Monday, January 23, 2006 

For Koufax Award voters...

Aetiology has been nominated for a Koufax Award for Best new blog. First, if you're stopping by via that link, welcome, and thanks for checking out this site. I hope you'll take some time to stroll through the archives here, and to check out recent activity on my new site, located here. Sorry for the confusion!

Wednesday, January 11, 2006 

Aetiology is moving!

Well, it looks like it's official, so I might as well spill the beans. Seed Magazine has launched a new feature, Science blogs, and Aetiology is one of the inaugural blogs. If you take a look at the list of other blogs here, you'll probably notice some other familiar names. It's a good deal for me: they pay for everything *and* provide technical support. Everything else will stay the same--I still control everything I write, and there's no editorial control or anything from the higher-ups.

So, I hope you'll continue reading, and join me over at the new address:

For those of you who have this site on your blogroll (and allow me to take a moment to thank you for that in the first place), I'd appreciate it if you updated your link. I think there's some way I can do a re-direct eventually, but I'll keep traffic coming to this page for awhile before switching it over. Additionally, all old content will remain archived here, so if you've linked to a post here, it should be fine in perpetuity.

Tuesday, January 10, 2006 

H5N1--does it live up to the hype? Redux

Okay, one more quick post. I've talked quite a bit on here (and over on Panda's Thumb) about the importance of surveillance, and how the current death rates from H5N1 influenza ("bird flu") are likely to be artificially high, since we're more likely to diagnose the very ill cases than the mild or asymptomatic ones. (See here and here for the relevant posts). Indeed, that first post linked discusses a study carried out here at the Center for Emerging Infectious Diseases at the U of Iowa, which found that swine workers were much more likely to be infected with swine influenza viruses than those without significant swine contact--showing that there's likely a heckuva lot more sub-clinical or unrecognized cases of zoonotic influenza than ever pop up on the radar. A new study from Vietnam suggests the same thing, only surveying for "bird flu" and bird contact rather than swine. The abstract:
Background The verified human cases of highly pathogenic avian influenza in Vietnam may represent only a selection of the most severely ill patients. The study objective was to analyze the association between flulike illness, defined as cough and fever, and exposure to sick or dead poultry.

Methods A population-based study was performed from April 1 to June 30, 2004, in FilaBavi, a rural Vietnamese demographic surveillance site with confirmed outbreaks of highly pathogenic avian influenza among poultry. We included 45 478 randomly selected (cluster sampling) inhabitants. Household representatives were asked screening questions about exposure to poultry and flulike illness during the preceding months; individuals with a history of disease and/or exposure were interviewed in person.

Results A total of 8149 individuals (17.9%) reported flulike illness, 38 373 persons (84.4%) lived in households keeping poultry, and 11 755 (25.9%) resided in households reporting sick or dead poultry. A dose-response relationship between poultry exposure and flulike illness was noted: poultry in the household (odds ratio, 1.04; 95% confidence interval, 0.96-1.12), sick or dead poultry in the household but with no direct contact (odds ratio, 1.14; 95% confidence interval, 1.06-1.23), and direct contact with sick poultry (odds ratio, 1.73; 95% confidence interval, 1.58-1.89). The flulike illness attributed to direct contact with sick or dead poultry was estimated to be 650 to 750 cases.

Conclusions Our epidemiological data are consistent with transmission of mild, highly pathogenic avian influenza to humans and suggest that transmission could be more common than anticipated, though close contact seems required. Further microbiological studies are needed to validate these findings.
Though intriguing, there are some major weaknesses in the study. First, it's all self-reported, without any serological evidence, and "flu-like illness" ain't exactly definitive of actually having influenza. But it's certainly suggestive, and once again highlights what so many in public health have been trying to pound into the heads of those who control the funds: we need better surveillance, period.

Other scientists seem to be a bit more optimistic. According to this AP article:
"I would call this the smoking gun," said Dr. Gregory Poland, a Mayo Clinic flu specialist. "All of us have been concerned and have guessed that the data we have so far has been the tip of the iceberg."

The human cases counted so far likely have been the most severely ill patients treated at major hospitals, Poland said.

"In the really rural areas, we know that this had to be occurring" too, and the study suggests that the prevalence "is pretty high," he said. "The data lines up biologically the way we would have expected it to."
I agree with a lot of that, but wouldn't call this a "smoking gun" in any way, shape, or form. Maybe it would have been if they'd definitively shown H5N1 seroconversion before and after bird exposure, but the "influenza-like illness" category is just too broad. Even other bird diseases that humans can acquire, such as psittacosis, can cause influenza -like symptoms--so I think Dr. Poland is overshooting. Hopefully this will help to get other studies funded, though.

I've not been writing much on the recent developments with H5N1, so for anyone who's not up to speed, check out Effect Measure, where they've been keeping up much better on the newest influenza news. And while those of us who report on the science are generally a bit more clinical about the suffering, Revere also reminds us of the more personal side, noting that one family in Turkey has now lost a son and two daughters to H5N1--a second son, age 6, survives. This is why it's so much easier to deal with stats--numbers, even when contemplating a large amount of deaths, are less difficult than the personal story of just one victim.

Edited to add this news story:
Two young brothers, ages 4 and 5, who have tested positive for the dreaded H5N1 avian virus but shown no symptoms of the disease were being closely watched at Kecioren Hospital here Tuesday. Doctors are unsure whether they are for the first time seeing human bird flu in its earliest stages or if they are discovering that infection with the H5N1 virus does not always lead to illness.

In any case, the highly unusual cluster of five cases detected in Turkey's capital over the last three days -- all traceable to contact with sick birds -- is challenging some of the doctors' assumptions about bird flu and giving them new insights into how it spreads and causes disease. Since none of the five has died, it is raising the possibility that human bird flu is not as deadly as currently thought and that many mild cases in Asian countries may have gone unreported.
Gee, no, really?? Why hasn't anyone considered that before? *smacks forehead, pulls out hair*

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New Grand Rounds!

Had a sick kid yesterday and am swamped today, so if you're jonesing for some good science reads, head over to Clinical Cases and Images for this week's Grand Rounds.


