Thursday, June 30, 2005

The milk of human dumbness

It's nice to see the scientific establishment getting its head screwed on straight regarding bioterrorism at last. At least this once.

A month ago the geniuses at Department of Health and Human Services (DHHS) asked one of the world's most prestigious scientific journals, The Proceedings of the National Academy of Sciences (PNAS, or "penis," in the trade) to delay publication of a scientific paper they deemed "useful" to terrorists. It was an analysis of areas in the dairy industry vulnerable to a bioterrorist attack. Specifically, a professor of management and a graduate student at Stanford laid out how easy it would be to pop some botulinum toxin into the milk supply and cause a major problem.
In an accompanying editorial, Bruce Alberts, president of the National Academy of Sciences, noted that PNAS decided to publish the article "as originally accepted," because they believed that, despite the government's concerns, the article "can be valuable for biodefense" by informing scientists and other key players working to strengthen food security. A PNAS spokesperson told The Scientist the editorial would serve as the journal's statement on the matter.

In a statement through a spokesperson, Stewart Simonson, HHS Assistant Secretary for Public Health Emergency Preparedness, said he regretted the journal's decision to publish the paper. "We recognize, of course, that this is an issue about which good and reasonable people disagree," he said. "But I must say that if the Academy is wrong, the consequences could be dire and it will be HHS–not the Academy–which will have to deal with it." (The Scientist)
The senior author, Lawrence Wein, denied the paper was sufficiently detailed to be a "road map for terrorism," pointing out the information was all available in public information sources (or by simple observation). DHHS's response:
Bill Hall, spokesperson for the HHS, who spoke to The Scientist after the paper was initially pulled, said this is the first time he knows of the HHS asking an academic publication to hold a paper due to terrorism concerns. Although many argue that newspapers and other outlets have exposed vulnerabilities in transportation, nuclear power and other sectors that terrorists could exploit, Hall said this paper stood out because of the "level of detail." It's one thing to say the dairy industry is vulnerable, he noted, it's another to specifically describe how to poison the country's dairy supply. "That's a level of granularity that's of no help to anyone but terrorists," he said.
So I took at look at the paper (available here in .pdf format). There is indeed a lot of detail ("level of granularity") in the paper, but it is mostly in the form of parameters for Wein's model. There is little not already known to the dairy industry or anyone else who wanted to find out. Wein says his intention was to "nudge" policy makers into better protecting the dairy supply.

That policy makers, and more importantly the industry itself, needs a "nudge" is not open to debate. The problem with Wein's paper is that it focusses on the wrong things and offers some pretty dumb recommendations. The very problem Wein invokes for botulinum, contamination of the milk supply, also holds true for contamination with other potent toxins, like 2,3,7,8-TCDD ("dioxin"). If DHHS (and USDA and the dairy industry) were to take this seriously, they would be thinking of many other ways the milk supply could be contaminated but "accidentally" or through negligence. They are not anxious to do this or have its vulnerability called attention to. More regulations? No thanks. Not for this administration or their patrons.

And some of Wein's suggestions, such as requiring security "checks" for farmworkers or laborers with access to raw bulk milk supplies are dumb, both for political and practical reasons (maybe they should have them take off their shoes before entering the cow barn?). It's tough to do a check when you hire undocumented aliens at cut rate wages.

Wein's paper should call attention to the vulnerability of the food chain, all the way up and down its length, not just to rare and unlikely bioterrorism incidents. It should include "terrorism" caused by uncaring and negligent food processors. But it won't, I am sure. Now that's really dangerous talk.

But at least PNAS published this paper and wasn't cowed by the jackasses at DHHS (note farm animal language). It's about time scientists got around to saying The Bioterrorism Emperor has no clothes.

EDs shrinking: Some "diversions" aren't that amusing

DemFrom CT called my attention to a May 26, 2005 Press Release from CDC that should give us pause as we stare into the face of a possible influenza pandemic. Here's an excerpt:
Visits to U.S. Emergency Departments at All-Time High; Number of Departments Shrinking

Visits to the nations emergency departments (EDs) reached a record high of nearly 114 million in 2003, but the number of EDs decreased by 14 percent from 1993 to 2003, according to a new report released today by the Centers for Disease Control and Prevention (CDC).

The report attributes the rise in ED visits to increased use by adults, especially those 65 years old and over. Among people aged 65-74, the ED visit rate was more than five times higher for those residing in a nursing home or other institution compared with those not living in an institutionalized setting.

The report also finds that Medicaid patients were four times (81 visits per 100 people) more likely to seek treatment in from an ED than those with private insurance (22 visits per 100 people.)

Emergency departments are a safety net and often the place of first resort for health care for Americas poor and uninsured, said Linda McCaig of CDCs National Center for Health Statistics and the reports lead author. This annual study of the nations emergency departments is part of a series of surveys of health care in the United States and provides current information for the development of policies and programs designed to meet Americas health care needs.

Other findings in the report include:
  • From 1993 through 2003, the number of ED visits increased 26 percent from 90.3 million visits in 1993 to 114 million in 2003. The U.S. population rose 12.3 percent during this period, and the 65-and-over population rose 9.6 percent.

  • The average waiting time to see a physician was 46.5 minutes, the same as it was in 2000. The wait time was unchanged despite increased visits. EDs have implemented a number of efficiencies, including fast track units, which may have kept the wait time constant. On average, patients spent 3.2 hours in the ED, which includes time with the physician as well as other clinical services.
Influenza is characterized by sudden onset. In an influenza epidemic, the Emergency Department (ED) will be the first place people will think of going or be taken to (can't get an appointment with your doctor until next February?). In many cities EDs are already on "diversion" (they shunt cases elsewhere). What will happen if the case load goes up by a mere 20% (not a rhetorical question)?

Not bad news is not necessarily good news

At least the latest news out of the WHO team visiting Vietnam isn't bad.
HANOI, June 29 (Xinhuanet) -- After spending one week in Vietnam studying bird flu, a WHO-coordinated international team of experts detected little change in the virus strain H5N1, concluding that there are no increased levels in the efficiency of transmission of the disease either from poultry to human or from human to human. (Xinhuanet)
But it's not quite clear exactly what the news is--or isn't. A team of international investigators went to Vietnam to see whether there was more infection with H5N1 than case counts indicated. Specifically there was question about whether investigation using Western blot of stored blood samples suggested this. Media reports, like the one from Xinhuanet above, are silent on this issue. Nor do we know on what basis the team made the judgment there are no increased (compared to what?) levels of transmission. It is not enough just assert this. Maybe the lack of information is a problem with the media, not WHO. But better and more detailed information is needed if pronouncements like this are to be accepted at face value.

The team also asked that future samples from suspect cases by shared with reference laboratories outside Vietnam "for external, independent confirmation as well as for quality assurance." We assume this will also give WHO access to sequence information to allow design of better primers for detection and confirmation as well as monitoring mutation. Not exactly a vote of confidence in Vietnam's ability to provide accurate information.

So the news wasn't bad. But just what it was, is less clear.

Update 6/30/05 (via Promed): excerpt of Statement from WHO
Some reports now circulating suggest that WHO has downgraded its assessment of the pandemic threat. These reports are unfounded. The experts were specifically asked to search for evidence that could substantiate concerns raised first at a WHO consultation of international experts held at the beginning of May in Manila. That consultation considered suggestive findings, largely based on epidemiological observations, that the H5N1 virus had changed its behaviour in ways consistent with an improved, though not yet efficient, ability to spread directly from one human to another. The specific epidemiological observations considered included milder disease across a broader age spectrum and a growing number of clusters of cases, closely related in time and place.

More recently, testing of clinical specimens by international experts working in Viet Nam provided further suggestive evidence of more widespread infection with the virus, raising the possibility of community-acquired infection. These findings have not been confirmed by the present investigative team.

Firm evidence of improved transmissibility would be grounds for moving to a higher level of pandemic alert. Because of the huge consequences of such a change, WHO is following a cautious approach that combines heightened vigilance for new cases with immediate international verification of any suggestive findings.

Because the detection of H5N1 in clinical specimens is technically challenging and prone to errors, members of the investigative team took sophisticated laboratory equipment with them to Hanoi for on-site testing. Tests were performed using WHO-approved reagents and primers.

While these first results are reassuring, further retesting of clinical specimens will continue over the next few weeks to provide the most reliable possible foundation for risk assessment.

Wednesday, June 29, 2005

EU gets ready, US doesn't get it

The European Union is getting its act together on bird flu. Influenza experts from the 25 member and others are meeting in Luxembourg to discuss integrated strategy.
Markos Kyprianou, Commissioner for Health and Consumer Protection, said: “The threat of a global influenza pandemic with serious human and economic losses is a very real one that must be addressed. In today’s globalised society, unilateral responses to such possible outbreaks are not a viable option. There must be a coordinated EU approach to prevent and control diseases such as influenza, and today’s workshop is a significant step forward in this direction.”

