm

Almost one year ago, Nature ran a blistering Editorial — “Libya’s Travesty” — on the tragic case of the HIV medics in Libya. Much water, and many articles in Nature have passed under the bridge since then, and tonight we publish perhaps our last Editorial on the case — “Free at last” — calling for Libya to go beyond the welcome political solution found to have them released, and at last face up to the facts. Exonerate the medics, is the message.

The Editorial in September 2006 was written at a time when the medics faced a serious threat of execution, and began:

Imagine that five American nurses and a British doctor have been detained and tortured in a Libyan prison since 1999, and that a Libyan prosecutor called at the end of August for their execution by firing squad on trumped-up charges of deliberately contaminating more than 400 children with HIV in 1998. Meanwhile, the international community and its leaders sit by, spectators of a farce of a trial.

Implausible? That scenario, with the medics enduring prison conditions reminiscent of the film Midnight Express, is currently playing out in a Tripoli court, except that the nationalities of the medics are different. The nurses are from Bulgaria and the doctor is Palestinian

Excerpts from tonight’s editorial are below, written in a different context now that their liberation has been achieved. But fundamental human rights issues have not yet been resolved, however, and so we demand that Libya now also finally face up to the scientific realities of this case.

In France this week, Libyan leader Muammar al-Gaddafi’s son Seif al-Islam Gaddafi — who played a significant role in resolving the case — declared that the six were “scapegoats” in a “made-up conspiracy” by Libyans, and that the outbreak was as we have long said, an accident.

His statements are courageous, and are to be welcomed; can Libya’s government now show the same balls, and give the six the least they deserve, after all they have suffered as innocent victims of a bigger geopolitical game – having their names cleared? It doesn’t seem like a lot to ask, under the circumstances. Is Libya big enough?

An important para in the Editorial below is this:

“The scientists quickly learned that effectiveness in such matters demanded tight liaison with defence lawyers and human-rights groups. One-off appeals and letters of protest can have some impact in raising public awareness, but effective advocacy requires sustained action, clear objectives and a strategy to achieve them.”

It gives a hint of the behind-the-scenes networking needed to work on this complex case, and I’d like to mention in particular among human rights groups, Physicians for Human Rights, who have really worked hard on the case.



The six medical workers held for eight years in a Libyan prison on false charges of deliberately infecting hundreds of children with HIV were finally freed last week. But Libya’s cynical insistence on their guilt is casting a pall over this long-awaited event.

Late in the negotiations that saw the medics’ sentences commuted from the death penalty to life imprisonment followed by their extradition to Bulgaria, Libya refused a request for the final settlement to state that it did not represent an admission of guilt. When Bulgaria freed the six, Baghdadi Mahmudi, Libya’s prime minister, denounced the pardon as a “betrayal”, arguing that the medics should have served life sentences. It is time for Libya to end this charade.

An important supporting role was played by scientists who took up the medics’ cause, including Nobel laureate Rich Roberts of New England Biolabs; Vittorio Colizzi, an AIDS researcher at Tor Vergata University in Rome; and Luc Montagnier, whose group in Paris discovered HIV. They all persistently dissected the emptiness of the prosecution case, showed multiple avenues of evidence pointing to a hospital infection as the true cause of the outbreak and campaigned tirelessly.

The scientists quickly learned that effectiveness in such matters demanded tight liaison with defence lawyers and human-rights groups. One-off appeals and letters of protest can have some impact in raising public awareness, but effective advocacy requires sustained action, clear objectives and a strategy to achieve them.

Libya has, unfortunately, won plaudits in parts of the Arab world for the way it has played its hand, winning normalization of its political and economic ties with the European Union (EU) and much else besides for releasing the six. The EU and the United States should make further normalization contingent on the Libyan government owning up to the real facts of the case, and exonerating the six.

July 26, 2007

Liberty, Justice, HIV and Libya

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 5:37 pm

Richard Charkin, the chief executive officer of Macmillan Publishers, the parent company of Nature kindly invited me to write a guest post today for his blog, Charkin Blog. The guest post is here, but I thought I’d also post a copy here.

Liberty, Justice, HIV and Libya

The liberation of six foreign health workers, held hostage in Libya, is a welcome denouement of this tragic affair. Today, the 5 Bulgarian nurses and a Palestinian medic woke up in Bulgaria, free at last from the threat that one morning, they might have woken up only to be instead led out, blindfolded, tied to a stake, and executed by firing squad. But the moral price of securing release of the hostages has been high.

The EU humanitarian aid package for over 400 infected Libyan children accidentally infected at a Benghazi hospital is desirable and commendable. But Libya’s tying it to the six’s release, in effect a ransom, sets a dangerous precedent for future unjustly condemned prisoners.

How much more ransom was really paid in the murky deal between the European Union and Libya will probably never be known. The $400 million in ‘blood money’ paid to the families of the infected children from an opaque international fund – which paved the way for the end of the crisis — may in fact have largely been paid by Libya, as part of a complex face saving deal. But Libya extorted concessions on debt relief, and many other fronts. The EU has also promised returns by normalizing its political and economic ties with Libya.

Moreover, Libya set the tempo for the prearranged choreographed diplomatic script. The sequence of the sorry spectacle went like this.

The Supreme Court upholds the death sentence to play to domestic opinion by being seen to stand up to the West, and to avoid calling into question the farce of a trial conducted by its judicial system.

The families then get bought off to gracefully pardon the medics. The Supreme Council then stalls for days, keeping the West waiting at its feet, before finally commuting the death sentences to life imprisonment, and opening the way for extradition of the six to Bulgaria.

Instead of extraditing the medics immediately, Libya continued its bad faith, knowing that with the West so close to resolution of the crisis, it could still try to raise its price. Right until the final hour of their release, Libya haggled as if the medics were carpets in a Tripoli souk, and used delaying tactics, to win further concessions.

In short, the West has been forced to appease Libya, and ultimately reward it for taking six health workers hostage for eight years. This all is difficult to swallow. The six were not given a fair trial, prosecution evidence was fabricated, and scientific evidence that would have exonerated the medics ignored. Their trials were a kafkaesque mockery that trampled on justice.

But that outcome was perhaps inevitable. From the outset, the six were pawns, caught up in global geopolitics. Once sucked into that quagmire, respect for fundamental human rights such as the right to a fair trial, became just one element in a wider basket, that included Libya’s renunciation of weapons of mass destruction, it’s utility as an ally in the war against terror, not to mention that Libya’s coming in from the cold opened up to for Western economic interests the goldmine of the world’s largest unexplored oil reserves.

Once the case had become politicized, it was inevitable too that the solution would have to be political. The campaigns by Nature, human rights groups, scientific organizations and lawyers, acknowledged this reality from the outset, and understood well that the only real pressure point available was to raise international public opinion and awareness to force Western governments to do more to resolve the case.

As well as defending the fundamental principles of a fair trial, and the right for relevant evidence to be heard, the focus on calling for the scientific evidence to be heard was considered by the defence as its best card in the run up to the end of the trial last autumn.

Had Libya accepted to have had the scientific evidence heard in court, the prosecution case would have collapsed like a pack of cards. But if as was most likely, it refused to do so, it would also expose with clarity that the trial was anything but fair, and provide a fulcrum, a focus, to leverage public opinion, and consequently political opinion.

The massive international outrage after the 19 December death penalty verdict was in large part prompted by the fact that science had demonstrated the emptiness of the prosecution case, leaving the world in no doubt that this was an appalling miscarriage of justice. The scale of the outrage led to more intense diplomatic activity, in particular by the EU.

The human rights case was also not entirely lost. After the verdict, the EU broke temporarily with its policy of ‘silent diplomacy’ — refraining from public criticism of Libya’s handling of the case and relying on behind-the-scenes discussions – and condemned in no uncertain terms the human rights violations, and abuse of scientific evidence in the case. This, combined with the fact that Bulgaria became a member of the European Union at the start of the year, led to pressure for a speedy resolution of the case.

The United States meanwhile has been absent from the case, and mute on the human rights abuses in the case. Its absence though was perhaps not a bad thing after all, given the current administration’s own abyssmal record on human rights, which deprive it of moral authority.

Unbelievable perhaps though, that the administration couldn’t find anything better to do on 11 July, the day the Libyan Supreme Court upheld the death verdict, than to announce it would appoint an ambassador to Tripoli for the first time in more than 25 years.

Realpolitik all along meant that the six could probably never have hoped that the international community would force Libya to give the six a fair trial. That the medics are free at last is already a major victory, and hat’s off to the EU and British diplomats who worked patiently to put together a solution to the case — they are right to be livid with France and the Sarkozy family’s shameless attempt to steal the limelight and take all the credit for the release.

The 1998 outbreak was a triple tragedy — for the six unjustly imprisoned, and for the infected children and families. Exoneration of the medics must be the next step. And as Vittorio Colizzi, an AIDS researcher at Tor Vergata University in Rome, Italy, who campaigned for scientific evidence exonerating the medical workers to be considered by the Libyan courts, says: “We must not forget the children.” The third victim, which has not often been mentioned, is the struggle to have nation states abide by the fundamental international principles of justice and human rights enshrined in treaties to which they are, on paper, parties to.

Declan Butler

July 24, 2007


Filed under: HIV,Justice,Libya,Uncategorized — admin @ 5:16 pm

By now you will all have heard the good news that the six foreign health workers have finally been freed. I’ve written an update in Nature tonight — Libyan ordeal ends: medics freed.