Aflatoxin found in pet food

I've been meaning to write something up about this for awhile, but keep forgetting. Anyhoo, because my own dog is currently ill and it's stressing me out watching her (not due to this, thankfully), I thought I'd do my own little part to get the word out to any dog owners who may not have heard of this recall.

Diamond Pet Food Recalled Due to Aflatoxin
Diamond Pet Food has discovered aflatoxin in a product manufactured at our facility in Gaston, South Carolina. Aflatoxin is a naturally occurring toxic chemical by-product from the growth of the fungus Aspergillus flavus,, on corn and other crops.

Out of an abundance of caution, we have notified our distributors and recommended they hold the sale of all Diamond Pet Food products formulated with corn that were produced out of our Gaston facility (see complete list below). Please note that products manufactured at our facilities in Meta, Missouri and Lathrop, California are not affected. The Gaston facility date codes are unique from other Diamond facility codes in that either the eleventh or twelfth character in the date code will be a capital "G" (in reference to Gaston). The range of date codes being reviewed are "Best By 01-March-07" through Best By " 11-June-07". Diamond's quantitative analysis records substantiate that Diamond's corn shipments were definitively clear of aflatoxin after December 10. As such, "Best By 11-June-07" date codes or later are not affected by this notice.

States serviced by our Gaston facility include Alabama, Connecticut, Delaware, Florida, Georgia, Kentucky (eastern), Maine, Maryland, Massachusetts, Mississippi, New Hampshire, New Jersey, New York, North Carolina, Ohio, Pennsylvania, Rhode Island, South Carolina, Tennessee, West Virginia, Vermont, and Virginia.

We are rapidly analyzing retained samples of all products produced in Gaston so we can isolate specific lot numbers impacted and provide this information to our distributors, retailers and customers as quickly as possible.

Meanwhile, if your pet is showing any symptoms of illness, including sluggishness or lethargy combined with a reluctance to eat, yellowish tint to the eyes and/or gums, and severe or bloody diarrhea, please consult your veterinarian immediately.
There's a list of the brands recalled, sold under the names Diamond, Professional, or Country Value. Unfortunately, several dogs have already died due to this contamination.

About aflatoxin: this is a fungal toxin made by several species of Aspergillus. You may have heard of it previously because it's a potential bioweapon. It's generally found in crops that have either gotten wet or have long been exposed to high humidity; like most fungi, Aspergillus grows best in moist conditions. When ingested, aflatoxin generally targets the liver, and can cause either acute effects (including death) or cause damage leading to cancer. Either way, it's nothing to mess around with, so please double-check your dog food and if you have the affected brand, contact Diamond pet foods. There was finally some news coverage of this last night (I think on NBC) and it was noted that Diamond would pay all vet costs related to treatment of affected pets (though as far as I know, dogs are the only ones affected so far, the Diamond site lists some cat foods as recall products as well).

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Friday, January 06, 2006 

South African AIDS activists sue denialists

South Africa has been a hotbed of AIDS denial, ever since President Thabo Mbeki invited noted HIV denialist Peter Duesberg and other HIV-deniers to his country to discuss "alternative" theories of AIDS. Though scientists and others (including prior president Nelson Mandela) in the country repeatedly spoke out against these ideas, they've lingered. Now, AIDS activists are taking it to the courts. In the current issue of Nature Medicine, they have a brief news report discussing the lawsuit.
Doctors and AIDS activists in South Africa have filed a joint lawsuit against the country's health minister and controversial vitamin supplier Matthias Rath as concerns mount over the government's lack of leadership amidst the country's worsening AIDS crisis.

The South African Medical Association (SAMA) and the prominent activist group Treatment Action Campaign (TAC), which together filed the lawsuit, say they aim to end the climate of what the TAC calls "politically-supported denialism" afflicting the country's fight against AIDS.

A key element of the lawsuit is the allegation that in at least two townships, Rath is running illegal medical trials for his multivitamins, which he markets to AIDS sufferers as an alternative to 'poisonous' antiretroviral drugs.
The lawsuit claims 5 deaths already due to this action, with reports of up to 12--while 2 people still living were found to be taking anti-retroviral drugs.

The saddest quote of the article:
A spokesman for Rath declined to speak to Nature Medicine about the case, saying he is convinced the journal is "funded to the hilt with drug money."
Man, these conspiracy theories are getting tiresome, and so hard to keep track of. Is Nature Medicine in bed with the EAC as well?

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Two potential rotavirus vaccines tested

Rotavirus, a member of the reovirus family, is one of the world’s leading causes of childhood death. This virus causes acute gastroenteritis and diarrhea, resulting in 600,000 fatalities every year in children younger than 5. Most of these deaths occur in the developing world, where there is poor sanitation and medical care, but even in the United States, about 40 deaths every year in children are attributed to rotavirus. Additionally, there are about 70,000 hospitalizations and billions of dollars in health care costs and missed work days for parents due to infection with this virus—-so the virus still causes a significant financial burden, even in a developed country.

A vaccine against the virus was first introduced in 1998 by Wyeth, with the name “RotaShield.” Based on a genetically engineered rhesus monkey rotavirus, the vaccine was withdrawn from the U.S. after only 11 months due to reports citing a potentially fatal intestinal blockage (intussusception) associated with use of the vaccine. Studies conducted following removal from the market showed that the risk of intussusception following vaccination with RotaShield was much lower than initially thought, and much lower than the risk of death from rotavirus, but the damage had been done and the virus remained shelved.

Two new vaccines may be able to take RotaShield’s place. Trials in a number of countries of these vaccines, GlaxoSmithKline’s Rotarix and Merck’s RotaTeq, showed that they worked well and had few side effects. In a trial involving 63,000 infants, the serially passaged, attenuated human rotavirus vaccine Rotarix reduced serious illness by 85% and hospitalizations for diarrhea by 42%. (Details here in the current issue of the New England Journal of Medicine). The RotaTaq vaccine, a genetically modified cow rotavirus, was given to 68,000 infants and was found to reduce severe disease by 98% and diarrhea-related hospitalizations by 63%. (Full study available here).