The current avian influenza epidemic in Asia is unprecedented. It is caused by a particular strain of virus that has already caused the death or killing and destruction of more than 125 million birds, major economic losses to the countries concerned which have been estimated at € 8-12 billion and the death of more than 50 people. Even more worryingly, it has given rise to grave concerns that an influenza pandemic is imminent. (EU statement)
This reminds us of the US response--because it's so different. Hello-o-o . . .

NB: EU Animal Health and Control Measures regarding influenza; Public Health; and the document, Towards Sufficiency of Pandemic Influenza Vaccines in the EU, links up at Flu Wiki

Flu Wiki marches on

Another big day over at the Flu Wiki. 1300 visits and 8000 page reads by mid-evening of the second day. More importantly, stuff is being added steadily: state plans, new EU links, edits to the Primers, offers of entries on the way.

Here's a good example of just how we hoped this thing would work. From an email to DemFromCT:
One issue I didn't see addressed in depth in the scenarios I've read, is what to do about municipal waste management in a pandemic. Refuse collection & disposal are essential public health functions, and if they break down, secondary epidemics are almost a certainty. I have an article in my files about how municipal government in one of the large cities in Holland managed to maintain essential sanitation services during the WW2 Nazi occupation and wartime conditions generally. It's the only published article I've ever seen on municipal sanitation under extreme emergency conditions. And even though those events occurred over sixty years ago, it may be a useful starting point for local governments to begin thinking about these issues in relation to a flu pandemic.
Are we interested? You bet we are!

Tuesday, June 28, 2005

Bird die-off in China, etc.

Influenza virus's home in nature is in wild birds. Most of the viral subtypes are found only in birds, although a few have become adapted to other species like humans, pigs, horses and, of course, domestic fowl (poultry), which, while birds, are different than their wild counterparts in many ways. What happens in birds is both a warning and an influence on what happens in humans. So health experts pay attention.

What we have seen over the last two years is not only unprecedented but extremely worrying. Influenza A virus for the most part is of low pathogenicity in birds, so the emergence of highly pathogenic forms like H5N1 in recent years was an unpleasant surprise. Recently there have also been die-offs of wild migratory birds in species previously unaffected. H5N1 infection now is regionally widespread in asia and is poised to spread further. The recent reports of 1000 geese dying in western China (Qinghai province) has now been increased to 5000, according to the UN agencies WHO and FAO (Food and Agriculture Organization), who have a team in the area.
"This is the first time we've seen large numbers of migratory birds dying from bird flu," Julie Hall, the WHO official in charge of communicable diseases in China, said.

"So the virus has obviously changed to be more pathogenic to animals. What it means to humans we don't know." (Daily Telegraph, Australia)
There is some urgency to studying the birds on the large nature sanctuary on Qinghai's large salt-water lake, but of the almost 200 species of birds, only five have been tested so far. Because they will begin migration in a month or so, there is some urgency. The concern is that asymptomatic birds will carry the virus to distant places and a bird pandemic with H5N1 will spread to domestic poultry elsewhere. But another source of uncertainty and concern is that there is little information on where many of the bird species migrate (Bloomberg).

Meanwhile Vietnam has continued to see human cases in the absence of florid outbreaks in domestic poultry, unlike previously. Just what this means is unclear, but experts consider it a warning sign the virus has changed once again.

Although the usual "flu season" is over in Vietnam, there seems no respite from continued appearance of human cases. So far the numbers of officially counted sick people has been relatively small (unofficial count in Vietnam since December 2003 is 90, with 38 deaths). But no one is confident it will remain that way.

Something wiki this way came: the first day

Somewhere around 7 am EDST on June 27, 2005, the Flu Wiki was announced on the three initiating blogs (Just a Bump in the Beltway, The Next Hurrah, Effect Measure). By midnight EDST the site had received almost 1500 visits and an incredible 8000 page views. Average visit length was over 20 minutes.

Whatever else this means, there is a lot of interest in this subject. We hope that interest will translate into contributions and participation in the wiki. We have already seen some copy edits, corrections and expressions of intention-to-contribute. For those who have yet to visit or haven't spent much time on the site, there are three areas you might look at now.
  • Under Basic Scientific Info (left sidebar) you will find several influenza "Primers", extended essays meant to provide basic scientific information on influenza as a respiratory infection, on the virus itself, and a new one on "cytokine storm." These essays were written to be read by lay people but they do not oversimplify the science. They are written by a scientist but it is important specialists in virology check, correct, expand, clarify, amend, delete or whatever is appropriate to make them the best, most accurate and up-to-date information available for the intended audience. Addition of links, references and images are especially needed. There is no pride of authorship on a wiki. Only pride in the best product.

  • In the Experience of Others and Draft Plans section, clicking on states, regions and countries will get you to a list. Clicking on a state will get you to a page that probably says "Content to be added" (but see California). Go to your state health department's website and see what's there. If they have a flu site or information, click "edit" in the upper right of the wiki page and enter the link and any additional annotation text you want to. Links are done like this: [[URL|link text]]. You need to put in a name (your choice) and some text in the summary box (in this case it might be "link added"). You can preview it, but before it will be posted you have to hit Save. That's it. You've contributed.

    Consider that when all the states are filled in we will have the first "all in one place" guide and comparison of what the states are doing on influenza. And we can accomplish this very quickly with everyone's help. They (and you) can use it to compare your state with others and get ideas.

  • Finally, there are two amazing scenarios you will find under Anticipated consequences and solutions, Imagined Scenarios. One was done seven months ago by a Canadian citizen who wondered what a flu pandemic would be like. It is a very impressive, fully imagined piece. The other is the (now famous) Nature fictional blog of Declan Butler. Also very impressive, scientifically accurate and chilling.
In less than a single day this wiki has gone from a standing start to almost full speed ahead. Hop on. There's a lot of work to do and we don't know how much time to do as much as we can.

Monday, June 27, 2005

Launch of the Flu Wiki

Just a Bump in the Beltway, The Next Hurrah and Effect Measure blogs announce the launch of a new experiment in collaborative problem solving in public health, The Flu Wiki.

A Wiki is a form of collaborative software that allows anyone to edit (change) any page on the site using a standard web browser like Explorer, Firefox or Safari.The purpose of the Flu Wiki is to help local communities prepare for and perhaps cope with a possible influenza pandemic. This is a task previously ceded to local, state and national governmental public health agencies. Communications technology has now become sufficiently available to allow a new form of collaborative problem solving that harvests the rich fund of knowledge and experience that exists among those connected via the internet, allowing more talent to participate.

What the Flu Wiki is not:
  • a news filter
  • a discussion board
  • a place to promote commercial products
  • a soap box
  • a place to advance pet theories
There is nothing wrong with these things. Many of us have blogs that do some or all of them. The wiki is not a replacement or competition for any existing blog or site. We hope existing sites will continue to grow, flourish and generally continue to carry out the important functions they have already done so well.

What we hope the wiki will be:
  • a reliable source of information, as neutral as possible, about important facts useful for a public health approach to pandemic influenza
  • a venue for anticipating the vast range of problems that may arise if a pandemic does occur
  • a venue for thinking about implementable solutions to foreseeable problems
No one, in any health department or government agency, knows all the things needed to cope with an influenza pandemic. But it is likely someone knows something about some aspect of each of them and if we can pool and share our knowledge we can advance preparation for and the ability to cope with events. This is not meant to be a substitute for planning, preparation and implementation by civil authorities, but a parallel effort that complements, supports and extends those efforts.

The open nature of the wiki format has shown itself able to develop surprisingly effective and sophisticated products, as in the Wikipedia. Whether it will work to fashion new solutions to a complex public health problem remains to be seen. This is in the nature of a grand experiment. We hope you will join us in it.

The initial offerings are small and illustrative, in keeping with the limited resources of those of us who are turning the keys in the ignition for the first time. While we will continue to administer and maintain the Wiki, we are turning the wheel over to the community, to take it where the road leads us. There is a bit of a learning curve to driving this rig. We hope you will find the instructions sufficient to get started. You'll soon be learning on your own. There is a "sandbox" page you can use to play with if you wish.

Here's the URL: Regularly updated content will be forthcoming in the days and weeks to come, both by us and by you. That's what wikis are for.

See you there.

Melanie Mattson (Just a Bump in the Beltway), DemFromCT (The Next Hurrah), Revere (Effect Measure).


Even when Morton Kondracke seems to be making sense he's full of crap. Consider his recent screed, "Avian flu may become top issue."

