Possessed: Parasite Video and Powerpoint

Carl Zimmer at his blog, The Loom:

Well, the talk at Cornell last week went very well. Thanks to everyone who came. If you want to hear me wax rhapsodic about parasite manipulations (and explain how scientists study their evolution), you’re in luck. Cornell has put the video of the talk online. The image is pretty small on the screen, so I decided to post the slide show on my web site here. I suggest opening two screens and advancing the slides as the talk progresses.

At first the sound is a little scratchy on the video and the light balance takes a while to get properly adjusted. But don’t give up–it evens out. You may also hear a baby gurgling from time to time.

Near the end, when I talk about cuckoo birds as parasites, I refer to their host in one of the pictures as a cowbird. I should have said a reed warbler.

And if you are curious to find out more, check out my book, Parasite Rex.

Update: Apparently the video doesn’t work for some readers. I am at a loss.



A tantalizing theory of consciousness

John Clark in Bookslut:

Can you define “consciousness”? Most of us understand the word in context and can use it properly in a sentence. But asked to define it, we are suddenly rendered mute or at best unintelligible. It’s a word that is both vague (cannot be precisely measured) and ambiguous (having multiple meanings). No wonder scientists, philosophers and religious scholars have debated the source, meaning and nature of consciousness for all of recorded history. The argument continues, but a fascinating new book, Second Nature, Brain Science and Human Knowledge may bring us one step closer to resolution.

Nobel laureate Dr. Gerald M. Edelman offers a tantalizing theory of consciousness aimed at satisfying both the scientist and philosopher alike, but also appealing to the reader, like me, who is neither. There isn’t much here for the fundamentalist though. By naming his theory Neural Darwinism, and invoking evolution throughout, I suspect believers in the literal truth of religious texts will summarily reject the book before they get through the preface. Deeper into the book, Edelman does cleverly use the word GOD as an acronym for “Generator of Diversity.” Who can argue with that?

The title, Second Nature, is intended to distinguish human nature from nature in general. It calls “…attention to the fact that our thoughts often float free of our realistic descriptions of observed nature.” Edelman aims to communicate his proposed theory of consciousness without resorting to complex technical detail.  Even so, it is not for the faint of heart in terms of vocabulary.

More here.

Global Health into 2030

In PLoS Medicine, Colin Mathers and Dejan Loncar’s projections of global mortality and disease through 2030.

We project that life expectancy will increase around the world for all three scenarios, fewer children younger than 5 y will die (a 50% decline under the baseline scenario), and the proportion of people dying from non-communicable diseases will increase (from 59% in 2002 to 69% in 2030 under the baseline scenario). Although deaths from infectious diseases will decrease overall, HIV/AIDS deaths will continue to increase; the exact magnitude of the increase will depend to a limited extent on how many people have access to antiretroviral drugs and much more on whether there are increased prevention efforts. Although a projected 6.5 million people will die from HIV/AIDS under the 2030 baseline projection, an even larger number will die from disease attributable to tobacco smoking (8.3 million). By 2030, the three leading causes of burden of disease will be HIV/AIDS, depression, and ischaemic heart disease in the baseline and pessimistic scenarios. Road traffic accidents are the fourth leading cause in the baseline scenario, and the third leading cause ahead of ischaemic heart disease in the optimistic scenario.

These updated projections of mortality and burden of disease have been prepared using a similar methodology to that of the original GBD study, but with some changes described above and with updated inputs and an updated base set of estimates for 2002. We have incorporated a number of methodological improvements and changes. These include carrying out the projections at country rather than regional level, use of separate regression equations for low-income countries, incorporation of information from death registration datasets on recent observed trends for selected causes, and calibration of the regression equations through a comparison of back-projections with observed child mortality trends from 1990 to 2002.

The Imperial Impulse of the Puritans

In the Globalist, Robert Kagan looks at Puritan culture and American expansionism:

The picture of Puritan America as a pious Greta Garbo, wanting only to be left alone in her self-contained world, is misleading.For one thing, Winthrop’s Puritans were not isolationists.

They were global revolutionaries. They escaped persecution in the Old World to establish the ideal religious commonwealth in America, their “new Jerusalem.” But unlike the biblical Jews, they looked forward to the day, they hoped not far off, when they might return to a reformed Egypt.

Far from seeking permanent separation from the Old World, the Puritans’ “errand into the wilderness” aimed to establish a base from which to launch a counteroffensive across the Atlantic.

Their special covenant with God was not tied to the soil of the North American continent. America was not the Puritans’ promised land, but a temporary refuge. God had “peopled New England in order that the reformation of England and Scotland may be hastened.”

The Massachusetts Bay colonists neither sought isolation from the Old World nor considered themselves isolated. The Puritan leaders did not even believe they were establishing a “new” world distinct from the old. In their minds New England and Old England were the same world, spiritually if not geographically.

