October 2008 Archives

Ghoulish Goulash

Happy Halloween. Over 23 million people have voted in early elections across the United States. People are now driven to distraction by the election, even Acronym Required at times. But we're also distracted by science topics.

  • Decidin'

    For instance take the cartoon that accompanied an article in last week's New Yorker. It was a drawing of a TinTin looking character, eyes wide, eyebrows arched, finger to his pursed lips, puzzling over two choices on a wall chart. On the left I saw a rooster. On the right I saw a Drosophila.

    The accompanying article "Undecided", by David Sedaris, discussed the baffling group of supposedly undecided voters:

    "I look at these people and can't quite believe that they exist. Are they professional actors? I wonder. Or are they simply laymen who want a lot of attention?"

    He placed the dilemma in terms of airline food:

    "The flight attendant comes down the aisle with her food cart and, eventually, parks it beside my seat. "Can I interest you in the chicken?" she asks. "Or would you prefer the platter of shit with bits of broken glass in it?"

    It still took me a while to figure out that the cartoon character was standing in a voting booth. The choice was not a silly Rooster or Drosophila but "chicken" or "shit with bits of broken glass" in it. The Drosophila wasn't that at all, just a giant red-eyed other type of more fuzzy fly, standing on a small brown mound that represented Sedaris' subject, "shit". In an effort to explain my confusion, I'll just say I was writing about C. elegans at the time, another model organism, so perhaps that's why I saw Drosophila melanogaster.

  • Buggin'

    It was a Drosophila kind of week. Scientists and many knowledgeable Americans (and French) were angry that V.P. candidate Sarah Palin dissed fruit fly research as waste. Of course she wasn't talking about Drosophila melanogaster, either, but olive fruit flies in a completely different taxonomic family. But the outrage over her perfunctory dismissal of California agricultural research is warranted.

  • Poisonin'

    Updating our melamine coverage from previous posts, this week brought China and Hong Kong melamine contaminated eggs, thus widening the scandal. The culprit may be melamine laced grain which has spread the toxic chemical throughout the food chain. China is now culling chickens. The past year has seen the demise -- through culling and dumping -- of some major protein sources, pigs, milk, eggs, chicken -- hopefully there's some unadulterated beans and soy and rice around.

  • Labelin'

    India passed the Prevention of Food Adulteration (Fifth Amendment) Rules, 2008, which will require food product labels starting in March, 2009. Fruit products cannot be labeled as such unless they contain fruit, etc. Cardiac conscious customers will now be able to identify transfats such as "vansapati", hydrogenated vegetable cooking oil which is commonly found in packaged food.

  • Trick-or-Treatin'
    The cost of drugs to treat type 2 diabetes doubled between 2001 and 2007, according to a report in the Archives of Internal Medicine, from $6.7 billion dollars in 2001, to $12.5 billion dollars in 2007. The higher cost is due to new drugs, which can be 10 times higher than old drugs, as well as increased numbers of patients. The number of patient visits increased from 25 million in 1994, to 36 million in 2007.

    But today's Halloween. So here's a carbohydrate chart (PDF!) from "DLife" ("Diabetes Life") For example:
    - 3 Musketeers 16 gram fun-sized bar: 12 grams
    - Gummy Bears 11 pieces: 30 grams
    - M&M's "Halloween" mini box: 10 grams
    - Tootsie Roll midgets 12: 30 grams
    - Heath Bar 1.4 oz. bar: 20 grams

  • Cravin' Palin

    One of this year's most popular costumes is a Sarah Palin costume. This would be a challenging one to pull off for three reasons. One, it's just gonna' be an icky couple of hours sitting in that particular suit. Two, do you really have her style down? Sarah Palin is hot, according to, well, everyone, which may be hard to live up to. I recently got an explanation of this relative hotness -- it's "niche hot". Therefore if she doesn't win the vice presidency maybe she'll vamp through Playboy, with a "hot" politician theme, and if not that, then she actually already has her Palin calendar awaiting your purchase.

    But she's a tricky act to follow, which brings us to your third challenge. You might be able to cackle "you betcha!" with the best of them, you might be able to wink wildly, you might be able bend the elite right wing news staff of the Weekly Standard, the National Review, The Hill, and the New York Times to your side by leading them around by the front of their pants, as a recent New Yorker article describes1.

    But do you really have her diction down? Can you remember to drop the "g" on pallin', and lyin' -- like Palin'? Maybe, but can you remember to leave the "g" on the word when necessary? Can you remember to say "cravING", as she does? As in, American's are craving that straight talk"? And Americans are craving something new and different..." You're not hearing "I'm Sarah and I'm cravin'". Americans are cravinG.

    Sure "it's genuine, not affectation", just like she's genuine in every other way, an "outsider" who didn't hire lobbyists to buff her image as Alaskan governor. I think it's a tough Halloween costume to pull off.

  • Swoopin' & Spookin'
    Merriam Webster's Word of the Day is Chiropteran:
    "Chiroptera" is the name of the order of the only mammal capable of true flight, the bat. The name is influenced by the hand-like wings of bats, which are formed from four elongated "fingers" covered by a cutaneous membrane. It is based on the Greek words for "hand," "cheir," and "wing," "pteron." "Cheir" also had a hand in the formation of the word "surgery," which is ultimately derived from the ancient word "cheirourgos," meaning "doing by hand."

    Acronym Required wrote a little about bats in "Bats, Riddles, and Viruses."

  • Mappin' not Spyin'

    The town of Molfsee, Germany, is rebelling against Google's "Street View". Google would dispatch vehicles with camera's to map the town's streets, but the 5,000 citizens have laid down the law. The company would need a special permit to photograph the city's streets, which the town politicians refuse to grant. The town's concerns about privacy are shared by state and federal privacy experts, according to Spiegel.

  • Votin'

    As for the election, some, like Larry David, are pacing and suspicious. There's been a steady stream of alarming reports about voting machines, it's no wonder that everyone's a bit on edge. On a positive note, voting turn-out so far is great. Pray; no Hope; no Work! for the most honest, cleanest result.


1 This article also contends that this one young Republican started a blog advocating Sarah Palin for Vice President, and that blog precipitated a lot of conservative enthusiasm: "In the month before Palin was picked by McCain, Brickley said, his Web site was receiving about three thousand hits a day". To put this in perspective Daily Kos gets about 2,604,779 page views a day, so if there's about 3-4 hits per page view, DKos gets about 6 million hits a day. Brickley was getting about 1000 pages a day -- not too much.

Aging: Maybe Not all Downhill and Shuffleboard?

A UCLA study published in the Neurobiology of Aging found that age related decreases in myelin correlate to decreased motor function after the age of 39. The researchers suggest that sensory and cognitive processing speeds are also effected by the loss of myelin.

That would be problematic for scientists. The age at which U.S. researchers get their first NIH grant increased from 34.3 in 1970 to 41.7 in 2004, according to a recent paper on arxiv.org by Yves Gingras et al. The authors studied 13,680 university science professors and showed that productivity rises between 28-40, rises more slowly between 41-50 and decreases until 50-55 years old. Although it's a measure with limited value, the authors counted "productivity" as published papers. For multi-author papers the study credited one paper per listed author. In short, the study found that scientists still produce papers up through retirement, publish in well respected journals, and are cited more frequently.

Neither study is earth shattering, but there's value to aging. Motor processing does slow down, but other studies have shown that with some motor function, movement accuracy improves, compensating for decreased speed. For many reasons, lab dynamics, prestige, networking, etc., older scientists may not publish more, but their quality of production (by measures by which people judge, anyway) may increase.

Books On-line

Book Search, More, Better

Google recently reached a settlement with the Author's Guild and the Association of American Publishers, which will pave the way for digitization of copyrighted books for on-line use. The authors and publishers brought suits against Google in 2005, accusing the company of copyright infringement. Google wanted to digitize books for internet perusal, but the publishers had their own opinion of that: "They keep talking about doing this because it is going to be good for the world. That has never been a principle in law. They 'do no evil' except they are stealing people's property."

Google paid $125 million to settle the suit, which will cover legal fees and fund the Book Rights Registry, to be modeled after the music industry's copyright clearing house ASCAP. Google will structure a deal to put thousands of digitized books on the web. Readers will be able to access books or buy a digitized copy and publishers and authors will get some percentage of the customer fees.

Newspapers Stop Printing

Print is steadily moving on-line. The Christian Science Monitor announced yesterday that it will soon (just about) cease printing:

"in April 2009 the daily print edition of The Christian Science Monitor will shift to a 24/7 daily Web publication. This will be combined with the launch of an attractive new weekly print publication that looks behind the headlines..."

The continued cuts to newspapers is not always seen as a good thing. Some papers aren't ready to give up their print editions (with much more lucrative advertising than on-line). Instead they cut staff. Noted one commenter:

New Jersey, a petri dish of corruption, will have to make do with 40 percent fewer reporters at The Star-Ledger, one of the few remaining cops on the beat. The Los Angeles Times, which toils under Hollywood's nose, has one movie reviewer left on staff.

