October 2009 Archives

Death Ascendency:

Scientists, pollsters and journalists like to complain that Americans can't be bothered to read or understand science. That distresses these pundits. I don't believe their contentions are altogether accurate or their hand-wringing justified, but true enough, Americans seem distracted or even obsessed with subjects other than science. Like what?

Death, for one. Remember, the hoopla over death panels, and fears about the death of a grandpa because of illegal immigrants? Maybe you've forgotten the multi-month media requiem for Michael Jackson, but can remember via Time Magazine's 100 page Special Commemorative Michael Jackson Issue, still on the news stands through October. And if you missed that, you can now watch the movie. If Jackson was reclusive in life, his death just won't die.

And it's not just Michael Jackson. This summer and fall, the string of newsworthy celebrity deaths led MSNBC, the New York Times and others to recount the "the endless funereal season". Trying to slip in a post on death over the last few months, if you didn't want to seem like you were milking the trend in an unseemly way, (because we're the unblog blog) was near impossible.

The preoccupation with death spanned news on politics, employment and entertainment. What did AP feature in a story on career advice? "Funeral science: One business that's still alive: Amid layoffs and a weak job market, interest in mortuary science surges." And after death it's not over, as the New York Times pointed out in: "After a Death, the Pain That Doesn't Go Away".

You can't escape death -- the theme I mean. It's what people are living, breathing and reading. Non-fiction? At least four new books focus on death. "Annililation: The Sense and Significance of Death", "The Philosophy of Death", "Our Stories: Essays on Life, Death and Free Will", and "Death". You get the gist, but for more, FT reviewed the books here. Not satisfied with new books? Someone along my route today poured over "Stiff: The Curious Life of Cadavers".

And in fiction? Mass-market fiction? Deaths by aliens, apparitions, and evil-doers, not to mention more than one bubble-gum romance featuring irresistible marble-chested vampires. In sunny, otherwise cheerful September, 12 of the 20 best selling titles from the NYT mass-market fiction list were: "Dead Until Dark", "Frankenstein: Dead or Alive", "From Dead To Worse", "Club Dead", "The Bodies Left Behind", "Dead To The World", "Living Dead In Dallas", "Dead As A Doornail", "Promises in Death" "Chosen To Die", "Definitely Dead", and "Altogether Dead".

The remaining 8 of the 20 best sellers didn't bother to include "Death" in the title, but don't despair, it's there. You could chose between "The Assassin" (subject obvious), a book on "scandalous deaths", or one each on death from lung cancer, a killer, a dead lover, a dead friend, the death of a child from acute promyelocytic leukemia, a string of dead medical tourists, and last but not least - a book that brings Elvis back from the dead to help investigate some mysterious deaths. Now at Halloween and moving into the darker, more appropriately morbid time of year, the media is naturally out of step so the mass market fiction list looks slightly more upbeat -- though Death still holds its own.

Until the Smell of Death Do Us Cart You Away

So what's a science writer do in The Demon Haunted World of deathly news and entertainment preoccupation? Science journalists struggling to work within this dreary paradigm last summer published versions of "The Smell of Death", a story about experiments on bugs by scientists at McMaster University.

Previous research had showed that noxious chemicals expelled by some animals upon death repel their live companions. It's true. Necrophoresis is the term for the behavior of ants and bees when they move their dead away from their nests. Scientists such as Henry Christopher McCook in 1879, E.O. Wilson, in 1958 first documented necrophoresis. Wilson showed that worker ants moved the dead bodies out of the living spaces, and the ants and were motivated by something other than the untidy look of their comrades carcasses strewn about the nest.

To investigate, Wilson's team sprayed what I'll call "eau de ground up dead ants" on live ants, and observed the ants move their perfumed but live fellow ants away from the nest as if they were dead. Following from that observation, researchers learned that the ants expelled a specific scent when they died that other ants of the same species could detect. Wilson determined that chemicals called oleic acids motivated movement of the dead bodies by their fellow worker ants. Scientists than discovered that while bees and ants remove their dead, termites merely avoid their dead -- they're necrophobic.

Building on a century of research on "necromones" then, the McMaster University scientists dispersed necromones among insects such as caterpillars, which aren't known to expel their own dispersants but do aggregate like social bees and ants as well as the semi-social termites. Their experiments showed that the fatty oleic acid compounds also repelled woodlice and pillbugs. Since necromones seem to effect multiple species, the scientists now suggest that the death chemical is common across many species.

Programmed Cell Death -- Upbeat, Hopeful, Vital

What else could scientists write about? Programmed Cell Death (PCD) springs to mind. Not only does it have "death" in the title, like all the best selling mass market titles, but it's actually vital to life and therefore a rather hopeful, non-dreary subject. PCD occurs in plants and animals, yeasts and bacteria. The human body creates more than a thousand billion of cells and just as many die through PCD, a carefully orchestrated event which allows some cells to be destroyed through a process that assures that healthy cells proliferate. PCD is different than necrosis, when cells die due to blood loss or insult. There's a bounty of research on PCD and it has it's own journals -- enough reading and writing that could see us well through the winter months and into spring.

Although the proliferation of cell death research and understanding is relatively recent, in the 19th century scientists noticed changes in the cells during insect metamorphosis and tadpole development which suggested cell death. Although early research focused on phagocytosis, in the mid-20th century evolving technology provided scientists with more sophisticated microscopes and histologic techniques which gave them a clearer view of cell processes. In their 2001 history of PCD in Nature Review Molecular Cell Biology¹, Richard A. Lockshin and Zahra Zakeri, describe how the 1960's at Harvard, afternoon teas attended by Carroll Williams' lab members served as humorous and informative exchanges for "ideas of the day", and in time coined the term "programmed cell death".

In 2002 the The Nobel Prize in Physiology or Medicine was awarded to Sydney Brenner, H. Robert Horvitz and John E. Sulston for their discoveries concerning "genetic regulation of organ development and programmed cell death." The researchers used the model organism nematode Caenorhabditis elegans (C. elegans) to study cell death and established for the first time that certain genes control cell death. That there were genes controlling death showed that cell death is an integral part of development, not an accident.

