Aetiology

For Koufax Award voters...

2006-01-23T12:14:00.000-06:00

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!

Aetiology is moving!

2006-01-11T00:18:00.000-06:00

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:

http://scienceblogs.com/aetiology

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.

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

2006-01-10T10:33:00.000-06:00

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*

Influenza, H5N1, Vietnam

New Grand Rounds!

2006-01-10T09:42:00.000-06:00

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

2006-01-10T09:36:00.000-06:00

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).

Aflatoxin, outbreak, Veterinary medicine, Dogs

South African AIDS activists sue denialists

2006-01-06T13:42:00.000-06:00

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?

AIDS, AIDS denial, HIV

Two potential rotavirus vaccines tested

2006-01-06T11:29:00.000-06:00

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.

Rotavirus, Vaccine, Virology, Global Health

Not gotten enough PZ Myers at Pharyngula?

2006-01-06T11:04:00.000-06:00

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? :)

What a difference a molecule makes...

2006-01-05T11:27:00.000-06:00

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

2005 Medical weblog awards--voting open

2006-01-04T03:57:00.000-06:00

Voting's open at Medagadget.com: 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

2006-01-04T02:12:00.000-06:00

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.

Evolution, Biology

Back from the net void...

2006-01-03T22:54:00.000-06:00

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.

Last grand rounds of '05

2005-12-27T19:41:00.000-06:00

...is 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!

Population-based surveillance for MRSA

2005-12-24T00:09:00.000-06:00

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.

Those who do not learn from history...

2005-12-23T11:33:00.000-06:00

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 http://users.erols.com/ziring/povray.htm)

Iowa Academy of Science supports Dover decision

2005-12-22T15:03:00.000-06:00

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

2005-12-22T14:32:00.000-06:00

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.

So, is it over?

2005-12-21T11:16:00.000-06:00

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

2005-12-21T10:34:00.000-06:00

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.

New Grand Rounds

2005-12-20T12:59:00.000-06:00

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.

Victory!

2005-12-20T10:36:00.000-06:00

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...

Bill Maher and his anti-vaccination claims. Again.

2005-12-19T11:22:00.000-06:00

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

2005-12-19T10:44:00.000-06:00

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

2005-12-19T08:46:00.000-06:00

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.

Doonesbury does ID

2005-12-18T07:24:00.000-06:00

Link

This illustrates nicely what *should* happen, but alas, all that antibiotic resistance stuff is only "microevolution," which even most die-hard young earth creationists (YECs) can accept: so, no second-thoughts about using modern medicines or vaccines that were developed using evolutionary principles. They just say that the evolution of antibiotic resistance is "evolution within the kind," which is peachy-keen. Of course, no one can say exactly what a "kind" is, and whether it's along the same lines as a "species," "genus," "family," etc. They obviously can't base it just on DNA similarity, either. Though what they will affirm, of course, is that "my grandpa wasn't no monkey!"--but chimps and humans are about 98% similar on the DNA level, while even within a species of bacteria, 2 different isolates can share as little as 70% of their DNA sequences. So, while these 2 isolates of E. coli would certainly be the same "kind" (heck, often you hear of one single "bacterial kind"), the 98% similar humans and chimps are different "kinds."

You may think the IDists are better--but not really. At least the YECs are fairly consistent in their position, while some IDists won't even go on record as accepting an old earth; some have said they don't believe in common ancestry, while some, like Behe, have said they do--but, y'know, God (oops, The Designer) just tinkered with certain parts along the way. Even the examples IDists use--bacterial flagella, blood clotting--would be examples of "microevolution," which even YECs accept in theory, yet the IDists feel those scenarios couldn't have happened without some kind of external intelligent guidance.

*scientist head go boom*

Edited to add: PZ weighs in, touching on similar points. Sadly, I think he manages to attribute a silver lining to the situation. (Okay, maybe a bronze one). I *must* be sleep-deprived when PZ is more optimistic than I am, yikes!

Secret of surviving sepsis, say scientists

2005-12-18T05:33:00.000-06:00

Infection is a complicated process. Every day, we're all carrying organisms that have the potential to kill someone. A recent article in the Journal of Infectious Diseases, for example, found that just under a third of us are colonized with Staphylococcus aureus, a leading cause of skin and soft tissue infections. From our noses, to our mouth, to our gut and elsewhere, we are literally teeming with organisms--so much so that, by the numbers, the cells in our body are more bacterial than human. But generally, we don't get sick. When epidemiologists investigate infectious disease, we consider a number of factors: the genetics of the pathogenic organism; the genetics of the host; environmental and cultural factors; host nutritional status; host immune status; and a plethora of other specifics which may affect development of disease. Still, when we discuss host genetics, we've mostly been looking at nuclear genes: those on our 23 pairs of chromosomes. An interesting study out in The Lancet today suggests that view is too narrow.

Recall that within our cells are organelles, each with a specialized function. One such organelle is the mitochondria, the "power plant" of the cell. Much evidence has been put forth that suggests these organelles evolved from bacteria, engulfed by primitive eukaryotic cells. As such, these organelles have their own DNA, separate from that in our nucleus. Differences in this mitochondrial DNA (mtDNA) has been previously shown to affect sperm motility, and to affect the risk of individuals for development of some late-onset neurodegenerative diseases. However, the current study looks at how differences in mtDNA can affect survival after sepsis (bacterial infection of the bloodstream).

Variations in the mtDNA were previously studied by the authors of the current study. By investigating single nucleotide polymorphisms (SNPs) in the mtDNA, they grouped people by mtDNA haplogroup (10 different ones were identified). Don't get confused with the terminology--basically, they just looked at changes, and grouped people together using the differences they found. One of these groups--haplogroup H--was found to be most common in their study population (41.3% of the population). They wanted to see if this had any bearing on survival after sepsis--if haplogroup H people survived more often than their non-haplogroup-H neighbors.

And, yep, indeed they did. Haplogroup H folks showed higher survival over 180 days than those without the haplogroup, and were a bit over 2 times more likely to survive to that point than those in other mtDNA haplogroups. They were also found to generate "a significantly higher core temperature" than those in other haplogroups--in other words, on average, they spiked higher fevers. This might sound like a bad thing, but a fever is actually one of the body's elegant defenses against infection: the increase in body temperature can slow the growth of , or even kill, some bacterial pathogens. Additionally, the increase in temperature also increases the rate of enzymatic reactions, increasing metabolism and speeding tissue repair. (The fever response is also one that's incredibly conserved, from an evolutionary standpoint. Even ectotherms--"cold-blooded" animals--create a "fever" by basking in the sun during an infection). It's not known if this higher fever temperature is the key to the differential survival in the groups, but it's an intriguing finding. It's also interesting to note that, though haplogroup H is the most common in the population, it's the most recently evolved. Could it have been selected for due to this, and potentially other, effect on infection mortality? Infectious disease has certainly played a role in shaping our genomes--for example, sickle cell carriers who are more resistant to malaria; or cystic fibrosis carriers who are more resistant to typhoid. This may be yet another example.

It should be noted that this was a fairly small pilot study--150 people were enrolled, so larger studies will be needed to see if this finding is repeated, and if so, just what the mechanism is that renders them more likely to survive. Definitely food for thought, and a reminder of yet another level of complexity to consider for those of us who seek to sort these kinds of things out.

Avian flu in Malawi?

2005-12-16T16:20:00.000-06:00

Avian influenza suspected in Malawi

Malawi dispatched blood and tissue samples to neighboring South Africa on Friday to be tested for avian influenza after thousands of migratory birds were found dead on a hill in the central Ntchisi district.

Agriculture officials expressed alarm after local villagers started scooping up the dead fork-tailed drongos -- known locally as namzenze -- to eat earlier this week in the district about 200km east of the capital, Lilongwe.

"Someone alerted police that people are feasting on mysterious manna from heaven," said Wilfred Lipita, director of livestock and animal health in the Ministr of Agriculture and Food Security. "We sent officials to caution the people not to eat them, since they may have the avian flu which has proved deadly to humans in other countries."

Note that it's not even certain yet that they died of influenza, much less the high-pathogenicity H5N1 strain. Still, H5N1 was said to be expected in northern and central Africa "within months"--and that was only at the beginning of December. I doubt anyone asked for avian flu in their stocking this year--hopefully Africa didn't get an unpleasant early Christmas present.

2005 Koufax nominations are open

2005-12-16T15:31:00.000-06:00

Here. (ETA: OK, they went and closed that thread on me. Read the first one to see who's already been nominated, then post yours here.)

What are they? From the FAQ:

The Koufax Awards are held annually to honor the best of left-leaning bloggers. A "Sandy" will be awarded based on reader votes in each of a number of categories. It is like the Oscars for lefty bloggers, except that we do not allow overly long, overly sentimental speeches by the winners.

***

What is the purpose of the Awards?

There are three purposes of the Koufax Awards. First, as I wrote last year:

At its core, the Koufax Awards are meant to be an opportunity to say nice things about your favorite bloggers and to provide a bit of recognition for the folks who provide us with information, insight, and entertainment usually for little or no renumeration. The awards are supposed to be fun for us and fun for you.

The second purpose of the awards is to provide some exposure for blogs that you may have overlooked for some reason or another. There are lots of good blogs out there (more everyday) and no one can keep track of them all. We hope to call your attention to new blogs or blogs that deserve a chance to capture your attention. That is the reason for our policy of providing a link to every blog mentioned in the nomination process (despite the fact that assembling such links is an incredible amount of work). Please use those links to visit the blogs you have not previously read. You will not often regret it.

The most important purpose of the awards is to help build a sense of community between and among lefty bloggers and readers of lefty blogs. The awards provide an opportunity to say something nice about bloggers you like and to have something nice said about you. Please try not to take the idea of winning and losing too seriously. The primary rules of the contest are be nice and have fun.

There are 15 different categories, so check them out and nominate your favorite blogs. Last year, Panda's Thumb was up for best group blog, and Pharyngula was up for best expert blog--but neither took home (um, figuratively) an award. I'm compiling my list of faves to submit and spread around some love...

Napoleon lice 'n' mites

2005-12-16T13:36:00.000-06:00

I've been meaning to blog this paper discussing evidence of louse-transmitted disease in corpses unearthed from Napoleon's army for a few days now, but haven't had the time to sit down with it. Now afarensis has saved me the work.

afarensis notes, however, that they extracted DNA from tooth pulp to amplify B. quintana (a louse-transmitted agent of trench fever), and says,

I will also be the first to admit that I have no idea how the DNA got into the pulp cavity in the first place...

Simple: via the bloodstream. Dental pulp is a living tissue, receiving a blood supply like any other tissue in the body—and any pathogens that are carried in the blood supply can end up there as well. Dental pulp is good for these ancient investigations because since it's surrounded by the tooth material, it's unlikely to be contaminated with other pathogen DNA, and it's more protected from decay and therefore a usable sample is more likely to be extracted. To my knowledge, this was pioneered by Michael Drancourt and Dider Raoult, both of whom are authors on the louse paper; the first publication on the technique was this one on Yersinia pestis DNA, which I'd not a half-hour ago mentioned in the comments to this thread. It's fascinating stuff--Drancourt and Raoult have also used it to examine B. quintana in a 4000 year old tooth, among other projects, which have significantly pushed forward the field of paleomicrobiology.

Did Macbeth have mad cow?

2005-12-16T00:15:00.000-06:00

I love these historical analyses of disease--real, or fictional. One historical event that has been the subject of much speculation over the decades has been the Plague of Athens, a mysterious outbreak that is thought to have changed the direction of the Peloponnesian War, and for which the cause still remains uncertain:

[2] As a rule, however, there was no ostensible cause; but people in good health were all of a sudden attacked by violent heats in the head, and redness and inflammation in the eyes, the inward parts, such as the throat or tongue, becoming bloody and emitting an unnatural and fetid breath.

[3] These symptoms were followed by sneezing and hoarseness, after which the pain soon reached the chest, and produced a hard cough. When it fixed in the stomach, it upset it; and discharges of bile of every kind named by physicians ensued, accompanied by very great distress.

[4] In most cases also an ineffectual retching followed, producing violent spasms, which in some cases ceased soon after, in others much later.

[5] Externally the body was not very hot to the touch, nor pale in its appearance, but reddish, livid, and breaking out into small pustules and ulcers. But internally it burned so that the patient could not bear to have on him clothing or linen even of the very lightest description; or indeed to be otherwise than stark naked. What they would have liked best would have been to throw themselves into cold water; as indeed was done by some of the neglected sick, who plunged into the rain-tanks in their agonies of unquenchable thirst; though it made no difference whether they drank little or much.

[6] Besides this, the miserable feeling of not being able to rest or sleep never ceased to torment them. The body meanwhile did not waste away so long as the distemper was at its height, but held out to a marvel against its ravages; so that when they succumbed, as in most cases, on the seventh or eighth day to the internal inflammation, they had still some strength in them. But if they passed this stage, and the disease descended further into the bowels, inducing a violent ulceration there accompanied by severe diarrhea, this brought on a weakness which was generally fatal.

