In anticipation of future performance: Rotary recognized Nigerian president Jonathan Goodluck in April for his vision of a polio free Nigeria. (Photo: Nigeria PolioPlus Committee)

Polio cases across Africa are near zero, with the exception of Nigeria where they are surging, jeopardizing a continent that is close to polio-free after decades of effort. Nigeria and international agencies are taking measures to halt the recrudescence and prevent spread outside the country, but the amount of disease and mobility of populations gives the virus a fighting chance to kindle outbreaks elsewhere on the continent.

With India having rid itself of polio, Nigeria now is the main front in the effort to eradicate the virus. Nigeria is the only African country which has never interrupted transmission of the disease, making it a supplier of poliovirus to its neighbors and the rest of the continent. Nigeria made huge strides, bringing cases down to 21 cases in 2010.  But then public health lost out to politics. Elections in early 2011 turned attention away from polio and cases bounced back to 65 for the year. Already in 2012 there are 35, even though it is the low season for cases. The only other country in Africa to report cases this year is Chad with three.

Vaccination rounds have been scheduled in countries neighboring Nigeria, but polio’s renewed momentum could carry it to any number of places in Africa where population immunity is low. “That’s the big question,” says the Gates Foundation’s Apoorva Mallya concerning the possibility of export. “We are trying a lot of new strategies, but it is definitely a tough challenge,” he said. Outbreaks could go undetected in remote areas, becoming larger and even seeding secondary outbreaks, undoing at least part of the work in getting rid of polio.  At the same time, the Global Polio Eradication Initiative has become adept at swiftly extinguishing outbreaks. And the initiative has returned to the some of the same countries several times already to stamp out recurrences of polio.

The World Health Assembly voted last week to make polio a global health emergency, raising the profile of the issue and perhaps attracting additional funding for a project continuously declaring funding shortfalls. The emergency declaration could also mean travel restrictions for countries that fail to bring polio under control, Nigeria being the obvious candidate. Leaving the country might come to require proof of vaccination.

Polio also continues to roam freely in parts of Pakistan and Afghanistan. That locus is considered a lesser threat for exporting the disease, although polio did cross from Pakistan into China before being quickly smothered.

Nigeria, hard pressed today, is perhaps at best several years away from putting an end to polio. President Jonathan Goodluck has set 2015 as his target, and global health authorities believe Nigerian leadership is sincere in its efforts. As in India, the tactics or “micro plans” for vaccination are changing to emphasize mobile and remote populations which have been consistently missed, perhaps since eradication efforts began decades ago. India shows eradication can be done and, in many ways how, but also the enormity of the effort required.

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Biology’s holy grail, a full mechanistic understanding of the workings of life, is beyond reach according to two recent papers. Computer models that closely replicate the phenomena of a single cell are not possible, and the goal has been dropped.

Over the last decade, researchers have tried to grapple with biological complexity by modeling less complicated organisms. Yeast proved too complex and was replaced by organisms with smaller and smaller genomes, all the way down to tiny Mycoplasma pneumoniae. Unable to reduce genomes any further, scientists have radically reduced expectations for models instead.

In Science last month, researchers described the “popular view,” in which “we progress linearly, from conceptual to ever more detailed models.” The popular, linear view is no more. From now on, models “should be judged by how useful they are and what we can learn from them,” according to the paper’s authors, “not by how close we are to the elusive ‘whole cell model’.”

Alex Mogilner, one of authors and a professor at UC Davis, believes some future discovery might make the whole cell model again possible. “Never say never,” he advised. However, a paper from the Institute for Systems Biology forecloses the possibility for all time:

[N]o practically conceivable model will ever represent all possible physical parameters in a system, nor will enough data ever exist to fully constrain them all. It is also experimentally infeasible to measure, and technically prohibitive to model all possible phenomena in a cell, all possible environmental contexts, and all possible genetic perturbations.

There will be no in silico model of a cell, one that fully recapitulates cell behavior and substitutes for wet lab experiments. “Anyone who thinks we can ever obtain a completely deterministic view of an organism will have a hard job to convince me,” said Marc Kirschner, chair of the systems biology department at Harvard. “It is probably true that the number of equations to describe the events in a single cell is so large that this approach will never work,” according to Kirschner. He does hope to be able to predict “to some accuracy” particular responses of a system.

The implications for the future have yet to be worked out, although Mogilner and colleagues observed that such models were envisioned as enabling personalized medicine. For historical purposes, however, these papers bring an end to a monumentally successful, physics-based program for biology that began roughly a century ago.

Biologist Thomas Hunt Morgan successfully pioneered the methods of physics in biology, elucidating the role of chromosomes in heredity. This “turned out to be extraordinarily simple,” as he wrote in 1919, and nature was entirely approachable. “[I]f the world in which we live were as complicated as some of our friends would have us believe,” Morgan wrote, “we might well despair that biology could ever become an exact science.”

Shortly thereafter, physics underwent a crisis of faith as the discipline moved from an intuitive, mechanistic basis into a new and unsettling quantum era which renounced the Newtonian ideal of casually linking everything in space and time. When DNA was discovered decades later, the Newtonian paradise was regained. As a theoretical physicist turned biologist Max Delbrück said in his Nobel Prize lecture:

It might be said that Watson and Crick’s discovery of the DNA double helix in 1953 did for biology what many physicists hoped in vain could be done for atomic physics: it solved all the mysteries in terms of classical models and theories, without forcing us to abandon our intuitive notions about truth and reality.

Not long after, Lee Hood decided to become a biologist after reading an article by Francis Crick in Scientific American. Crick wrote how “the sequence of the bases acts as a kind of genetic code…” which was unknown. Many years later, Hood expressed the belief that “the core of biology is ultimately knowable, and hence, we start with a certainty that is not possible in the other disciplines,” like physics. He forecast being able to predict the behavior of a biological systems “given any perturbation.” His lab at Caltech invented the DNA sequencer.

A draft sequence of the human genome was published in 2000 and Hood founded his Institute for Systems Biology (ISB). The same year, Matt Ridley published his best-selling Genome which predicted a leap from knowing “almost nothing about our genes to knowing everything,” which he described as “the greatest intellectual moment in history. Bar none."

For the next dozen years, researchers from ISB heaved with might and main to realize Hood’s vision. Instead, they now say it is unattainable.

Undoubtedly, there will be disbelief. But Robert Millikan, a founding father of Caltech, didn’t want to believe in Einstein’s photoelectric effect. He won a Nobel Prize for being wrong and proving Einstein right.

This may still be one of the greatest intellectual moments in history, just not what we expected.

Image of yeast adapted from Nelson et al. DOI: 10.1073/pnas.0910874107

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Alternatives are being sought, but the world has not produced a novel frontline malaria drug in over 30 years.

From my article in Ars Technica, second in a series on malaria.

Read the full story

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In Southeast Asia, drug-resistant falciparum malaria may have evolved resistance to another frontline therapy and established itself in new territory in western Thailand, according to the World Health Organization. The new area in Thailand joins previous hot spots in Cambodia, Vietnam, and Myanmar, with the latter being badly equipped to stanch further spread. Despite containment efforts, the possibility this strain may spread to Africa, which has the most significant malaria burden, remains very real.

From my article in Ars Technica, first in a series on malaria.

Read the full story

Robert Semeniuk's stirring photo shows a man from Myanmar with severe malaria who walked with his wife for four days to cross the border into Thailand, coming to the Mao Tao clinic in the village of Mae Sot. A forthcoming Lancet paper will describe the detection of artemisinin resistance arising in that region of Thailand. http://www.robertsemeniuk.com

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A two-woman vaccination team in Firozabad, Uttar Pradesh, (Photo: UNICEF)

From my article on Ars Technica:

In the year since January 13, 2011, India has had zero cases of polio. Previously, India led the world, accumulating over 5,000 cases since 2000. Polio's last victim in India was 18 month-old Rukhsar, a girl in West Bengal who began showing signs of paralysis on this day in 2011. Now, epic immunization efforts have brought global eradication of the disease a giant step closer. Outside India, however, backsliding Pakistan and Nigeria and splotches of polio across Africa have blocked the final stamping out of the disease worldwide...

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Read my story on Ars Technica

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"India, ravaged by polio like no other place on the planet, has seen only a single case this year, back in January. Although the global polio eradication effort is neither celebrating nor relenting, it may have already succeeded in eliminating polio from India."