A 2,000 Year Old Computer

In The New York Times:

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A computer in antiquity would seem to be an anachronism, like Athena ordering takeout on her cellphone.

But a century ago, pieces of a strange mechanism with bronze gears and dials were recovered from an ancient shipwreck off the coast of Greece. Historians of science concluded that this was an instrument that calculated and illustrated astronomical information, particularly phases of the Moon and planetary motions, in the second century B.C.

The Antikythera Mechanism, sometimes called the world’s first computer, has now been examined with the latest in high-resolution imaging systems and three-dimensional X-ray tomography. A team of British, Greek and American researchers was able to decipher many inscriptions and reconstruct the gear functions, revealing, they said, “an unexpected degree of technical sophistication for the period.”

The researchers, led by Tony Freeth and Mike G. Edmunds, both of the University of Cardiff, Wales, are reporting the results of their study in Thursday’s issue of the journal Nature.

They said their findings showed that the inscriptions related to lunar-solar motions and the gears were a mechanical representation of the irregularities of the Moon’s orbital course across the sky, as theorized by the astronomer Hipparchos. They established the date of the mechanism at 150-100 B.C.

Mahfouz’s grave, Arab liberalism’s deathbed

“The Arab world’s passage from progressive secularism to conservative religiosity in the last fifty years is illuminated by the work of Egypt’s greatest writer.”

Tarek Osman in openDemocracy.net:

The death on 30 August 2006 of the Egyptian novelist Naguib Mahfouz – the sole Arab writer to receive the Nobel prize in literature – was marked around the world, and by many of those unable to read a word of his work in its original language. This universal moment, however, was primarily an Egyptian and Arab one, and for more even than the loss of a great writer. For Naguib Mahfouz’s death is also a symbol of the demise of Arab liberalism. It is a century’s story, and the “Dostoyevsky of Cairo” was the one whose books embodied it.

A century ago, the west was not worryingly eyeing the Arab world, with a fear of suicide-bombers and plane hijackers. It was colonising the Arab world – for a number of reasons: the strategic location, the Suez canal, securing trade routes, access to the Indian subcontinent, protection of minorities, exploitation of economic resources, building empires, civilising the savage Saracens.

In resisting the colonists, the Arabs were broadly divided into two camps: the rejectionists and the integrationists.

The rejectionists were predominately Islamists and Salafis: the group that saw the Arab world’s humiliation and defeat as a consequence of its abandonment of the righteous path prescribed in the Qu’ran and the Prophet Mohammed’s sunna.

The integrationists, on the other side of the intellectual spectrum, saw the Arabs’ defeat as a consequence of their lagging behind in all aspects of modern thinking; they saw a dire need for the integration of western modernity into the traditional Arabic/Islamic culture. As one notable integrationist – Taha Hussein, the legendary Egyptian education minister in the early 20th century – put it: “it’s the enlightenment”.

More here.

Trained bees sniff out bombs

From Cosmos Magazine:

Screenhunter_2_17Researchers at the Los Alamos National Laboratory in New Mexico, USA, said they trained honeybees to stick out their proboscis – the tube they use to feed on nectar – when they smell explosives in anything from cars and roadside bombs to belts similar to those used by suicide bombers.

“Scientists have long marveled at the honey bee’s phenomenal sense of smell, which rivals that of dogs,” said Tim Haarmann, who led the research, dubbed the Stealthy Insect Sensor Project. “But previous attempts to harness and understand this ability were scientifically unproven. With more knowledge, our team thought we could make use of this ability.”

Using Pavlovian training techniques in which bees were exposed to the odour of explosives followed by a sugar water reward, researchers said they had trained bees to recognise substances ranging from dynamite and C-4 plastic explosives to the Howitzer propellant grains used in improvised explosive devices in Iraq.

More here.

Ask a Nobel Laureate

From Scientific American:Nobel_1

The Nobel Prize is the highest award in science. Its recipients include nearly every member of the pantheon of secular gods we revere–from Albert Einstein to Marie Curie, along with more recent notables such as James Watson and Francis Crick.

Every December, the current year’s crop of new science Laureates travel to Stockholm to receive their Prizes. While they are there, Nobelprize.org, t he official website of the Nobel Foundation, interviews them for the archives. This year, Nobelprize.org is offering visitors to Scientific American.com the chance to pose questions to the Laureates.

More here.

Does everyone smell different?

From Nature:

Smell There are many good reasons to believe that we all have our own unique smell. Dogs, for example — as pets or police sniffers — seem to be able to distinguish individuals by their smell. And the mother-baby bond is cemented by their own distinctive odours. Now a large and systematic study led by Dustin Penn from the Konrad Lorenz Institute for Ethology in Vienna, Austria, has provided stronger support for the notion that your smell might distinguish you from others — maybe even as much as your face. The researchers further suggest that profiles of individual odours may also fall into two groups according to gender — men more commonly have some smelly compounds, women more commonly others.

