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Last week, U.S. District Judge Royce Lamberth issued a preliminary injunction to stop Obama's reinstatement of some of the federal funding for embryonic stem cell research.

The plaintiffs included Christian Medical Association; the Nightlight Christian Adoptions, an agency that sells the use of frozen embryos it calls "snowflakes" - from fertility clinics; two PH.D. scientists, James Sherely of Watertown, Massachusetts, and Theresa Diesher of Seattle, who do research on adult stem cells and claim that allowing embryonic stem cell research wrecks their chances of getting federal grants; clients for adopted embryos; and the embryos frozen in IVF clinics.

Judge Lamberth's decision was based on the Dickey-Wicker Amendment attached to every Department of Health and Human Services (HHS) bill since 1996. The rider was a pro-life fueled measure, intended to prevent cloning for research purposes. Since 1996, the Dickey-Wicker Amendment has ostensibly prohibited the use of federal funds for:

• "the creation of a human embryo or embryos for research purposes;" or
• "research in which a human embryo or embryos are destroyed, discarded, or knowingly subjected to risk of injury or death greater than that allowed for research on fetuses in utero under" certain existing laws."

Nevertheless, three administrations, the Clinton, Bush, and Obama, have allowed various levels of federal funding on research on embryonic stem cell lines. The judge's injunction goes so far as to roll back former President Bush's limited acceptance of federally funded stem cell research for certain stem-cell lines created by 2001. The Federal government has requested a stay (.pdf) of the injunction. Who will prevail? The government? Plaintiffs?

Science Community Stunned

The legal move was a blow to the science research community. Said NIH Director Francis Collins: "The NIH was frankly, I was stunned - as was virtually everyone here at NIH - by the judicial decision yesterday".

But remember, back in 2001, prior to the 2002 elections in which Republicans gained seats, and when President Bush was making decisions about stem cell research. A similar group of plaintiffs sued the government. The plaintiffs in Nightlight Christian Adoptions et al v. Thompson included Nightlight Christian Adoptions, the Christian Medical Association; two couples who wanted to adopt embryos and said that stem cell research reduced availability of embryos for adoption; and Dr. David Prentice, a former professor of life sciences at Indiana State University who said that there were better alternatives to hESC, who is now a fellow at the Family Research Council.

Now, nine years later, right before mid-term elections and after Obama plans to expand funding for stem cell research, we have basically the same lawsuit, from basically same plaintiffs.

People have various opinions about what the injunction means and how it will progress in the courts. A lawyer and commenters here at concurringopinions.com discuss why the government will prevail (or won't).

Some scientists speculate that the importance of federally funded embryonic stem cell research has faded, because so much work is done privately. Others, including the plaintiffs, argue that inducible pluripotent stem cells (iPSC) or adult stem cells are just as promising. But most people don't find these arguments too persuasive, and agree that embryonic research is at least a necessary prong to pursue potentially life-saving research. Of course "pro-life" and Christian groups argue that the blastocysts are people which shouldn't be used for research, even if it will save lives.

The plaintiffs' arguments do not persuade for many reasons. Their claim to economic injury is not only unconvincing on its face, considering the plaintiffs and NIH funding structure, it's dwarfed by the impact that stopping the research would have on the lives of sick people. As well, the livelihoods of the researchers are in jeopardy, as is the investment of millions of dollars of government funding that the judge's order seeks to abandon. 24 research projects in which the government has spent $64 million are currently threatened (.pdf) because they had been scheduled to receive $54 million in continuing NIH funding at the end of September.

Should Scientists Have Been Surprised

I was. But maybe I wasn't paying close enough attention. Or maybe I didn't want to believe that such anti-reason would even get a chance. But apparently, all it took was the "right" plaintiff and the "right" judge, at the "right" time.

It's sometimes easier for people (including scientists) to perfunctorily dismiss as terminally unenlightened or misguided, those who hold politically opposing views, for instance those who believe in Creation over evolution. Maybe it's not as head-splittingly frustrating as arguing or teaching. Perhaps a quick witted turn of phrase can morph anti-reason into fodder for jokes, yay! And why not deflect an ugly stand-off with some humor?

James Taranto, of the Wall Street Journal, for one, says that dismissive attitudes (here's one example I thought of: "Poll: So You Want to Build a Mosk?") harms liberal causes because 1) they tend to "mainstream those supposedly fringe notions" (ie: Pew Research Polls that constantly highlight subjects of "culture wars"), and 2) they "put the ugly attitudes of the liberal elite on display."

Scientists discuss these things frequently and blogging scientists have consumed years writing, discussing, comparing and vehemently arguing about various approaches -- hostility, framing, teaching, patience, humor, tolerance, diplomacy, "accomodationism", to deal with anti-reason. (Personally, I can't get attached to one approach or think another is "bad", I believe different writers and audiences will gravitate towards one communication method or another. They complement each other. )

But regardless of whether scientists are "civil", hostile, sarcastic, or choose to ignore what offends them, I wonder if all approaches are fatally flawed not only because of the reasons Taranto and scientists usually discuss, but because scientists are so up to their necks in scientific method. Do we then let ourselves believe that reason will prevail? And does that lead us to ignore what's at stake? The incredible belief everyone had in Obama that he could somehow transcend politics, indicates this may be so. Francis Collins "stunned" response indicates this may be so. Collins, if anyone, with his position and overt religiosity -- he's written books on this! -- should have had his ear to the ground.

Maybe it's a tempest in a teapot, as many seem to think. Maybe Lamberth had an off day and will change his mind, maybe the courts (moving right every day) will come to their senses. But at the moment, those who want to stop hESC seem to be determinately bulldozing things their way, decade after decade.

The ruckus over Obama's proposal to extend only part of Bush's tax breaks -- not the part to ultra-ultra-ultra wealthy individuals -- is maybe playing second fiddle to the mosque ruckus. Maybe this should be obvious, since one involves a little math and reasoning, while the other can be argued from straight from the gut, therefore more people can chatter about Muslim community centers.

News Aimed to the Lowest Common Denominator

But it's a shame more people aren't talking about the tax cuts, because the GOP driven (w/ some Democrats on board) arguments against tax-breaks make no more sense than the ones against the Muslim Community Center, so they should be gossiped about. Plus, the tax-cuts arguably have more impact on the average American than the presence of a community center in downtown New York City.