[7] For the disorder first settled in the head, ran its course from thence through the whole of the body, and even where it did not prove mortal, it still left its mark on the extremities;

[8] for it settled in the privy parts, the fingers and the toes, and many escaped with the loss of these, some too with that of their eyes. Others again were seized with an entire loss of memory on their first recovery, and did not know either themselves or their friends.

This plague has been attributed to bubonic plague, toxic shock syndrome and/or necrotizing fasciitis due to Streptococcus pyogenes or Staphylococcus aureus, Salmonella, yellow fever, malaria, Ebola, influenza, and smallpox, to name just a few. Typhus seems to fit the description best, but it's likely that a cause will never be known with certainty.

Another much-wondered-about historical disease is the English sweating sickness. The New England Journal of Medicine has an article on the sickness here for those of you with access:

In the summer of 1485, a rapidly fatal infectious fever struck England: "A newe Kynde of sickness came through the whole region, which was so sore, so peynfull, and sharp, that the lyke was never harde of to any mannes rememberance before that tyme."

Sudor Anglicus, later known as the English sweating sickness, was characterized by sudden headaches, myalgia, fever, profuse sweating, and dyspnea. Four additional epidemics were reported in the summers of 1508, 1517, 1528, and 1551, after which the disease abruptly disappeared. Contemporary observers distinguished the condition from plague, malaria, and typhus. Later suggestions included influenza, food poisoning, an arbovirus, and an enterovirus as possible causes.

(For the record, the authors suggest a rodent-borne virus, such as a hantavirus, as a potential causal agent.)

Historical diagnoses aren't limited to epidemics; historical figures are also fair game. Those of you familiar with the story of how Jeffrey Taubenberger eventually came to sequence the 1918 influenza virus probably know that it all began with an investigation of chemist John Dalton's eyeballs. Dalton was color-blind, and left instructions that, upon his death, his eyes be preserved and examined to figure out why he saw the world differently than everyone else. A 1995 Science paper found that Dalton was a deuteranope; that is, he had trouble discriminating small differences in hues in the red, orange, yellow, green region of the spectrum. And while Dalton may have wanted to know what ailed him, it's likely that Shakespeare never expected the suggestion made in this paper published almost 400 years after his death that the Bard had syphilis.

And don't think fictional characters and epidemics are off the hook just because, y'know, they're not real or somethin'. A 1989 Journal of the American Medical Association paper concluded that porphyria was the disease that caused the fall of Edgar Allan Poe's house of Usher. And a few years ago, a paper in Emerging Infectious Diseases explored the idea that Poe may have been inspired by Ebola or another hemorrhagic fever for his short story, "The Masque of Red Death."

Now, in the current issue of Clinical Infectious Diseases, Norton et al. suggest that Macbeth may be an account of an early prion disease.

Macbeth's descent into madness often elicits psychological interpretations, but he experienced neurologic and cognitive deterioration as well. This brings into question whether a psychiatric disorder alone could fully account for his condition. Any patient today, particularly one from Scotland, presenting with a similar rapid decline in neurologic, psychiatric, and cognitive function, accompanied (as in Macbeth's case) by involuntary movements, hallucinations, and insomnia, would require an evaluation for variant Creutzfeldt-Jakob disease.

They even have a whole table dissecting the passage, sign or symptom described, and prion diseases that share these symptoms. Does it get any better than this?

They continue,

Although we contend that Macbeth's presentation is compatible with a spongiform encephalopathy, no evidence corroborates that this is what Shakespeare intended. Nevertheless, Shakespeare showed an uncannily prescient understanding of prion disease transmission via exposure to neural tissues: "[Once], when the brains were out, the man would die / And there an end; but now they rise again / With twenty mortal murders on their crowns" (3.4.78–80). Conceivably, Macbeth was exposed to infectious prions during an early encounter with the weird sisters, whose necromantic brews contained a variety of human and animal organs. Proclaiming, "Round about the cauldron go / In the poison'd entrails throw," (4.1. 4–5), they added, for example, a human nose and liver tissues that are capable of carrying infectious prions. It is not clear that anyone consumed the witches' brews, but if Macbeth had, that could explain the exposure. Furthermore, Shakespeare foreshadowed current culinary controversies in prion disease epidemiology by warning his audiences to "eat our meal in fear" (3.2.17) until the time when "we may again / Give to our tables meat" (3.6.33–34). (A character in Twelfth Night declares "I am a great eater of beef, and I believe that does harm to my wit" [1.3.85–86]).

Just another reason to study those classics...you never know what you might glean from them.

New Ebola outbreak in African primates?

2005-12-15T11:52:00.000-06:00

From ProMed:

Early reports of great ape mortalities from local people in the Cuvette-Ouest region of the Congo Republic are currently being investigated by a wildlife health team including Dr Alain Ondzie of WCS in coordination with government authorities and researchers in the area. If carcasses can be found, samples will be sent for diagnostic work to CIRMF/IRD network partners. The RoC Ministry of Health is mobilizing community outreach efforts while the wildlife investigation is underway.

This is in the same area where there was an Ebola outbreak earlier in 2005.

Ebola in African primates has been a real problem since about 2001. While, as I mentioned previously, human cases of the disease have been fairly minimal, primate researchers estimate that thousands of gorillas have died in the past decade from Ebola during outbreaks in Gabon and Côte d'Ivoire. In Gabon, gorilla sightings (or other evidence of their presence, such as dung and trails) decreased by 50% in a few short years; chimpanzee sightings decreased by 88%. Eight groups of gorillas that had been monitored by primatologists for 10 years disappeared completely between October 2002 and January 2003. Several gorilla carcasses that were found were positive for Ebola, suggesting this played a role in the population decrease.

I mentioned here that fruit bats may be a reservoir for Ebola, and that a hypothesis has been put forth that Ebola may be a plant virus. Gorillas are, of course, vegetarians; some species eat up to 200 different plant species. Chimpanzees are omnivores, but fruit and leaves still make up a large percentage of their diet. Again, this idea is still unconfirmed, but it's intriguing.

Refs and further reading:

Formentry et al., 1999. J Infect Dis. "Ebola virus outbreak among wild chimpanzees living in a rain forest of Côte d'Ivoire." 179S1:S120-126.

Leroy et al., 2004. Science. "Multiple Ebola virus transmission events and rapid decline of central African wildlife." 303:387-90.

Vogel, G., 2003. Science. "Can great apes be saved from Ebola?" 300:1645.

More than just a pretty face

2005-12-15T10:21:00.000-06:00

Staphylococcus aureus. The name means, literally, "golden grape clusters." Upon staining, these round bacteria are visualized in clumps that resemble bunches of grapes. Every microbiology student is familiar with the most notorious member of the Staphylococcus species, S. aureus, which often produces a distinct yellow pigment when grown on agar plates containing blood. This bacterium itself causes a wide range of illnesses, ranging from food poisoning to deadly skin infections. Of great concern is the fact that strains that resist a number of antibiotics--including methicillin--have been increasingly isolated no only in hospital settings, but also in the community. Vancomycin-resistant strains have also been isolated, but are not yet widespread.

It was recognized almost 25 years ago that the S. aureus yellow pigment consists of a number of carotenoids, similar to those produced in carrots and other fruits and vegetables. Studies of these carotenoid pigments have revealed their free-radical scavenging properties, protecting cells and tissues from the damaging effects of free radicals and singlet oxygen. (In other words, they’re antioxidants). Interestingly, one mechanism by which phagocytic cells of the host immune system destroy pathogenic invaders is via release of reactive oxygen species. Do these bacterial carotenoids protect S. aureus against damage initiated by the host immune system?

This question was investigated in a paper published this summer in the Journal of Experimental Medicine. Here, they investigated a mutant in the crtM gene, a critical gene in the carotenoid biosynthesis process. crtM mutants lack pigment and do not produce carotenoid, but other than that, were similar to the wild-type bacterium. In vitro, the mutants were more easily killed by oxygen and hydrogen peroxide—but when the crtM gene was added back in on a plasmid, the bacterium could again resist oxidative killing at a level similar to the wild type.

Looking at this mutant in a mouse model of infection, they also saw that the mutant did not cause skin lesions as the wild-type isolate did, suggesting the carotenoid is important in vivo. Finally, they also transformed an isolate of group A streptococcus (Streptococcus pyogenes) not known to produce carotenoids with the plasmid carrying the crtM gene—causing the isolate to produce a faint yellow pigment. When they examined the lesion pathogenesis in mice injected with the wild-type and the crtM-positive isolates of S. pyogenes, they found that lesions formed were larger with the crtM-positive isolates. So, while the wild-type was already invasive, addition of the carotenoid gene made them even nastier.

I wrote previously about pili being discovered in gram-positive bacteria: once it’s found in one species, it begins a search in other, related, species—and indeed, pili have now been found in groups A and B streptococci, and will probably be found in other gram-positives. Likewise, carotenoid pigments were first investigated as an antioxidant virulence factor last year in the group B streptococcus (GBS, Streptococcus agalactiae). This is another gram-positive bacterium; clinically, it is an important cause of neonatal meningitis and other invasive infections. This bacterium also produces a carotenoid pigment that can give the colonies a slightly orange tinge. Interestingly, it was found that knocking out the gene that produces the GBS hemolysin cylE (a protein that breaks open blood cells, producing a characteristic clearing around a colony on a blood agar plate) renders the colonies both non-hemolytic and non-pigmented, though it’s not yet known whether this is a direct or indirect effect. Additionally, these cylE knockouts were reduced in virulence in a mouse model of infection and more easily cleared by the host. They were also more susceptible to oxidative damage in a macrophage killing assay—so, similar to S. aureus, presence of the carotenoid increases the virulence of the bacterium.

Previous studies examining the role that the GBS hemolysin plays in disease pathogenesis has focused on damage the hemolysin is able to inflict upon host cells. Investigating it from the angle of protection of the bacterium, rather than damage to the host, represents a shift in thinking about bacterial virulence. It also opens up a new avenue for antimicrobial targets—creating drugs to render the bacteria’s defenses inadequate, thereby allowing the host’s own immune clearance mechanisms to operate more effectively. Finally, it suggests that other microbes that produce antioxidant carotenoids or melanin, such as cystic fibrosis pathogen Burkholderia cepacia--an organism that is often notoriously difficult to kill once patients are colonized—and fungus Aspergillus fumigatus, the leading cause of fungal infections worldwide. The challenge here, of course, will be to design drugs that target these microbial carotenoids but are safe to humans. With this research, an observation that has been more of a curiosity and diagnostic determinant has become a possible way to get a handle on these important pathogens.

Six years ago today

2005-12-13T02:43:00.000-06:00

...I was suffering the worst pain I'd ever experienced. I arrived at the hospital a bit before 1AM, and spent the next four hours or so walking around in agony. By 5AM, I decided I was ready for some of the good drugs, but the nurse informed me it was too late--time for the real fun to start. My daughter was born at 5:23AM, December 13, 1999--five long grumpy days after her due date. I was supposed to have a final exam that day.

My daughter wasn't exactly, erm, scheduled--but no contraceptive is 100% effective. I'd just been accepted to grad school, married less than 6 months, and hello, baby on the way. Kids had always been in the long-term plan, and since where my husband and I grew up, 23 was practically ancient to have your first baby, we bought a crib, set up a nursery, and hunkered down to become parents. It occurred to me for all of a minute to postpone grad school, but I've always been up for a challenge, so never gave that option serious consideration. I admit, though, that it was unnerving to say the least to be sitting in class during the last trimester of my pregnancy, discussing every possible chromosomal and developmental abnormality that can happen during development, with outcomes ranging from mildly bad to, of course, fatal. *Not* recommended for the faint of heart.

Luckily, she had pretty good timing. A mid-December birth meant that I already had Christmas and New Year's off, so I didn't have to miss too much time in the lab. I took off exactly 4 weeks (though I made up the missed exam a week after she was born), then headed back to the lab. Since daycare was a huge financial burden on a grad student's stipend, we got creative. My husband had a 7-to-4 job, so I worked around that, going in a lot of weekends and generally staying home one or two days during the "normal" work week to cut daycare costs. Again, I was fortunate: I'd already worked in the lab for almost a year prior as a technician, so even though I'd officially been a grad student for only a few months, I was already independent in the lab and didn't need someone to watch over my shoulder--allowing me to be in there on a Sunday at 7AM or a Wednesday at 1AM and get my work done.

Being a parent and a graduate student ain't easy. Obviously, the money sucks--at that time, my stipend was just over $13,000/year, and then they took out more every month for parking and health insurance. At my school, the health care also was pretty terrible: incredibly, though well-baby checkups were paid for, infant vaccinations weren't even covered. To top things off, I had (make that *have*) pretty hefty student loan payments from undergrad. Nothing like using the ol' charge card for diapers and groceries.

Anyway, since Baby #1 was the model of cherubic perfection (as of course, everyone thinks their own children are), and since my husband and I both have siblings who are close to us in age and we wanted that for our own children, we decided to confirm the fact that we were, indeed, insane. Baby #2 came along toward the other end of my PhD. (He was right on time, and no test that day--I was scheduled to give a journal club presentation. I'd already passed the file along to someone else, "just in case.")