Apoptosis (from the Greek word "falling off") is the most commonly studied form of cell death, although there are others. The most common example of cell death is the development of hands and feet, which start off as spade-like clumps of cells, then through apoptosis of the cells in-between, the fingers and toes emerge. In the developing brain millions of nerve cells get "pruned" through apoptosis to assure that proper connections are made. For instance in the development of the retina in the eye, 90% of certain types of cells die. Rather than being limited by cell biology techniques to observing cell death, scientists can now also use molecular biology techniques to understand specific proteins and genetic processes involved in regulating cell death.

When cell death goes awry, the repercussions are serious. In cancer, the cell death pathways malfunction and too many cells are allowed to proliferate. In Parkinson and Alzheimer diseases, cell death pathways allow the destruction of too many cells. Now scientists are zeroing in on specific proteins or pathways that could be altered to prevent aberrations in cell death that result in disease. From not knowing that cell death was an important part to living organisms, scientists are realizing how much it dominates life - sort of like the paperback mass-market fiction list.

¹"Programmed cell death and apoptosis: origins of the theory" 545-550 (July 2001) | doi:10.1038/35080097

Superfreakonomics authors Levitt and Dubner make it out like solving global warming is no more complicated than cooling off on the patio on a hot summer day. First, someone else puts up the umbrella, then they unwind the hose and spray all the kids so they stay cool. This may sound good to you, but it's not logical, despite what the Superfreaks insist. They're appealing to your laziness, your ennui, your fear, and your cynicism, all in the name of books and businesses that you don't hold stock in. Do you buy it?

Daily Show Economics

When Steven Levitt appeared on the Daily Show to talk about Superfreakonomics and the giant umbrellas that could be used to ward off climate change, Jon Stewart apologized for the collective response by scientists to Levitt and Dubner's unscientific treatment of climate change. : "I'm sorry you're taking so much shit for it".

For Levitt, climate change is an easy problem. He told the Guardian "We could end this debate and be done with it, and move on to problems that are harder to solve", (hat tip Curious Capitalist). But isn't climate change a more tenacious problem? What was Stewart up to, dismissing it?

When Your Advertisers Are Auto Companies?

But if you think about it, trashing "environmentalists" isn't new territory for Levitt or for Jon Stewart. The Freakonomics blog has argued repeatedly that recycling makes little sense. The Daily Show host has previously criticized actions to lower carbon emissions, for instance in his show "Auto-Neurotic Gas Fixation", May 20, 2009. At the time, Obama had announced his intention to set new, ambitious CAFE standards for gas mileage. Stewart chastised him for it: "Dude...Obama...don't blow your load on mileage baby, save it for when the Chinese invade."

On that show, Stewart claimed that gas efficient cars, being smaller, put people "in harm's way because they're in a lighter vehicle", that "safety" was a "valid", "reasonable concern" - mirroring lines from the Competitive Enterprise Institute (CEI). A nod to all the automobile companies that advertise with Comedy Central perhaps? Or ignorance? We thought that this ancient CEI argument died back in 2007, once people thought through their elementary math and physics and realized that yes, if you run your Prius into a Hummer, you may get hurt, but the more Priuses on the road, and the fewer Hummers, the less likely you will be to run into a Hummer, therefore less likely you'll get hurt. Alas, there we were in the spring of 2009 and Jon Stewart was giving us his schoolboy version of the old auto industry fueled CEI argument.

Coincidentally, at the same time -- April/May 2009 -- car sales had recently dropped to their lowest point in thirty years. A flurry of editorials pronounced the danger of small vehicles and so Stewart fit right in with The Wall Street Journal which droned on about about the "lethal effects" of CAFE standards and light vehicles. Lesson? Comedy Central is not always all that "progressive" people, really, don't leave your brain in the cold on 11th Avenue.

Just When You Thought Superfreak was Finally Gone

So Jon Stewart's accommodation to Levitt's argument isn't a surprise, nor is Superfreakonomics' bid to attract attention by rousing populist appeal. As the sequel to Freakonomics SuperFreakonomics seems to run aground the way many movie sequels do -- Rocky V, Clerks II, Caddyshack II... It maintains sufficient audiences to grind through talk-shows, stimulate blog chatter, and generate pay-out, but it disappoints fans.

Here's a collection of about 90 blog links that criticize Chapter 5 of the book. They call the authors on many points, for instance:

• Of distorting the science and misquoting scientists - From an atmospheric scientist (Ken Caldeira) in response to the book's quote - "Carbon dioxide is not the right villain": "I don't believe I said anything remotely like that...we should be outlawing the production of devices that emit carbon dioxide...I do see CO2 as the problem...it's like if you got shot by a bullet and you said, well, it wasn't really the bullet that was the problem, it was just that I happened to have this hole through my body..."

• Of distorting science consensus - From many economists: "it is terribly misleading that the two scientists you quote are BOTH skeptics. What are the odds of that? Probably a billion to one, so my unavoidable conclusion is that you are deliberately trying to cast doubt on the scientific consensus."

• Of presenting facile, improbable solutions to climate change like pumping SO2 into the atmosphere with a giant hose - From scientists: "'..thinking of geoengineering as a substitute for emissions reduction is analogous to saying, 'Now that I've got the seatbelts on, I can just take my hands off the wheel and turn around and talk to people in the back seat.' It's crazy.'"

• Of deceiving the American public - From a congressman: "We have seen a similar effort to hoodwink, defraud, and deceive the American public now to cover up the toxicity to the world environment...I want to note a book...that basically said or asserted we don't have to control CO2..They purported to quote a scientist named Ken Caldeira from Stanford...Which is an absolute deception."

Like the Daily Show, the Superfreakonomics authors have a history of distorting reality. But the two entertainers talk about the irrationality of environmentalists!

Stripping Away Moralism and Giving You Freedom: The Ruse

Note how Stewart barely batted an eye when Levitt offered his other offensive assertion aside from diminishing the seriousness of climate change, that prostitutes should retain pimps in order to earn more money. It's true, shrugged Levitt, as if nothing can to be done because the invisible hand has sealed womens' fates the world over -- as if he didn't just twist up that statistical interpretation to get people tittering and buying books.