The first sentence at least isn't toxic:
While Washington, D.C., is consumed by issues ranging from the important to the downright petty, there's something huge lurking out there to really worry about: infectious diseases.
Then it goes downhill. Fast. A few sentences about the widely reported Foreign Affairs symposium, followed by:
The combined threat of infectious disease and bioterrorism presents a quandary for U.S. politicians. Do they urgently prepare for the worst, possibly wasting vast resources, or cross their fingers and hope that nothing happens?
Like taking off my shoes at the airport? Or like invading Iraq (Kondracke's favorite project)? There an even dumber "analysis" of the rivalry between Frist and Lieberman on who can give more away to Big Pharma in the name of combatting bioterrorism and "infectious disease" (no contest, by the way: Lieberman).
Frist and Sen. Joe Lieberman, D-Conn., are backing rival bills that offer tax, liability and other incentives to now-reluctant biotech companies to begin producing vaccines and diagnostics and to guarantee a market if they produce them. Lieberman contends that his bill is more comprehensive, and his aides question whether Frist is pushing various Senate committees hard enough to get legislation enacted this year.

"You have a fascinating conflation of presidential politics and serious substance at work here," said Chuck Ludlam, a former biotechnology lobbyist who's retiring this week as a top Lieberman aide.
Nothing "former" about it. Ludlum was Big Pharma's patsy and Lieberman was only too happy to lie back and enjoy it.
Whether a disease is spread by nature or by terrorists, Lieberman says, "we have essentially none of the diagnostics, therapeutics and vaccines we need to treat those who might be exposed or infected.

"If we don't have these medicines, we are likely to see quarantines and panics, which will amplify the damage and disruption."
Besides being a bald-faced lie, this is straight out of Big Pharma's talking points for why they should be given truly obscene patent extensions of the very drugs they prefer to make instead of vaccines (Viagra, etc.). According to Mr. Kondracke, however:
Clearly, this issue transcends Washington's daily political games.
Oh, clearly. Very, very clearly.

Sunday, June 26, 2005

It can't happen here

Who could imagine our government acting like this?
Bird flu is now as much of a danger to Britain as terrorism, ministers have been told by the Government's official emergency body.

Top officials from the Civil Contingency Secretariat (CCS), part of the Cabinet Office, told a cabinet subcommittee last week that a flu pandemic - which it believes could kill 700,000 Britons - is now one of the most serious threats facing the country.

Plans are being made to close schools and cancel sporting fixtures in an attempt to limit the spread of the virus, and official advice on how to try to avoid being infected will be ready for publication this summer.

Cobra, Britain's emergency committee, will co-ordinate attempts to fight the virus. But the Government accepts that, if the flu reaches Britain, there is no hope of stopping an epidemic, and that the only hope is to mitigate its effects. (The Independent)
George W.'s cabinet obviously knows something the British cabinet doesn't. Like evolution is a secular hoax, so we don't have to worry about the virus adapting. That means I don't have to worry about reports like this:
The unusual behavior of the avian flu has gotten stranger: The virus, which caused no confirmed cases last summer in Vietnam, is continuing to infect people this year.


"Everything suggests, that the situation we are in now, there is a greater risk for a pandemic than for many decades," said Dr. Peter Horby, a medical officer and epidemiologist for the World Health Organization in Hanoi. "The situation is much more complex than a year ago."


"This year, there doesn't appear to be a stop," said Klaus Stöhr, head of WHO's global influenza program in Geneva. "Every human case is worrisome because there is another chance for the virus to [mutate] and a higher chance for a pandemic to occur."

WHO confirmed four human cases this month in Vietnam, and news reports suggest two more cases have been identified this past week. By comparison, the country had no reported cases between April and late summer last year, Stöhr said.


When the avian flu first started infecting people in late 2003 in Vietnam, Horby said, it was expected to be around weeks or maybe months before subsiding. But now, he said, "we are almost in a chronic outbreak situation."


Stöhr said it was unclear why human cases have not receded this summer. It could be better surveillance or more instances of bird-to-human transmission. Or perhaps the virus has become more adept at infecting people.

"We have to plan our actions more urgently now that the virus is with us," Horby said. "There is no respite."


Unlike previous pandemics, where a virus underwent a major genetic overhaul all at once, [Dr. Michael] Osterholm said the avian strain has been changing gradually since it was first identified in 1997. He believes the virus will continue to transform, increasing the likelihood it will ultimately lead to a pandemic. (Philadelphia Inquirer)
I'm glad I live in the US, where avian flu isn't a problem. I'd be pretty scared if I lived in the UK.

P.S. If despite this, the threat of bird flu still bothers you, look for the launch of the FluWiki (announcement tomorrow).

Sunday Sermonette: Upon this rock I will build my church

Sunday, and once again time for our homily to freethought. Today, the words of the late Carl Sagan:
“There is something stunningly narrow about how the Anthropic Principle is phrased. Yes, only certain laws and constants of nature are consistent with our kind of life. But essentially the same laws and constants are required to make a rock. So why not talk about a Universe designed so rocks could one day come to be, and strong and weak Lithic Principles? If stones could philosophize, I imagine Lithic Principles would be at the intellectual frontiers.”

( Carl Sagan, Pale Blue Dot, New York: Random House, 1994, p. 38. )

Saturday, June 25, 2005

Joke of the Week

The set-up:
In an announcement made Friday afternoon, Agriculture Secretary Mike Johanns confirmed that a second case of bovine spongiform encephalopathy (BSE) has been found in the U.S. The latest case is believed to be in a cow from Texas, which was initially tested for the disease more than six months ago.

The second case of BSE to impact the U.S. cattle industry has come as a surprise to many in the business, as the cow was slaughtered last November. At that time the animal was determined to have first tested as inconclusive for BSE, but was later declared negative through a series of testing conducted by USDA.

However, a review by the department’s Office of the Inspector General determined that further testing was needed. Agriculture officials announced two weeks ago that the animal had once again been classified as inconclusive for BSE, and thus, additional testing would be done. USDA tested samples of the animal’s nervous tissue at a disease lab in Ames, Iowa and also had testing completed by a world-renowned lab in Weybride, England. (Josh St. Peters, Brownfield Network)
The punchline:

"The Food and Drug Administration, along with the USDA, is committed to ensuring the safety of the U.S. human food and animal feed supply from BSE (bovine spongiform encephalopathy). Today we saw that the system worked. The safety measures that FDA and USDA have put in place successfully kept this animal that has tested positive for BSE out of the food and feed supply. These existing safeguards have proven extremely effective, and the American public should feel secure in knowing that the current animal feed rule already provides significant protection against the spread of BSE. We will continue to work closely with the USDA on this important public health issue and evaluate every option to strengthen the 1997 animal feed ban."
Update (6/25/05, 11:15 am EDST: The system worked so well, they decided to change it on Friday.
Federal officials on Friday changed how they test for mad cow disease after a British lab confirmed the ailment in a U.S. animal earlier declared free of the disease.

The U.S. Department of Agriculture asked for more tests only after its inspector general reported "an unusual pattern of conflicting test results" on the cow killed in November. From now on, the USDA will conduct expanded tests on any animal that fails initial screening for bovine spongiform encephalopathy, or BSE, Agriculture Secretary Mike Johanns said.


Confusion and mistakes caused the delay between the cow's slaughter and Friday's announcement. Two initial screening tests showed signs of the disease, which the USDA announced in November. But the agency decided it was not BSE after its Iowa lab did two more specific tests -- called immunohistochemistry, or IHC -- that were negative.

The conflicting results led the USDA's inspector general to request another kind of test, called a Western blot. The USDA ran it and another IHC earlier this month. Both were positive for BSE. So were all but one of the tests run at the world's top BSE lab in England.

Johanns revealed Friday that the Iowa lab had run a second, experimental IHC test in November that found "abnormalities." Regulators ignored the results because the test was not proven, he said. The unapproved test was one of "four areas of concern" Johanns cited Friday, along with workers inappropriately freezing the brain sample, and the Iowa lab's failure to finish paperwork on the tests. The fourth error was storing the cow's carcass with four others during testing, making the sick cow hard to identify. All five carcasses were incinerated, Johanns said.

From now on, Johanns said, the USDA will run both IHC and Western blot tests on any brain samples flagged by initial screenings. A positive result on either follow-up will be considered a BSE case, he said. (Andy Dworkin in The Oregonian)
If this system works any better, I may give up eating altogether. What would be the point?

Flu: "We're not in Kansas anymore"

I won't dwell on the new report (.pdf) by The Trust for America's Health (TAH) on US unpreparedness for an influenza pandemic. It's all over the newswires and says the same things this and many other sources (including TAH) have been saying for a long time. Here's the gist, boiled down to two paragraphs and three sentences from the story on Yahoo:
"The U.S. lags in pandemic preparations compared to Great Britain and Canada based on an examination of leadership, vaccine development, vaccine and antiviral planning, health care system surge capacity planning, coordination between public and private sectors, and emergency communications planning."