The Tax Policy Center made a great chart showing who, exactly, would be touched by the Obama tax-cut extension plan. Not until you made $196,549/year would you your tax break be impacted even one cent by Obama's plan.

Once you made $196,540, the Obama plan would take an average of $2 off your $5,508 tax cut - two dollars. The most you would "lose" under Obama -- if you happened to make over $8,367,274 -- that is you were in the top 99.9 percentile in income, making $8.4 million dollars or more, would be $61,500.

The Tax Policy Center notes that the Obama plan will actually only cut a very small part of the overall deficit - 7%. Obama would only change a very small, small number of peoples' incomes (not "small businesses" that would feel the pinch). The TPC says:

"How much will the President's proposal save? Unfortunately, not nearly enough to close the cumulative budget deficit. The administration's proposal shaves off about $680 billion from the 10-year deficit--a modest $68 billion per year"

But the cost of extending all the cuts is worse news. The Tax Policy Center writes: "From a budgetary perspective, the price of extending all of the cuts is steep; full extension would contribute $3.7 trillion to the deficit over the next ten years..."

The Battle Between Math & Rhetoric (hint: math is losing)

Paul Krugman also points out that the insistence on extending the tax cuts as opposed to going with Obama's plan makes no sense. He brings our attention to the craziness of what the GOP is quibbling over, rather than the insignificance of the cuts to the overall budget.

He writes:

"According to the nonpartisan Tax Policy Center, making all of the Bush tax cuts permanent, as opposed to following the Obama proposal, would cost the federal government $680 billion in revenue over the next 10 years. For the sake of comparison, it took months of hard negotiations to get Congressional approval for a mere $26 billion in desperately needed aid to state and local governments."

Even Alan Greenspan, forever shocked that the markets let him down, recommends suspending all the 2001 and 2003 tax cuts. Aside from FOX News, where John Stossel is "tired of Greenspan", and finds it "ironic" that Greenspan once wrote for Ayn Rand, and (not ironic the way I do), what's up with the rest of the people?

Update 08/13: AB 70 was defeated. However, the Bring Your Genes to Cal program was altered because they planned to do the analysis in Berkeley labs, which are not certified medical labs. In accordance with state demands the students will not receive their own results.

Legislation usually moves along at a crawl, slowly, glacially -- except if you're the California State legislature trying to corral the University of California, Berkeley's personal genomics walkabout offered to incoming freshmen. The state bill AB 70 was introduced in December, 2008 to encourage transparency on how school districts classify "English learners" to "proficient".* Now, the text of AB 70 the "English learners" bill has been parasitically devoured and replaced with text to impede the University of California, Berkeley's program for incoming students, known as: "On the Same Page: Bring Your Genes to Cal".

How the State Tries to Come Between Cal...and Your Genes

Like many universities, freshmen are welcomed to UC Berkeley with some thematic program. Historically that's meant they all read a book, for instance last year they read Omnivore's Dilemma, by Michael Pollan. This year they decided on a more interactive learning experience, asking incoming Freshman to spit in a cup and submit that for analysis of lactose, alcohol metabolism, and folate gene variants. The idea seemed fresh and relevant, and Berkeley went forward with it apparently without much internal debate. Certainly getting students involved in their own health can't be bad can it?

Some people actually thought it was bad, however, and eventually the state legislature got involved -- very late to the game, of course. But as the university mailed out saliva spit kits to students, AB 70 suddenly gained what seemed like unprecedented speed and "urgency". If passed, it will be "enacted immediately."

The original AB 70 proposed adding a section to the education code requiring that school districts report their criteria for assessing English proficiency. The bill languished until being amended June 24, 2010. The amended title reflected not-too subtle changes. The old sponsor and bill purposes were simply crossed out, and the new sponsor and purpose inserted so it read:

"Duvall Norby English learners. Public postsecondary education: genetic testing."

That's how an English learners bill morphed into a bill to stop UC Berkeley from teaching about genetic testing.

Legislation 101

English learners text was crossed out:

....This bill would require the department, as part of its duties in administering the English language development test, to gather from each school district that has one or more English learners the criteria that the district uses for the reclassification of a pupil from English learner to proficient in English and to summarize and report the criteria it receives...

And in its place, text warning about allowing "On The Same Page: Bring Your Genes to Cal":

• Collecting, testing and storing genetic material presents "unique challenges to protecting individual privacy".
• Medical testing "subjects" should receive "substantial" written and verbal explanation before supplying consent
• Students "may feel coerced to participate in official activities involving widespread genetic testing"
• A 2006 GAO report showed that tests are "unproven, misleading, meaningless.."
• Students could "suffer consequences later in life" because of privacy breaches.

The June 24th version demanded that the school report quarterly, all the costs of the "solicitation" so that the state of California could recoup those expenses. The trouble with that legislation was that the solicitation already happened and was funded with a gift (probably, the funding is unclear). (The state only provides Berkeley with a small percentage of its funding.) So the August 02 amended version of AB 70 struck out "prohibits" and entered "requests" instead. The August version also struck out the demand for accounting of "unsolicited requests", and replaced that for a demand to account for "legal judgements or settlements resulting from violations of the informed consent requirements".

On Different Pages

The August amendments show the state adjusting to meet the realities of the program moving forward. It's a learning experience for all. Clearly the legislature is trying to wrap its head around the project, and adjusting as needed. As is Berkeley. As are organizations who oppose the program.

The text of the bill reflects very closely the rhetoric of the Massachusetts based Council on Responsible Genetics (CRG). Their primary concern seems to be privacy, and their multiple letters to California legislators practically dictate the content of AB 70. But as they gather more information about the project, they too change their rhetoric. In their most recent letter to California legislators, the Council For Responsible Genetics joined with the ACLU, Privacy Rights Clearinghouse, The Electronic Freedom Foundation and others, urging the legislators to "request a full accounting" of the "On the Same Page: Bring Your Genes to Call" program, specifically issues of conflict of interest, funding, privacy, and data confidentiality.

The Berkeley program certainly brings relevant topics to the fore, and who can challenge the importance of this? But Berkeley scientists and the Council on Responsible Genetics have stuck doggedly to their talking points. Scientists advocating the program stress the need for education about genomics, and accuse critics of being anachronistic and paternalistic. They stress individuals personal right learn genetic information. Therefore, they would argue, this is a relevant topic worthy of the attention of the program.

