But to understand why the story is wrong means recognizing a weakness of science as it’s often practiced today.

Wade’s claim is based on two papers published this month.  A relatively well done study by Haensch et al. in PLoS Pathogens earlier in October tested human remains from well-identified plague pits — burial sites for medieval plague victims — in different parts of Europe.  Researchers amplified DNA sequences of the plague bacterium, Yersinia pestis, at specific genetic loci, and tested to see whether the DNA matched known sequences of contemporary Y. pestis genes.

The findings published in PLoS suggest that the Black Death and perhaps subsequent waves of plague in Europe were indeed caused by Y. pestis — which would tend to debunk the theory proposed by some British researchers that the Black Death was some kind of viral hemorrhagic fever outbreak.  And they suggest that there were at least two widely different Y. pestis strains involved in different parts of Europe.  Here’s a bit of the abstract:

[O]n the basis of 17 single nucleotide polymorphisms plus the absence of a deletion in glpD gene, our aDNA results identified two previously unknown but related clades of Y. pestis associated with distinct medieval mass graves. These findings suggest that plague was imported to Europe on two or more occasions, each following a distinct route.

The main weakness here is that DNA could not be amplified from all of the plague pits the researchers studied, but after using alternative means to test the DNA debris against contemporary gene sequences the investigators concluded that the absence of genetic material reminiscent of one strain of Y. pestis was evidence that that strain was not in play in that part of Europe at the time.  Probably right, but stretching the available evidence.

It’s a common mistake, alas.  To paraphrase Karl Popper:  just because you see DNA from white swans and don’t see any DNA from black swans, doesn’t mean that black swans don’t exist.

Still, the PLoS paper is persuasive that more than one strain of the plague bacterium was circulating, and probably causing deaths, in the plague period in Europe.  Of course, it says nothing about China.

So where does the NYT reporter get his headline-grabbing story?  A paper to be published in Nature Genetics online (still embargoed at the time I’m writing, but a summary appears here) states that the sequences of plague DNA amplified from plague pit remains, as well as contemporary isolates, can be placed on a molecular clock because of the occurrence of unique mutations.  Winding the clock backward, the researchers conclude that the Ur plague organism, ancestor of all Y. pestis, came from the far east.

The molecular biology may be unimpeachable, but the inferences about history aren’t supportable by molecular evidence.  That might explain why they’re almost certainly wrong.

The problem (scientists, I hope you’re listening!) is that you may know very well what you know, but you can never know what you haven’t seen.  The hereditary tree has its roots in China.  Here is one proposed by some of the same authors in a 2004 PNAS paper:

In this set-up, isolates of Y. pestis from China seem closest to the primordial strains.

But of course, the molecular clock doesn’t take account of strains that are no longer extant.  And ones that haven’t been unearthed.  The contemporary researchers don’t see them (or don’t know how to look), so they don’t exist.

It’s a bad mistake, inferentially.  And historically.  It’s where the NYT writer goes wrong.  Almost certainly, plague did not begin in China.  It began as an enzootic infection of small mammals in the uplands of central Asia.  This is the story convincingly relayed by William H. McNeill in Plagues and Peoples a generation ago, and none of the many accounts I’ve read since then has debunked it.

Plague would have had to begin in an ecosystem in which it could circulate at moderate transmission rates with little pathogenicity among small mammals (the natural host of the bacterium).  Exactly where it started remains open to question, but it was probably in the area that is now Turkestan/Uzbekistan.  With the development of trade between that region and China, intermixing of local (central-Asian) animals with caravan-accompanying rats would have allowed Y. pestis to adapt to the latter.

Quite possibly China was the source of the first human outbreaks of plague — because the river valleys of China were settled and agricultural (therefore offering feeding opportunities for rats as well as multiple opportunities for rat-human interaction) long before Europe was.  That fact probably accounts for the biologists’ (mistaken) belief that their early samples show that Y. pestis started out in China.

But plague began as — and remains — a disease of animals.  To acknowledge that human outbreaks in China preceded the human outbreaks in Europe (the Justinian plague that began in the mid-sixth century, the Black Death that began in the 1340s, and subsequent visitations) is not the same as saying that plague originated in China.

Which it didn’t.  Plague is an animal disease from Central Asia.  Plague’s long history is the usual one:  ecosystem change, trade, animal-human interactions, alterations in climate and economic conditions, and occasional opportunities for mass human illness.   (One world, one health.)