The researchers took samples of armpit sweat, urine and spit from 197 adults. Each subject was sampled five times over a ten-week collecting period. They extracted thousands of volatile chemicals from the samples — the type of compound most likely to have an odour — and identified them by chromatography and mass spectrometry. The team found many more different volatile chemicals in sweat than in urine or saliva, it reports in Journal of the Royal Society Interface. This could be because humans have a reason to be able to distinguish themselves by general body odour, more than by marking territory as many other animals do.

More here.

Tuesday, November 28, 2006

Getting Development Right

In Foreign Affairs, Nancy Birdsall, Dani Rodrik, and Arvind Subramanian on economic devlopment:

The contrasting experiences of eastern Asia, China, and India suggest that the secret of poverty-reducing growth lies in creating business opportunities for domestic investors, including the poor, through institutional innovations that are tailored to local political and institutional realities. Ignoring these realities carries the risk that pro-poor policies, even when they are part of apparently sound and well-intentioned IMF and World Bank programs, will be captured by local elites.

Wealthy nations and international development organizations thus should not operate as if the right policies and institutional arrangements are the same across time and space. Yet current WTO rules on subsidies, foreign investment, and patents preclude some of the policy choices made, for example, by South Korea and Taiwan in the past, when rules under the WTO’s predecessor, the General Agreement on Tariffs and Trade, were more permissive. What is more, new WTO members typically confront demands to conform their trade and industrial policies to standards that go well beyond existing WTO agreements. The new Basle II international banking standards, better fitted to banks in industrialized nations, risk making it more difficult for banks in developing countries to compete.

To be sure, not all internationally imposed economic discipline is harmful. The principle of transparency, enshrined in international trade agreements and many global financial codes, is fully consistent with policy independence, as long as governments are provided leeway with respect to actual policy content. A well-functioning international economic system does need rules. But international rules should regulate the interface between different policies and institutional regimes, not erase them.

Bruce Robbins on Bérubé

Bruce Robbins in the Valve on Michael Bérubé and liberalism.

Could I try out one view of Michael Berubé’s book I haven’t heard mentioned? Sure, he’s speaking for academics in the humanities and social sciences whom non-liberals would properly see as liberal. And sure, these people (myself included) are a majority in our departments. But do they see themselves as liberal? Maybe on the phone at home, when reluctantly answering some pollster’s questions in a tongue they know to be alien. But at work, I don’t think so. In literature departments (I teach in one) “liberal” is more often than not a dirty word.

For example, Berubé’s liberalism means secularism. But secularism is by no means English department dogma. On the contrary, the big fashion these days is to declare oneself post-secular; it’s everywhere. This unbending to religion should not be a surprise. After all, the critique of Enlightenment rationality is what English departments were founded on. You can still get more or less automatic assent, if not necessarily wild cheering or a reputation for originality, by rising to denounce any of that rationality’s assumptions or moving parts. Remember, Nietzsche is still the biggest philosopher in this neighborhood. Not a democrat, and not a liberal.

No, I’m not crazy about this. But there are sides of the deep anti-liberal bias in English departments that I have more time for. The active discussion about Burkean conservatism where I live–and you should know that there is one– centers on whether Burke wasn’t after all the true leftist, given that the people to his left never had the qualms he had about British imperialism and that his version of agricultural organicism, though it didn’t stop him from welcoming enclosures, certainly offered a better defense of India than anything else in the British public sphere.

the ghost in the machine

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ONE OF THE great broken promises of the 20th-century view of the future, right up there with personal jet-packs, was the promise of artificial intelligence. AI was supposed to lead to computers that wouldn’t just calculate and organize, but reason and analyze; computers that could really think, like HAL in “2001” or KITT on the 1980s TV show “Knight Rider.” (Of course, HAL turned out to be a homicidal psychopath and KITT was a smug know-it-all, but still, it seemed like a good idea.)

Recent efforts to realize the promise of AI have centered on teaching computers to better deduce meaning from the vast content of the Web, but there’s still a long way to go. In the meantime, however, there’s an alternative type of computerized system that is actually making big strides toward getting computers to think like humans. Publisher Tim O’Reilly calls it intelligence augmentation (IA for short), and it uses a very clever technique. It cheats.

more from Boston Globe Ideas here.

alternative modernity

China_shanghai

The ruins of Shanghai come as a surprise in a city so defiantly modern. Demolished low-rise houses lie in downtown streets next to luxury condominiums with names such as ‘Rich Gate’, the wreckage reflected in the glass façades of tall office buildings. In Dongjiadu, Shanghai’s oldest quarter, bulldozers were expected within the fortnight, the old women squatting silently in the cramped alleys helpless before them.