Certainly healthcare in America is at such a nadir that anyone with half a brain in their head who has visited a doctor lately would agree that giving individuals more information to take more ownership of their own healthcare would be great. Personal genomics could give such insight, democratize information, and benefit health consumers. But this is one (there are others) big hitch. Direct to consumer genetics testing (this is related) walks a fine line between being innocuous information and a "medical test". Bring Your Genes to Cal proponents simultaneously push the importance of the students learning about genomics - and by pushing this they get necessary support, while at the same time belittling the relevance of the tests and their results - so as not to attract unwanted attention.

Meanwhile, critics are focusing on the very issues that the University is trying to downplay. CRG insists on repeatedly labeling the Bring Your Genes to Cal tests "medical tests" in order to prompt alarm and greater scrutiny. The critics dwell on privacy, data confidentiality, and interpretation of data. To me, if genomics data is important enough that it's worth building this program around (as innocuous seeming as these variants may be), than it's important enough for the critics' issues to matter -- even if the involved scientists twist themselves into knots to avoid those discussions.

The state, for its part, is trying to respond, quickly at that, without having a clear handle on the issues. Perhaps they yearn for 2008, when AB 70 was stymied in controversy over adding a webpage to assure transparency in schools' English Learner programs.

------------------------

*AB 70 was also once a bill about state dams.

The University of California, Berkeley always amazes. It has an ultra-liberal reputation, yet it defies its label by harboring some of the most controversial figures, and protects them under the auspices of academic freedom -- an excellent institution -- strreetttched at Berkeley to fit many circumstances. The law school dean used it to protect John Yoo, the law professor who crafted the Bush administration's torture policy, for instance. Now the school has invoked the useful catch-all to clear scientist Peter Duesberg of wrong-doing over a paper he wrote denying the HIV viral link to AIDS. The University said there was "insufficient evidence" to do anything else.

Berkeley Did Not Judge the "Accuracy or Validity of the Article"

Although UC Berkeley didn't judge the "accuracy or validity of the article", those issues lie at the heart the ongoing Duesberg controversy. This was only Dueberg's latest foray, that he initiated last year by publishing a paper in a non-peer review journal called "Medical Hypotheses". He claimed in his paper that the HIV virus didn't cause AIDS, something he's been promoting for years. The paper did not undergo peer-review. Scientists refuted his false theories in a collective uproar, the journal retracted the paper, the journal editor was fired, and Elsevier, the publisher, promised to rethink the journal format.

Then the University received two letters, one from Treatment Action Coalition (TAC) in South Africa, criticizing Duesberg's paper for conflict of interest and for "making false claims". The letters asked the University to investigate. The school did so, however yesterday's action clearing Duesberg of wrongdoing indicates that the UC Berkeley mission, policy and conduct documents don't contain anything that's applicable to Duesberg's situation.

Duesberg's Legacy In South Africa

The main problem is not necessarily the statements Duesberg published last year, but the fact that for years he's been publishing them and they've significantly influenced policy and beliefs about AIDS and science in general. It's his actions outside the University, like Yoo's, that cause the most distress. Duesberg sat on former South African President Mbeki's advisory panel on AIDS back in 1999-2000, and the South African government frequently cited his AIDS ideas to support their policies. Mbeki didn't treat AIDS in his country, letting hundreds of thousands of people die.

Whether Duesberg was a handy foil for Mbeki's pre-determined policy -- whether Mbeki's countrymen died because the president was more driven to toe conservative economic and social policy the procure available AIDS drugs -- is unclear. What is clear is that the country had the highest death rate from AIDS in history, while wielding the most mendacious policies, which Mbeki backed-up with "science" created by Duesberg.

Yet there's nothing in Berkeley policy that specifically calls this a crime.

Peer-Review? Whatever. Duesberg = UC Berkeley= AIDS Denial = Mbeki's AIDS Policy = Death

A Berkeley spokesman told Nature: "The university relies on the scholarly peer-review process, rather than disciplinary procedures, for evaluating the value of scientific work." There. Very official. However AIDS denialists don't rely on peer-review. They revel in non-peer-review.

And unlike the University and scientists who care about peer-review, for Duesberg's purposes, getting a paper retracted by some flaky non-peer-reviewed tabloid called "Medical Hypotheses" doesn't matter. He has his audience. For years he's had a self-promoting website up, and his ideas have gained an audience. Next they'll go after "my parking permits" he says. His audience laps this stuff up -- the underdog, taking on the big evil science establishment.

UC Berkeley has their policies and official responses. Academic freedom, the concept, is inarguably beneficial, the heart of academia. But the fact remains, one of the most renowned research universities in the world supports a scientist largely responsible for some of the most deadly anti-science claims in history. If you search "Duesberg" in Google, his site is featured at the top. Here's how the Google results page text reads today:

"Peter Duesberg on AIDS - Duesberg.com - HIV / AIDS research ... Infectious AIDS - Have We Been Misled? This is the official HIV/AIDS research from the University of California Berkeley, Department of Molecular and Cell ... www.duesberg.com/ - Cached - Similar"

"Official" HIV/AIDS "research" from the University of California, Berkeley. The Wikipedia entry for Duesberg appears third today on the same Google search page. Here's how it reads:

"Duesberg hypothesis - Wikipedia, the free encyclopedia The Duesberg hypothesis is the claim, associated with University of California, Berkeley professor Peter Duesberg, that various non-infectious factors such ... en.wikipedia.org/wiki/Duesberg_hypothesis - Cached - Similar"

UC Berkeley policy has nothing to say. Peer-review? Here's what the world sees: Duesberg = UC Berkeley= AIDS Denial = Mbeki's AIDS Policy = Death. Somewhere deep in the heart of hearts of university bureaucracy, under all the official, vague missions, purposes, and policies, doesn't this cause angst?

Exonerated?

Interestingly, it's Duesberg himself whose been spear-heading the reporting on the investigation. Apparently Duesberg has enough confidence in the support of anti-science, AIDS denialist community, to know the outcome would work for his purposes. And since now Duesberg is claiming that he was "exonerated", it's like free marketing for his theories. How tragic.

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¹PLoS One, the audience reviewed journal, is also tangentially affiliated with UC Berkeley via PLoS co-founder and esteemed scientist Michael Eisen.