A current problem, however, is the cost of these vaccines. These new vaccines are projected to cost approximately $100 each, or more, putting them far out of the reach of most third world countries, where even $1 for a vaccine is often more than most people and the government can afford. More widespread use in countries that can afford them, such as the United States, could serve to drive these prices down, but this will still take time—-and meanwhile, over half a million children are dying each year from this virus. (To give some numbers for comparison, about 4 million babies are born each year in the U.S.--imagine waiting for a vaccine for a disease that killed 15% of them every year. ) Not surprisingly to anyone who follows global health issues, the Bill and Melinda Gates Foundation, among others, are working to accelerate this process, and get this vaccine to those who need it most.

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Not gotten enough PZ Myers at Pharyngula?

Just in case you're not getting enough of everyone's favorite "mad scientist," today over at DailyKos, DarkSyde's published an interview with Pharyngula's PZ Myers. Love him or hate him (and I can already see some of his quotes in there again being mined by the Discovery Institute...), you gotta admit he's an interesting fella. And I won't even dig at him too badly for this quote regarding the administration at his university:

They don't agree with everything I say -- in particular, I suspect my anti-religious stance might give a few of our administrators' ulcers -- but they're also committed to the principles of academic freedom.

That "stress-->ulcers" thing ain't ever gonna die, is it? :)

Thursday, January 05, 2006 

What a difference a molecule makes...

Microbial ecology, and its relation to the development of infectious disease, is an ever-growing field of study. Of course, there are a vast number of bacterial species living amongst us, most of which do not cause us any harm. Others may infect us only when, so to speak, the stars align in a certain manner: when a number of factors collide that result in the development of a diseased state. For instance, we may already be immunocompromised due to the presence of another infection—something minor, such as a rhinovirus, or something more serious, such as HIV—and this chink in our armor allows another organism to more easily infect, and potentially damage, us.

Other agents in the environment also play a key role in the ecology of potentially pathogenic microorganisms. A recent study in Science highlighted one of these that appears to play an important role in the ecology and evolution of Vibrio cholerae, a major human pathogen of the past several centuries.

V. cholerae is the bacterial agent of cholera, a deadly water-borne disease. The bacterium itself is somewhat of a boomerang or kidney bean shape, and can be found in a number of aquatic environments of varying salinity. Cholera has killed millions over the past 200-odd years, frequently re-appearing in pandemic form after initially emerging from India in the early 1800s. Infection with the bacterium can lead to severe gastrointestinal problems, and the production of copious amounts of "ricewater stool." Death is generally due to severe dehydration. It’s also a bacterium that has played a key role in the development of the very science of epidemiology. John Snow, considered the “grandfather” of epidemiology, became famous for tracing a 1854 outbreak of cholera in London to a contaminated well, introducing the basic principles of epidemiology along the way.

More recent research has shown that in nature, the bacterium uses the polymer chitin as both a food source and an anchor. Chitin is the second most common polymer on earth (beaten only by cellulose), and is the most abundant in the marine environment, where V. cholerae thrives. Chitin can be found in a number of diatoms, in the exoskeletons and fecal material of arthropods, and in fungi, just to name a few sources.

Why does this matter? V. cholerae that are associated with chitin have been found to be more highly resistant to acid—a primary defense mechanism against food (including water)-borne pathogens. Chitin surfaces can also serve to concentrate these bacteria. Biofilms of V. cholerae on a single chitin-containing plankton, for example, may be enough to constitute an infectious dose of the organism-—meaning you’d have to ingest an incredibly small amount of contaminated water in order to develop disease. If this wasn’t all bad enough, the new study by Meibom et al. shows that chitin causes V. cholerae to become naturally competent—-it makes it take up DNA.

Previously, V. cholerae wasn’t thought to be naturally competent (also referred to as "naturally transformable"). Though it was known that there was a large amount of genetic diversity within the species, it was thought this was largely due to transduction--movement of genetic material between bacteria by viruses, since in laboratory culture, V. cholerae didn't readily take up DNA. Meibom et al. showed that when V. cholerae were grown in the presence of chitin polymers, they took up a Kanamycin resistance gene at much higher rates than isolates grown in the same medium without chitin--the chitin caused them to become competent.

Now, to return to microbial ecology and evolution. I already mentioned that chitin is the most abundant polymer in the aquatic environment, and that the results of this new study show that chitin can greatly increase the possibility of horizontal gene transfer in V. cholerae. Imagine, now, what can happen when there’s a copepod bloom (literally "oar foot;" this is simply a general name for a number of aquatic crustaceans)—-a giant increase in the population of these (chitin-containing) animals, in water that’s contaminated with V. cholerae. Under these conditions, the potential for rapid evolution of these populations of bacteria--and hence, the transmission of novel strains to humans--may be immense, if the laboratory findings hold up under natural conditions.

Indeed, it was already known that weather conditions that can lead to these copepod blooms played a role in cholera outbreaks--and scientists have been working on modelling the conditions that may lead to cholera outbreaks, as well as testing additional potential environmental conditions that play a role in disease. Will this help prevent--or at least provide advance warning of--cholera outbreaks in the future? Time will tell. In the meantime, I wonder how many other bacteria that aren't considered to be naturally transformable (such as Group B strep, which I discussed here) would be if we only found the right set of conditions.

Biology, Cholera, Evolution

Wednesday, January 04, 2006 

2005 Medical weblog awards--voting open

Voting's open at you can go here to vote. Aetiology is up for best new blog and best clinical blog. I don't have a chance in hell 'cause my readership's still pretty low compared to some of the other sites listed, but I'd appreciate it if y'all could help me not get my ass kicked *too* badly. Thanks muchly to those of you who nominated this blog in the first place, and more thanks to those of you who take the time to head over there and vote. This certainly isn't the biggest place in the blogosphere, but it's cool to be appreciated by those of you who do check in regularly.


This view of life

Over my "vacation" (which unfortunately ended up being more work than play), I was at a dinner with two of my best friends from the past 15-odd years. For whatever reason, the topic turned to evolution--and we quickly realized that we had, erm, differing opinions on whether evolution actually occurred or not. Now, this was pretty depressing to me, as both of them are very intelligent women, and one happens to work in a scientific field. So, we retreated to a coffee shop for some animated conversation on science, religion, and politics. I don't know if I changed any minds or not, but that wasn't really my goal anyway--rather, just to talk about the evidence that supported evolution, and to discuss their own reservations and objections. Obviously there were only so many things we could cover, but it was an interesting chat (and I hope I wasn't too harsh. It's a topic that makes me a bit...excitable.)