"The heroes turn out to be the pimps", he said. Shrug. "Get rid of the moral part" he insisted, and you have pure unadulterated economics, that's what we're about. Jon laughed -- hahaha, heeheehee. Levitt shrugged again.

What Levitt claims, is that he simply "strips away the moralism" - then, all you have is the economics and prostitution, or economics and climate change. Glib. This is not uncommon rhetoric in economics, politics and public policy -- the ultra-rational, just do the math approach. It's used, for instance, to justify radical cost-benefit-analysis, where people argue that you can put a monetary value on everything - the price of one member of an endangered species, the price of the life of an old person, the price of the life of an infant, the price of a chemical to an industry - and otherwise complicated policy decisions fraught with difficult ethical choices can be reduced to simple math. Voilà.

The problem is, when the authors decided to write that prostitutes are better off with pimps then dug up some statistics to support that assertion, they made a moral decision. First Levitt and Dubner had to decide that this particular slant on prostitution was what they wanted to focus on, then they had to cherry pick some "data" to support it. Similarly, as we wrote in an earlier post, deciding that a male mule deer is worth $525.50, whereas a female mule deer is worth $163, while a just plain deer is worth $1, is not a decision without "moralism".

Moral sentiments are part and parcel of human decisions. Numbers and words that appear in print on a piece of paper or screen in front of you came from a formula or process derived by a human, based on that human's views, perceptions, expectations and desired outcomes. It didn't come from some superior amoralistic all-knowing power, intent on providing answers and comfort to confused humans beings -- despite what people say.

Ironically, by asking his audience to "strip away the moralism", Levitt is appealing to ethos or pathos, but certainly not logos. He's saying -- be logical like me, I'm being logical. Shrug. But he's dismissing tons and tons of scientific proof of climate change (as well as some about prostitution) and the need to decrease emissions as pathetic "moral" arguments (ethos), when those scientific studies are actually the logical ones (logos). He's appealing to his audience's laissez-faire tendencies, their desire to do nothing, their habits not to change, their pathos.

The Ploy: Technology will Suffice in Lieu of Action

Then, offering the equivalent of the old, chintzy plastic prize at the bottom of the box of Crackerjacks, he gives the audience something to grasp on to in the impending and threatening flood of unpleasant scientific reality, although again, it's not logical. Levitt insists that there's a simple scientific solution to solve the problem. Of course, there is no technological solution. The authors offer untested pie-in-the-sky idea that many, many scientists find problematic.

But this is what we all want to hear, right? The irrational, busy, lazy or pathetic side of all of all of us wants to be assured that electronic records will solve healthcare failures, that tsunami warning systems will prevent catastrophic losses, that ankle bracelets will prevent recidivism, that massive fences along international borders will prevent terrorism and drug trafficking, and that electronic surveillance will prevent crime. But giant garden hoses suspended up in the sky, are not even in the realm of feasible technical solutions. Yet we're so happy to slough off responsibility that Jon Stewart, and although he's a modern icon of cynicism, he doesn't even bother to ask questions.

Levitt plays to the audience's sentiments perfectly, first by laughing off science and scientists who present scary ideas as flimsy moralistic hogwash, then by presenting his very own special version of "science". I'm the logical one, he says, but I'm not dorky like a scientist.

His flavor of rhetoric is commonly used by those who oppose scientific evidence because it presents the type of science society likes, that which solves our problems, but is seemingly stress-free, simpler to understand than Tivo, and doesn't require you to have liked high school science. Therefore Superfreakonomics presents magic "technology solutions" in terms that the average American (is there such a thing?) will know and like.

According to them, solving global warming is no more complicated than cooling down on a hot summer day on the patio. First someone else puts up the umbrella to shield you. Then a kindly neighbor unwinds the hose and sprays away, and all the kids stay cool. Sound good? But its not logical. It's doesn't strip away moralism. It doesn't give you freedom. You do have to worry about global warming, you may have to change your lightbulbs. Superfreakonomics appeals not to your logical side but to your laziness, your ennui, your fear, your cynicism, all in the name of books and businesses that you don't hold stock in.

The Solution

This isn't to say that we don't need technology, quite the opposite, technology is imperative to global warming attenuation. But it's not the only effort we need, we need to conserve and to decrease emissions also.

Underlying Superfreaks' argument is the contention that people won't change. And true, people tend to squirm and stall when pressed to adjust, as we noted in "Sea Change or Littoral Disaster", Cars: Buying Cognitive Dissonance", Science Communication, Communicating Climate Change, and Climate Change, Fueling the "Debate", "Curvilinear Thinking on Climate Change", and other posts. But Real Climate's good point is that - people will change with the right incentives. People can work collectively for the better, they don't need a solution to be imposed from nigh. They do have a long history of employing morals as well as logic to solve problems, both are good, both are necessary. And given all that, it may simply be immoral for Superfreak authors to distort the truth of climate change and insist on selling implausible solutions.

Notes:

"Smart Choices and Jiffy Pop"
"Calculating Carbon Emissions"
"Polar Bears at Sea"
"Manufacturing Sugar and Cynicism"
"Scientist Falsified Data, Embezzled Research Funds, and Illegally Bought Human Embryos -- But is Very Popular"
"Corporations, The Working Stiffs, The Rebels"
"Transparency: A Solution for Research Bias or A Refuge for Secrets?"

• Smart Choices and Jiffy Pop: If a rudderless man seeking fame can enthrall a whole nation -- the leader of the free world, at that -- with what Frank Rich referred to as an "supersized Jiffy Pop bag", we could bet that the largest food companies in said nation could easily pass off junk food like Froot Loops cereal as "Smart Choices". And so they did (or do).

  When the Food and Drug Administration (FDA) warned that it would scrutinize food labels in the "Smart Choices Program", have a look at the ingredients in "smart choice" sugary treats like Cocoa Crispies cereal, the program's leaders suddenly announced they would "suspend" operations. Let Frank Rich judge us smug, but we should award "Smart Choices" companies, along with balloon boy fiasco participants (viewers and all), with hearty back slaps for shamelessness.