As everyone knows, this won't be too good for many blogs and on-line media outlets either.

And Textbooks?

The textbook publishing industry should be next to change models and offer more open content. Congress recently passed a law that helps keep textbook prices transparent to students, professors and colleges. Six states have similar laws.

In the past couple of years the textbook and learning divisions of several publishing companies have changed hands, including Houghton Mifflin in the US to Riverdeep, Thomson Learning, Worters Kewer's educational arm, and Reed Elsevier's Harcourt Education. The companies weren't adept at changing their business strategy to meet the increasingly web savvy customer base, and alternative on-line options were increasing. Although five textbook publishers have now launched CourseSmart to offer online textbooks cheaper, it's not clear that this is a burgeoning enterprise.

In addition to the "traditional" textbook model, the Christian Science Monitor mentioned in a recent article a couple of "radical" textbook alternatives. One, Connexions (cnx.org), is a project of Rice University. Connexions offers Creative Commons licensed learning tools that are "non-linear modules" authored by independent authors and hosted on their site. The Connexions philosophy is based on their contention that the traditional textbook "system is broken." California State University has a site called Merlot, which I can't say I understand after spending, well, not very much time browsing through. There's also Wikibooks, and of course many professors simply write their own books from lecture notes.

Notes on Science when the Economy and the Election Dominate News

Once Red State - Blue State, Now Internetland - Radioland?

The news is all economy and election: Warren Buffet, accustomed to being courted by the press, software tycoons and presidential candidates flexes his muscles and asks that everyone go buy stocks. The people totally ignore him. Greenspan rears his head, a haunting apparition, moaning about 'the one thing he didn't know'...The market swoons again....

Sarah Palin goes for the rich little poor girl image...McCain supporters stage increasingly hostile and bizarre threats to Obama supporters and all the media...The liberal Internet pulls for a landslide Democrat win that I believe parts of the blogosphere could accomplish by sheer force of editorial will. The liberal-nets feature daily reports from conservatives and their sons and daughters and commentators who either disapprove or are defecting from the Republican Party (Goldwater,Schwartzenegger, Powell, Buckley, Brooks, Adelman...) If Huff Po ran out of Republican offspring essays to feature I'm sure campaign enthusiasm would give editorial space to increase the pixel size of their headlines from 70-80 to 700.

Bloggers predict that the internet is bringing an end to the era of Rove style politics...Karl Rove writes a letter to the editor of Harper's to point out that Grover Norquist, not him, said: "We can go to students at Harvard and say, 'There is now a secure retirement plan for Republican operatives'"

The media talks about back-stabbing and Republican Hill staff's curriculum vitae reportedly flying out to corporations...Nobody's too happy that Imelda Palin spends a lot on make-up in addition to shoes. (Still, I think it's way to soon too start cheerfully humming 'We never promised you a rose garden')

Meanwhile in science news:

The Oddities in Commodities

  • Chinese Milk Scandal: We last reported on melamine in milk made in China when the tainted milk had killed three kids and sickened a couple of thousand. Now 5000 are hospitalized in China, and products across the world are found to be toxic with melamine. Along with the "rabbit hole" of the economic despair and the "rabbit hole" of the McCain's campaign strategy, there's the imported melamine tainted "White Rabbit" candies found on candy shelves throughout the world. The United Nations noted this week that the Chinese government's oversight system needs "urgent review and revision".

  • Scientists are Eager to Explore your Genome: Last month Sergey Brin advertised on his blog that his genome indicated an increased risk of Parkinson's. This week George Church announced the first 10 volunteers had signed up for the Personal Genome Project and release parts of their genetic information and medical records to Harvard investigator. Church is "hoping to offset ethical concerns" that the data may breed discrimination in jobs, health insurance and how volunteers and their families are perceived."

    Before you sign up, the "Personal Genome Project" wants you to know a couple of things. On the positive side they say you're doing good for "society" and your "donation" (if you will) might allow you to indulge in a little "self-curiosity". One possible negative they mention is that someone could "claim statistical evidence that could affect employment or insurance or the ability to obtain financial services for the participant."

  • Open Access: In "Publish and be Wrong", earlier this month, the Economist pointed to a PLoS Medicine article that argues the science publishing model is seriously flawed. According to he authors, there's a false scarcity of publication slots at top science journals, and the criteria for publication doesn't assure that quality papers get published.

    The weight of the article rests with its title: "Why Current Publication Practices May Distort Science". Along with some familiar points, the writers offer shaky economic comparisons, vague criticism and recommendations. In one line of argumentation, the authors rework the idea that journals should include more negative results and fewer positive results. However its hard to see how publishing negative results (along with analysis, peer review, time) would help solve the problem of too much data and too few publication outlets, which is their primary concern. Peer review is so flawed they say, let's allow the more unprepared, less science literate readers, as opposed to scientists familiar with the research, sort through the data. Make sense?

    The team writes that many top journal publication results turn out to be flawed, and bases this on previous research by lead author John Ioannidis, an epidemiologist at Ioannina School of Medicine, Greece, who in 2005 wrote "Why Most Published Research Findings Are False". I didn't pick through the 2005 study, but assuming his assertions are true -- for the sake of discussion -- lots of published results get overturned. Therefore my take is lots of research is both "negative" and published. So why isn't that "negative" research coveted as much by the authors of the current PLoS Medicine as the unpublished "negative" research they say are so important?

    Ioannidis et al assert that "scientific information is a commodity" and say there's a "moral imperative" to consider how its judged and disseminated. Maybe so, but if that then why separate the publishing from the foundation that its built upon (academia, tenure, granting)? And to be consistent, can we talk about drugs as commodities? And the moral imperative for generics?

    There's more to say, but in short, from my view, some of the most spurious research emanates from public relations departments of universities, or lobbyists in the form of press releases. Some of the most flawed research (sometimes what seems like reworked press releases) shows up in esteemed media outlets (for instance FT and the related Economist). And if I were a certain type of policy advocate who wanted to push policy under the guise of science I'd welcome the chance to elevate my editorial -- I'd pay to publish my "research" in PLoS Medicine along with all the genuine great research, and if I got rejected there than I'd settle for PLoS One, with all its real research. Upon publication I'd mail out press releases touting my PLoS research.

    Sure we have far from a perfect system, but open access has its pitfalls too.

    Along with Ioannidis, the collaborating authors are Neal Young, an MD at the NIH, and Omar Al-Ubaydli, an assistant professor of economics at George Mason University and a research fellow at the Mercatus Center.

Seen In Space

  • India to the moon: India is aiming for the nation's first lunar exploration by putting an unmanned spacecraft, Chandrayaan1, into orbit for a 2 year mission on the moon.

  • NF3: The journal nature Nature reports that scientists found much higher levels of nitrogen trifluoride 3 from plasma TV's in the atmosphere then they had predicted.3 replaced perfluorcarbons and is "12,000-20,000 times more efficient at trapping heat than carbon dioxide". A UC Irvine scientist correctly predicted earlier this year that the emission rate of the chemical was more that previously assumed by scientists. An alternative technology to the plasma screens is LCD screens.

Picking Teams

  • The American Bar Association lists lawyers who might be chosen by Obama or McCain to serve their administrations. For Obama they list Robert Sussman for the EPA, a former Clinton administration deputy administrator. They name Cass Sunstein as possible White House Policy Advisor (a libertarian, but "no idealogue" writes ABA). Sunstein has written extensively on various topics; see for instance "The Paralyzing Principle" about the precautionary principle in the December, 2002-2003 issue of Cato's journal Regulation. ABA also picked Massachusetts governor Deval Patrick as possible attorney general choice.

The Green Fluorescent Protein Men

The Prize

The background story of almost every Nobel Prize awarded includes the biographies of one or more people who did lots of research but didn't get the prize. The New York Times published an article today about Douglas Prasher, who first cloned and sequenced Green Fluorescent Protein (GFP).

Prasher didn't share the Nobel Prize awarded to Osamu Shimomura, Martin Chalfie, Roger Y. Tsien, who worked to make GFP into the versatile tag that scientists use to visualize the inner workings of live cells and organisms. The GFP Chemistry Nobel Prize committee could only award three of the hundreds of people who developed GFP to its current state of usefulness. Prasher didn't pursue the scientific process of making GFP useful, and acknowledges that the winners deserved the prize over him, telling the Times reporter: "They worked their butts off over their entire lives for science, and I haven't." But his part is an interesting and keen choice for the New York Times human interest story, because science stories focus most often on the "winners", and in fact every major advance in science involves whole teams of research techs, students, contributors, most of whom don't share credit or fame, in fact some don't even eek a living out of it. The Times report explores the funding Prasher didn't get, as well as his difficulties finding employment and depression.

