Recently in Basic Research Category

The NIH narrowed an AIDS vaccine trial planned for U.S. testing. The trial, called Partnership for AIDS Vaccine Evaluation (PAVE 100) will be pared down to focus on the question of whether the vaccine lowers amount of HIV virus in the blood of those who are subsequently infected after vaccination. Scientists questioned the sense of moving forward with this larger trial last year in light of the failure of the multi-country Merck vaccine trials, as we commented in "New Directions for AIDS Research Funding".

In other AIDS research news,Weijing He and a team of colleagues in the US and UK found that a protein called DARC (Duffy antigen receptor for chemokines), that makes some African people resistant to malaria may influence HIV infections and AIDS outcomes. The small study published by Cell Host & Microbes shows that the existence of certain DARC mutations enables resistance to some malaria parasites -- though not Plasmodium falciparum, the most prevalent and deadly parasite.

The DARC mutation that prevents infection by some malaria parasites also seems to influence how successfully HIV invades and attacks the immune system. DARC codes a receptor on the surface of red blood cells that binds or tethers the HIV virus. The researchers found that a particular mutation of DARC increases the odds of acquiring HIV-1.

However the mutation also seems to increase the DARC protein's interactions with chemokines. Chemokines are proteins in the immune system that trigger inflammation, and they interact with HIV virus. Researchers have shown that the DARC protein acts by scavenging, retention, or transporting chemokines, and mutated DARC protein seems to lower levels of chemokines. In this study, once infected, people with the mutated DARC lived 2 years longer than those with the normal copy of the protein. While the study helps pave an outline of these interactions the authors predict (with understatement) that future research will show "the net effect of the relationship between DARC and chemokines on HIV disease in vivo is likely to be much more complex."

A Face that Sticks in Your Mind

Why is the crust of Mars up to 30 kilometers thinner on one half of the planet than the other, one side of the planet rugged terrain, the other plains? Twenty-five years ago a couple US scientists theorized that a collision had impacted the planet in a way that caused the dichotomy between the two hemispheres. However geological tools couldn't validate the theory, which also wasn't the only possible explanation.

Mars' mantle, like Earth's, shifts over time, and an alternate theory was that the 30km difference was due to upwards shift of the mantle. Overturn from magma ocean melting could have also produced the differences. Then some scientists thought that an impact of great magnitude would create different features from those found, or would simply obliterate all evidence.

Last week Nature (subscription) published studies by three research groups who used new modeling techniques to provide evidence for the collision theory. Jeffrey Andrews-Hanna, Maria T. Zuber, and Bruce Banerdt's team from MIT estimated that >4 billion years had passed since the Mars dichotomy formed, and that in the intervening time geological activity had obscured evidence from the original event. They programmed specific assumptions about gravity and terrain into their model to account for changes such as activity from Mars' Tharsis volcanic range.

The group then determined the original boundaries of the dichotomy, which happened to match their measurements of the elliptical area formed by the theorized impact. The huge elliptical area formed in the event is 10,600 by 8,500 kilometers (6,586 X 5,281 miles) covers about 20% of the planet and is bigger than than largest country on Earth -- Russia's width is ~5,000 miles. At about the same time as the Mars collision a similar event occurred on Earth which threw off the moon and lots of debris. It was a violent time in the solar system.

Margarita M. Marinova et al., from California Institute of Technology and University of California (UC), Santa Cruz, used modeling to determine the type of impact that would create the unique geology, The team calculated that an object 1,600-2,700 km wide hit the planet with about 3 X 10²⁹ Joules of energy. Scientists believe that the collision not only created a giant crater and changed the planet's crust, but that it was responsible for some of the other features of Mars. F. Nimmo and team, also from UC Santa Cruz, produced a third study to round out current understanding of the possible impact.

What's The Problem on the Water Front?

In other exciting Mars news, robots earlier in the month discovered what looked like it could be ice. Scientist programmed robots had taunted us for years, foraying around the planet then duly reporting back no signs of water. Last weekend the "NASA Phoenix Mars Lander" scooped up some of the icy soil for analysis. By vaporizing it in an oven analyzing the gases emitted, and by determining the minerals in the clumps of icy soil retrieved by the robot, scientists will try to ascertain what the substance is, whether it was at some time liquid, and how it formed. The lab tried to run this experiment a few weeks ago, but it went awry when the robot deposited the soil into the oven but the oven reported back that the soil wasn't there. Scientists were planning to process the soil sample differently or use a different oven in order to complete the analysis.

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For many years, the defense ministries in allied states like the US, Canada and the UK have denied that exposure to depleted uranium (DU) could produce negative health effects. Depleted uranium is a byproduct of uranium 238 (U238) enrichment, and contains a higher percentage of U235, a more fissile isotope that makes DU useful in the production of nuclear weapons and energy. This depleted byproduct is 1.7 times the density of lead, and because of its durability, has been used extensively by militaries for things like armor piercing projectiles and anti-tank weapons. During the Iraq and Balkans wars, when vehicles and weapons clashed together, dust from depleted uranium was released. Bullets made with the depleted uranium were scattered in battle, and shrapnel was strewn about and embedded in wounds. Depleted uranium ordnance now lays scattered throughout previous war zones where children play and civilians attempt to carry on their lives.

Civilians and other species are exposed to depleted uranium not only during war, but via dust in the air around weapons factories and in groundwater near firing test ranges like in Solway, Scotland, where scientists find worms that carry uranium isotopes. All of this exposure could prove toxic to animals and humans.

Depleted uranium is not as radioactive as U235 but it is suspected of causing various illnesses, from cancer, immune disorders like Gulf War Syndrome and even birth defects in offspring born of soldiers who inhale or ingest it. Research shows that in lab animals, depleted uranium is an immunotoxin, neurotoxin, and teratogen and carcinogen. Although the deteriorations in the health of some soldiers seems to show the the dangers of DU, there's limited government recognition of these dangers, from military, medical, and science establishments. Even in the face of accumulating evidence and significant public outcry about depleted uranium, militaries give mixed messages about DU safety. The US Department of Defense says:

• "The health effects of uranium have been studied extensively for over 50 years."
• "The Department of Defense has comprehensively studied the environmental fate of depleted uranium both before and after the Gulf War."
• "Fortunately, DU is only mildly radioactive emitting alpha and beta particles, and gamma rays.....The risk of chemical toxicity is also minimal because there is little likelihood that sufficient quantities of DU could be inhaled or ingested to cause a heavy metal concern."
• "Since the Gulf War, the DoD has dramatically stepped up its emphasis on increasing soldier and leader awareness of the hazards associated with the battlefield use of depleted uranium..." through training, handbooks and "support materials".
• "...there is no reason to believe that other exposed Service members have any elevated risk to their health due to their DU exposures."

Similarly, the Ministry of Defense (MOD) for the UK has repeatedly asserted minimal health effects from exposure to depleted uranium, but the MOD also gave warning cards to all UK servicemen deployed to Iraq stating possible health effects of DU. The Ministry of Defense suggests that it's reducing use of DU, noting cryptically of all the accounting of the depleted uranium used by the military: "In 2003, during the recent Iraq conflict, UK tanks expended 1.9 tonnes of DU ammunition and none has been fired since the official ending of the conflict." The MOD urged soldiers to get monitored for depleted uranium, but after testing the urine of returning servicemen the Ministry of Defense told papers in 2006 that "no evidence of DU was found in their urine". Critics question the sensitivity of their tests.

Clearly, the effects of depleted uranium are still disputed and perhaps not a problem, but new research suggests a potential solution. Scientists have discovered a fungus that will break down depleted uranium to a less toxic mineral, research sponsored in part by the Ministry of Defense, produced by scientists at the University of Dundee in Scotland and published in the recent issue of Current Biology. They describe how a plant symbiotic fungus can be grown on the surface of depleted uranium, where it will transform the depleted uranium into uranyl phosphate minerals, a more stable form of the metal that is less likely to be absorbed into plants, animals and water. The mycorrhizal fungi usually lives in the roots of plants, where it transforms carbon into nutrients that plants use. When colonizing uranium, moisture in the air helps the fungi cover the surface of the metal, where the fungi helps accelerate the corrosion process of the uranium into products that can be take up by the fungi or broken down to less toxic uranium holding minerals. The fungi could be used for various bioremediation projects in uranium polluted soils.

Charlie Rose concluded a thirteen part series on science earlier this week, with another interesting episode, "The Imperative of Science". Sharing his table were Paul Nurse, who shared the Nobel Prize of Physiology or Medicine in 2001 and is currently President of Rockefeller University; Bruce Alberts, a biochemist, author of texts like the definitive Molecular Biology of the Cell, former two time president of the National Academy of Sciences and Editor-in-chief of the journal Science; Lisa Randall, Harvard particle physicist and author; physicist Shirley Ann Jackson who is the President of Rensselaer Polytechnic Institute; and Harold Varmus, who shared the 1989 Nobel Prize in Physiology or Medicine, headed the NIH through a heady science period and is now the president of Memorial Sloan-Kettering Cancer Center. The focus was the importance of science and it naturally was an interesting, convivial, and lively, if general, discussion.

The group said that the US has become complacent about its long time position as a world leader in science and that increased global competition in science demands decisive action if the country is to maintain its status. The participants emphasized the need for better science education. Alberts brought up primary and secondary education, and they all discussed the importance of improving college curricula. They stressed that appreciation of the scientific process and experimentation should be a more central part of liberal arts education, and that all students, not just those who show great promise to be scientists, should learn and experiment at science.