  "Smart Choices" had been under heavy fire since its inception, and no one, not even FOX Business News, thought the program was anything but "a cynical way" for food manufacturers to sell products -- "dumb and dumber", as John Stossel put it. The Center for Science in the Public Interest (CSPI) called out Kraft for putting the "Smart Choices" logo on its Strawberry Bagel-fuls -- confections chocked full of cream cheese, sugar and red dye. So program's taking a hiatus and getting out of the heat, at least for now.

• Calculating Carbon Emissions: Scientists and policymakers who rely on biofuel carbon emission calculations to set policy have been using figures that underestimate total emissions, according to an article in last week's issue of Science (Searchinger et al. "Fixing a Critical Climate Accounting Error": Vol. 326. no. 5952, pp. 527 - 528). The current estimates ignore "CO2 emitted from tailpipes and smokestacks when bioenergy is being used", and also ignore "changes in emissions from land use when biomass for energy is harvested or grown." The errors will increase deforestation, the authors report, because the resulting incentives favor clearing established forest to plant biomass. Environmental Defense Fund's (EDF's) Chief Scientist Steven P. Hamburg told the Washington Post: "We made an honest mistake within the scientific framing of the debate, and we've got to correct it to make it right". Both the Waxman-Markey and the Kerry-Boxer energy bills include the miscalculation.

  Bioenergy and biomass company representatives loudly disagree with the Science study's conclusions, insisting that biomass is "carbon neutral". But of course we know that that's not true, nothing is carbon neutral -- not cars, not electric buses, not biomass. An "emissions free" electric bus, for instance, is filled with seats and upholstery and metal and paint that produced emissions during manufacturing, assembly, and transport. Emissions accounting is only reliable when it includes all the emissions produced over the full life cycle of the product.

• Polar Bears at Sea: The US Fish and Wildlife Association in the U.S. Department of the Interior proposed to set aside 128 million acres for the polar bear, following a lawsuit by the Center for Biological Diversity, the Natural Resources Defense Council, and Greenpeace. Simultaneously, the Minerals Management Service, also in the Department of the Interior, approved oil-company plans for exploratory drilling in the polar bear's habitat in the Beaufort Sea. Brendan Cummings, senior attorney with the Center for Biological Diversity called The Interior Department "schizophrenic".

  Image Copyright Greenpeace/Daniel Beltrá (via Google Images "labeled for reuse" search).

• Manufacturing Sugar and Cynicism: If you feel sad about the loss of "Smart Choices", rest assured that there's more where that came from. Coke and other food manufacturers have launched the "Healthy Weight Commitment Foundation", which advises people to exercise more in order to balance sugary, fatty food and soda intake. The food industry insists the sugar is not the culprit in the obesity epidemic, lack of exercise is. Acronym Required wrote about this industry strategy against soda critics in 2005.

  Now with governments raising the specter of taxes on sugary drinks, Coca-Cola has introduced its own little "smart choice" -- a smaller can of Coke, containing 90 kilocalories per serving. Coke markets its "portion-control option" as one that will help people "manage their calorie intake while still enjoying the beverages they love". Sort of like like our preferred way of dealing with carbon emissions -- don't lower them, just figure out a way to store them, deny them, or incorrectly calculate them.

• Scientist Falsified Data, Embezzled Research Funds, and Illegally Bought Human Embryos -- But is Very Popular: Hwang Woo-suk was a national hero in Korea after he claimed he had cloned stem cells. Then a long investigation involving co-researchers in the US and Korea found that his lab falsified data -- he had not cloned cell lines, as we noted in "The Emperor Has No Clones". Now, not only has he falsified data, a South Korean court has now found scientist Hwang Woo-suk guilty of embezzling research funds and illegally buying human embryos.

  The Korean government long ago revoked Hwang's title of "Supreme Scientist" and stopped selling Hwang Woo-suk postage stamps. But the fraud-besotted scientist hardly missed a beat. Since the court's last finding of guilt, Hwang Woo-suk published papers and started a research foundation -- Sooam Biotech Research Foundation. As a professor at Sooam put it: "Dr. Hwang has conducted his research tirelessly under terrible conditions." And despite his crimes, Dr. Hwang attracts tremendous public support. Hundreds of "hard-core fans" were waiting outside of court, and "dozens of lawmakers filed petitions asking the court for leniency", according to the Los Angeles Times.

• Corporations, The Working Stiffs and The Rebels: Michael Moore's recent movie "Capitalism: A Love Story" reminded people about Dead Peasant's Insurance, which may be the ultimate indignity to workers in the super-capitalist world. But the workers sometimes find ways harangue corporations. The Guardian looks at the campaign of a 92 year old's "gripe site" against Shell, as well as the Twitter campaign against Trafigura and social media's impact on so-called corporate responsibility.

Frogs Die and the Silence Screams:

When talking about all the ways that science was great to a junior high school relative recently, he protested that pursuing science would mean he'd have to dissect frogs very soon. I don't remember dissecting anything until college myself, but the idea of formaldehyde infused frogs and scalpels is apparently quite off-putting to young people these days. However this isn't a post about education or the many misperceptions of teenagers, but the fate of the frogs that have garnered scientists a bad reputation in some circles.

Scientists and doctors are not (usually) sadistic, as suggested by youthful rumors of ritualistic frog dissections. Rather, the drastic decline in frogs as they die en masse across the globe has absolutely dismayed herpetologists and ecologists, who scurry up scarce funds to research the cause of the frogs' demise. "The subsequent silence left a long-lasting impression on me", Australian scientist Jamie Voyles told the journal Science recently, speaking of her experience watching frogs die in a Panama rainforest in 2004.

In 1999 researchers at the University of Maine identified a fungus responsible for 90 of the 120 frog extinctions since 1980. In this week's Science, Voyles and her colleagues describe how this fungus, Batrachochytrium dendrobatidis, kills frogs. The resulting disease first upsets the electrolyte balance across the skin of the amphibians. The skin regulates respiration and osmotic balance inside the frog, and as the disease progresses it disrupts sodium and chloride ions and causes a drop in blood electrolytes causing systemic physiological failure and heart attacks for the frogs.