I’d like to thank the many hands, from the EU and British diplomats who worked patiently behind-the-scenes, to the many bloggers, scientists, journalists, lawyers, and human rights groups, who have all contributed to resolution of this politically-complex case.

It has been a long and tumultuous campaign, and over the past months, I’ve had the pleasure and opportunity of working closely with many incredibly committed people all pulling in the same direction to achieve one goal — today’s liberation — with many of their efforts often far from the public glare of the cameras.

Today is a great day, so let’s celebrate it. The full legal and diplomatic history of this case will take time to dissect, as will its implications. On the longer-term implications, Physicians for Human Rights, an organization that has been highly-active behind the scenes has issued a very pertinent statement tonight — “Exonerate Pardoned Bulgarian Nurses and Palestinian Medic“.

And as Vittorio Colizzi, an AIDS researcher at Tor Vergata University in Rome, Italy, who campaigned for scientific evidence exonerating the medical workers to be considered by the Libyan courts, says: “We must not forget the children.” The 1998 outbreak was a double tragedy — for the six unjustly imprisoned, and for the infected children and families.

And as a historical note, here’s a list of everything Nature published on this case recently

Libyan ordeal ends: medics freed

Declan Butler (24 July 2007) doi:10.1038/448398a

High noon in Libya

Declan Butler (17 July 2007) doi:10.1038/448230a

Libyan court upholds death sentences

Declan Butler (11 July 2007) doi:10.1038/news070709-6

Supreme Court hearing starts for medics facing death penalty
Declan Butler (20 June 2006) doi:10.1038/news070618-12

Diplomatic talks spur hope in Libya HIV case

Nature 447, 624—625 (7 June 2007) doi:10.1038/447624b

Libya and human values
Nature 445, 2 (4 January 2007) doi:10.1038/445002a

Europe condemns Libyan trial verdict
Declan Butler
Nature 445, 7 (4 January 2007) doi:10.1038/445007a

Medics sentenced to death in Libya
Declan Butler (18 December 2006) doi:10.1038/news061218-3

Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak
Tulio de Oliveira et al.
Nature AOP (6 December 2006) doi:10.1038/444836a

Molecular HIV evidence backs medics
Declan Butler
Nature 444, 658-659 (7 December 2006) doi:10.1038/444658b

Libya death penalty trial ends; verdict 19 December
Declan Butler
News@nature (6 November 2006) doi:10.1038/news061106-3

An open letter to Colonel Muammar al-Gaddafi
Richard J. Roberts and 113 fellow Nobel Laureates
Nature AOP (2 November 2006) doi:10.1038/444146a

A shocking lack of evidence
Declan Butler
Nature 443, 888-889 (26 October 2006) doi:10.1038/443888a

Protests mount against Libyan trial
Declan Butler
Nature 443, 612-613 (12 October 2006) doi:10.1038/news060925-2

Forgotten plights
Nature 443, 605-606 (12 October 2006) doi:10.1038/443605b

Dirty needles, dirty dealings
Charlotte Schubert
Nature 443, (2 October 2006) doi:10.1038/news061002-3

Bloggers rally for liberation of the ‘Tripoli Six’
Declan Butler
news@nature (25 September 2006) doi:10.1038/443612a

Libya’s travesty
Nature 443, 245 (21 September 2006) doi:10.1038/443245b

Lawyers call for science to clear AIDS nurses in Libya
Nature 443, 254 (21 September 2006) doi:10.1038/443254b

Excerpts from my brief article tonight:

A French government aircraft carrying six medical workers convicted of deliberately infecting children with HIV touched down in Sofia, Bulgaria, on 24 July, ending their 8-year ordeal in a Libyan prison.

Their release is the final scene in meticulously crafted negotiations between the European Union (EU) and Libya, which sought a way for Libya to climb down on the case without being seen to concede to Western pressure. Diplomatic efforts intensified as a result of international public and political outcry after the six medical workers were sentenced to death in a retrial on 19 December 2006.

“The efforts to mobilize Western governments to act by increasing international public opinion have paid off,” says Emmanuel Altit, a lawyer from the medical workers’ international defence team. The concerted efforts of the scientific community around the case played a “fundamental role” in changing the trajectory of the case and helping to secure today’s outcome, he adds.

Libya has long used the six medical workers as bargaining chips and political pawns in its international relations. Right until the final hour of their release, Libya haggled to win further concessions to improve its political and trade ties with the EU.

Benita Ferrero-Waldner, the European commissioner for external relations, was also on the aircraft with the freed health workers. She, the EU and Britain, were the main players working patiently behind the scenes to secure the release. On the Libyan side, the key force in freeing the workers was Seif al-Islam Gaddafi, son of the Libyan leader Muammar al-Gaddafi, through his charity the Gaddafi Development Foundation. He is thought to be personally convinced that the outbreak was accidental.

More controversial is the role played by another passenger on the plane, French first lady Cécilia Sarkozy. France has not had a prominent role in the negotiations, and her last-minute intervention is widely considered to be a thinly veiled bid by her husband to steal the limelight that may, in fact, have weakened the EU’s negotiating position in the talks.

July 17, 2007

High Noon in Libya

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 4:19 pm

Still waiting on a decision from the Supreme Council. Meanwhile, I’ve written a long article in Nature, “High Noon in Libya,” available online tonight, tracing scientists efforts in the case

June 20, 2007

Update on Libya death penalty case

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 5:42 pm

I’ve a brief update on the Libya case on Nature news online tonight – see ‘ Supreme Court hearing starts for medics facing death penalty ‘ . It’s an update to one earlier this month in Nature — Diplomatic talks spur hope in Libya HIV case.

We are now in the crucial final phase of the Tripoli six case. This morning, Libya’s Supreme Court heard the appeal of the six. There will be no further hearings, and it will rule on 11 July. Meanwhile, the families of the Libyan children are discussing a possible settlement with the European Union, and an announcement on that is expected Friday.

As in the past in this case, details and plans keep shifting — eg until very recently, a verdict had been expected today – but the overall thrust now looks cautiously optimistic for a rapid resolution of the case.

The campaigns by scientists and others to draw attention to the science of this case during the course of the trial last autumn have borne fruit, contributing to the depth of international protests after the 19 December death penalty verdict. This — combined with the fact that Bulgaria became a member of the European Union at the start of the year — – see ‘ Europe condemns Libyan trial verdict‘ – has resulted in increased diplomatic activity, in particular by the EU, to find a solution. Libya too increasingly seems sincerely to want to turn the page on this tragic affair.

Talks have intensified over the past month
, with visits to Libya by Tony Blair, Benita Ferrero-Waldner, the EU Commissioner for External Relations, and Frank-Walter Steinmeier, the German Foreign Minister.

The contours of the solution remain hinged on international humanitarian aid to provide high-quality life-long treatment of the infected children, and support for their families. That’s important, and addresses one of the concerns of the families: that once the spotlight turns away from the case, following any release of the healthcare workers, the children’s care might be forgotten about. With lifelong care, including existing modern anti-retrovirals, as well as anticipated therapeutic advances, the children might expect to lead reasonably normal lives.

The EU’s Ferrero-Waldner, who has condemned the conduct of the medics’s trial, has shown sensitivity to the children’s plight. “We have come here to acknowledge the suffering of the children,” she said 10 June during her Libya visit, “and have understanding and sympathy for the families, who must have been shocked by the horrible events of the AIDS case.”

In terms of negotiating an outcome, she said “I think we have advanced a lot.” Clearly if the families and the EU do reach agreement on a humanitarian package, this will greatly improve the climate for the 11 July ruling – Islamic law can interpret this as blood money, which could allow the charges to be dropped. But irrespective of what the verdict is on 11 July, the death sentences could still be annuled, or commuted, by the Supreme Council for Judicial Authority, a political body spanning Libya’s executive and judiciary authorities.

Amidst the flurry of diplomatic negotiations a key player is Seif al-Islam Gaddafi, a son of the Libyan leader.
He heads the Kadhafi Foundation for Development, a non-governmental charity, and helped mediate the compensation deals for both the bombings of a US airliner over Lockerbie in Scotland in 1988, and of a French airliner over Niger the following year. Those who have met the young Gaddafi have been impressed by what they describe as his thorough grasp of the circumstances of the HIV outbreak, and his sincere commitment to finding a solution.

Many scientists, human rights bodies, lawyers, and others have articulated clearly and publicly throughout this case the principles of the need for justice, a fair and impartial trial, and the proper hearing of scientific evidence.
I think that message has been received, and helped move matters along at an important point in the case. Although exoneration of the medics must be the ultimate goal, the immediate emphasis of European Union diplomats seems more on securing that the six might soon touch down on a tarmac in Sofia. That would already be a large step forward for the six still facing the death penalty in Libya.
Fingers crossed…

April 26, 2007

Families of Bulgarian nurses meet France’s presidential candidates

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 7:28 pm

The families of the Bulgarian nurses met today in Paris separately with Ségolène Royal and Nicolas Sarkozy. Both candidates pledged to make resolution of the case a priority if elected, and to have it on the agenda at the next EU summit on 22 June. This high-level political support is a very important, and welcome, development in the case.