Thinking scientifically is not only important to understanding science, these leaders pointed out, but to processing of all complex problems; the goal is not only to resist "the dogma of talk radio" but to be an active participant in democracy. (they ran with the science is democracy idea)

They all nodded, agreeing with one scientist who crisis in science to a frog sitting in the pot of water as the heat gets turned up. According to this allegory a frog that sits in cold water will stay and perish when the temperature is raised (by some demented frog torturer). When I heard this I applied the critical thinking and research skills that only scientific training can hone, and learned that the frog tale is an urban myth. The good news is that apparently frogs save themselves rather than fatally habituating to hot water -- though to be honest, mine is second hand information. Apart from urban myths, the urgency for science in America is real, as is the human tendency to disastrously ignore problems that creep up on us.

The group discussed various ways to reinvigorate American science as was done with focus and enterprise after Sputnik. Perhaps a problem like global warming could rouse national science spirit, they said. (Coincidentally, Al Gore applied the frog allegory to this problem in An Inconvenient Truth)

The scientists expressed nervous concern that our leaders be able to "connect the dots". A president needs to lead the nation to an understanding of science's central place in society and needs to focus attention on fundamentals like education and funding in order to assure both the nation's preeminence in science and increased public understanding of science. Politicians need to support science in a broad cross-disciplinary way, they said. The goal should not be to tackle a series of individual problems but to recognize the commonalities across disciplines and build a foundation upon which science progress thrives with long-term bipartisan support.

Rose asked whether there was enough interest in science among voters to warrant a presidential science debate, adding ""voters are there if you can get on the right side of it". The scientists righted course, expressing incredulity that there weren't already strong public science platforms, and supporting a debate to reassure Democrat and Republican voters of candidates' commitments to national competitiveness via science.

Here's the link to watch/listen to the video its entirety.

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When Merck's AIDS vaccine candidate failed in clinical trials, the National Institute of Allergy and Infectious Diseases (NIAID), in the National Institutes of Health (NIH) called a summit. The drug candidate did not reduce HIV infections, in fact the adenovirus based vaccine seemed to increase the risk of infections.

The meeting of scientists on March 25th in Washington focussed on the future of HIV/AIDS research in light of the fallout of Merck vaccine trials. Scientists including Anthony Fauci, who heads the NIAID, agree that funding needs to be redirected towards a broader research agenda and ideas beyond drug development and vaccines. Science last week noted that the decision about whether to proceed with the large NIH clinical trial planned for its HIV vaccine is still pending. ("Review of Vaccine Failure Prompts a Return to Basics" DOI: 10.1126/science.320.5872.30)

Nature also reported on the summit last week, pointing out that these clinical AIDS trials went forward not necessarily based on the strength of the science -- one of the vaccine candidates had a unimpressive track record -- but because programs needed to "show the public that progress is being made, thereby justifying the millions of dollars from philanthropists and taxpayers". ("Broken Promises" doi:10.1038/452503a).

The Nature editorial offers analysis of this HIV-AIDS vaccine experience, noting that ambitious commitments made in a flush funding environment in the early part of this decade short-changed basic research. These choices to heavily fund drug development are regarded less forgivingly in light of the trial failures and the budget shortfalls of recent years, according to the journal. Nature warns other fields, for instance stem-cell research, autism, and Parkinson's disease, are repeating these same mistakes.

The business approach comes with a high stakes mentality and ample, vigorous marketing that can ratchet up expectations both within the organization, the field and the public arena. The business-oriented nature of many philanthropic organizations influences the focus on development and can distort public expectations. But investors can and do influence the direction of an entire field. When a field becomes dominated by a few foundations it can gather tremendous productive momentum, but it can also stampede so hard down a particular path with such strong momentum in a particular direction. If that direction proves to be less fruitful than hoped research cannot turn around on a dime.

Each high-funded disease has its own idiosyncratic pitfalls, but behind the good works and fine intentions of charities, but the science research rarely responds to pressure, unlike many entrepreneurial ventures. When scientists request research funding, the results don't always yield answers as quickly as businesses might hope -- research is the mythical man myth on steroids. Some people investing in biotech and international public health come from businesses very unlike public health with its vagaries of not only politics and human behavior, but biology.

In today's fast paced communications and computing climate, intense focus on "results" is inherent to our culture. Expectations carry over from the successful and extraordinarily speedy progress of the genome sequencing. Scientists and politicians built hopes during that time that drug development and an accelerated understanding of human disease would follow. It has, but did we expect more? TV drug advertising gives the impression that scientists are developing a pill for every insignificant hangnail, when many of these drugs aren't new, just the subjects of new marketing campaigns. Meanwhile tougher diseases and conditions remain elusive.

High profile funding can influence the research environment and lead to a very public dead end. In the larger picture, despite the wisdom that should be accruing from these experiences, politicians, technology leaders, and pundits sometimes wax-on about technology's potential to produce solutions not only for specific diseases but for extremely complicated social problems such as global warming and healthcare. But while science research may yield pharmaceuticals and oil extraction techniques but one cannot look to science or technology to solve the healthcare crisis in the United States. Science and technology contextualize these problems and are integral in our lives but despite heady declarations, they are not central to the solutions.

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Acronym Required has written previously about these subjects, AIDS and research directions, and vaccines. Here are a couple of our vaccine articles:

Vaccinations -- Why Worry?
Polio Vaccinations - The end of a scourge?
Group B Strep Vaccine Development
Vaccine Development For Infectious Diseases

Before scientists went snorkeling in Borneo and plucked a frog, the charming looking Barboroula kalimantanensis, out from under a large rock in a fast moving body of water, the elusive species had been found only twice before. In 1978 Djoko Iskandar described the new species of frog in the journal Copeia (Dec. 28, 564-566), cataloging its webbed toes, rugose skin, flattened head, and the myriad anatomical features that distinguished it as a unique species. The second find was sighting was almost 20 years later, 1995, by the same scientist, Iskandar, who also collaborated on the current research.

As an endangered species, the frog is perhaps lucky that it's so difficult to locate, although it's still subjected to environmental pollutants and habitat encroachment from logging and mining. Not so fortuitous for these primitive frogs, the scientists decided to dissect the specimens for the first time and found that the species has no lungs. David Bickford, an evolutionary biologist at the National University of Singapore, explained that "because these specimens were so rare, they had never been dissected. If you have just one...in your museum, you don't want to rip it open!" (a different approach then some scientists take with their newly found marine species, Acronym Required has found). If unlucky for these frogs, the discovery was lucky for the researchers, as they got their name splashed across headlines around the world. ¹

The biologists hypothesize that the frog adapted to the highly oxygenated fast moving water by losing lung capacity. Since the frog lost its lungs, its body became more flattened and less buoyant, which researchers deduce helps it stay under rocks. As well, with its increased surface area respiratory capacity through its increased skin surface area.

Tetrapods without lungs are rare. There are lung-less salamanders and one species of caecilian, an earthworm-like amphibian, that don't have lungs, and some frogs with very diminished lungs, but this is the first species to have only cartilage in the place of lungs.

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¹ This news was in an advance press release supposedly ahead of a April 8th Current Biology article which we could not locate. Acronym Required usually doesn't publish research without reading the original source, but will update this post if needed. Update 05/06 - The article was published May 06, 2008 in Current Biology: Bickford, D.; Iskandar D.; Barlian, A; "Lungless frog discovered on Borneo": Current Biology, Vol 18, R374-R375, 06 May 2008.

A couple of years ago in "The Microbes Win", Acronym Required wrote about research done by Wright et al at McMaster University, who found that many species of microbes isolated from soil samples had significant antibiotic resistance to clinically useful antibiotics. Last week researchers at Harvard published a study in the journal Science (Dantas et al, "Bacteria Subsisting on Antibiotics":Vol. 320. no. 5872, pp. 100 - 103), advancing research in this area a step further.

The scientists managed to culture a significant number of soil isolates using antibiotics as the sole source of carbon. The bacteria that proliferated most proficiently on a diet of antibiotics were from the Pseudomoniale and Burholderiale orders. Bacteria in the genuses Pseudomonas or Burkholderia, like Pseudomonas aeruginosa and Burkoholderia cepacia are responsible for infections involved in meningitis, skin, lung and bone infections, swimmer's ear, and opportunistic infections in immunocompromised patients and those afflicted with cystic fibrosis.

The Harvard group suggest that the large genomes of Pseudomonas and Burkholderia species give them many diverse mechanisms of resisting bacteria and adaptive versatility, and that catabolism of antibiotics is just one tool in their arsenal of antibiotic resistance mechanisms.

These bacteria are very relevant clinically but scientists haven't observed utilization of this antibiotic catabolism, probably because there are many sources of carbon at infection site therefore catabolism of antibiotics isn't the most useful method of resistance. Since soil residing bacteria are exposed to natural sources of antibiotics, the research isn't extremely surprising, but may lead to further understanding of shared and unique antibiotic resistance mechanisms.

Update: The New York Times reported March 3, 2008 that David L. Allison resigned as the incoming president of the Obesity Society. He said in his email statement that "I stand behind the scientific statements I made, my right to make them, and the manner in which I made them", however he apologized for the "distress" he might have caused the Obesity Society. The economic tensions that interfere with frank science presentation and reporting remain.

Conflict of Interest?