But you can’t get too sentimental about Shanghai, a place built, like Bombay, in the 19th century on the back of the opium trade. An axis of gangsters, politicians and foreign businessmen ruled the city until the Communist takeover in 1949. Those decades of semi-colonial occupation, when Shanghai came to be known as the ‘Whore of Asia’, glow with old-fashioned glamour in Chinese cinema, in Zhang Yimou’s Shanghai Triad, or Chen Kaige’s Temptress Moon. But the corpses of thousands of the poor were collected every year from the pavements of the International Settlement.

more from the LRB here.

a not entirely disagreeable claustrophobia and a few flashes of light

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So there are three more-or-less mutually exclusive spheres of influence at play in “Magritte and Contemporary Art”: those displaying formal visual correspondences with the Belgian’s paintings (Charles Ray, Ed Ruscha, Vija Celmins), those exploring strictly language-based paradoxes in their art (Mel Bochner, Lawrence Weiner, Joseph Kosuth), and those dealing with Magritte’s legacy of pop-culture market saturation (Douglas Huebler, Jim Shaw, Sherrie Levine). In terms of the works assembled for the exhibition, the last category predictably gets the short shrift, although Pierce Brosnan gives plenty of audio-tour airtime to Shaw’s deliciously prole reading of Magritte’s significance.

But overwhelming that token populist concession, overwhelming the gift shop with its bowler hats and “Ceci n’est pas une pipe” ashtrays —overwhelming everything else when it comes right down to it — is the dazzling, absurd installation designed by John Baldessari. Alongside subtler homages (the security guards wearing bowler hats), Baldessari has carpeted the entire first floor of the Ahmanson with cloud-patterned wall-to-wall and paneled the ceiling with aerial photos of an L.A. freeway interchange, creating a sandwich of disorientation from which Magritte’s cheese emerges triumphant. It’s a courageous and unexpected elevation of Magritte’s stigmatic kitsch-cred to a transcendent and domineering immersiveness. The ridiculous has seldom looked so sublime.

more from the LA Weekly here.

Weekly Review

From Harper’s:

Lauraclassroom_350 Senator John McCain said that American troops in Iraq were “fighting and dying for a failed policy”; Henry Kissinger said that he didn’t believe a military victory in Iraq is possible;[The New York Times] and Army Specialist James Barker admitted that he had raped a 14-year-old Iraqi girl and helped murder her family in March 2006.[BBC News] Tony Blair told Al Jazeera that western intervention in Iraq had been “pretty much of a disaster,”[Times Online] and 40 firefighters in the United Kingdom carried out a two-hour rescue operation to bring a sheep down from a ledge.[Sky News] Syria’s foreign minister visited Iraq to discuss renewing diplomatic relations between the two nations,[Al Jazeera] and a researcher in Germany claimed that the swords of Damascus, which were made from a type of steel known as wootz, have a microstructure of carbon nanotubes.[Nature] Economist Milton Friedman died[The New York Times] and the price of oil stabilized;[BBC News] football coach Bo Schembechler died and Ohio State beat Michigan 42-39.

More here.

Hawaii Survey Yields Many New Species

From The National Geographic:Crab_1

With its conspicuous blue eyes and shiny orange claws, this colorful crab seems hard to miss. But it’s one of many species that had likely never been seen until scientists went exploring in the Northwestern Hawaiian Islands Marine National Monument this fall.

An international team of biologists made the discoveries in October during a three-week survey of a remote coral atoll called French Frigate Shoals.

More here.

Monday, November 27, 2006

The Future of Science is Open, Part 2: Open Science

In Part 1 of this essay, I gave an outline of the scholarly publishing practice/philosophy known as Open Access; here I want to examine ways in which the central concept of OA, the “open” part, is being expanded to encompass all of science.

Terms
Though I am adopting the term “Open Science”, there are an number of similar and related terms and no clear overriding consensus as to which should prevail.  This year’s iCommons Summit saw the conception and initiation of the Rio Framework for Open Science.   Hosted on the iCommons wiki, the Framework is presently an outline consisting mainly of a useful collection of links and does not offer a formal definition.  In a 2003 essay, Stephen Maurer noted that:

Open science is variously defined, but tends to connote (a) full, frank, and timely publication of results, (b) absence of intellectual property restrictions, and (c) radically increased pre- and post-publication transparency of data, activities, and deliberations within research groups.

Jamais Cascio and WorldChanging have been talking about open source science, making a direct analogy to open source software, for some timeChemists Without Borders follow Cascio’s definition in their position statement:

Research already in progress is opened up to allow labs anywhere in the world to contribute experiments. The deeply networked nature of modern laboratories, and the brief down-time that all labs have between projects, make this concept quite feasible. Moreover, such distributed-collaborative research spreads new ideas and discoveries even faster, ultimately accelerating the scientific process.

Richard Jefferson, founder and CEO of CAMBIA, uses the term BiOS (either “Biological Innovation for Open Society” or “Biological Open Source”), and the Intentional Biology group at The Molecular Biosciences Institute talks about Open Source Biology.   Peter Murray-Rust has recently put together a Wikipedia page on Open Data; he writes:

Open Data is a philosophy and practice requiring that certain data are freely available to everyone, without restrictions from copyright, patents or other mechanisms of control.