It’s a pity therefore that there is a slightly bitter aftertaste of political recuperation. TF1, one of the main national TV channels here, again demonstrated its political impartiality by running images of the meeting with Sarkozy as headline evening news, but failing to even mention that the nurses’ families met with Royal. Both meetings were arranged by a coalition of European NGOs and individuals, of which I’m part of.

Moreover the families also met, not only with Royal, but Jack Lang, Royal’s adviser — who a few weeks ago visited the nurses in their prison in Libya — and Robert Badinter, who as Socialist interior minister under Mitterrand, abolished the death penalty in France, and has long been a solid supporter of the nurse’s case, and also contributed his political sagesse and experience to the cause. Political credit should be given in such human rights issues — even by electoral and parochial TF1 — where it is due.

April 25, 2007

Virtual Globes and environmental science

Filed under: GIS,Google Earth,Open data,Semantic web,Standards,Uncategorized — admin @ 10:51 am

The UK National Institute for Environmental eScience (NIEeS) recently organized a scientific workshop at Cambridge University on environmental research applications of Google Earth and other virtual globes; some of the presentations are now available online here.

April 18, 2007

Bush commends Darfur Google Earth layers; I recount the history of the project

Filed under: Blogging,GIS,Google Earth,Open data,Uncategorized — admin @ 9:11 pm

For what it’s worth, Georges Bush tonight commended the Darfur layers in Google Earth built by a group of volunteers (including yours truly), and endorsed by Google and the United States Holocaust Memorial Museum. On tonight, I tell the story of how this project evolved.

To read more of that history, see below:

Nature on France’s presidential elections

Filed under: Uncategorized — admin @ 6:06 pm

In the week of the first round of France’s presidential elections, Nature takes a unique 9-page look at what the incoming president will mean for French research. Segolene Royal, Nicolas Sarkozy and Francois Bayrou, the only contenders in the race who might ultimately win the presidency, go into unprecedented detail on their plans for French science and technology in response to Nature’s questions.


April 10, 2007

Genocide information in Google Earth

Filed under: GIS,Google Earth,Justice,Open data,Uncategorized — admin @ 3:12 pm

I’m pleased to let you know about Crisis in Darfur, a Google Earth layer that assembles data, photographs, and eyewitness testimony and which will be officially announced today by Google and the US Holocaust Memorial Museum. It will appear in Google Earth under the Global Awareness layer in the left hand panel of Google Earth .

April 6, 2007

Send Senators Joseph Biden and Patrick Leahy an appeal on the Libya death penalty case

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 6:02 pm

Physicians for Human Rights has launched a web page to send a message to the US administration on the need to resolve speedily the case of the medics facing the death penalty in Libya. You can access the sign on page here. Bloggers, please sign up, and forward this link to other bloggers/media. See PHR’s recent letter to Colonel Gaddafi here.

Bianca Jagger to support medics in Libya

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 5:55 pm

Bianca Jagger will arrive in Bulgaria tomorrow to lend support to the “You are not alone” campaign.

George Michael will also hold a concert in May in Bulgaria to back the cause. The two join a list of celebrities moved by the double tragedy; the children infected with HIV, and these health professionals unfairly imprisoned and sentenced to death.

Let’s hope their support can help mobilize public opinion to galvanize ongoing political and diplomatic efforts to alleviate both tragedies.

US Deputy Secretary of State John Negroponte to visit Libya next week

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 5:36 pm

I’ve already posted on the public ambivalence of the US State Dept on the Libya death penalty trial — see post here.

John Negroponte, the number 2 in the State Dept will visit Libya next week, the highest-ranking US official to visit Libya since the US and Libya resumed full diplomatic relations last May. The talks will focus on Darfur. The US must ensure that the case of the six condemned medics is also high on the agenda.

See Reuters report here

“Justice in Libya? Let Scientific Evidence Prevail”

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 5:24 pm

That’s the title of a recent editorial in the Journal of Infectious Diseases, one of the top journals in this field. You can access the full article here.
Concluding paragraph:

How will this sad and deplorable episode end? Six foreign health care workers have now been jailed in Libya for ∼8 years, reportedly tortured, and now once again (on 19 December 2006) sentenced to death. Appeals are being considered, and ransom negotiations continue. Assuming the presumption of innocence as a basis for a fair trial, it must be stated that, by any objective standard, there is no scientific evidence to convict anyone of deliberately infecting unfortunate Libyan children. Moreover, epidemiologic and molecular evidence demonstrates that the HIV strain that caused the nosocomial outbreak was circulating in the hospital before the arrival of the foreign health care workers, and poor hygiene standards, such as the reuse of needles, were reportedly widespread. We can only hope that world pressure will continue until this miscarriage of justice is reversed. As noted by Ahuja et al., what has happened in Libya has sent “a chilling message to all health care workers who choose to work in difficult circumstances to deliver life-saving care to HIV-1–infected or at-risk people worldwide” [9, p. 924]. At a time when enormous progress is being made in the rollout of antiretroviral drugs to the developing world, we can ill afford such chilling messages. Let us all continue to exert whatever individual and collective pressure we can to bring this injustice to an end.

April 4, 2007

10 major US medical groups call for release of hostages in Libya

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 9:33 pm

In the run up to the Supreme Court hearing of the appeal of 5 Bulgarian nurses and a Palestinian doctor in the death penalty trial in Libya — expected as soon as end month — there will be growing international activity. On 23 March, 10 major medical associations wrote to Colonel Mu’ammar al-Qadhafi arguing the case for the release of what some describe as political and judicial hostages. A coalition of European organizations will be launched this month also.

Exclusive: Joan of Arc’s relics exposed as forgery made from Egyptian mummy

Filed under: Uncategorized — admin @ 4:34 pm

I’ve a quirky but fascinating exclusive in a news article in tonight’s Nature. Here’s the link.


The relics of St Joan of Arc are not the remains of the fifteenth-century French heroine after all, according to European experts who have analysed the sacred scraps. Instead, they say the relics are a forgery, made from the remains of an Egyptian mummy.

Philippe Charlier, a forensic scientist obtained permission to study the relics — cloth, a human rib and a cat femur — from the French church last year. He says he was “astonished” by the results. “I’d never have thought that it could be from a mummy.”

The researchers used a range of techniques to investigate the remains, including mass, infrared and atomic-emission spectrometry, electron microscopy, pollen analysis and, unusually, the help of the leading ‘noses’ of the perfume industry: Sylvaine Delacourte from Guerlain, and Jean-Michel Duriez from Jean Patou.

A series of clues led to conclusion that the relics were of the mummy origin, reinforced by carbon-14 analysis dating the remains to between the third and sixth centuries BC. And the spectrometry profiles of the relics matched those from Egyptian mummies from the period, and not those of burnt bones. Charlier points out that mummies were used in Europe during the Middle Ages in pharmaceutical remedies.

Millennium development holes

Nature recently published an Editorial “Millennium development holes” on problems with the underlying data used to assess progress to the goals.


Every year, the UN rolls out reports with slick graphics, seemingly noting with precise scientific precision progress towards the goals. But the reports mask the fact that the quality of most of the underlying data sets is far from adequate. Moreover, the indicators often combine very different types of data, making aggregation and analysis of the deficient data even more complicated.

There are decent data for just a handful of indicators, such as child mortality, but for most of the 163 developing countries, many indicators do not even have two data points for the period 1990–2006. And few developing countries have any data for around 1990, the baseline year. It is impossible to estimate progress for most of the indicators over less than five years, and sparse poverty data can only be reliably compared over decades.

Meanwhile, here are links to a few of my recent articles:

Nature launches avian flu site

Filed under: avian influenza,Uncategorized — admin @ 3:33 pm

Nature helped launch interest in addressing the risks of a flu pandemic back in 2005. One of may favourites still is the fictional blog I wrote; The flu pandemic: were we ready?

Since then awareness of the threat has grown and there is extensive blog and media coverage on developments, as well as governmental and other sites providing information.
As an archive of reliable scientific information, Nature has now brought all its avian flu content together on one site, with almost all on free access. Here’s the link.

January 3, 2007

Libya verdict follow-up in Nature

Filed under: HIV,Justice,Libya — admin @ 9:37 pm

The lead story in the first issue of Nature in 2007 is an update on the Libya death penalty case — link here. It is accompanied by an Editorial — “Libya and human values.” Both should be on free access.

A few excerpts from the Editorial:

December 26, 2006

Christmas day and Libya death penalty case

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 12:40 am

I haven’t posted since the death penalty verdict last Tuesday, because I’m still analysing carefully all the different responses and positions. But it is Christmas Day, so I thought I’d post symbolically, just to point out it was on this very day last year that the six were cleared by the Supreme Court of Libya of the charges against them.

One year later, Valya Chervenyashka; Snezhana Dimitrova; Nasya Nenova; Valentina Siropulo; and Kristiana Valcheva, the five Bulgarian nurses, along with Ashraf Ahmad Jum’a, a Palestinian intern trainee doctor, have again been given the death sentence following the 19 December court ruling in the retrial at the Benghazi criminal court.

That is despite the fact that this was not a fair and impartial trial, and that the court refused to hear the considerable body of international scientific evidence that could exonerate the medics, and show that this is a typical hospital-borne spread.

