Steve Kass

Yesterday, I wrote about the emerging public alarm over the fungus Cryptococcus gattii. Alarm continues to emerge, though some welcome voices of moderation are also appearing. (Time magazine’s writer Alice Park, for example, insightfully explored both the fungus and the alarm in “The ‘Killer Fungus’: Should We Be Scared?”)

Today’s topic is another fungus, a fungus of my childhood.

Like every nerdy kid in the 1960s, I could say and spell the words “antidisestablishmentarianism” and “pneumonoultramicroscopicsilicovolcanoconiosis.” But unlike most nerdy kids outside the desert Southwest, I could also say and spell “coccidioidomycosis.” When I read about C. gattii yesterday, I couldn’t help but think about it — coccidioidomycosis, or Valley Fever. Like the killer disease du jour, Valley Fever infects humans and animals who inhale fungus spores. In the case of Valley Fever, the fungus is Coccidioides immitis, which resides in the local soil around Phoenix and other parts of the Southwest. After a dry spell, rain and wind dislodge the spores and carry them into the air, where they float, free for the breathing.

I breathed in my share. Whenever a dust storm rolled in, my brother and I would don our swim masks, run outside, and play in the carport until rain and lightning arrived, if it did. Driving through the desert on dirt roads or off-road probably kicks up spores, too, and Dad took us on more than a few dirt-road and off-road trips in the Wagoneer.

Like C. immitis, C. gattii, according to some sources, usually causes no symptoms or minor ones. Sciencemag.org’s Robert F. Service writes that “most of [Vancouver Island’s] 750,000 residents have been exposed to C. gattii multiple times with no symptoms.” That’s not to say these fungal infections are innocuous; serious infections have occurred particularly in the immunocompromised, such as transplant recipients or (especially before HAART) persons with AIDS.

I like a fair bit of what I read in Time magazine, despite the “Partners with CNN” thing. For example, in today’s Time, Alice Park insightfully explored both the fungus I wrote about yesterday and the alarm surrounding it in “The ‘Killer Fungus’: Should We Be Scared?”

There’s one thing that gets me, though. Time punctuates many of its online stories with red links to related articles — or to articles someone, or perhaps some bot, thinks are related. It’s not that they distract me; I don’t tend to click on them and forget to come back and finish what I’m reading, for example, which would be a problem. What annoys me is that they frequently seem incongruous with the article I’m reading. They make my brain go “Huh? Why did I just read that?” It happened again today.

Ok, I get that Morales is a leader, but does anyone else see a gay ↔ fashion subtext lurking here? Not that there’s anything wrong with that, but maybe a link to the best-dressed leaders would have been more gracious, if they’re going to call this out in the first place. Oh, and that shade of red is too, too Nancy Reagan — it should be really more Reba.

The popular press is beginning to report on an article that appeared in PLoS Pathogens today, and you can bet public alarm will spread incomparably faster than the “highly virulent fungus” discussed in the article.

The Los Angeles Times was one of the first to pick up on the scare. They interviewed the article’s lead author, Edmond J. Byrnes, III for their report. In PLoS Pathogens, Byrnes and his coauthors described an “increasingly fatal fungal outbreak” in their discussion, without providing statistical support or an inline reference. The Times knows what readers will glom onto, however, and they devoted a couple of paragraphs to this “more lethal” angle.

The spread is also a concern because the strain of the fungus that moved into the United States in 2004 has mutated to become more lethal than the original strain that invaded British Columbia in 1999.

Five of the 21 people who contracted the fungus in the United States have died (about 25%), compared with 8.7% of the 218 infected people in Canada. The fungus has also infected many different species of mammals.

These details aren’t in today’s PLoS Pathogens article. Today’s article focuses on the molecular biology of C. gattii, not its epidemiology. My admittedly cursory search for the source of the Times’s numbers turned up one mention of an “over 25%” U.S. fatality rate. That was in a previous article of Byrnes’s, where he referenced the figure as the “unpublished observations” of two other scientists. But let’s give Byrnes and the Times the benefit of the doubt and suppose the numbers are reliable.

Math time. If you know only a handful of small numbers about a disease, drawing any epidemiological conclusions — especially alarmist ones that might be misconstrued — is risky, but mathematics can still help us evaluate the numbers. There will be lots of ifs, but that’s to be expected when you have limited data. The standard way to proceed is to ask the following question: If in fact nothing scary is happening (meaning that the infections in the U.S. are not more deadly than they are in Canada), might we really see as many as five deaths in 21 cases?