Acronym Required has written frequently on South Africa and AIDS, occasionally about HIV/AIDS deniers, and once in a while about UC Berkeley.

Haiti!

Help, donate: Partners in Health, or Medecins Sans Frontiers, or the Clinton Foundation, or the International Red Cross or text-to-give.

• PLoS and Elsevier: On the Same Page?

  One of our favorite things, in the Obama era, is to see would be foes band together. So we look fondly upon the unlikely albeit fragile "alliance" that PLoS and Elsevier ended up in at a recent open access publishing roundtable. The occasion was a meeting around the report issued by the Scholarly Publishing Roundtable. The U.S. House Committee on Science and Technology and the White House Office of Science and Technology Policy (OSTP) convened the meeting of a group of fourteen publishers, university leaders, librarians, and other experts at the round table, who drafted basic agreements about how public access to journal publications. They emphasized:

  "the need to preserve peer review, the necessity of adaptable publishing business models, the benefits of broader public access, the importance of archiving, and the interoperability of online content"

  However, the Elsevier and PLoS representatives refused to join the other 12 members in signing the consensus agreement, although both agreed that points of the agreement were "positive". PLoS and Elsevier apparently both have a lot a stake, since they each sent extra representatives to the panel. Elsevier sent their General Counsel/Senior Vice President, and PLoS sent their Managing Editor as well as their CEO.

  Predictably, YS Chi, speaking for Elsevier, stated that he couldn't sign the agreement because it "supports an overly expansive role of government and advocates approaches to the business of scholarly publishing that I believe are overly prescriptive." No question about where giant, monopolistic, Elsevier ever stands.

  PLoS representative Mark Patterson's statement was a little more difficult to unpack. He said that the agreement "stops far short of recognizing and endorsing the opportunities to unleash the full potential of online communication to transform access to and use of scholarly literature." What did he mean? He didn't include "the need to preserve peer review" as one of his "positive" points of agreement....But does PLoS want more Federal support for PLoS? Explicit endorsement of pay to publish? A more "expansive role for government"? Who knows.

  For more information on open access and this agreement in general, there's a great public access policy forum here at the Office of Science and Technology Policy, and the "ever-enthusiastic public access policy team" at OSTP has extended the comment period. So you can comment, and there's lots to read.

• H1N1

  The World Health Organization (WHO), has hit back at accusers who say that the organization, along with pharma companies, created a "fake epidemic" in H1N1. WHO reiterated its role to balance urgency and expediency with the uncertain nature of the epidemic. In an editorial generally praising the organization's response, Nature wrote this week:

  "The danger now is that last year's relatively mild pandemic will create a false sense of security and complacency. The reality is that next time we might not be so lucky -- especially given that this time most of the world's population, living as they do in developing countries, had no access to either vaccines or antiviral drugs."

  It's apparently easy for otherwise smart people to be cynical about the H1N1 pandemic. It is truly a challenge to explain risks and uncertainty of pandemics and the fact that the scientists and public health organizations are actually doing a great job.

Judge Overrules FDA on Electronic Cigarettes, Whatever They Are

Some people believe that a president's most lasting legacy is in the judges he appoints; George W. Bush appointed judge Richard Leon of the Federal District Court in Washington. Leon recently moved to stop the FDA from regulating e-cigarettes, on grounds that they aren't tobacco. In fact, e-cigarettes are battery-powered tubes that vaporize nicotine with tobacco flavoring, that simulate cigarette smoking for the user. I can't make that sound good. Seems like the next best thing to sex robots. But anyway, these devices deliver addictive nicotine to the body, but the judge says the FDA can't regulate e-cigarettes as devices anymore.

In other tobacco regulation news, an article in the New England Journal of Medicine (NEJM) discusses opposition to the Family Smoking Prevention and Tobacco Control Act on First Amendment grounds. Even the ACLU objects to the Act, which prohibits the use of certain words by cigarette advertisers, saying that

"regulating commercial speech for lawful products only because those products are widely disliked -- even for cause -- sets us on the path of regulating such speech for other products that may only be disfavored by a select few in a position to impose their personal preferences."

Instead advised the ACLU, "the antidote to harmful speech can be found in the wisdom of countervailing speech -- not in the outright ban of the speech perceived as harmful." But as the NEJM authors wrote:

"How did we come to believe that the exchange of commercial appeals in the marketplace of goods and services should be equated with free exchange in the marketplace of ideas? Are our freedoms really secured by a constitutional doctrine that would limit our capacity to inhibit the promotion of toxic goods? This is an opportune moment to reflect on these questions and their implications for the relationship between public health goals and the rules that should be foundational in a democracy."

• EPA's Updated Smog, Ozone Standard

  The EPA proposed new standards for smog last week, which would update the Bush Administration standards. The agency will set the "primary" standard, which protects public health, at a level between 0.060 and 0.070 parts per million (ppm), measured over eight hours, and will also propose a new secondary standard. These standards were recommended by scientists years ago to decrease deaths and smog levels dangerous to children, the elderly, and those with asthma and respiratory disease. As we wrote earlier, the Bush's EPA pushed the weaker standard of .075 ppm. We also wrote about the Obama EPA's stated intention to change the standard last fall.

• Airport Screening to Double as Healthcare?

  "We are headed toward the moment when screeners will watch watch-listers sashay through while we have to come to the airport in hospital gowns, flapping open in the back", wrote Maureen Dowd recently, commenting on holes in airport security processes. But I think she's seeing a cup half empty. We may well be headed for a moment when airport screening, reviled as a breach of privacy to some, is the closest thing to healthcare people can get.

  The public option has fallen "off the table" again, by now "fallen off the table" so many times that even when it intermittently appears back "on the table", it's obviously shopworn, if not smashed to bits.

  But the glass could still be half full. Think of the savings, if airport screening could double as healthcare screening : "You're cleared for flight sir, and don't worry about that lump..."

• What to Call It? Science Terminology

  For various reasons, political, scientific, logical (or not) or historical, people refer to the same thing using different terms. Here are two examples.

  Canada does not call the tar sands "tar sands", anymore, they're "oil sands". Of course "tar sands" is more descriptive of the energy-intensive process, of extracting oil, but "oil sands" sounds like something that you would naturally siphon some oil out of, it sounds better.