Postdoc ensues, then I get to move up in the world as an assistant professor. Though family issues have always been a worry, now is when it really starts to kick in. (See, for example, this discussion, or this horror story). Again, I'm lucky on one level--I'm not planning on having any more children, so I don't have to worry about pregnancy, or maternity leave, or any of that jazz. I don't need to stress and tear my hair out trying to find the "right time" to start a family, since I already finished mine during probably the least-recommended stage of my career. My daughter is in kindergarten and my son goes to preschool, so our childcare expenses aren't quite as horrible as they once were. My husband now has his own business, so if I need him to watch the kids for some reason, he's flexible. But like many women in all different kinds of careers, I still feel pulled in a million different directions, and still worry about how taking time out for my kids will impact my career, and how spending so much time at my job will affect my children.

I'm all too familiar with the arguments on both sides of the "academics and children" fence. "Overall, academics have it good." We're "spoiled, whiny complainers;" we "want it all and don't want to sacrifice job or family;" our "ambitions are too high, we should lower them" (especially true for women who want a satisfying family life); "hey, the system as it works now gave us quantum mechanics and the Internet, so why fix what ain't broken?" On the other side, "academia loses a lot of good teachers and researchers when it comes down to a choice between family and career"--and besides, "how would we con those naive, innocent grad students into aspiring to stay in academia without some kind of move forward on family issues?"

In the discussion referenced above, physicist Ann Nelson left this comment (which sums up my feelings pretty well, and having an authority say it is even better):

The problem is that most people ASSUME that a woman cannot be a good mother and a good scientist. So at work we always feel we have to prove ourselves and do extra so people don’t say “see, she can’t be serious about science because she is a mother”. Then women who do need to take some leave or some time to breastfeed or need to leave work to pick up a sick kid worry that this is going to lead their colleagues to assume they have lost their committment to science. The other side of the pressure and stress is caused by the very large number of people who assume that only a SAHM [stay-at-home mom] can be a good mother, and a career oriented woman must be some kind of neglectful mother who is having her kids raised by strangers.

So, yeah, there's this too--guilt from all sides. You're never good enough as a scientist because you have a life away from the lab. You're never good enough as a mother because you have a life away from the kids. Is this just our paranoia, or does it really represent what people think? Do people really *say* this to us? Rarely--but it does happen. More often, I'll read it somewhere: a comment from a scientist about other scientists with families, and how their priorities aren't in line (or, one of the more overtly insulting lines I mentioned above). Or I'll see or hear a similar comment from a SAHM who is sure I'm screwing up my kids' psyches by having a demanding career.

Anyway, I worry, and I stress, and at the same time, I make the most of it. By all reports, my kids are doing great in school, both academically (well, as academic as kindergarten and preschool get) and socially. I've been here for almost a year now, am currently working on getting some more manuscripts submitted, and think I've had a pretty productive year. Things aren't going quite as swimingly in the lab, but I'll be starting at least 2 new projects after the new year, which will (hopefully) mean more papers and more grants, potentially by this coming summer. Next fall will bring more teaching duties, but it's a course I've taught before, so at least I'm not quite starting from scratch. In between, there will be birthday parties, and trips to the park and the lake, and Disney movies, and ice skating. And lots of creature-catching: we currently have about 5 wolf spiders in various jars around the house, and a small frog she caught in the creek out back in late fall as "pets." And yes, it will probably mean a few weekend mornings spent coloring in Mom's office while I finish up some work. If they need therapy as adults because of this horrible treatment, maybe I'll chip in for half.

Happy birthday, baby girl. I hope that 20 years down the line, the idea that you have to make a choice between your dreams and your family will seem a backwards and archaic notion, and that you go as far as you want along whatever path you choose. I may have to come with a journal article and highlighter in hand, but I'll be there, cheering you on.

Everything old is new again

2005-12-13T00:30:00.000-06:00

...as Nick Matzke reveals.

I'm sure some of you paid attention to the goings-on in Cobb county, Georgia, earlier this year. To sum up, evolution-deniers had placed the infamous "evolution is a theory, not a fact" disclaimer sticker on biology textbooks in the district. Other parents sued to have them removed. In January, U.S. District Judge Clarence Cooper said that the sticker violated the Establishment Clause of the First Amendment--bye-bye stickers. The ruling was appealed, and the hearing for that appeal is scheduled to be held later this week.

So, now what you're up to speed, check out Nick's finding: a 1925 quote from the LA Times discussing evolution as a "theory, not a fact." Man, can't *anyone* on their side come up with some new material?

Whole hog analysis of emerging diseases

2005-12-12T12:11:00.000-06:00

As I've mentioned a bunch of times now, I work with the Center for Emerging Infectious Diseases here at the U of Iowa. Our primary focus is zoonotic diseases (diseases which are transmitted between species), and being in an agricultural state, we have a special interest in pathogens of agriculture. A new analysis by Mark Woolhouse and Sonya Gowtage-Sequeria in the journal Emerging Infectious Diseases has taken a closer look at the origin of zoonotic diseases. By the numbers:

Of the 1407 human pathogen species, 816 (58%) are known to be zoonotic.
Of the 177 emerging or reemerging pathogens, 130 (77%) are known to be zoonotic.

Therefore, zoonotic pathogens are disproportionately likely to be associated with emerging and reemerging infectious diseases.

First, they looked to see *what* is driving the emergence of these pathogens--what factors are causing them to "emerge?" They came up with a number of variables, and ranked them by the number of pathogen species associated with them:

Changes in land use/agricultural practices
Changes in human demographics and society
Poor population health
Hospitals and medical procedures
Pathogen evolution (e.g., antimicrobial resistance, increased virulence)
Contamination of food or water supplies
International travel
Failure of public health programs
International trade
Climate change

There's both good and bad in the ranking. The top two factors both give us many areas in which to intervene and prevent the emergence of additional pathogens. Agricultural practices can be analyzed to see exactly what it is that leads to disease emergence (crowding, new animals brought in and out, etc.), and this can be somewhat controlled. I'd guess demographics of humans are similar--more people in big cities and living in crowded conditions are great breeding grounds for new diseases. It's a challenge, but not as tough to deal with as climate change or poor population health. A real criticism is that, of course, the drivers of emergence to look at in the first place were chosen based on things the authors already assumed played a role in disease emergence, and we may be either missing something or falsely inflating one factor, but it's a start.

Breaking it down by groups of organisms, this association (between emerging disease and zoonotic pathogens) is strongest for bacteria and fungi, less so for viruses and protozoa. (The other category, helminths--parasitic worms--are already almost all zoonotic anyway, and very few are considered emerging or reemerging). Ungulates (hoofed mammals--deer, horses, swine, etc.) were found to be the most important species overall, see figure below. So, thus far, we have 1) importance of agricultural practices, and 2) hoofed mammals (including many you'd find on a farm). I have a feeling this paper is going to be oft-cited in our future grant proposals.

They next grouped the pathogens according to host range, and found that greater than 40% of the pathogens with the broadest host range (3 or more types of nonhuman host) were emerging or reemerging:

Finally, they looked at transmissibility. Most zoonotic pathogens aren't easily transmitted between humans--humans are either a "dead-end" host, or minimal human-to-human transmission occurs. To look at this graphically, they plotted the R₀ (the "basic reproductive number" for each pathogen; the number of secondary cases due to each case) on the X axis, and the relative size of each outbreak an organism caused on the Y:

So, the good news is that most zoonotic pathogens don't cause major epidemics. But, as they note in the discussion, we don't have a good way right now to predict whether a new pathogen will behave more like rabies (frequently introduced into the population, but doesn't cause major epidemics) or HIV (likely rarely introduced, but capable of causing a global pandemic). This is why we take things like H5N1 so seriously--especially because that's a virus family which, historically, is out in the upper right corner of that graph above. Right now H5N1 is in the opposite corner--introduced fairly frequently in the last year (~130 odd times thus far), but without significant transmission between humans. Hopefully it will stay that way, as many zoontic pathogens do. But as the authors also point out, good surveillance is, once again, the key--and to be thorough, we should go even beyond humans and ducks in an effort to better understand our microbial neighbors.

Synopsis of Maggiore's Primetime Live Appearance

2005-12-12T10:16:00.000-06:00

I didn't have a chance to blog this, but Christine Maggiore appeared on ABC's Primetime Live last week. For those of you who may be new to the story, she's the HIV denier whose 3-year-old daughter, Eliza Jane, died of AIDS-associated pneumonia. Maggiore dismissed the coroner's report, and had her own, erm, "expert" do a second autopsy; Orac discussed those findings here.

Orac has a good summary of the Primetime Live appearance; I was busy making snacks for my daughter to take to school the next day while Maggiore was on, so I wasn't able to take good notes. The whole incident was so sad; they played parts of the 911 call, and as Orac notes, it seemed clear from the story that EJ was much sicker for a longer period of time than Maggiore had previously suggested. Additionally, as Orac mentioned, she wasn't even convinced when the reporter gave her the exact evidence she asked for: pathology slides that showed that Eliza Jane had pneumonia. It was heartbreaking to watch her talk about her daughter, and the love she had for her was clear. But the bottom line remains: she went against consensus medical advice, and took risks with the lives of her children. And the worst part is that she continues to encourage others to do the same. Maybe their children won't get the national attention that Eliza Jane did; maybe some have already died due to advice from Maggiore and others like her. I don't know, and to my knowledge, no good studies have been done investigating how HIV denial groups like hers affect the opinion of others on the issue of AIDS causation. I hope EJ's legacy will make some of those deniers at least think twice about what they may be doing, not only to themselves, but to those close to them.

ID rumblings in Muscatine, Iowa

2005-12-09T10:20:00.000-06:00

From The Muscatine Journal:

Although they don’t all agree on the merits of intelligent design, most members of the Muscatine School District Board of Education believe that students should know about it, and they agree that it will likely be discussed by the Board within the next two years.

Ann Hart, vice president of the Muscatine School Board, said she would not remove evolution from the school district’s curriculum, because of its scientific basis, but that students should also know about intelligent design.

“I think somewhere along the line, intelligent design should be brought up because a lot of people believe in it; and, otherwise, kids aren’t going to understand it as well as they should,” Hart said. “I don’t think we should go in-depth with it, just let kids know what it’s about and that it’s what some people believe and then go on to evolution. I believe in evolution, for sure, but we do need to let kids know this is something that people believe.”

I wonder if she's contemplated that there are thousands of things "that people believe" that are not taught in schools, and by opening the door to one of them, you're leaving a crack for all the other nutty ideas that are out there.

Muscatine School Board member Clyde Evans said he would not be opposed to the teaching of intelligent design in Muscatine’s schools, and agreed that it would probably be discussed when the science curriculum was being reviewed.

Evans compared the workings of the human body, universe and nature to a fine watch in their design and operation. “I think if you look at how very complicated and very sophisticated it is, there’s probably as much credit for (intelligent design) as for (evolution), and probably more,” he said.

Ah, yes, Paley's Natural Theology...which, of course, ID isn't, according to Gonzalez et al. What's not noted is that many people believe in evolution *and* give credit to God at the same time. Earlier in the article (that I snipped out for brevity), the reporter describes evolution as an "unguided" force, but theistic evolutionists have no problem believing God played some role in how things turned out. Maybe someone should ship the school board a copy of "Finding Darwin's God" as a Christmas gift.

Board member Tom Welk was also supportive of intelligent design in school curriculum, although he said he had not studied the subject to the extent that he had an exact definition of intelligent design.

“Personally, I’m a believer,” he said. “We have not discussed it as a Board, but I would probably be supportive of it being taught. Of course, I’d still need an exact definition of it.”

*Snicker* Good luck with that--even the ID supporters don't agree on an "exact definition" of it.

Welk said that should intelligent design be discussed, he expected Iowan’s reactions and thoughts to be similar to the residents of Kansas.

A comparison to Kansas is not a good thing, as they just received a big fat F on their science standards.

Board member Paul Brooks said he was still deciding his position on intelligent design.

“I know what I believe, but I guess my feeling is I don’t know if I want atheist people in teaching positions trying to talk about intelligent design,” he said. “If I could determine who the instructors were, that’d be different. Right now, I’m confident our teachers give students a fair assessment of the creation.”

Hmmm, what "assessment of the creation" are your teachers now giving?? Sounds like Mr. Brooks is saying that if his teachers agree to indoctrinate kids in the specific way he agrees with, he'd be OK with it--but none o' them atheist teachers telling the young-ins that ID's hokey, now, y'hear??

But at least one Board member, president Jerry Lange, said he would feel uncomfortable with intelligent design in school curriculum. Lange did agree that it was likely to be an issue in the next two years.

Lange believed intelligent design was an attempt to put religious doctrine into schools, and while he did think it would be acceptable to introduce the idea to students as far as explaining its purpose, he would not support any significant teaching of intelligent design.

Thank you, Mr. Lange, for being the voice of reason.