Under the probabilistic assumptions of this kind of analysis, getting infected with C. gattii is treated like a crap shoot as to whether you die or not; you die with probability 8.7%, the Canadian fatality rate. If 21 people get infected and for each one God rolls the dice to see who dies, what’s the likelihood at least five of them will succumb? Well, it’s around 3%. To put that in context, imagine that tomorrow’s traffic is terrible, like once-a-month terrible. Would you chalk it up to bad luck or a real change in traffic congestion? I’d chalk it up to bad luck and assume a real change only if traffic was similarly terrible again tomorrow or maybe next week. (Even then I would probably look for other explanations, like an announced construction project or a visiting dignitary.)

Other factors should be considered when comparing fatality rates to test the hypothesis of increasing deadliness, particularly with such small numbers of cases. Were the U.S. persons infected by C. gattii diagnosed as promptly (or not) as the Canadians and given identical treatments? If not, the higher U.S. fatality rate could be due to late diagnosis or ineffective treatment. Were the U.S. persons infected or killed similar to the Canadians in age, general health, and other factors known to be independent predictors of mortality from disease? If not, the higher U.S. mortality might not be due to greater virulence.

PLoS Pathogens is a peer-reviewed journal, and that provides some assurance that the scientific conclusions were based on accepted scientific practices. Unfortunately, published science has the potential to affect society and policy via the popular press, and reviewers need to think about how a publication might be construed by a journalist.

To Byrnes’s credit and the Times’s, readers who ventured a few paragraphs past the alarming headline will read this more moderate assessment of the situation: “Overall, I don’t think it is a large threat at this time. But the fact that it is continuing to spread geographically and the number of cases is rising makes it a concern.”

Whether or not Byrnes et al. were more justified than I can tell in calling this a “increasingly fatal fungal outbreak,” sure, this could be the next black plague. So could any number of currently very rare or unknown pathogens. But based on the science I’ve seen, you shouldn’t be any more worried about C. gattii today than you were last week, when I’m guessing you’d never heard of it.

References

• PLoS: Emergence and Pathogenicity of Highly Virulent Cryptococcus gattii Genotypes in the Northwest United States
• LA Times: Potentially lethal fungus moves south from Canada

Updated at 2010-04-22 at 23:28. I added the words Deadly and Fungus to the post title hoping to get more play. A list of headlines on this story follows.

One rebuttal of the alarm: Ore. DHS questions article statements about deadly fungus
(DHS is Department of Human Services, not Homeland Security)

Alarm and alarm in all the other headlines, though.

• Airborne fungus claiming lives
• New strain of virulent airborne fungi, unique to Oregon, is set to spread
• New Deadly Fungus Found in US, Has Already Killed Six
• Potentially Lethal Airborne Fungus May Spread to California
• Deadly Oregon fungus may spread on West Coast
• Deadly airborne fungus in Oregon set to spread
• Killer fungus seen in Pacific Northwest
• Potentially deadly fungus spreading in US and Canada
• Deadly Oregon fungus may spread on West Coast
• Deadly Fungus In Oregon: New Strain Of Fungus Killed 6 in Oregon
• Fungus Cryptococcus gatti Threat to Healthy People
• New Likely Deadly Fungus Invading US & Canada – Signs & Symptoms
• Emerging Northwest fungal disease develops virulent Oregon strain
• Oregon Fungus Spreading South
• Toxic Airborne Fungus From Oregon Spreading Across West Coast
• New Concerns About Deadly Fungus Found in Oregon
• Deadly strain of airborne fungus spreading among healthy people and animals
• Life threatening tropical fungus seen in Pacific Northwest
• Fungus Spreading Throughout US, Canada
• Killer Fungus Migrates To The US
• Killer Lung Fungus Hits Northwest
• ‘Highly Virulent’ Strain of Killer Fungus Found in Ore

Thanks to my friend Andy for posting the outrage. Thanks also to Ashley, whom I don’t know but whose blog Google helped me find, for her summation: Why I hate you if you voted Yes on 8.

UPDATE (July 24, 2010) Clay Green and Sonoma County have settled the case, and this PBS report of the settlement suggests both parties are happy with the outcome (not to mention Green’s lawyers, who should also be satisfied). Green and his partner’s estate receive cash compensation for the county’s actions, Green’s lawyers get paid, and the county alters its policies for property disposition and case management.

Funeral services were held today for the late President Lech Kaczynski. The Washington Post let this slip into its report of the event, which Barack Obama and others couldn’t attend, Eyjafjallajökull’s ash cloud having interfered with air travel:

But Kaczynski’s family, led by his twin bother, Jaroslaw, insisted the ceremony go ahead, apparently in an attempt to allow normal life to resume in a country that has been seized in mourning.

Whatever the Post or anyone else thinks of Jaroslaw, if it’s not something nice, don’t mention it on the funeral day.

On a more serious note, it was a dozen or so years ago, walking along the Jersey City waterfront, that I first learned about the Katyn Massacre. I’m years overdue to take a few minutes of time and reflect on the striking memorial at Jersey City’s Exchange Place. It’s worth a visit if you haven’t seen it.