Read my article on Ars Technica

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IBM’s Watson, with a 15 terabyte chunk of human knowledge loaded into it like a Game Boy cartridge and set to hair trigger, poured out a high-precision fact fusillade that left no humans standing in the (aptly-named) Jeopardy. Is machine omniscience upon us?

“I, for one, welcome our new computer overlords,” said defeated Jeopardy champion Ken Jennings. But Jennings has buzzed in too quickly. Watson might point not to the inevitability of artificial intelligence but its unattainability. Barring unexpected revelations from IBM, Watson represents exquisite engineering work-arounds substituting for fundamental advance.

Questionable progress
In 1999, early question answering systems, including one from IBM, began competing against each other under the auspices of the National Institute for Standards Testing (NIST). At the time, researchers envisioned a four-step progression, starting with systems batting back facts to simple questions such as “When was Queen Victoria born?” A few tall steps later, programs would stand atop the podium and hold forth on matters requiring a human expert like “What are the opinions of the Danes on the Euro?”

Getting past step one proved difficult. While naming the grape variety in Chateau Petrus Bordeaux posed little difficulty, programs flailed on follow-up questions like “Where did the winery’s owner go to college?” even though the answer resided in the knowledgebase provided. These contextual questions were deemed “not suitable” by NIST and dropped. The focus remained on simple, unconnected factoids. In 2006, context questions returned—only to be cut again the following year. In the consensus view, such questions were “too hard,” according to Jimmy Lin, a computer science professor at the University of Maryland and a coordinator of the competition.

The entire contest was dropped after 2007. “NIST decides what to push,” explained Lin, “and we were not getting that much out of this…” Progress had turned incremental, like “trying to build a better gas engine,” according to Lin. Question answering wasn’t finished, but it was done. Although James T. Kirk asked the Star Trek computer questions like whether a storm could cause inter-dimensional contact with a parallel universe, actual question answering systems like Watson would be hard pressed to answer NIST level one questions like “Where is Pfizer doing business?”

ABC easy as 1, 2, 3
Kirk spoke to the computer. Watson’s designers opted for text messages—which says a lot. Speech recognition software accuracy reaches only around 80% whereas humans hover in the nineties. Speech software treats language not as words and sentences carrying meaning but as strings of characters following statistical patterns. Seemingly, Moore’s law and more language data should eventually yield accuracy at or conceivably beyond human levels. But although chips have sped up and data abound, recognition accuracy plateaued around 1999 and NIST stopped benchmarking in 2001 for lack of progress to measure. (See my Rest in Peas: the Unrecognized Death of Speech Recognition.)

Much of speech recognition’s considerable success derives from consciously rejecting the deeper dimensions of language. This source of success is now a cause of failure. Ironically, as Watson triggers existential crisis among humans, computers are struggling to find meaning.

Words are important in language. We’ve had dictionaries for a quarter millennium, and these became machine readable in the last quarter century. But the fundamental difficulties of word meanings have not changed. For his 1755 English dictionary, Samuel Johnson hoped that words, “these fundamental atoms of our speech might obtain the firmness and immutability of… particles of matter…” After nine years’ effort, Johnson published his dictionary but abandoned the idea of a periodic table of words. Concerning language, he wrote: “naked science is too delicate for the purposes of life.”

Echoing Johnson 250 years later, lexicographer Adam Kilgarriff wrote: “The scientific study of language should not include word senses as objects…” The sense of a word depends on context. For example, if Ken Jennings calculates that Oreos and crosswords originated in the 1920s, does calculate mean mathematical computation or judge to be probable? Well, both. Those senses are too fine-grained and need to be lumped together. But senses can also be too coarse. If I buy a vowel on Wheel of Fortune, do I own the letter A? No. This context calls for a finer, even micro-sense.

The decade of origin for Oreos and crosswords was actually the 1910s—as Watson correctly answered. In what decade will computers understand word meanings? Not soon; perhaps never. Theoretical underpinnings are absent: “[T]he various attempts to provide the concept ‘word sense’ with secure foundations over the last thirty years have all been unsuccessful,” as Kilgarriff wrote more than a decade ago, in 1997. Empirical, philosophy-be-damned approaches were tried the following year.

In 1998, at Senseval-1, researchers tackled a set of 35 ambiguous words. The best system attained 78% accuracy. The next Senseval, in 2001, used more nuanced word definitions which knocked accuracy down below 70%. It didn’t get up: “[I]t seems that the best systems have hit a wall,” organizers wrote. The wall wasn’t very high. Systems struggled to do better than mindlessly picking the first dictionary sense of a word every time. Organizers acknowledged that most of the efforts “seem to be of little use…” and had “not yet demonstrated real benefits in human language technology applications.”

Disambiguation was dustbinned. Senseval was renamed Semeval and semantic tasks subsumed word sense disambiguation by 2010. Today no hardware/software system can reliably determine the meaning of a given word in a sentence.

That’s imparsable
Belief continues unfazed, however, regarding whether language can be solved with statistical methods. “The answer to that question is ‘yes,’ “ declares an unabashedly partial Eugene Charniak, professor of computer science at Brown University. Whatever the trouble with word meanings, at the sentence level, computer comprehension is quite impressive—thanks to probabilistic models. Charniak has written a parsing program that unfurls a delicate mobile of syntax from the structure of a sentence. 

Such state-of-the-art parsers spin accurate mobiles about 80% of the time when given sentences from The Wall Street Journal. But feed in a piece of literature, biomedical text or a patent and the parses tangle. Nouns are mistaken for finite verbs in patents; in literary texts, different kinks and knots tug accuracy down to 70%.

Performance droops because the best parsers don’t apply universal rules of grammar. We don’t know them or if they exist. Instead parsers try to reverse engineer grammar by examining huge numbers of example sentences and generating a statistical model that substitutes for the ineffable principles.

That strategy hasn’t worked. Accuracy invariably declines when parsers confront an unfamiliar body of text. The machine learning approach finds patterns no human realistically could, but these aren’t universal. Change the text and the patterns change. That means current parsing technology performs poorly on highly diverse sources like the web.

Progress has gone extinct: parsing accuracy gained perhaps a few tenths of one percent in the last decade. “Squeezing more out of the current approaches is not going to work,” says Charniak. Instead, he concludes, “we need to squeeze more out of meaning.”

Surface features don’t provide a reliable grip on sentence syntax. Word order and parts of speech often aren’t enough. Regular sentences can be slippery, like:

• President F.W. de Klerk released the ANC men along with one of the founding members of the Pan Africanist Congress (PAC).

Not knowing about apartheid, the parser must guess whether de Klerk and a PAC member together released the ANC men—although the PAC figure was also in prison. The program has no basis for deciding where in the mobile (pictured above) to hang up the phrase “along with…”

Notice that winning Jeopardy is easier than correctly diagramming some sentences. And Watson provides no help to a parser in need. Questions like, “What are the chances of PAC releasing members of the ANC?” are far too hard, the reasoning power and information required too vast. Watson’s designers likened organizing all knowledge to “boiling the ocean.” They didn’t try. Others are.

Unobtanium
But it’s called mining the World Wide Web and aims to penetrate to the inner core, the sanctum sanctorum, of meaning.

In the beginning was the word. But the problem of meaning arises in word senses and spreads, as we have, seen to sentences. Errors and misprisions accumulate, fouling higher level processing. In a paragraph referencing “Mr. Clinton,” “Clinton,” and “she,” programs cannot reliably figure out if “Clinton” refers to Bill Clinton or Hillary Clinton—after 15 years of effort. Perhaps because of this problem, Watson once answered “Richard Nixon” to a clue asking for a first lady,

Evading this error requires understanding the senses of nearby words, that is, solving the unsolved word disambiguation problem. Finding entry into this loop of meaning has been elusive, the tape roll seamless, thumbnail never catching at the beginning.

Structuring web-based human knowledge promises to break through today’s dreary performance ceiling. Tom Mitchell at Carnegie Mellon University seeks “growing competence without asymptote,” a language learning system which spirals upward limitlessly. Mitchell’s Never Ending Language Learning (NELL) reads huge tracts of the web, every day. NELL’s blade servers grind half a billion pages of text into atoms of knowledge, extracting simple facts like “Microsoft is a company.” Initially, facts are seeded onto a human-built knowledge scaffold. But the idea is to train NELL in this process and enable automatic accretion of facts into ever-growing crystals of knowledge, adding “headquartered in the city Redmond” to facts about Microsoft, for example. Iterate like only computers can and such simple crystals should complexify and propagate.