The optimistic news, if any could be so framed, is that other scientists recently discovered a bacteria species that releases the chemical violacein, which stops the lethal fungal infection. This bacteria is symbiotic to some frog species which manage to repel the fungal infections. This finding suggests that perhaps sometime the devastating fungus could be controlled by managing the bacterial ecology of amphibian skins.

• "Beyond Yottabytes" -- The NSA Will Know Who's Been Naughty and Who's Been Nice: The New York Review of Books reports on the government's information quest:

  "As the sensors associated with the various surveillance missions improve," says the report..."the data volumes are increasing with a projection that sensor data volume could potentially increase to the level of Yottabytes (1024 Bytes) by 2015."[1] Roughly equal to about a septillion (1,000,000,000,000,000,000,000,000) pages of text, numbers beyond Yottabytes haven't yet been named."

  NYRB continues: "Once vacuumed up and stored in these near-infinite "libraries," the data are then analyzed by powerful infoweapons, supercomputers running complex algorithmic programs, to determine who among us may be--or may one day become--a terrorist. In the NSA's world of automated surveillance on steroids, every bit has a history and every keystroke tells a story."

• FedThread: FedThread A newly launched Federal register where you can annotate documents, customize feeds, and search the Federal Register back to 2000. Not to be confused with Threadfed, an embroidery site.

• Health Map: Allows you to see various outbreaks like H1N1, and recalls like salmonella, by geographic area.

• Open Access How-To: SPARC issued a guide for publishers wanting to support open access, along with supply and demand side revenue models.

• Government is an Arm of the Banks: We know that the banks have a phone line to Tim Geithner. But in case you doubted the effect of that on bank behavior, or if you trusted there were no future implications of that relationship for regulation, watch Bill Moyers' show last week with Congresswoman Marcy Kaptur (Ohio-9) and Simon Johnson, the Ronald A. Kurtz (1954) Professor of Entrepreneurship at MIT's Sloan School of Management. Don't read the transcript. Watch the show.

• Telecoms are Agencies Within The Government?: The banks aren't the only ones with a disconcertingly close relationship with the White House. Wired reports that the Electronic Frontier Foundation (EFF) is investigating the influence of telecom lobbying on the Justice Department's coup of winning retroactive immunity for AT&T and others accused of spying on citizens. EFF requested related documents under the Freedom of Information Act and the government refused, arguing that the documents were protected because they were "intra-agency", that is, telecoms were an arm of government.

  Last month U.S. District Court Judge Jeffrey White reversed that decision, ruling for the EFF that the Justice Department was obligated to release the names of telecom employees who contacted the Justice Department and White House.

• Is Transparency Is Over-rated? Is Lessig The Fifth Column?: Lawrence Lessig used to argue that culture needed to be free. People should be able to mash it up, he said, make what they wanted out of songs and books and writing. He founded Creative Commons, whereby people can use your work for free, with attribution if they feel like it. He started what turned into the Google Books settlement when he legally challenged copyright laws by pursuing the release from copyright of "orphan" books. At the time, he was at Stanfords' Center for the Internet and Society, funded by 2 million dollars from Google.

  Now Lessig is pursuing a different cause while he is at Harvard and on the board of the excellent Sunlight Foundation (biased, maybe, but I have no stakes), which funds projects to make government more transparent. Paradoxically, perhaps, Lessig argues in The New Republic this month that transparency is dangerous because people have short attention spans and mashing up the data will connect money to politicians in seemingly nefarious ways when in fact none may exist. The citizens, simple as they are, will become cynical, and government will fall apart. Something like that. The Sunlight Foundation disagrees. More later.

• Google's Fast Flip: You can browse multiple sites simultaneously. Small print. To note: Google chooses which sites participate.

• States Can Sue Utilities: States had tried to sue utilities for being a "public nuisance", releasing CO2 which creates global warming and the court had ruled against them. Now, as the NYT reports: "a panel of the United States Court of Appeals for the Second Circuit, in New York, ruled that eight states -- California, Connecticut, Iowa, New Jersey, New York, Rhode Island, Vermont and Wisconsin -- as well as New York City and three land trusts could proceed with a suit" against American Electric Power, Southern Corporation, the Tennessee Valley Authority, Xcel Energy and Cinergy Corporation, all large coal-burning utilities."

• Economist Changes User Access: The Economist will remove much of the online content for perusal by non-paying subscribers, including the Table of Contents of the print edition - clever. Subscribers will get access to an audio version, archives and all content.

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Image from Wiki Commons

Now, at PNAS Three Papers in Question:

The science journal Proceedings of the National Academy of Sciences (PNAS) offers special publication privileges to members of their Academy, a group of elite scientists chosen by other esteemed scientists based on their unique contributions to science research. Now the editorial board has retracted some of those privileges in light of papers that recently appeared in the journal.

Nature News reported on a "row" caused when PNAS published research that didn't meet the journals' standards for peer review. The dispute is now heating up. The controversy began in August when one article published on-line at PNAS forwarded a theory by author Donald Williamson, on what he called "larval transfer hypothesis".¹

Williamson suggests that the process of metamorphosis, whereby larvae turn into butterflies, arose when butterfly Leptidorae larva "mistakenly fertilized their eggs with sperm from velvet worms", as Scientific American put it (funnily twisting agency). Velvet worms, Onychophora, look like larvae but have completely different life cycles -- they don't turn into butterflies. According to Williamson, evolutionary transfer of genetic material causes butterflies to have essentially two lives, one as a worm-like larva, and one as a butterfly.

But there are problems with the theory. First, he offers no proof, just a "testable" hypothesis. And while interspecies fertilization is not unheard of within the animal kingdom, velvet worms are too distinct from butterflies to make this feasible, say scientists. The sperm could not fertilize such a distantly related egg and produce a viable embryo, and even if it did, it wouldn't "explain the process of metamorphosis".