Yesterday, the New York Times published “Why Do Educated People Use Bad Words?” on the Opinion page as part of its series Room For Debate: A Running Commentary on the News. The Times piece was dull, but it gave me an excuse to visit and play at the never-dull Google News archives.

Search:

Selected results:

Today’s earthquake is about 150 miles from the much larger 2004 earthquake.

[This would be a real interactive map if Google Maps embedding weren’t broken.]

The USGS page on today’s earthquake is here.

A recent numerical expedition led me to these summary statistics from a 2009 Pew survey on Religion and Public Life.

Looks like a typo to me. At a glance, the breakdown by age seems inconsistent with the aggregate result.

Most (about 85%) of the survey participants fell into one of the three oldest age groups, all of which favored gay marriage at a lower rate than the general population. The 65+ crowd, numbering 507, favored gay marriage at a rate a full 17 points lower than the rate for all ages combined. Although young’ens favor allowing Adam¹ and me (or Autumn and Eve) to get married legally, and they smile with approval at a rate almost 20 points higher than the rate for all ages combined, there are too few of them (only 283) to balance out the manier² old grumps and middle-aged semigrumps.

I have no reason to suspect the Pew folks of vulpigeration, so I tried to find an honest basis for these apparently contradictory figures.

Pew’s full report on survey question Q146a revealed one potential source of slop: the number under “Favor” seems be the sum of two individually rounded percentages: one for “Favor” and one for “Strongly Favor.” The actual survey instrument included both possible answers. Therefore, 39% could mean anything between 38% and 40%. Survey percentages are routinely rounded, but one expects 39% to mean somewhere between 38.5% and 39.5%.

Even allowing for extra slop, the numbers don’t agree. Here’s a tabulation (using the increased slop allowance) that gives the minimum and maximum numbers of favorers in each age group and (by summing) the minimum and maximum number of favorers among those in any age category.

According to these numbers, between 34.8% and 36.8% of 1,980 respondents would be cool with my marrying Adam legally.

According to Pew’s summary chart (at the top), though, between 38% and 40% of 2,010 responses, or between 764 and 804 people, answered “Favor.” That’s quite a bit higher than the breakdown figures show, and even if the 30 people in no age category (who presumably withheld their age or were under 18) all favored gay marriage, the maximum (and an unlikely maximum, because it would require all the rounding and missing information to be skewed favorably) number of favorers is 759.

As another plausible scenario, I calculated a Total percentage based on the age breakdown but weighted according to the actual histogram of age in the U.S. Still no dice. If anyone has an idea, let me know.

¹ For the record, I’m currently Adamless and available

² manier, adjective. Comparative of many; more numerous. To be coined presently. Many and numerous are synonyms; if things can be more numerous, I see no reason they can’t also be more many, or manier.

A letter to the editor about Daylight Saving Time is today’s most-viewed article in the Panama City (FL) News Herald today, and it deserves more attention than it got over at whatwelookat.com. Letters to the editor routinely begin with their first sentence, but Gene Cabot’s letter begins with its first and longest sentence.

It’s daylight saving time again — called “summer time” in some of the many countries around the world that yearly move their clock hands and pretend that it’s earlier than it really is according to the sun.

Except that we don’t pretend it’s earlier than it really is according to the sun when we move our clocks forward for daylight saving time. We pretend it’s later than it really is. So much for Gene’s viewpoint that we should move daylight saving time to winter. If we had it backwards like he seems to think, it might make sense to move it to winter, but we don’t have it backwards.

Gene goes on to write,

The rationale now for daylight saving time is to save fuel, as people wouldn’t use as much electricity in the mornings because the sun was up.

Except that it’s in the evening, not the morning, that daylight saving time can cut down the amount of electricity used for lighting. With or without daylight saving time, in most parts of the U.S., the sun is up when people start their day, so there’s no effect on morning energy use.

Gene wraps up his confusing argument against a misconception by noting,

… in Miami with a Dec. 21 sunrise of 6:41 a.m. and sunset of 5:15 p.m. — they still had more than 11½ hours of sunlight, plus the twilight hours.

Except that in Miami (or anywhere else on Earth), 5:15 p.m. is only 10 hours and 34 minutes after 6:41 a.m. Unless I missed the news about Miami slipping into the Bermuda Triangle.

In today’s number news (State-by-state cremation rates in U.S.), we learn that “slightly more than a third of all persons who died in 2006 were cremated, according to the Cremation Association of North America.” Happily, the article contained the raw data, but only as an alphabetical-by-state table of numbers.

Here’s an illumination, as MapPoint is my amanuensis. Click to embiggen.

Explanation: Pie areas are proportional to the number of deaths; the yellow slice is cremations, the red non-cremations.

Pies for our nation’s two newest states are not shown. Alaska’s looks like a two-thirds size Vermont pie; Hawai’i’s looks like a one-third size Oregon pie.