But instead NELL slumps lifelessly soon after human hands tip it on its feet. Accuracy of facts extracted drops from an estimated 90% to 57%. Human intervention became necessary: “We had to do something,” Mitchell told fellow researchers last year. The interventions became routine and NELL dependent on humans. NELL employs machine learning but knowledge acquisition might not be machine learnable: “NELL makes mistakes that lead to learning to make additional mistakes,” as NELL’s creators observed.

The program came to believe that F.W. de Klerk is a scientist not a former president of South Africa—providing little help in resolving ambiguous parsing problems. At the same time, NELL needs better parsing to mine knowledge more accurately: “[W]e know NELL needs to learn to parse,” Mitchell wrote in email. This particular Catch-22 might not be fundamentally blocking. But if NELL can’t enhance the performance of lower-level components, those components might clamp a weighty asymptote on NELL’s progress.

Represent, represent
An older, less surmountable, perhaps impossible problem faced by NELL is how to arrange facts, assuming they can be made immaculate. Facts gleaned by NELL must be pigeon-holed into one of just 270 categories—tight confines for all of knowledge. Mitchell wants NELL to be able to expand these categories. However, while incorrect individual facts might compromise NELL, getting categories wrong would be fatal.

But no one knows how to write a kind of forensic program that accurately reconstructs a taxonomy from its faint imprint in text. Humans manage, but only with bickering. Even organizing knowledge in relatively narrow, scientific domains poses challenges, small molecules in biology, for example. Some labs just isolate and name the different species. Other researchers with different interests represent a molecule with its weight and the weights of its component parts, information essential to studying metabolism.  However, 2D representations are needed for yet another set of purposes (reasoning about reaction mechanisms) whereas docking studies call for 3D representations, etc.

What a thing is or, more specifically, how you represent it, depends on what you are trying to do—just as the quest for word senses discovered. So even for the apparently simple task of representing a type of molecule, “there is not one absolute answer,” according to Fabien Campagne, research professor of computational biomedicine at Weill Medical College. The implication is that representation isn’t fixed, pre-defined. And new lines of inquiry, wrote Campagne, “may require totally new representations of the same entity.”

One of NELL’s biological conceptions is that “blood is a subpart of the body within the right ventricle.” Perhaps this and a complement of many other facts cut in a similar shape can represent blood in a way that answers some purpose or purposes. But it will not apply in discussions of fish blood. (Fish have no right ventricle.) And when it comes to human transfusion, blood is more a subpart of a bag.

Particular regions of knowledge can be tamed by effort or imposition of a scheme by raw exercise of authority. But these fiefdoms resist unification and generally conflict. After millennia of effort, humans have yet to devise a giant plan which would harmonize all knowledge. The Wikipedia folksonomy works well for people but badly for automating reasoning. Blood diamonds and political parties in Africa, for example, share a category but clearly require different handling. One knowledge project, YAGO, simply lops off the Wikipedia taxonomy.

The dream of a database of everything is very much alive. Microsoft Research, from its Beijing lab, recently unveiled a project named Probase which its creators say contains 2.7 million concepts sifted from 1.68 billion web pages. “[P]robably it already includes most, if not all, concepts of worldly facts that human beings have formed in their mind,” claim the researchers with refreshing idealism. Leaving aside the contention that everything ever thought has been registered on the Internet, there still are no universal injection molds—categories—ready to be blown full of knowledge.

A much earlier, equally ambitious effort called Cyc failed for a number of reasons, but insouciance about knowledge engineering, about what to put where, contributed to Cyc’s collapse. Human beings tried to build Cyc’s knowledgebase by hand, assembling a Jenga stack of about one million facts before giving up.

NELL may be an automated version of Cyc. And it might succeed less. NELL’s minders already have their hands full tweaking the program’s learning habits to keep fact accuracy up. NELL is inferior to Cyc when it comes to the complexity of knowledge each system can handle. Unless NELL can learn to create categories, people will have to do it, entailing a monumental knowledge engineering effort and one not guaranteed to succeed. Machine learning relies on examples which simply might not work for elucidating categories and taxonomies. Undoubtedly, it is far harder than extracting facts.

NELL may also represent a kind of inverse of IBM’s Watson. NELL arguably is creating a huge Jeopardy clue database full of facts like “Microsoft is a company headquartered in Redmond.” NELL and Watson attack essentially the same problem of knowledge, just from different directions. But it will be difficult for NELL to reach even Watson’s level of performance. Watson left untouched the texts among its 15 terabytes of data. NELL eviscerates text, centrifuging the slurry to separate out facts and reassembling them into a formalized structure. That is harder.

And Watson is confined to the wading pool, factoid shallows of knowledge. The program is out of its depth on questions that require reasoning and understanding of categories. That may be why, in Final Jeopardy, Watson answered “Toronto” not “Chicago” for the United States city whose largest airport is named for a World War II hero and second largest for a World War II battle. Watson likely could have separately identified O’Hare and Midway if asked sequential questions. And pegging Chicago as the city served by both airports also presumably would be automatic for the computer. But decomposing and then answering the series appears to have been too hard. NIST dropped such questions—twice—for their perceived insuperability. And yet they are trivial compared to answering questions about the relations between F. W. de Clerk, the African National Congress, and the Pan Africanist Congress, questions of the kind which have stalled progress in parsing.

Google vs. language
Google contends with language constantly—and prevails. Most Google queries are actually noun phrases like “washed baby carrots.” To return relevant results, Google needs to know if the query is about a clean baby or clean carrots. Last year, a team of researchers crushed this problem under a trillion-word heap of text harvested from the many-acred Google server farms. Statistically, the two words “baby carrots” show up together more than “washed baby.” Problem solved. Well, mostly.

The method works an impressive 95.4% of the time, at least on sentences from The Wall Street Journal. Perhaps as important, accuracy muscled up as the system ingested ever-larger amounts of data. “Web-scale data improves performance,” trumpeted researchers. “That is, there is no data like more data.” And more data are inevitable. So will the growing deluge wash away the inconveniencies of parsing and other language processing problems?

Performance did increase with data, but bang for the byte still dropped—precipitously. Torqueing accuracy up just 0.1% required an order of magnitude increase in leverage, to four billion unique word sequences. Powering an ascent to 96% accuracy would require four quadrillion, assuming no further diminution of returns. To reach 97%, begin looking for 40 septillion text specimens. 

More data yielding ever better results is the exception not the rule. The problem of words senses, for example, is relatively impervious to data-based assaults. “The learning curve moves upward fairly quickly with a few hundred or a few thousand examples,” according to Ted Pedersen, computer science professor at the University of Minnesota, Duluth, “but after a few thousand examples there's usually no further gain/learning, it just all gets very noisy.”

Conceivably, we are now witnessing the data wave in language processing. And it may pass over without sweeping away the problems.

Let the data speak, or silence please
In speech recognition too, according to MIT’s Jim Glass, “There is no data like more data.” Glass, head of MIT’s Spoken Language System Group, continued in email: “Everyone has been wondering where the asymptote will be for years but we are still eking out gains from more data.” However, evidence for continuing advance toward human levels of recognition accuracy is scarce, possibly non-existent.

Nova’s Watson documentary asserts that recognition accuracy is “getting better all the time” (~34:00) but doesn’t substantiate the claim. Replying to an email inquiry, a Nova producer re-asserted that programs like Dragon Naturally Speaking from Nuance “are clearly more accurate and continuing to improve,” but again adduced no evidence.

Guido Gallopyn, vice president of research and development at Nuance, has worked on Dragon Naturally Speaking for over a decade. He says Dragon’s error rate had been cut “more than in half.” But Gallopyn begged off providing actual figures, saying accuracy was “complicated.” He did acknowledge that there was still “a long way to go.” And while Gallopyn has faith that human-level performance can be attained, astonishingly, it is not a goal for which Nuance strives: “We don’t do that,” he stated flatly.

Slate also recently talked up speech recognition, specifically Google Voice. The article claims that programs like Dragon “tend to be slow and use up a lot of your computer's power when deciphering your words,” in contrast to Google’s powerful servers. In the Google cloud, 70 processor-years of data mashing can be squeezed into a single day. Accurate speech recognition then springs from the “magic of data,” but exactly how magic goes unmeasured. Google too is mum: “We don't have specific metrics to share on accuracy,” a spokesperson for the company said.