Health officials are aware of the warnings and say they are developing a plan. The heads of the Centers for Disease Control and Prevention, National Institutes of Health and Health and Human Services Department are regularly called to hearings before Congress on the issue.
Regarding the first paragraph, TAH points out (for starters) the US has under a million staffed hospital beds while reasonable estimates of the number that could require hospitalization are up to two million. That will be quite cozy.

Regarding the second paragraph . . . aaargh! It's accurate all right. Health officials have been testifying: "Yes, it's a serious concern. But we're doing the best we can and we are actively getting ready and we will be ready." (my paraphrase of their prevarications). And don't forget: "We've broken the backs of the insurgency in Iraq," "Social security will go broke," and "There's no scientific proof on global warming."

Note to the Administration: The influenza A virus doesn't know evolution is a hoax. We're not in Kansas anymore.

No surprise (which isn't good)

Reuters is quoting Vietnam's agriculture ministry today to the effect that the H5N1 virus was mutating in a way to make human-to-human spread more likely. State-run media were reporting that laboratory results had shown the virus's "antigen structure" had changed and that was why recent major outbreaks in poultry had gone undetected. The report does not make clear what this change entailed. The team of international experts noted here yesterday is looking into this.

The situation seems to be developing as expected. Which is not encouraging.

Friday, June 24, 2005

Expiration dates for staples

The last thing we want to encourage is a purely survivalist response to the threat of an influenza pandemic. We all want to protect ourselves and our families but we will need a community response and should be working on ways we help each other through what might happen.

Sermon over (for the moment).

What about the staples you are laying in "just in case"? How long will they last? Brown sugar? Beer? Hershey bars? Even these have expiration dates on them. Fortunately the folks at Real Simple have bothered to look into this for us. Here are a few examples (via Boingboing). Click this link for the full roster, including pasta, coffee and mayonnaise (you'll be surprised).
Frozen dinners
Unopened: 12 to 18 months

Frozen vegetables
Unopened: 18 to 24 months
Opened: 1 month

Juice, bottled (apple or cranberry)
Unopened: 8 months from production date
Opened: 7 to 10 days

Maraschino cherries
Unopened: 3 to 4 years
Opened: 2 weeks at room temperature; 6 months refrigerated

Olives, jarred (green with pimento)
Unopened: 3 years
Opened: 3 months

Protein bars (PowerBars)
Unopened: 10 to 12 months. Check "best by" date on the package.

Soda, regular
Unopened: In cans or glass bottles, 9 months from "best by" date
Opened: Doesn't spoil, but taste is affected

How much H5N1 infection in Vietnam?

A nagging question about H5N1 infection in Vietnam is whether there is considerably more mild, clinically undetected or inapparent infection than accounted for by only considering the most seriously ill cases admitted to the hospital. Since the most seriously ill are the tip of the iceberg in most human viral diseases this is a plausible concern. Its significance would be that there is more transmission of the virus either from poultry to humans or from human to human than has been conceded at present.

Equivocal evidence to suggest this has apparently been obtained by a joint Vietnamese-Canadian research team working in Hanoi. Using a method called a Western blot, the researchers tested hundreds of stored blood samples to see if they showed evidence of antibodies to H5N1. Rumors are that "scores of samples came back positive." As a consequence Vietnam asked for international assistance:
A team of international influenza experts is in Hanoi, at the invitation of the Vietnamese government, to investigate worrisome signs the avian flu virus known as H5N1 may be adapting in ways that may make it more likely to spark an influenza pandemic, the World Health Organization has confirmed.

The group of about a half-dozen virologists and epidemiologists from the United States, Britain, Japan and Hong Kong will be following up on concerns raised at a special WHO avian flu summit held last month in Manila, spokespersons for the organization said Thursday.

The team will also be analysing some potentially disturbing but hard-to-assess test results that could suggest a significant number of additional human infections have occurred but went undetected. (via Canadian Press)
That's what we know at this point, but it hasn't prevented the spin machine from going into action. Apparently the results aren't that hard to assess for WHO the spokesman:
"These are highly questionable results," said Dick Thompson, director of communications for the WHO's communicable diseases branch in Geneva.
The official explanation for this diffidence is the possibility the Western blot is not sufficiently specific to rule out it is detecting antibodies to other influenza strains than H5N1, although for other viruses "Westerns" are used as confirmatory tests because they are more specific than the usual ELISAs. Westerns are "antibodies against antibody" tests and are not especially easy to do, but are easier and less hazardous than the current gold standard, the neutralization test. Neutralization tests use live H5N1 virus and tissue culture cells. If the subject's serum contains antibodies to H5N1 it will block its infectivity. This is not only a technically demanding test but requires adequate biosafety measures, not available in Vietnamese laboratories. The Canadian team was trying to see if Westerns could substitute for neutralization tests, so this effort could properly be considered a research study.

However that doesn't mean it is of no significance. There is good reason to believe Westerns are both sensitive and specific and would make a good substitute for neutralization assays. The next step is to verify the Westerns with neutralization tests, which will necessitate sending the blood sera outside of Vietnam to a WHO reference laboratory. Without analyzing the results it is hard to understand how the WHO spinmeister is able to dismiss the results so blithely. Indeed the dispatch of a high level team--a half-dozen virologists and epidemiologists from the United States, Britain, Japan and Hong Kong--could hardly be justified if the results and the general situation seemed unproblematic. Once again, WHO is playing the part of the World Reassurance Organization.

Meanwhile a systematic seroprevalence survey in Vietnam and Thailand is long overdue, either with Westerns if prove reliable, or neutralization tests if need be. Let's get on with it.

Thursday, June 23, 2005

Star Trek: the pledge

This falls into the don't-know-whether-to-laugh-or-cry category, but I decided to agree with this young lad's mother and laugh. Here is the story of an eight year old suspended from school over the Pledge of Allegiance, which he duly recited, although apparently his allegiance got pledged to the wrong thing--everything. Here is the complete post from Ms. Jaworski's Beauty Dish blog (via Boingboing):
I got a call from the elementary school administrative assistant this morning.

"Mrs. Jaworski?" I could hear her tapping a pencil against the desk.

"Uh yes, and it's Ms., please."

"Your son, 8, has been suspended for the day. Come here and pick him up."

She didn't give me time to answer, to ask questions, her voice disappeared as if someone cut the line. I stood in the kitchen, my bare feet aching from yesterday's marathon, and I took a deep breath. My son can be a nut at times, but he's never done the kinds of things that troubled kids do. He doesn't talk back, he doesn't pick fights, and he's never destroyed property. I couldn't picture him doing anything scholastically evil. Maybe he stripped and ran around the school naked, I thought. I grabbed my keys and headed out the door.

The principal met me in her office. She closed the door tightly behind me and invited me to sit in a stuffed orange vinyl chair.

"Mrs. Jaworski, 8 has been suspended from school for one day." She wore an arctic blue power jacket over black slacks, and I self-consciously tried to pull my hooded sweatshirt further over my pink pajamas.

"It's Ms., please. And sorry for my attire, but I ran a marathon yesterday and I'm too sore to change this morning." I tried to infect her with my smile, but she wore a tight-lipped expression as frosty as her jacket. "So, anyway. What did he do?" I picked at the hem of my sweatshirt, looked just to the right of her face. I couldn't meet her eyes. I felt nervous. I felt underdressed. I wondered where 8 was.

So she told me what he did. And as she told me, I started to laugh. I didn't laugh a little, either, but I belly-laughed and grabbed my stomach. My son stood with his class this morning, put small right hand over heart, faced the American flag, and recited his own personal pledge of allegiance:

"I pledge allegiance to the flag of the United Federation of Planets, and to the galaxy for which it stands, one universe, under everybody, with liberty and justice for all species."

"Mrs. Jaworski. This isn't humorous. The Pledge is an extremely important and patriotic moment each morning in the classroom. I am ashamed of your son's behavior, and I hope you are, too."

I wanted to say, Hey Lady, it's a big universe. Why should we pledge allegiance to a mixed-up country? Why shouldn't my son embrace the potential of stardust? But I stood, extended my hand, apologized for my laughter, slung my purse over my shoulder, opened her door to find my son, 8, red-eyed sitting on the wooden bench bordering the World Map wall.

I'm sitting here, working on computer things, and Mr. 8 sits in the living room. He has to write the "real" pledge of allegiance fifty times before he can return to school. But first he's watching Star Trek. Damn straight.
Hey kid. I'll boldly go with you on this one.