Above all, remember that science is only capable of drawing conclusions about what scientists can observe.  Don’t be taken in by hair-raising stories.  Even in the NY Times.

What I value about H5N1 is the tracking of the mosquito-borne viral diseases, like dengue and chikungunya as well as H1N1, that reveal the effects of the elision of ecosystem boundaries; the close attention to outbreaks that stem from changes in human-animal interactions — like the recent outbreak of plague in Tibet and, of course, H5N1; and the watch it keeps on the vaccine trade, as in yesterday’s post picking up a report in The Nation on the purchase of flu vaccine from France and one last week on a US tech company’s trials of a new flu vaccine (which won’t help the public but is, apparently, already helping the company to get richer).

The kind of close attention to the details of complex interactions amongst humans, animals, and both the natural environment and the economic one that H5N1 shows is indispensable.   It should spur more interest in wresting public health away from the simple-minded mass-vaccination schemes of medical officials in the U.S. and other wealthy countries — the point of which is usually to transfer public monies into the hands of pharmaceutical companies.  And move us to toward a more complex and inclusive view of the nature of health.

But this AP article grabbed me.  According to New York City, over 6 percent of residents who responded to a community health survey claimed to have dealt with bedbugs in the past year.  In response, the city will withhold half-million dollars normally budgeted for the city’s health department  and redirect the funds to an anti-bedbug campaign.

Some might argue that the $500,000 would be better used for preventing deadly illnesses and accidents, not just bug bites.  Still, the campaign seems right.  According to the AP story, environmental health people will work with a “top entomologist.” (Professionals collaborating across sectors:  One City, One Health.  Good.)  A note by Javier Hernandez at the NY Times‘s City Room blog is guarded, but some (like Molly Fischer at the NY Observer) seem relieved that there will be a big anti-bedbug crusade at last.

Not a very big crusade, but at least a multifaceted one, as the Bed Bug Advisory Board’s Report suggests.

But how can every day not be AIDS Day?  Over 5,000 people die of AIDS each day, worldwide — even now, in the era of effective therapy.  In south Asia alone, more people die of AIDS every two weeks than have died of the H1N1 swine flu worldwide in the past six months (about 8,000).  In Africa, AIDS takes that toll every two or three days.

AIDS is a big problem in far-away poor countries, in other words.  But unlike the usual poor-nation problems that are easily ignored in comfortable North America — malaria, sleeping sickness, dengue, diarrhea, and more — AIDS is still a problem here, too.   Surely, you might think, we ought not to need any reminders about AIDS.

Much has been said about AIDS, and much has been done.  What does World AIDS Day add?

A harder question, perhaps: why can’t AIDS just be an ordinary disease? Surely, you might think, it isn’t special anymore.

Here are some thoughts on the problem of ordinariness, published in the American Scholar a few years ago.  The occasion was the 25th anniversary of the announcement of the first U.S. cases of AIDS.

Joshua Holland’s post at AlterNet yesterday tries to explain why H1N1 swine flu shouldn’t be cause for hysteria.  He puts this outbreak in the context of flu history and the threat posed by other, more harmful, conditions — malaria for instance.  Holland plays a little bit fast and loose with the numbers:  it probably isn’t accurate to extrapolate, from the number of confirmed flu deaths so far, to get a total number of deaths that will be caused by the swine H1N1 strain this year — more efficient spread in the  cities of the Northern hemisphere in the coming few months is likely to produce fatalities at a higher rate than the more sporadic outbreaks here in April and May.  And he’s overly critical of the media — a point brought out by Revere in a response to Holland at Effect Measure today.

But, as Frank Furedi has been telling us (recently in Erasmus Law Review, for example), try to explain how people’s deep-seated anxieties drive perceptions that risk is extraordinary and unprecedented (and contribute to demands for more and better high-cost technology to deal with it) and you get some people riled up.  Disappointingly, even Effect Measure, whose assessments are consistently level-headed and cogent, slips here, flashing the moral-entrepreneur card at Mr. Holland:

Joshua Holland has never cared for a critically ill person with Acute Respiratory Distress Syndrome (ARDS), which is often the terminal event for flu patients. So I’ll tell him. It doesn’t matter if it’s caused by bacteria (many are). Half of them die no matter what you do and no matter what intensive care unit you have available to you or what antibiotic or what computer controlled respirator. We still can’t do much.