Anyhoo, I wish I'd had this op-ed on me. Written by evolutionary biolgist Olivia Judson, it highlights just a few things that make evolution so amazing:
Organisms like the sea slug Elysia chlorotica. This animal not only looks like a leaf, but it also acts like one, making energy from the sun. Its secret? When it eats algae, it extracts the chloroplasts, the tiny entities that plants and algae use to manufacture energy from sunlight, and shunts them into special cells beneath its skin. The chloroplasts continue to function; the slug thus becomes able to live on a diet composed only of sunbeams.

Still more fabulous is the bacterium Brocadia anammoxidans. It blithely makes a substance that to most organisms is a lethal poison - namely, hydrazine. That's rocket fuel.

And then there's the wasp Cotesia congregata. She injects her eggs into the bodies of caterpillars. As she does so, she also injects a virus that disables the caterpillar's immune system and prevents it from attacking the eggs. When the eggs hatch, the larvae eat the caterpillar alive.

It's hard not to have an insatiable interest in organisms like these, to be enthralled by the strangeness, the complexity, the breathtaking variety of nature.
This is what I find so incredibly cool about biology. It's not quite like any other science--life makes it messier.

In Jurassic Park, Jeff Goldblum's character, skeptical of the measures that have been implemented to control the park's dinosaur inhabitants, notes that "life will find a way." And indeed, it does--in nature as well as in the movies. And for me, it's so interesting to learn about, as Judson describes it, the "breathtaking variety" of those ways. Hairworms making their grasshopper hosts take a dive. Tiny molecular changes that can result in drastic effects on an outcome, or even lead to a cultural phenomenon. Sure, sometimes it's gruesome; the dearly departed WinAce's collection of organisms that look designed has a plethora of fascinating--if somewhat nasty--organisms that are part of this variety. Life ain't always beautiful butterflies and flowers--it's also parasites, and bacteria, and a whole lot of "kill or be killed" situations. And while biology doesn't rely as much on equations and formulas as some of the other natural sciences, Judson notes:
It's that small facts add up to big pictures. For although Mother Nature's infinite variety seems incomprehensible at first, it is not. The forces of nature are not random; often, they are strongly predictable.

For example, if you were to discover a new species and you told me that the male is much bigger than the female, I would tell you what the mating system is likely to be: males fight each other for access to females. Or if you discover that the male's testicles make up a large part of his weight, I can tell you that the females in his species consort with several males at a time.

Suppose you find that a particular bacterium lives exclusively in the gullets of leeches and helps them digest blood. Then I can tell you how that bacterium's genome is likely to differ from those of its free-living cousins; among other changes, the genome will be smaller, and it will have lost sets of genes that are helpful for living free but useless for living inside another being.
And while we find much that is predictable, many interesting areas of research seek to discover why we see something that, on the surface, *doesn't* fit those patterns. Why would some populations, for example, have a higher rate of the gene that causes sickle cell anemia, an often-fatal condition in people who possess 2 mutant copies of the gene? It didn't seem to fit--until it was noted that the heterozygotes had greater resistance to malaria, and thus, there was a reason for this unexpected pattern.

It truly is humbling to think about all that we've discovered about the variety of life on this planet, and even more humbling to consider the vast amount we know little or nothing about. Alas, the experience of Judson is all too common:
When I was in school, I learned none of this. Biology was a subject that seemed as exciting as a clump of cotton wool. It was a dreary exercise in the memorization and regurgitation of apparently unconnected facts. Only later did I learn about evolution and how it transforms biology from that mass of cotton wool into a magnificent tapestry, a tapestry we can contemplate and begin to understand.
I think I've mentioned before that this my high school bio class was like this as well--lots of memorization, a good dose of anatomy, but no emphasis on evolution to tie it all together. In fact, I thought biology was boring before I took an intro course in college. I'm happy to admit I was totally wrong (something I don't do very often!).
Some people want to think of humans as the product of a special creation, separate from other living things. I am not among them; I am glad it is not so. I am proud to be part of the riot of nature, to know that the same forces that produced me also produced bees, giant ferns and microbes that live at the bottom of the sea.

For me, the knowledge that we evolved is a source of solace and hope. I find it a relief that plagues and cancers and wasp larvae that eat caterpillars alive are the result of the impartial - and comprehensible - forces of evolution rather than the caprices of a deity.

More than that, I find that in viewing ourselves as one species out of hundreds of millions, we become more remarkable, not less so. No other animal that I have heard of can live so peaceably in such close quarters with so many individuals that are unrelated. No other animal routinely bothers to help the sick and the dying, or tries to save those hurt in an earthquake or flood.
I very much agree with this. Elsewhere online, I was involved in a discussion about evolution with a number of people with a host of different beliefs, from atheist to a self-described fundamentalist Christian. One Christian (who actually happens to be in seminary) stated his view on the topic:
And for me, there is something deeply spiritual about that idea, of connectedness to all of the planet on some level. I don't find that evolution challenges my spirit; rather, learning more about how nature interconnects allows me to find more footing with my own life and walk with God.
This feeling of interconnection is something any of us can experience, regardless of our religious beliefs (or lack thereof). To steal a quote from Darwin, there is grandeur in this view of life--and I'm happy I evolved.


Tuesday, January 03, 2006 

Back from the net void...

I love heading home and seeing family, but man, does it get exhausting. I'm ready for a vacation from my "vacation" now (in scare quotes 'cause I spent way too much time working on a book manuscript), but alas, it's time to get back to the real work--after I wade through a mountain of email. Ugh.

Tuesday, December 27, 2005 

Last grand rounds of '05 up a The Health Care blog. Still mostly out of internet contact for a few more days, so check out the best of 2005 over there!