The paper doesn't go into the broader picture of the GFP protein discovery, which is interesting in itself and also helps one understand the process of scientific discovery.

The Long History Behind the Making of Useful GFP

The history of GFP research in the past 50 years traces the history of biology itself over the last half a century. In 1961, Osamu Shimomura discovered the protein while purifying and characterizing aequorin. Shimomura came to the US from Japan, when as a teenager, he was only 12 kilometers from the Nagasaki bomb explosion. After piecing together his education and life, he worked in a lab in Japan isolating and characterizing another protein, thereby earning his Ph.D. Shimomura was recruited to Princeton by Frank Johnson, co-author of the 1962 paper that first mentioned GFP. 1 Their paper gave a nod to the history of bioluminescence research to that point:

"In experiments that have become classic in bioluminescence, Dubois (1885, 1887), first prepared from a luminous elaterid, Pyrophorus, and a luminous clam, Pholas, respectively, crude extracts containing a substrate, luciferin, and an enzyme, luciferase, which luminesced on mixing in aqueous solution containing dissolved oxygen."

The 1962 paper gives the reader a view into some of the techniques used by cell biologists and biochemists at that time. It also give insight into the sort of fortitude of successful researchers. It's perspective that's useful to understanding how science research works.

Thousands and Thousands of Jellyfish

Shimomura collected tens or hundreds of thousands (the accounts vary) of the Aequoria jellyfish to learn about GFP and aequorin. Non-scientists probably can't imagine the tedium of collecting tens of thousands of jellyfish. And that's only the start. How would you figure out how to extract of luminescent parts of the jellyfish "squeezate" without destroying it? How would you determine a method for purifying a protein via repeated chromatography? How many trial and errors would finally lead to the chemical conditions in which a protein glows and at what wavelength? Scientists had to work through many questions before making GFP useful.

In 1962, the GFP protein find was incidental to his aequorin study. The authors only mentioned it in footnote number three:

"A protein giving solutions that look slightly greenish in sunlight though only yellowish under tungsten lights, and exhibiting a very bright, greenish fluorescence in the ultraviolet of Mineralite has also been isolated from squeezates. No indications of a luminescent reaction of this substance could be detected."

In later work Shimomura et al went on to determine the emission spectrum of GFP and learned that the protein absorbs light in the blue spectrum emitted in Aequorea victoria by the calcium activated aequorin, that is, it exists because of aequorin. Then they found that it emits its own fluorescent green light. Over the next few decades, many other scientists advanced the work, as Roger Tsien wrote in review paper of the GFP in 1999:2

"Morin & Hastings found the same color shift in the related coelenterates...and were the first to suggest radiationless energy transfer as the mechanism for exciting coelenterate GFPs in vivo. Morise et al purified and crystallized GFP, measured its absorbance spectrum and fluorescence quantum yield, and showed that aequorin could efficiently transfer its luminescence energy to GFP when the two were coadsorbed onto a cationic support. Prendergast & Mann obtained the first clear estimate for the monomer molecular weight. Shimomura proteolyzed denatured GFP, analyzed the peptide that retained visible absorbance, and correctly proposed that the chromophore is a 4-(p-hydroxybenzylidene)imidazolidin-5-one attached to the peptide backbone through the 1- and 2-positions of the ring...The crucial breakthroughs came with the cloning of the gene by Prasher et al and the demonstrations by Chalfie et al and Inouye & Tsuji that expression of the gene in other organisms creates fluorescence."

Traditions of giving credit in papers varies widely across labs, but in general the more generous inclination to list all contributing authors on a paper runs counter to that you might see at the Academy Awards, where winners give thanks a whole list of people including their mothers, wives and extended families. Behind each of the papers noted by Tsien was a who team of scientists, advisors, and I'm sure familial support that went unmentioned.

Rainbows of Fluorescent Proteins

Prasher's cloning and sequencing contribution defined GFP research. Sequencing in the late 1980's was laborious, much more so than it is today, where the most tedious parts of it were automated. Prasher spent years accomplishing his research, but then didn't get the funding to take the work forward from there. As Tsien and Chalkie acknowledged, their work depended on his, and Prasher passed his results on to Chalfie and Tsien and moved to another lab. In the light of the Nobel prize, Prasher's current job as a driver seems like a dreary "human interest" tale typical of the New York Times or NPR.

But this is actually typical for both "successful" and "unsuccessful" scientists. Progress moves in fits and starts -- fits and starts of research progress, of funding, and of luck, layered with varying dispositions of the people who read the grants, support the researchers, and whose labs the funding ends up in. Science might have more than it's share of unrewarded contributors.

Of the three prize winners, Chalfie lab constructed GFP to be used as a reporter protein in C. elegans, a transparent roundworm used as a model organism for research. C. elegans were put to use as a model organism in 1974, long after the discovery of GFP. Because the worms are transparent, Chalfie saw the potential to use GFP in genetic experiments, and to use it in place of other reporters like beta-lactamase which was used extensively at the time. Chalfie first noted his positive result in the October 1993 edition of the humble Worm Breeder's Gazette and went on to publish the research in Science.

In his 1998 review of GFP protein Tsien wrote:

"Unfortunately, Aequorea GFP genes are the only GFP genes that have been cloned... Painstaking research like that undertaken by the pioneers of Aequorea and Renilla GFP would be needed before cloning efforts could begin. It is unclear whether any investigators or granting agencies are still patient enough to undertake and fund such long-term groundwork."

(A little understandable lobbying for continued funding there.)

Rewarding, But Only One Award

While many scientists worked on GFP, many of the same scientist would have imagined its current utility. GFP was became important as technology changed the nature of science research, as the questions that scientists asked changed over time, and as successive bench developments proved the protein's potential.

Tsien's lab wrote another review of the protein in 2002, and by that time at least 30 other fluorescent proteins had been cloned and sequenced, thanks to continued funding and increased evidence of their utility. High throughput methods of sequencing and cloning accelerated work and allowed faster identification than in Prasher's Wood's Hole days. In 2005 Tsien wrote another review advising researchers how to choose the most appropriate fluorescent proteins among all that were available. Today, Martin Chalfie has said, uses of fluorescing proteins are only limited to scientists imaginations of what they want to do.


1Osamu Shimomura, Frank Johnson, and Yo Saiga."Extraction, Purification and Properties of Aequorin, a Bioluminescent Protein from the Luminous Hydromedusan, Aequorea'", Journal of Cellular and Comparative Physiology October, 1962

2 Tsien, R. "Green Fluorescent Protein" Annual Review of Biochemistry Vol. 67: 509-544 July 1998.

3 Tsien, R. "A guide to choosing fluorescent proteins Nature Methods" 906 Vol. 2 No. 12, 905 - 909 (2005)

Notes on Peripheral News

Barack Obama and John McCain square off for their third debate. Sarah Palin draws predominantly males at "dude rallies". Obama surges ahead, but people are a little nervous, nervous about another GOP October surprise that's not an unlicensed plumber with a chip on his shoulder who doesn't pay all his taxes, a surprise that's not voter fraud accusations drummed up by the DOJ. On and on it goes. Here's news that's not about the election campaign.

  • US Department of Justice eases up on Ranbaxy:

    A couple of weeks ago the FDA banned 31 Ranbaxy drugs imported by the Indian company after an unfavorable inspection. The Department of Justice became involved, and last time we reported, Ranbaxy had just hired Rudolph Giuliani to help them appeal to the regulators. This week the Department of Justice has decided not to pursue legal action against the company, causing Ranbaxy's shares to increase by 10%. The New Delhi Business Week reports that India's commerce department and chemicals ministry are saying the curbs weren't justified but the work of US drug lobbies. Typical international politics?

  • Greening Your Lawn in Global Warming:

    In the US, many cities and towns have responded to global warming and water shortages by instituting voluntary water bans, especially on lawn watering. But this doesn't please everyone. Realtors chide people for not keeping their lawns watered, green, sellable. Global warming be damned. According to My Fox Tampa Bay, the man jailed for not keeping his sod attractive enough now faces court charges and fines, although he's out of jail. A home association in Florida had the man jailed because he didn't resod his lawn according to their specifications.

    The man, distracted from sod-care when his family was beset by hard times, spent his punishment time at the correction facility called Land O' Lakes (LOL) [this blog author adds the acronym, although its one I already intensely disliked]. The jail's homepage features a picture of prisoners sporting black and white striped prison-wear, bent over cultivating hydroponic lettuce. As LOL puts it: "This program joins the inmate garden and the aquaculture program, all designed to both reduce taxpayer's costs of funding the jail and to teach marketable skills to the inmates." There you go. Marketable skills to keep you eating in LOL and on the right correct side of your homeowners' association outside of jail.

    On the bright side, as with every problem faced by man LOL;) -- there's a promising technical alternative to back-breaking sod cultivation. In this case, LOL, a company that spray paints dead lawns green. Their business niche is foreclosed homes. LOL.