Nobody thinks it’s a good idea to let people get ARDS, and Holland acknowledges that flu is a problem that should be dealt with.  But that’s not always enough.  Question the intensity of perceived risk or the need for all the technology, and you find this out fast.

But Revere is back on track when noting that lots of problems — including malaria — are horrendous and deserve attention, and probably don’t get it because they happen to people far away.

Where would the impetus to deal with global problems besides flu come from?  A global organization that can keep things in perspective would be useful.  Poor W.H.O. isn’t positioned to do that.  Yesterday’s flu advisory from W.H.O. emphasizes the use of antivirals (oseltamivir and zanamivir) to treat people with severe or possibly severe flu:

Early treatment is especially important for patients who are at increased risk of developing complications, those who present with severe illness or those with worsening signs and symptoms.

Yet, the W.H.O. also warns against hastening the development of resistance.  This agency gets a lot of flak for not doing more and for panic-mongering when it does do more.  But, really, it’s only doing its job:  offer advice, and support interventions when invited.  It isn’t consistent, naturally.  It can’t make binding policy.  It faces a limitless and essentially insuperable legitimation problem.  In a way, W.H.O.’s hardest job is simply to maintain its own legitimacy.

Still, in a world poised to interpret signs of illness as evidence of risk and eager for technical fixes to alleviate the sense of vulnerability risk instills, the W.H.O.’s announcements can seem authoritative — and look like beckoning to the drug makers.  A Reuters story yesterday is entitled “Early Use of Antivirals Key in H1N1 Flu: WHO,” and highlights the value of the two antiviral medications more than the caution W.H.O. wants to instill.

Meanwhile, agencies that should be making real policy are focusing on immunization.  In today’s Washington Post, Rob Stein reports on health care workers’ resistance to mandatory flu vaccination.  New York State made flu immunization mandatory early on, not only for salaried health care workers but for anyone — including medical and nursing students — who might come in contact with patients, and is putting teeth into the requirement with sanctions for refuseniks.  The state resorts to high  moral rhetoric to justify its policy.  The state’s health commissioner told Stein that “the rationale begins with the health-care ethic, which is: The patient’s well-being comes ahead of the personal preferences of health-care workers.”

And at CDC, the director is cautioning that there might be a rough start-up to the swine flu immunization campaign, as the first doses of vaccine will be made available in early October.  According to the NY Times, there should be 40 million doses of vaccine available by mid-October.

We wonder whether immunization will be of any public health value at all, by the time there’s enough vaccine that it can be offered to anyone other than health care workers and a few of the people who really need protection (young people, infants’ caregivers, and pregnant women, especially — DemFromCT’s round-up at DailyKos is always worth reading).  Given the rapidity of spread of flu — in 37 U.S. states, H1N1 spread is already regional or widespread; flu is spreading locally in 12 more states, Puerto Rico, and Washington, D.C. — and based on the usual course of flu outbreaks, it seems possible that this outbreak will peak by mid November.  There’s no knowing if that will be so, obviously.  Even if it is, immunization would continue to be useful to prevent severe cases among people who are likely to get very sick if infected.

But mass immunization would no longer be of much use in preventing further incidence of infection on a population level if high levels of acquired immunity are reached across much of the population by the time vaccine is widely available.

That’s the problem with relying on mass immunization as the centerpiece of public health response: as in the old joke about comedy, timing is everything.  In 1976, there was too much immunization, too soon.  It might turn out that this year, there’s too little, too late.  The dynamics of vaccine availability and the dynamics of flu spread have to be watched in tandem, and policy updated accordingly.

In any case, with vaccine at the center, the rest of the story — the complex environmental interactions that allow flu genomes to recombine, the trade in animals and feed that allow viruses to move around, the problems of affordability and immune status and competing viral subtypes, the health care facilities to handle severe cases, and so on — gets shoved to the side.

Last Tuesday, a post by Revere at Effect Measure highlighted the effect that cultural anxieties have on the production of scientific knowledge — specifically with regard to modes of contagion.   In the 1920s, a time of worry about immigrants and socialists, public health “concentrate[d] on society’s most marginal people, in keeping with the Zeitgeist.”  Thus Typhoid Mary, and other concerns about germ carriers.  By contrast, when the environment is of most concern, people worry about transmission via objects — fomites in our odd epidemiology jargon (from Latin fomes:  touchwood or tinder).  There are reminders to wash hands after touching the subway handholds, not to handle other kids’ toys, to think about doorknobs.