Saturday, December 24, 2005 

Population-based surveillance for MRSA

NHANES is an abbreviation that's quite familiar to epidemiologists of all stripes: the National Health and Nutrition Examination Survey. This survey dates back to 1956 with the passage of the National Health Survey Act, providing legislative authorization for "a continuing survey to provide current statistical data on the amount, distribution, and effects of illness and disability in the United States." Generally, information from these surveys has been used to look at the effect of nutrition, particularly micronutrients, on the health status of the population, or subgroups within the population. However, survey data and biological samples obtained from those enrolled in these studies can be used for other purposes as well—-and one recent study took advantage of this. A new publication by Kuehnert et al. uses NHANES samples to examine colonization with Staphylococcus aureus. As with many pathogens, a significantly greater number of us are asymptomatic carriers of this bacterium than are sickened by the pathogen. Additionally, strains of S. aureus that is resistant to the antibiotic methicillin (methicillin-resistant S. aureus, MRSA) appear to be increasing in prevalence in the community. I say, “appear to be,” because no good, population-based study had been carried out to date. This new study begins to fill that void.

Samples from 9,622 people enrolled in the NHANES study in 2001-2 were examined for S. aureus colonization; almost a third (32.4%) were found to be positive. Extrapolating to the U.S. population, that means that almost 90 million people are colonized with this pathogen. Prevalence was found to be highest in the 6-11 year age group, and males were slightly more likely to be colonized than females.

75 of the S. aureus-colonized individuals were carrying MRSA--.8% of the population, or about 2.3 million Americans. In this analysis, MRSA was found more frequently in older age groups, and in females. However, when community-acquired MRSA (in contrast to nosocomially—or hospital-acquired—isolates) were analyzed separately, the groups most at risk again were young children and African-Americans. As previous studies have shown that those who are colonized are at a higher risk of subsequent MRSA disease, this puts a significant amount of our population--and particularly, our children--at risk of developing serious disease due to this bacterium, which is extremely difficult to treat.

Additionally, MRSA disease in individuals who have no nosocomial exposure has increased in the past several years. Since the data from this study comes from samples taken in 2001-2, these results can be compared to more recent data. For example, other studies conducted at various sites in 2001 found MRSA prevalence rates of .6-2.8%. However, by 2004, a study of 500 healthy children using identical methods found colonization rates of 9.2%, an increase of greater than 10-fold in that community. Likewise, a 2004 study of youths in San Francisco found a MRSA colonization rate of 6.2%, and a Texas study earlier this year reported a 22% MRSA colonization rate. Certainly with these numbers, the increasing find of community-acquired MRSA becomes much less surprising. The bad news is, we don't currently have a way to keep this from increasing even further, and there are few options in the pipeline as far as treating MRSA. A vaccine is in the works, but clinical trials--for both vaccines and new drugs--take time and money. Meanwhile, thousands of people worldwide are dying from this pathogen each year. As usual, the best prevention is simply to wash your hands and generally practice good hygiene--something to keep in mind while you gather with your loved ones during this holiday season.

Cheers, and have a good one--I'll be out for a few days with the kiddos and extended family myself.

Friday, December 23, 2005 

Those who do not learn from history...

My favorite essay arguing against intelligent design isn’t one of Gould’s, or Dawkins’, or Sagan’s. Rather, it’s one that has portions I disagree with, but the eloquent prose simply can’t be beat:
"The analogy which you attempt to establish between the contrivances of human art, and the various existences of the Universe, is inadmissible. We attribute these effects to human intelligence, because we know beforehand that human intelligence is capable of producing them. Take away this knowledge, and the grounds of our reasoning will be destroyed. Our entire ignorance, therefore, of the Divine Nature leaves this analogy defective in its most essential point of comparison.

You assert that the construction of the animal machine, the fitness of certain animals to certain situations, the connexion between the organs of perception and that which is perceived; the relation between every thing which exists, and that which tends to preserve it in its existence, imply design. It is manifest that if the eye could not see, nor the stomach digest, the human frame could not preserve its present mode of existence. It is equally certain, however, that the elements of its composition, if they did not exist in one form, must exist in another; and that the combinations which they would form, must so long as they endured, derive support for their peculiar mode of being from their fitness to the circumstances of their situation."
These come from an 1814 essay by Percy Bysse Shelley, analyzing the claims in William Paley's Natural Theology, a text which explores arguments very similar to those used by modern-day ID advocates. So similar, in fact, that although some of the minor details have changed, Shelley's refutation of it can be easily used today.

As this essay demonstrates, and as recently highlighted in this post, it behooves us to know our history—and none know this better than those who teach the subject. University of Iowa history professor Douglas Baynton wrote an interesting letter to the Washington Post this past Saturday, offering a unique perspective on the “controversy” regarding Intelligent Design by using 19th century geography texts to speculate about how a course using intelligent design might look. He cites three precendents: “Physical and Intermediate Geography” (1866), the 1873 “Physical Geography,” and “Elements of Physical Geography” from 1868. Baynton writes,
These textbooks seem also to have been intended to provide solace for the existentially anxious. All of them offered in one form or another the reassurance that “Geography eaches us about the earth which was made to be our home.” Earth by itself “could not be the abode of man,” advised one. “Therefore, two indispensable agents are provided—the sun and the atmosphere.” The entire vast history of the planet was summed up as the “gradual formation by which it was made ready for the reception of mankind.” The lay of the land had been thoughtfully arranged for our benefit: “As the torrid regions of the earth require the greatest amount of rain, there are the loftiest mountains, which act as huge condensers of the clouds.” Because the breezes that blew down mountainsides cooled the inhabitants below, the highest were located in the hottest pars of the world “for the same reason that you put a piece of ice into a pitcher of water in summer, rather than in winter.”
Of course, these are very similar to the arguments put forth in Natural Theology and a number of other texts over the centuries, reviewed briefly here.