Though Science Commons, which grew out of Creative Commons, doesn’t use the term “Open Data”, they have a “data project” and the concept is clearly central to their efforts.  Best and most open of all (in my opinion), Jean-Claude Bradley has coined the term Open Notebook Science, by which he means:

…there [exists] a URL to a laboratory notebook (like this) that is freely available and indexed on common search engines. It does not necessarily have to look like a paper notebook but it is essential that all of the information available to the researchers to make their conclusions is equally available to the rest of the world. Basically, no insider information.


Conditions
For what I am calling Open Science to work, there are (I think) at least two further requirements: open standards, and open licensing.

In his introduction to the chemistry-focused Blue Obelisk (group? movement?), Peter Murray-Rust refers to Open Standards as “visible community mechanisms which act as agreed protocols for communicating information”.   What he is talking about is metadata and a semantic web for science.  To see this idea in action, consider the following citation:

Hooker CW, Harrich D.  The first strand transfer reaction of HIV-1 reverse transcription is more efficient in infected cells than in cell-free natural endogenous reverse transcription reactions.  Journal of Clinical Virology vol 26 pp.229-38 (2003)

You can read that, but a computer cannot do anything really useful with the text string as given: it has no idea which part of the string means me and which means Dave, where the title begins and ends, which numbers are page numbers and which are a date, and so on.  Now remember that PubMed, the database from which I got it, contains millions of such citations (and abstracts, and links between papers that cite each other, and so on).  Stored as text strings, they would be impossibly clumsy, but with the addition of a little simple metadata:

Author/s: Hooker CW, Harrich D.
Title: The first strand transfer reaction of HIV-1 reverse transcription is more efficient in infected cells than in cell-free natural endogenous reverse transcription reactions.
Journal: Journal of Clinical Virology
Volume: 26
Pages: 229-238
Year: 2003

the citation is broken down into meaningful fields, each of which can be searched or otherwise manipulated separately.  The computer can now treat each string after “Author/s:” as a series of substrings (author names) separated by commas and ended with a period, the numbers after “Pages:” as a numerical range, and so on and on — which means you can ask the database useful questions, like “show me all the papers written by Hooker, CW between the years 2000 and 2006 and published in J Virol”.  There you have (a very simple example of) the two pillars of a semantic web: metadata and standards.  Examples abound: the Proteomics Standards Initiative, MIAPE, MIAME, Flow Cytometry Standards, SBML, CML, another CML, the Open Microscopy Environment and dozens of others.  Metadata and associated standards are going to be increasingly necessary to scientific communication and analysis as more and more of it takes place online and as datasets grow ever larger and more complex.  Science commons makes the point using the tumor suppressor TP53:

There are 39,136 papers in PubMed on P53. There are almost 9,000 gene sequences […] 3,800 protein sequences [and] 68,000 data sets available. This is just too much for any one human brain to comprehend.

Quite apart from lack of brainspace, there are answers in those datasets to questions that their creators never thought to ask.  In the same way that Open Access accelerates the research cycle and facilitates collaboration, so too does Open Data — and Open Standards is the infrastructure that makes it possible.

In a similar vein, Open Licensing also provides a kind of infrastructure — in this case, for dealing with intellectual property issues.  It’s fine to simply put your product on the web and let the world do as it will, but many people prefer (or, depending on where they work, are legally required) to retain some control over what others do with their work.  In particular, if you are concerned with openness you may want to ensure that the original and all derivative works remain part of the commons (e.g. copyleft rather than copyright). That means reserving at least some rights, which is where licensing comes in. 

As with Open Access, the original model comes from software licenses.  The Free Software Foundation publishes three licenses designed to provide and protect end-user freedoms and maintains a list of other software licenses classified according to compatibility with FSF licenses.  The Open Source Initiative also maintains a list of approved licenses which meet their (slightly less restrictive) standards for Open Source.  If you are looking for a publishing license (for audio, video, images, text and/or software), Creative Commons is the place to go: they offer six main licenses which provide varying degrees of freedom to end-users, a think-before-you-license guide and a handy tool for choosing which license suits you best.  They also offer a number of more specialized licenses and the FSF GPL and LGPL software licenses.  Every CC license is provided in three formats: legal code that will stand up in court, a plain-language summary and a machine-readable version (built-in Open Standards!) that CC-savvy search engines can use to filter results by CC end-user freedoms.  As with the copyleft protections in the GPL, CC offers “share-alike” licenses that maintain end-user freedoms throughout derivative works.  The example that impresses me most strongly with the power of CC licenses is that Public Library of Science journals, collectively the flagship of Open Access publishing, are all released under a CC attribution license.  If you find yourself dealing with someone else’s license — for instance, a publishing company — and you want to provide Open Access, you can use the SPARC author addendum: simply attach a completed copy of the addendum to the publishing agreement and bring the publisher’s attention to it; more than 90% of journal editors will comply.  You can also get an author addendum from Science Commons, who are working with SPARC and will soon offer plain-language and machine-readable versions like those that accompany CC licenses, as well as a web-based tool for choosing and preparing the appropriate addendum.