On Thursday, “Swine flu this fall:  turbulence ahead” took the time to work through the results of mathematical modeling — a highly readable post which explains why some modeling results suggest a rationale for the belief that swine flu might spread intensely in the northern hemisphere this fall.  Revere does the favor of reminding the reader that models are not always good predictors of what will happen.

History shows that the metaphors that guide scientists’ focus in tracking contagion aren’t always perfectly either/or.   They don’t alternate neatly between people-directed or environment-directed, that is — more typically, many myths and metaphors compete for attention, with certain ones winning out at any given moment.  Now, the alleged toxicity of the environment seems very compelling to some people, and there are also contagion concepts based on fears of foreigners, suspicions of supposedy nefarious corporations, worries about open borders, anxieties about public education, concerns that governments keep secrets, and so forth.

The guiding metaphors for contagion breathe life into moral, political, or profit-making campaigns.  The magic-bullet concept remains compelling, for instance, and perhaps accounts for some of the interest not only in Tamiflu but in whether or not flu strains are resistant to it, and whether or not it will be made available,  to whom, and at what cost.  There’s a post at H5N1 on this today.

But there’s an overarching truth about swine flu:  our society can’t seem to leave it alone.  No matter how small the tally of confirmed H1N1 flu deaths (WHO counted 1154 as of the end of July, the European Centre for Disease Prevention and Control‘s report today puts the number of deaths at 1645 — but even the higher number yields an exceptionally low case-fatality ratio:  under 0.1%, roughly on the order of seasonal flu.  So this remains a far-reaching but so-far mild outbreak.

Yet the question of whether or not it will become more severe — more virulent, more deadly — remains front and center for public health people, and stays alive as a media story.

Okay, yes, it’s important to be prepared.  It would be shameful if there were deaths that would have been preventable with a little forethought and planning.

That accounts for the assiduous tracking by serious public-health people.  But what accounts for the prominence of this rather mild outbreak in the public consciousness?

This is an era of epidemics.  Which is to say, it is an era of fear.  There must be something wrong, it is so easy to think.  This is not just the work of media (although they help, and it doesn’t hurt that playing on fear sells).  It runs deeper than that.  Our modern civilization seems, sometimes, deeply uncomfortable with the world we’ve created.

Last Thursday, for instance, the  New York Times ran a story featuring a study that claimed TV viewing is linked to blood pressure increases in kids.  It’s a story of toxicity in the constructed environment — of the ways contemporary arrangements are inherently and latently harmful (yes, latently:  TV isn’t causing kids to shoot other kids, at least not in this story; it is allegedly causing them to develop a so-called risk factor for later harm).

How do we keep an eye on flu, or other outbreaks, and seek ways to protect everyone from harm as best we can, but avoid hysteria about contaminated toys, subway riding, TV viewing, processed foods, and so forth?  This is a challenge.  It means examining what makes us anxious, and it means understanding that life has risks that can’t be avoided.

The CDC’s travelers’ health website recommends vaccination against typhoid (as well as hepatitis A and B, and routine childhood immunizations) for travelers visiting small towns and villages in Ukraine.  Since we expect to be doing exactly that, we opted to be immunized.

Picking up the oral typhoid vaccine at a pharmacy in the Bronx made us reflect on inequities in health, and inequalities of opportunity.  How odd, to stand in an air-conditioned pharmacy on a busy street in New York City and prepare to fortify oneself against a disease that, here, we consider of historical interest.  Typhoid makes us think of the sad episode of Mary Mallon, the infamous typhoid carrier, and the struggles of Almroth Wright to develop a vaccine that would limit the terrible toll that typhoid took on British troops in the Boer War.  All a very long time ago.

That typhoid is still a public health problem in much of the world attests to real differences in opportunity.  Clean drinking water, and the sanitary systems that allow water to stay clean, being aspects of opportunity.

The American conversation about health uses the grammar of risk.  Our health professionals talk about the possibility that illness will ensue if people persist in some behavior (smoking, inhaling others’ cigarette smoke, using certain pharmaceuticals, driving while intoxicated, etc.), if authorities fail to inform, if vaccine isn’t produced on time.  But a sense of scale is lost.

Flu preoccupies the risk conversation right now, for obvious reasons having to do with the current outbreak of H1N1 influenza.  The risk conversation sometimes appeals to the terrible pandemic of 1918, the worst single-strike disease outbreak of all time.  But it doesn’t often recall that, in the United States, the 1918 flu spared over 99% of the population.