China syndrome

Word now is that Chinese authorities will allow the independent scientists from WHO and FAO to visit the Xinjiang autonomous region, where the lastest outbreak of avian flu in domestic geese has been confirmed in Tacheng, while additional reports of ducks and geese die-offs come from Xinjiang's capital, Urumqi (International Herald Tribune). Whether they will be able to confirm or disconfirm additional reports of numerous patients being admitted to the hospital with pneumonia is unknown.

Meanwhile the brouhaha over use by Chinese farmers of adamantine in poultry farm drinking water continues. The Chinese Ministry of Agriculture has denied any official or unofficial part in this practice, which some believe might have contributed to drug resistance of H5N1, although this is far from clear at the moment. However, it is a plausible consequence and the practice should never have been allowed.
WHO spokesman Dick Thompson said the issue of oseltamivir was raised when Henk Bekedam, the agency's chief representative in China, met earlier this week with senior Ministry of Health officials to express concern about agricultural use of the precious few antiviral drugs that combat flu in humans.

"He specifically brought up the issue of Tamiflu - oseltamivir - in agriculture....We wanted to clarify whether or not it had been used. Or was being used," Thompson said from Geneva.

"It's clear to us that the Ministry of Health shares our concerns about this and they understand the importance of ... the possible use of this antiviral in agriculture, that it might force or speed (development of) a resistant strain. (Helen Branswell, Canadian Press)
It is not clear whether this question was prompted by an abundance of caution or whether it was based on evidence (hard or soft) that use of oseltamivir or oseltamivir-like drugs was occurring in agricultural practice. While the drug is too expensive and scarce for that purpose (unless diverted in the black market) and although one starting point is a plant product (Chinese Star Anise), its manufacturer, Roche, says that there is a complex and time-consuming series of steps required to turn it into Tamiflu (trade name for oseltamivir). Roche spokesperson doubted it could be done as "knock-off," unlike adamantine.

Dr. Frederick Hayden, an antiviral expert at the University of Virginia, isn't so sure, as reported by Helen Branswell (Canadian Press, link above):
Hayden recalls a chilling conversation he had with a Chinese physician at a WHO meeting in Hanoi awhile back. She told him of the rumours of amantadine use in poultry operations. He asked if oseltamivir was used much in China. Too expensive, she replied, but noted a Chinese company made an oseltamivir-like drug.

He admitted he can't vouch for the accuracy of the information but remains worried nonetheless that inappropriate use of a drug similar to oseltamivir might have serious consequences for the future usefulness of the drug.
Well, maybe. Not enough information to go on here. But the practice of prophylactic feeding antimicrobials of any kind to farm animals should stop. It is not just a Chinese problem, or even mainly a Chinese problem. It is done my many countries, including the US. The same antibiotics used to fatten farm animals might be the ones we will need to treat a secondary infections in an influenza pandemic (not to mention a routine surgical wound infection).

Meanwhile, let's find out what's happening on the ground in western China.

Wednesday, June 22, 2005

Chinese antiviral practice is chickenfeed

Chinese authorities are denying they advocated or encouraged the practice of feeding the antiviral drug amantadine in poultry flocks as a preventive for avian flu.
Agriculture Ministry spokesman Xu Shixin, quoted by the government-run China Daily newspaper, denied a report by The Washington Post that officials encouraged farmers to give the drug amantadine to millions of chickens in their drinking water in the late 1990s to suppress bird-flu outbreaks, the China Daily said.

The report didn't say when or how widely the amantadine was misused or whether farmers still use it. Phone calls to the health and agriculture ministries yesterday weren't answered.

"The report was groundless," Xu was quoted as saying.
Groundless? I rather doubt it. I don't know if the government encouraged it or just looked the other way, but I'm fairly confident it was one or the other. The Chinese authorities are lying.

Avian influenza A/H5N1 in China and southeast asia is reported to be resistant to amantadine, but circulating strains outside this area are sensitive (see Henry Niman's interesting post on this issue here). The role that the practice played in this resistance is unknown. Influenza A readily and rapidly develops resistance to amantadine, often after only two to three days of treatment. It is an empirical question the geographic extent of resistance now and its source. But the policy issue is quite clear. This is an impermissible and irresponsible practice and the Chinese authorities should have known better. It probably doesn't even work to protect poultry.

But here's the catch. The US has been doing this with antibiotics of medical importance in animal feed for decades and refuses to condemn or stop it (see a recent post about it here). Whether or not the Chinese practice will have clinical significance in the future, the US practice has impact now. As someone once said, when you point your finger at someone, three fingers are pointing back at you. Whatever one thinks about the Chinese in this case, it goes triple for the US.

"Which side are you on?"

Lila Guterman writes for The Chronicle of Higher Education on public health topics. Her story on The Lancet epidemiological study of civilian casualties in Iraq was superb. Now she has another timely article on the vexing question of corporate influence on research in occupational and environmental health. As you would expect, it is a nuanced and balanced treatment, quoting academics on both sides of the fence regarding some ethical issues that arise when researchers work for industries with a stake in the outcome of their research. [Disclaimer: the Reveres know almost everyone quoted in this article (there are a few exceptions) and our views may be influenced by that. Another disclaimer: the Reveres also have been involved in numerous court and regulatory proceedings on the side of plaintiffs, consumers or the public interest, so you would be wise to take this into account.]

Several questions are raised by Guterman's article, among them the extent to which researchers working with corporate sponsorship can be truly independent. It has not been a hot topic in academic circles:
"There's not been a lot of debate," says Arthur L. Frank, a professor of public health and chair of the department of environmental and occupational health at Drexel University. "Most academics live in their ivory towers and do their own work: 'You leave me alone, I'll leave you alone.' It takes a certain amount of guts to stand up and say the emperor has no clothes."
Debate or not, the Bush administration's blatant interference with independent scientific advisory committees and crude manipulation of science policy has increased sensitivity to the problem. Federal research funds for environmental and occupational health are miniscule and getting even smaller when compared to other biomedical research areas, which together with fainthearted federal scrutiny of corporate health and safety has made researchers more dependent upon industry for access to data. As scientists find themselves more and more entangled with industry, they also become drawn into adversarial proceedings, with scientists facing off over multimillion dollar regulatory rules or tort claims.

New rules of scientific evidence in the wake of the Supreme Court's Daubert decision have compounded the problem. That case required federal trial judges to make a determination on the relevance and reliability of scientific evidence before allowing a jury to hear it. Industry now routinely files legal challenges to plaintiff's expert witnesses and the legal form of these challenges assert the opposing expert's testimony is neither relevant or reliable. This requires the support of other academics to say that their opposing colleagues do not use accepted or proper scientific methods, since mere differences of opinion about scientific results are not sufficient to win a Daubert challenge. Thus industry witnesses must show the other side's science is irremediably flawed and unacceptable (plaintiffs don't usually raise Daubert challenges because they are too expensive). It is easy to see hard feelings might result.
Some researchers in these fields think any collaboration with industry taints the science. "This isn't a matter of minor ethics," says Joseph LaDou, a clinical professor of medicine at the University of California at San Francisco. "These are bought scientists."


Daniel T. Teitelbaum, a doctor in Denver who specializes in medical toxicology and occupational epidemiology, says: "Industry doesn't give you money to do research. Industry gives you money to do research that favors them."
Guterman quotes Kenneth Rothman, one of the world's most prominent epidemiologists, the author of an authoritative text and who frequently has testified for industry: "You're not biased if you're correct." Again a disclaimer: I know Rothman and respect him, although our politics and sympathies are very different. I wouldn't work for many of the companies he has willingly collaborated with, but at the same time I don't consider him a corporate whore. In my opinion he is intellectually honest and technically flawless, dissenting opinions of colleagues whose politics are close to mine, notwithstanding. However there is also a substantial cadre of scientists, some of them with academic standing, who are willing to say anything in the service of their corporate consulting clients and they are joined by a virtual army of industry-pandering consulting companies whose science is almost as bad as their ethics (or vice versa).

But the real problem is not these blatant violations of scientific integrity, as bad as that is. It is the distortion of the research agenda itself. Money doesn't have to buy answers as long as it can control the questions, directing them toward things of interest to industry and away from things that are dangerous. A scientist doesn't have to alter results to serve corporate interests. We have posted here previously about how this works in the pharmaceutical industry (here and here). We have also noted the tactic of "manufactured uncertainty", a theme that comes up frequently from those Guterman interviewed:
Aside from the obvious pressures that industry exerts over research, it can influence academic scientists in subtler ways. For example, when companies cast doubt on academic studies, they often force university researchers into long and draining debates that lead to years of additional work, tying up proposed regulations or court cases in endless debates about the validity of the science.