  • Economics Nobel Laureate:

    Paul Krugman won the Nobel Prize in Economics for his "analysis of trade patterns and location of economic activity". In first year economics or political economics class most students learn the benefits of trade from comparative advantage. If one country sells bicycles, and the other cars, each will benefit from trade even if it intuitively seems like the car producing company could easily whip out a couple of bicycles. Students learn the simple math that proves this. However in real life sometimes countries with similar goods tend to trade a lot with each other, so one country that makes Volvos will trade a lot with one that makes Audis. Europe and the US trade extensively. Krugman's model from 20 years ago refined trade theory to explain why this apparent disparity occurs. He showed that there are economies of scale in industries that will make one city or country the best source of a particular specialized product and that these areas with similar capital and labor resources will preferentially trade. He extended this theory to explain how certain cities will become geographic centers of growth.

    Krugman's name didn't appear on the lists economist betting pools set up to predict the winner, but after all, leading economists sometimes make bad predictions. Greg Mankiw, for instance, detailed in Fortune, November 13, 2000 how Bush is a Leader The Economy Can Trust".

    Some reporters and economists took exception to Krugman's award in light of his vocal criticism on his "liberal" blog and newspaper column. However some people miss that Krugman's economics practice and philosophy are quite "liberal" in the free trade - open market sense. Some commentators would like to see him change his work balance. For instance the Financial Times wrote last week:

    "It is not too late for Paul Krugman to return to what he does best: explaining how the economy works, why it matters, and what wrong-headed policies can do to it. In fact, that change may soon come. If so, it will not be because of the Nobel prize, but because the Republicans no longer hold the White House."

    But, but, but....isn't that what Professor Krugman is doing?

Joe the Scientist Takes His Hits

Science and Math by Armies of Uncertified Teachers, My Friends

I would have liked to see more science and technology issues discussed at the presidential debates, things like funding, education, and public policy. However, as we all know, the debates are not aimed at scientists, they're aimed at plumbers.1 So Acronym Required had low expectations for meaningful science discussions in the debates and rightly so. In the first two debates, even the word "science" got fleeting mention. It was inevitably paired with the words "research" or "scientists", or "important". Obama thrilled us because he said "science" three times in the second debate.

Republican John McCain also threw out a couple science key words, and managed to appeal to us as well as the science haters in his base. He trashed "bear research" as we previously discussed here, and he went on about the money wasted on "an overhead projector at a planetarium in Chicago, Illinois" -- not just in one debate, but in two. "My friends, do we need to spend that kind of money?", he repeated Wednesday night, despite the constellation of criticism from scientists who already disproved his planetarium misrepresentations in the previous debate -- here, and here and here and elsewhere.

The word "science" got another incidental airing last night when Bob Schieffer posed this question:

"The U.S. spends more per capita than any other country on education. Yet, by every international measurement, in math and science competence, from kindergarten through the 12th grade, we trail most of the countries of the world. The implications of this are clearly obvious. Some even say it poses a threat to our national security. Do you feel that way and what do you intend to do about it?

Obama noted: "I think it's going to be critically important for us to recruit a generation of new teachers, an army of new teachers, especially in math and science...

And Have I a Job for You....

Continued Barack Obama:

"I meet young people all across the country who either have decided not to go to college or if they're going to college, they are taking on $20,000, $30,000, $50,000, $60,000 worth of debt, and it's very difficult for them to go into some fields, like basic research in science, for example, thinking to themselves that they're going to have a mortgage before they even buy a house..."

Times are tough if you're a scientist trying to find a job, or if you're trying to fund your lab. To Obama's point, if you scan available research jobs the pay offered often looks like a misprint. Here's one recent job from theChronicle of Higher Education:

"Chief Architect of the Genome Commons: Lead design, engineering, and deployment of the Genome Commons and Navigator. Develop and articulate a vision for using personal genomes to enhance human wellbeing."


  • Outstanding software architecture and development skills; proven ability to independently carry out a complex software engineering project.
  • Understanding of human genetics.
  • Commitment to open access and open source development.
  • Savvy to medical, legal, and sociological influences in this project. Exceptional communication skills.
  • Keen scientific acumen, intense technical ability, and broad social awareness.
  • M.D. or Ph.D. in biological sciences highly desirable.
  • Appointment: 1 year, renewal contingent on performance and funding.

Range: $48,372-$55,464."

Perhaps if your parents paid your tuition or subsidized your expenses this would be tenable position. Otherwise, despite college presidents who implore graduates to follow their bliss -- no doubt irritating endowment fund managers -- why not consulting or banking? Don't even start about "wishlists" of hiring criteria. It's basically a postdoc job at UC Berkeley for that person who's an MD, a research scientist, an accomplished software architect, and an "intense" techie, but paradoxically, who is also socially aware, astute about legal and sociological issues, and an excellent communicator. Someone with all those incredible accomplishments will no doubt sign on to work as a developer/lab-rat for half the money that either an MD, an accomplished developer, communicator, or a technical architect anywhere in the Bay Area could earn.

If you are this person, the MD/developer/communicator god, the top end salary for this position is $55,000. Minus $10,000 for federal tax and $3,000 for state taxes, gives you $42,000 to live on in one of the most expensive areas of the country. Sales tax is about 8-9%, health insurance will set you back more than you think, and the balance you can use to cover your dependents, car, gas, food, and housing, movies, books, etc. Then, once you move here you should be prepared to be up and packing at the end of a year.

Should you be so lucky to get a grant renewal, a recent search of Berkeley houses on MDLS gives you a better idea of how far that $2900 a month take-home will go. A very modest 1,170 square foot house in a very "modest" area of Berkeley is priced at $589,000; a 1,451 square foot house is priced at $769,000, and a 1,583 square foot house is $899,000. You get the drift -- bungalows on tiny lots in a temperate climate. The $589,000 house, which may need some work from the looks of it, can be had at a fixed rate 6.25% 30 year loan that will require a monthly payment of over $3600 per month. So you'll be renting.

Obama voices an understanding of the difficulty of these difficulties when he says: "I've proposed a $4,000 tuition credit, every student, every year..."

Plumbers Get Lots of Appreciation....

McCain answered Schieffer's question on math and science education like this:

"Well, it's the civil rights issue of the 21st century...There's no doubt that we have achieved equal access to schools in America after a long and difficult and terrible struggle. We need to encourage programs such as...Troops to Teachers where people, after having served in the military, can go right to teaching and not have to take these examinations which -- or have the certification...

As far as college education is concerned, we need to make those student loans available."

McCain continued his concise, to the point answer:

"I'm sure you're aware, Senator Obama, of the program in the Washington, D.C., school system where vouchers are provided...That was vouchers. That was voucher, Senator Obama. And I'm frankly surprised you didn't pay more attention to that example...3

And more: "town hall meeting after town hall meeting, parents come with kids, children -- precious children who have autism. Sarah Palin knows about that better than most. And we'll find and we'll spend the money, research, to find the cause of autism."3

Plumbers make $250,000 a year? We should all be plumbers.


1 And about that plumber and the "spread the wealth around" remark. It wasn't Obama's best moment -- although, really, how much campaigning can one do and still keep standing? If it was a conspiracy, they were brilliant about making Obama say those words. Leave it to Joe the plumber and Fox News cherry-pick the whole 5 minute Obama response for that one phrase.

I do admire the self reliance of those who don't want to pay taxes, who blithely scoff at the need of policemen, fire stations and social security -- who complain mightily about taxes and government, but are first to yell when public spending cuts effect them. But how many miles does Joe drive everyday on the job, house to house to house via Ohio's deteriorating roads? Has he ever tested his truck axles out on a road that's really in disrepair? What about Ohio's building booms, supplemented with state funded roads, water and sewer -- new developments and houses that in turn assure plumbers business?

2 Obama has paid attention to vouchers I'm sure. The book "Nudge", which includes a chapter on vouchers, was written by Cass Sunstein, an advocate of "paternal libertarianism" who is an advisor to Obama. The book illustrates the gist of "paternal libertarianism" by explaining that cafeterias can position carrots in a more conspicuous place than pizza to encourage healthy eating. It uses this innocuous example to "nudge" you to its conclusions that this paternalism would be a good for bringing government public policy to fruition -- healthcare, education, and retirement benefits. The Freakonomics blog explains it like this "it is a lot easier to trick them into doing what you want than to try to educate them or incentivize them to change their behavior. There are many ways to trick people, but one of the easiest is simply by giving thought to the way choices are arrayed to them, or what they call "choice architecture." Like it? The Nudge authors would like the government to entice people to accept vouchers, heathcare plans, and other government crafted choices.

Some interesting recent research by economists at the Federal Reserve Bank and Princeton concluded that achievement levels of students using vouchers were "not significantly different than zero", and that "very little evidence about the potential for public schools to respond to increased competitive pressure generated by vouchers also suggests that one should remain wary that large-scale improvements would result from a comprehensive system." The work, "School vouchers: Recent findings and unanswered questions", was published in 3Q/2008, Economic Perspectives.