The Libyan children are being treated in European hospitals — thanks in part to a humanitarian fund established by the international community –and this Christmas, our thoughts are also with them and their families. But denial of the problems all health systems face will not help these children, or those children who risk being infected in future through hospital infections in many countries, such as the almost 100 children infected with HIV in a Kazakhstan hospital this summer — see older BBC story here.

Bulgarian media have launched a “You are Not Alone” ribbon campaign for the six — see logo at top of this post. I endorse it, as defending the most basic of human rights; the right to a fair trial. This case is not only about fundamental human rights principles, but also about the role of scientific evidence, and how we face up to, and not deny, the potential health threats to us and our children, posed by deficiencies in all our health systems.

This case should be an issue of health and science, not a power play between governments as it is turning out to be. Let’s get back to the fundamental principles of health, science, and law in this case. And think of the two groups of innocent victims in this case; the six, falsely accused, and the infected children.

December 19, 2006

Libya condemns Tripoli Six to death

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 4:16 pm

By now, I am sure you all will have heard the grim news from Libya. I’ve written a short factual account here: Medics sentenced to death in Libya.

I’ll blog more later, after taking stock. The six health professionals have 60 days to appeal to the Supreme Court — their ultimate chance to obtain justice.

December 18, 2006

Background information resources for Libya HIV case

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 5:45 pm

The verdict in the Libya HIV death penalty trial is expected to be announced tomorrow. Here are a few information resources that may be useful if you are blogging or writing about the trial.

The Council of Europe has a good and succint factual account of the case and the human rights violations.
This blog also has a resource page for the trial providing other background, and links to key media Editorials. This WSJ account by Judy Miller, who visited the prisoners recently, is also well worth a read.
ScienceBlogs has considerable coverage.
Nature has a special focus with free access to articles about the trial.
A selection of recent media and blog articles are bookmarked here.
European efforts to help the affected children are described here.

US State Department’s public face on Libya HIV case

Filed under: HIV,Justice,Libya — admin @ 12:33 am

Sean McCormack is the US State Department’s official spokesman. But he doesn’t seem to be very well-briefed on the death penalty trial in Libya of 5 Bulgarian nurses, and a Palestinian doctor, accused of injecting over 400 children with HIV, even though the verdict is expected next Tuesday.


December 17, 2006

Libyan scientist defends prosecution case in death penalty trial

Filed under: HIV,Justice,Libya — admin @ 8:57 pm

This link is to videos of a press conference held in Geneva last Friday, where the speakers defend the prosecution case in the Libya HIV trial.

One speaker is Mohamed Daw, head of the Department of Microbiology at the Faculty of Medicine, al-Fatah University. Daw was one of five independent Libyan experts, who authored of a 2003 report to the court. Here he defends his report; for an independent assessment of this report, see here. He shares the platform with Ramadan Ali El Faiture, speaking on behalf of the infected children and families.

I will leave you to judge for yourself the depth, rigour, and validity, of the scientific evidence presented.

December 10, 2006

Google Earth avian flu maps updated

Filed under: avian influenza,GIS,Google Earth,Open data — admin @ 11:08 pm

I’ve updated the flu maps to this weekend — link here.. Since August, the spread of avian flu, as reported, has shown a lull, with only a few animal outbreaks, reported, in Indonesia, Vietnam, Cambodia, Egypt, China and South Korea. Over the same period there have been 10 human cases in Indonesia, and 1 in Egypt.

December 8, 2006

Leading international medical bodies plead for charges to be dropped in Libya case after new scientific evidences

Filed under: HIV,Justice,Libya — admin @ 5:44 pm

Citing the new scientific evidence published in Nature this week, “the World Medical Association and the International Council of Nurses have sent a joint letter to the African Union, Amnesty International, the Libyan Government, the Council of Europe and Physicians for Human Rights drawing their attention to new scientific findings casting doubt on the evidence against the accused health professionals.”

The full text of their statement is given below. The World Medical Association,represents more than eight million physicians worldwide. The International Council of Nurses is a federation of 129 national nurses’ associations representing 13 millions nurses worldwide.

Full text below:


December 6, 2006

New scientific evidence in Libya death penalty case

Filed under: HIV,Justice,Libya — admin @ 6:50 pm

New molecular evidence, published online by Nature tonight — “Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak” — and supplementary info — see hereprovides a firm alibi for the six medical workers facing the death penalty in Libya. They are charged with deliberately contaminating more than 400 children with HIV in 1998.

An international team has used the genetic sequences of the viruses isolated from the patients to reconstruct the exact history, or “family tree” of the outbreak. Analysing mutations that accumulate over time has allowed the researchers to work out when different events occurred. The Brief Communication shows that the subtype of HIV involved was present and spreading locally well before the medical workers arrived in Libya in 1998.

The trial of the six ended in Tripoli on 4 November, and a verdict is expected on 19 December. A body of scientific evidence already indicates that the outbreak was caused not by deliberate transmission, but by poor hospital hygiene. These results, by Tulio de Oliveira and colleagues, provide the first independent molecular confirmation.

I’ve an accompanying news article — Molecular HIV evidence backs accused medics — that discusses the case case and how important this new evidence could be — the full pdf, with box is here. Phylogenetic HIV analyses have been used in court cases worldwide involving allegations of accidental or deliberate HIV infection. Thomas Leitner of Los Alamos National Laboratory has provided forensic HIV evidence in more than 30 such cases over the past 15 years. He describes the Nature paper as “compelling evidence that the outbreak had started before the accused could have started it.”

The news article cites several other assessments by scientists who have been involved in HIV phylogenetic evidence presented in court cases of the new findings.

Here are two more comments, that came in after we had gone to press:

The scientific data presented by de Oliveria et al. convincingly establish multiple infections in the children prior to the arrival of the Bulgarian staff in March, 1998 at the hospital. These data sufficiently refute any connection with the staff, directly or indirectly. This is a real travesty given the refusal by the Libyan courts to consider key scientific evidence that gets to the truth of the matter.”

Mike Metzker, Baylor College of Medicine, Human Genome Sequencing Center

Using state of the art evolutionary analyses, they demonstrate that the likely dates for the most-recent common ancestors (MRCAs) of the HCV and HIV-1 viral sequences pre-date the presence of the Bulgarian nurses in the Al-Fateh Hospital. Taken as a whole, the results of the analyses of de Oliveira et al. are highly inconsistent with the allegations of the Libyan prosecutors.”

Gerald Learn, evolutionary geneticist at the University of Washington

Related resources
Nature Libya Focus
My resources page for the trial

November 30, 2006

Blog anniversary, and latest news

This blog is 1 year old today. I’d like to say thanks to all of you for visiting, and often getting in touch.

It’s been an eventful year, with content mostly a mix of posts — too-infrequent 🙂 — on GIS, avian flu and public health, computing, and, of late, the venue for disseminating information on the Libya HIV case, and the campaign to free the six medical workers facing the death penalty — see here and here.

I’ve an article in today’s Nature — Amazon puts network power online — on an interesting form of computing-on-demand from Amazon, that might appeal to many scientists — it is in beta. It costs $0.10 per computing hour, and to store data for $0.15 per gigabyte per month. To get started, see the FAQ, and a guide here.


November 15, 2006

Article on WHO’s new DG — Margaret Chan

Filed under: avian influenza,Uncategorized — admin @ 10:26 pm

With the death penalty trial in Libya and the Nature supplement on Islam & Science, I’ve had to put avian flu and the World Health Organization (WHO) on the backburner over the past few weeks.

In this week’s Nature, though I take at look at Margaret Chan’s election as director general of WHO, and what this might mean for global health.

Update on Iraq kidnapping

Filed under: Justice — admin @ 7:55 pm

I’ve published an update to yesterday’s news item in Nature.

Almost all those taken hostage in yesterday’s mass kidnapping in Baghdad, now appear to have been freed in a series of security force operations.

November 14, 2006

As many as 150 kidnapped at science ministry in Baghdad

Filed under: Justice — admin @ 5:48 pm

I’ve written here before about the assassination of Iraq scientists. Today as Nature went to press as many as 150 were kidnapped at the science/education ministry. We have published a short article online — “Gunmen seize academics at Baghdad ministry.”


November 8, 2006

Scholars at Risk calls for action against murders of Iraqi academics

Filed under: Justice — admin @ 10:37 pm

I’ve written here before about the targetted assasination of academics in Iraq. Tonight, Scholars at Risk has launched an appeal. I’ve appended its text below.


November 4, 2006

Libya HIV trial ends: verdict 19 December

Filed under: HIV,Justice,Libya — admin @ 1:52 pm

The trial of 5 Bulgarian nurses, and a Palestinian doctor, accused of deliberately injecting 426 children with HIV in 1998, has just ended in Tripoli. The court said that the verdict would be announced on 19 December.

More to come later (Update; I’ve just published a very short article in Nature on the end of the trial). For background, and recent news on the case, see Nature’s Focus on the trial, and my “Resources page.“.

November 2, 2006

114 Nobel laureates call for fair trial for Tripoli Six

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 7:50 pm

More than one hundred Nobel laureates have written to Colonel Muammar al-Gaddafi to express their concern over the death-penalty case of 5 Bulgarian nurses, and a Palestinian doctor, accused of deliberately infecting more than 400 children with HIV in 1998.

In the letter, to be published online this week by Nature, 114 laureates affirm the need to ensure a fair trial, and for the appropriate authorities to permit evidence from internationally recognized AIDS experts to be used in this case. It notes that: “Strong scientific evidence is needed to establish the cause of this infection. However, independent science-based evidence from international experts has so far not been permitted in court.”