By contrast, The Wall Street Journal, recently reported on how Google Voice is laughably mistake prone, serving as the butt of jokes in a new comedic sub-genre.

There is no need for debate or speculation: the NIST benchmarks, gathering dust for a decade, can definitively answer the question of accuracy. The results would be suggestive for the prospects of web-scale data to overcome obstacles in language processing. Computer understanding of language, in turn, has substantial implications for machine intelligence. In any event, claims about recognition accuracy should come with data.

Today, all that can be said is this:

To be || not to be
That is the question about machine intelligence.

When Garry Kasparov was asked how IBM might improve Deep Blue, its chess playing computer, he answered tartly: “Teach it to resign earlier.” Kasparov, then world chess champion, had just soundly defeated Deep Blue. Rather than follow this advice, IBMers put some faster chips in, tweaked the software and then utterly destroyed Kasparov not long after, in 1997. It was IBM’s turn to vaunt: “One hundred years from now, people will say this day was the beginning of the Information Age,” claimed the head of the IBM team. Instead, apart from chess, Deep Blue has had no effect.

If Deep Blue represented an effort to rise above human intelligence by brute computational force, Watson represents the data wave. But we have been inundated by data for some time. Google released its trillion word torrent of text five years ago. Today the evidence may suggest that the problems of language will remain after the deluge. If the rising tide of world-wide data can’t float computing’s boat to human levels, “What’s the alternative?” demands Eugene Charniak. He perhaps means there is no alternative.

A somewhat radical idea is to revise the parts of speech, as Stanford University’s Christopher Manning has proposed. Disturbingly, Manning asks: “Are part-of-speech labels well-defined discrete properties enabling us to assign each word a single symbolic label?” Recall that words don’t cleanly map to discrete senses, and similarly that things in the world don’t fit into obvious, finite, universal categories. Now the parts of speech seem to be breaking down.

Manning is skeptical that machine learning could conjure even 0.2% more accuracy in the tagging of words with their part of speech. Achim Hoffmann, at the University of New South Wales, believes more generally that machine learning now bumps against a ceiling. “New techniques,” he adds, “are not going to substantially change that.” Hoffman points out that relatively old techniques “are still among the most successful learning techniques today, despite the fact that many thousand new papers have been written in the field since then.”

For Hoffman, the alternative is to approach intelligence not through language or knowledge but algorithm. Arguably, however, this is just a return to the very origins of artificial intelligence. John McCarthy, inventor of the term “artificial intelligence,” tried to find a formal logic and mathematical semantics that would lead to human-like reasoning. This project failed. It led to Cyc. As Cyc founder Doug Lenat wrote in 1990: “We don’t believe there is any shortcut to being intelligent, any yet-to-be-discovered Maxwell’s equations of thought.” Forget algorithm. Knowledge would pave the way to commonsense. Cyc, of course, also did not work.

Are we just turning circles, or is the noose cinching tighter with repeated exertions? There is something viscerally compelling—disturbing—about Watson and its triumph. “Cast your mind back 20 years,” as AI researcher Edward Feigenbaum recently said in the pages of The New York Times, “and who would have thought this was possible?” But 20 years ago, Feigenbaum published a paper with Doug Lenat about a project called Cyc. Cyc aimed at full blown artificial intelligence. Watson stands in relation to a completely realized Cyc the way J. Craig Venter’s synthetic cell stands to the original vision of genetic engineering: a toy.

John McCarthy derided the Kasparov-Deep Blue spectacle, calling it “AI as sport.” Jimmy Lin, the former NIST coordinator, is not derisive but more ho-hum, wordly-wise about Watson: “Like a lot of things,” he says, “it’s a publicity stunt.” Perhaps an artificially intelligent computer wouldn’t fall for it, but people have. The New Yorker sees the triumphs of Deep Blue and Watson as forcing would-be defenders of humanity to move the goalposts back, to re-define the boundaries of intelligence and leave behind the fields recently annexed by computers. But the goalposts arguably have been moved up, so that weak artificial intelligence—artificial AI—can put it through the uprights.

The New York Times contends that Watson means “rethinking what it means to be human.” Actually what needs redefinition may be humanity’s relationship to dreams of technological transcendence.