Less charitably, scientists said that the paper was better suited to a a tabloid than to a science journal, and called the paper "absolutely ridiculous". They also scoffed at his attempt to show the "superficial similarity between adult velvet worms and larval moths and butterflies" with "very poorly reproduced line drawings that really need to be seen to be believed".

In short, the August PNAS paper brought a torrent of harsh criticism for the octogenarian's ideas. Moreover, while some people tolerated Williamson's submission as an attempt to generate discussion, nobody thought that PNAS should have published such a speculative paper. Scientific publishing is very competitive and many scientists who produce worthy research with real results are summarily rejected from high profile journals like PNAS. So how did the research get published? The tale gets even more interesting.

When Push Comes to Shove

Shortly after Williaimson's PNAS article saw daylight, Scientific American published an interview with evolutionary microbiologist Lynn Margulis, an editor at PNAS who shepherded Williamson's work through the peer-review and publishing process. In recounting her story of how the paper got published, Margulis mentioned that she had been trying to publish the work for twenty years. After convincing Williamson to ask the question of how the worms fertilize caterpillars -- rather than the more conceptually challenging idea that worms breed with butterflies, she told SA it took 6 or 7 peer reviews before she got 2 or 3 that were positive enough to push the paper through to publication. Her narrative raised more eyebrows in the science community.

But now it's not just that paper. Another PNAS paper by Margulis and co-authors that's being questioned apparently proposes a treatment for Lyme disease that's "800" times more effective than doxycycline -- "it is very important to get this paper published", co-author Oystein Brorson told Nature.

A third paper in question is a computational biology paper by an adjunct professor of the Margulis lab. PNAS has asked Margulis to withdraw that paper because of problems with the methods. Margulis told Nature she would do no such thing, and when asked in turn for comment, PNAS told Nature: "We don't want to respond to any questions or complaints she [Margulis] has through the media." Sounds like more entertainment is forthcoming.

The three PNAS papers all circle themes that Margulis has been pursuing for decades -- Spirochetes, desiccation, spores, symbiosis and more symbiosis than you'd ever believe, and disease. Is the recent spate of publishing from the Margulis camp a final push for these ideas? And even more controversial ones?

Another 2009 paper has been published on-line in the (less well-known) journal Symbiosis (another journal that Margulis edits), by the same authors -- Hall, Brorson, Margulis and others. This "position paper" proposes that antibiotic treatment of Lyme and Syphilis, both caused by Spirochetes, induces the formation of cysts, or "round bodies", that then revert to their original Spirochete form in a favorable (antibiotic free) environment, causing secondary infections, long-term human symbioses, and compromised immunity.²

Although the abstract is pretty straight-forward, the paper quickly leaps out on a limb to suggest that AIDS is not caused by HIV but by Spirochete round bodies. Again, there's no evidence. The authors draw tenuous connections between quotes made by public health officials after a 2007 HIV vaccine trial, and their own round-body theory of AIDS. They reason that HIV seems not to infect heterosexual partners as much as men who might be infected with syphilis but not fully treated with antibiotics even though medical professionals say they are. So the authors have an idea:

"Is the situation [AIDS] better described as an obligate and ancient symbiosis where the bionts (spirochetes and humans) are integrated at the behavioral, metabolic and genetic level rather than a new viral infection such that HIV equals AIDS? ...We urge that the possible direct causal involvement of spirochetes and their round bodies to symptoms of immune deficiency be carefully and vigorously investigated."

So then HIV might not be caused by a virus but by Spirochete-round bodies. See? Someone test this right away.

Forget Crabs, Look Out For Round Bodies and Symbiosis

Margulis told Nature her attitude about the three PNAS papers in question: "If they definitively reject these papers I will make it very clear to the reading public (because they make it clear in their anonymous letters) that, as usual, they don't like my ideas." Two years ago, we posted on Margulis's controversial ideas and public relations skirmishes. Our post followed her debut on PZ Myers blog, where unchallenged, she forwarded her idea that HIV didn't cause AIDS. If HIV causes AIDS than why doesn't NIH write back to me, she asked? We wrote:

"Margulis relishes controversy and slings mud far better than most people, a well-honed and essential skill....[but] famously, despite her formidable offense skills, she forever portrays herself as someone who has been pushed in a mud puddle."

The PNAS controversy is interesting, although it wouldn't leap out at everyone so much if the papers in question weren't so blatantly ludicrous. PNAS's publication "favoritism" is far from unusual in the science world. Margulis has been publishing these ideas for years, drawing connections based on thin research (often foreign, often Russian, somehow lost on Americans), and asking the science community to run some experiments to test her ideas. In our previous post we talked about her theory of Spirochete symbiosis forming nerves:

"Think of the nerve as coming from what had formerly been a bacterium, 'trying' but unable to rotate and swim. Thought involves motility and communication, the connection between remnant spirochetes. All I ask is that we compare human consciousness with spirochete ecology."

That was in 1991. But the gulf between what she "asks" and a warm reception from scientists has grown as science has advanced. Williamson is an 87 year old retired scientist, who himself is no stranger to forwarding controversial ideas. Sketched drawings weren't so ludicrous 60 years ago when he was starting. But now, the idea that a paper could simply describe what you see, like generations and generations of cell biology papers before us, seems ridiculous. As an educator at Princeton said recently, "The days of sort of naturalistic walking around and looking at flowers are long gone". (Look at the emphasis on clinical description in this excerpt from a ptomaine poisoning paper from the early 1900's. Williamson was a scientist not too long after that.)

Margulis has always published in PNAS. Some of the labs' older papers have similar themes and a little research. But it's a different world now. Margulis still has the prestige to gather a cast of characters around her in symbiotic relationships, to continue to push ideas out, and to entertain admirers like PZ Myers and his followers. But while her fame draws admirers and moths it also draws vipers, many of whom are now online.

PNAS claims they were going to change their Track I policy anyway. OK, sure, but no doubt the deluge of online criticism didn't tempt them to tarry with the announcement. Just as high-tech science has redefined what a good science paper looks like, online science criticism has become blood sport. And that's a good thing, don't get me wrong. But imagine what would we'd learn if all papers and journal publication policies got such a thorough raking over?