The next, and probably last, session of the trial is scheduled on 4 November, with a verdict expected shortly thereafter. If the six are convicted, the case would go to appeal in the Supreme Court.

For background, and recent news on the case, see Nature’s Focus on the trial, and my “Resources page” for the trial.

Update on status of Libya HIV trial

Filed under: HIV,Justice,Libya — admin @ 12:26 pm

Apols for not posting earlier, but past 48hrs have been busy. I’ve posted a very brief update on the adjournment of what should have been the last session in the Libya HIV trial here.


The death-penalty trial of six foreign medical workers in Libya, which was scheduled to end yesterday, 31 October, has been extended until this weekend at the earliest.

The medics are accused of deliberately injecting 426 children with HIV at the Al-Fateh Hospital in Benghazi in 1998. Yesterday’s hearing — the eleventh of the trial that began 11 May — was the first time that the defence had argued its case.

The sitting was scheduled to be the last day of the trial, but the prosecution argued that they needed a further extraordinary court sitting to respond to the defence arguments. This has been granted for 4 November.

Special issue on Islam and Science

Filed under: Uncategorized — admin @ 12:03 pm


Nature today published a huge special on Islam and Science. I’ve listed it’s contents below, with direct links to the pdfs. It is also available on free access here.

The special, which will also be translated into Arabic, covers a series of issues dealing with science in the 57 member states of the Organization of the Islamic Conference (OIC). Producing the special, the brainchild of Philip Campbell, Nature’s Editor-in-chief, has involved substantial work and preparation by the Nature team. Many of the themes emerged in a meeting earlier this year — held under Chatham House rules — organized by Nature at the Rockefeller Foundation’s Bellagio Centre in Italy, where Nature editors, and eminent scientists, intellectuals and politicians, from several Muslim countries, spent 4 days in fascinating discussions of the many issues.

I’ve been involved in the preparation of the special, and also have written two of its articles, one an analysis of science and other statistical indicators for OIC countries, and the other a Q&A with Mostafa Moin, a medical researcher, former minister of Iran for higher education and for science, and the reformist candidate in Iran’s presidential election last year.

October 29, 2006

Libya trial next Tuesday — update

Filed under: HIV,Justice,Libya — admin @ 9:18 pm

With the Libyan death penalty trial of the Tripoli Six scheduled to end next Tuesday in Libya, I thought I’d post an update on some on the buildup of international pressure over the past few days.

October 28, 2006

Map of press freedom

Filed under: GIS,Google Earth,Justice — admin @ 5:57 pm

Reporters Without Borders released its annual worldwide press freedom index on 23 October. Ive made a quick Google Earth map of the data — click here to view and see screenshot below.

October 25, 2006

Exclusive: Nature article demolishes prosecution’s scientific evidence in Libya HIV death penalty trial

Filed under: HIV,Justice,Libya — admin @ 6:37 pm

Nature has obtained an Arabic to English translation of the ‘scientific evidence’ which has been key to the prosecution’s case in the trial of six medics in Libya, and asked top international AIDS and health scientists to assess it. They unanimously conclude that the evidence is a compilation of conjecture and supposition, that could not even justify suspecting the medics, let alone holding them in prison for 7 years on death penalty charges. The next, and last, session of the trial is next Tuesday (31 October), and a verdict will come in the days or weeks after.

Nature took this exceptional action of asking internationally-renowned scientists to review prosecution evidence, because the Tripoli court has denied requests by defence lawyers to have evidence from international scientists heard. So if the Libyan court refuses to hear what independent top scientists have to say, I feel it is my duty to at least have them aired before the international community, so that it can judge for itself.

October 24, 2006

44 top scientists call for Tripoli Six release in Science Magazine

Filed under: HIV,Justice,Libya — admin @ 4:18 pm

Science magazine has today joined the campaign on the Tripoli Six. Great to see the world’s two largest science magazines brothers in arms on this case. The full letter is available here.

Scientists Call for Release of Healthcare Workers in Libya Wrongly Accused of Intentionally Infecting Children with HIV.


October 23, 2006

UK Times on Tripoli Six

Filed under: HIV,Justice,Libya — admin @ 5:42 pm

The UK Times has an Editorial piece in today’s edition: Science rallies to save the Tripoli Six from Gaddafi’s firing squads

October 20, 2006

Mp3 available of Leonard Lopate broadcast on Libya medics case

Filed under: HIV,Justice,Libya — admin @ 5:47 pm

If you would like to listen to last nights Leonard Lopate WNYC show on the Tripoli Six the MP3 of the half-hour segment is now available online. Leonard discussed the case with me and David Stamps, vice president of Amnesty International USA. To download the MP3 file — click here.

Update: WYNC tell me that I can embed the audio in my blog post, so here goes my attempt.

October 18, 2006

The New York Academy of Sciences writes to Mu’ammar al-Gaddafi

Filed under: HIV,Justice,Libya — admin @ 8:56 pm

The New York Academy of Sciences has let me know that the letter they sent on the Libyan case is now available on the Web here.

I’ve reproduced it below:

Federation of the European Academies of Medicine writes to Mu’ammar al-Gaddafi

Filed under: HIV,Justice,Libya — admin @ 5:55 pm

The Federation of the European Academies of Medicine (FEAM) has written this letter to His Excellency Mu’ammar al-Gaddafi. The letter concludes:

October 16, 2006

New York Public Radio to air 1h broadcast on Libya case

Filed under: HIV,Justice,Libya — admin @ 6:23 pm

The Leonard Lopate Show on New York Public Radio (WNYC) will run a 1h broadcast on Thursday on the Tripoli Six and the current trial as part of its weekly “Underreported Series.” I’ll be the invited guest, and the live broadcast (1-2 pm EST) will cover the background of the case, where the trial stands now, and discuss its implications for the scientific community, for foreign health professionals, for human rights in Libya, etc, and the mounting protests against the trial.

It will also be broadcast on the Web here, or you can sign up to get the podcast here. This will be an excellent opportunity to get the facts of this poorly-publicised case out to a wider public, as the title of the series suggests.

Update (20th October): finally we had a half-hour segment. What was great was that David Stamp, vice president of Amnesty International USA, also joined the show. The MP3 file of the show is now available — to download click here.

October 15, 2006

Resource page for HIV Libya trial

Filed under: HIV,Justice,Libya — admin @ 7:28 pm

Many of you have expressed difficulties in being able to quickly obtain information on the Libya HIV case, or actions that can be taken. To try to help with this, I’ve today created a very rough “resources page,” where I will try to centralize key reports, links, and action guides. I will keep this updated, so if you have any good links please send me them on

I will also shortly add court and other key documents.

October 14, 2006

Pressure grows for fair trial for Tripoli Six

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 7:49 pm

This post is a word of thanks to all bloggers for their posts — now more than 200 — helping to keep up attention in this crucial phase of the Tripoli Six trial before the court’s last sitting on 31 October. Here are just two good examples among the many: today The Daily Kos, the world’s largest political blog, and Effect Measure, a progressive science blog, both published updates — see here and here.

This is in addition to renewed efforts this week, by the New York Times, who should be congratulated for being the first mainstream media to grasp the new current urgency in this long-running trial, and the many human rights and science bodies who have likewise weighed in over the past week with their renewed support — see here, here, here, and here.

This effort is all the more admirable as one of the biggest difficulties of maintaining sustained attention on this issue is that events occur only very sporadically, with long intervals in between, making hard news angles few and far between.

There are now less than three weeks before the end of the current trial in Libya, three weeks where sustained pressure can influence the outcome of the verdict — and remember that the verdict will be the only news on the case that most of the mainstream news agencies will likely report on in the coming weeks.

New York Times editorial on Libya case

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 9:33 am

The New York Times today published a strong editorial — “A Medical-Legal Travesty in Libya” —
As one can seen from my last few posts, momentum — for international pressure for a fair trial and for the scientific evidence to be heard in the case — is now building in the crucial run up to the next and last court session in Tripoli on 31 October.

Excerpts below:

October 13, 2006

UK science bodies call for fair trial in Tripoli Six case to avoid “judicial murder.”

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 10:24 am

The UK Times has today published a letter — link here — from Lord Rees, president of the Royal Society, Sir Keith Peters, president of the UK Academy of Medical Sciences, Ian Gilmore, president of the Royal College of Physicians, and Thomas Lehner, from Kings College, London. The letter, “Foreign workers at risk in Libya,” concludes with this sentence:

“We ask the medical and scientific authorities of the United Nations, Arab countries, United States and European Union (Bulgaria will join the EU in three months) to exert their utmost influence on President Gaddafi to prevent what might amount to judicial murder.”

October 11, 2006

Three pages of Nature on Science & Human Rights

Filed under: HIV,Justice,Libya — admin @ 9:56 pm

Dear all
Broadening out on the Libyan HIV case, given that the trial will not resume until 31 October, tomorrow’s issue of Nature takes a look at the Libyan case within the wider context of science and human rights. I’ve a two-page story in, and Nature itself also has an editorial on the topic — they should be on free access. I’m up to my neck in deadlines, but will also endeavour to so some digging on this case in the weeks to come.

Here are a few excerpts from the Editorial.