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Statistics at left, tragedy at right Closer to victory than ever, polio eradication efforts have intensified, with 2011 bringing new initiatives and funding to most every front in the global war on the virus. The encirclement extends from presidential palaces to the streets of Luanda, Angola to tent villages on the Kosi River in India. “[T]he reach is incredible,” said Ellyn Ogden, USAID’s polio eradication coordinator, “to the doorstep of every child in the developing world, multiple times… It is an extraordinary human achievement that is hard for most people imaging in a peace-time program.” In India, for example, an army of 2.5 million vaccinator visited 68 million homes and immunized 172 million children; the president of India kicked off the January campaign. Cumulative efforts have driven cases in India to historic lows, just 42 cases last year versus 741 in 2009. In Africa, 15 African countries launched a synchronized immunization campaign late last year with 290,000 vaccinators targeting 72 million children. But a similar campaign took place the year before—and the year before that. Yet despite these huge efforts, polio keeps coming back. Some countries like Burkina Faso have gotten rid of polio three times. Nigeria once exported the most polio in Africa, but record-setting progress has occurred there. However, polio has developed a new stronghold—in Angola, which has fed explosive cross-border outbreaks. This year Angola will likely be the source of one third of the world’s polios cases. Continued transmission there has caused the Global Polio Eradication Initiative (GPEI) initiative to miss a major end-2010 milestone. “Angola now is almost the most important front in the global war on polio, and the whole world is watching to see how we do here," said UNICEF Executive Director Anthony Lake. Lake visited Angola with Tachi Yamada, president of global health at the Bill & Melinda Gates Foundation, in January. Angola freed itself of polio in 2002 only to suffer re-importation—from India. Since then, 33 vaccination campaigns over half a decade have failed to stamp out the disease. Lack of political commitment explains these failures, according to multiple sources within the eradication initiative. Angola’s vaccination rounds have been staffed to a large extent by children. Inadequate supervision has meant just a few hours of vaccinating a day, with efforts dropping off further over the course of three-day campaigns. Political commitment now appears solidly locked in. Visiting Angola, Lake and Yamada met with President José Eduardo dos Santos. “ ‘I’ll lead the campaign,’ ” Yamada said the president told him. The following day, Angop, the state-run news agency, ran the headline “Head of State committed to eradication of polio.” Subsequent news releases showed a domino effect down the political chain of command from the vice-president, to governors, to administrators of individual districts. One release identified a district manager by name and as acknowledging “the availability of the necessary conditions for vaccinators to reach all areas of the district,” likely coded language for placing direct responsibility on the manager for ensuring vaccination of the 156,000 children under five in that district. The World Health Organization (WHO) places equal emphasis on community involvement in its formula for effective immunization campaigns. In the past, vaccination plans have been centrally created and handed down for execution. WHO finds that the best “microplans,” which map out block-by-block strategies and awareness efforts, are developed by the communities involved. In this way, “communities hold themselves accountable,” as Tim Petersen, a program officer at the Bill & Melinda Gates Foundation, puts it. Angola conducted a three-day polio vaccination campaign, February 23-25, across five high-risk areas of the country. A WHO spokesperson said the new decentralized planning led to some “hiccups” in execution. A report from independent monitors, expected in about a week, will reveal the quality of the campaigns which aim to immunize 90% of children under five. [Note: I attempted to travel to Angola to cover the vaccination campaigns but was not granted a visa. The Angolan consulate in New York informed me four days before my flight that the signature page of my application was “missing,” that my letter from WHO did not meet requirements for documentation related to the purpose of travel and, still less plausibly, that the consulate had been trying unsuccessfully to reach me concerning these problems.] High risk areas will be covered twice more in upcoming nation-wide vaccination campaigns. However, “It is clear that Angola has a tough few months ahead,” says Sona Bari, communications officer for polio at WHO. But Angola has beaten polio before. Today cases are relatively few, at about 30 a year, certainly in comparison with 1999 which saw more than 1,000. Also, the intensity of transmission is much lower in Angola than that faced by, say, India. While political commitment seems to be in place, stability might be an issue. Some political tremors from Tunisia and Egypt have reached Angola, such as a call for public protest on March 7. (Recently Angola was without internet access for about two days which state media attributed to a cut cable.) Prior to the 7th, US State Department spokesperson Hilary Renner said she was not aware of “significant demonstrations in Angola.” The Associate Press report on turn out and reaction on the 7th suggests revolutionary force so far is not strong. Rest of the World: Key Fronts The eradication initiative must close out the major global sources of polio, India and Nigeria. India is closer to the goal and mostly needs to sustain its exertions. Nigeria trails but has made enormous progress; there are risks but today the country is essentially on track. If Angola too has turned in the right direction, Pakistan becomes the next focus. Pakistan presents almost all possible obstacles to polio eradication. Like India, the oral polio vaccine in Pakistan fails to immunize among a significant number of children, usually under conditions of very low health and hygiene. Some parents in Pakistan refuse to allow their children to be immunized, a problem also once seen among Muslims in Nigeria who feared the vaccine had been purposefully tainted. Much of Pakistan’s polio burden falls on border states with Afghanistan where security issues prevent vaccination teams from operating. The virus travels to more secure areas of the country where poorly run, corruption-riven vaccination campaigns fail to stamp it out. Even the house of a former minister of health was bypassed—twice—by polio vaccinators. “I had to call them to get my kids vaccinated,” reported the former minister. Pakistan’s political stability is low. Natural disasters—huge flooding—have made a difficult situation worse. Last year saw a jump to 144 cases, up from 89. And so far in 2011, cases are accumulating more rapidly. Fortunately, the Pakistan/Afghanistan polio complex has not exported the virus to the rest of the world—so far. Pakistan figured prominently in the careful eradication orchestrations of early 2011. Bill Gates met with President Asif Ali Zardari on January 15th. On January 25th, an emergency plan to immunize 32 million children was announced. The same day brought a joint announcement of $100 million in funding from the Gates Foundation and Mohammed bin Zayed Al Nahyan, crown prince of Abu Dhabi, to support vaccination efforts, with $34 million earmarked for polio immunization in Pakistan and Afghanistan. Afghanistan offers ample challenges, including security problems. However the absolute number of cases, about 30 per year, is not extreme. Described as a “pretty strong program” by the Gates Foundation’s Tim Petersen, the Afghan polio eradication team appears to already enjoy the confidence of the members of the global eradication initiative. The least controlled polio rampage is taking place in the Democratic Republic of Congo (DRC). Cases last year exploded to 100 versus three in 2009. The DRC and its northeastern neighbor, Angola, comprise an epidemiological block like Afghanistan and Pakistan. There is “huge cross-border traffic” between Angola and the DRC, according to Apoorva Mallya, a program officer at the Bill & Melinda Gates Foundation. A lack of roads and transportation infrastructure greatly complicate operations. For example, biological samples from possible polio victims sometimes must be floated down the Congo River en route to a lab for analysis. The eradication initiative is looking at “local, local solutions,” according to Mallya. At the same time it seeks high level political commitment, just as in Angola and indeed all countries. WHO Director-General Margaret Chan travelled to the DRC in February to meet with President Laurent Kabila. UNICEF’s Anthony Lake then visited in in the first week of March and called for “an absolute commitment” to vaccinate every child. New Trends in Media Coverage The front in the polio war has been discouragingly broad and variable. Countries have been won and lost—some more than once. Low numbers or even single cases perpetually spatter the map. Gabon just reported a case, its first in more than ten years. Seemingly safe areas like Tajikistan and Congo have recently seen blowout epidemics. Transmission has become fully re-established in four African countries, not only Angola but also, for instance, Chad. Total cases globally have rarely dipped under a thousand a year over the last decade, giving rise to the view that this “last one percent,” like Jell-O, will squish somewhere else no matter how hard it is squeezed. But the polio eradication initiative has focused on choking off the sources, following the strategy of von Clausewitz, who in, On War, recommended subduing the enemy “center of gravity.” In polio, that’s India and Nigeria. No other countries come close in polio burden. It’s not over, but India is astonishingly near to eliminating polio. The states of Bihar and Uttar Pradesh, where polio has been worst in India, haven’t seen a single case in six months. Among much else, this required tracking and immunizing enormous mobile populations. As many as six million people are on the move each day, according to a WHO estimate, with accessibility complicated by flooding of the Kosi River in Bihar. In addition, India’s eradication effort has overcome vaccine failure by achieving very high levels of population immunity: the virus basically can’t penetrate the thicket of immune people to access the vulnerable, those children in which the vaccine didn’t take. The Associated Press recently recognized these developments in "India brings hope to stalled fight against polio."  ABC News posted a story in which progress in India provides hope for polio becoming “just the second disease to be wiped off the planet since smallpox.” (ABC News received $1.5 million from the Gates Foundation to support a television series on global health, making the representativeness of their current coverage more difficult to ascertain.) Most recently, The Globe and Mail ran a polio package driving off successes in India, saying “Polio is all but gone from India…” (I have written to similar effect in Scientific American.) One article is entitled: “Anti-polio battle on verge of victory.” No country has been as difficult as India. The obstacles in the countries of the rest of the world are largely different combinations of known problems which have been surmounted somewhere already. Polio has been expunged from anarchic, conflict-ridden states like Somalia. Rejection of vaccine by parents on cultural or religious grounds has been overcome in Nigeria. The quality and coverage of vaccination campaigns has been lifted even amidst rife corruption. Clearly, however, past performance doesn’t guarantee future results. Completely novel problems could arise. Failure on one or more of the numerous fronts in eradication is likely; compound failures could wreck the broader enterprise. However, while feasibility remains an issue, coverage appears to be shifting—to whether the polio “endgame” can be won. The wild poliovirus is not the only threat to eradication. Very rarely, the oral polio vaccine, which uses a live attenuated virus, mutates into virulent form. Thus, in a sense, the eradication effort is fighting fire with fire, as a recent op-ed piece in the Los Angeles Times points out in “The Polio Virus Fights Back.” Not long after, Myanmar reported just such a case of vaccine-derived poliovirus. These mutants can—and have—spread. So far no related cases have been reported because the vaccine protects against it. And in Myanmar, “Immunization demand is high and the country conducts good quality campaigns,” according to WHO’s Sona Bari. In India, where oral polio vaccine dosing has been most intense, 2010 saw only one case of vaccine-derived virus. Rightly, however, the subject will likely gain in prominence in media coverage. Not only has the nature of feasibility questioning changed, shifting to whether the next phase can be won, the position of arch critic of eradication now appears to be open. Donald Henderson played a key role in smallpox eradication but has long been skeptical of polio eradication. According to a January Seattle Times article, however, Henderson changed his mind six months ago and now believes polio could be eliminated. But not long after, The New York Times cited Henderson as a vehement critic of eradication. In mid-February, however, they ran a different story, Can Polio Be Eradicated? A Skeptic Now Thinks So, which (re-)disclosed that Henderson had changed his mind. The title of the earlier article in which Henderson was a critic also appears to have been changed online from “Critics Say Gates’s Anti-Polio Push Is Misdirected” to “Gates Calls for a Final Push to Eradicate Polio.” At present, this leaves only the desirability of polio eradication in question. While no one argues for polio, there are other diseases which are more widespread, taking more lives and causing greater suffering. According to The New York Times, Richard Horton, editor-in-chief of The Lancet tweeted that: “Bill Gates’s obsession with polio is distorting priorities in other critical [Bill &Melinda Gates Foundation} areas. Global health does not depend on polio eradication.” The Gates Foundation, however, embraces the accusation. “We are overemphasizing polio,” says the foundation’s Tachi Yamada. Polio became the foundation’s number one priority late last year. And it’s not just Bill Gates or his foundation. In 2008, WHO Director-General Margaret Chan said “I am putting the full operational power of the World Health Organization into the job of finishing polio eradication… I am making polio eradication the Organization’s top operational priority on a most urgent, if not an emergency basis.” But the emphasis on polio is indeed disproportionate. Both the Gates Foundation and WHO recognize that eradication would not just rid the world of a horrific disease: it would be a giant symbolic victory for global health. Chan, in her 2008 speech, also said “We have to prove the power of public health,” a goal which eradication would achieve. Similarly, Gates Foundation’s Yamada doesn’t want to give “fuel to cynics” by having eradication fail but instead to demonstrate that “this is what development assistance can do.” Returning to the matter of eradication critics, The New York Times also quoted bioethicist Arthur L. Caplan, a professor at the University of Pennsylvania as saying “We ought to admit that the best we can achieve is control.” In June, 2009, Caplan wrote an opinion piece in The Lancet entitled, “Is Disease Eradication Ethical?” Caplan wondered if eradication was possible since it hadn’t worked after more than two decades of effort. The financial cost was high and diverted resources from better, more life-saving uses. Caplan declined to comment for this article. However, questioning eradication as a strategy in global health, as polio demonstrates, is a worthwhile endeavor. And if polio resurges, so will skepticism of eradication. Space Race to Human Race The upcoming retirement of the Space Shuttle likely will attract enormous coverage. The Shuttle is not being replaced, however. And there are currently no plans for even a single human to permanently leave the planet. Still, the expectation of a spacefaring humanity persists although the 1960s might remain the golden age of manned space exploration. In other words, the world has missed that the next giant step for humankind will take place on planet earth. The polio eradication effort might actually be larger than the Apollo program. Already in India, the number of cases can be counted down to zero; other countries might follow. It’s a good story.