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¹ Proceedings of the National Academy of Sciences: Caterpillars evolved from onychophorans by hybridogenesis Donald I. Williamson, Communicated by Lynn Margulis, University of Massachusetts Amherst, Amherst, MA, July 24, 2009 (received for review May 19, 2009)

²SYMBIOSIS Vol. 47, No. 1 (2009) Position paper. Spirochete round bodies. Syphilis, Lyme disease & AIDS: Resurgence of "the great imitator"? L. Margulis, A. Maniotis, J. MacAllister, J. Scythes, O. Brorson, J. Hall, W.E. Krumbein, and M.J. Chapman

Better than Chicago 2016: ""Who will win?", they wondered: "Morgan Tsvangirai, the Zimbabwean opposition leader; two Chinese dissidents, Hu Kia and Wei Jingsheng; Afghan: Human rights activist Seema SamarSo; Prince Ghazi bin Muhammad of Jordan; the Western-educated Islamic scholar; Eighty-year-old Vietnamese Buddhist monk Thich Quang Do; Colombian senator Piedad Cordoba?"

Obama won the Nobel Peace Prize. The reaction, needless to say, was mixed, with the Taliban, Syria and Hamas weighing in, and praises from folks like the Mandela Foundation and Desmond Tutu. And where are the photos of the Weekly Standard staff members, who cheered when Obama's entreaty to the Olympic Committee failed to bring the games to Chicago? Snapshots of them crying into their coffee cups?

We think it's all working out for the best though. Olympics in Chicago would have no doubt snared and infuriated millions of people at the O'Hare airport we know and hate. Chicago 2016 would not have been peaceful.

Nobel Prize To Push the World In a Direction We Norwegians Can Endorse

But if you're feeling like Nicholas Kristof, who thinks that perhaps a prize for Obama would be more apt at the end of his eight years, "after he has actually made peace somewhere", whereas someone else should have won this year, know that all those left out are in good company. Foreign Policy lists other deserving candidates who failed to win in the past.

One committee member said that the prize should be viewed as "support and a commitment for Obama." In a way, the Nobel Peace Prize given to Al Gore and the IPCC in 2007 was a similar statement in its overt political support for one side of the contentious arguments about whether climate change was real.

Obama, charming, said:

"Malia walked in and said, "Daddy, you won the Nobel Peace Prize, and it is Bo's birthday!" And then Sasha added, "Plus, we have a three-day weekend coming up." So it's good to have kids to keep things in perspective"

He said he doesn't see the prize as recognition for his accomplishments, rather as recognition for the goals he's set. The committee therefore rewards Obama for being very Obama...and nudges him to do more?

The EPA and Me

Last week Environmental Protection Agency (EPA) Administrator Lisa Jackson addressed the issue of chemical regulation at the Commonwealth Club in San Francisco. The speech, posted on the EPA's website, succinctly addressed some of the EPA concerns we've had over the years at Acronym Required. First, Jackson reviewed the EPA's accomplishments in the last eight months:

"[A]s EPA Administrator, I was proud to be able to bring the California waiver back from the dead - more Obama environmental health care...We've hit the ground running on priority issues: first-ever national initiatives to confront climate change; restoring the rightful place of science as our cornerstone and rebuilding public trust in our work; revitalizing protections from toxic chemicals, smog, water pollution; and expanding the conversation on all of these issues, so that communities most affected by environmental degradation have a voice."

All these things we like. Jackson cited the EPA's dedication to science, public trust, protection from chemicals, smog, pollution, and she promised to listen to affected communities. Of course she listed these things as both short-term accomplishments as well as long term goals because quite a few of these "accomplishments" aren't quite accomplished yet -- but oh well. Her speech, anyway, followed the goals she set out for the EPA. She warmed the audience up with her likable personality and her biography of typical Obama-era public trust credentials -- dedicated, hard working family, public service orientation, significantly accomplished career.

And how she spoke to our concerns! She talked about about the EPA's recent response to the Supreme Court's endangerment finding. She recounted her mother's losses in Hurricane Katrina and how it affected her attitude towards public service. We covered Katrina (here, and here, and here, and here, and here, and here). She spoke of the failure of the Toxic Substance Chemical Act to adequately protect us from chemicals, which we last wrote about here. She spoke about bisphenol A, a popular topic at AR -- one of our latest posts is here.

The guts of her talk involved chemical safety and again she spoke to us. Evaluation of risks must be based on risks, not economics, she said, eluding to cost-benefit analysis debates. Jackson asserted the EPA's need for authority to take action when necessary to enforce the rules. She spoke of the mishaps of Love Canal and Superfund sites, reassuring gestures since people like Cass Sunstein, head of OIRA, has disconcertingly denied the toxic dangers of Love Canal (Chapter 4: "Risk and Reason", Cambridge, Cambridge University Press, 2002). Jackson noted the uneven burden on the EPA over industry to generate and pay for information and resources. We agree, the agencies are overburdened.

The EPA and Everyone

However, while at first buoyed by Jackson's upbeat announcements and the pleasant departure from the Bush EPA's Administrator Johnson, as I read on I began to question my naively egocentric notion that Jackson spoke to me, to us. Indeed, what will be the place of science? Should science really be the "cornerstone" of public policy, as she said? No, despite what many scientists clamor, it neither can nor should be. Granted, this very real point is too subtle for her speech, but she reiterated the very popular sentiment to approving nods, I'm sure, from the crowd in San Francisco.

But wait, before your applaud her endorsement of science defining public policy. Further along in her speech, she brought the point up again, but subtly changed it, saying that Americans wondered whether EPA decisions were guided by "science and law". Appealing to lawyers in the crowd, perhaps. But law is different from science, and with different outcomes often at odds with environmental science -- as anyone who follows the Supreme Court decisions on science will know. Here, the Supreme Court doesn't really understand the environmental argument that the Navy and whales can co-exist while national security is insured. Here we talked about legally influenced decision that forsook whales, as well as the legal finaglings of the Exxon Valdez settlement. The EPA under Bush used the law to effectively stall in every direction on the environment. Use science to inform policy? Yes. Use the law as needed? Yes. But, in our edgy post-Bush, trying not to be cynical phase, we'd prefer them separated by periods not conjunctions.