As mentioned yesterday, Iowa doesn't have state science standards, so each district sets their own curriculum. This is good and bad for us: good, because the national ID groups can't simply target a state school board to push for inclusion of ID, but bad, because instead of potentially fighting one battle, we could potentially have to deal with this in every district individually. For Iowans interested in these issues, I'll again mention that we now have a Iowa Citizens for Science organization in our state, so keep an eye on that website and email me at iowascienceATgmailDOTcom for more information.

Thai 5-year-old becomes 70th known H5N1 death

2005-12-09T08:12:00.000-06:00

Death toll from bird flu hits 70

A Thai boy has become the 70th Asian to die of bird flu, authorities said on Friday, as reports warned a flu pandemic could cost the U.S. economy hundreds of billions of dollars as well as millions of lives.

The death of the 5-year-old boy from the central province of Nakhon Nayok, 110 km (70 miles) from Bangkok, took Thailand’s bird flu death toll to 14 out of 22 known cases since the virus swept through large parts of Asia in late 2003.

It was not certain how the boy caught the virus, which usually strikes those in close contact with infected fowl or their droppings, senior health officials said. The boy, who died in hospital on Wednesday, was not known to have had direct contact with chickens, health officials said.

“We believe that the boy contracted the virus from his surroundings because, although his family does not raise chickens, there are chickens raised in his neighbourhood,” said Thawat Suntrajarn, head of the Health Ministry’s Disease Control Department.

China also reported a new case of H5N1, the fifth person in the country known to have been infected with the deadly virus. The 31-year-old woman, who lived in Heishan county of Liaoning province, has since recovered.

The news that the boy didn't have any known direct contact with birds is worrying. Hopefully this is an anomaly, or there's some unrecognized contact with birds that his family may not know about. If more of these "no known fowl contact" cases start showing up, it's really time to start battening down the hatches and preparing for the worst.

Science year in review

2005-12-09T07:42:00.000-06:00

MSNBC has an article on the year in science. High on the list is the intersection of science and politics: cloning, climate,

The developments of the past year show that the "accepted wisdom" on science isn't as quickly or as widely accepted as perhaps it once was — partly because of a skeptical political climate, and partly because the Internet provides wider access for dissenting views. Those societal challenges are sparking the rise of a new breed of scientists: media-savvy folk who aren't afraid to join the fray themselves.

And this is both good and bad. They mention Gavin Schmidt of the RealClimate blog:

Schmidt and his co-bloggers get into the nitty-gritty of climate research, interacting earnestly with fans as well as foes in long strings of reference-rich commentary. It's not an approach meant to attract a mass audience or stir a political movement — and Schmidt doesn't mean it to be.

But while RealClimate, as they mention, is "reference-rich" and run by experts in the field, there are also, of course, sites like that by the Discovery Institute and other creationist groups, which, to many lay people, seem to be scientific and convincing, while the experts in the field scoff. It's great that we scientists are becoming better able to take new findings and explain them directly to the public, but it's unfortunate sometimes that there's so much "background noise" with the conspiracy theorists and anti-science brigade that it becomes difficult for many people to separate the wheat from the chaff.

Anyway, other hot topics of the year will come as little surprise to regular science readers: bird flu, hurricanes, evolution, and end-of-life issues, including Terri Schiavo and advances in neurology. I'd love to have a time machine and see how this year is reviewed 20 or 50 years from now. So many of the issues that we've gone through in the past year seem to be a tug-of-war between those of us who want to move forward, and those who want to send the country back to the "dark ages," where creationism is taught and the environment is ours to mutilate.

Is Indonesia even dumber than the United States?

2005-12-08T10:22:00.000-06:00

Over on SciAm Observations, they report that Indonesia has threatened to close down NAMRU-2. For those of you unfamiliar, NAMRU-2 is an acronym for "U. S. Naval Medical Research Unit No.2", and they work over in Indonesia (and extend to other countries in the region) to do infectious disease surveillance, outbreak investigation, and a number of other public health activities. Most recently, they've also been vital in working on the diagnosis of avian flu cases in that country, as it's the only facility with a BL-3 laboratory in the country. From the sounds of things, the country is valuing playing the game of politics rather than securing the health of its people (I know, a familiar ring):

The official justification for shutting down the lab is that the memorandum of understanding between the governments of Indonesia and the United States, which set up NAMRU-2 in 1970, expired in 2000 and has yet to be renewed. Since 2000, however, the lab has continued its activities--which in addition to large diagnostic and surveillance programs includes training medical workers to recognize and treat H5N1-infected patients--without interruption. "From 1 January 2006," the letter dictates, "all NAMRU-2 activities will be terminated until a new M.O.U. between the Government of Indonesia and the United States Government has been signed."

The letter does not mention what concessions Indonesia aims to obtain from the U.S. But it closes by reminding health officials that every scientific article they produce in collaboration with a foreign researcher must be cleared by the ministry of health before it can be published.

This hits close to home for me, as a technician in my lab is supposed to head over to Jakarta next semester, after finishing her MPH degree this month. This is the first time I've heard of these threats...I'll have to check with her to see if they've been more forthcoming in her communications.

Edited to add: Effect Measure's take on the situation

State science standards are in

2005-12-08T10:15:00.000-06:00

How did your state do? More info in this post on Panda's Thumb, with a table broken down by state rank here. Note: Iowa isn't on there. We don't have a set of state standards; it's left up to each district to decide what to teach.

Institute of Medicine lays the smackdown on SpongeBob

2005-12-07T10:51:00.000-06:00

The Institute of Medicine, an arm of the National Academy of Sciences, has gone on record saying that Food Marketing Aimed at Kids Influences Poor Nutritional Choices:

Food and beverage marketing targeted to children ages 12 and under leads them to request and consume high-calorie, low-nutrient products, says a new report from the Institute of Medicine of the National Academies. The report offers the most comprehensive review to date of the scientific evidence on the influence of food marketing on diets of children and youth.

Concern has focused on food and beverage marketing practices because of the increase in new products targeted specifically to children and youth over the past decade and the media's increasing role in socializing young people. Companies spent an estimated $10 billion to market foods, beverages, and meals to U.S. children and youth in 2004, and four of the top 10 items that children ages 8 to 12 say they can buy without parental permission are either foods or beverages.

The committee assessed hundreds of relevant studies and rigorously reviewed evidence from more than 120 of the best designed to determine what effects marketing may have on children's diets and health. Most of these studies focused only on television advertising, a shortcoming that should be addressed in future research, given that marketing strategies are rapidly evolving and now employ many tactics beyond television advertising, including Internet marketing, mobile phone ads, and product placements in video games and other media. For the most part, the committee did not have access to the substantial body of proprietary market research data held by marketing firms and food, beverage, and restaurant companies.

The committee found strong evidence that television advertising influences the food and beverage preferences and purchase requests of children ages 2 through 11 years old and affects their consumption habits, at least over the short term. Most advertising geared toward children promotes high-calorie, low-nutrient foods, beverages, and meals, which, the committee concluded, influences children to request and choose these products. There is not enough evidence to determine the extent to which marketing influences the preferences and consumption habits of 12- to 18-year-olds; too few studies have focused on teens.

The evidence on whether television advertising directly affects children's long-term dietary patterns is limited and less conclusive. However, nutrition studies show that America's children and youth are consuming too many calories and too much added sugar, fat, and salt. Moreover, they are consuming less-than-recommended amounts of many key nutrients, including calcium, vitamin E, and fiber.

You can find the report at this link to read all of the findings (note: it ain't free).

As a parent, I'm of a mixed opinion on this. I was still home for the Today show this morning, and the report was discussed, saying that pressure would be put on companies first to stop this kind of marketing, and if that failed, the legislature may very well take up the issue. Even as a public health professional, though, I think the bulk of the responsibility lies with the parents, not the government, to help our kids make smart choices. My kids are age (almost) 6 and 3 1/2, and of course they'd rather eat SpongeBob cereal than, say, Raisin Bran, or have a Barbie pop tart as a snack instead of a banana. But how much blame lies with the parents for buying the junk food in the first place (even if we're cajoled into it by our kids)?

There are lots of parents out there who absolutely ban "junk food" from their homes. I can understand that--it's not healthy, it's mainly empty calories, whole grains are better. But I don't know that's the way to go either--you're not teaching your children about temptation and smart choices, you're simply shielding them from it.

I don't know what the right answers are. My kids generally eat healthy. My husband or I cook something homemade almost every night. We try to limit the processed foods as much as possible, and my kids generally drink milk or water, with the occasional juice. But we do have "junk" around the house, and our kids definitely love cookies and potato chips and ice cream. I don't think that's necessarily a bad thing--even if it's junk food being marketed by Dora the Explorer and Shrek. I respect the IoM's work and trust their conclusions, but I wonder that the wrong things are going to come out of this--more regulation by the government, without a coincident increase in concern by parents.

What's causing the "Grisis Signis?"

2005-12-07T10:05:00.000-06:00

This came over the ProMed email last week:

A new outbreak of widespread "madness", known as "Grisis Signis" among native Central American tribes, is affecting native Miskito communities on the northern Caribbean Nicaraguan coast, and health authorities have not offered any scientific explanation for this phenomenon.

The information, published today by "El Nuevo Diario" newspaper, indicates that this region of the country is also suffering famine caused by a plague of rats that devoured crops. It adds that at least 31 native persons in the northern Caribbean coast had been affected by "Grisis Signis", which provokes attacks of violence and hysteria.

Saul Miranda, head of the health center in Waspam, the main municipality on the Coco River at the Honduras border, told the newspaper that 21 cases were detected in the Raiti community, 729 km northeast of Managua. He added that 4 additional cases were detected in the community of Santa Fe, while in Krin Krin village, indigenous leaders reported 6 ill persons.

The illness causes seizures and hallucinations, affecting only Miskito natives, who interpret the affliction as the result of a curse or sorcery. Those affected become quite strong, attacking households and becoming violent when somebody tries to disarm them. Some walk around the villages armed with sticks and machetes, sometimes returning to their homes after having been absent for some days. The only way in which affected persons return to normal is by taking herbs given to them by a traditional healer ("curandero"), but after the episode they do not remember anything at all.

Duing other outbreaks [a similar outbreak was reported in October 2003], Health Ministry authorities have not offered any scientific explanation for this illness.

Meanwhile, Coco River communities have been suffering for many months from famine caused by a plague of rats, which devoured their crops, and they have also been affected by floods caused by the recent tropical storms and hurricanes. Government authorities, with support from the World Food Program (WFA), have brought food and support for these communities that have been historically affected by natural disasters.

Comments on the email mention that there are a number of infectious agents that have been previously noted to cause psychosis in sufferers, including brucellosis, leptospirosis, and even Lyme disease. Other possibilitites mentioned include mycotoxicosis, due to a fungal toxin that can cause hallucinations that has been implicated in the Salem witch trials. Non-infectious causes, such as vitamin deficiencies, may also play a role.

I don't know how closely this outbreak is being examined, but I wonder if they're checking the rats for other parasites as well, in addition to the agents mentioned above. For those of you who haven't read Carl Zimmer's Parasite Rex yet, you're missing out on a fascinating exposition of all kinds of ways that parasites make their hosts do crazy things--"attacks of violence and hysteria" seem mild compared to causing animals to become sterile and raise parasite progeny as their own "young," for example; or causing a grasshopper to commit suicide.

This outbreak also allows me to mention another one of my pet interests, as I've noted before: infectious causes of chronic illness. It's long been known that infectious agents can mess with our minds: rabies was associated clinically with hydrophobia before the agent was ever isolated; similarly with the neurological effects of Treponema pallidum, the causative agent of syphillis. Are we seeing a new microbe here? A new clinical manifestation of an old one? Simple vitamin deficiency? I don't know, but I hope someone in the area is finding out.

U.S. unprepared for health disaser

2005-12-06T11:09:00.000-06:00

What. A. Surprise.

WASHINGTON - Hospitals are not prepared to handle the patients who would arrive after a disaster or a pandemic, most states have few plans in place for coping and the federal government has not taken charge of such preparation, according to a report released Tuesday.

Although President Bush released an influenza pandemic plan with great fanfare last month, and even though federal health experts have been issuing dire warnings for years, little has actually been done to get the nation ready, according to the Trust for America’s Health, or TFAH.

“While considerable progress has been achieved in improving America’s health emergency preparedness, the nation is still not adequately prepared for the range of serious threats we face,” the report from the non-profit health education group reads.

Well, knock me over with a feather. Who could have seen this coming?

On the more positive side

2005-12-06T10:35:00.000-06:00

So, that NYT article discussed below about how difficult it is to receive funding for innovative research was a bit depressing, so as an antidote, check out this article, also from today's New York Times.

Addressing 275 of the world's most brilliant scientists, Bill Gates cracked a joke:

"I've been applying my imagination to the synergies of this," he said. "We could have sorghum that cures latent tuberculosis. We could have mosquitoes that spread vitamin A. And most important, we could have bananas that never need to be kept cold."