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Whether polio eradication should be pursued or whether it is central to global health are questions that should be and are asked by The New York Times in “Critics Say Gates’s Anti-Polio Push Is Misdirected.” However, the Times also contends that “Victory may have been closest in 2006…” when victory may be closer now than ever before. And the latest blast of polio funding and initiatives, described by the Times, comes not because the eradication effort is on its heels but because it’s going for the kill.

Eradication hinges less on the number of countries suffering polio cases than on knocking out the sources—or “reservoirs”—of the disease. The two largest such reservoirs are India and Nigeria. Today, both countries have historic, record low cases. The Times describes this as “doing much better.” Perhaps also underappreciated by the article, wiping out the reservoirs of polio will stop outbreaks. The Times mentions outbreaks in Nepal, Kazakhstan, Tajikistan, Turkmenistan and Russia. All originated from India.

Further, the case of India seems to demonstrate that there are no scientific or technological barriers to eliminating polio. In particular, the Indian states of Bihar and Uttar Pradesh once were the most impregnable redoubts for the poliovirus anywhere on the planet. Yet, because of the huge expense and exertions described by The New York Times, Bihar and Uttar Pradesh saw nearly zero cases even during the “high season” for polio. (See my Polio in Retreat: New Cases Nearly Eliminated Where Virus Once Flourished.)

In Africa, Nigeria has been the most intractable polio problem. No sooner is eradication on track in that nation, than new sources—Angola, Chad, Congo and Sudan—arose to continue infecting the continent. Indeed, Angola and Sudan have even reverted back into polio reservoirs, the disease spreading within and across borders. The Times properly draws attention to this indisputable, highly problematic regress. But the obstacles to eliminating polio in Angola do not compare with those of India where the degree of difficulty approached near impossibility. And Angola has gotten rid of polio before. How did it come back? Cases imported from India, a reservoir now drawn down to historic lows.

The New York Times represents a crucial exception to the influence of the Gates Foundation on global health coverage. It is important to question whether, in retrospect, polio eradication ought to have been undertaken, given all the costs. Also, whether today polio ought to be treated as the number one priority in global health is likewise a valid inquiry. And the Times is right that the Bill & Melinda Gates Foundation has doubled down on polio eradication several times before in the aftermath of setbacks to the program. However, the recent slew of polio announcements and initiatives is not in response to setbacks. It’s to unload a knock-out punch while the opponent is staggered. It might work.

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A National Science Foundation study cast doubt on the idea that scientific progress is accelerating--or even maintaining speed. Nearly two dozen scientists, science administrators, members of Congress and the Executive branch declined to comment. The study elicited almost no coverage.

I explain these phenomena in Columbia Journalism Review:

Science Faltering? Obama wants more R&D, but few willing to discuss research productivity

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A historic downward shift in U.S. research efficiency is described in a new report on science publication trends, showing that while funding rose, the quantity of research yielded, measured by an analysis of published scientific papers, fell

Read the story at Scientific American

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"The world's largest, most intractable source of polio may be on the brink of elimination."

Read the rest...

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Read the rest: The Web Grows Wider: Gates Foundation partnerships with the Guardian and ABC News further complicate global health coverage

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As CJR's editor's note says:

This article was originally published on the author’s personal blog in July. With a few updates, we are running it as the first in a two part series exploring the implications of the Bill and Melinda Gates Foundation’s increasingly large and complex web of media partnerships. This part deals with a partnership between the PBS NewsHour and the Gates Foundation formed in 2008. Part two, running tomorrow, will examine a partnership with the Guardian, a British newspaper, announced in September, and one with ABC News announced on Wednesday.

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The 20th century broke open both the atom and the human genome. Physics deftly imposed mathematical order on the upwelling of particles. Now, in the 21^st century, systems biology aims to fit equations to living matter, creating mathematical models that promise new insight into disease and cures. But, after a decade of effort and growth in computing power, models of cells and organs remain crude. Researchers are retreating from complexity towards simpler systems. And, perversely, ever-expanding data are making models more complicated instead of accurate. To an extent, systems biology, rather than climbing upwards to sparkling mathematical vistas, is stuck in a mire of its own deepening details.

Read the rest....

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Oral polio vaccine (Photo credit: quilty2010)  

Polio eradication may be entering a new phase in India where incidence of the disease has become so faint, it’s sometimes undetectable. Yet polio is still very much there and capable of spreading. Sewage in New Delhi tested positive for poliovirus six straight weeks recently. (Polio is usually spread by oral contact with water contaminated by the feces of people infected by the virus.) But no cases of polio have been reported in the entire state of Delhi for more than a year. How can there be circulating virus and no cases?

Only about one in 200 polio infections results in paralyzing disease. But these cases must be detected to be counted and to prevent further spread. Across India, more than 20,000 people comprise the detection network, in theory at least one to every block of every district in the country.

But in the states of Uttar Pradesh and Bihar, one of the world’s largest polio redoubts, the challenges of detecting polio cases are immense. The sheer reproductive force of the region astonishes: 500,000 children are born every month in Uttar Pradesh. Poverty, illness and death are likewise extreme in degree while infrastructure is scant. And many people are highly mobile, migrating far and wide, all of which makes detecting polio cases from this oceanic flux difficult. And it is getting harder.

Frequent, massive vaccination campaigns have beaten polio down. Uttar Pradesh hasn’t seen a case since April and only six in total this year. But the disease is cropping up elsewhere. New cases were reported in the state of Jharkhand, which borders Bihar, but also in Maharashtra on the other side of the country. And a spectacular outbreak ignited in Tajikistan a few months ago. 452 people became infected with a poliovirus traced back to Bihar. A smaller outbreak occurred in Nepal, again originating in neighboring Bihar.

But even giant outbreaks don’t threaten polio eradication. Make it rain oral polio vaccine and new outbreaks can be fairly reliably extinguished, albeit at significant cost. The problem facing eradication efforts is that the gauges read “zero” when clearly the actual number of polio cases sits above zero. As the World Health Organization put it, new cases in India last week and the sewage samples in New Delhi are “evidence of ongoing, low-level [poliovirus] transmission in the country.” (Wild Poliovirus Weekly Update, 11 August 2010).

The level of transmission has dropped to where it can’t always be seen but it remains high enough to sustain the cycle of infection.  The good news is that strenuous vaccination efforts have driven cases down. The bad news is that polio is not eradicated and now might fly too low to be picked up by the existing detection network, hindering efforts to stamp the virus out for all time.

Today the Bill and Melinda Gates Foundation invited proposals to address exactly this problem. According to the foundation, “as eradication nears the signal provided by paralytic disease will be eventually lost; new methods to monitor poliovirus circulation are increasingly necessary.” The foundation identified other obstacles to eradication that need to be addressed but the overarching theme was for what it described as the “poliovirus endgame.”

How close is this endgame? The steep fall in cases evokes guarded optimism from Steve Wassilak at the Center for Disease Control, which is part of the Global Polio Eradication Initiative. In email, he said:

We, the interested parties, do need to avoid over-weighing any decline in cases as a clear path to zero, given the ups and downs in the past, particularly in India. However, we are squarely now in the high season and the total number of cases is at an historical low…

The outlook for 2010 appears good, although according to Dr. Yash Paul, a pediatrician in Jaipur, India, “In India high incidence of polio starts June onwards, so we shall know the likely polio scenario in end August” because of reporting lags. Also, one good year doesn’t automatically beget another. While 2005 saw just 66 cases, 2006 brought over 600 cases while 2007 produced more than 800.