That covers copyright-based licensing, pretty much; but patenting is a whole different headache for Open practices.  Copyright inheres automatically (though there is a registry) in “original works of authorship” as soon as they are created, but patents are granted for inventions by way of a drawn-out administrative process and on a more complex basis than “who made this?”.  There are also important differences between patent laws in different countries.  The primary test-bed for open licensing approaches has been biotechnology and especially genomics, with particular emphasis on specific gene sequence data and databases .  The concern is that too much patent protection, combined with patents of too broad a scope, will stifle research and in particular exacerbate the difficulties faced by poorer nations in trying to establish research and development infrastructure.

One possible soution, at least for database information, is offered by the HapMap Project‘s “click-wrap” license.  Rather than assigning property rights, this is an end-user agreement that specifically disallows the patenting of genetic information from the database, unless such claims do not restrict others’ free access to the database.  This license has since been abandoned by the HapMap project, however, in order to allow integration of HapMap data into other public databases such as GenBank. 

Other solutions focus on assigning property rights in such a way as to permit Open practices.  Yochai Benkler suggests what he calls publicly minded licencing for universities and academic institutions.  This form of licensing would consist primarily of an “open research license”, whereby the institutions would reserve the right “to use and nonexclusively sublicense its technology for research and education”, and would require a reciprocal license to research such that any (sub)licensee must “grant back a nonexclusive license to the university to use and sublicense all technology that the licensee develops based on university technology, again, for research and education only”.  There is a model for this sort of scheme in PIPRA, a collaboration among public sector agricultural research institutions which employs licensing language that aims to protect humanitarian use.  In a similar vein, Benkler also suggests a second variety of licence, a “developing country license”, which would extend the open protections through development and manufacture to end-products such as drugs, so long as distribution was limited to developing countries.  Noting that University revenues from government research grants and contracts are at least an order of magnitude greater than those derived from patents, Benkler points out that the loss of certain licensing revenue would be minor at most.  The loss of the small possibility of a “gold-mine” patent would be more than compensated by gains in research efficiency and public perception of universities as public interest organizations rather than puppets of big business.

Science Commons has a more specific focus with its biological materials transfer project, which is aimed at retooling materials transfer agreements.  These are the contracts under which research laboratories exchange the physical objects of research — DNA, proteins, chemicals, whole organisms, and so on.  There is no standard format, since even the NIH Office of Technology Transfer‘s Uniform Biological Materials Transfer Agreement (UBMTA), despite wide support, does not cover all eventualities and is frequently modified or replaced with institution-specific MTAs.  I can tell you from experience that these things can be a nightmare.  The one I remember most clearly came from a large pharmaceutical firm which shall remain nameless; they were willing to send us some of their antiretroviral in pure form, provided we signed over our firstborn children and their children unto the seventh generation.  (I exaggerate, but you get the idea.  In the end we crushed up pills supplied by friendly clinicians, and the damn drug did nothing in our assay anyway.)  Science Commons’ efforts in this field have yet to bear fruit (that I know of), but given the Science Commons/Creative Commons track record I have high hopes.

There is also a more fully-developed model available.  The international nonprofit organization CAMBIA offers two BiOS licences designed to create and protect a “research commons” (the Plant Enabling Techology License and the Genetic Resource Technology license) and is currently drafting a third license for health-related technology.  The essence of these licenses is a reciprocality agreement similar in concept to copyleft or “share-alike”, such that

…licensees cannot appropriate the fundamental “kernel” of the technology and improvements exclusively for themselves.  The base technology remains the property of whatever entity developed it, but improvements can be shared with others that support the development of a protected commons around the technology, and all those who agree to the same terms of sharing obtain access to improvements, and other information, such as regulatory and biosafety data, shared by others who have agreed.

To maintain legal access to the technology, in other words, you must agree not to prevent others who have agreed to the same terms from using the technology and any improvements in the development of different products.

In addition to the licenses, CAMBIA maintains BioForge, an open-source platform for research collaboration on which the licenses and other open practices can be, as it were, field-tested.


Definition

I think “Open Science” is the banner under which the various Open X clans might most profitably assemble.  It is punchy, fairly self-explanatory and does not carry any of the potential confusion with related movements in software that might plague “Open Source Science”.  (Nor, for that matter, will it give rise to daft analogies about what exactly is science’s “source code”.)  Moreover, it seems a natural counterpart to the established term Open Access, and is apparently the term of choice for Science Commons/iCommons, which puts the considerable weight of the Creative Commons behind it.  My personal favourite (term and practice) is Open Notebook Science, but this seems better suited to being the name of the most open subset of Open Science practices since, as with Open Access, it is likely that a range of applications will co-exist and co-evolve.