October 10, 2006

Map for World Day Against the Death Penalty.

Filed under: Justice — admin @ 10:31 pm

Today is World Day Against the Death Penalty. It is also the 25th anniversary of the abolition of the death penalty in France.
To commemorate the events, I’ve made a GE map of the status of legislation worldwide, based on data from Amnesty International.

October 7, 2006

Physicians for Human Rights adds its voice to Libya medics’ case

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 8:40 pm

Physicians for Human Rights has tonight weighed in again on the Tripoli Six case, with this alert. I’ve appended its text, which is a good explanation, below.


October 6, 2006

More on CIESIN data

Filed under: GIS,Google Earth — admin @ 6:47 pm

Greg kindly posted a comment to my earlier post on the CIESIN poverty maps, to let me know that CIESIN is making GE versions of its data via WMS. I’m promoting it to a post. I’ve made a network link to view some of his files here; the resolution of the images increases as one zooms in.

October 5, 2006

Amnesty International issues alert on Tripoli Six

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 10:24 pm

See statement here.
The full text is appended below:

October 4, 2006

AAAS issues alert on Tripoli Six

Filed under: HIV,Justice,Libya — admin @ 5:50 pm

The American Association for the Advancement of Science (AAAS) Science and Human Rights Program has just released this urgent alert to its extensive human rights network on the news developments on the case described here. Their appeal page also contains a useful letter generating tool.
The AAAS has taken an active interest in this case in the past, and it is good to see it weighing in again, as it has significant clout. Other scientific human rights organizations tell me that they will also be shortly issuing renewed alerts. I will keep you posted.

The full text is appended below:

October 2, 2006

Nature review of ‘Infection!’ documentary

Filed under: HIV,Justice,Libya — admin @ 6:41 pm has a review up this evening of Mickey Grant’s documentary on the six medics risking execution in Libya on concocted charges of infecting 426 children with HIV. You will remember that Mickey made his full length 1h22min documentary free on Google Video last week to help the blog campaign requesting that Libya’s courts order an independent international scientific assessment of the case, so that the medics’ innocence can be proven.


October 1, 2006

Stunning, and important, new GIS maps of Poverty

Filed under: GIS — admin @ 9:41 pm

Columbia University’s Center for International Earth Science Information Network (CIESIN) released 28 September an important set of new GIS data related to poverty; the project homepage is here. Most of the data are also available as shapefiles — after getting to this page, click “global” or “national” to get them (with comprehensive metadata) — and so allows one to analyse the data against other relevant datasets.

The CIESIN datasets provide global views of indicators such as infant mortality and hunger, with some surprizing results:

Tripoli Six update

Filed under: HIV,Justice,Libya — admin @ 6:09 pm

Effect Measure has published a brief update on the situation, including useful links, such as how to write appropriate, polite, letters. Mike Dunford at The Questionable Authority also has useful links on what you can do.

September 25, 2006

Filmmaker makes full documentary on Libya HIV case available free online

Filed under: HIV,Justice,Libya,Uncategorized — admin @ 7:25 pm

Mickey Grant, a filmmaker from Dallas, Texas, has, in response to the blog campaign, today made his full, 1h 22 min, 2003 documentary on the Libya HIV case, Infection, available free, on Google Video — link here — it’s a raw upload, so for the moment you have to endure a 30 second test pattern before the film actually starts. I mentioned this in my earlier post, but I think his initiative deserves a post of its own.

Bloggers rally for liberation of the ‘Tripoli Six’

Filed under: HIV,Justice,Libya — admin @ 7:08 pm

Last week, I posed a question on this blog: “Can the blogosphere help free the Tripoli six?
Although its too soon to give a definitive answer to that question, it is not too soon to say that it will not be for want of trying. The response of the science blogosphere over the past 5 days has been astonishing, with over 125 posts so far.

So much so, that I’ve written a news article on this evening — Bloggers rally for liberation of the ‘Tripoli Six’ — on the phenomenon.

September 20, 2006

Can the blogosphere help free the Tripoli six? — innocent medics risking execution in Libya

Filed under: HIV,Justice,Libya — admin @ 6:50 pm

“Imagine that five American nurses and a British doctor have been detained and tortured in a Libyan prison since 1999, and that a Libyan prosecutor called at the end of August for their execution… on trumped-up charges of deliberately contaminating more than 400 children with HIV in 1998. Meanwhile, the international community and its leaders sit by, spectators of a farce of a trial, leaving a handful of dedicated volunteer humanitarian lawyers and scientists to try to secure their release.

Implausible? That scenario, with the medics enduring prison conditions reminiscent of the film Midnight Express, is currently playing out in a Tripoli court, except that the nationalities of the medics are different. The nurses are from Bulgaria and the doctor is Palestinian.”

These are the opening paragraphs of an unusually strongly-worded editorial — ‘Libya’s travesty‘ — published in tomorrow’s issue of Nature.

September 17, 2006

The spread of avian flu with time; new maps exploiting Google Earth’s time series function

Filed under: avian influenza,GIS,Google Earth — admin @ 8:44 pm

Google Earth last week introduced new functionality that allows one to map events against time. Clearly this is the ideal way to view the spread of avian flu worldwide, so I have adapted my existing flu maps to it. Only the new maps will be updated. The new link for the time-enabled maps is this one (the KML file).

You WILL NOT be able to view these maps correctly using the standard Google Earth client. You MUST FIRST install the latest GE 4.0 beta — download link here.


September 1, 2006

NASA World Wind Moon

Filed under: GIS — admin @ 7:08 pm

Nature online has a special out tonight on the Moon.

The occasion:

“On 2 or 3 September 2006, Europe’s latest mission to the Moon, a robotic craft called SMART-1, is scheduled to perform a spectacular crash landing, visible to Earth-bound professionals and amateurs alike.
Here takes a close look at the Moon, from its geology to its effects on mankind, from its birth to the future missions planned to build a base on its surface.”

The reason, I mention it here is that alongside I’ve a lighthearted Q&A with Patrick Hogan, project manager of NASA World Wind, on World Wind Moon. It’s a fun general public piece, and not one of my ever-so-serious analytical Nature articles, so I let Patrick get away with a few superlatives as to what he claims is upcoming in the next release of World Wind (1.3.6), due out this month. Let’s see if it is as good as he says:

August 30, 2006

More on flu data access scheme

Filed under: avian influenza,Neglected diseases,Open data,Standards — admin @ 7:33 pm

Nature has an Editorial in this week’s edition — ‘Boosting access to disease data’ — on the Global Initiative on Sharing Avian Influenza Data (GISAID) — see previous post. It also has a short news story — ‘Plan to pool bird-flu data takes off.’

Some excerpts from the Editorial:

August 24, 2006

Global Initiative on Sharing Avian Influenza Data

Filed under: avian influenza,Open data — admin @ 1:45 pm

In a Correspondence published online today by Nature, 70 top flu scientists and health officials, including six Nobel laureates, back a plan to end secrecy over avian flu data. The published letter is available on free access here, and the signatories here.

An accompanying news article — Bird flu data liberated — describes this Global Initiative on Sharing Avian Influenza Data (GISAID), which is intended to encourage scientists and nations to share data rapidly with other scientists worldwide.

I’ve compiled some links to recent related events and Nature coverage here.

I will post related media and blog articles to the Connotea social bookmarking service under the GISAID tag

August 1, 2006

FAO reiterates data sharing policy on H5N1

Filed under: avian influenza — admin @ 9:41 pm

Last week I revealed that since summer 2005 almost no avian flu poultry isolates have gone from Indonesia to the joint network of national and international reference laboratories run by the UN Food and Agriculture Organization (FAO) and the World Organization for Animal Health (OIE).

I therefore found it interesting that today the FAO issued a statement reiterating the policy on data sharing which it announced earlier this year. I’ve pasted its statement below.

July 29, 2006

When new news is old news

Filed under: Blogging — admin @ 11:21 pm

Bob Cringely, the self-acclaimed IT guru who describes himself as a “sex symbol, airplane enthusiast and adventurer [who] continues to write about personal computers and has an active consulting business in Silicon Valley, selling his cybersoul to the highest bidder” has been sounding off — “The Wrap Fish, Don’t They? — about the short half-life of news on the Internet. His story is based on a paper — that he thinks was just published, but which was in fact *just republished*– in Phys. Rev. E 73 066132 – see here.

July 28, 2006

International community driving blindfolded in Indonesia flu battle

Filed under: avian influenza,Neglected diseases — admin @ 7:17 pm

Indonesia is the world’s current hotspot of avian flu, with the concomitant risk of emergence of a pandemic flu strain. Despite this risk, almost no avian flu poultry isolates have gone from Indonesia to the joint FAO/OIE network of national and international reference laboratories since summer 2005, I reveal in a short article tonight.

Some excerpts from the article:


July 25, 2006

More ‘Aaargh plop;’ cat flu in Iraq

Filed under: avian influenza — admin @ 10:02 pm

Back in March I reported on what we know, and don’t know, about the avian flu virus H5N1 in cats. The issue has new resurfaced with a paper in Emerging Infectious Diseases reporting avian flu in cats in northern Iraq — see my story today; “More cats found with bird flu“.

The earlier post commented on the fact that cat infections were more common than recognized:

July 20, 2006

WHO’s in charge?