Baynton continues,
Another book explained that all the plants and animals that lived and died for eons did so precisely because humans, during their industrial era, would need the coal. The author observed that “the wisdom of this Plan is further recognized in the fact that the coal is found, mainly, in those parts of the earth that are best fitted for human habitation—in the United States, Great Britain, Western Europe, British America, and China.”
I wonder what these same authors would say today if they were aware of our efforts to extract oil in the Gulf of Mexico, Siberia, Alaska, etc.-—not exactly the best fit areas for human habitation. This is the problem with correlating religious ideas to natural phenomena, and assigning purpose in a scientific setting. One may be able to make a theological argument outlining what God’s Plan is, but it’s not a scientific endeavor. Baynton notes this:
Design arguments…reverse such practical explanations, replacing natural causality with supernatural predestination. In doing so, useful answers that open up further questions are replaced by answers that are emotionally satisfying but intellectual and practical dead ends. After all, once you know that mountains exist because they were meant to exist, what is left to do but sit in your armchair and mediation on the wisdom of their design?
And this is a big reason why scientists are so frustrated with intelligent design—it doesn’t provide us with anything useful. When ID advocate Guillermo Gonzalez was asked at his talk at the University of Northern Iowa what the practical applications of ID were; how it could be used in a practical sense to explore avenues not possible with current scientific methodology? He answered (paraphrasing) that it was "a truth that can be known, leading us to ask more questions and examine the evidence more carefully"--but that's something scientists do, anyway. And sure, who can disagree that the pursuit of truth is a noble thing? But ID is not a scientific truth. It is a religious conjecture, identical to those pointed out by Baynton. Consider, for example, Gonzalez’s thesis in “The Privileged Planet:” that habitability and observability must correlate, because God (oops, The Designer) meant for us to be able to see the magnificence of the Universe. Isn’t this just as silly, and just as arbitrary, as the idea that coal was placed in the specific spots on this earth that “were most fit for human habitation?” Additionally, how does one ascertain the motivations of this mysterious Designer—-the central tenet of The Privileged Planet and other ID writings-- without first knowing their identity; a question which Discovery Institute Senior Fellow Johnathan Witt notes here, is religion.

I suppose, however, that my suggestion that the premise of Gonzalez’s book is silly will be construed as a personal attack. A recent EvolutionNews article regarding a seminar led by Iowa State University professors Hector Avalos, Jim Colbert, and Michael Clough titled “Why the Overwhelming Consensus of Science is that Intelligent Design is not Good Science” contains another Gonzalez assertion that “Avalos and the other critics of ID on campus have to date resorted to misrepresentations of ID and personal attacks on me.” Rather ironic, considering Gonzalez's own attacks and accusations of lying, and the fact that ID is, in essence, little more than a giant misrepresentation of evolutionary theory.

Additionally, Witt complains that the authors of the Iowa State Daily article gave Gonzalez only one sentence: as they mention, “one sentence for the man at the center of the Iowa State controversy,” and call it “fishy.” My, my, what egos—and a bit of misrepresentation of their own. Though they’ve spun all of the activity in Iowa as an attack on Gonzalez, not once in the petitions that over 400 Iowa faculty signed is there a mention of “the man at the center of the Iowa State controversy.” It’s not an attack on Gonzalez, or Fred Skiff, or any other Iowa faculty who may support intelligent design. The Discovery Institute tries to play this as an “academic freedom” issue: that by criticizing ID, we’re scientific “McCarthyites”. So, where is *our* academic freedom to say that we feel ID is a load of garbage? No one has said Gonzalez shouldn’t be able to research ID, should he actually manage to find some way to do so. No one has said he can’t believe in it. No one has questioned his credentials as an astronomer. What has been said is that we don’t believe that ID is suitable for teaching in science classes, and that ID “theory” is intellectually vacuous. It’s a dead end. ID proponents have repeatedly said it’s not a theory of mechanism, so even once it has been established that something has “been designed,” there’s no way to determine *how* it was designed; and it’s a question of theology, not science, to ask “why” The Designer created it that way.

Baynton ends his essay with the thought:
The details have changed, but the fundamental habits of thought at issue have not. Do we want children to learn what is currently known and, more important, what remains to be discovered, about the physics of planetary motion? Or rather should they learn that “As the earth is round, only half of it can be lighted at once. In order that both sides may be lighted, the Creator has caused the earth to rotate”?
It may be, as Baynton notes, a solace to think that this is the explanation for the Earth’s rotation. It may even be a correct explanation; I’m not in a position to say. But either way, it’s a theological stance, not a scientific one.

A quote from Patrick Hazard states, "History in our kind of society is not a luxury but a necessity." Perhaps if more people were aware of the history of intelligent design "theory," less time would be wasted working to keep it out of science classes.

[Note: I'd planned to post this Tuesday, but didn't want it to get lost in all the Dover issues. I think, given the decision and the role the history of the ID movement played in that, it's even more relevant today that this history is considered.--T]

(Geography image from

Thursday, December 22, 2005 

Iowa Academy of Science supports Dover decision

IAS president Paul Bartelt has a piece in today's Des Moines Register.
Respect religious beliefs, but don't teach them as science
Proponents of intelligent design are working in many states to legally incorporate ID into the science curricula of public schools. On Tuesday, however, U.S. District Judge John Jones ruled that ID is not science and cannot be taught in Dover, Pa., public-school science classes. The Iowa Academy of Science agrees with this decision.

The Dover trial made it very clear that the arguments of ID are not scientific, and the basic message of ID is the same as young-earth creationism: Evolution is wrong, and a literal interpretation of Genesis explains everything we see in our world. The argument of ID that there is an "intelligent designer" behind the universe may be a good theological topic, but it has no place in science classrooms.


The Iowa Academy of Science and the science community, in general, respects religious belief and has no intention of diminishing religion in society. Central to the academy's mission, however, is to educate Iowa's citizenry about science. Science hasn't all the answers to questions about life on earth, but evoking a supernatural explanation, as ID advocates, will not advance our understanding of our physical world.

ID proponents press school districts to provide "equal time" and to "teach the controversy." Even on the campuses of Iowa's universities, discussions are being held on whether or how to teach ID.

Americans place a high value on fairness, and providing equal time for ID seems only fair, right? The Iowa Academy of Science has high regard and respect for the value placed on fairness; however, it is not that simple. ID proponents would have science teachers recognize a deity "behind the universe." If so, to be fair (and constitutional), teachers would have to include discussions about the many different deities revered by human societies. Our government cannot give preference to any one religion, including Christianity.

What many people do not understand is that within the science community, there is no controversy about evolution. The controversy is among the general public.

Entire text available at the link.


Mike Argento weighs in

One of the best commentators on the Dover trial (IMO, of course) was local reporter Mike Argento, of the York Daiily Record. (Previous posts on his stories here and here.) He has a new story on the final "smackdown" here.
Just wait until Pat Robertson gets a load of this.