Would you believe a nutrition researcher working for Coca-Cola who said that restricting foods might backfire in preventing obesity because 'birds put on weight when food is scarce'? Would you choose him to be president of your "Obesity Society", if your club's mission was to "be the leader in understanding, preventing and treating obesity and in improving the lives of those affected"?

A recent New York Times article, "Conflict on the Menu", threw light on the "food fight among the nation's obesity experts". The New York State Restaurant Association hired the president-elect of the Obesity Society, Dr. David Allison, to support their suit against New York City's regulation requiring chain restaurants to list the kilocalorie values on menu items.

Allison submitted an affidavit warning that listing calories on menus might encourage overeating. According to the NYT he suggested the regulation would either tempt patrons with "the forbidden-fruit allure of high-calorie foods", or leave them so hungry they'd "later gorge themselves".

Somewhat less creatively, the American Medical Association, the American Academy of Pediatrics, the American Heart Association, the American Diabetes Association, the American Public Health Association, the California Center for Public Health Advocacy, the Medical Society of the State of New York, the Trust for America's Health, and many other organizations back the city's regulation.

Obesity & Personal Freedom

While the New York Times keeps the focus of the story on the skirmish within the Obesity Society, many stakeholders have a foot in this game. Public interest groups of all stripes, including "consumer freedom and choice" advocates, fight tooth and nail over the city's plan.

The Center for Consumer Freedom (CCF) is a group that lobbies against government regulation. They wrote histrionically about New York City's labeling plan in "Menu Labeling Meltdown", warning that "the food cop campaign will plaster our nation's menus with warning labels.." Their consolation was Dr. Allison's "damning evidence" that labeling "might be harmful". CCF reveled in the idea that Allison's affidavit dealt a "major blow" to the city's plan and that Burger King might not have to label their Whopper with its energy value: 670 kilocalories.

CCF claims to fight for Americans' right to "guilt free eating". Their stated mission is "promoting personal responsibility and protecting consumer choice" and their especially belligerent towards specific targets, individuals or groups like the Center for Science in the Public Interest (CSPI) -- "the food cops". Sourcewatch offers a more blunt profile of CCF, calling them "a front group for the restaurant, alcohol and tobacco industries". Phillip Morris started the organization under the name "Guest Choice Network" years ago for the purpose of organizing restaurants against government smoking bans.

CCF wields the same arguments that tobacco lobbyists used to oppose government smoking bans by supporting the claim that the city's rules violate the First Amendment. However Sandra Wootan, director of nutrition policy at the Center for Science in the Public Interest (CSPI), says: "The restaurant industry isn't concerned about defending the First Amendment, as its lawsuit laughably claims. It just wants to keep its customers in the dark. People need nutrition information to exercise personal responsibility and to feed their children healthy diets."

It seems like "personal freedom" stands for "corporate freedom" in this context. While personal freedom is important, governments are obliged to work on behalf of the community, for instance by mandating vaccinations, sanitary conditions in restaurants, anti-smoking laws, etc. The city regulation basically requires chain restaurants that have caloric information elsewhere, like on a website, to post in on the customer menus. This is not the cumbersome requirement that CCF makes it out to be.

Science & Policy

Despite the Center for Consumer Freedom's approval of Allison's recent position they haven't always been so friendly. In 2001 the group contested Dr. Allison's 1999 finding that obesity caused 300,000 deaths a year, calling the research "bogus". The organization accused him of "voicing support for an onerous and unnecessary 'Twinkie Tax'", and having "ties to the weight-loss industry". In 2004 and 2005 the group opposed Dr. Allison in articles like "Hypocritical Food Cops Preach 'Integrity'", accusing him of conflict of interest and citing Allison's many industry affiliations to discredit his research.

In 2005 Allison was one of ten authors on a New England Journal of Medicine paper showing that the average lifespan in the US would decrease because of the obesity epidemic. (Olshansky et al, "A Potential Decline in Life Expectancy in the United States in the 21st Century", March 17, 2005 Vol. 352:1138-1145.) The accompanying editorial said the group's assumptions were "excessively gloomy", but scientists generally thought the findings important despite the data estimates.

Although this was a science research paper, the authors pointed out policy implications, as they often do. There were possible up-sides to the research, for instance: "the U.S. population may be inadvertently saving Social Security by becoming more obese". The findings were grim, but policy interventions might reverse the death trends, they said: "Unless effective population-level interventions to reduce obesity are developed, the steady rise in life expectancy observed in the modern era may soon come to an end and the youth of today may, on average, live less healthy and possibly even shorter lives than their parents."

An accompanying editorial gave more detail. "Deadweight? --The Influence of Obesity on Longevity", by Samuel Preston, Ph.D., mentioned other research showing that only "30 excess calories a day during an eight-year period for Americans 20 to 40 years of age" produced the obesity epidemic. (NEJM Volume 352:1135-1137). Given the morbid implications of small increases in daily calories, Dr. Preston said: "reversing the increase in body mass might be accomplished through small behavioral changes...the food and restaurant industries would be valuable allies in this effort..."

So the authors recommended that government interventions were critical to maintaining current longevity, and that nominal calorie reduction might help reduce obesity if restaurants cooperated. Which makes it particularly ironic that Allison, the co-author, chooses the role of a hired gun fighting calorie labeling on behalf of restaurants.

In contrast to their opinion of Allison since 2001 CCF's coverage of the current NYC regulation does an about face. Now, abruptly, his "facts showed" and "the evidence was damning". They decided not to fill their story about his affidavit for the Restaurant Association with long lists of "conflicts of interest", which served as the meat and potatoes of their previous irate stories about his research.

News of Allison's affidavit supposedly caused a fracas among members of the Obesity Society, who got ''completely mad that a president-elect of [an] organization that cares about obesity and cares about healthy eating, wants to hold back information from people that helps them make healthy choices'', according to the NYT. This forced the current president of the Obesity Society to put out a separate statement opposing Dr. Allison's that supported the city's labeling rules.

Which made me wonder -- if Allison's position is so disagreeable, why did the nominating committee and 2,000 members in the society select him to be their future president? His consulting positions were a significant piece of his resume. He has been a paid industry consultant for at least 15 years. There must be more to this story.

When Truth Pays

A professor at the University of Alabama, Dr. Allison is an obesity statistician with a background in psychology. He's more than just a statistician with an affidavit that appears to be a conflict of interest. He's has published over 300 papers and 5 books. His home page shows him clad in a sporty warm-up jacket as if back from a jog, rather than posing with the more traditional professor air, before a pile of books or a math covered blackboard . He regards the camera a little too ravenously, as if he had picked the Veggie Delite Salad (51 kcal) at Subway, instead of the Footlong Meatball Marinara (1160 kcal), and was photographed hungry, about to grab the Ben & Jerry's New York Super Fudge Chunk from the freezer. [Although, if he wasn't getting paid to introduce doubt, we wouldn't be wasting our time here because he would have sensibly chosen the 6 inch Turkey Sandwich (280 kcal) instead of the Delite.(Subway lists their calories on menus)]

For his efforts and accomplishments Dr. Allison was honored by George Bush last year in a White House ceremony for recipients of the Presidential Award for Excellence in Science, Mathematics and Engineering". The award recognizes mentoring of women, minorities, and persons with disabilities.

Dr. Allison noted that the award was not just about mentoring but also about making sure the students "understand the ethical foundation on which science is based." It's a mission he apparently takes seriously, as The Birmingham News reported: ''In science, we are not just doing a job,'' he said. ''I was chosen. I think of it like a calling. It is a special and sacred profession. Our sacred duty is truth.''

When he was questioned by the New York Times about his support of the restaurant industry he said, "I'm happy to be involved in the pursuit for truth....Sometimes, when I'm involved in the pursuit for truth, I'm hired by the Federal Trade Commission. Sometimes I help them. Sometimes I help a group like the restaurant industry."

Speaking his truth though he may, Allison remains agnostic in his choice of client. He's widely consulted by government, industry and the media for his expertise in obesity, science, and integrity. When Eric Poehlman, the University of Vermont obesity professor was accused of falsifying data on metabolism and aging in research papers and federal grant applications, Dr. Allison interviewed the media in his defense: "I believe he's innocent, and I believe that he is being broken financially to the point where he's ready to give up the fight because he has no more money to fight with, and that's the way the game works", (Boston Globe, March, 2005). Poehlman served a year in jail, paid fines and recieved penalties.

Dough Boy

The Center for Consumer Freedom discredited any research Allison was involved in except when it ran in their favor. They accused Allison repeatedly of conflict of interest especially with companies selling "weight control product and services". CCF may be a bottom feeder, but it doesn't exaggerate Allison's impressive industry ties. In the 2005 NEJM paper about obesity longevity, nine authors disclosed zero financial interests or affiliations. Dr. Allison however, gave new respect to warm-up jackets and statistics by listing about 150 organizational affiliations in a three page single spaced PDF, attached to the paper.

Dr. Allison's list of grants, monetary donations, donations of product, payments for consultation, contracts, honoria and commitments include consulting assignments for numerous parties, like lawyers engaged in litigation, pharmaceutical companies including Pfizer, Eli Lily, Wyeth Ayerst, Glaxo, as well as Corning, Frito-Lay, Coca-Cola, the Wheat Council, Kraft Foods, Nabisco, the FDA and ILSI. He has impressive experience doing everything from serving on the United Soybean Panel's Nutrition Advisory Board, to being an expert witness for defendant Lockheed Martin at $350 an hour in a groundwater contamination lawsuit.