3 Autism research won't benefit from Sarah Palin's vow to tell the government to "get out of the way." Nor will it benefit from McCain's proposal in the first debate for a "spending freeze on everything but defense, veteran affairs and entitlement programs."

Spies On the Line

You watch me and I watch you and the government watches us and we watch the government. If everyone is in on the surveillance then the cameras all around us shouldn't make us paranoid right? Citizens can access the images as well as government, and through all this benevolent spying, we'll decrease crime and preserve liberty. Life will be good in a "transparent society", better than in the old fashioned privacy days, in fact some thought think this "transparency" was is the only way liberty would be preserved. Although I'm simplifying a bit, David Brin's article and book about his "Transparent Society" received laudatory attention when it was published ten years ago.

Even a couple of years ago, before cell phones with cameras were ubiquitous and before governments accelerated post-9-11 surveillance was still under wraps "technoprogressive" critics continued to argue the pros (often) and cons (sometimes) of the "transparent society". A couple of years ago the corner cameras didn't have quite the omnipresence they now have in the UK and it was easier to imagine what the technology could be before the technology was in our midst, fully realized.

I was a "Transparent Society" critic for many reasons which could be summed up by saying I thought the ideas naively utopian. However I marveled how the technology Brin predicted became commonplace and how cell-phone cameras, for one, offer citizens ready opportunities to document events. But no matter how many times people update their Facebook, despite how many times technology companies market their newest freedom enhancing device, citizens don't usually get the upper hand in the information arbitrage, regardless of the medium of exchange. One of the most compelling recent criticisms of the "transparent society" was written by Bruce Schneier last March in his column "Security Matters", published by Wired. He criticized the idea that "mutual disclosure" could stop the inevitable erosion of privacy via technology:

"...it doesn't work, because it ignores the crucial dissimilarity of power. You cannot evaluate the value of privacy and disclosure unless you account for the relative power levels of the discloser and the disclosee."

This seems more obvious now than it did in March, more obvious in March, 2008 than few years ago. Brin's ideas now seem as facile as John Perry Barlow's A Declaration of the Independence of Cyberspace. Barlow's 1996 piece told governments to stay out of Cyberspace, which he declared a "civilization" and promised a "more humane and fair than the world your governments have made."

Each year's technology evolutions make those original manifestos seem even more nostalgic, even more quaint. China now monitors and archives Skype messages. Ah, but I don't live in China you say. Then for you the New York Times writes today about the newest book by James Bamford "The Shadow Factory: The Ultra- Secret NSA From 9/11 to the Eavesdropping on America". The author's third book on the NSA focuses on "the agency's growing partnership with private companies to tap into the fiber-optic cables that now carry most telephone and Internet traffic." As he documents in the book, ABC reported that the NSA had been recently eavesdropping on ordinary citizens abroad.

What are citizens to do if it ends up they can't hold a candle to the state's spying? Get creative. Via BoingBoing, we're led to Open Rights Group's (ORG) 4 X 5 meter collage of photos of surveillance "ephemera" all over the UK. The group collected photos capturing what they call "UK's wholesale transformation into the surveillance society/database state". ORG then arranged the photos into a "Big-Brother-esque photo of Gordon Brown looking over Parliament Square against a background of barbed wire, handcuffs and double helice."

The (new) US government has plenty of ideas of it's own. Like the so called "Google government" proposed by Obama in 2006 or Palin in 2008. Will that correct the imbalance of power by making more information available to citizens? Ease our minds?

Whales in The Supreme Court

In Winter v. Natural Resources Defense Council (NRDC), the court heard arguments fromthe Navy and the NRDC about probable injuries to marine animals due to sonar. The question was, did the Navy have to file an environmental impact statement (EIS) as established under EPA law? The justices seemed to clearly lean on the side of the Navy and the Navy's interpretation of the science. In fact Justice Scalia basically coached the Navy's counsel through his arguments. Is this deference to the military justified? How does that bode for whales? For environmental impact statements?

What Environment?

In February 2007, the Navy initiated training exercises without filing the environmental impact statement (EIS) required by the National Environmental Protection Act of 1969 (NEPA). The EIS is required by law and is meant to predict possible environmental harm from the sonar training. Following the Navy's action, various groups including the Natural Resource Defense Council (NRDC) challenged the action in court. The case wound up in the Supreme Court yesterday, where the prosecution and defense presented their arguments. (transcript.) The counsel for the Navy, General Garre, summarized for Justice David Souter the Navy's decision to go ahead without the EIS, arguing that the Navy broke the law because: "it doesn't specifically say what happens if they [the laws] are not followed".

A District Court had originally found in favor of NRDC, deciding that the Navy had violated NEPA. But instead of complying with the court injunction, the Navy wrote its own environmental assessment EA, and presented this to an executive-branch administrative agency called the Council on Environmental Quality (CEQ). The CEQ found that the Navy's mission constituted "emergency circumstances", thereby allowing the Navy to circumvent the law.

The Navy took this CEQ opinion back to the court, arguing that the court should dissolve its injunction. In more court reviews, Los Angeles U.S. District Judge Florence Marie Cooper sifted through scientific evidence and determined criteria for when the Navy should turn off sonar. According to the NRDC brief, the District Court reviewed "thousands of pages of briefing and evidence over the course of many weeks, and tour[ed] a Navy destroyer--to assess the Navy's contention that the mitigation measures would risk the Navy's ability to train and certify its strike groups."

The mitigations the NRDC asked for weren't new, in fact the Navy had followed those very same mitigation procedures previously. The District Court considered that in previous Navy training exercises, the Navy had "trained and certified its strike groups using the two mitigation measures at issue in this appeal". In fact, following the lower court's decisions, the Navy successfully continued training exercises in the Pacific Ocean, "completing the last 13 of 14 training exercises, 8 of which were under the current rules". The Navy followed the mitigation procedures and did not appeal to the court for relief. Richard Kendall, who argued on behalf of NRDC pointed this out to the Supreme Court as well as the fact that the LA District court had already loosened its initial ruling to accommodate the Navy.

But the Navy doesn't want to take any more steps to mitigate environmental damage (It too, conceded several points before bringing its case to the high court.) Despite the fact that the Navy's training was not impeded by the mitigations the LA court requested, the Navy and the President appealed to the Supreme Court to overrule any measures imposed by the lower courts, and yesterday the Supreme Court questioned the two sides about whales, sonar, and impact statements. It considered issues of standing and equity, as well as the role of the executive branch in determining the fate of endangered species.

Sometimes the court seemed aloof to the information in the briefs. In balancing the possible harm to marine animals, Chief Justice Roberts hyperbolically suggested that one possible harm was: "the potential that a North Korean diesel electric submarine will get within range of Pearl Harbor undetected". NRDC counsel Kendall corrected the Chief Justice, noting that the questions in the case concerned only military training, not combat. Justice Breyer also seemed confused, and elicited a laugh by suggesting that all military exercises were destructive: "You go on a bombing mission, do they have to prepare an environmental impact statement first?" Mr. Kendall said again: "No", since NRDC was arguing for basic mitigation measures during training, ones that the Navy had previously followed, which had not stopped training.

Whales & Sonar: It's Not Pretty

Research shows that whales become disoriented, injured, and die after sonar testing. Strandings and deaths that have been frequently documented; in North Carolina (2005); in Haro Strait off the coast of Washington State (2003); in the Canary Islands (2004, 2002, 1989, 1986, 1985); in Madeira (2000); in the U.S. Virgin Islands (1999, 1998); Greece (1996), and the Bahamas (2000), and off the coast of Spain (2006), just for starters. The coincidence of whale strandings or deaths and naval sonar testing exercises seems too obvious to ignore. Recent research indicates how the marine mammals become injured and die, although cause and effect is sometimes difficult to pinpoint.

After the 2003 mass strandings in the Canary Islands, Nature published a report by Jepson et al, showing that beaked whales had gas filled cavities and emboli in their organs and tissues. The animals tend to hemorrhage around their ears and brain and according to Jepson, the whales died from decompression sickness.1 A subsequent study in Science, 2004 found the same effect in sperm whales. 2. Jepson later reported that embolisms were also present in whales stranded off the coast of Spain in 2006. 3 More studies of strandings found the same. 4 So, common to the many government funded reports, and consistent with observation, tagging, and corpse analysis, whales become disoriented when subjected to sonar, leading to decompression sickness 5.

Recent research by teams in the Ian Boyd lab at St Andrews University and in the Peter Tyack lab at the Woods Hole Oceanographic Institute suggest that the whales try to escape the sound, causing them to dive frantically, which upsets their usual feeding and breeding habits. This erratic diving behavior causes the bends, hemorrhaging and injuries, Tyack told Times Online in a story published September 28, 2008:

"[The Navy] uses pulses of similar frequency and duration to the pulses emitted by killer whales and is very loud. It seems to have a particularly strong effect on species, such as small beaked whales, of which killer whales are the primary predator."