They laughed. Perhaps that was to be expected when the world's richest man, who had just promised them $450 million, was delivering a punchline. But it was also germane, because they were gathered to celebrate some of the oddest-sounding projects in the history of science.

Several of the grants awarded are described in the article; the entire list is here. Goes to show you that not everyone has to give up on innovative research to get ahead, or get funded.

...what if?...

2005-12-06T09:52:00.000-06:00

I mentioned in October that ulcer researchers Barry Marshall and Robin Warren won this year's Nobel Prize in medicine for their research showing that Helicobacter was a cause of gastric ulcers. However, Marshall and Warren weren't the first to come up with that idea; indeed, there were earlier reports suggesting a connection. Antecdotal evidence from several hospitals suggested that ulcer sufferers improved when prescribed antibiotics, and a curved bacterium had even been seen in the stomachs of Boston ulcer patients back in the 1940s. Reports of this bacterium date back to even earlier in the century, but none were conclusively followed up. Indeed, the doctor who made the observation in Boston, A. Stone Freedberg, was discouraged from pursuing that line of research. Now, a half-century later, he will award the Nobel prize to the researchers who were able to do what he could not: grow Helicobacter pylori, and show that it was a cause of gastric ulcers. Today's New York Times discusses more of the story, a tale not only of "what ifs" but also of the role chance plays in science--even science good enough to win a Nobel.

New Grand Rounds!

2005-12-06T09:02:00.000-06:00

This week's Grand Rounds is up at The Examining Room of Dr. Charles. These seem to be growing every week (maybe because now Medscape is publicizing it?). Lots of good posts this week. At the Biotech weblog, they discuss the use of fumarones to prevent biofilm formation, with the goal of making catheters and other implanted devices that are prone to infection safer. Red State Moron fleshes out the newest battle in the abortion debate: laws suggesting doctors "inform women seeking abortions that a fetus is developed enough after 20 weeks to feel pain." As RSM discusses, this is something that's not even been decided in the medical world, yet now they want to bypass that and write it into law. MedSleuth discusses the newest Clostridium difficile news--and s/he should know, having gone through a bout of C. difficile infection. Finally, over my med body! has a late submission on pattern recognition, and why it's not always a good thing.

About your "poo print"

2005-12-05T11:04:00.000-06:00

I admit it. I am not the most organized person. My office is one of those "don't touch anything--I know exactly where it is" kinds of places, in sharp contrast to the colleague I work with most frequently, who was in the Navy for 20 years and never has so much as a pencil out of place. I blame it on my business; I like to have everything within reach when I'm working on something, therefore it's more likely to be "filed" on the floor or on my desk than in an actual cabinet until the grant or manuscript is out the door. In the last month I've sent off 2 grant proposals, finished a new course submission, and sent off a journal manuscript (with another to follow shortly), so alas, the clutter is closing in on me, forcing me to spend today filing, reading journals that have been piling up on my desk, and just generally making my office space presentable to students once again. (Though after reading this post via Pharyngula, maybe it's better to keep it messy in here...)

Anyhoo, in the meantime, you might want to check out a discussion of probiotics over at Immunoblogging. The discussion of the introduction of new bacterial species into your native flora (your "poo print--" I'm totally going to steal that for a lecture on intestinal flora) goes nicely with my post on Clostridium, below.

Emergence of epidemic Clostridium difficile

2005-12-05T10:29:00.000-06:00

Clostridium difficile has joined MRSA, SARS, avian influenza, and West Nile as a hot new emerging disease. This bacterium, a cousin to Clostridium tetani–the causative agent of tetanus--and Clostridium botulinum--the botulism bacterium—is a spore-forming anaerobe. Carried by about 3 percent of healthy adults, the bacterium is generally present as a metabolically inactive spore. The bacterium typically causes problems in the nosocomial (hospital) environment, where up to 40 percent of hospital patients may be colonized. Clinical disease generally presents as watery diarrhea and cramps, and is the most frequent infectious cause of nosocomial diarrhea, resulting in about 3 million cases per year. Mortality is generally low (less than 3 percent). Though not commonly fatal, these infections have a high monetary cost: each infection results in ~$3600 in excess health care costs, for a total of over $1 billion in the United States alone every year.

Ironically, it is antibiotic treatment that often precipitates manifestation of disease. In the 1974, a study by Tedesco et al showed that, in 200 patients given clindamycin, 41 developed diarrhea, and 20 had pseudomembranous colitis, a pathological finding characteristic of infection with C. difficile. Indeed, in the 1970s, the most common antibiotic associated with C. difficile disease was clindamycin; cephalosporins in the 1980s; and, in 2 new papers published in the New England Journal of Medicine, fluoroquinolones.

Like other disease-causing Clostridia, C. difficile produces a repertoire of toxins. Toxins A and B, released by the bacteria after colonization of the gut, are thought to be the main cause of disease pathogenesis. These toxins cause illness by disrupting the cytoskeleton of fibroblasts.

An increase in both the rate and severity of C. difficile infections has been noted since the 1980s—what underlay this increase? The emergence of a new, virulent strain was hypothesized, and that hypothesis was tested and confirmed in the reports by Loo et al. and McDonald et al., describing a new variant of this bacterium. This variant strain is resistant to fluoroquinolones, and contains an 18 base pair deletion in the tcdC gene. As this gene has been proposed to be a negative regulator of expression of the A and B toxins, it is likely that this mutation leads to the significantly higher toxin levels observed in these variants—reported to be16 to 23 times higher than strains without the deletion.

This isolate has been found not only in the US, but also in Canada, where it was responsible for 100 deaths over an 18-month period in a Quebec hospital. Additionally, analysis of the pulsed field gel electrophoresis (PFGE) patterns of 6000 historic isolates show that this variant has been present in hospitals dating back at least to the late 1980s. It is thought that the recent increase in incidence is due to increasing use of fluroquinolones. For instance, in one hospital studied in Pennsylvania, increase in disease incidence was correlated with a switch from levofloxacin to moxifloxacin; however, in another hospital, levofloxacin was found to be used in the largest percentage of patients who developed infection with C. difficile.

These outbreaks—again—underscore the need for active surveillance for infections. In a hospital situation, infections can be controlled by using careful procedures to avoid exposing non-colonized patients to C. difficile. Patient care equipment, including blood pressure cuffs and stethoscopes, should be used either only for the colonized patient, or thoroughly cleaned before using it on a second patient. Additionally, health care workers need to use actual soap and water to wash their hands between patients, as alcohol-based hand sanitizers aren’t effective in killing C. difficile spores. Finally, in the past, outbreaks of C. difficile disease have been controlled by restricting the use of antibiotics associated with disease outbreak—a difficult proposition for fluoroquinolone antibiotics. Therefore, we must be careful to use them in a more judicious manner--something microbiologists have long called for, anyway. Finally, as a greater percentage of our population is being housed in nursing homes and other long-term care operations, this is a problem we’re unlikely to see vanish anytime soon, unfortunately.

Further reading:

McDonald et al.. 2005. An Epidemic, Toxin Gene-Variant Strain of Clostridium difficile. NEJM, 353:2433. Link.

Loo et al.. 2005. A Predominantly Clonal Multi-Institutional Outbreak of Clostridium difficile-Associated Diarrhea with High Morbidity and Mortality. NEJM, 353:2442. Link.

Bartlett and Perl. 2005. The New Clostridium difficile -- What Does It Mean?. NEJM, 353:2503. Link.

Anonymous. 2005. Severe Clostridium difficile--Associated Disease in Populations Previously at Low Risk --- Four States, 2005. MMWR. 54:1201. Link.

AMA Op-Ed: "loopy times," and what medical professionals can do

2005-12-02T11:48:00.000-06:00

Though I'm not an MD myself, much of my research and my reading centers on medical issues, while another passion (as regular readers certainly must have noticed) is the "controversy" over evolution, and educating the public about the issues involved with that. So, in a nice convergence of these two topics, the American Medical Association has published an Op-Ed on the topic of evolution denial.

I’m afraid we live in loopy times. How else to account for the latest entries in America’s culture wars: science museum docents donning combat gloves against rival fundamentalist tour groups and evolution on trial in a Pennsylvania federal court. For those keeping score, so far this year it’s Monkeys: 0, Monkey Business: 82. That's 82 evolution versus creationism debates in school boards or towns nationwide—this year alone.

The most important part of his piece, IMO, addresses the role of the medical community in this "controversy:"

The medical community as a whole has been largely absent from today’s public debates on science. Neither the American Medical Association nor the American Psychiatric Association has taken a formal stand on the issue of evolution versus creationism. When physicians use their power of political persuasion in state legislatures and the US Congress, it’s generally on questions more pertinent to their daily survival—Medicare reimbursement, managed care reform, and funding for medical research. Northwestern’s Miller believes that the scientific community can’t fight the battle alone and that, as the attacks against science accelerate, the medical community will have to use its privileged perch in society to make the case for science. “You have to join your friends, so when someone attacks the Big Bang, when someone attacks evolution, when someone attacks stem cell research, all of us rally to the front. You can’t say it’s their problem because the scientific community is not so big that we can splinter 4 or more ways and ever still succeed doing anything”

So what does one do? How can a medical student, a resident, or a physician just beginning to build a career become active in these larger public battles? Burt Humburg, MD, a resident in internal medicine at Penn State’s Hershey Medical Center, is one role model. He’s been manning the evolutionary ramparts since his medical school days in Kansas in the late 1990s when he became active in Kansas Citizens for Science. On a brief vacation from his residency volunteering as a citizen advocate for the federal trial in Pennsylvania, he said education is the key role for the physician. While he realizes that medical students, residents and physicians might not view themselves as scientists, per se, he sees himself and his colleagues as part of the larger scientific collective that can’t afford to shirk its duty. “The town scientist is the town doctor, so whether we want it or not, we have the mantle—the trappings—of a scientist”.

There are many ways to get involved; from the most rudimentary—attending school board meetings, sending letters to the editor, and volunteering at the local science museum—to the more demanding—running for office, encouraging a spouse or partner to do so, or supporting candidates (especially financially) who are willing to speak out for science.

I hope Costello's call is answered. Those of you who may feel that this topic isn't your concern--you're wrong. Many of the same people who deny evolution are the same ones who refuse vaccination, who deny that HIV causes AIDS (such as Phillip Johnson), who claim that abortion causes breast cancer (such as DI petition signer Joel Brind), who think that there's some big conspiracy by the "scientific elite" against the common man. Many have a fundamental mistrust and misunderstanding about science, and evolution denial is only one way it manifests itself.

I know, it's much easier to stay in your office and not deal with the issue, but please, we can use your help. Write a letter to the editor--people seem to respond better to those "M.D." initials after a name than the "Ph.D." (="ivory tower elitist") ones. Especially if you're a well- known and respected member of your community, showing that you support the teaching of evolution in your school district can really help. There are other ways you can help listed here, and every little bit helps.

New Archaeopteryx fossil provides further insight into bird, dinosaur evolution

2005-12-02T09:25:00.000-06:00

Early-bird fossil features dinosaur feet

When it comes to feet, the earliest-known bird species had more in common with Velociraptors than cardinals.

Modern bird feet have a hind toe that points backward and helps the birds perch on branches, power lines, and pirates' shoulders. And until a recent discovery of an extremely well-preserved skeleton of the earliest-known bird species, Archaeopteryx, scientists believed it too had a "perching toe."

The new fossil, known as the "Thermopolis specimen," is incredibly well-preserved. It left clear impressions of its wing and tail feathers in the limestone it was encased in, and the skull is the best-preserved of all the 10 specimens ever discovered. But it may be the feet that prove to be the most important aspect of the find.

Other links:
Science summary
Science research article

Also posted on Panda's Thumb since I'm too far behind even in lay reading in this area to be able to make any insightful comments beyond, "this is so cool!" :) Hopefully some of the experts there will pick up my slack.

Are fruit bats a reservoir for Ebola?

2005-12-01T03:58:00.000-06:00

As I've mentioned before, Ebola is a virus near and dear to my heart. (Figuratively, not literally. I'm not quite that enamored of it). In that previous post, I mentioned that we didn't know the reservoir of Ebola in nature. It certainly isn't for lack of trying that it wasn't determined previously. The first field studies took place shortly after the initial 1976 outbreaks in the Democratic Republic of Congo (DRC) and Sudan. In the former, 818 bedbugs, 1500 mosquitoes, 10 domestic pigs, one cow, seven bats, 123 rodents, eight squirrels, six Cercopithecus monkeys, and three small antelopes were sampled--all negative when viral isolation was attempted. In Sudan, almost 500 vertebrates were similarly tested--zilch. Similar results in 1977 and 1979 in the DRC. Following that outbreak, Ebola did not re-surface for a decade and a half, popping up again in a large 1995 outbreak in Kikwit, DRC. A total of 2814 vertebrates and a whopping 27,843 arthropods were captured during respective periods of 3 and 6 months after the end of the outbreak. Viral isolation was attempted from both categories of animals, and vertebrates were also tested for Ebola-Zaire specific IgG. No positive IgG reactions were obtained, and no viruses were isolated on Vero cells. The vertebrates included 1759 rodents, 539 bats, 114 insectivores, 184 birds, and 127 reptiles and amphibians. The arthropods included 15,118 mosquitoes, 124 blood-sucking flies, 6538 bedbugs, 144 fleas, 103 lice, and 5816 ticks.