Researchers feel forced to expand studies or repeat their work after such attacks, says David Ozonoff, a professor of environmental health at Boston University, "to dispel the doubt that industry has created."
Ozonoff could have added that industry can also create entire research agendas by constructing hypotheses that favor their position (e.g., that some chemicals which cause cancer in animals can't do so in humans because humans lack the same mechanism), forcing others to do the experiments that show it isn't the case for that chemical. The Chemical Industry Institute of Technology has made a particular specialty of doing this and it has sucked up the energies of many independent scientists who must refute the nice "scientific" stories they tell.

But in the last analysis it comes down to where one's sympathies lie. I do not testify or do research for industry for a practical reason and a personal one. Practically, my time and energy are limited. Industry has the money to buy the services of whomever they wish. They don't need me, so I save what resources I have for those who need them more and have a harder time finding them. It is not a judgment that industry can never be right, but a choice about where and how I want to devote my energies and how I want to integrate my work and my hopes for the world I live in. Others have made different choices. I wish they wouldn't but that's the way it is.

There are charlatans and good scientists on both sides. About the former, there is little to say. And for the latter, the question becomes that of the old Labor song, "Which side are you on?"

Tuesday, June 21, 2005

History lesson from Recombinomics and more on China

Henry Niman at the Recombinomics site has a very useful summary of the development of the H5N1 problem, since its first appearance as a public health issue in 1996 to the present. He traces the development through the six phases of a pandemic, bringing us to our current position on the threshold of phase 6: "increased and sustained transmission in the general population." For those following this situation on a daily basis, it is extremely helpful to step back to look at the "Big Picture." If you haven't read his post yet, by all means do so.

Meanwhile, Bloomberg reports (via the Asian Wall Street Journal) that international teams from WHO and FAO (the UN Food and Agriculture Organization) have arrived in Qinghai, China, the remote western province that was the site of a large migratory bird flu die-off and unconfirmed reports of many human cases with flu-like symptoms (see here and Niman's post for links).

This is welcome news, although the degree of access wasn't specified, and more to the point, China is said to have denied a request for a visit by independent scientists to the neighboring Xinjiang autonomous region where China has reported another large die off of geese, and as in Qinghai, there have been unconfirmed reports of many admissions to special "fever units" set up in the hospital at Tacheng city. Since the international teams are already in the area, this refusal to permit a visit is hard to understand and will not help dispel suspicions that China is not making full disclosure of their bird flu problem.

It never ceases to amaze how stupid some bureaucrats and the governments they serve so badly can be.

Republicans oppose capital punishment for murderers

Republicans seem almost unanimous in their opposition to capital punishment--for companies who murder their employees, family members and the general public. Their latest attempt at light sentencing is the WR Grace Bailout Asbestos Bill which would establish a federal compensation trust fund of $140 billion for victims who can show they were harmed by asbestos products.

The WR Grace Company is a named defendant in 129,ooo personal injury suits and their executives have been criminally indicted for a conspiracy to cover up crimes, obstruction of a federal agency and fraud. The company made asbestos products and chemicals and was the defendant in the "Civil Action" case that received the Hollywood treatment. Independent experts put Grace's actual financial liability for compensating the many victims of their criminal negligence at somewhere between $1.6 billion and $3.2 billion. Under the Republican bailout bill (there are also some Democrat collaborators), Grace will pay into the trust fund an estimated $418 million and end all uncertainty about future liability from this source. Pretty good return on their lobbying investment.

The company is currently in bankruptcy proceedings and is "attempting" to reorganize.
"I hesitate to use the word windfall, but it would definitely be a favorable outcome for them," said Crystal Skinner, who tracks asbestos legislation for Susquehanna Financial Group. She pegs the odds of the bill passing this year at 30 percent.

Grace won't realize any of those savings if it emerges from bankruptcy before the bill passes, experts said. The company's reorganization plan requires it to create its own asbestos compensation fund, which the company says would be capped at $1.6 billion. Once that fund is established, the company is stuck paying that amount instead of the $500 million or less that it would pay under the proposed federal legislation.

"No one will say it publicly, but I think a majority of the larger asbestos cases have been stalled due to the efforts in Washington on the federal [asbestos] bill," said Peter Kelso, a senior editor for Asbestos Bankruptcy and International Asbestos Report newsletter. "Obviously, it is going to benefit them greatly, so the longer they play it out ... the more it will benefit them." (The Baltimore Sun)
A frequent excuse for this inexcusable coddling of corporate murderers is that financially executing the company would leave many people jobless (of course the ones they killed are also out of a job). By that reasoning, outsourcing to India should be a corporate crime, too, but never mind:
[S]ome industry experts and economists say Grace remains a fundamentally sound company if the uncertainty associated with the personal injury suits is stripped away. The company reported a 14 percent increase in 2004 sales and pretax income from core operations of $179.3 million, up nearly 21 percent from 2003. Asbestos liability charges resulted in a loss of $402.3 million for the year.

"The managers -- at least the ones running the company now -- are doing a good job," said Emory University economics professor George J. Benston, who published a study of companies forced into bankruptcy by asbestos lawsuits. "The sensible thing to do is let them keep running and extract as much as you can from them short of killing them."
So no capital punishment for WR Grace (or the others in the asbestos death squads). If you think it would be too harsh, let's recall a little corporate history. J. Peter Grace, a scion of the Grace fortunes and company capo after WWII, had an eye for talent. After the war he sprung from prison, hired and employed for thirty years one Otto Ambros, a convicted Nazi war criminal who also had expertise in chemistry, useful for a big chemical company. What was Ambros's chemical specialty? Before and during the war he worked for the German chemical conglomerate I.G. Farben and help develop "Zykon B," the gas used in the Nazi gas chambers. Ambros also gave us the nerve gases Sarin and Tabun. But he was a chemist. Useful fellow.

Oh yes, there was also this:
…Conviction at Nuremberg for the enslavement and mass murder of two hundred thousand inmates at Auschwitz did not bar Otto Ambros from later employment as a high level technical advisor to a major American corporation, W. R. Grace and Company, and as a consultant to the United States Department of Energy. When queried about Ambros in March 1982, a representative of W. R. Grace said 'We do not feel there is anything wrong in employing this man in a technical position years after whatever he did.' The spokesman added that J. Peter Grace, chairman of the board, 'is extremely proud' of his relationship with Ambros and did not find the appointment 'embarrassing in any sense.'

James W. Nance, a special assistant to President Ronald Reagan for national security confirmed with apparent approval that Ambros had "recently" served as a consultant to the Department of Energy. A White House spokesperson declared that Ambros, who served only three years for his crimes, 'had paid his debt to society.' (my emphasis; from Rubenstein and Roth, Approaches to Auschwitz, quoted in Joanne Tuck Preliminary Study on Ethics and German Engineers During the Nazi Period)
Republicans may get WR Grace out of financial bankruptcy, but they'll be keeping them company in moral bankruptcy.

But you know how it is with Republicans: always coddling criminals.

Monday, June 20, 2005

The body yields some evidence on bird flu

The online version of CDC's scientific journal Emerging Infectious Diseases has just put up a paper detailing laboratory and autopsy findings in a little 6 year old Thai boy who died last year. The patient died of a primary viral pneumonia and acute respiratory distress 17 days after onset of his illness. One of the first entries in the forthcoming Flu Wiki will explain a bit about primary viral pneumonias but for now think of it as an infection of the delicate cells in the part of the lower respiratory tract where gas exchange takes place. Intensive oseltamivir therapy was not started until day 15 because of unavailability of the drug in Thailand.

Using a variety of techniques to verify that the infection was from H5N1 virus and to locate those organs and tissues where the virus could be found and replicating, the authors obtained surprising findings in this tragic case (I feel compelled to keep reminding myself that this object of medical inquiry in a scientific journal was somebody's little boy, an older or younger brother or a best friend).

Of particular interest was evidence that the virus was present and replicating in the intestinal tract, although evidence of viral proteins weren't detected there. In addition, the pathologic damage was more or less confined to the extremities of the respiratory tree (the Wiki will also explain this). In other influenza infections (like the common H1 and H3 infections) there is evident damage to the upper respiratory tract, giving rise to the symptoms of running nose and hacking cough we associate with the disease. In this case it was just the areas where gas exchange takes place that were infected (the type II pneumocytes), with fluid in the spaces between the gas exchange sacs (interstitial pneumonia). There was also sign of a secondary fungal infection of the lungs, possibly a terminal event. While there was evidence of replicating virus in the intestines, the tissues looked normal. In keeping with other findings, there were increased levels of certain cytokines (chemical signalling substances induced by infection). While only suggestive, this is consistent with a role for a dysregulated defense reaction playing a part in making the infection more severe.

The presence of the virus in the intestinal tract raises the question of whether stool is infective in these patients, an important point for transmission. The localization of the virus to the lower respiratory tract also suggests that the usual nose and throat specimen swabs may be less reliable for H5 infection than for other influenza viral subtypes.