Filed under: avian influenza,Neglected diseases — admin @ 9:42 pm

That’s the title of an editorial in this week’s Nature looking at the shift in balance of governance in global health away from the World Health Organization, prompted by the plethora of new actors, including the G8 (see the Saint Petersburg communiqué on infectious diseases) the Global Fund to fight AIDS, Tuberculosis and Malaria and the Bill & Melinda Gates Foundation.

Some excerpts

Academics targetted in Iraq

Filed under: Justice — admin @ 8:44 pm

Following a recent news special I wrote on academics being targetted for assassination in Iraq, the International Council for Science (ICSU) has contacted me to let me know that they have issued a statement in response; I hear Pugwash are also looking at the issue.
The 2-page news special on Iraq is here.

Some excerpts:


July 15, 2006

Media pickup of Indonesia sequences

Filed under: avian influenza,Open data — admin @ 11:19 pm

My article on the Indonesia flu mutations has generated a fair bit of press coverage, making the front page of Google News — see here. Reuters, and many other media outlets, have picked up on it also, but the best article I’ve seen so far I think is this one, which gives balanced credit to both WHO’s core data needs in handling outbreaks, while also discussing its difficulties in making data more widely available. Le Monde also has good coverage — in French, as has CIDRAP.

The article has also generated considerable discussion in the blogosphere — see for example, the comments here.

July 12, 2006

Indonesia cluster mutations

Filed under: avian influenza,Open data — admin @ 10:54 pm

Just a quick signpost to an article I’ve published in Nature tonight revealing the full mutations in the recent Indonesian cluster where human to human transmission occurred. Some abbreviated excerpts:

A strain of avian flu that spread through a family in Indonesia, killing seven of the eight people infected, was accumulating mutations as it spread from person to person, according to confidential sequence data seen by Nature. The functional significance of the mutations isn’t clear — most of them seem unimportant. But influenza researchers say the finding reiterates the need for sequence data to be made more widely available, if the virus is to be better understood.

July 6, 2006

Top 50 science blogs

Filed under: Blogging,GIS — admin @ 9:27 pm

Quick pointer to an analysis I’ve done of where science blogs rank in the overall blogosphere; its on free access at
1. Top Five Science Blogs
2. Top Five Science Writer Blogs
3. Top 50 Science Blogs
4. Note on how I did the rankings
5. Five odd facts about the ranking

A note for my fellow flu bloggers; Effect Measure comes in at number 9 of all science blogs with a Technorati rank of 6186, and H5N1, not listed, came in at number 9 in the writers’ category with a Technorati rank of 10159.

Congress members call to free H5N1 gene sequences

Filed under: avian influenza,Open data — admin @ 9:10 pm

I mentioned in a previous post that:

“Dennis Kucinich (Democrat, Ohio) and Wayne Gilchrest (Republican, Maryland) are circulating a letter in the House of Representatives that calls on Michael Levitt, the US health secretary, to require H5N1 sequences and other publicly funded research data “to be promptly deposited in a publicly accessible database, such as GenBank”.

The letter has now been sent, signed by 16 members of Congress: you can read it here.

June 29, 2006

The time for sitting on flu data is over.

Filed under: avian influenza,Uncategorized — admin @ 9:12 pm

Nature has a short but strong editorial today on the problem issue of access to flu data, which I’ve already blogged about here and here. It follows up on our much longer March editorial on the issue — Dreams of Flu Data.

Here are a few excepts, from today’s:

June 20, 2006

PLoS financials

Filed under: Uncategorized — admin @ 7:14 pm

For a change, something other than avian flu. I’ve an article in Nature this week on the finances of the Public Library of Science (PLoS]. I’ve been a longtime advocate of the principles of open access, and open data, but at the same time also keen on experiments to verify its feasibility across various sorts of publications; ie not simplistic “one solution fits all” models — see previous debate here. — This weeks article, published online here, which takes a hard look at PLos’s finances, will I hope contribute to the debate. Comments welcome.
Here’s some excerpts:


May 31, 2006

Breaking the silence: “If this was a test to see whether Indonesia could contain a virus, they failed miserably”

Filed under: avian influenza — admin @ 10:10 pm

The latter quote is from a front-page article I’ve published in Nature tonight on what the experience of the large human cluster of avian flu cases in Indonesia says about the realities of attempting to slow the spread of, much less extinguishing at source, an emerging pandemic in the context of a developing country, with poor health infrastructure.

May 30, 2006

Map update

Filed under: avian influenza — admin @ 11:09 pm

I’ve posted a quick update to the maps. Obvious things to note are the large cluster of human cases in Indonesia, widely discussed in the media, and the less obvious spread of animal outbreaks, almost entirely confined to Europe, over the past two weeks. I’ll have a detailed article on the Indonesian cluster coming out in Nature tomorrow night, and will post about that then.

May 16, 2006

Map update

Filed under: avian influenza,Google Earth — admin @ 11:24 pm

H5n1 maps have been updated — link here. You will notice that there has been a large decrease in the number of outbreaks reported over the last month.
We had a couple of pieces in last week’s Nature on the threat of H5N1 to the Americas — all free access- see :
Avian Flu and the New World
How might it get there?
State’s flu response raises concern.

April 16, 2006

Easter avian flu map update

Map update

This weekend’s update adds a minor change to make it easier to see the latest human cases and animal outbreaks. The initial screen will by default only show — in yellow — those events that have occured since the last map update (see screenshots below). Download the new maps directly to Google Earth by clicking here. For a more detailed explanation of the new maps, click here.

April 6, 2006

Avian flu map weekly update

Filed under: avian influenza,GIS,Google Earth — admin @ 6:37 pm

Last weekend’s scheduled weekly update to the flu maps finally went up tonight, after I found the bug that was causing export errors in the update. Download map directly here.

This week’s update, including the first bird case in Scotland, will go up this weekend.

Featured image from this week: Egypt
(Circles = animal outbreaks; triangles = human cases)

March 26, 2006

A guide to using Arc2 Earth to get data into Google Earth

Filed under: GIS,Google Earth — admin @ 11:18 am

I’d been thinking of documenting the process of using Arc2Earth to quickly export existing GIS data to Google Earth format, as used in the avian flu maps. But Brian Flood, who built Arc2Earth, has now posted a walk-through guide that does the job. See Getting Data into Google Earth using Arc2Earth

March 24, 2006

Mapping avian flu in almost real-time using Google Earth

Filed under: avian influenza,GIS,Google Earth,Neglected diseases,Open data — admin @ 11:53 pm

UPDATE — SEPT 2006; the links below are to the old maps; to see the new time-enabled versions, click HERE — UPDATE

New Google Earth maps of avian flu spread

This is the new beta of an operational service designed to provide Google Earth maps of avian flu spread on a weekly basis for the first time. As well as mapping human cases and poultry outbreaks, the maps also provide additional data on each event, and additional datasets, such as poultry densities worldwide, to let you explore avian flu.

The fact that the maps can now be regularly updated has been made possible largely through technical improvements in the initial beta map computing infrastructure , and new volunteer support in data management.

March 22, 2006

The future of computing; science in 2020

Barely a month after Google Earth made the front cover of Nature, computing is back on the cover again. Tomorrow’s issue contains a big special on the future of scientific computing. All the articles are free, thanks to sponsorship from Microsoft; the special was produced in conjunction with the 2020 report published today by an international group of experts convened by Microsoft. The special is, however, of course completely editorially-independent of Microsoft

The special, by journalists and top computing experts, looks at some of the key emerging technologies and concepts that look set to have a major impact on scientific computing by 2020. I’ve a three pager on “sensor webs” – “2020 computing: Everything, everywhere” — in it; there is also a short pop-up box — “Batteries not included” — on the problems of powering these small remote devices.

March 9, 2006

Cat flu — ‘aaargh plop’ , and next-generation GIS

Filed under: avian influenza,GIS,Google Earth — admin @ 12:31 am

I’ve a short article in Nature tonight summarising the situation on H5N1 and cats. I first raised this issue in an article a month back, before the first cases of cat infections in Germany and Austria.

Thought you might enjoy this excerpt.

March 1, 2006

Reinventing the world’s disease surveillance system

Filed under: avian influenza,Uncategorized — admin @ 11:50 pm

Quick post; I’ve a 2-page article in Nature tonight on the need to reinvent the world’s disease surveillance systems, in particular with respect to avian flu. The problem is so large, that it could have been 15 pages, or a book.

I have my thoughts on what are the roles and responsibilities of international agencies such as WHO, FAO, and OIE, and their own agendas, and their diplomatic and other constraints, and also what are the glaring elements lacking in the current international system, but I’ll save that for a later date in Nature… And yes we can also talk about cats and H5N1; see my article from two weeks ago on this risk.

Here are a few excerpts from tonight’s article:

Arc2Earth now available

Filed under: GIS,Google Earth — admin @ 9:20 pm

In an earlier post, I discussed one of the big obstacles to wider use of Google Earth in science: much professional spatial data are in shapefile format and need to be converted to KML, the format GE uses, to be viewed in Google Earth. Several converters have emerged including KMLer, KML Home Companion, and Export to KML, and the Pro version of Google Earth allows import of shapefiles.