Around the same time as the Kikwit outbreak, a case of Ebola was retrospectively identified in a primatologist who had been working on the Ivory Coast. So, scientists trudged back out there, collecting 1642 vertebrates (652 bats, 283 rodents, 398 insectivores, 27 monkeys and 282 birds) between 1996 and 1997. One red colobus monkey was seropositive, but virus was never cultured.

Finally, 242 vertebrates (24 bats, 163 rodents and 56 insectivores) were captured in the Central Africal Republic in 1998. Small Ebola-specific genetic sequences were amplified from organs of six mice and a shrew. However, although these results constitute the only biological evidence that Ebola may be present in healthy animals, no firm conclusions as to the reservoir status of these animals can be drawn, given the lack of specific serologic responses, the lack of nucleotide specificities in the amplified viral sequences, the failure of virus isolation, and the non-reproducible nature of the results. Still, it was heartening to finally have some positive results after so many dead ends. (All of this reviewed in Pourrut et al., "The natural history of Ebola virus in Africa." Microb Infect 7:1005-14).

Now, a new study in today's Nature has found similar results in fruit bats.

Like previous studies, the authors trapped a number of species while Ebola epidemics were occurring (this time, in Gabon). In total, 1,030 animals were captured, including 679 bats, 222 birds and 129 small terrestrial vertebrates. They found Ebola-specific IgG in 3 different bat species (a total of 16 positive individuals). Viral RNA was detected in the liver and spleen of a total of 13 of the individuals of these species as well, and found to be the Zaire subtype. (There are 4 known Ebola subtypes: Zaire, Sudan, Ivory Coast, and Reston, listed from highest to lowest virulence in humans). However, the bats that were antibody-positive weren't the same individuals that were PCR-positive. The authors suggest that the IgG+ individuals had likely already cleared the virus, and the PCR+ individuals had not yet mounted a significant immune response to the virus.

Is it biologically plausible that bats are a reservoir of Ebola? In a word, yep. Bats have long been suspected to play a role in Ebola transmission. Studies have shown that the virus can replicate in experimentally-infected bats, and index cases in outbreaks of not only Ebola, but also its filoviral cousin Marburg virus, have been traced to bat-infested locations: caves, warehouses. However, this is the first direct evidence of bat infection in the field. Finally, the authors note that each of the three bat species has a broad geographical range that includes regions of Africa where human Ebola outbreaks occur, and also suggest that changes in the bat's diet during the dry season (when Ebola mortality increases in the great apes) may make them more likely to spread the virus during that time.

Does this close the book on an Ebola reservoir? Hardly. This will, however, give scientists some targets to focus on.
The three species identified include Hypsignathus monstrosus (which has to win some kind of ugly animal award), Epomops franqueti, and Myonycteris torquata, pictured in that order. Future investigation can examine more closely the ecology of this species, and particularly its interaction both with humans and with the great apes in this region. The current study also cannot address how the bats themselves become infected. Is there another reservoir that they acquire the virus from? Is it transmitted between bats via secretions? Feces? Blood? Acquired from nursing on an infected mother, or during birth? Does it come from their diet? All the positive bats were fruit eaters, and it's been previously suggested that Ebola may be a plant virus (though the evidence for that is currently pretty sketchy). Nevertheless, all are potentially testable hypotheses in the field and/or in the lab.

Finally, an awareness campaign can be instituted, as they mention that villagers in the area may eat these bats. Some previous outbreaks seem to have correlated with the consumption of bush meat (in one case, a chimpanzee who had likely died from Ebola); therefore, this is one potential way the virus could enter the human population. Education may potentially ward off a future outbreak. It won't help the gorillas, but it's definitely a start, after a long and mostly fruitless (wink, wink) search.

(Images (c) N. Ebigbo for E. franqueti and (c) J. Fahr for M. torquata).

You go, (Professor) girl!

2005-12-01T03:10:00.000-06:00

Meet Dr. Kristi S. Anseth. Dr. Anseth is a tissue engineer--reassembling life's basic building blocks into something that becomes living tissues within a body. At the age of only 37, she also has the distinction of becoming the first engineer to become a Howard Hughes medical investigator, "a prize usually reserved for Nobel-worthy researchers in the basic sciences," as noted in the article.

I've been lucky to have several good female mentors in biology and epidemiology; it's good to see an increase in female role models in other sciences as well, especially fields that are traditionally very male-heavy like engineering. Kudos.

Science blogs getting noticed by the big guns

2005-12-01T01:40:00.000-06:00

PZ noted that Science magazine contained a blurb about Panda's Thumb in this post:

Darwin's contemporaries Thomas Huxley and Joseph Hooker championed his theory in print and in lectures. If they were alive today and had a little attitude, they might craft something like The Panda's Thumb, a Web log in which a cadre of Darwin's modern-day defenders pummels antievolution pseudoscience such as "intelligent design" (ID). The site gets its name from a Stephen Jay Gould essay about the giant panda's adaptation for stripping bamboo leaves--it's a jury-rigged feature a clever designer wouldn't engineer. Panda's Thumb regulars--who range from Ph.D.s and grad students to a businessman and a lawyer--comb the news media for follies to expose and errors to correct. The site provided blanket coverage of the recent trial on the Dover, Pennsylvania, school board's decision to require teaching of ID (Science, 18 November, p. 1105). Panda's Thumb also highlights evolution-related research, such as a study showing that the antibiotics produced by our immune systems may not be a panacea for drug-resistant bacteria.

Today, Nature gets into the game, featuring quotes from PZ as well as Revere from Effect Measure:

Scientists who blog see their activities as a useful adjunct to formal journals, not a replacement. "The standard scientific paper is irreplaceable as a fixed, archivable document that defines a checkpoint in a body of work, but it's static, it's very limited," says Paul Myers, a biologist at the University of Minnesota, who blogs at Pharyngula. "Put a description of your paper on a weblog, though, and something very different happens," says Myers. "People who are very far afield from your usual circle start thinking about the subject. They bring up interesting perspectives." By sharing ideas online, you get feedback and new research ideas, he says.

A senior US epidemiologist who blogs once or twice a day under the pseudonym 'Revere' on his public-health blog Effect Measure, has attracted a diverse readership. "About 1,500 people visit each day," he says. "If someone told me that I could show up at a lecture hall every day and deliver a short opinion, and that 1,500 people would show up to hear me, I'd be pretty satisfied — 1,500 is twice the subscription of many speciality journals."

But for most scientists and academics, blogs and wikis remain unattractive distractions from their real work. Many consider them an online version of coffee-room chatter, background noise that goes against the very ethos of heavily filtered scholarly information.

Sounds pretty rosy, so they do include a counter-point:

Yet even the most web-savvy scientists remain unconvinced that blogs have any useful role in science. "I have my doubts that blogging reduces information overload, but blogging will survive as it appeals to all the exhibitionists," quips Rolf Apweiler, a bioinformatician at the European Bioinformatics Institute in Hinxton, UK, and head of the UniProtKB/Swiss-Prot protein-sequence database.

Ouch. Rolf's certainly entitled to his opinion, but I wonder how much science weblog reading went into formulating it. Me, I write not to be an "exhibitionist," but because I am, quite simply, a complete science geek. I love reading about this stuff, and sharing what I read with others (and my friends and family are getting sick of it, heh). And even if no one reads it, just the act of writing about various topics forces *me* to give deeper thought to them, and improves my own understanding of the issue. I think (hope) this also makes me both a better scientist and a better teacher. And finally, one of my pet issues is making science available (and understandable) to the general public. Scientists often bemoan science journalists for not getting things quite right, so why not let them hear it straight from the horse's mouth, so to speak?

"Face/off"...and back on again

2005-11-30T10:47:00.000-06:00

Doctors in France perform partial face transplant
Okay, so it's not quite Travolta/Cage switching places, but it's a start.

French doctors on Wednesday claimed a world-first partial face transplant, saying a nose, lips and chin were grafted onto a 38-year-old woman disfigured by a dog bite.

The woman was in "excellent" condition and that the transplanted organs look "normal," the statement said. She wants to remain anonymous, it said.

Dr. Jean-Michel Dubernard, one of the surgeons who collaborated on the transplant, told The Associated Press when reached Wednesday that the transplant was the world's first of its kind.

Scientists elsewhere have performed scalp and ear transplants in the past. However, the claim is the first for a mouth and nose transplant. Experts say the mouth and nose the most difficult parts of the face to transplant.

The woman was disfigured by a dog bite in May that made it difficult for the woman to speak and chew, the statement said. Such injuries are "extremely difficult, if not impossible" to repair using normal surgical techniques, it added.

The organs were taken from a donor who was brain dead, with the family's consent, the hospitals said.

I'm a big advocate of organ donation, but I wonder if this would creep me out a bit if I was the donor's family. I'm curious how much she'd resemble the donor from the nose-down? I'd assume her own bone structure must play a part in that, so that it's not exactly the same as the donor. I hope they show some pictures once she heals. Since it's only the bottom half of her face, they could easily block out the top portion to conceal her identity.

Just following the cool kids...

2005-11-30T09:50:00.000-06:00

PZ has a post up today wondering about international visitors and left/right leaning tendencies. His blog received about 57% of its visitors from the U.S., compared to the "right-leaning" blog that was compared, Powerline (94% U.S.). Mine is in the middle, with 30% international:

Just for the record, and all.

(Oh, yeah, and I totally knew my sitemeter could do that before today. Not clueless at all, nope, not me...)

Check out Tangled Bank #42

2005-11-30T09:25:00.000-06:00

A new Tangled Bank is up at Dogged Blog, and it is giant and awesome. First, the host herself is a writer about veterinary medicine--interesting to me since I work with zoonotic diseases (diseases that are transmitted between species) and work with veterinarians myself quite a bit. Beyond that, there are a ton of great posts. I'm adding Science and Politics to my blogroll right now, just 'cause he's a disease geek like I am, as evidenced by his post about his love of malaria. Same goes for Christie at Dogged Blog, actually:

One of my favorite subjects is disease. I was happy to get so many submissions about sickness and plague and pestilence. It may be that I'm not a well woman, but it seems I am in extremely good company.

Obviously I'm biased, but I agree.

One final post to highlight: this gem from bootstrap analysis about judging a middle school science fair (hilarity ensues). I also judge a few of these every year, so the comments were familiar, but if you've not been to one of those since you were a middle-schooler yourself, stop by and see what the kiddos are up to. I guarantee a chuckle.

Berenstain Bears co-creator, Stan Berenstain, dies

2005-11-29T12:32:00.000-06:00

Link to CNN story.

Stan Berenstain, who with his wife created the popular children's books about the Berenstain Bears, has died.

In more than 200 books, the Berenstain Bears, written and illustrated by Stan and Jan Berenstain, helped children for 40 years cope with trips to the dentist, eating junk food and cleaning their messy rooms.

The first Berenstain Bears book, "The Great Honey Hunt," was published in 1962. The couple developed the series with children's author Theodor Geisel -- better known as Dr. Seuss, then head of children's publishing at Random House -- with the goal of teaching children to read while entertaining them.

I know a post about a children's book author may seem out of place on a blog mostly devoted to science issues, but I read tons of Berenstain Bears book when I was a tot, and I now have a bunch more for my own kids. They actually have a number of books with a science theme:

The Berenstain Bears' Big Book of Science and Nature
The Berenstain Bears' Science Fair
The Berenstain Bears on the Moon
The Berenstain Bears Don't Pollute
The Berenstain Bears and the Missing Dinosaur Bone
The Berenstain Bears: Brother Bear Loves Dinosaurs (for really little tykes)
Heck, even one now for the information age: The Berenstain Bears Lost in Cyberspace

Plus, they had a woman doctor, back before Barbie taught girls that "math is hard."

I wonder sometimes how much books like these and many others shaped my early interest in science. When I was a bit older, I loved Nancy Drew books...my mom had probably 25 of them from when she was young. I'd always buy the Encyclopedia Brown mysteries from the book club in elementary school. I used to read encyclopedias, too, and now that everything is online, it's rare to even find an actual set of those. As an older child, I graduated to science fiction and "classic" literature, but I could never get into anything too romantic and stereotypically "girly." And today, I've definitely benefited from all that reading and varied interests from my childhood. My daughter is at that age where she's starting to read more independenly--I hope she learns to love it as much as I do. Thank you, Mr. Berenstain.

Grand Rounds 2.10

2005-11-29T03:54:00.000-06:00

Best of the medical blogosphere is up and runnin' at "Over my med body" (great title!) with a Thanksgiving theme. Ones that drew my attention: antimicrobial chewing gum on the Biotech Weblog; a discussion on the issues related to VBAC (vaginal birth after Cesarean) at Red State Moron; Polite Dissent discusses a pet peeve of mine as well: ridiculous headlines; Catallarchy has more on the autopsy of HIV-denier Christine Maggiore's daughter, Eliza; and Orac lays the smack-down on chelation therapy for autism.