A formal definition will have to wait for future conferences at which scientists and their allies can hammer out the Open Science equivalent of the BBB Declarations.  For now, I think the Wikipedia Open Science stub has the right idea in propounding a sort of meta-definition: “a general term representing the application of various Open approaches… to scientific endeavour”.  Andrés Guadamuz González ventures “the application of open source licensing principles and clauses to protect and distribute the fruits of scientific research”.   In a recent paper (sorry, subscription only; see how useful OA is?) Ibanez et al. put it this way:

The Open Science movement advances the idea that the results of scientific research must be made available as public resource. Limiting access to scientific information hinders innovation, complicates validation, and wastes valuable socio-economic resources. Open Science is an effective way of overcoming the nearsightedness of the contemporary obsession with intellectual property. The practice of Open Science is based on three pillars: Open Access, Open Data, and Open Source.

It seems to me that Access and Data are crucial by definition; you could do Open Science which relied on proprietary software, provided you made the raw data and your publications openly accessible.  It is, of course, more efficient to use software that is available to everyone without intellectual property or cost barriers.  Similarly, open standards and open licensing might not be fundamental to the practice of Open Science, but both make possible such vast increases in efficiency that I would argue for their inclusion in any comprehensive definition or declaration.

In short, Open (Access + Data + Source + Standards + Licensing) = Open Science.


Coda

Once again, this is an enormous topic and I have given only a brief overview; if you spot anything I have missed or got wrong, please leave a comment.  (I am a scientist, after all; I am thoroughly inured to being wrong in public.)  This was supposed to be the second of two essays on the future of science, but I have run out of room and time so there will now be a third instalment.  In that piece I will try to show what Open Science looks like now, in its infancy, and to sketch some of the directions in which it might grow.

Update: part 3 is here.

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Monday Musing: Some Random Thoughts on the Trial of Saddam Hussein

On November 5, one year and 17 days after his trial began, Saddam Hussein was found guilty. Predictably, the trial was subject to criticism and questions of legitimacy before it began, and from quite different sides of the issue no less.

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In the lead up to the war but especially in the wake of the failure to find weapons of mass destruction, the brutality of Saddam Hussein’s regime was used to justify the invasion. Over his reign, Saddam’s attacks on his own civilian populations left nearly a few hundred thousand corpses, even by conservative estimates. If we hold him responsible for the Iran-Iraq War, we can add an additional 1 million killed or wounded.

Against this backdrop, the decision to try him for the massacre in the village of Dujail of 150 Shi’a men and boys following an assassination attempt was a surprise. Images of the weirdly named Anfal massacre of at least 50,000 Kurds (other estimates range into 100,000 to 180,000), especially of the chemical weapons attack on the village of Halabja, had been played regularly in the build up to the war. What the Dujail massacre had going for it was that it was straightforward and the great powers weren’t complicit. The trial thus already began with sweeping the dirt of the great powers, East and West, under the rug.

Halabjadavari_1

From the outset, questions of whether a government set up by foreign victors could legitimately try Saddam Hussein loomed over the trial. Mahathir Mohammed, Ahmed Ben Bella, Roland Dumas, and Ramsey Clark (now, there’s an interesting set) all moved to set up a joint committee to insure a fair trial. Respectable organizations such as Amnesty and Human Rights Watch questioned the independence and impartiality of the court and raise concerns about the trials fairness.

The trial itself saw assassinations, the resignation of judges, death threats against defense attorneys—all of which leads to questions of not whether Saddam did it, but whether the trial process itself was fair. It certainly wasn’t orderly.

I only sporadically followed the trial. I was skeptical that it would achieve much in terms of personal or political justice. Moreover, I was doubtful that it would do much in establishing the political legitimacy of the new Iraqi government. All of which just lead to me cringe or sigh as the reports came in on the trial’s progress.

I couldn’t really imagine anything other than a death sentence, rumors of Rumsfeld’s offer of leniency in exchange for Saddam’s calling on insurgents to disarm and surrender notwithstanding. The task for and before Iraq was its own transformation. Given the regime’s treatment of Shi’as and Kurds, and de facto Kurdish independence in the northern Iraq, it had to reconstitute itself as a polity if it was, is going to stay together. It was also to transition to a democracy. Against this backdrop, Saddam’s execution would have to be something like Cadmus’ slaughter of the cow to the gods in order to establish Thebes or the execution of Louis XVI, that is, something of a foundational sacrifice.

The trial, verdict and execution would be truth and reconciliation, memory and a break with the past, and the legitimation of the new political order and the nation, all of which would have to be achieved in the midst of occupation and civil war, as well as the patronage of the some of the more incompetent political figures in recent and even not so recent history.