If you thought the election and the removal of that inflamed boil on democracy that was the Dover school board had doomed Dover to an eternity of perdition, filled with pain and suffering and the lamentations of the damned echoing over a Muzak-like soundtrack of Britney, Clay and other soulless pap, you ain't seen nothing yet.

You should take a few minutes - well, an hour or so - to read federal Judge John E. Jones III's ruling in the case of Kitzmiller v. Dover.

If the election convinced Robertson that Dover will fall into the hands of Satan, he will most certainly interpret the judge's ruling as a sign that Armageddon is truly upon us.

It was telling that, moments after Jones' ruling landed, Dover was beset upon by a plague of locusts, poisonous toads rained from the sky and some obsequious jerk from Fox News arrived in town to interview residents about their role in the coming apocalypse.

OK, none of that happened, except for the Fox News thing.

Dover is once again driving the national SUV down the highway to hell by, as Robertson has famously said, turning its back on God. And now the judge is providing the map.

If only national reporters covered science with his combination of humor and a no-holds-barred bullshit detector...I can dream, I guess.

Wednesday, December 21, 2005 

So, is it over?

One question I received from a reporter yesterday asked, essentially, if the fight against intelligent design is over with yesterday's decision. MSNBC has an article along a similar theme today, and those interviewed in the article say the same thing I did: it ain't over by a long shot. (PZ has some similar sobering thoughts on the topic). While I do think the decision handed down yesterday will make it more difficult for anyone contemplating introducing ID into the classroom, as suggested in the MSNBC article, all that means is that the focus will have to shift a bit. I suspect we'll see more of "teach the controversy" and less push to teach intelligent design--something the Discovery Institute has already moved to, anyway.

Additionally, while ID has been the major thorn in the side of pro-science groups, it's obviously not the only bad science out there: just the best-funded. As discussed a few days ago, we still have huge challenges to deal with regarding science education in this country--and ID is but one facet of that. We still have groups that regularly spew misinformation about HIV/AIDS, vaccination, global warming, etc.--and certainly, the evolution deniers won't be going away. Answers in Genesis is working on their "creation museum", the Discovery Institute is still crying about the decision, and certainly ID proponents around the country are going to regroup and work on a revised strategy. This isn't something that's going to go away, and it's not time to rest on our laurels.

My central passion has always been working to teach good science, and get both students and the general public interested in and educated about scientific topics--and that won't change just because we've achieved a major victory against one faction of the anti-science movement. Thus, while I whole-heartedly salute and appreciate the efforts of all of those involved with this trial, the fact remains that we still have much more work to do. I hope many of you who've become interested in these issues during the Dover trial will stick with us as we deal with future challenges as well.


Kitzmiller decision--required reading

Okay, after going through the whole Kitzmiller decision last night, and damn, it's good. Really, incredibly good. This should be required reading. Jones' disgust at the whole thing comes through loud and clear. On page 29:
Although proponents of the IDM (Intelligent Design movement) occasionally suggest that the designer could be a space alien or a time-traveling cell biologist, no serious alternative to God as the designer has been proposed by members of the IDM, including Defendant's expert witnesses.
He discussed this at length, clearly connecting the dots between the Discovery Institute, the Wedge Document, Pandas and People, right up to the Thomas More law center and the Dover school board. On page 31,
A "hypothetical reasonable observer," adult or child, who is "aware of the history and context of the community and forum" is also presumed to know that ID is a form of creationism...The evidence at trial demonstrates that ID is nothing less than the progeny of creationism. What is likely the strongest evidence supporting the finding of ID's creationist nature is the history and historical pedigree of the book to which students in Dover's ninth grade biology class are referred, Pandas. Pandas is published by an organization called FTE, as noted, whose articles of incorporation and filings with the Internal Revenue Service describe it as a religious, Christian organization. Pandas was written by Dean Kenyon and Percival Davis, both acknowledged creationists, and Nancy Pearcey, a Young Earth Creationist, contributed to the work.

As Plaintiffs meticulously and effectively presented to the Court, Pandas went through many drafts, several of which were completed prior to and some after the Supreme Court's decision in Edwards, which held that the Constitution forbids teaching creationism as science. By comparing the pre and post Edwards drafts of Pandas, three astonishing points emerge: (1) the definition for creation science in early drafts is identical to the definition of ID; (2) cognates of the word creation, which appeared approximately 150 times were deliberately and systematically replaced with the phrase ID; (3) the changes occurred shortly after the Supreme Court held that creation science is religious and cannot be taught in public school science classes in Edwards.
The Pandas book was definitely a slam-dunk, though many other factors clearly contributed as well: the history of the decision by the Dover board to have their teachers announce the disclaimer, and the adoption of the Pandas book as an "alternative" text (and the lies that were told about it during the trial); the Wedge document; Behe's arrogant testimony (dissected further at Pharyngula); and the overwhelming view from the community that ID was indeed religious, as measured by opinion letters in the local newspapers. The latter is something that could be very important in any future trials of this nature: even if the proponents are careful to say that the designer in ID can be "a time-travelling cell bioloist" or whatever, the community is going to be more vocal in their belief that ID is a religious idea, and the designer is God.

This, truly, has given those of us who've been fighting ID a "merry Kitzmas."

Edited to add: Ed and Burt's Skeptic article about the trial has been released here with some more "behind the scenes" material. Check it out. Additionally, for a one-stop-shop of links to discussion of the trial and the decision, check out The Questionable Authority.

Tuesday, December 20, 2005 

New Grand Rounds

This week's Grand Rounds is up over at Medpundit. Lots of good stuff. If that doesn't keep you busy, check out DarkSyde's inteview with Chris Mooney over on DailyKos. Busy today, but I'll have more up tomorrow.



Plaintiffs Prevail
The much-awaited decision in the Kitzmiller et al. v. Dover Area School District is now available.

The 139 page document finds for the plaintiffs.

Judge Jones finds that “intelligent design” is not science. The DASD ID policy violates both purpose and effect prongs of the Lemon test, and also violates the Pennsylvania constitution.

Much more here, here, and here, and I'm sure more will follow. (Update: Ed has a "thank you" list here, and Mike mentions others here. As someone who got to watch a bit behind the scenes, there was definitely an amazing amount of work that went into this case--and what I saw was only the tip of the iceberg. Kudos to everyone involved.)