  In 2005, physicist Lisa Randall urged that "global climate change" was the appropriate phrase to use, because "global warming" would lead people to argue that their winter was actually very cold. Others argued that "climate change" sounded less dangerous, so therefore would be used to manipulate people who would be fearful enough about "global warming" to urge policy changes, whereas "climate change" seemed benign. But it gets even more complicated for some agencies. NASA differentiates between "global warming", which is surface climate change, and "climate change", and "global change", and "global climate change", which deems the most accurate term. I think everyone pretty much knows what everyone's talking about now, though I dare not make conclusions about that.

• Oh, and Happy Not-So-New Year

  Did you travel over your break? Have fun?

  In the US, marketing aimed at tourists is off the rails. Perhaps marketers have learned that people who travel in a heightened state of orange level stress will sooth themselves by buying absurd products. You may argue that it's a global trend, and indeed, the badminton set peddled to me by a man on the muddy backroad of a major city in Asia seemed ridiculous, until I flipped through Sky Mall Magazine and spied the "King Tut Life Sized Sarcophagus Cabinet" that can be "delivered curbside" (to impress your neighbors). Personally, I would rather pay to bat around a little white badminton birdie in a mud puddle, while talking baksheesh with kids who speak, at will, touristica French, German, English or Japanese. By comparison, traveler oriented products in the US seem conceived by desperate marketing departments who've lost their wits. Case in point -- the sarcophagus cabinet. Or:

  • If you were assigned to seating group 2 or above recently, on my least favorite airline I still fly on, you heard this announcement: "Board now. Enter via aisle closest to the wall, NOT THE RED CARPET." Because "the red carpet", actually a two foot doormat, is reserved for first class customers.

    Some people bemoan the lot of the economy passenger, the so-called "poverty parade", and the herd animal like treatment. But as a first class customer you pay an extra few thousand dollars to traipse across a red mat with bars on each side to keep you in bounds. Sure the legroom's nice, I won't argue, but you have to walk "the red carpet" to get there, and once there in that bigger, comfier seat, you're subjected to complimentary cheesefood snacks. Supposedly smart people actually buy this privilege.

  • At your hotel, you will be sold the usual-- rooms, room service, laundry services, shoe shines and upgrades, not to mention the mini-bar. But what if the five dollar peanuts in the mini-bar are too devilish a temptation for you and your New Year's resolutions? No worries, there's a market-based solution. Pay $50 to have the mini-bar hauled away at one hotel I was recently at.

  • Want to use the hotel refrigerator for your water? $50 fine at another hotel. And the same people who stay at these hotels complain that the EPA's bureaucracy confines their business style.

  • Maybe you actually love business travel and want to bring home a bit of the experience, like the "pulsating" showerhead that your can actually buy from one hotel's glossy catalogue. The catalogue carried other mundane household hardware and dog cushions stamped with the hotel's logo. Pretty special.

  Couldn't we just travel unsolicited sometimes? Definitely not in 2010. Happy New Year.

Letter From Berkeley

In March, 1965, Calvin Trillin wrote "Letter From Berkeley" for the New Yorker (abstract), about the Free Speech Movement (F.S.M.) at the University of California, Berkeley. At that point, the end of the movement, F.S.M. was working on the trial of 800 students who had been arrested, out of 4000 who had occupied Sproul Hall. Police had carried students out "wearing blue jeans and singing hymms".

By Trillin's arrival, the students "conscientiously presented themselves, in quiet, well-dressed groups of fifty, in a make-shift courtroom", to enter their pleas. The now compliant group, having once "attacked the computer as the symbolic agent of its followers' alienation", was "borrowing the university's I.B.M. machine to keep track of all the people [including 20 lawyers] involved in its legal affairs".

Trillin's description of the protestors is pretty much how students at Berkeley are today -- organized, smart and generally compliant. Despite that, they're often depicted almost instinctively as carrying the torch of the 1960's era "rebels".

The C.I.A., the F.B.I. and the F.S.M.

The student protests in the 1960's were movements, they actually moved things and people, not only cars and police but ideas of powerful people. The federal and state governments looked at the F.S.M. as a force to be reckoned with -- a threat. The C.I.A. and the F.B.I. attempted to associate Berkeley's free speech movement with an imaginary Bay Area hotbed of Communism in order to turn citizens against 'unruly' youth.

Reagan and conservatives ran election campaigns depicting the corrosive nature of the F.S.M. and student activities at the University of California, and in one speech Reagan declared that the F.S.M. leaders should be thrown out by "the scruff of their necks". He decried the shocking occasion of "a dance" held on campus featuring acts so reprehensible that he couldn't talk about it for fear of shocking his audience. He then read a list of the horrifying acts anyway: three "rock and roll bands playing simultaneously" and movies where "persons twisted and gyrated in provocative and sensual fashion".

The future governor and president presented himself as a complete square, but keep in mind that Reagan, Greenspan and other budding neoliberals had been poring over bodice rippers like Ayn Rand's, "The Fountainhead" for years. It was the threat to political economics that perhaps perturbed them -- the "free" next to "speech", instead of next to "markets". But the ascending neoliberal movement made it about sex and drugs and rock and roll -- they successfully painted it as a culture war.

Despite conservative outrage and Reagan's condemnation, the F.S.M. succeeded. Today students have the right to set up card tables in one area of campus and give passing students information about churches and student clubs they may join, as well as various petitions they can sign. It's radical.

But although in the end the F.S.M. prevailed, the movement seems altogether impotent compared to the power of neoliberal ideas that took root during Reagan's acts as governor and president. Regardless of the relatively weak power of Free Speech Movement, UC Berkeley, the university has never really shaken its reputation as the somewhat sinister, hippy-dippy, center of California left-wing ideas.

Today's Protests, and Those 40 years Ago

When people think of UC Berkeley they think of the 60's protests. But look closely at today's protests. On the occasion of, for instance, BP's massive energy collaboration with the university in 2007, there on the steps of California Hall, 40 students held signs, gave speeches, and then spilled a little bit of organic molasses ("oil") on the steps. Forty strong, the protestors proved they meant no harm by licking molasses off the steps of California Hall. Police in riot gear, wearing shields over their faces surrounded them. A biohazards team was called in to clean up the molasses, despite the students offers to clean it up themselves.