Much of this was listed in Allison's resume, which I assume the Obesity Society recieved prior to selecting him to their leadership council. If not it was summarized at the Integrity in Science project at CSPI, or in disclosure documents in his publications. His insouciant transparency, extensive network (I assume), precocious achievement. and ethically unencumbered attitudes to choosing clients no doubt secured him a Obesity Society leadership position.

Hungry Scientists, Money

Sometimes when you travel or walk down the sidewalk you encounter kids so poor they come running up, dozens of them -- "pen"? "dollar"? "cigarette"? Science seems like this sometimes these days. It seems there's no party that doesn't have an interest in this obesity science/business -- pharmaceutical companies, lawyers, labs, product companies, insurance companies, NGO's, government. Science results create more work and profits for some, and/or less work and profits for others. You can imagine the repercussions of some of the science results we mention above.

Allison co-authored a study published in NEJM, where the policy implications proposed are the opposite of the "expertise" Allison now sells. This costs the state in legal fees and customer choice, not to mention making a mockery of science. Poehlman's false data of age related metabolic depreciation affected policy. Doctors and researchers based study and clinical practice on his results, and granting Poehlman funding, other scientists were denied money for their research. Then there was the CDC study in 2004 which incorrectly calculated the statistics and overestimated the annual deaths from obesity. This created false public perceptions and policy implications, and raised the ire of public health advocates in other areas who eying the competitive pie of public health money (especially anti-smoking advocates who were nervous that the results would make obesity public health priority number one).

Some people think that science should remain separate from policy -- like an old TV dinner, the cut vegetables separate from meat product and the syrupy peaches, each one in its own plastic mold -- compartmentalized, never mixed. Combining "science and policy" confuses the public they say. Others, claiming pragmatism, suggest everything is already mixed up, a big stew. Indeed, this seems true when scientists recommend policy, or when results are seized upon by lobbies. In many fields results have direct policy and/or business implications.

The media impedes the first approach, separating science from politics, by blending everything together in their stories, the science, the policy, the personalities, the business, the lobbyists. This mush is extracted by the press, drained of color and interesting nutrients and doled out as an equally portioned product of pro and con, like symmetrical freeze-dried blocks. We're fed an easily digested story with the predictable arch of a food fight and a neat two part conflict: "Scientists found this...but others found that".

Unfortunately, one of the largest problems resulting from this information processing by media and various lobbies, politicians, and interest groups, is that many of us -- citizens, reporters, politicians, scientists out of their field... have not clue as to who's the lobbyist, who's the "unbiased researcher", who's the expert, and who is an apostate. If headline news runs a "science piece", separating the chaff doesn't always matter because it might ruin the storyline, and anyway, who could be bothered? But this is not and never has been an isolated conflict of interest problem, a media problem, the scientists' problem, or a government agency problem. It's a larger more thorny economic conundrum that affects us all.

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Acronym Required has previously written about obesity in public health.

Long ago, as our ancestors hopped up and started getting around on two feet, their musculoskeletal systems evolved to accommodate the new bipedal locomotion. The size of the vertebrae increased, the lumbar region of the spine elongated, and the number of vertebrae in the lumbar region of the lower back eventually decreased from six to five.

In the female, further adaptations helped her endure pregnancy and carry up to 30% more of her body weight. Scientists wrote in Nature¹ last week about sexually dimorphic features in the lumbar spines of women, such as larger joints and greater curvature of the spine, that appear to ease the biomechanical strain of pregnancy. The lumbar lordosis (curvature) in women's spines extends over three vertebrae rather than two, as it does in men.

The authors proposed an evolutionary benefit to this increased flexibility in women's spines. During pregnancy, they said, the greater lordosis probably reduces the pain and stress on the spine caused by spinal shearing forces which intensify with the increased load bearing. The scientists also compared modern human spines to chimpanzees and early hominins such as Australopithecus africanus. From their measurements of the different lumbar regions and fossil vertebrae the scientists concluded that these adaptations were present in some of the earliest hominins, but not in chimpanzees. Male and female spines evolved for their bipedal locomotion, but then women's spines are distinguishable from men's, which helps them through childbearing.

Many evolutionary adaptations aid gestation and birthing. But some of these changes seem to simultaneously compromise other activities, like locomotion. The female pelvis is wider then males', to accommodate the birth of a baby. Scientists debate whether this adaptation increases the Q-(quadriceps) angle in women, which may cause injury (mostly knee tracking issues) during running or walking. Hormones during pregnancy make the ligaments temporarily lax, which doesn't help overall stability. But the authors suggest that this newest finding about the sexual dimorphism in lumbar lordosis probably benefited women by decreasing pain during pregnancy. It therefore may have helped females "forage effectively or escape predators".

Foraging, ok. But I was trying to visualize how the new and improved physique would help our ancestors escape predators as I flipped through the meretricious "Fine Times" section of the Financial Times last weekend ("The Game Generations"). In the story, the author's safari group tracked a female cheetah as she unsuccessfully hunted with her cubs. After days of failed forays, the hungry female cheetah chose to attack two rutting impala. The female interrupted the two fighting males, brought one down, left it to her cubs to the kill, but they bungled it -- so she stepped in and finish off the job.

Granted our ancestors were a heartier bunch, not yet reduced to reading about "wild Africa" in the glossy pages of an insert subtitled "How to Spend It". Still, I have trouble visualizing the flexible but ponderously gravid Australopithecus effectively escaping a cheetah or tiger or leopard. An impala is about 75kg, with horns, and can make 30 feet jumps as high as 8 feet off the ground -- but is still prey to every other beast. Women may leap tall buildings but they're no match for the impala, never mind a wildcat in the bush.

The "Fine Times" author may indeed have experienced an "awesome lesson in the savage ways of nature", but she was removed from the action, at a distance sufficiently safe for hominins. Which made me realize that despite the superbness of this newly discovered evolutionary feature, our pregnant female ancestors might not have chosen to run with the wolves at all. Instead, while four or five months pregnant, perhaps they recognized their inferior speed, smaller teeth and duller claws, and chose instead to forage around for some sticks and stones, before retiring to a cave to fashion some proper weapons.

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¹Whitcome et al., "Fetal load and the evolution of lumbar lordosis in bipedal hominins" Nature 450, 1075-1078 (13 December 2007) | doi:10.1038/nature06342.

²The Q angle is an acute angle found at the knee. It's formed by at the the intersection of one line drawn from the patellar midpoint to a point on the anterior lateral (outside front) of the pelvis called superialic spine (ASIS), and another line drawn through the tibial tuberosity (on the front part of the top of the leg bone called the tibia) (See Fig. 2 here)

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Acronym Required has written previous articles on biomechanics, such as "The Stalwartness of Nepalese Porters", and hominins, such as "The Hobbit Species of Indonesia"

Summary:

Just a thought: If bisphenol A were a therapeutic drug going to market, instead of a chemical with an established global market, and there were 700 studies (LA Times) showing hormone effector effects in animals, but also "two dozen" human studies showing the same responses in humans-- therefore if bisphenol A, the hypothetical drug, had passed through the equivalent of Phase I safety, Phase II efficacy and was well into Phase III trials-- the stock of a certain pharmaceutical company would be skyrocketing based on the evidence. Financial analysts would be jumping up and down in their Aeron chairs predicting sales of the next blockbuster drug... But bisphenol-A is not a drug. It's a chemical used in mostly polycarbonate products such as baby bottles and sport's drink bottles, but ubiquitously in toys, dental epoxies, food cans... 2.8 million tons of bisphenol A were produced in 2002. So manufacturers, politicians and organizations like the American Dental Association deny that the animal studies mean anything. They insist that bisphenol A is safe. Is it? If not why did city legislators in San Francisco decide not to restrict its use in products?

Plastic People

Chemical & Engineering News published an article August 6, 2007, titled "More Concerns Over Bisphenol A: Human Exposures are Usually as High as Those Causing Profound Effects in Rodents". The article presented evidence from four toxicology studies that "bolstered" the link between "bisphenol A (BPA) and adverse health affects". Bisphenol A is used extensively in producing certain hard plastics used for various products. It is an endocrine disruptor that in mice causes a myriad of deleterious physiological effects, and when scientists do corresponding studies in humans, they produce the same results as in mice.

Makers of bisphenol A and the chemical industry label anyone who questions the safety of chemicals a "green activist" with "anti-chemical agenda". But the American Chemical Society hardly fits into this category. When the American Chemical Society notes the "profound effect" of bisphenol A, won't industry lobbyists and Fox news temper their caustic comments towards anyone who dares questions the safety of a chemical? Will they realize how out of date and trenchant they sound and change their tune? Doubtful. As the American Chemical Society also notes, "despite growing evidence of toxic effects in lab animals, manufacturers of BPA insist that their product is safe."

It's curious that the chemical industry has manage to conceive and manufacture hundreds of thousands of chemicals for millions of "better living through chemistry" applications, but seems hamstrung by the challenge to create less toxic options. Instead, they vehemently oppose the idea of taking a toxic product like bisphenol A off the market. Once production is in place and market share is established, removing a product from the market is as much an anathema to industry as it is to the politicians and media who represent industry. Of course there are "economic repercussions" to such a move. But industries remove consumers favorite products all the time when it benefits their bottom line. In fact isn't "planned obsolescence" a foundation of capitalism? But rather than focusing on the potential profit that would come from a new, less toxic product, these industries cling like traumatized children to their old business.