Arendt

Maybe it was the constant invocation of the Nazis as an analog for Saddam, but part of me was hoping that out of the coverage of the trial would come the sort of reportage that Hannah Arendt filled the pages of The New Yorker with during the trial of Adolph Eichmann, pieces which became the basis of Eichmann in Jerusalem: A Report on the Banality of Evil.

There were enough parallel issues: the legitimacy of the court trying Saddam; the attempt to have the horrors of Iraqi Ba’athism become the foundation myth (in the sense of mythic, not in the sense of false or not true) which would create a continuity between the peoples of Iraq and a new Iraqi polity; the issue of complicity of Shi’a and Kurdish leaders, the West, the East bloc, China, the rest of the Arab world; the Pontius Pilate like reaction of much of the world to the trial; the nature of international law, crimes against humanity, and genocide. Moreover, there is a tale to be told of the hope and tragic descent into corruption and brutality of much of the post-colonial experience, a trajectory and narrative captured only on occasion and waiting to be captured in the form of the political theory-cum-reportage that Arendt deployed so well. Eichmann in Jerusalem, whatever its limitations, help us to understand something about modernity, the officialese of modern bureaucracy and ethics.

In Saddam Hussein and the experience of Ba’athism in Iraq, I imagine a similar tale could be told of the colonial aftermath, the Cold War, and the devolutions into thuggery.

I thought of Arendt and Eichmann in Jerusalem at the outset of the trial, but was strongly reminded of it after the verdict was read. Arendt famously writes of Eichmann as he goes to the gallows:

He begun by stating emphatically that he was a Gottgläubiger, to express in common Nazi fashion that he was no Christian and did not believe in life after death. He then proceeded: “After a short while, gentlemen, we shall all meet again. Such is the fate of all men. Long live Germany, long live Argentina, long live Austria. I shall not forget them“. In the face of death, he had found the cliché used in funeral oratory … It was as though in those last minutes he was summing up the lesson that this long course in human wickedness had thought us–the lesson of the fearsome, word-and-thought-defying banality of evil.

Right after the verdict was delivered, Saddam’s lawyer delivered a message from the convicted dictator.

“The message from President Saddam to his people came during a meeting in Baghdad this morning, just before the so-called Iraqi court issued its verdict in his trial,” Khalil al-Dulaimi told The Associated Press in a telephone interview from Baghdad.

“His message to the Iraqi people was ‘pardon and do not take revenge on the invading nations and their people’,” al-Dulaimi said, quoting Saddam.

“The president also asked his countrymen to ‘unify in the face of sectarian strife’,” the lawyer added.

If in the original idea of the war crimes and at the same time political trial, verdict and execution were to pave the road for the creation a new democratic, and unified Iraq, then Saddam was clearly attempting to steal the thunder and make his death the founding of a new Iraq in a different way. He would go off to the gallows like a patriarch whose last request of his children is to be more decent and united. It echoed a bad Bollywood movie. But if he was acting like a patriarch whose dying request of his children was to be generous, tolerant, and forgiving, it was more as a patriarch who had molested and brutalized them through out his life. Needless to say, the pleas weren’t being heard.

I avoided watching or following the trial because it was, despite its attempts at uncovering the crimes of Saddam Hussein in Dujail, an exercise in self-deception for all parties involved, and not because it was a victor’s justice. Self-deception, as the late political and moral philosopher Bernard Williams liked to point out, involves a conspiracy between the deceiver and the deceived. The idea that the choice of the Dujail massacre was anything other than a political choice, that the court was really interested in truthfulness, or even the creation of a new Iraq was the deception that all but a few purchased. If the trial of Saddam Hussein was to be one of the first attempts to address the new Iraq responsibly, then it has failed miserably. And we’ve lied to ourselves in thinking so.

Back to back, the self-delusions of Saddam Hussein and the self-deception of the coalition forces do offer lessons. But these seem hard to articulate. The trial, the verdict and the response itself seem to be lessons in (and the inversion has been used before) the evil of banality, of what happens when the quest for deeper political truth and the pressing political concerns of the community are subsumed to the interests of narrow parties. Let’s hope the Anfal trial fares better and that Iraq, its past, and future are more responsibly addressed.

Sunday, November 26, 2006

WHY THE US SHOULD SPRING FOR A NEW PARTICLE ACCELERATOR

“The US must develop a compelling bid to host the International Linear Collider in order to safeguard American science.”

Harold T. Shapiro in Seed Magazine:

Screenhunter_8_6Physics in the United States is at a crossroads. There are scientific discoveries just within reach whose impact is likely to transform and even transcend the field. Yet US particle physics facilities are being closed or converted to other uses, federal investments are stagnating, and the intellectual center of gravity is moving overseas with the construction of new facilities in Europe and Japan.

These were the conclusions of the committee for the National Academy of Sciences, which I had the honor of chairing. Our mandate was to examine the current state, and make recommendations regarding the future shape, of a US particle physics program that has yielded innumerable discoveries and played a defining role in American scientific leadership.

More here.