That's the nature of the nice, if limp spirit of today's student rebellions. But people still think Berkeley as radically "left wing". They tend not to associate "Berkeley" with its conservative influences, like John Yoo, who wrote the Bush torture memos and teaches constitutional law, or the law school that defends Yoo's position in the name of "academic freedom". They ignore the power differential that makes such protests anemic.

People think of UC Berkeley and think science and politically liberal values. They tend not to think of retired law school professor Phillip E. Johnson, conservative born-again Christian, who is the father of the intelligent design movement, and who, along with Berkeley science professor Peter Duesberg, denies that the HIV virus causes of AIDS. People ignore the existence of the vibrant libertarian and student Republicans groups (the student Republican group is the largest student organization on campus), and probably don't know about the Center for the Comparative Study of Right-Wing Movements, established last year. What prevails is the cliche of a subversive, pot-smoking, Birkenstock wearing, long-haired, provocatively liberal university.

Letter From California, The Reality

Last fall, the cliche was reinforced when students took over Wheeler Hall, protesting increases to student tuition. The erosion of state support for the University is a travesty, but the students protests were very personal. Their cries were not about wars (either of them), or free speech, in fact in many cases they were not even about higher education. Some negotiators had a hard time figuring out what the students demands even were -- something about janitors jobs being reinstated? But this 21st century student uprising concerned the increased costs of higher education that would be in part coming out of their (or their parents') pockets.

It was a protest not without irony. Tours of campus routinely compare Berkeley to Stanford University, and the sense of competition is so fierce, apparently, that some Berkeley denizens will not wear any article of clothing that is maroon (Stanford's color). Stanford, a private school, is more costly than Berkeley, so now, financially at least, the comparison will be more apt. So what did the protestors want? Like the rest of America, don't 21st century protestors basically want Bergdorf Goodman quality at Walmart prices?

Not to mention that even as they they protest now, some of the students' parents no doubt voted for California Proposition 13, which gutted the state's ability to raise taxes and support things like higher education.

There was mixed tolerance for the protests on campus. Certainly some students participated, as did some faculty, like negotiator Ananya Roy, who the New Yorker recently profiled in its column "Letter From California". Some faculty and students were very sympathetic to the students, some of whom were in fact savagely batoned by police. But most students and certainly most faculty didn't protest, they were too busy with their own affairs.

Other onlookers complained about the student's behavior in Wheeler Hall, because apparently they "partied"" and "ordered pizzas". I asked one critic: "What should they be doing?", thinking about how boring it must be to sit in an administrative office building for hours on end -- I mean, even back in 1964 they had music, such as it was -- Joan Baez singing "We Shall Overcome". They should be "writing manifestos", came the answer, rather sternly.

Indeed, today's protests somehow fall short of expectations and cliches -- no manifestoes, students marching against fee increases rather than for world peace or the weighty issues of the centuries, and in the November 2009 protests, a piddly sixty-six protestors arrested, not 800, like back in the day.

Not to say certain actions can't stir up memories of students behaving very badly. Once police cleared protestors from Wheeler Hall (and not by blaring Joan Baez into the building, but with some bone breaking), a fringe group got out of hand when they marched to the home of Berkeley Chancellor Robert Birgeneau. Here's how the New Yorker wrote about this subsequent act of violence in the last paragraph of their "Letter From California":

"That night, more than forty people carrying torches marched on Birgeneau's residence. A handful of the protesters smashed the outdoor lights and threw cement planters and burning torches at the house, scattering only after the chancellor's wife, who was writing Christmas cards, woke her husband and he called the police."

Since Birgeneau is well-respected for his leadership and contributions to this and other campus problems, this action was universally reviled. The New Yorker paints a good picture, if inaccurate. A more accurate account than the New Yorker's would include the fact that only eight "protestors" were arrested at Birgeneau's house and only two of those were students, and subsequently none of them were charged. While the act was reprehensible, this wasn't quite the scary spectacle described. One professor who witnessed the event questioned the official accounts.

Concert Tickets and The Cost of a Credit

All and all, this wasn't thousands of students convening in 1964 to make speeches about free speech while standing on a police car, any more than the Wheeler protests in November at all resembled the Sproul Hall protests in the 1960's. December's protests, for the most part strictly shut down by police, culminated in a handful of misaligned adults (some in their 40's) committing random and spontaneous acts of violence against someone who is actually working very hard on behalf of higher education. It was pathetic.

But so was the New Yorker's coverage in the "Letter From California". Today's protests aren't a continuation of the Berkeley of the 60's. The facts reflect the ennui of the noughts. The 2009 protests weren't a movement, and it wouldn't impede the changes in public education or privatization. Politicians barely batted an eye. Most people favor privatization, students included, unlike in 1964 when Mario Savio spoke about "the operation of the machine -- so odious...".

The 1960's were the cusp of major social-economic change, but in 2009/2010 everything that was novel and threatening back then -- from computers, to privatization, to liquid colors moving across movie screens, is part of who we are. It's outdated to fight against privatization, whether your aged or youthful. Increased fees, increased tuition? How is that any different than higher housing costs, more expensive medical care, and $150 concert tickets?

Berkeley the University is clearly not the place it was in 60's, when the state provided over 50% of funding; today the state only provides 28% of UC Berkeley funding and that's still shrinking. Although the funding cuts have been damaging, overall, the change in Berkeley is good -- institutions need to keep up with the times. California is privatizing education system like other states such as Virginia and Michigan -- higher education is ripe to be privatized.

Of course the question remains, how will the changes alter the institution of higher education? And how will that benefit society? Moreover, can California remain an economic powerhouse, in the top ten in the world, without the commitment to education it had in the 1960's under the original Master Plan? The state is perennially burdened by a government that promises the quintessential American dream to naive citizens who demand the whole pie for nothing -- safety nets, education, comprehensive services, and low taxes. California state government is ahead of the federal government in assuring citizens that there's no conflict in citizens' wishes, how will this work out?

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.

• Transparency: A Solution for Research "Bias" or A Refuge for Secrets?: Last year we wrote about The Obesity Society's indignation, after Dr. David Allison, on behalf of a restaurant association suing New York City, submitted a legal affidavit criticizing the city's plan to require fast food restaurants to post caloric information for customers.