Chemical & Engineering News doesn't need to tell us that the Chemical, Plastics and Toy Manufacturing industries might not be the most reliable source of information for toxicity of chemicals. This is not strange or unprecedented business practice, rather a predictable one. The car industry bucked seatbelts for years, the tobacco industry denied that dragging on cigarettes caused cancer, and the oil industry launched/launches vigorous attacks against all science and scientists who observed and predicted climate change and global warming. We've come to expect this of industries. They bombard the market with new and exciting products on the their own terms. They find infinite new uses for chemicals; for phthalates and bisphenol A that make plastic products pliable or rigid or just plastic-y so. They create and manufacture plastic products en force, to strong demand, with impressive budgets that buy marketing, press releases, opinion pieces, disclaimers, liability notices, and a bevy of braying lobbyists and complicit politicians.

When it comes to our health, consumers are learning not to depend on industry information. Since Acronym Required first started reporting on bisphenol A and phthalates a couple of years ago, public awareness of the potential dangers and the lack of industry transparency about them has grown tremendously. Despite this self-determination, however, consumers remain dependent on the media to inform us, and the legislature to protect us. We're the largest constituency of politicians, and the largest consumer group of newspapers, and TV networks. However to the media and politicians, citizens are just one of many constituencies -- not necessarily the loudest, the most consistent, or the most generous. Politicians and the media are also indebted to their own bottom line; to donors, partner businesses, trade groups, and advertisers, not only readers and voters. Health and environmentally conscious citizens sometimes discover that their influence is relatively small, just one line on a whole balance sheet of competing interests.

The Press and Poison, The Press and Pills

Media coverage on potential toxins can be good, as in a USA Today article on October 30th about bisphenol A, but it can also be confusing if not downright bad. Consider the editorial decisions that Los Angeles Times made last month, in publishing an article titled: "Some Chemicals May Affect the Reproductive System, Growing Research Suggests. But as Consumers seek Alternatives, Scientists Point out that Human Studies are Few."

Discussing the bisphenol A, the article relayed the warning of a panel of 38 scientists working for a EPA and NIH panel on bisphenol A, who surveyed "700 studies of bisphenol A". The scientists concluded:

"human exposure to BPA is within the range that is predicted to be biologically active in over 95% of people sampled. The wide range of adverse effects of low doses of BPA in laboratory animals exposed both during development and in adulthood is a great cause for concern with regard to the potential for similar adverse effects in humans."¹ [emphasis ours]

Said the Los Angeles Times "the vast majority of studies" looked at BPA effects in animals, but "only two dozen studies measured levels of the chemical in people, and three have examined the health effects of everyday exposure to the chemical". "Hundreds of studies" in lab animals, the article notes, found that "bisphenol A damages the reproductive system by interfering with the effects of reproductive hormones. Male rats have reduced sperm counts and enlarged reproductive glands; female rodents have altered mammary glands, hit puberty faster than normal and have trouble getting pregnant."

If bisphenol A were a therapeutic drug going to market, and there were 700 studies, many in animals, but "two dozen" human studies showing the same responses in humans as mice, and if therefore the hypothetical drug had passed through the equivalent of Phase I safety, Phase II efficacy and was well into Phase III trials, the stock of pharmaceutical company would be skyrocketing. Financial analysts would be jumping up and down in their Aeron chairs predicting the company's astronomical growth based on the "exciting" news. They would be exclaiming about "surpassed expectations" of a "new blockbuster drug", and headlines would be shouting about the "cure" for diabetes, cancer, heart disease, or arthritis in very very large font.

For an extreme example of this see the Times Online article this week titled "'Magic Bullet' Devised to Beat Cancer", a piece optimistic about a strategy to cure cancer based on an experiment that "eliminated ovarian cancers in five out of six mice, and greatly reduced the tumour's size in the sixth mouse." Six mice. Yet when it comes to evidence that points to the deleterious effects of bisphenol A based on hundreds of studies in mice, the Los Angeles Times chooses a presentation that intermingles hair raising evidence with reminders of how meaningless this all is; the studies are "small and few", "few", "nonexistent", "paltry", "little", and "we mostly don't know" -- their list of belittling adjectives is impressive.

"Paltry" Proof of Phthalates

There is even stronger data on phthalates than there is on bisphenol A. The LA Times acknowledges that "phthalates and other chemicals" are toxic to animals, but emphasizes that "in humans, the data are still inconclusive". Combining a couple of different ideas the writer says:

...In fact, when it comes to humans, the data are nearly nonexistent. Very little research has examined the health risks associated with consumer use of plastics. And because of suggestive evidence from studies of lab animals, much of that research has focused largely on chemicals in two types of plastics: those marked with recycling No. 3 and No. 7.

No. 3 is polyvinyls that contain phthalates. Despite the paper's assurances, here is what the article actually says about phthalates in animals:

"...high doses of phthalates cause a conglomeration of health effects that suggest the chemical may either block the activity of male sex hormones (such as testosterone) or hamper their synthesis in the developing embryo...[and]...lowered testosterone levels; a shortened distance between the anus and scrotum; testes that fail to descend; reduced sperm counts; and defects in the urethra, prostate and seminal vesicles."

As for humans, the author notes that the National Toxicology Program issued a report about DEHP (a particularly worrying phthalate)¹ expressing "'serious concern' that critically ill male infants exposed to the plasticizer could suffer damage to their developing reproductive systems". In 2002 the FDA notified healthcare providers that they shouldn't use tubes, bags or equipment containing DEHP "when treating premature babies, adults undergoing dialysis, heart transplant recipients and women pregnant with male fetuses", because the DEHP leaches out. (Many hospitals are currently phasing out DEHP.) The LA Times also lists the following research results for phthalates in humans:

• A study showing elevated mono-(2-ethylhexyl) phthalate in men corresponded with "50% more sperm DNA damage ."
• A study showing that men with elevated monobutyl phthalate "were more than three times as likely to have a low sperm count than men with the lowest levels of the phthalate"
• A study of "85 mother-and-son pairs, showing that, as in rats", higher levels of phthalates were associated with "shorter ano-genital" distance in infants, as well as "undescended testes, smaller scrota and smaller penises". The level of phthalates associated with these reproductive effects was lower than what was considered acceptable by the EPA.
• Another study showing that the longer newborns spent in intensive care the higher their levels of phthalates.
• Another study showed that high levels of phthalates correspond to "decreased levels of thyroid hormones".
• Studies showing increased levels of phthalates in dust corresponded to "decreased lung function" in men and asthma in children.
• A study showing that increased levels of phthalates was also linked to "insulin resistance" and larger waist size in men.

None of this seems particularly healthful. The European Union, Mexico, Japan, Fiji and Argentina have banned phthalates. But the LA Times, either in a desperate attempt to balance competing interests or because they have phthalate syndrome, has a higher bar of proof than Fiji. The paper reminds us once again that phthalates data is in its "infancy", and bisphenol A data "in the womb".

In light of what scientists tend to consider proof, if this were a drug going to market, wouldn't such evidence be trumpeted, as proof of efficacy? Indeed, drugs for breast cancer, leukemia, Huntington's Disease, brain tumors, Down's Syndrome, MS, various tumors, Alzheimer's, Gleevec resistance, diabetes, H5N1 infection, lupus, and hundreds more -- are touted as showing "promise" based on far less "data in mice". If this were a potential drug wouldn't the money be pouring into determining the proper dosage? Instead, any testing of these hazardous chemicals is incumbent largely on government and occurs, slowly, slowly, and only as "time and resources allow", as San Francisco recently put it in legislation on phthalates.

Precautionary Principle

When public concern is high enough, as it is for bisphenol A and phthalates, a toxin might catch the attention of politicians. But even then, when push comes to shove, politics can water down the most well intended legislation. Take, for example the short sequence of events in San Francisco's recent legislation effort on bisphenol A and phthalates.

• On June 6, 2006, the San Francisco supervisors passed a ban on phthalates and bisphenol A .
• On October 25, 2006, bisphenol A manufacturers, the American Chemistry Council, California Retailers Association, California Grocers Association and Juvenile Products Manufacturers Association and a local store called CitiKids sued the city.
• On November 16, 2006 manufacturers of phthalates, the California Chamber of Commerce, the Toy Industry Association and Ambassador Toys, a local store, filed another lawsuit against the city (notice, always a local merchant as a plaintiff?).
• November 19, 2006, the San Francisco Chronicle published an article showing that the chemicals showed up in plastic toys, despite the fact that they were labeled free from chemicals. The story alarmed parents. It also gave support for the supervisors' subsequent changes to their ban based on the fact that plastic products lacked any labeling and enforcement of the ban would be too difficult.
• November- January, 2006: The Chronicle published a couple of opinion pieces that opposed the ban, including ones from the American Council on Science and Health (ACSH - an industries lobby group), and the American Plastics Council. The Chronicle also ran its own editorial, writing that however "well-intended", the ban lacked the "appropriate planning and consultation with public health authorities, retailers and toy manufacturers."
• On December 1, 2006, the ban was slated to go into effect, but it was postponed by city officials, who told businesses the city would wait until after the holidays to begin enforcement.
• On January 23, 2007, Supervisor Angela Aliota-Pier proposed changes to the ban which were approved by the Board of Supervisors in April, 2007. All bisphenol A legislation was removed. Instead of banning certain phthalates, under the changed legislation labs would be hired to test specific products over the next couple of years (as resources permitted, the legislation noted). The products were only those that were specifically meant to be put in the mouths of children under three. If these products had certain levels of phthalates sale of those specific toys could be punishable. The fine for the first offense would be $100.
• In response to the amended legislation Bisphenol A manufacturers and parties of that lawsuit dropped their case against the city.