Additionally, it was noted that applications are being accepted for the 2005 Medical Weblog Awards. Nominate your favorite blogs in the following categories and spread some love around:

-- Best Medical Weblog

-- Best New Medical Weblog (established in 2005)

-- Best Literary Medical Weblog

-- Best Clinical Sciences Weblog

-- Best Health Policies/Ethics Weblog

-- Best Medical Technologies/Informatics Weblog

Finally, my career prospect if I don't get tenure. DB reports on a trend in drug reps: hiring former cheerleaders. Bet it pays better than academia, too.

Super-sized needles

2005-11-29T00:16:00.000-06:00

I suppose there are stories about obesity every day, but this one caught my attention after just posting about watching "Supersize Me:"

Fatter rear ends are causing many drug injections to miss their mark, requiring longer needles to reach buttock muscle, researchers said on Monday.

Standard-sized needles failed to reach the buttock muscle in 23 out of 25 women whose rears were examined after what was supposed to be an intramuscular injection of a drug.

Two-thirds of the 50 patients in the study did not receive the full dosage of the drug, which instead lodged in the fat tissue of their buttocks, researchers from The Adelaide and Meath Hospital in Dublin said in a presentation to the annual meeting of the Radiological Society of North America.

Besides patients receiving less than the correct drug dosage, medications that remain lodged in fat can cause infection or irritation, researchers Victoria Chan said.

23 out of 25 women?? That seems too high.

I have a love/hate relationship with stories like this. Love 'em because I enjoy reading about any new findings, but hate 'em because, since this apparently was just a conference abstract, I can't comment further on the methods. Was this some kind of population that was more likely to be obese anyway? Even if you figure that 65% of the population is overweight or obese, they found that 92% of the women in their population had too much ass fat to be able to use a regular needle. It could very well be simply a sample size effect--25 ain't much of a population to generalize from. But still, it's baffling to think that only 8% of those patients received the correct dosage of drug. Shouldn't this have been noticed before?

It’s a small world, after all

2005-11-28T13:13:00.000-06:00

Have you ever wondered how Kevin Bacon and the lights of fireflies related to malaria and power grids? I know it’s something that’s kept me up many a sleepless night. One word: interconnections.

Many of you have probably heard of the “Six degrees of Kevin Bacon”game. This is based on the work of Stanley Milgram beginning in the 1960s, and brought up again more recently in a 1998 Nature paper, "Collective Dynamics of ‘Small-World’ Networks,” by mathematicians Watts and Strogatz. Milgram conducted a number of studies using his “lost letter technique,” in which letters were sent out and then needed to be forwarded onto reach their destination. In one instance, Milgram sent out 160 letters to individuals in the midwest, with instructions to pass them along to acquaintances who would be most likely to reach his stockbroker friend back east. Almost all of the letters that reached the stockbroker did so via one of 3 friends, and most did it within 6 steps--hence the “six degrees of separation” idea. Similarly, Duncan Watts first became interested in the “small world problem”—the idea that all of us are more closely connected than we realize—after watching fireflies flash in synchrony, and wondering how they accomplished that. What Watts, Strogatz, Milgram, and others were investigating boiled down to a series of links in a network—hubs and connectors. As Watts and Strogatz showed in their 1998 paper, all it took to make a "small world" from a regular network was the addition of a few "short cuts" (see figure from their paper, above). This elegant and seemingly simple structure of networks explains not only connections between movie stars and scientists but also cellular metabolism, ecology webs and the World Wide Web itself.

Another “small world” phenomenon is disease transmission. Social architecture affects, and explains, factors that impact the spread of disease—the people we are in contact with, and in the cases of sexually transmitted diseases, the people we sleep with. At the base of this phenomenon in infectious diseases is an idea called the "tipping point." This is something epidemiologists have discussed much in recent months regarding the potential of an avian influenza pandemic—tiny influences can have startling effects. A simple mutation may make a virus more easily transmitted between humans. Given the right environment, this may allow the virus to sweep through a population, causing a world-wide outbreak. Under different conditions, it may cause a few infections and fade away; a few factors may make all the difference. Mathematical modelers can examine these factors in computer simulations in order to determine if a disease will burn out, remain endemic in a population, or become an epidemic. A critical determining factor affecting these outcomes is the basic reproductive rate of a disease (R0). If R0 is less than 1 (each case infects less than one additional individual), a self-sustaining epidemic is not possible. If it is equal to 1, the disease will become endemic in a population. If R0 exceeds one, the disease may become epidemic; the larger the number, the more likely this outcome is. But, while this number is useful, one must keep in mind that R is an average over the population—it may be much higher or lower in subsets of the group.

Early work in this area did not take this difference into account, and assumed that individuals in a population had an equal chance of transmitting the disease. However, reality does not bear this out, leading to the proposal of the "20/80 rule," which suggests that approximately 20% of the most infectious individuals are responsible for 80% of the disease transmission. This was most recently demonstrated by an analysis of the 2003 SARS outbreak (see figure, from MMWR 52(18);405-411), but has also been seen with AIDS and other STDs. With AIDS, we recognize that "core groups" of infected individuals are often responsible for large outbreaks of disease. What we see when we examine this graphically is a "small world" network: a series of hubs and connectors, with the largest hubs—-termed "superspreaders" (the numbered dots in the picture above)--responsible for a disproportionately large number of secondary cases. This may be due to the fact that the superspreaders simply have a higher number of contacts; they may have a co-infection that leads to increased pathogen shedding, meaning the contacts they have are more efficiently exposed; they may have an undiagnosed illness, leading to an extended period of transmission; or they may have a combination of the above. For example, imagine a sex worker with both HIV and a secondary STD, such as gonorrhea. By virtue of her occupation, she will be in contact with a large number of individuals. HIV may lead to an increase in bacterial load, exposing her clients to a larger dose of N. gonorrhea than the "average" infected person; and her lack of health care means she has been treated for neither STD—potentially spreading both for years, until she is too sick to continue working. In this case, there are multiple explanations for why she would be a superspreader.

It takes careful epidemiological analysis to identify these superspreaders, however. One limitation of epidemiological analysis is that populations are generally divided into homogeneous subgroups--people of the same age, or race, or occupation, etc. This makes it possible to carry out studies comparing groups of individuals, but at the same time, it creates false divisions; life is always messier. A new paper published in Nature seeks to investigate some of this "mess," addressing the heterogeneity of transmission number among individuals and its effect on spread of disease. This new study by Lloyd-Smith et al., instead of using R0, investigates ν, the individual reproductive number. To examine this, they looked at previously published accounts of disease transmission where contacts had been traced, and determined ν for a number of different diseases and patients (see figure, below).

To sum up their findings, they suggest that disease with a high variation in ν show infrequent, but explosive, epidemics after introduction of a single case, a statement again borne out by an examination of the epidemiology of SARS, a disease which showed a high variation in ν. Indeed, many cities were exposed to SARS, but very few had explosive outbreaks. Is this universal? It will take more careful studies to determine that, but it suggests a new avenue of investigation.

Indeed, knowledge of the architecture of these outbreaks has immediate real-world applications. If the superspreaders could be identified early in an outbreak, interventions (vaccination, isolation/quarantine, treatment) could be targeted to this group. For example, another recent report highlights this same conclusion for malaria: identifying and targeting the superspreaders could reduce the disease burden enormously. Additionally, this work suggests, again, that we need better surveillance in order to detect these events while they are in progress. We can’t control superspreaders that we aren’t aware of, or only identify retrospectively, weeks, months, or years down the line.

Finally, this work—and indeed, much of the work done in the field of network theory--also points out, again, how things that appear to be “designed” can be the product of chance and circumstance. Each of these “small worlds” reveals a very similar architectural design. Each is dominated by hubs—a few extremely well-connected individuals, or web sites, etc. Additionally, this is not merely a qualitative difference: instead, they have a specific mathematical signature, which is nearly identical from one network to the next. I won’t go into the details, but Mark Buchanan has written a very layman-friendly book on the subject. (To be complete, Watts and Strogatz have also written books on the subject, but I've not read them yet). In Nexus, Buchanan notes:

What we see then is a kind of natural order that for mysterious reasons seems to well up in networks of all kinds and that does so despite the complexities of their individual histories….In biology, Charles Darwin’s idea of evolution by natural selection offers an extremely powerful organizing framework within which historical accidents take place. In the context of networks, there must also be some deeper principle at work.

Along a similar line of thought, Nobelist Herbert Simon once said, “The purpose of science is to find meaningful simplicity in the midst of disorderly complexity.” Network theory has shown how this can be done, and unlike “intelligent design,” has immediate practical applications in a vast range of fields.

China--being as forthcoming as they claim?

2005-11-28T09:59:00.000-06:00

Saw this while I was away, but wanted to find out more details. Reports had surfaced that China was covering up H5N1 cases. The initial ProMed email report:

Dr. Masato Tashiro, a Japanese WHO consultant, believes that China has had 300 human deaths from avian influenza and is hiding the true extent of the disease from the rest of the world. Dr. Masato Tashiro, Director of the WHO Collaborating Center on Influenza at the National Institute of Infectious Diseases, Tokyo, and head of the Department of Virology of the National Institute of Infectious Disease (Japan), astonished colleagues with this information during a speech at a recent retirement dinner for a fellow virologist, Hans-Dieter Klenk.

Having just returned from the Hunan province of China on behalf of the World Health Organization (WHO), [Dr. Masato Tashiro] claimed that a reliable source had provided him with details of the true nature of the H5N1 virus in China. "We are systematically deceived," he is reported to have said.

Tashiro visited China on behalf of the World Health Organization (WHO) in Hunan province. His laboratory, at the National Institute for Infection Research in Tokyo, as one of the Asian points of contact for the United Nations, had been particularly entrusted with investigations into avian influenza in Asia and China. Dr. Masato gave his lecture in the University of Marburg Clinic before some the most outstanding virologists in the world and shocked the meeting with his unauthorized data [report] from inside China.

The Japanese virologist [said he] firmly believes in the reliability of the source and its data. The secrecy of the Peking government is still causing concern as it was at the beginning of the SARS epidemic disease, complained Tashiro. At least 5 medical co-workers who should be reporting on the situation in the provinces were arrested, and [other] publication-willing researchers were threatened with punishments [he said].

A kind-of denial was then issued (see here), but the situtation still lacks clarity. Given China's population, agriculture practices, and past history of being, err, less than forthcoming when it comes to releasing information about disease to international authorities, this doesn't bode well, even if Dr. Toshiro's comments were played up or misunderstood.

Back!

2005-11-28T09:52:00.000-06:00

Well, this past week has been interesting. I traveled back to Ohio early to throw my sister a baby shower, then stayed with my in-laws over the Thanksgiving weekend. Saturday night my husband and I ended up watching most of "Supersize Me." My husband's reaction to the film: "I'm hungry for a Big Mac." As a public health professional, this made me weep. At least I've edumacated him about many issues in infectious disease epidemiology; guess I must now move on to nutrition epi.

More microbial tools

2005-11-26T14:16:00.000-06:00

I mentioned a real "microbial machine" in this post last month. Now, they're appearing as living photographs:

Researchers at the University of California, San Francisco and the University of Texas announced in the journal Nature that they had created photographs of themselves by programming the bacteria — — best known for outbreaks of food poisoning — to make pictures in much the same way Kodak film produces images.

***

Voigt and colleagues took from algae light-sensitive genes that emit black compounds and spliced them into a batch of E. coli bacteria. The organisms were then spread on a petri dish that resembles a cookie sheet and placed in an incubator. A high-powered projector cast photographic images of the researchers through a hole on top of the incubator, exposing some of the bacteria to light.

The result: Ghostly images like traditional black-and-white photographs of the researchers responsible for the invention, at a resolution Voigt said was about 100 megapixels, or 10 times sharper than high-end printers.

Nature paper (vol 438, 441-442):

Synthetic biology: Engineering Escherichia coli to see light

Anselm Levskaya1, Aaron A. Chevalier, Jeffrey J. Tabor, Zachary Booth Simpson, Laura A. Lavery, Matthew Levy, Eric A. Davidson, Alexander Scouras, Andrew D. Ellington, Edward M. Marcotte and Christopher A. Voigt

Abstract:We have designed a bacterial system that is switched between different states by red light. The system consists of a synthetic sensor kinase that allows a lawn of bacteria to function as a biological film, such that the projection of a pattern of light on to the bacteria produces a high-definition (about 100 megapixels per square inch), two-dimensional chemical image. This spatial control of bacterial gene expression could be used to 'print' complex biological materials, for example, and to investigate signalling pathways through precise spatial and temporal control of their phosphorylation steps.

Very cool stuff. The MSNBC article discusses a bit of the ethics behind it (the ubiquitous "bioterrorism applications" and such), but those fears have been applied to essentially every advance in technology probably since fire. ("Put it out, Snog! That may be used against us someday!")