  To note, before Allison became an advocate for restaurants, he had worked for "the other side", publishing studies which urged government intervention to stem the obesity epidemic. Nevertheless, we thought The Obesity Society's ire somewhat ironic since Allison's CV is public and he's been very transparent about all his affiliations including his industry ones. As we noted:

  "In the 2005 NEJM paper about obesity longevity, nine authors each disclosed zero financial interests or affiliations. Dr. Allison, however, listed 150 organizational affiliations in a three page single spaced PDF, attached to the paper..."

  Apparently not too many people read the .PDF, including The Obesity Society, since the cause of their ire, Allison's consulting (against NYC's public health measures) was nothing new. In the glare of media exposure from a New York Times article and under pressure from The Obesity Society, Allison stepped down from his president-elect position. But he maintains an active career. Last week, the journal Science published a letter from Allison, who advised an "antidote" to "research bias" (Vol. 326. no. 5952, pp. 522 - 523).

  "Bias", is actually a soft label for the real problem of discerning the influence of industry funding on research or policy recommendations. Addressing the ongoing debate in Science about "bias", Allison wrote that the solution is data transparency: "When data are public, no one need take analyses on faith". Allison is attentive to the possibility that industry payment could color expert opinions, but apparently considers himself above the fray: "'I was chosen" - he said last year, "I think of it like a calling. It is a special and sacred profession. Our sacred duty is truth.'"

  The problem -- aside from the sense of "sacred duties" -- is his suggestion that transparency in our data prolific world will assure scrutiny or integrity. Raw data is made into policy by experts, but unanalyzed raw data is fairly meaningless, transparent or not. Experts don't have time. The Obesity Society demonstrated this last year in their apparent oblivion to the record of their president-elect and their surprise when Allison challenged New York City's labeling laws. His resume was very accessible and his conflict of interest statements clearly showed him to be the hired gun he was (for the truth, of course). But the ~2000 experts in the Society who had voted him president only noticed his conflict of interest once it became public concern via the New York Times.

  The error of assuming that transparency is adequately informative is also shown in a recent study of those same New York City labeling laws, now in effect. On behalf of the restaurant association, Allison had insisted that the labeling laws would backfire and cause customers to "gorge themselves". But a recent study showed that the calorie information may not change customers' food habits at all. Not only won't they gorge, they might not cut back on their intake either.

  Transparency for nothing? Beyond Dr. Allison and obesity, this isn't good news for the growing trend in government -- now enthusiastically endorsed by Allison -- to push transparency in lieu of regulatory policy. ¹

¹ The study was published in the October issue of the journal Health Affairs, and I couldn't access the full text. But since this is one of the first studies to analyze this policy, the authors do caution that it's too soon to jump to conclusions, similar studies will shed further light on the behavior associated with the new policy.

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, all about 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, they asked, incredulous? 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 answer 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. More eyebrows raised in the science community.

It turns out that Lynn Margulis "communicated" Williamson's paper to PNAS, a method of publishing offered to Academy members that differs from "submissions". Via this method, members can suggest for publication papers by non-members, along with reviewers selected by the member. PNAS recently announced it will eliminate this "Track I" publishing in 2010. In the meantime PNAS editors will not publish Williamson's paper in print edition pending further discussion with Margulis about the review process.

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. And really, 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 (remember "behavior" from the quote above?):

"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."

"All I ask". 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?

------------------------

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

Update: 9/11/09: Cass Sunstein, subject of the note below, was nominated to the OIRA post. The list of Yeas and Nays from yesterday's vote is here.

• Scientist says Nerds are Happy: The New York Times Sunday op-ed section featured advice from educators to students. Nancy Hopkins wrote:

  "Passion is the mysterious force behind nearly every scientific breakthrough. Perhaps it's because without it you might never be able to tolerate the huge amount of hard work and frustration that scientific discovery entails...For the next four years you will get to poke around the corridors of your college, listen to any lecture you choose, work in a lab...You may be the person who constructs a new biological species, or figures out how to stop global warming, or aging. Maybe you'll discover life on another planet..." More here.

• China Surges Ahead With Solar: Inner Mongolia in China will be the location of the world's largest solar facility. China is working with the US company First Solar. The new solar farm is due for completion in 5 years and will generate 2 gigawatts of energy by 2019. Plans are also in the works in India and the US for other giant solar facilities.

• Awesome Hubble Photos: NASA upgraded the 19 year old Hubble telescope this summer and released photos that showed impressive improvements due to the upgrade. Compare the Omega Centauri starfield from 2002 to a recent one taken after the scientists completed the Hubble renovations. The photo to the left is a from the planetary nebula NGC 6302 -- a dying star in the middle -- also known as the "Butterfly Nebula".

• Phoenicopterus ruber falsus: Madison, Wisconsin has named the pink plastic flamingo the city's bird, in honor of a college prank from 30 years ago which Alderwoman Marsha Rummel said "signifies something that makes us a very special place" and "captured in our imaginations forever." Why worry about endangered species when there's plastic so real politicians lose their minds?

• Constitution Day: Federal law now requires that schools receiving federal funding offer an education day to celebrate the signing of the Constitution. September 17th, which used to be called Citizenship Day, was renamed Constitution Day and the education requirement added to the 2004 Omnibus Spending Act by Senator Robert Byrd (D-WV). Wikipedia suggests that the holiday began as I Am American Day, a May holiday designated by Congress in 1940 after being championed by newspaper tycoon William Randolph Hearst. Now that newspapers are dying and some Americans are going cuckoo, it seems like a fine time to reinvigorate the holiday. It's a shame that some hosts on certain television networks aren't required to take a refresher course.

• Nudge in Action Despite Opposition to Sunstein: We previously wrote about the preposterous protest of Cass Sunstein's nomination not because of his cost-benefit analysis views (.pdf), but because hunting enthusiasts fear he's too enthusiastic about animal rights. They continue to foam at the mouth oppose his nomination for the same ill-conceived reasons we noted before. But yesterday, despite efforts of Glenn Beck to derail the Obama administration and move the "conversation" to the right towards McCarthyism, Democrats pushed Sunstein's nomination forward.

  Even as opposition foot-dragging continues (an anonymous third Senator has apparently placed another hold on the nomination), Sunstein isn't languishing idle. With more two books published since his nomination, his influence can also be seen in Obama administration policy changes such as the retirement savings plan changes, announced by the President on Labor Day.