Wassilak pointed out that the passing of the high season for polio could snap the few remaining chains of transmission. Or not. “[A]n alternative,” Wassilak hypothesized, “is can mobile populations be sustaining/contributing to transmission but cases of paralysis among these populations be missed?” The sewage tests in New Delhi, at Swaran Cinema, might support this hypothesis if the moviegoers are from neighboring Uttar Pradesh.

Other known problems obstruct eradication. Notably, the oral polio vaccine quite often fails to elicit immunity. WHO began addressing this in April. (See Polio Eradication: Harder Than it Looks.) Similarly, the Gates Foundation, in its invitation for polio eradication proposals today, included investigating why “vaccines have shown reduced efficacy in children living in certain resource-poor environments.”

A newer potential problem is re-infection among persons who were earlier protected by prior immunizing exposure. Such re-infections might be helping sustain the poliovirus cycle in areas with long-running eradication efforts—a vicious circle.

Finally, India is not the only endemic source of polio. Nigeria, Pakistan and Afghanistan also have never interrupted transmission, although a decade ago, 20 countries fell in this category. Unfortunately, transmission has become re-established in several nations in Africa and is unlikely to be stopped in those places by the end of the year, a revised goal for the eradication effort which originally was supposed to conclude in 2000.

Still, the potential is there for this be the turning point.

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Related:

Gates Seeks to Close Out Polio in Nigeria (June 7, 2010)

Heavy Lifting: Raising Health Beyond Polio's Reach (May 13, 2010)

Wall Street Journal: Pulling the plug on polio eradication? (April 26, 2010)

Polio Eradication: Harder Than it Looks (April 14, 2010)

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Tom Markusic, of Space Exploration Technologies (SpaceX), recently warned that spaceflight on its present course “will devolve into social welfare for nerds.” To escape federally funded self-indulgence, Markusic proposes developing a potentially game-changing technology: nuclear thermal propulsion.  But its nominal prospects only make his unhappy prediction for the future of spaceflight more likely.

NASA chief Charles Bolden called for new ideas after President Obama earlier this year cancelled the Constellation project, which looked much like its antecedent, the half-century old Apollo program. Nuclear thermal propulsion, which Markusic advocates for getting to Mars, also dates back to the golden age of space. Beginning in the 1950s and continuing into the ‘60s, NASA extensively investigated thermal nuclear technology which combusts hydrogen at the extreme temperatures of a nuclear reactor, providing much greater thrust than the chemical reaction used in conventional rockets.

Clearly it’s not a new idea. Rather it underlines the paucity of new, workable technologies that meaningfully enhance the prospects for human exploration of space.

Nuclear thermal does work and it delivers about twice the kick from a given amount of hydrogen compared to burning it the usual way. But it’s expensive. And it’s nuclear.  In the 1950s we looked forward to everything atomic. But no longer.

SpaceX founder Elon Musk contradicted Markusic a few days ago saying “I don’t think nuclear thermal is the way to go.” Musk, perhaps wanting to keep his company out of the nuclear fray, said the weight of the reactor would offset the benefit of greater combustion energy. However, Stanley Borowski and colleagues at NASA firmly contend that nuclear thermal rockets would roughly halve the transit time for a Mars mission from about 4.7 years to 2.5. But a not-quite-factor-of-two improvement has failed to captivate.

When Musk entered the rocket business, he was looking for a “Moore’s law of space,” exponential advances which would make humanity a spacefaring species. Markusic appears to have truer insight into the future of spaceflight.

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Related:

Goodbye Mars, Hello Malaria: Bill Gates’ Imprimatur on Science and the 21st Century

 Human Space Exploration: Scaled Back to Vanishing 

Space Age entering eclipse—unnoticed

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The Gates Foundation, global health and the media

How did Ray Suarez catch the global health bug? Simple, he said in a recent talk answering  that exact question. Suarez explained: “The executive producer of the NewsHour, Linda Winslow, came into my office and asked me if I was interested in covering global health for the program and I said ‘yes.’ ”

But the actual reason is, following that conversation, Suarez wrote a proposal for the Bill & Melinda Gates Foundation resulting in $3.6 million of funding for NewsHour programming on global health. The Gates Foundation also sponsored the event at which Suarez was speaking. The moderator came from the foundation too, posing questions and selecting others from the audience, the funder interviewing a journalist whose global health education it had financed.

Suarez has heard gripes about Gates Foundation funding before. He defended the arrangement as giving an under-reported subject increased coverage while preserving “complete editorial independence.” Continued Suarez: “The foundation doesn’t hold the purse strings, encouraging some stories and discouraging others. And we don’t get approval before we embark on projects.”

But could Suarez’s own internal process for selecting stories and storylines be susceptible to influence? Certainly there are no stories thus far that seem contrary to foundation views. On the other hand, hardly every Gates-funded story examines an issue high on its agenda, obesity in China, for example. Malaria eradication does sit near the top of the foundation agenda. But NewsHour coverage of Tanzania mostly spoke of malaria elimination which targets specific regions rather than worldwide eradication which is more difficult and controversial.

Suarez went to considerable effort to avoid covering global health projects also funded by his funder. He described this as an accomplishment given “the remarkable number of pies around the world that the foundation has its fingers in…” However, the ubiquity of the Gates Foundation in global health is itself important. The malaria vaccine trial Suarez covered on his trip to Tanzania, for example, would never have taken place absent Gates Foundation support. The vaccine was shepherded forward by the Gates-funded PATH Malaria Vaccine Initiative. Both the event and its coverage are products of Gates money.

Every story has more facets than can be examined. But Gates Foundation funding discourages or even forecloses examination of certain storylines. Suarez can’t credit the foundation for making gigantic contributions to global health, for example. At the same time, the elephant in the room—the Gates Foundation—remains out of frame even as it pays for the camera.

Does that matter if the main effect of Gates funding is to increase awareness of global health? As Suarez pointed out:

A few months ago in Washington, I watched Bill & Melinda themselves give a presentation on global health research to an auditorium packed with a who’s who of Congress, the executive branch, think tanks and the media, not demanding one policy approach or another or recommending one drug protocol or another as much as hammering home the idea that public knowledge creates support for [global health] efforts…

By funding the NewsHour as well as Public Radio International, the foundation heightens general awareness of and support for global health. However, while the Gateses might not have advocated for specific programs, they and their foundation do have distinct policy preferences and require strict compliance.  Furthermore, the foundation’s policy-agnostic advocacy efforts link together with its policy-shaping efforts, again by influencing the media.

In October 2008, the same time it awarded the NewsHour funding, the Gates Foundation granted the Kaiser Family Foundation (KFF) $2 million with a remit to “inform policy making and program development and implementation” for U.S. global health policy. The Kaiser Family Foundation doesn’t specify precisely how it uses these funds and publishes no annual reports on its website. Concerning its spending and governance, the KFF website only alludes to the possibility of such funding:

With an endowment of over half a billion dollars, Kaiser has an operating budget of over $40 million per year.  The Foundation operates almost exclusively with its own resources, though we do occasionally receive funds from grant-making foundations, primarily to expand our global programs.

Prominent among these programs is KFF’s US Global Health Policy portal. The portal selects and summarizes global health news from more than 200 worldwide sources spanning mainstream media outlets to blogs. KFF sends a daily email news digest to policy makers, opinion leaders and journalists. Also, KFF offers its own original research and analysis, from cheat sheets for journalists to extensive reports on subjects such as the US global health architecture.

Gates Foundation financing of the enterprise is, arguably, hidden. KFF’s daily emails carry no boilerplate mention of Gates funding. The only disclosure on the KFF US Global Health Policy site resides under the “About” link at the bottom right of page, which says only that KFF’s work on global health and the global health gateway receives “substantial support” from the Gates Foundation.  

In other respects, however, the influence of the Gates Foundation is more apparent. Not only does KFF have the power to choose what constitutes global health news but, in summarizing the stories it selects, it can give them a construction of its choosing. In key instances, the Kaiser Family Foundation’s global health news coverage suggests bias both in story selection and preferential treatment of the Gates Foundation.

In May 2009, the Lancet ran two papers and an accompanying editorial offering multiple, sharp criticisms of the Gates Foundation. The KFF summary muted the few criticisms it repeated and dismissed the one paper it discussed as “marred by ideological assumptions.” The summary quoted the Gates Foundation as saying “We welcome the article and its findings…” although, as the Lancet editorial noted, the foundation had actually “declined our invitation to respond…” Unusually and perhaps uniquely, KFF did acknowledge in its daily email that it “receives substantial support from the Bill & Melinda Gates Foundation for the Kaiser Daily Global Health Policy Report.”