This report is one of very few autopsy reports in the scientific literature, despite the fact that 59 deaths have occurred from this disease in southeast asia. Cultural reasons clearly play a part (as they do in the current low autopsy rate in the US). While we continually seek important viral gene sequence information, this case reminds us we have much to learn from examining the damage done to real people.

More surprises are clearly in store.

High caliber guns in a low caliber Congress

The National Rifle Association and their toadies in the House of Representatives (whom do they represent?) have won another one, defeating an effort to stop their patron merchants of death from exporting the absurdly high-powered .50-caliber guns, supposedly powerful enough to take down a jet liner at a distance of a mile (AP via LA Times).

The vote on Virginia Democrat James Moran's bill to block the export wasn't even close: 278-149.
The .50-caliber rifle is the most powerful firearm in wide circulation. It can penetrate thick steel used to armor personnel carriers and is accurate at distances greater than a mile. Moran said that if someone were to use the weapons from such distances, he easily would evade law enforcement.

The risks associated with .50-caliber weapons gained attention this year after CBS' "60 Minutes" aired a report demonstrating the ease with which .50-caliber rifles could be exported to overseas militias.

But the NRA said the amendment was an unnecessary infringement on gun rights and that existing laws provide penalties for smuggling the rifles.
This is so irresponsible and reprehensible that it defies one's ability to express adequate condemnation, and while Representative Moran should be praised for trying to stick his finger in the dike, it is telling he didn't have the gumption to ask for everything he should have:
"These are unparalleled weapons, and I'm not trying to restrict them in the United States," said Moran, D-Va. "I just don't want them sold by arms dealers."
Question: why wasn't he trying to restrict them in the United States, too? Does anyone with an ounce of sense feel safer knowing these monstrosoties might be in our communities?

More cases in Vietnam

The newspaper Siagon Liberation is reporting two more bird flu cases in northern Vietnam, along with three more suspect cases (via XinhuaNet). The cases were said to have been admitted to the Institute of Tropical Diseases in Hanoi over the weekend. This raises the unofficial case count since the first of the year to 63 (although the newspaper counts 64). The paper also reports that the Hanoi hospital currently has under care 28 people with flu symptoms, of whom 13 are confirmed cases.

It is becoming difficult to sort out the newly reported from the already reported, but it is quite clear that new cases are now appearing at an accelerating pace.

Sunday, June 19, 2005

The Flu Wiki

Sometime next week (we hope) three collaborating bloggers (Revere of Effect Measure, Melanie Mattson of Just a Bump in the Beltway, and demfromct of The Next Hurrah) plan to launch a new experiment in public health. Many knowledgeable people believe a serious pandemic from avian influenza is possible in the near future. In a highly interconnected world, the consequences could be grave, with widespread illness and mortality accompanied by major stress on the social system in almost every affected locality. Few, if any, national governmental authorities have prepared for this, despite adequate warning.

Because such an event would be geographically widespread it will leave each local area to cope with and solve problems on their own. In such a circumstance, any preparation, however limited, can save lives and suffering. And to make these local preparations, knowledge is not only empowering, but essential. Rather than leave these preparations solely to governmental authorities and rather than restrict knowledge to designated "experts," both of whom have failed to prepare adequately, it is necessary to begin to undertake many needed tasks ourselves. The Flu Wiki is our first try at a mechanism to facilitate this.

Many readers of this site know what a wiki is. But probably many more don't. Here is one description, taken from the site that makes the software engine we plan to use (pmwiki):
WikiWikiWeb is an "open-editing" system where the emphasis is on the authoring and collaboration of documents rather than the simple browsing or viewing of them. The name "wiki" is based on the Hawaiian term "wiki wiki", meaning "quick" or "super-fast". The basic concept of a WikiWikiWeb (or "wiki") is that (almost) anyone can edit any page. While at first this sounds like a recipe for complete anarchy, the truth is that sites using this system have developed surprisingly complex and rich communities for online collaboration and communication. Yes, it's possible for someone to go and destroy everything on a page, but it doesn't seem to happen often. And, many systems (including this one) have built-in mechanisms to restore content that has been defaced or destroyed.

The point of the system is to simply make it as quick, easy and rewarding as possible to create or edit online content.

Using any standard Web browser, a person can edit (almost) any page on the system using relatively simple TextFormattingRules. [In fact it's] not even necessary to learn the Text Formatting Rules; others will often come in and reformat things for you. After all, anyone can edit!
The most famous example of a wiki is the huge free encyclopedia, Wikipedia. Our intention is not to compete with wikipedia, but instead establish a venue for knowledge compilation and generation relevant to epidemic avian influenza. How it will evolve and be configured will be determined by its contributors (you!), but we are hoping eventually to have city, region and country specific sections, entries explaining important elements of biology and drug actions, anticipation of consequences and solutions for them, and many other things beyond our imaginations but within the ken of our collective intelligence.

Sunday Sermonette: prophecies of the present

Satan may not be real, but he exists as a human impulse. Listen as he speaks:
"The good Christian should beware the mathematician and all those who make empty prophecies. The danger already exists that the mathematicians have made a covenant with the devil to darken the spirit and to confine man in the bonds of hell."
- Saint Augustine (354-430), Christian church father, bishop

Secular schools can never be tolerated because such a school has no religious instruction and a general moral instruction without a religious foundation is built on air; consequently, all character training and religion must be derived from faith.... We need believing people.
- Adolf Hitler, April 26, 1933, from a speech made during negotiations leading to the Nazi-Vatican Concordat of 1933

"Today we are engaged in a final, all-out battle between communistic atheism and Christianity."
- Sen. Joseph McCarthy, in his famous address to the Ohio County Women's Republican Club on February 9, 1950

"I hope I live to see the day when, as in the early days of our country, we won't have any public schools. The churches will have taken them over again and Christians will be running them. What a happy day that will be!"
- Rev. Jerry Falwell, America Can Be Saved, 1979 pp. 52-53, from Albert J. Menendez and Edd Doerr, The Great Quotations on Religious Freedom

"The Constitution of the United States, for instance, is a marvelous document for self-government by the Christian people. But the minute you turn the document into the hands of non-Christian people and atheistic people they can use it to destroy the very foundation of our society. And that's what's been happening."
- Pat Robertson, The 700 Club television program, December 30, 1981

"The "wall of separation between church and state" is a metaphor based on bad history, a metaphor which has proved useless as a guide to judging. It should be frankly and explicitly abandoned."
- William Rehnquist, Chief Justice of the U.S. Supreme Court, Dissenting Opinion in Wallace v. Jaffree (1985)

"We at the Christian Coalition are raising an army who cares. We are training people to be effective -- to be elected to school boards, to city councils, to state legislatures, and to key positions in political parties.... By the end of this decade, if we work and give and organize and train, THE CHRISTIAN COALITION WILL BE THE MOST POWERFUL POLITICAL ORGANIZATION IN AMERICA."
- Pat Robertson, in a fundraising letter, July 4, 1991

"Evolution is a bankrupt speculative philosophy, not a scientific fact. Only a spiritually bankrupt society could ever believe it. ... Only atheists could accept this Satanic theory."
- Rev. Jimmy Swaggart

“I want you to just let a wave of intolerance wash over you. I want you to let a wave of hatred wash over you. Yes, hate is good. Our goal is a Christian nation. We have a Biblical duty, we are called by God, to conquer this country. We don’t want equal time. We don’t want pluralism.”
- Randall Terry, founder of Operation Rescue and advocate for Terry Sciavo, quoted in The News-Sentinel, 8-16-93

"Therefore, I, George W. Bush, Governor of Texas, do hereby proclaim June 10, 2000, Jesus Day in Texas and urge the appropriate recognition whereof, In official recognition whereof, I hereby affix my signature this 17th day of April, 2000."
- George W. Bush, "Jesus Day 2000" Proclamation
Source: Ethical Atheist

Addendum to the peoplethings above
: You lose.

Saturday, June 18, 2005

War, peace and bird flu

As the slow trickle of hard information on new bird flu cases in Vietnam forces us into another start-stop cycle of hurry-up-and-wait, we catch only incomplete glimpses of what is happening. The most amazing report (not because it reports anything new but because of the source) is this one:
Washington -- Health officials in Vietnam have confirmed four new human cases of bird flu since June 1, and all are being treated at a Hanoi hospital. The total number of humans stricken with avian influenza during the Southeast Asian outbreak now comes to 107, according to the World Health Organization.


If the [H5N1] virus becomes able to cross the species barrier with ease, U.S. health officials warn of catastrophic consequences to life and the global economy.

"A pandemic of influenza could result in 350 million deaths globally,” said Michael Osterholm of the U.S. Department of Homeland Security, “and would cripple the global economy with the suspension of international trade." [Dr. Michael] Osterholm, associate director for the National Center for Food Protection and Defense, [said] at a Council on Foreign Relations meeting June 16.