• Media Wars: A number of "11th-hour filers" are challenging the Google book deal, including Germany and France. The head of the US copyright office expressed reservations. At a recent Google Books conference, James Love said that Google benefits from people's perception that if Google makes it it must be free and good, and if it were called (I paraphrase) AnyOtherCorporation Book Deal, it would have never progressed this far. People aren't consoled by the Google image as the lovable, do no evil, benevolent adopter of just a small number of orphan books. But was copyright really meant to extend life plus 70 years? In the interest of the public, hopefully they'll settle on the "right" book deal.

• Clues to Potato Blight: Scientists collaborating from 36 institutions across the globe completed sequencing the water mold responsible for late blight and the Irish Great Famine of 1840's-1850's. Phytophthora infestans consumes the plant's leaves and tubers and just as it wiped out potato crops in the 19th century, today the mold causes ~$6.7 billion dollars of damage annually to tomatoes, potatoes and other crops.

  Researchers identified genes that may help the organism evade scientists fight against the costly blight, and also found that about 75% of the genome contained repeat sections of DNA called transposons. Transposons duplicate and jump from one section of the genome to another, where they can disrupt genes and introduce mutations. This could allow the organism to adapt and evolve more quickly and continue to cause havoc in potato crops despite scientists' best efforts to engineer blight resistant crops.

  The part of the genome that contains the transposons also contains genes that code proteins responsible for virulence. Researchers theorize that the instability of this greatly expanded and rapidly changing part of the genome gives P. infestans its lethal power. The sequence data will help scientists understand the mold in order to prevent the destructive blight. Nature published the report: 9 September 2009 | doi:10.1038/nature08358.

Doctors Fret On Behalf Pharma: Pro Bono For What? No Free Lunch?

Vermont and Massachusetts recently passed strict conflict of interest laws that require certain drug and medical-device manufacturers to inform state health officials of gifts made to doctors. At least half a dozen states have similar laws. Pharmaceutical companies spent $2.93 million on marketing in Vermont in 12 months. Payments and gifts to some Vermont psychiatrists totaled more than $100 thousand dollars a year. Nationwide, pharmaceutical companies spend between $20 billion and "$57 billion per year" on marketing per year.

The majority of Americans approve of the measures. In a survey of the public opinion, 64% of Americans think it's important to know their physician's financial ties to pharmaceutical companies and 68% support legislation requiring pharmaceutical companies to disclose gifts to doctors according to the results of a Prescription Project survey.

The regulations aim to bar some gifts from industry to doctors and researchers and more closely monitor which doctors and researchers pharma pays. The Vermont Medical Society supported the new regulations, noting that trust is necessary to build doctor patient relationships. The president of the physicians group commented: "Gifts from the pharmaceutical industry can create at least the appearance of conflict of interest, so in our minds that has a negative impact on our relationship with patients."

Just Don't Say "Corrupt"

However, opposing the conflict of interest regulation is the Association of Clinical Researchers and Educators (ACRE), a group of 100 physicians led by Harvard hematologist Thomas Stossel.¹ ACRE acknowledges that some physicians or researchers may take too much money from industry but argues that regulation of conflict of interest is not the answer. ACRE says that regulation will encroach on the free give and take between industry, physicians, and researchers that has yielded great research and medical progress. Nature reported frustration on the part of physicians who attended ACRE's July 23rd meeting:

"One attendee complained that he couldn't buy a $12 hamburger for a consultant who had agreed to speak for free. 'They're giving us a pro bono service and we're going to ask them to pay for their own lunch?' he lamented." ²

Really? Should free consulting from a pharma representative or consultant raise feelings of obligatory angst in attendees? If a pro-bono talk motivates such laments, what guilt do free samples provoke? What about a vacation trip? Will a $12 dollar hamburger fulfill the obligation? Or perhaps just a few prescriptions orders for patients?

ACRE's Stossel objects to the gift ban because it suggests that physicians have "'have a corruption problem'". In Marcia Angell's January, 2009 NY Review of Books article, "Drug Companies & Doctors: A Story of Corruption", the author reviewed three books on pharmaceutical corruption.^3,4 The books were published after the congressional inquiry into drug company payments that uncovered quantities of drug money flowing into psychiatry doctors' pockets.

A Senate investigation led by Chuck Grassley (R-IA) (pdf!), uncovered payments to three Harvard psychiatrists who received over a million dollars each over a several year period. One psychiatrist at Stanford and one at Emory also received payments of over a million dollars.

A study in 2007 by Columbia University researchers showed that doctors don't feel that their personal integrity is compromised by taking gifts or money from pharmaceutical companies. But they do feel that other doctors would be compromised by such gifts. Chimonas et al concluded: "Our findings suggest that voluntary guidelines, like those proposed by most major medical societies, are inadequate. It may be that only the prohibition of physician-detailer interactions will be effective."

Marcia Angell points out that although the cases highlighted by the media tend to be more extreme, most physicians (94%) do have some relationship with drug companies. And certainly many of these payments are inconsequential and/or don't sway research or influence prescribing patterns. But clearly many do, or else pharmaceutical companies wouldn't be spending tens of billions of dollars on doctors and research.

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¹ The group is now supported by membership fees, according to Nature and the organization website. However in 2008, according to a note accompanying a British Medical Journal article, Stossel was on the boards of several pharmaceuticals, and received fees for speaking to corporations and other organizations about conflict of interest.

² Willard, Cassandra, "Physicians fight back against disclosure rules" Nature 460, 556-557 (2009) | doi:10.1038/460556b. Also published in Nature Medicine.

³ The NY Review of Books received a letter from the legal representative of one of the doctors covered in her article, complaining about the use of the word "corruption" in the headline and text of Angell's review, because it inferred the doctor had been engaged in "bribery" or "similar dishonest dealings". The weekly disagreed.

⁴ The three books are: Side Effects: A Prosecutor, a Whistleblower, and a Bestselling Antidepressant on Trial by Alison Bass (Algonquin Books of Chapel Hill); Our Daily Meds: How the Pharmaceutical Companies Transformed Themselves into Slick Marketing Machines and Hooked the Nation on Prescription Drugs by Melody Petersen (Sarah Crichton/Farrar, Straus and Giroux); and Shyness: How Normal Behavior Became a Sickness by Christopher Lane, (Yale University Press).