In June, USA Today ran a largely positive story on the Gates Foundation. But the article also said:

…the Gates Foundation has been painted by critics and even admirers as sometimes too heavy-handed in saying how its money is used and too prone to listening to the recommendations of experts vs. grass-roots groups when setting its strategies to battle global poverty.

In Kaiser’s rendering, this became: “The article reports on different perspectives about the Gates Foundation's influence and approach to global health and other work.” While not strictly false, such gentle treatment does appear to be reserved for the Gates Foundation.

A June 19 Lancet story entitled, “WHO heads back to the drug development drawing board” became in KFF’s version “WHO Scraps Old Drug Development Group, Creates New One” and featured quotations about “unclear methods, a lack of transparency and signs of industry interference” as well as “suspicions of impropriety.” Although the Lancet story quoted one source as saying “We think this is a landmark decision,” that more positive perspective was not included in the KFF summary.

 BMJ recently alleged improper ties between WHO H1N1 advisors and the pharmaceutical industry. KFF quoted the editor-in-chief of BMJ saying “The WHO's credibility ‘has been badly damaged.’ ” However, four days later, Nature News/Scientific American wrote:

To judge from media coverage last week, a major scandal had been exposed in the handling of the H1N1 flu pandemic by the World Health Organization (WHO). But nothing could be further from the truth.

However, after this debunking, KFF only reported that “the authors of the BMJ piece agreed the timeline they presented in the article was off.”

KFF lets hard knocks for some organizations through, but cushions blows for the Gates Foundation and sometimes ducks them entirely. The Los Angeles Times ran a series of stories in January 2007, beginning with “Dark cloud over good works of Gates Foundation.” The Times contended that the foundation’s endowment investments worked against its global health objectives:

The Gates Foundation has poured $218 million into polio and measles immunization and research worldwide, including in the Niger Delta. At the same time that the foundation is funding inoculations to protect health, The Times found, it has invested $423 million in Eni, Royal Dutch Shell, Exxon Mobil Corp., Chevron Corp. and Total of France — the companies responsible for most of the flares blanketing the delta with pollution, beyond anything permitted in the United States or Europe.

The Kaiser Daily Global Health Policy Report never mentioned the series.

KFF frequently mentions coverage of the Gates Foundation appearing in the Seattle Times. But the Times' recent, June 15 story, “Gates Foundation gets low marks in relations with non-profits” went ignored. The foundation actually surveyed not just non-profits but all 1,544 of its grantees from a recent one-year period. There was good news, according to the foundation: “strong ratings for our work in grantees’ fields,” and “a positive impact on knowledge, policy, and practice in our strategy areas.” However, the Gates Foundation received “lower than typical ratings on many other aspects of the grantee experience,” such as communication and clarity with respect to goals and strategy.

The foundation paid out roughly $3 billion to its grantees over the timeframe examined yet the obvious potential story about the effectiveness of foundation spending received neither mention nor exploration, an omission true of all media organizations, not just the Kaiser Family Foundation. Concerns about transparency, raised by KFF in different circumstances, here go dormant.

The lens of KFF’s portal gives particular shape to reader perception of the world’s coverage of global health. KFF is also studying global health journalism in a project led by former Boston Globe global health writer and Pulitzer Prize winner John Donnelly. Donnelly left the Globe in 2008 to join Burness Communications, a media consultancy, where he is vice president and senior editor. At the same time, Donnelly became a media fellow at Kaiser Family Foundation. (I was interviewed in June by a member of Donnelly’s project.)

“Newspapers,” Donnelly said in a telephone interview, “have very strict ethical standards that assure you’re unbiased.” He characterized his past work for the Globe as “independent,” his stories involving consultation only with editors. As budget cuts swept the newspaper industry, the Globe closed its foreign bureaus, about a year before Donnelly departed. “In global health,” said Donnelly, “there are really very few of those jobs left.”

Asked about the possible influence of Gates Foundation funding on journalism, Donnelly explained in email:

I'm rarely doing much pure journalism now, so I don't know if I can answer the question of whether Gates' underwriting of journalism creates a conflict for journalists. I would think that journalists working on global health issues at NewsHour and NPR would be in the best position.

Donnelly seemed to defend non-disclosure of Gates Foundation funding to certain media organizations. “Indirect funding is not really seen as independent journalism,” he said by phone. “It’s seen as advocacy-based journalism.”

Donnelly currently writes for Global Health, a magazine published by the Global Health Council. The council has a three-year, $10 million grant from the Gates Foundation to “to foster policies that accelerate scale-up of cost-effective, proven health approaches and diffusion of best practices and innovation that have policy significance.” The grant was awarded in October 2008, like those won by the NewsHour and KFF. Global Health, which began publication in the winter of 2009, does not disclose Gates funding, as of this writing.

Donnelly said he didn’t know if Gates funding supported Global Health. He recently blogged the Pacific Health Summit for that publication. The invitation-only summit paid most of his airfare with the balance coming from another non-profit receiving Gates Foundation support.  “I don’t know who funds the summit,” said Donnelly, other than numerous different organizations. On the summit website, the National Bureau of Asian Research (NBAR) sits atop the marquis of the four organizations behind the event, including the Gates Foundation. However, the Gates Foundation paid part or all of NBAR’s share of the Summit, $700,000. Again, the event and its coverage originate from the foundation whose role is larger than it appears.

Is this ubiquity simply a property of global health, a consequence of a generosity both welcome and immense? Should air have to disclose that it is 21% oxygen?

I used to write about the Gates Foundation for the Seattle-based Crosscut. I stopped in November of 2009 after Crosscut, following financial struggles and a switch to non-profit status, announced it had received a $100,000 grant from the Gates Foundation. Some weeks after learning about the Gates grant in Crosscut, I inquired of the editor, David Brewster: “Any thoughts about editorial policy with respect to coverage of the Gates Foundation under Crosscut's new funding paradigm?” Brewster responded:

No change at all. You should get it out of your head that Gates is funding us, and they insist they would be embarrassed if their funding in any way altered our independent reporting on them.

The episode is suggestive of the ubiquity of Gates funding in the media, from unknown Crosscut to the PBS NewsHour. The subject of Gates funding is uniformly uncomfortable to those receiving it—which should perhaps suggest that something is wrong. Finally, the effects of foundation funding are quite universal:  journalists who need the money seem to believe they can remain objective about their coverage.

John Donnelly says his study of global health journalism examines “what’s going on, how things have changed,” and what the future might look like. Perhaps it will conclude that the objectives of global health might not be harmed by increased transparency of funding sources. Journalism and the processes of an open society, quite obviously, are harmed when money influences coverage invisibly.

Certainly, Ray Suarez should be asking questions of the Gates Foundation, not the other way around.

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Polio is way down in Nigeria, in part because of Gates' first visit there early in 2009. A year and a half on, polio cases are nearly zero, just three so far in 2010 compared with 288 in the first half of 2009. Gates' arrival coincides with the first of two large-scale vaccination sweeps in Nigeria this month. Also, rather than directly fund polio vaccination efforts and hope for good results, the Gates Foundation agreed in 2009 to indirectly buy down existing World Bank loans to Nigeria when the country achieves specific vaccination targets. (See the picture Gates posted on Twitter which he entitled: "Reviewing statistics with leaders...")

Nigeria has 42 million children under 5; reaching 80% vaccination coverage takes an army of about 200,000 vaccinators. If polio can be dispatched in Nigeria, that would leave only India as a major polio epicenter, which Gates visited just three weeks ago. India also has seen its case rate fall precipitously but, unlike Nigeria, the oral polio vaccine doesn't always work even after repeated doses in the most polio-intensive regions of India. After Nigeria and India, the remaining polio redoubts are Aghanistan and Pakistan where vaccination campaigns are often impossible because of war-time conditions. Those are likely the only polio frontlines Gates won't visit.

Note on graphic: The location of the three cases reported so far in 2010 comes from AllAfrica.com. The map for 2009 is for illustrative purposes. It shows only half of 2009's cases with little fidelity to actual location.

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Related:

Polio Turns Stealthy in India (August 19, 2010)

Heavy Lifting: Raising Health Beyond Polio's Reach (May 13, 2010)

Wall Street Journal: Pulling the plug on polio eradication? (April 26, 2010)

Polio Eradication: Harder Than it Looks (April 14, 2010)

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