The ordinance that was eventually passed seemed to take in mind "retailers and toy manufacturers", as the of the San Francisco Chronicle had suggested. The city understandably pushed some of the work up to the state and federal levels. The supervisors say they intend to remain abreast of developments in bisphenol A research. But if San Francisco's citizens were looking for guidance from the city on which plastic toys they should allow their children to teethe on, at what age, or whether using bisphenol A containing Nalgene bottles for water might cause breast cancer, they are still left to their own devices.

The state has also passed a phthalates bill (not bisphenol A) sponsored by Fiona Ma. Governer Schwarzenegger commented upon signing, "I do not believe that addressing this type of concern in the legislature on a chemical by chemical, product by product basis is the best or most effective way to make chemical policy in California". It remains to be seen how California will enforce the legislation.

The San Francisco supervisors invoked the "precautionary principle" when they proposed their first ban in June of 2006. There is a huge body of literature and argumentation about the precautionary principle which we're going to skip over here, but basically it says "When an activity raises threats of harm to human health or the environment, precautionary measures should be taken even if some cause-and-effect relationships are not fully established scientifically".

Specific to the examples of phthalates and bisphenol A, what really does it really mean to say that "cause-and-effect relationships are not fully established scientifically"? What about the standards we use for drug development? Wouldn't all these results in BPA and pthalates "establish" the science if this were a drug? If this were drug development with a potential market similar to the size of the population effected by BPA and phthalates use, the pharmaceutical company would be pouring money into further testing. Despite this reasonable sounding premise, the precautionary principle consistently fails to gain traction with city, state and federal politicians, who are realistic to all interests.

If the city is "precautionary", it's NOT on the side of health or the environment, but (if inadvertently), on the side of industry. While San Francisco has made a admirable public statement about these chemicals its hard to see how this is going to diminish the threats to kids. Since plastic toys aren't labeled, is the city going to go into the plastics product testing business? What city can afford to regulate products? I'm not criticizing politicians -- this is the system we have -- but let's be realistic about implementing the "precautionary principle". Does it even make sense for politicians to invoke the phrase? Perhaps at the federal level or state levels we could be precautionary. But on the local level, so far it looks more like the "pragmatic principle": all interests considered.

Perhaps the precautionary principle is only personal ideal for individuals to follow. Fortunately, to be optimistic, individual families can decide to make product choices (basically by finding plastic alternatives like glass and wood) despite inevitably slow legislative efforts and still conflicting -- though on the whole increasingly good -- coverage in the media.

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¹ A second study released by the National Toxicology Program concluded that bisphenol A raised "some concern" about "neurological and behavioral effects in developing fetuses, infants and young children." This study was controversial, as it was conducted after the original contractor, Sciences International, was fired by NIH under a cloud of conflict of interest concerns. Acronym Required documented the conflict of interest issues.

Acronym Required also wrote about bisphenol A in the following articles:

Plastic Bottles- Protecting Your Baby, by the ACC (July, 2005)

Bisphenol-A and Phthalates Bill in California (January, 2006)

San Francisco Bans Bisphenol A, Phthalates (July, 2006)

San Francisco phthalates & Bisphenol A Ban (November, 2006)

Summary: As children we accept stories of history, science, and politics that are doled out to us as simple little lessons. Rikki-Tikki-Tavi is a children's story about a mongoose, which the National Endowment for the Arts uses to teach about anthropomorphism and the differences between "truth" and "fiction". Yet, despite our childhood training, many grown adults are smitten with syrupy accounts of reality -- simplifications, whitewashes or even outright lies. What about accounts of science? What happens in real life when another mongoose species, the meerkat, meets a puff adder? Does National Geographic's account ring true? Or does research that uses the result to bolster theories about learning in meerkats seem more plausible?

Rikki-Tikki-Tavi: Truth or Fiction?

Rikki-Tikki-Tavi is Rudyard Kipling's mongoose in The Jungle Book famous for saving a human family in India from predatory snakes. First the young mongoose takes on a venomous krait ("Karait") when the snake threatens the young boy Teddy: "Rikki-tikki's eyes grew red again, and danced up to Karait with the peculiar rocking, swaying motion that he had inherited from his family". Next the mongoose engages in an epic fight with a family of cobras. Rikki-Tikki-Tavi takes on "Nagaina", of "Nag" and "Nagaina", when the snakes attempt to kill off the humans in order to inhabit their home and raise their own expanding brood:

"Rikki-tikki was bounding all round Nagaina, keeping just out of reach of her stroke, his little eyes like hot coals. Nagaina gathered herself together and flung out at him. Rikki-tikki jumped up and backward. Again and again and again she struck, and each time her head came with a whack on the matting of the veranda and she gathered herself together like a watch spring. Then Rikki-tikki danced in a circle to get behind her..."

Rikki-Tikki-Tavi may be agile, however the animal is naive at first, taking cavalier risks like following after Nagaina when she plunges down into a rat hole during battle. Rikki-Tikki-Tavi reckons with his youthful inexperience:

"...just under him whizzed by the head of Nagaina, Nag's wicked wife. She had crept up behind him as he was talking, to make an end of him. He heard her savage hiss as the stroke missed. He came down almost across her back, and if he had been an old mongoose he would have known that then was the time to break her back with one bite."

Rikki-tikki-tavi is fiction of course. Mongooses and snakes don't converse or plot to kill each other. But although it may be fiction, the story holds many lessons, some of which the National Endowment of The Arts (NEA) -- funded by the U.S. government -- sees fit to teach. The NEA created a learning website for teachers that uses the tale of Rikki-Tikki-Tavi for lesson plan called "'Rudyard Kipling's "Rikki-Tikki-Tavi": Mixing Fact and Fiction'". The site cues teachers about appropriate background information to impart to the students. "You may also wish to tell your students that, like the United States of America, India is no longer a British colony....". Of course one could also say, "like Britain once, the United States of America sometimes attempts at empire-building", but no, that account of history wouldn't win favor.

The NEA links to maps, and suggests lesson questions and answers. Lesson number 3, "Fact, Fiction, and Personification", notes that it's a "fact", that Rikki-Tikki-Tavi, like many mongooses:

"....[l]ives in India, has a pink nose and eyes, has a fluffy tail, hunts snakes, lives in a burrow, eats meat, has a rocking gait when about to attack, makes a ticking sound when aggressive."

But NEA notes that it's "fiction", that Rikki-Tikki-Tavi or mongooses, "have conversations like humans do". And when Kipling has the female cobra Nagaina say to resident bird and Rikki-Tikki-Tavi ally, Darze:

'"You warned Rikki-tikki when I would have killed him. Indeed and truly, you've chosen a bad place to be lame in." And she moved toward Darzee's wife, slipping along over the dust."'

The NEA website says that students should be taught:

"Animals do not try to have their revenge on other animals; vengeance is a human invention. A snake would hunt a bird for food, but it would not seek to kill the bird for revenge. To assess students' understanding, you may wish to have your students find one or more other passages in which an animal thinks or acts like a human being."

If only it were so simple. Indeed, snakes don't seek revenge, "a human invention", nor do mongooses express scorn or pride, as Kipling's hero does. But scientists are finding that some animal behaviors, like learning and teaching young, do look like human behaviors.

Oh Meerkcat, You're No Rikki-Tikki Tavi

Mongooses comprise the taxonomic family Herpestidae, of which there are about 35 species. Various mongoose species can differ in appearance and behavior. Meerkats, Suricata suricattais, are a smaller mongoose, with a thin tail that they use for balance. Rikki-Tikki-Tavi, by comparison, "...could fluff up his tail till it looked like a bottle brush, and his war cry as he scuttled through the long grass was: "Rikk-tikk-tikki-tikki-tchk".

Rikki-Tikki-Tavi washed up on his hosts' doorstep after a storm and took it upon himself to protect his host's home single-handedly. Meerkats, by comparison are always described as "gregarious", spending much of their time in social groups where they together face down foes and handle prey, and perhaps assess dangers. Meerkat groups of several families band together to form "mobs". The word conjures images of roving gangs of thugs with dubious purposes, sneers and leather jackets, but meerkat mobs on the lookout for predators stand-up in sentinel position looking more like a gaggle of girls or chattering tweens. They're so fetching that they undoubtedly need to gang up together to get any traction whatsoever on the rough and tumble Kalahari.

The meerkat social structure and the ease with which they can be habituated to humans makes them attractive research subjects, and more science could help us all understand just what meerkats do and don't and can and can't do. However in the course of studying meerkats, scientists have captured hours and hours and hours of meerkat interactions on film. What to do with that? Enterprising producers make television shows, one of which is the well-known Meerkat Manor on Animal Kingdom.

Apparently the show offers audiences what might well be the zenith of anthropomorphism, or "personification" as NEA would have it, as it follows the life and times of a mob of meerkats that centers around a family called "The Whiskers". Now in its third season, the show keeps viewers as engaged as any soap-opera. This is probably a win-win situation, since researchers at the Cambridge University Kalahari Meerkat Project might well benefit from having their hundreds of hours of observation tapes turned into a hit television series -- and audiences are smitten. But does the creation of soap operas starring characters like family encourage further anthropomorphism of the carnivores?