Osterholm characterized a pandemic influenza as "the perfect storm" for the global economy because of its potential effect on countries that depend on overnight international trade for critical services.

"Collateral damage from the pandemic would also be significant because a suspension in trade would mean that countries will not have access to imported products used for manufacturing, life-saving medications and other consumer items," Osterholm said.
The writer is Todd Bullock, Washington File Staff Writer for an online publication of the U.S. State Department. Does Condi know what her minions are saying while she warns us about non-existent WMDs?

Meanwhile Agence France Presse (via Vietnam Tribune) says that the six new suspected patients reported yesterday have tested positive, although a second test on the doctor reported infected is now negative . Whether the doctor was a false positive followed by a true negative or a true positive followed by a false negative is impossible to say, but the latter has been common in Vietnam [and see this report from today's Thanh Nien News which says he is a case and is in stable condition]. The six new cases are said to be from the northern provinces and to be in stable condition at Hanoi's Institute of Tropical Diseases.

These media reports notwithstanding, Vietnam notified WHO on Friday about four new cases (not six). WHO could not determine if these four cases were part of the six or yet another four cases.
"The data which we have received do not suffice to determine whether these are the cases which we became aware of yesterday," Dr. Klaus Stohr said.

"We are not sure."


On Thursday the WHO received unofficial confirmation it felt was sufficiently strong to issue a statement saying it believed the media reports [about the six cases] were accurate.

But the Vietnamese government statement that came forward on Friday listed only four cases. And there was not enough identifying information to determine if they match up with the earlier reported cases.


Stohr could not explain the discrepancy in the numbers.

"It could be the case that two more cases could be reported tomorrow. We don't know," he said. "The reality is that is the piece of information that we have." (Canadian Press via myTELUS)
These are cases confirmed between now and the beginning of the month and bring to seven the number one source said are being treated at the moment in Hanoi (but see below).
The World Health Organisation says while it is still waiting for official confirmation from the Vietnamese Government, it believes the report [of six cases] is credible.

Peter Cordingly from the WHO's Asia Pacific headquarters in Manila says the fact that there are so many cases in one hospital is worrying.

"Clusters always send our blood pressure up, this is the biggest one," he said.

"The previous one was five so it's not an enormous jump but they do catch our attention and we need to have very swift information of this.

"While we dont know how a pandemic will start it will almost certainly start through a cluster so every cluster has to be very closely examined." (ABC Net [Australia])
Where does this leave us? Six new cases, maybe four more (or maybe just six that include the four), not to mention yesterday's media reports (local daily, Young People) of "23 local people with bird flu symptoms, of whom 11 have been confirmed to have contracted bird flu virus strain H5N1 by the hospital's officials." (via Xinhuanet; see also Thanh Nien today which reports specifies further 11 hospitalized cases and 12 more "being treated")

Maybe there is a reason why there is so much confusion here. This does happen, especially in chaotic and rapidly changing circumstances. But if the cause is a chaotic and rapidly changing situation, this in itself is a danger signal. If this is not the reason, then that leaves incompetence and disorganization or intransigence. The choices here are not palatable.

There is understandable impatience with WHO for not getting to the bottom of this faster. But while I have been critical of them in the past, their options here are fairly limited in the face of the conventional claims of national sovereignty. The US also resists acting in the global interest when it suits its parochial national interests. For policies like climate change, the global consequences might be as bad or worse than an influenza pandemic (climate change is a catastrophe in slow motion but just as unstoppable potentially devastating as bird flu).

An impending pandemic, global climate change, acts of genocide and wanton war-making all suggest the same thing: that a formal international social contract be forged that allows national sovereignty only to the extent a state's leaders act in accordance with fundamental norms of justice toward their own peoples and in ways that do not endanger the peoples of their region or the world. Failure to honor this social contract should result in ostracism from the comity of nations and presumptive abrogation of existing treaties, commercial agreements and reciprocal arrangements; and when crimes against humanity have been perpetrated those responsible should be subject to apprehension, detention and fair trial in the International Criminal Court once they enter the jurisdiction of another nation.

Many people would immediately assent to these sanctions in the case when the behavior of a nation's leaders increase the danger of a disastrous disease pandemic and would allow WHO to force a government like Vietnam's to provide urgently needed public health information. If it is desirable in tis circumstance, why not the same desire regarding matters of war, peace and fundamental human rights?

Under the surface, the serious public health situation of responding to an impending pandemic reveals a deeper connection with matters of war, peace and crimes against humanity. Something to ponder, even as we scramble to prepare for avian influenza.

Friday, June 17, 2005

What is to be done

If an influenza pandemic is indeed on the way, there is much to be done and little time. And many potential problems need to be anticipated and some solutions devised and readied. This task has proven beyond our governments (federal, state and local) and there is no reason to believe they will suddenly acquire the ability to accomplish it in the midst of chaos. So we'll have to do it ourselves.

With luck from the techno gods, next week the Reveres will join The Next Hurrah's DemFromCT and Just a Bump in the Beltway's Melanie Mattson in a new effort, a collaborative resource on influenza. Henry Niman will join us, and so, we hope, will many of you. We have chosen the "Wiki" format because it is the one that can take advantage of the substantial amount of "raw brain power" and latent expertise in the vast blogosphere community. This means it will be a shared endeavor. You will be able to add to or edit existing entries or submit a new one. For the most part quality control will be of the "self-correcting" kind, i.e., those who see errors in entries will correct them. But some control will be exercised by us as we try to guide things along constructive and useful lines according to principles suitably adapted from the wikipedia.

This will not be a discussion board, news filter or soap box. We have our blogs for that and we hope the many and still growing number of existing bird flu sites will continue to function as they have. Our objective is to provide an accurate and responsible base of scientific information, collaboratively developed, about influenza and the means to prevent it, treat it and control it. The emphasis will be on community solutions to a community problem. If you choose to go off to a cabin in the woods, this will not be the place to explain how to build and supply it. While individual actions will not be avoided, our intention is to empower people in their local communities to initiate and encourage innovative, humane solutions to the problem of a serious epidemic disease in our midst. Thus it will be a place to suggest how your community hospital can better prepare, how your community leaders can think ahead to the inevitable problems that will appear, and where you can contribute your ideas and experience to make everyone's community better able to endure an onslaught from nature's bioterrorist.

This is an experiment borne of necessity, anxiety, and hope. Our three sites will post further information as we scramble to get this thing ready to go. At that point it will be up to all of us to make it useful and constructive.

Eat, drink and be merry, for tomorrow . . .

Canadian Press (the reliable Helen Branswell) has more from the famous Osterholm "we're screwed" press briefing. Osterholm reiterated what he and others have said elsewhere and often. Planning is essential and there hasn't been enough of it. He pointed to the need to ensure food supplies as especially critical:
Osterholm said the "just-in-time" delivery model by which modern corporations operate means food distribution networks don't have warehouses brimming with months worth of inventory.

Most grocery store chains have only several days worth of their most popular commodities in warehouses, he explained, with perhaps 30 days worth of stock for less popular items.

He pointed to the short-term shortages that occur when winter storms threaten communities, then suggested people envisage the possibility of those shortages dragging on for somewhere between 18 months and three years as the expected successive waves of pandemic flu buffet the world.

"I think we'll have a very limited food supply," he said in the interview.

"As soon as you shut down both the global travel and trade . . . and (add to it) the very real potential to shut down over-land travel within a country, there are very few areas that will be hit as quickly as will be food, given the perishable nature of it."
Given the non-local nature of so much of our food supply, we can add (possibly severe) food shortages to the list of woes a shutdown of both local and international trade and commerce will produce. The list is long. A few other items (from WebMD):
Osterholm complains that U.S. officials and companies have not planned for the widespread logistical disruptions that would result if bird flu were to spread within the next couple of years. His warnings range from inadequate planning for hospital overcrowding to the fact that the U.S. market has only 2.5-week supply of caskets.

Local and federal agencies have not planned for widespread disruptions to schools and workplaces as the public is told to stay home and gymnasiums are converted to emergency medical facilities, he says. Travel restrictions and a run on vital supplies, such as masks able to filter flu viruses, would "no doubt" lead to an economic shutdown, he adds.


Others offer equally stark warnings that the U.S. has not engaged foreign governments over how nations will react in the event of a global pandemic and economic standstill. Poor and middle-income governments have already begun to complain that they are being left out as industrialized countries make deals to buy stockpiles of antiflu medications, says Laurie Garrett, the council's senior fellow for global health and a former journalist.

"We have no agreed-upon mechanisms of any kind," Garrett says. "This could turn into a big, bloody mess."
So here's my question to our national health officials: WHAT'S THE PLAN NOW?