Beaked whales are most susceptible to harm because of their behavioral response of abnormal diving in the presence of sonar. Scientists are closing in on the mechanisms for injury and possible ways to avoid them. In the meantime, the Navy publicly denies all of this this research.

This Won't Hurt at All, Says the Navy

The justices of the Supreme Court acknowledged they can't evaluate science. When presented with rationale by the Navy about needing to train at night because of thermal layers, here's what Justice Breyer said about the Navy's stance: "Fine, they went on some exercises and they didn't run into these layered things. So obviously they couldn't have training." (Thermal layers and sonar are not too complicated for a lay person to understand at a basic level, as here in the book, "How To Make War", by James Kunnigan, Chap. 10: Navy: Run Silent Run Deep.)

The court only anemically challenged the Navy's General Garre, who repeated asserted that the Navy's sonar causes no harm. Garre also claimed that the respondents hadn't shown "irreparable harm". For instance General Garre referred the court to a Navy document listing "all the species of beaked whales and explained that the harms that are predicted in the environmental assessment are non-injurious, temporary harms". Justice Samuel Alioto asked Garre to explain this in "lay terms". Garre led Alioto to conclude there wasn't "physical injury", rather the whales might, as Alioto put it, just: "swim in a different direction"? (As if your child was whining in the living room so you wandered into the kitchen to get yourself a snack, rather than, that you were suddenly subjected to unending earth-shatteringly loud, nerve-ripping noise that caused you to flee up to the attic window, cover your exploding ears and plunge from the roof.) Garre assured Alioto: "that's right". But here's how the noise sounds to the mamals according to the NRDC:

"In sound intensity, in this courtroom if we had a jet engine and you multiplied that noise by 2,000 times, correcting for water, that's the sound's intensity that would be going on in the water if you were a marine mammal near that source."

That's loud. Despite the Navy's assertions, the NRDC presented significant evidence of harm in its briefs. Kendall disputed General Garre that sonar caused "no harm." He described the noise, the embolisms, the gas filled pockets, and the hemorrhaging.

What the Navy Doesn't Want Us Know?

People have long suspected the Navy knows more then they're letting on about how sonar effects marine life. According to the NRDC brief (PDF) the Navy predicted in their environmental assesment that the SOCAL sonar training would result in 170,000 incidents to marine mammals -- harassment, injuries, or deaths -- and 548 permanent injuries for beaked whales.

The Navy denied and backpedaled about the possible harm to marine animals during Supreme Court questioning, but there is plenty of evidence that militaries of the world understand sonar's effects. The science journal Nature obtained an unpublished 2007 report from the UK Military under the Freedom of Information Act 2000 documenting that sonar negatively effects whale behavior and can lead to death. 6 The UK military ran Operation Anglo-Saxon 06 in 2006 and reported on whale activity during the "submarine war-games". Using hydrophones, researchers found the number of whale recordings dropped by 75% over during sonar exercises. The whales stopped vocalizing and foraging for food, and the UK military predicted this would lead to '"second and third order effects on the animal and population as a whole"', including starvation and death, according to the report.

To the extent the research is sparse perhaps it's because the US Navy has tried to suppress its findings. Nature reported in "Panel quits in row over sonar damage" in 2006, that the US Navy pressured scientists to suppress evidence of harm from sonar. 7 The US Marine Mammal Commission (MMC) was convened by Congress in 2003 to advise Congress on a plan to research whales and sonar, however the commission broke apart, plan-less, after 2 years of meetings.

Nature spoke to members of the failed MNC who said that the science had been "highly politicized". According to one participant, "the Navy, as well as other groups that use sonar, including geophysical researchers and the oil and gas industry, blocked a consensus." Lindy Weilgart of Dalhousie University in Nova Scotia, Canada, told the journal: '"This process has been a travesty of fiscal responsibility, scientific integrity, and environmental stewardship."'

Environmental Law, by the Navy: "What He Said."

In the beginning of the hearing Supreme Court pursued the facts pertaining to the Navy's decision to ignore the law requiring the EIS, and simply construct its own environmental assessment (EA) according to it's own criteria, that was not vetted by anyone but the Navy, and not subject to public comment.

Different justices questioned General Garre about the CEQ's authority as an office in the White House to override environmental law set out in NEPA. They suggested that perhaps the only "emergency" was that the Navy had ignored the legal requirement for the EIS before starting training. Then Justice Scalia proposed a tactic of argumentation for General Garre:

Scalia: "Look, the problem you face and maybe you're being whipsawed, is that you are effectively estopped from the argument that no EIS is necessary by the fact that you have agreed to these alternative arrangements. But you should not be estopped from arguing that at the time the EA was issued that was not a good faith completion of all the Navy's responsibilities....It assumes that the EA wasn't enough. And I'm not sure that we -- that that assumption is valid."

General Garre: "Well, that's right....the Navy believes that its EA was not only prepared in good faith, but was appropriate and reached the right conclusions...." Garre had repeatedly stated that the sonar training would cause little "likelihood of irreparable injury..." But Justice David Souter wondered whether: "without the EIS, the Navy is acting in -- in a state of -- of some degree of ignorance greater than would be the case if -- if it had done -- done the EIS."

Scalia addressed Garre again:

"The EA demonstrates in your view that the EIS would -- would very likely say that this -- this action by the Navy is okay. And since that is the case, there is -- there is no probability of irreparable harm; to the contrary, there is the probability of no irreparable harm because of the EA."

Said General Garre: "Well, we agree with that." (The Navy does agree with that, even though the EA predicted over 500 serious injuries and 170,000 incidents, it concludes no harm, no harm, again and again.)

Scalia later suggested:

"In all -- in all of these cases it is controverted, or in most of them, whether an EIS is either necessary -- is even necessary. So if the mere allegation that it was necessary gives rise to an allegation of irreparable harm, you are going to get a preliminary injunction in all cases?"

General Garre replied: "I think that's right."

However, earlier in the questioning, General Garre had assured the court that he recognized the Navy's original "duty to prepare the EIS". He had told the justices about the Navy's steadfast commitment to completing the tardy EIS document per previous legal agreements. Now, suddenly, Garre asserted he was "contesting" what he had before agreed to -- that the Navy needed to complete an EIS. This confused Justice Ginsburg, who remembered that 30 minutes earlier Garre had stated his commitment to "meet the goal" of producing the EIS by January, 2009 (although, disconcertingly, the training ends in 2008). Ginsburg said: "I thought you conceded that point". General Garre the quickly apologized for his earlier concession: "if I misspoke".

Who needs Scalia's book "Making Your Case Persuading Judges"? Just show up for the tutorial, let him argue your points, and nod -- "what Scalia said".

Good Stewards of The Environment

In the end, the Supreme Court justices puzzled over why the Navy was dragging its heels if the agency had completed the EA, was committed to completing the EIS, and if there was "no irreparable harm" to mammals.

Garre, perhaps emboldened after Scalia's pat on the back, suggested in closing that the NRDC did not even have standing on the issue of whether beaked whales were harmed.

One justice queried the two parties about why they hadn't worked it out, as opposed to leaving it to the courts. Judges aren't experts on Naval exercises or marine biology, the justices pointed out. NRDC's Kendall answered that "the Navy is focused on having it its way or no way". Chief Justice John G. Roberts retorted, "that's not fair"; the Navy had continually compromised, he said, but "no good deed goes unpunished".

Scientists warn that the beach strandings may indicate an even larger problem -- not all animals may be washed ashore, many more may be dying and lost at the sea. In a review of research on whale injuries, causes, and mitigation by Marine Pollution Bulletin. 8, the authors write: "...the greatest user of military sonars in the world, the US Navy, appears to be in denial about the situation." While the US has taken significant action to weaken cetacean protection in national and international waters, especially with regard to sonar, the Navy continues to boast about its commitment to being "good stewards of the environment".

The Supreme Court will issue its decision later this session.


1Jepson et al, Gas-bubble lesions in stranded cetaceans: was sonar responsible for a spate of whale deaths after an Atlantic military exercise? Nature, 425, 575-57, 9 October 2003: doi:10.1038/425575a.
2 Moore and Early; Cumulative sperm whale bone damage and the bends, Science 306, Vol. 306. no. 5705, p. 2215. 2004: doe: 10.1126/science.1105452
3 Dalton, Rex; More whale strandings are linked to sonar : Nature 440, 593 30 March 2006 doi :10.1038/440593a.
4 Fernandez, A. Gas and fat embolic syndrome" involving a mass stranding of beaked whales (family Ziphiidae) exposed to anthropogenic sonar signals.Veterinary Patholology 42:446-457 2005.
5 Tyak et al. Extreme diving of beaked whales. Journal of Experimental Biology 209, 4238-4253. 2006 doi: 10.1242/jeb.02505).
6 Cressey, Daniel; Sonar does affect whales, military report confirms. Nature, Aug 1, 2008. doi:10.1038/news.2008.997.
7 Dalton, Rex; Panel quits in row over sonar damage. Nature 439, 376-377 26 January 2006 doi :10.1038/439376a;doi:10.1038/439376a
8 Parsons et al., Navy sonar and cetaceans: Just how much does the gun need to smoke before we act? Marine Pollution Bulletin, July, 2008 doi:10.1016/j.marpolbul.2008.04.025


Acronym Required previously wrote on this subject in "Whales In A Time of War", and "Whales in Court".