Many people fell for a recent hoax reported by the Telegraph, when wardens at the Longleat Safari Park released photos that were described as meerkats taking family snapshots. People thought it was so cute, and apparently believed that a meerkat would be motivated to take portraits of its mob. The scam was only exposed once an Amateur Photographer's magazine threw doubts on the tale, forcing folks to face the fact that it's "fiction" that meerkats take snapshots of their families with Canon cameras.

Meerkat Mobbing, A Purpose Driven Life

Animal learning has always fascinated scientists, and on a smaller scale anyone can play at it. For instance, when dogs hear the mailbox clatter open on the front porch, do they bark so ferociously because they forgot the lesson from the day before -- that the mailman is not a threat? Or does the dog think its barking makes the mailman going away, which therefore reinforces the ritualized barking frenzy in its little dog brain? Or is it something entirely different? Does one's human brain limit ones ability to interpret a dog's behavior? I don't know. But how do animals learn? Cooperate? Evolve to learn? These are all interesting questions.

Last year Science (summary) published research by Alex Thornton and Katherine McAuliffe, who observed that meerkats were learning survival skills from their older kin. Adult meerkats would respond to unique age dependent calls of meerkats by preparing scorpions for the young meerkats according to the youngster's developmental ability to deal with the scorpion and its poisonous parts. The older meerkat would then present the age-appropriate, dead/non-poisonous, half-dead or live-ish scorpions to the young meerkats. The research is briefly described in this blurb from NPR.

Meerkats don't engage in the single-handed acrobatic mortal duels that made Rikki-Tikki-Tavi famous, and they seek out prey smaller than cobras -- insects or lizards or venomous scorpions perhaps. But that doesn't mean that the meerkats don't have run-ins with large snakes. The Meerkat Manor clan has quite a few encounters with snakes, and they don't always end well. The show left viewers hanging at the end of one season after a meerkat called Shakespeare (a viewer favorite) had a run in with a puff adder. It was a life and death situation for Shakespeare, who remained unaccounted for when the show resumed the next season.

Similarly, researchers record encounters that meerkats have with snakes all the time. A study in Animal Behavior last month, called "The function of mobbing in cooperative meerkats", sought to learn whether mobbing behavior is used simply to deter predators or for other purposes. Animal Behavior doi:10.1016/j.anbehav.2006.11.021, online August 17th. Also available via this direct link at ZORA (Zurich Open Repository and Archive) The authors first established previous thinking on meerkat mobbing:

The three main functional hypotheses for mobbing, namely predator deterrence, predator risk assessment and transfer of information, as well as the self-advertisement hypothesis, all predict that mobbing intensity will be correlated with threat level and the recruitment of others.

Then the authors frame their research question. Here's an excerpt:

"If meerkats mainly mob to deter predators, they should show a strong response to predators but not to nondangerous animals, and continue this behaviour until the predator leaves the vicinity. Additionally, meerkats should only mob in situations where a predator is likely to leave, and avoid mobbing in situations where this is unlikely, such as on encountering predators hiding in boltholes or hollow trees...."

The authors looked at 564 natural mobbing encounters that recorded over six years. In these instances, did the meerkat lose interest in the subject? Or did the snake or hawk or other animal retreat? These two options were observed in only about 72 of the 564 cases. In all other cases, however, the outcome of the encounter is unknown. The researchers also rounded up various snakes, a pet cat, a pet squirrel, a dead squirrel and other miscellaneous animal subjects and presented them to the meerkats in a cage that the meerkats had been habituated to. The authors concluded that mobbing behavior in meerkats differs according to variables like the age and sex of the animal as well as the threat of the animal being mobbed. They wrote:

"The observations from natural encounters and the experiments showing that meerkats not only mobbed potential predators, but also frequently herbivores, suggest that this behavior is not only to deter predators. They also spent regularly a considerable amount of time mobbing predators that were unlikely to leave the area, such as predators sheltered in burrows (Kalahari Meerkat Project, unpublished data) and puff adders, which were never observed to move in response to meerkat mobbing. This supports that the purpose of mobbing in meerkats, besides deterring predators, is likely to be assessing the risk of the encountered animal and recruiting other group members to the stimuli, which may also serve to transfer information to the others."[emphasis mine]

The authors concluded that the adaptive behavior of the meerkats is used to "chase away predators", and to "gather information about the threat and/or motivation of a predator", which allows the meerkats to "coordinate group movement and group vigilance accordingly". In addition, they concluded "young meerkats learn to recognize predators and to respond to the varying degrees of threat". The final conclusion is arguably the most exciting because it supports the idea that (like humans), meerkats teach their young.

Puff Adders Retreat For National Geographic But Not for Researchers?

The author's puff adder data consisted of 106 observations, and in 94% of those the mongooses mobbed the puff adders. In 12 encounters the meerkats lost interest, and in 0 encounters the puff adder retreated. But in all of the other puff adder mobbing instances, which is as far as I can tell around 88/100 instances of mobbing, the outcomes were unknown. What happened?

The researchers use their evidence that the puff adders never respond to meerkat mobbing to help build their theory that mobbing behavior must be for a purpose other than meerkat saber rattling....so to speak. But here in this video, National Geographic films a puff adder retreating as a mob of meerkats kick dirt at it. How does National Geographic manage to capture such privileged puff adder and meerkat shows when the researchers had been at it for years? How many takes did it take National Geographic? Perhaps meerkats were having some off days for the researchers? What's real? Did National Geographic stage the story? Puff piece? (Did they even use a real sportscaster to narrate the snake-meerkat stand-off?) Maybe the puff adder slinks away every 13th encounter with a meerkat? Would this new evidence be a chink in the meerkat learning story?

We scoured the National Endowment of the Arts site for lessons that might help us understand this, but to no avail. Unfortunately we may never know why the puff adders caught on National Geographic cameras readily slink off when dust is kicked on them by the vigilant meerkats, whereas for the researchers puff adders "never" retreat.

There are other things we don't understand about the meerkat study in Animal Behavior. The meerkats continue to mob herbivores despite the fact that the animals are no threat. The authors say indicates information transfer -- a teaching moment. But couldn't it just be a senior moment? Perhaps meerkats just perpetually forget about which threats are which? Or, on the other hand, if young meerkats mobbed innocuous squirrels more than older ones do, which the author says means they're naive, maybe young squirrels are just confident about their squirrel mobbing abilities-- like the fierce dog marauds the mailman safely behind the front door. Could meerkats be teaching themselves with and without the adults? Clearly I haven't been out there on the Kalihari with my notebook so you'll have to read the study yourself -- it has far more information of course, we've only skimmed the surface.

In concluding that mobbing serves as a classroom for young meerkats the authors build on previous animal behavior research, as well as their own. Perhaps it seems intuitive (wait--that's not science) that young meerkats would learn from their elders and indeed previous studies have shown that. But how does the puff adder data support their hypothesis? Given that meerkats do learn in these tight social interactions as has been shown, when did mongoose species evolve as independent self learners? How is that meerkats seem to need so much special tutoring? Do mongooses like Rikki-Tikki-Tavi engage in fewer interactions, that are just as relevant to learning in their unique species or are they truly independent learners? We await future research.

In "March On Penguins", March, 2005, we wrote about anthropomorphism in penguin movies.

Today, Craig Venter published his genome sequence in the journal PLoS Biology, along with a self-portrait so large, in the journal's 'Synopsis' version, that this startled reader recoiled with fright.

Sheesh. Science should be soothing...first you have your abstract, your introduction, the methods, results, discussion...No unassuming reader seeking to understand science's newest frontiers, for the greater good, should ever be confronted with SO MANY individual facial hairs, in such...lewd...detail. Shotgun sequencing indeed, he's a bit in the reader's face, as they say.

The published sequence is diploid, both his mother's and father's contributions. Much of the sequence may seem familiar, due to the fact that Venter contributed his DNA to the first composite sequencing human genome effort made by Celera (his company, which is also behind the current effort), the results of which were published in 2001. His genetic contribution to that effort was 60%. According to today's Financial Times unique scoop, Venter is predisposed to "novelty-seeking behaviour and a preference for evening rather than morning activity". News you can use.

However both the journal and the author stress that individual human traits are each influenced by many genes. The PLoS paper concludes that human-to-human sequence variation is five- to seven-fold greater than earlier estimates, which Venter says, proves that we are in fact more unique at the individual genetic level than we thought.

Yawn. Good enough. Nevertheless, maybe next time, a composite photo? Perhaps? To display your essential humanity?

UC and Tobacco

Wednesday was perhaps a typical University of California (UC) day. En route to their commencement celebrations, UC Berkeley students passed custodians who were picketing for raises. In support of the protesters, their scheduled speaker, Danny Glover, canceled his talk. A few dozen UC students on several campuses started a solid food hunger strike to protest nuclear research, in what U.S. News and World Report suggested might be "a boon for the pudding industry". Meanwhile, the UC Academic Senate, for its part, defeated RE-89, a measure aimed at barring tobacco industry funding of academic research.

The senate voted 43-4 against RE-89, with 3 abstentions. RE-89 represents the most recent push by some UC faculty to ban tobacco industry sponsorship. It follows last year's D.C. District Court decision, which confirmed in 1,742-pages that, among other transgressions, five tobacco companies lied about the hazards of tobacco and smoking for 50 years, enticed children to smoke, and used university researchers to help undermine anti-tobacco litigation efforts.

