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.

May CDC become a force for real public health, not an advocate for the risk-avoidance canard.  May the new director, Dr. Frieden, stop favoring pharmaceutical companies’ profit making through expansion of immunization.  And may he direct the agency to begin to address legitimate public needs, like sound answers about vaccines and autism, and clear communication about what is — and isn’t — dangerous about obesity.

May WHO officials stop playing with the pandemic threat barometer.  May WHO begin demanding that the world’s wealthy countries devote at least the same resources to stopping diarrheal diseases, malaria, and TB as they do to dealing with high-news-value problems like new strains of flu.   Diarrheal illness kills as many children in Africa and Asia in any given week as the 2009 swine flu killed Americans in eight months.  So does malaria.   Direct policy, and money, toward sanitation, pure water free of parasites, adequate treatment of TB, mosquito control, and prevention of other causes of heavy mortality in the developing world — not just flu strains that threaten North America, Europe, and Japan.

May public health professionals lose their obsessions with bad habits. May the public health profession return to the problem of ensuring basic rights — access to sufficient food, clean water, decent housing, good education, a livable wage, and adequate child care — and ease up on its moralistic obsessions with nicotine and overeating (for recent examples of the preoccupation with tobacco, see this article or this one (abstracts here; subscription needed for full articles) in recent issues of the American Journal of Public Health).

May science be what Joanne Manaster does at her incomparable website: looking at the world with wonder, asking without dogmatic preconceptions how it works, and accepting that its irrepressible quirkiness makes it impossible to know the world perfectly.  May science not be the crystal-ball-gazing thing whose so-called “scientific” forecasts are really doomsday scenes worthy of the medieval Church — predictions of liquefied icecaps and rising seas,  hundreds of millions of deaths in a flu pandemic, or catastrophic plagues sparked by people with engineered smallpox virus.  There are plenty of reasons to be concerned about both the environment and disease outbreaks based on sound here-and-now observations; leave the forecasts of Apocalypse to the clergy, who know how to handle dread.

A new year’s wish (from the valedictory exhortation in Tony Kushner’s Angels in America):  “More life!”

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At Smallpox2009, Robert posts a note following Abigail Zuger’s review of Dread, which appeared in the NY Times on 26 May.  The post picks up Zuger’s wording as to whether fear of epidemics is “hard-wired” — not the most felicitous term but an apt question to ponder.  More happily, it also picks up her evident fascination with the question of why our society is so intrigued by epidemics.

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At change.org, Kristina Chew wonders about the question of whether autism is an epidemic.  She picks up the idea from Dread that once we call something an epidemic we give it “a story line, with a beginning and an end.”

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Crawford Killian reviews Dread at The Tyee, homing in on the links between the epidemic narrative and social anxieties — and economic disparities.  “Much of what we consider hygiene is little more than an attempt by the anxious middle class to control the dirty, lawless, sexually profligate poor,” he reminds us.