The EPA's Public Relations Jambalaya

The more I read, the more Jackson's speech looked like a veritable public relations jambalaya. She spoke to those committed to wetlands, spotted owls, to asthma sufferers, climate change, to those concerned about coal and gas emissions, to the Clean Air Act, to trash incineration, dioxins, pesticides, green chemistry, research, unions, medical professionals, public health groups, industry, environmentalism, to those who want jobs, fast food packaging, to unborn children, African Americans, Native Americans, Latinos and postal workers, as well as everyone who emails public comments to the EPA or who's concerned about health care and health.

It sounds like public relations to me. Not that we don't want to believe in the EPA's intentions. And the EPA should be far more visible with its message. But we know that promises on a podium cannot foretell the outcome of all the very hard policy work that needs to be done before something can be called an accomplishment.

We felt like we had our expectations in line when we reported on Obama's ambitious announcements for the environment, in which we jestingly placed the fairy and wand image to the right above. Our realism last November (no, not cynicism), assured that we were not disappointed with the Obama administration as so many others now are. We know that Obama administration speeches are not promises -- they're just speeches.

So we see Jackson's speech as a marketing tool, and conversation generator but not a public policy statement. The goals of business were largely missing from the speech, perhaps because business doesn't need reassuring or because they're already sitting at the EPA's table. (Cynical or realistic?)

In keeping with the goal to restore public trust and provide information, after the speech, the EPA sent out another press release about Jackson's talk. "Leaders Praise EPA Administrator Lisa P. Jackson's Plans for Chemical Reform", the agency applauded.

Preserving the Brilliance?

FCC Chairman Julius Genachowski spoke on net neutrality last month, promising an open and robust internet that would continue to benefit business and individuals, commerce and democracy:

"...we are here because 40 years ago, a bunch of researchers in a lab changed the way computers interact and, as a result, changed the world. We are here because those Internet pioneers had unique insights about the power of open networks to transform lives for the better, and they did something about it. Our work now is to preserve the brilliance of what they contributed to our country and the world."

Freedom to Tinker's David Robinson recently critiqued net neutrality proposals now the works. In addition to the FCC's announcement, Robinson reviewed a legislative proposal by Representative Ed Markey (D-MA).

Promulgating Ambiguity?

Legislation like Markey's could, if written right, solidify the goals of net neutrality more robustly than leaving the process entirely to the FCC. However Robinson writes that as it stands, The Internet Preservation Act of 2009 assumes too much in the way of regulatory authority from the FCC. Secondly it depends on an ill-defined standard of "reasonableness", as reasonableness would be judged by unidentified "interests". For example:

"We are discussing the actions of ISPs, who are generally public companies-- do their interests in profit maximization count as compelling? Shareholders certainly think so. What about their interests in R&D? Or, does the statute mean to single out the public's interest in the general goods outlined in section 12 (a), such as "protect[ing] the open and interconnected nature of broadband networks"?

Robinson calls for clearer language that leaves less ambiguity about what's being proposed. More here.

Monarchs? Where Do They Go? How Do They Get There?

Monarch butterflies, Danaus plexippus, migrate from the Northern US and Southern Canada to Central Mexico beginning in late August, then migrate north once the weather gets warm. It's a journey of up to 2000 miles, and an individual monarch butterfly doesn't live long enough to make the full journey. ¹ Monarch butterflies only live two to six weeks once they metamorphose into butterflies.

Interestingly, however, while most generations of monarchs born in the spring and summer live two to six weeks, the last generation of monarchs that emerge in late summer undergo arrested development called diapause, brought on by less daylight. Missing a reproductive chemical called juvenile hormone, these monarchs can live seven months or more. During this time they migrate to Mexico, hibernate, then begin the flight back north, all before reproducing. But even this longer living generation of butterflies will not finish the trip, nor, most likely, will their shorter lived progeny. It will usually take one or two more generations of monarchs to complete the trip to North America from Mexico.

Scientists have long investigated how it is that these monarchs in successive generations can travel thousands of miles and manage to navigate the route so precisely that they often overwinter in the same tree year after year. Previous scientific research revealed that, like other insects, monarchs use the sun for navigation. More research showed that as the sun moves across the sky, the butterflies also use circadian clocks to adjust their route and maintain a southerly course. Then, as years passed scientists identified genes which control various circadian clock functions, and evidence from their research suggested that these genes could reside in the brain.

Public domain photo from US Fish and Wildlife, via Wikimedia Commons.

Where The Clock Lies

However new science last week brought an unexpected turn in the path of monarch circadian clock research. Science published a paper by monarch butterfly researchers at the University of Massachusetts Medical School who have long been studying monarch circadian clocks. Steven Reppert's lab showed that circadian clocks which control the monarchs ability to navigate the long migration reside not in the brain but in the antennae.

Following up on research done in the 1960's the scientists studied the influence of butterfly antennas on navigation. They found that butterflies without their antennas were unable to navigate a southerly course, nor could butterflies navigate whose antennae researchers blocked from light. They found that neither eyesight nor smell influenced navigational ability which was solely determined by light interacting with the antennae.

The current research, building on all the previous research, shows that circadian clock in the antennae are necessary for navigation, whereas the brain circadian clock may have different or complementary purposes. The paper, "Antennal Circadian Clocks Coordinate Sun Compass Orientation in Migratory Monarch Butterflies," was published in Science last week.^{2 3}

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¹ Monarchs hatch from eggs after four days to become caterpillars for about two weeks. They then enter the pupa or chrysalis stage which lasts about two weeks before molting and undergoing metamophorsis to mature butterflies. They can then flit around as butterflies for two to eight weeks before dying.

² Christine Merlin, Robert J. Gegear, Steven M. Reppert*, "Antennal Circadian Clocks Coordinate Sun Compass Orientation in Migratory Monarch Butterflies" Science 25 September 2009: Vol. 325. no. 5948, pp. 1700 - 1704 DOI: 10.1126/science.1176221

³ Send Acronym Required your suggestions, questions or comments.