Nobel Prize in Physiology or Medicine for Viruses Linked to Disease

The The Nobel Assembly at Karolinska Institute awarded the 2008 Nobel Prize in Physiology or Medicine to Luc Montagnier and Francoise Barre-Sinoussi for their discovery of the human immunodeficiency virus that causes AIDS. Montagnier is the director of the World Foundation for AIDS Research and Prevention in Paris. Barre-Sinoussi works in the virology department at the Pasteur Institute in Paris. The two scientists split the prize with Dr. Harald zur Hausen of the University of Dusseldorf who discovered the viruses that cause genital warts and cervical cancer.

The Nobel Prize committee commended the French scientists for their work identifying the virus that caused AIDS, work that established the foundation for further scientific characterization of HIV. In the 1980's Montangier and Barre-Sinoussi isolated and cultured cells from the lymph nodes of patients suspected to be infected with acquired immune deficiency syndrome (AIDS). In lab experiments they found the enzyme retroviral enzyme reverse transcriptase, which indicated the presence of a retrovirus in the lymph nodes. They then infected lymphocytes from donors with their retrovirus and found that the virus killed healthy lymphocytes which helped show that this virus was the infectious agent responsible for changing the immune response in the body and causing AIDS.

The discovery of the HIV virus was contentious, with US scientist Robert Gallo and Luc Montagnier each saying that they were first to discover the virus. Some early news media reports on the discovery in the 1980's said that the French team discovered the virus, while others indicated it was Gallo who first identified the virus. The French and US teams published papers in 1983 and 1984, and each filed patent claims for their discovery. It got a little heated with both teams vying not only for recognition but for the profits associated with the development of the test for HIV. New Scientist called the long running dispute "the tackiest sagas in the history of medicine..." (albeit with a lot at stake)

The two governments led by President Ronald Reagan and Prime Minister Jacques Chirac finally agreed to let both teams share recognition for the discovery. You can get a sense of how sharing worked for them in an article published in Scientific American in 1988 (when the magazine actually published full length articles). Gallo and Montagnier wrote the article, describing the scientific unraveling of the AIDS mystery at length and punctuating the interesting account with "clarifiers": "one of us ([Gallo or Montagnier])" or "the other of us [(insert name)]. Gallo later acknowledged that the strain of the HIV virus the French isolated had contaminated his lab's work. On yesterday's announcement of the Nobel Prize both teams cordially commended the other for the work each did.

The Nobel Foundation will announce more prizes this week and next. The physics prize was awarded today to three physicists from Japan and the US for their discovery of nature's broken symmetry. The announcement for the prize in Chemistry will be tomorrow. Literature and Peace will follow this week, with the Economics prize awarded next Monday.

New Minister of Health For South Africa. Change Afoot?

Change, Change, Change

People chant for change, yet some political observers say change in presidency is of over-rated importance. Nevertheless, the US electorate has basically thrown George Bush out in their excitement to welcome a new chief executive who promises change. For his part, Bush addresses the nation with familiar threats about the nation's security and citizens' well-being, delivered with alarmingly monotonic disassociation, as if drugged.

Anxious to move on, the voters gather their remaining hopes and dreams in bundles and strew these along the campaign trail like flower petals at the feet of the new king and they vie for the attention of the incoming administration. The electorate anxiously tracks the presidential campaign and chooses, gaffe by gaffe, who to entrust with their future.

But there is a certain mystery to this all. People clamor for change but most of them just want security -- to work in the day and scurry to safety back at the den for food and sleep and family; they want their hunger abated and to be warm. With their fundamental securities established, the gold watch of yore really was icing on the cake. Today many people can't count on a job or a home. The change people yearn for is to feel more secure.

Of course it's never that simple. US presidential candidates also court constituents who would like to be assured that the dinosaurs roamed around with the humans 5000 years ago and that there's no such thing as evolution. Preachers urge parishioners to vote according to the bible, which of course means no evolution, no modern social awareness that reflects new science knowledge, no change. Perhaps being able to read your future from The Good Book feels secure for it certainly promises no change. To these people McCain also paradoxically promises "change", as he embraces the religious right via Palin. Those mavericks.

Change in the US, Change in the World

The US population is not alone in being seduced by the "change" promised by new leaders. In South Africa last month, Thabo Mbeki resigned as he was being ousted from his post of the last eight years as president representing the African National Congress party (ANC). As the successor to Mandela, the West considered Mbeki a steady leader of a nascent democracy on a continent with too few democracies. The west did well by the president who advocated neoliberal policies and expanded the economy with predictable policies.

In Mbeki's place, the ANC installed Kgalema Motlanthe as the interim president until Jacob Zuma, the presumed future winner of the 2009 election and future president is elected into office. Zuma was the populist choice to lead the ANC and has strong support of unions and the Communist Party. He was imprisoned during apartheid and still revels in the glory of liberation movement, singing "Bring Me My Machine Gun" at gatherings.

Zuma's strong populist appeal and support from unions makes investors and middle class South Africans very nervous and so to them, he promises no change. But his populist message appeals to many voters who were disenfranchised under Mbeki. Mbeki's South Africa was a fragile economy which created glaring gaps between extreme wealth and extreme poverty. The Mail & Guardian wrote of South Africa's growing discontent with Mbeki:

"the mounting failure of the criminal justice system to prosecute and convict criminals, the increasingly disturbing nature of violent crime, burgeoning inequality and unemployment, the HIV/Aids catastrophe and the culture of impunity for corrupt and incompetent public officials."

Change is needed on South Africa's domestic front, and Zuma's message promises a forum for the poorer populations. But will Zuma deliver this change? And can his policies at the same time appeal to international investors the way Mbeki's did?

Barbara Hogan, New Minister of Health for Africa

Before Zuma_The_Unnerving takes office, there is a chance for interesting, perhaps positive and real change in the form of the new interim government of Kgalema Motlanthe. Motlanthe has already appointed a new Health Minister, Barbara Hogan, to replace the infamous "Dr. Beetroot" -- Manto Tshabalala-Msimang -- who ably and stridently propagated Mbeki's AIDS denialism. Dr Molefi Sefularo is the new Deputy Minister of Health.

The proactive organization Treatment Action Africa (TAC) and the AIDS Law Project, along with many others both inside and outside of Africa -- scholars, public health communities, researchers and NGOs around the world -- have embraced the new choice for Minister of Health. TAC and the AIDS Law project joined to serenade Hogan at her Cape Town flat last Friday, toasting her appointment with champagne. Her neighbors wondered what all the ruckus was about, then joined the party. TAC expressed their opinion of Hogan on their website:

"We are confident that Hogan has the ability to improve the South African health system. She has been one of the few Members of Parliament to speak out against AIDS denialism and to offer support to the TAC, even during the worst period of AIDS denialism by former President Thabo Mbeki and former Health Minister Manto Tshabalala-Msimang. 0n 14 February 2003, she received the TAC memorandum to President Mbeki for a treatment plan. She was removed as Finance Portfolio Chairperson by Mbeki in part for her stand on HIV/AIDS. She has a reputation for being hard-working, competent and principled."

The new minister has her work cut out for her. Various groups clamor that she should work to clean up the "rot in public hospitals", to "protect us from toxic foods", and to intervene and uncover the truth beneath the secrecy surrounding "tragic deaths of 142 babies in the Eastern Cape" at Frere Hospital. They ask that Hogan stop the brain drain of medical personnel in South Africa and restore confidence in the public health system.

In an interview with News24 radio last week, Barbara Hogan acknowledged the amount of work that needs to be done in her new post as Minister of Health and warned that with such a short tenure she can only focus on a couple of things. Top of her list was the "morale of healthworkers" and revamping healthcare to a "system that is functional and responsive to people who are using it". Hogan said the "biggest challenge is HIV/Aids and all the strains that it places on the health system." None of these seem like low-hanging or modest, easily achievable goals for Hogan's short tenure, nevertheless, she seems sincere, which is why there is so much hope.

Change You Can Believe In?