February 22, 2006

Malaria message in a bottle

Filed under: Neglected diseases — admin @ 10:44 pm

I came across an intriguing post on Boing Boing tonight. It reads:

“Little magazines that come stuck to pop bottles
A marketing student’s project to produce little magazines that are shipped under the removable label of a pop bottle is going into commercial production. The idea is to bypass traditional distribution systems and economics, and piggyback on the far-more-sophisticated soft drink distribution infrastructure.”

The coincidence is that when I attended the UN Millennium Project’s Nobel Forum meeting in Stockholm at the end of last month, I discussed the problems in getting information on malaria and other diseases out to remote villages in Africa with Kenya’s health minister, Charity Kaluki Ngilu. I mentioned that even in the most remote areas of Africa one could almost always find soft drinks, and suggested that perhaps she should think about piggybacking health programmes on top of such distribution infrastructures. I haven’t thought about this in detail, but it seems like an idea worth pursuing.

Collection of several hundred bookmarks on virtual globes, science, and GIS

Filed under: avian influenza,GIS,Google Earth,Open data,Social bookmarking — admin @ 2:04 pm

Journalists researching articles come across many interesting web resources, but whereas a few key ones might be linked to in the final published articles, most remain on the journalists’ hard drives, never used or exploited again by themselves, let alone others. During my research into scientific applications of virtual globes, such as Google Earth — articles linked to here — I checked out many web resources. Given that these resources might be useful to others, I’ve now made them all public on Connotea, the free social bookmarking service for science professionals.

In a sense, I’m sharing with everyone some of my effort put into researching the topic, with the thinking that my link collection might provide starting points that are an alternative, and more select, starting point than a Google search for virtual globes and science.

February 15, 2006

Google Earth on the cover of Nature

Filed under: GIS,Google Earth — admin @ 7:34 pm

What on Earth is Google Earth doing on the front cover of Nature, the international weekly journal of science?

This week’s issue contains several pieces on virtual globes, and all are on free access. I’ve written a three-page feature — Virtual globes: The web-wide world — on the various ways scientists are beginning to use virtual globes, such as Google Earth and Nasa’s World Wind. And Al Gore, former US vice-president, who envisioned the Digital Earth in 1998, also gives his thoughts on the new developments, and his initial vision. “Its highest purpose was to use the Earth itself as an organizing metaphor for digital information,” he says in the article.

I discuss the feature in an accompanying podcast.

February 13, 2006

Avian flu — Africa, Thai dogs, catching up

Filed under: avian influenza — admin @ 10:40 pm

Some quick pointers/quick catch up.
I’ve published tonight a piece showing the first scientific evidence of possible widespread infection of dogs with the avian flu virus H5N1; in Thailand: see “Thai dogs carry bird-flu virus, but will they spread it?

January 24, 2006

GIS software

Filed under: GIS — admin @ 9:26 pm

I’ve come across what’s seems to be a large and useful listing of open-source GIS software. Over at Very Spatial, bloggers are also trying to build the definitive list of desktop GIS software. Such initiatives are useful for others to discover what is out there.
My own, less-organized, bookmarks to many GIS resources can be found on my GIS ‘thin blog’ here; the section on GIS & science will be vastly expanded in mid-February.

January 19, 2006

More on Turkey mutations

Filed under: avian influenza — admin @ 5:01 pm

Just a pointer to a long article I’ve published in Nature today on the three mutations found in human cases of H5N1 in Turkey — “Alarms ring over bird flu mutations.
It’s a follow up to last week’s article “Bird flu mutation sparks concern.

For more avian flu news, see my flu ‘thin’ blog or sign up to its RSS feed.

January 13, 2006

Turkey updates to avian flu maps

Filed under: avian influenza,GIS,Google Earth — admin @ 11:00 pm

Given the current interest in the outbreak of H5N1 in Turkey, I’ve exceptionally manually updated the Google Earth global avian flu outbreak maps to show the location of the latest human cases in Turkey (red dots), and links to relevant WHO updates.

January 11, 2006

BBC Radio 5 has a piece on the Google Earth flu maps

Filed under: avian influenza,GIS,Google Earth,Uncategorized — admin @ 12:07 am

Here’s the link

January 4, 2006

Google Earth featured in Nature’s podcast

Filed under: avian influenza,GIS,Google Earth — admin @ 11:21 pm

This week’s Nature podcast features a short interview with me on Google Earth.

Avian flu maps in Google Earth

Filed under: avian influenza,GIS,Google Earth — admin @ 8:16 pm


Nature has a Google Earth map of avian flu outbreaks online tonight.

Download the network link directly from here.

It accompanies an article I’ve published in Nature: “Mashups mix data into global service.” The article also has a box on methods; a shorter version of this post: “Nature gets mashed up.”

The visualization of avian flu outbreaks is the first online map, to my knowledge, of each of the more than 1800 individual outbreaks of avian flu in birds that have been reported over the past two years. It also provides a geographical overview of confirmed human cases of infection with the H5N1 influenza virus.

December 20, 2005

Official: ‘Intelligent design’ is not science

Filed under: Creationism — admin @ 10:45 pm

A Pennsylvania judge has ruled that the Dover, Pennsylvania, school board cannot have “intelligent design” taught in schools. The 139-page verdict concludes: “The secular purposes claimed by the board amount to a pretext for the board’s real purpose, which was to promote religion in the public school classroom.” It concluded that ID was “not science.” Click here for full ruling

December 15, 2005

SETI@home moves home

Filed under: Distributed computing — admin @ 3:47 pm

I’ve a story in today on the BOINC platform developed by SETI@home as a sort of distributed supercomputing operating system for the Internet. SETI@home itself moves onto the new platform today.


December 14, 2005

Wikipedia rivals Encyclopedia Brittanica

Filed under: Wikis — admin @ 7:10 pm

This week’s issue of Nature contains a survey ( it’s on free access) of the quality of a sample of scientific entries in Wikipedia. They emerged as having hardly any more errors than corresponding entries in Encyclopedia Brittanica, often considered the gold standard of encyclopedias. In the survey, in which I was involved, entries were reviewed by external experts in each of the topics.

December 13, 2005

Getting GIS data into Google Earth

Filed under: GIS,Google Earth — admin @ 11:45 pm

Google Earth has set new standards for visualizing geographical information systems (GIS) data. Great for viewing the world’s sightseeing spots, your house, or the nearest hotels and restaurants at your business, or, holiday destination. But that’s a bit limited. The full extent of rich scientific, and other, GIS datasets often cannot yet be easily converted for viewing in Google Earth, because of differences in formats. Speak to anyone at various geographical or scientific databases these days and you often hear the same question: “How can we get our data into Google Earth?” New computing tools are now emerging, however, that are changing this situation.

December 9, 2005

Google Earth for Mac

Filed under: GIS,Google Earth — admin @ 1:19 pm

A Mac version of Google Earth is finally on the way. It’s reviewed here.
Via Ogle Earth

December 8, 2005

Looking for a great open source WYSIWYG web page editor?

Filed under: Software suggestions — admin @ 10:14 pm

One of the best open source WYSIWYG web editors I’ve come across is the cross-platform NVU; it has much of the functionality of Dreamweaver or Frontpage, but it’s free. Also if you are looking for the ultimate open source text editor try VIM; it’s light, powerful, and can handle huge datasets.

More on threatened Indonesian flu lab closure

Filed under: avian influenza — admin @ 9:43 pm

Scientific American today reported on the threatened closure of Namru-2 in Indonesia (see previous post). Associated Press also report that the laboratory may now be given a stay of execution, and that this may be tied to financial terms of any vaccine produced from Indonesian viral samples.

December 7, 2005

Indonesia threatens closure of US military lab that’s key to avian flu fight

Filed under: avian influenza — admin @ 10:41 pm

In tomorrow’s issue of Nature, I’ve a short exclusive on Indonesia seeking to close down Namru-2, a US military lab which has played a key role in helping build the country’s influenza surveillance and testing infrastructure.

Here’s a couple of snippets:

‘Thin blogs’, RSS and ‘social bookmarking’

Filed under: avian influenza,Blogging — admin @ 7:45 pm

Journalists are information professionals. We handle, and select, huge amounts of information every day, and add to it through our own investigations. That’s what we are paid for. But can we use new technologies to help us share our research better, rather than leaving it in notebooks and on our hard drives? I think so; here I kick off with just some personal reflections on bookmarks and web resources.

December 3, 2005

Skype launches video messaging

Filed under: VOIP — admin @ 10:40 pm

Skype, the voice over Internet telephone company, has just launched a free video beta, Skype 2.0, allowing videoconferencing calls. I’ve downloaded it, and it seems to work; more later…
My Skype tel number is declan6016

December 2, 2005

Science Commons details use of Creative Commons licenses for data

Filed under: Open data,Web services — admin @ 11:08 am

John Wilbanks, executive director of Science Commons has responded to the Nature editorial on data access and web services with a FAQ explaining in detail the application of Creative Commons licenses to databases.

From the Science Commons website: “Our goal is to encourage stakeholders to create areas of free access and inquiry using standardized licenses and other means; a ‘Science Commons’ built out of voluntary private agreements.”

November 30, 2005

Nature on blogging in science

Filed under: Blogging — admin @ 9:49 pm

I’ve published in Nature an article on blogging in science; Science in the web age: Joint efforts (pdf here). It’s all now on free access.

It’s part of a special on new developments in science communication on the Web; read the intro, and other articles on search , and digital libraries.
Nature also has an accompanying editorial on web services.

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