Haven't read the (139 page!) decision yet--perhaps my reading for tonight.

Update: Discovery Institute pans the ruling, calls Jones an "activist judge:" link. Funny that Jones was appointed by GW...

Monday, December 19, 2005 

Bill Maher and his anti-vaccination claims. Again.

Bill Maher has again discussed his anti-vaccination views, this time on Larry King. Among other claims, Maher says that polio was wiped out due to better sanitation, and that getting the flu shot increases your chances of developing Alzheimer's. Orac has more detail on the claims and the dubious source of the "Alzheimer's/flu shot" link. I wonder how Maher would explain the decrease in African measles that's followed an increase in measles vaccination there?

Funny how so many of these people who label themselves "skeptical of Western medicine" (including Maggiore and her brand of HIV-deniers) don't apply that same skepticism to their "alternative health" claims. Maher decries vaccination, a cornerstone of modern public health, by apparently spouting the unlikely claims of an seemingly disgraced MD. Maggiore et al/ say HIV doesn't cause AIDS, and instead of treatments shown by medical science to be effective, she advocates homeopathy and nebulous "toxin elimination" as a healthy alternative. No wonder it's so hard to get young people in the U.S. interested in science; it's all just a big conspiracy and we're always wrong anyway, so why bother?


Breakthroughs in progeria research

Progeria, (officially, "Hutchinson-Gilford Progeria Syndrome"), is a rare fatal disease that makes the victim appear, as the name suggests, prematurely old. Although these children are born looking healthy, onset of the disease occurs around 12-24 months, affecting about 1 out of 4 million children. Symptoms include growth failure, hair loss, and other diseases of aging: atherosclerosis and stroke, arthritis, hip dislocation, aged-looking skin. Most children die of heart disease by the age of 13; life expectancy averages between 8-21 years. (A marked contrast to the story of Brooke Greenberg, a 12-year-old who still looks like an infant).

First described over a hundred years ago, progeria is caused by a mutation in the LMNA gene. This gene produces the Lamin A protein, which is the structural scaffolding that holds the nucleus of a cell together. It's thought that this mutation makes the nucleus unstable, leading to premature aging seen clinically. It was reported earlier this year that a class of anti-cancer drugs called farnesyltranferase inhibitors may help children with this condition. In tissue culture, these drugs finish a job that is blocked in progeria patients--snipping off a farnesyl group thought to somehow "gum up the works" in the cell and lead to progeria. Now, new research suggests possible reasons for this "gumming."
One study found that some of the lamins turn up in the wrong place—too tightly linked to the membranes of the nuclear envelope to participate properly in key stages of cell replication.

The researchers said this would disrupt DNA replication, and be a likely factor in the rapid march of cells toward premature “senescence,” a cellular version of aging. Whether similar missteps and miscues by nuclear lamins are part of normal human aging is the question that draws researchers onward, said Goldman. But the findings are consistent with a widespread belief among biologists that a key cause of ordinary aging is damage to DNA and mistakes in gene replication, two interrelated problems.

Another study found that the most common type of mutant lamin re-organizes regions of chromosomes that are key in controlling gene expression. These portions of chromosomes, known as heterochromatic regions, are kept inactive for various reasons; for example, one of the two female X chromosomes is deactivated in this fashion in order to avoid having them duplicate their work.

One of the hallmarks of the X chromosome heterochromatic region is that it is linked to molecules known as methylated histones. But the researchers found that in a girl with the progeria syndrome, the quantities of these molecules and of an enzyme required to form them were abnormally low.
It's often said that funding for research is unbalanced. Why do we spend so much money on a disease that only affects a relatively few people? Why isn't more money spent on heart disease and stroke, leading killers in the U.S., for example? If heart disease causes, say, a third of all deaths, shouldn't it get a third of the research dollars? This case shows why it shouldn't be quite that simple. Progeria is a rare disease, affecting only a handful of children in this country--but research in this area may lead not only to treatment and/or prevention of progeria, but also to a better understanding of the molecular mechanisms that cause us all to age. You simply don't know where the next brilliant insight is going to come from, whether it be specific disease-related research, or your morning breakfast cereal.


Persons of the year

Time names Bono, Bill and Melinda Gates Persons of Year
Bono is a co-founder of the DATA (Debt, AIDS, Trade, Africa) organization, which fights poverty and HIV in the developing world. From that organization was spawned the ONE Campaign to Make Poverty History.

"It has been a great year for global health to get more visibility," Bill Gates said Friday. "The more people know about it, the more they want to act."

The magazine said that while sudden disasters grab the headlines, other tragedies unfold daily.

"And who is proving most effective in figuring out how to eradicate those calamities? In different ways, it is Bill and Melinda Gates, co-founders of the world's wealthiest charitable foundation, and Bono, the Irish rocker who has made debt reduction sexy," Time's managing editor Jim Kelly writes.

In January, the Bill and Melinda Gates Foundation committed $750 million to improving access to child immunizations, accelerating introduction of new vaccines and strengthening vaccine delivery systems.

The foundation focuses on education, global health, improving public libraries and supporting at-risk families, according to its Web site.

2004's Man of the Year: George W. Bush. I think Time made a better choice this year; kudos to them for emphasizing global health and poverty.

About me

  • I'm Tara C. Smith
  • From Iowa, United States
  • I'm a mom and a scientist, your basic stressed-out, wanna-have-it-all-and-do-it-all Gen Xer. Recently transplanted from Ohio to Iowa, I've spent most of my life in the midwest (with 4 years of college spent out east in "soda" territory). My main interest, and the subject of my research, is infectious disease: how does the microbe cause illness? What makes one strain nasty, and another "avirulent?" Are the latter really not causing any disease, or could some of those be possible for the development of chronic disease years down the road? Additionally, I've spent a lot of time discussing the value of teaching evolution, and educating others about "intelligent design" and other forms of creationism. My interest in history of science and medicine is also useful as a way to tie all of the above interests together. [Disclaimer: the views here are solely my own, and do not represent my employer, my spouse, that guy who's always sitting by the fountain when I come into work, or anyone else with whom I may be remotely affiliated.]
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