However last week the science journal Nature cautioned in Nature News that a new law passed by the South African parliament may hamper the country's adoption of more progressive HIV policies. ("Incoming South African health minister raises hopes on HIV" (doi:10.1038/news.2008.1138))

The law creates a regulatory authority (South African Health Products Regulatory Authority (SAHPRA)) which will oversee all medicines including "medicine, medical device or cosmetic in respect of which a medical claim is made". The Minister of Health will become the final arbiter of which drugs get to market according to criteria that includes nebulous goals like "public interest", the experience of other countries, and consideration of whether the product is "supportive of national health policy goals". The agency is not independent, rather its under the thumb of the Health Minister.

The previous Minister of Health had had run-ins with the former science based drug regulatory agency, so the law seems tailored to Manto Tshabalala-Msimang's reign and Mbeki's intense suspicion of Western pharmaceuticals. As Nature sees it, the concern is that the new bill gives the new minister "sweeping authority over the approval of new medicines and a remit to regulate traditional medicines alongside of conventional pharmaceuticals", Considering all the enthusiasm for the new Health Minister, Nature's observation seems almost ill-conceived. Or does it?

Mbeki's Legacy

Hogan has a lot of obstacles to overcome with the standard Mbeki set for public health. When he emerged from prison after apartheid with strong ideas about African solutions. The growing HIV/AIDS epidemic must have seemed cosmically unfair as the nation finally sloughed off apartheid. AIDS treatment is costly, especially for a country with a fledgling public healthcare system. Yet rather than approaching the national crisis head on, Mbeki for years refused to acknowledge that HIV was the viral cause of AIDS. As a result, according to the Mail & Guardian, "Death certification by Stats SA shows more than 1.5-million deaths in the ages 0-49 and more than two million new infections during his rule." Now, almost 30% of pregnant women in antenatal clinics screen positive for HIV and best estimates show that approximately 50% of patients with Stage IV AIDS who need AIDS drugs, do not receive anti-retroviral treatment (ART).

Throughout his tenure, Mbeki steadily dragged his feet on the HIV/AIDS crisis. He juggled the tensions of his mixed world-view -- his South African heritage, his survival during apartheid, and his education as an economist in Europe. He mixed up neoliberalism, anti-colonialism, and crony politics, and ended up intensifying public unrest during his tenure as his policies created increasingly stressful social conditions. These tensions were apparent in the long, oblique letters he wrote to the citizens published by a weekly newspaper and at the website of the African National Congress (ANC). Here he spent considerable energy trying to diffuse serial national outcries.

Last year Acronym Required wrote about Mbeki's mini-skirt memo, in which he took the media to task for their criticism of the infant death cover-up at the Frere Hospital in Eastern Cape. At the time of that August 2, 2007 memo, Mbeki had just fired the assistant health minister Nozizwe Madlala-Routledge who had been addressing the AIDS crisis and who had devised an HIV/AIDS strategy while she stood in for Manto Tshabalala-Msimang. Tshabalala-Msimang had received a liver transplant and newspapers were reporting that she was a heavy drinker before and after the transplant, had skipped the organ donor cue, and was abusive to hospital staff during her transplant operations.

Mbeki addressed the outcry of the public health situation again in his 6000 word August 31, 2007 memo. The memo shows his cunning ability to twist the facts around, to say first one thing, then the opposite. He accused anyone who criticizes Manto Tshabalala-Msimang (("cadre of the revolution") of being a traitor or weakling:

"...some, at home and abroad, who did nothing or very little to contribute to the immensely difficult and costly struggle to achieve our liberation, have chosen to sit as judges over who she is, what she has done for the welfare of our nation, and what she represents, today, with regard to the pursuit of the goal of a better life for all our people."

He defended his administration's handling of HIV/AIDS and railed on national and international papers for questioning his stance, including The New York Times, BBC and The Guardian. He eviscerated all media for distorting his and Manto Tshabalala-Msimang's position on nutrition as it relates to AIDS:

"Manto Tshabalala-Msimang's mortal sin in the eyes of our opponents, in which regard she has faithfully represented the convictions of the ANC and the ANC directive to those we had deployed in government, is that she upheld this view, insisting that it must constitute an important and integral part of our national response to the serious challenge of HIV and AIDS....they [her critics] will continue to do their best to denigrate a principled fighter for a democratic, non-racial and non-sexist South Africa, who has dedicated her entire life to the achievement of this outcome, Dr Manto Tshabalala-Msimang, whom history will honour as one of the pioneer architects of a South African public health system constructed to ensure that we achieve the objective of health for all our people, and especially the poor."

His extensive rationale for promoting nutrition to help prevent AIDS included citing the judgment of everyone from small babies to Romans, all who he claims understand, as he does, the importance of nutrition.

"they [the critics] have deliberately falsely presented the arguments of our Minister of Health about the known nutritional (and micro-nutrient) value of olive oil, lemon, beetroot, garlic, and other foods, as well as the efficacy of traditional medicinal prescriptions based on herbs and other natural plants, as an argument against the use of modern drugs and medicines, including antiretrovirals (ARVs)."

He wrote that the media and critics contorted his message to represent that he proposed nutrition and opposed ARV's. Mbeki criticized the national Cape Times for reporting the Minister of Health's own words:

"Nutrition is the basis of good health and it can stop the progression from HIV to full-blown Aids, and eating garlic, olive oil, beetroot and the African potato boosts the immune system to ensure the body is able to defend itself against the virus and live with it."

He didn't deny that Manto Tshabalala-Msimang said that, but recruited to his side a doctor who wrote in a letter to the editor that good food bolsters the immune system. Mbeki quoted the doctor, then re-established his party's position: "It is our sustained opposition to the fundamentally wrong proposition that in our response to HIV and AIDS we must rely almost exclusively on ARVs." He added that because of "our poverty", the country had "fallen victim to three pernicious influences", as he put it:

"One of these is the medicalisation of poverty. Another is the politicisation of disease. The third is the commercialisation of health care, in all its elements. As a revolutionary movement we have fought against all these, and must continue to do so.

Mbeki recruited the US as an ally for his position:

"US Secretary of Health Mike Leavitt had the courage and honesty to acknowledge this reality, fully understanding the need to respond to the health needs of our people, liberating our health care obligations from the dictates of partisan political and commercial interests."

Secretary of Health Leavitt, who now has his own disapproval to face on a controversial contraception bill, unsurprisingly didn't mention anything about "liberating South African from commercial interests" on his blog back in 2007 when he visited South Africa.

Mbeki managed to play all angles in his August 31, 2007 memo. He bragged about the excellent modern health care system, describing at length the surgical excellence and technology afforded to the Minister of Health during her liver transplant. Meanwhile his administration was busy covering up the Frere baby death scandal and mounting evidence of a failing public health care system. He accused anyone who complained about Tshabalala-Msimang of being either a traitor, someone who wanted to see South Africa fail, or someone who would "have allowed Manto Tshabalala-Msimang to die." He accused the media and any critic of misrepresenting the ANC's position on AIDS drugs vis a vis nutrition. Then he defended the importance of nutrition to the immune system and his government's advocacy of nutrition in AIDS, recruiting to his side a letter to the editor and the US Secretary of Health.

Neoliberal Economic Policies or Public Health -- One or the Other?

Despite outcry from the international public health community for his AIDS policies, Mbeki built relationships in the West because of his adherence to neoliberal economic policies. He welcomed foreign investment and freed up capital from the demands of deteriorating infrastructure in order purchase goods abroad and foster national participation in the world economy. Supporters from the west, including many consultants, would argue that Mbeki made progress with his motions to rebuild shantytowns and provide better healthcare. They will point to Zimbabwe, which roils at South Africa's northeast borders, and note that similar unrest that could just as easily overflow into S. Africa -- as it recently did. Some of these business leaders talk about the new struggling capitalist economy and say -- 'isn't it obvious? Public health just couldn't be the highest priority with the economic stakes so high'. People are apparently able to look past the charges against Zuma, for extortion, for reportedly having unsolicited sex woman who had AIDS, among other charges, and see someone who's "change" promises more security.

In the meantime, will the interim government and Minister Hogan be able to balance international economic pressure for open markets with the yawning gap in public healthcare and carry through her stated mission? Were Mbeki and Manto Tshabalala-Msimang merely carrying out the demands of the ANC as Mbeki always emphasized? Will party politics of the ANC to which Barbara Hogan is so loyal to allow reform? Or will the ANC continue to let laggard public health policies associated with Mbeki's reign prevail? Or will the ANC give the people reason to trust in the ANC and reason to hope -- as they did during the short tenure of Nozizwe Madlala-Routledge, before Zuma takes office? Can you grow a liberal state without tending to the population's basic needs for shelter, security and healthcare? Will change really come to Africa's public health system? We remain hopeful.


Acronym Required previously wrote on this subject in these posts:

"Mbeki's AIDS Legacy and Ours"

"South Africa: Peddling Beetroot, Courting AIDS"

""Not in Paradise Anymore - AIDS in Africa - Reason for Optimism?"

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