In trying to ban tobacco funding across the UC system, faculty were responding to a recent UC policy limiting individual schools from setting policies to ban tobacco money. That measure, enacted in 2005, overturned the tobacco funding policies set by the nursing, medical, public and family health schools, on the Berkeley, UCSF, UCLA, and San Diego campuses. By setting policy, University leadership forbid those schools, with their public health missions and first hand experience with the devastating tobacco related morbidity and mortality, from declining tobacco money. Other universities, such as Ohio State University, Harvard, and John Hopkins, have no such limits on individual schools whose academic missions clash with the goals of tobacco companies.

Why Tobacco?

Stanford University is also considering a campus-wide ban on tobacco funding, and professors there argue divisively along the same lines as the UC faculty. Some contend that professors should be free to pursue whatever research they choose, including tobacco. Others say that if any business ever earned the label "evil", it's the tobacco industry, and that continuing to welcome tobacco's dollars on campuses undermines university goals.

Faculty who disapprove of tobacco funding are often associated with public health or medical schools, in some cases they've devoted their scholarship to studying the tobacco industry. The UCSF contingent of the Academic Senate voted for the UC ban, and the UCSF campus is dedicated solely to medicine and graduate science research. Stanford tobacco industry historian Robert Proctor noted, "We really don't want to be collaborating with an industry that is producing the world's largest preventable cause of death."

University presidents, on the other hand, generally argue for what they call academic freedom. They maintain that academic integrity and conflict of interest guidelines for research cover any touchy issues that might arise in sponsored research. Evidence doesn't always support this claim. A 2003 study by a UCLA professor was one of four examples of academic research tainted by tobacco funding cited by Judge Kessler in her court decision. (In response to various ethical breaches, all UC staff and faculty are required to take a 30 on-line minute ethics class this year.)

Stanford President John Hennessy said "This is a political message, and I am very concerned that we are changing our academic policy to send a political message." His statement no doubt meant that the university doesn't need to send a political message to tobacco companies, condemning their toxic products. But since the primary charge of University presidents is to raise money for campus, they wouldn't necessarily be too eager to muddy the waters of fund raising goals by implying that their university might be choosy about where it gets its money. That would be the wrong political message to send to tobacco companies.

University administrations across the United States are sensitive to the issue of tobacco funding. Although universities often post conflict of interest policies and publicly list their funding sources, when we called universities with questions about their tobacco research funding policies, we received a wide variety of interesting responses from administrators. Some talked very openly about their decision making processes, but others were especially guarded. Coincidentally these were generally the universities who posted affiliations with the tobacco industry.

It's a tricky balancing act for universities. Although many have divested their tobacco interests, these universities often continue to accept tobacco money for research. Since university communities are increasingly hostile to the tobacco industry and its smoke, these universities seem reluctant to discuss their nuanced policies. Tobacco industry money doesn't generally amount to a large percentage of research money but universities are quietly vigilant about protecting their rights to it.

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Acronym Required wrote more about the UC tobacco policy decision process a few months ago in "My Lab Thanks You For Smoking".

A number of books have been written on the relationships between corporations and universities.

The Wall Street Journal posed a challenge to scientists in yesterday's paper: "Is an Economist Qualified To Solve Puzzle of Autism?" Author Mark Whitehouse looked at the controversy stirred up by Cornell economist Michael Waldman's study¹ last October that linked TV viewing to autism. In "Does Television Cause Autism?" Waldman used precipitation records and cable subscriptions as proxies for TV viewing, then performed statistical analysis to correlate television watching with incidence of autism.

Waldman was motivated to study autism by his family's experience with his young son, who was affected by Autism Spectrum Disorder. In response to his son's diagnosis, and in addition to doctor recommended therapies, he curtailed his son's television watching. To his surprise the child recovered completely. However he was unable to engage doctors to study whether TV caused autism, so he studied the connection himself. He found a causal effect in his study and recommended that parents not allow young children to watch TV. As the WSJ article recounts, many researchers don't agree with his conclusion. Scientists, autism researchers especially, were most critical, but economists also questioned his methods. Although his methods weren't unheard of, some economists said the "instrumental-variables technique" was imperfect and others said it tempted economists to study topics they're "not particularly well-trained" to study. Acronym Required wrote a satirical post on the study last October².

Despite the impression given by the Wall Street Journal, Waldman's self-reliant approach to setting a science research agenda is not unprecedented. Other people whose kids are afflicted by autism have also poured personal resources into autism research. A 2005 Wall Street Journal article, "A Hedge-fund Titan Stirs up Research into Autism", mathematician James Simons, who, motivated by his daughter's autism, founded an organization that plans to spend over 100 million dollars on autism research. The 2005 WSJ article noted the controversy over Simons' funding:

"When the Massachusetts Institute of Technology asked him for money for brain research, he demanded that the project focus on autism and include scientists he liked. He has provided his family's DNA for study, pitched in to help solve research problems and is pushing scientists to probe a genetically based explanation for the disease."

"Many are cheering this influx of cash, hoping Mr. Simons' riches can buy a breakthrough. Others complain that Mr. Simons isn't working with existing autism groups and that his focus on finding a genetic explanation could miss the disease's true cause."

Yesterday, two years later, the WSJ article cautions:

"by suggesting that something within parents' control could be triggering autism, Prof. Waldman has reopened old wounds in the realm of autism research, which is littered with debunked theories linking the disorder to the family environment."

The WSJ quoted senior vice president of Autism Speaks and mother of an autistic child, who said: "Autism is a genetic disorder. The only thing the parents do wrong is they have bad genes." Autism Speaks was founded by two years ago by Bob Wright, Vice Chairman and Executive Officer and GE Chairman of NBC Universal, whose grandson is autistic. However, if Waldman's research was solid, why shouldn't economists study autism? Wouldn't parents appreciate a solution in hand, as opposed to one that entails decades of research and development?

The connection between autism and TV would best be studied in controlled experiments between groups of children, but according to the WSJ, economists don't have the "money or the access to children" to perform this kind of research. The WSJ quoted "Ami Klin, director of the autism program at the Yale Child Study Center, [who] says Prof. Waldman needlessly wounded families by advertising an unpublished paper that lacks support from clinical studies of actual children." In other words, Klin said, Waldman's conclusions conflicted with results of clinical trials that were already done.

The genetic links to autism are currently being studied intensely and the effort is fruitful. Scientists have discovered genes that could account for one or more aspects of Autism Spectral Disorder. The Yale Child Study Center is partially funded by the Simon's Foundation.

The WSJ also quoted Klin sayng: "The moment you start to use economics to study the cause of autism, I think you've crossed a boundary." Yet is the question really about whether economists can study science problems? Economists contribute significantly to fields including psychology, ecology, and international development.

Scientists distort the issue by focusing on parental blame, or whether an economist can contribute to research. Shouldn't we just look at whether a specific paper more approximates rigorous research or Swiss cheese? Waldman's paper was criticized because it drew speculative conclusions and was advertised in a what amounted to a sensationalist press release as opposed to being published in a peer reviewed academic journal. While the researchers and authors may have been swayed by conviction, their resulting study didn't meet the standards of the autism community, psychologists or neurobiologists. As WSJ reported, Joseph Piven, director of Neurodevelopmental Disorders Research Center at the University of North Carolina, said of the confounding variables, "It is just too much of a stretch to tie this to television-watching...[W]hy not tie it to carrying umbrellas?"

Did the paper meet economist's standards, a skeptical reader's standards, or for that matter the own researcher's standards? Scientists ideally start from a neutral position then work to disprove their theories, in order to prove them to themselves, their peers, and the world. Social scientists approach problem solving similarly. If the paper was representative of the field of economics, we might look at economics and its influence with renewed skepticism.

Why not just conclude that this particular exploration, however well intended, wasn't that rigorous, and/or didn't seem to support the author's conclusions and final recommendations. Waldman perhaps used his reputation in another field to build media interest around this hypothesis. He's not the first researcher to flip the scientific process on its ear. Other scientists have announced "results" prior to publication, with various motives. Perhaps his move was strategic, but it remains to be seen whether this economist can circumvent the research process to successfully demand that the science community study his hypothesis.

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¹ The original paper "Does Television Cause Autism?", is posted online at NBER working papers and from the Cornell website. Read it for yourself. What do you think?

²Last October, Acronym Required wrote "Autism, TV, Precipitation: Dismal Science", a satirical 10 step research how-to for repeating the results of Waldman's original paper.

Last year, as avian bird flu H5N1 skipped around the world decimating bird populations and fatally infecting clusters of humans, governments near and far felt increasingly threatened by the possibility of a influenza pandemic. Tension and mistrust increased among countries at a time when full cooperation among them was essential to public health.

Countries promised $1.9 billion to a United Nations avian flu program but had yet to fulfill their pledges. The World Health Organization (WHO) established a repository for virus information from member countries at the Influenza Sequence Database (ISD) at Los Alamos National Laboratory in New Mexico in 2004, but the agency had a spotty history trying to deal effectively with infectious disease and was accused of beholden to the "gang of fifteen" labs given access to the data. The World Organization for Animal Health (OIE) and the United Nations' Food and Agriculture Organization (FAO) also committed to sharing data, but like the WHO, answered to their member states and could do little to compel countries to share resources. Private labs, the CDC, and individual countries like Russia, and China, had all been withholding data and biological samples, sometimes because of poor international relations, concern about intellectual property rights, or concern about credit for their contributions.

In response to the fragmentation in the research community, scientists, politicians and public health officials fulminated, concerned that hording virus and sequence samples would hobble effective responses to outbreaks. In February of 2006, Italian influenza scientist Ilaria Capua called on fel