The talk of risk, the sometimes-lurid conversation about what might happen, almost always occupies itself with the tiny tail of the broad distribution of health – the minuscule proportion of the population that, even in a frightening outbreak, actually dies from it.

What’s left out is the real situation that confronts most people, most of the time.  Not the sudden outbreak, but the persistent struggle to stave off more mundane problems that rarely appear in the media.

Junkfood Science this week reminds us to keep the care in health care.  Care seems relevant here.  The risk conversation gives us clues – sometimes valuable ones – about how to diminish somewhat the number of people who are sickened or killed by a threat, like flu.  But to really get at people’s health – to offer a more thoroughgoing and humanistic form of care – will mean moving past the narrow conversation about risk, and asking about opportunity.

It isn’t risk that keeps most people from achieving capabilities — from escaping poverty, living comfortably, or being free of disability.  It’s more usually bad water, bad food, or just bad government.  A broader and more effective health conversation would start with the conditions of living, and not be preoccupied with the risks of illness alone.

And now it’s Toll House chocolate chip cookies.  The dough has been recalled by Nestlé because some batches contain E. coli O157:H7, a potentially dangerous strain, with at least 66 cases in 28 states.  There have been 7 severe cases of hemolytic-uremic syndrome, although no deaths.

At the Center for Science in the Public Interest, food safety lawyer Sarah Klein says “If there was anyone left in America who didn’t realize we need to reform the food safety functions at the Food and Drug Administration, this latest recall of Nestle Toll House Cookie Dough provides a sobering wakeup call,” telling the NY Times that “If there was ever any doubt that we’ve reached a crisis, this should provide the proof.”

But crisis of what?  The FDA itself isn’t sure how the bacteria got into the dough, and CDC is still investigating. What are we supposed to wake up to?  Is it toxicity?

According to research recently reported in the Milbank Quarterly, the metaphor that Americans most commonly hold responsible for obesity is a toxic food environment. — over 75 percent of respondents subscribed to this view of the obesity epidemic.

With foodborne disease, it isn’t obesity that’s at stake, but it seems that the same view of American eating shapes responses.  That the foods recently associated with bacterial outbreaks are so quintessentially American helps.  So does awareness of the tortuous journey that many foods take to market now, which is what makes it hard to know exactly how, where, and when contamination might occur.

But surely the U.S. doesn’t face a food crisis of the sort that the impoverished countries of the world do — a crisis of environmental change, political struggles over land use, access to clean water, and food shortage for a billion people worldwide.

Americans generally manage not to talk about the lives of people for whom food crisis means dirty water and the questionable availability of cassava flour or cornmeal mush, but are pleased that our own food crisis does not involve such deprivation.

At the same time, a lot of people here feel suspicious of the technical apparatus that has afforded us our cornucopia.  They are suspicious of the ways Americans (or most Americans) have access to the modern groaning board without our having to hunt, scrape the soil, haul water, or collect firewood – just park the car, enter the store, and take out cash or a debit card.  It seems too easy.  It isn’t traditional, natural, organic.

The occasional news story on food contamination validates those concerns, tells anxious people that they were right to be suspicious – that American food producers are poisoning us all.

To say that an event (cookie-related or other) is a wake-up call is to demand surveillance and control.  It says that someone has done something wrong (CSPI doesn’t need to tell us who that is – they mean the usual suspect:  big business, aided by lax government).

If someone has done something wrong, then surveillance – better food-plant inspection, for instance – and control will fix the problem.  But the wake-up call doesn’t really wake anyone up to the larger problem, or its nuances.

We’d like everyone worldwide to have enough to eat.  And not just enough rice or roots – we’d like everyone to be able to eat a diverse and nutritious diet.  We’d also like to be able to have chocolate chip cookies and other tasty processed food, at least from time to time.  We’d like all that to happen with a minimum of suffering caused by the food itself.  It’s unreasonable to think that nobody will ever get sick from contaminated food — but we’d like foodborne disease to be limited.

The technology and the transportation know-how exist to make that future possible.  But people concerned about food content, food safety, and food plenty have barely started the sort of conversation that would allow all the many pieces to be fit together globally.  The way to make such a vision of food adequacy and diversity possible still isn’t clear.  To argue for better surveillance and oversight of American food production is fine – but it doesn’t move us far along the road to solving the larger food crisis.  It’s going to take more than FDA inspection to get us there.