Influenza series from LiveScience

2005-11-26T12:17:00.000-06:00

As the start of the influenza season is upon us, LiveScience has done a 3-part series on the virus, the disease, and the pandemic potential.

Part One: A guide to the biological basics of influenza and its effects

Part Two: Defending yourself against the flu. Vaccines and healthy habits keep harmful viruses at bay

Part Three: A pandemic primer.

Could arsenic poisoning have led to the development of Chilean mummification techniques?

2005-11-25T13:49:00.000-06:00

Maybe.

Living in the harsh desert of northern Chile's Pacific coast more than 7,000 years ago, the Chinchorro fishing tribe mysteriously began mummifying dead babies — removing internal organs, cleaning bones, stuffing and sewing up the skin, putting wigs and clay masks on them.

The Chinchorro mummies are the oldest-known artificially preserved dead, dating thousands of years before Egyptian mummies, and the life quest of the archaeologists who study them is to discover why this early society developed such a complex death ritual.

"I was reading a Chilean newspaper that talked about pollution and it had a map of arsenic and lead pollution, and it said arsenic caused abortions. I jumped in my seat and said, 'That's it,'" Arriaza said.

Arriaza says high levels of arsenic in the water in the region, which persist to this day, meant more premature births, stillbirths, spontaneous abortions and higher infant mortality among the Chinchorro.

"We've always known that the Camarones (the area where the mummies are found) had a lot of arsenic, and the first mummies were children," he said.

He posits the Chinchorro began preserving dead babies to express personal and community grief and later began mummifying adults as well, and the practice became more elaborate.

Interesting how something as seemingly minor as a trace chemical in the water could have led to a cultural revolution.

Only in America...

2005-11-25T13:41:00.000-06:00

...could a man as incompetent as Michael Brown turn lemons into lemonade, by starting a consulting company on disaster preparedness.

“If I can help people focus on preparedness, how to be better prepared in their homes and better prepared in their businesses — because that goes straight to the bottom line — then I hope I can help the country in some way,” Brown told the Rocky Mountain News for its Thursday editions.

Brown said officials need to “take inventory” of what’s going on in a disaster to be able to answer questions to avoid appearing unaware of how serious a situation is.

Boy, I hope he's going to provide more pearls of wisdom than that. According to the article, "companies already have expressed interested in his consulting business." Hey, companies considering hiring Mike Brown--I have actual experience and education in this area, and I work cheap! I'll even throw in a money-back guarantee: no disasters bigger than the one Brown made of Katrina.

(Seriously, though, someone please tell me this is a joke...please?)

Followup to "dragons and microbes" post

2005-11-25T12:54:00.000-06:00

I discussed here new research on venom evolution that topples some old conventional wisdom. It seems this and another study are already making large waves in that field.

Genealogy of Scaly Reptiles Rewritten by New Research

The most comprehensive analysis ever performed of the genetic relationships among all the major groups of snakes, lizards, and other scaly reptiles has resulted in a radical reorganization of the family tree of these animals, requiring new names for many of the tree's new branches. The research, reported in the current issue of the journal C. R. Biologies, was performed by two biologists working at Penn State University: S. Blair Hedges, professor of biology, and Nicolas Vidal, a postdoctoral fellow in Hedges' research group at the time of the research who now is a curator at the National Museum in Paris.

Vidal and Hedges collected and analyzed the largest genetic data set ever assembled for the scaly reptiles known as squamates. The resulting family tree has revealed a number of surprising relationships. For example, "The overwhelming molecular-genetic evidence shows that the primitive-looking iguanian lizards are close relatives of two of the most advanced lineages, the snakes on the one hand and the monitor lizards and their relatives on the other," Vidal says.

"We gave this group the new name, 'Toxicofera' because of another discovery, reported in a related paper, that some lizard species thought to be harmless actually produce toxic venom, as do some snakes--including some large monitor lizards in the same family as the giant Komodo Dragon and some large species of iguanians." Vidal, Hedges, and other researchers report this and other discoveries about the early evolution of the venom system in lizards and snakes in a paper led by Bryan G. Fry, of the University of Melbourne in Australia, published in the current issue of the journal Nature. "It's a really startling thing that so many supposedly harmless lizards actually are venomous," Vidal comments, "but their sharing of this characteristic makes sense now that our genetic studies have shown how closely they are related."

This is a great example of how science works. Important new findings have come to light, and the rest of the evidence is re-examined in that light, to see what stays and what thinking may need to be revised. No one expects it to happen overnight, and a call is put out for others to investigate and test the new conclusions:

"Because the current tree has been widely accepted for nearly a century, I think there is going to be a delay of maybe a few years before the general scientific community gets used to the new tree," Vidal says. "If other research groups working in this area find the same pattern with additional genes, then I believe the scientific community may accept these results more quickly."

Note how there are no politics involved, no pressure to teach these new results. The investigators are confident enough in their own data that they can wait for other scientists to examine it, express skepticism, test it themselves, and add their own conclusions to the scientific literature. It may take several years, but if the data stand up and are repeated by others, the way students are taught *will* change--not because anyone was lobbied to do so, but because the evidence is strong and it would be folly not to acknowledge that. I look forward to following this in the coming years.

Flu and asymptomatic infections

2005-11-22T13:03:00.000-06:00

I've mentioned many times on here reservations I have over the current avian flu numbers--how many subclinical or mild infections are being missed? Are they indeed offset by the number of serious disease cases we're also missing? There's a reason for these questions, and it's now out in electronic form in Clinical Infectious Diseases.

A bit of background. I work in Iowa as part of the Center for Emerging Infectious Diseases. One of our pet pathogens happens to be influenza virus, and we have ongoing studies looking at serological evidence of prior infection with swine and avian viruses in people who are exposed to these animals. This current paper looks at a cross-section of people who are in several of these groups: swine farmers, veterinarians, and meat-processing workers. The results:

Using multivariable proportional odds modeling, all 3 exposed study groups demonstrated markedly elevated titers against the H1N1 and H1N2 swine influenza virus isolates, compared with control subjects. Farmers had the strongest indication of exposure to swine H1N1 virus infection (odds ratio [OR], 35.3; 95% confidence interval [CI], 7.7–161.8), followed by veterinarians (OR, 17.8; 95% CI, 3.8–82.7), and meat processing workers (OR, 6.5; 95% CI, 1.4–29.5). Similarly, farmers had the highest odds for exposure to swine H1N2 virus (OR, 13.8; 95% CI, 5.4–35.4), followed by veterinarians (OR, 9.5; 95% CI, 3.6–24.6) and meat processing workers (OR, 2.7; 95% CI, 1.1–6.7).

To boil it down a bit, farmers were about 35 times more likely than the control group to react positively to the swine H1N1 virus used--indicating they'd been previously exposed. Similarly for the swine H1N2 virus--13 times more likely. It appears there is a good deal of zoonotic transmission occurring in this population--it's just not manifesting with serious clinical symptoms, so we're missing much of it.

This has implications for what's going on in Asia with H5N1 as well. How many sub-clincial or mild infections are there with that virus? We don't know yet--we need good surveillance and seroprevalence studies to address that question. Do these milder infections allow the virus more time to adapt to humans, so that human-to-human spead will become more efficient? We don't know. It's largely a black box at this point. It also is something that's largely been ignored at the response level--do we vaccinate and/or treat these groups early, along with first responders and others? Will doing so prevent a significant number of new infections, protecting not only the human population, but also domestic animals? During the 1918 pandemic, pigs also were susceptible to the virus, and suffered high mortality rates, but this isn't something that's garnered much discussion in the current pandemic plan.

This is just a pilot study, and limitations are discussed in the paper. A prospective study is ongoing, which should be able to pick up seroconversion events. Still, even though this is a small study, it hopefully will be food for thought, and will draw attention to including agriculture workers and others in contact with animals in pandemic response plans.

Edited to add other media coverage:
Des Moines Register
Cedar Rapids Gazette
NIAID press release
IDSA news release

Of dragons and microbes

2005-11-22T11:22:00.000-06:00

Carl Zimmer has a post today about the work of Dr. Bryan Grieg Fry on the evolution of snake venom. If that name sounds familiar to those of you who aren't reptile specialists, you may have run across Dr. Fry's homepage, or you may have seen his research profiled previously on Panda's Thumb here, or you may have read comments by the good doc in this thread. Zimmer, as always, has an excellent overview of Fry et al's new paper in Nature (link ), but he didn't emphasize the one sneak peek I received from Bryan.

This tasty bit of information involved monitor lizards, such as the Komodo dragon. The conventional wisdom has been that these lizards kill by infecting their prey with bactera during a bite, featured on many sites such as this one:

[The komodo dragon] can run as fast as a dog for short stretches and prey they merely injure are brought down shortly by the deadly bacteria in their mouths.

and this one:

[The komodo dragon's] saliva is not venomous, but the mouth of a Komodo dragon is so full of bacteria that a bite from one almost always leads to infection. If untreated, the infection is usually fatal.

Only thing is, it's wrong. I can't say how much bacterial infection plays a role in the killing of a komodo dragon's prey, but the research by Fry's group shows that indeed, these lizards are capable of producing venom, via previously undescribed venom glands. (Carl Zimmer has posted a figure from the Nature paper; the komodo dragon is in the Varanidae group).

Previously, it was thought that venom production in snakes and lizards had evolved independently, since the venom glands in these lineages had a different structure. However, using new DNA sequence data, Dr Fry and his colleagues found nine venom toxin types that were shared between lizards and snakes. Seven of these were previously only known from snake venoms, including one that had only previously been reported in rattlesnake venom but was sequenced by the team from the Bearded Dragon. Looks like yet another paradigm-shattering paper; y'know, the kind all the IDists say scientists are so afraid of...

Grand rounds 2.09

2005-11-22T09:51:00.000-06:00

This week's grand rounds is up at codeblog. Of particular interest to me is Orac's post, a response to Dean Esmay's post here. Some of you may remember the story of the death of Eliza Jane, whose mother, Christine Maggiore, is a prominent AIDS-denyer. The coroner had listed the cause of Eliza's death as AIDS-related pneumonia; of course, those in the AIDS-denial community scoffed. They had their own "expert" analyze the coroner's report, and they eventually came out with a different cause of death, detailed at Esmay's blog. Orac points out that their alternative version just doesn't add up:

1. A previously completely healthy girl developed PVB19 infection leading to both encephalitis and aplastic anemia (possible, but highly unlikely, and, even if PVB19 were found, it would be far more likely that it was able to cause anemia because of immunosuppression due to AIDS).

2. This same girl also developed an acute allergic reaction to amoxicillin that led to cardiovascular collapse and--oh, by the way--also caused steatosis of the liver within a day after starting the drug, the steatosis being something even Dr. Al-Bayati's own references do not seem to support as being likely.

3. This same otherwise healthy girl had sufficient quantity of P. carinii in her lungs to show up on Gomori methenamine silver staining at her autopsy.

4. The medical examiner and neuropathologist either botched the staining for the p24 protein (or that it was a false positive) and an experienced neuropathologist didn't know the pitfalls of the diagnosis of HIV encephalitis using brain tissue sections.

Other grand rounds posts that caught my eye include this one reminding us that heart attacks are the leading cause of death in women (with a link to the story of a near-fatal heart attack in a 37-year-old woman); posts at Parallel Universes on a connection between antibiotic use and non-Hodgkins lymphoma (and an update), and a rant on Science Creative Quarterly about people who wear their lab coats and scrubs out in public (I don't get that one, either!). Lots of good reading this week.

40 million infected with AIDS; but, some good news

2005-11-21T14:14:00.000-06:00

The global HIV epidemic continues to expand, with more than 40 million people now estimated to have the AIDS virus, but in some countries prevention efforts are finally starting to pay off, the United Nations says.

AIDS has killed more than 25 million people since it was first recognized in 1981, making it one of the most destructive epidemics in history. An estimated 3.1 million people died from the virus last year and another 4.9 million people became infected, according to a U.N. update published Monday.

However, for the first time there is solid evidence that increased efforts to combat the disease over the last five years have led to fewer new infections in some places, said UNAIDS chief Peter Piot.

Previously improvements had been seen in places such as Senegal, Uganda and Thailand, but those were rare exceptions.

"Now we have Kenya, several of the Caribbean countries and Zimbabwe with a decline," Piot said, adding that Zimbabwe is the first place in Southern Africa, the hardest-hit area, to show improvement.

These are all countries that have invested heavily in safe-sex campaigns and other prevention programs, with the result that prevalence of HIV among the young has declined.

"People are starting later with their first sexual intercourse, they are having fewer partners, there's more condom use," Piot said.

These are key ingredients in the "ABC"s of AIDS, a program first widely used in Uganda. A=abstinence (or delayed sexual experiences), B="be faithful", C=condoms. This simple strategy has resulted in increased awareness of disease transmission, and has resulted in a decrease in the rate of new infections diagnosed--showing just what good sex education and condom availability can do.

However, there is, of course, some bad news as well:

The epidemics continue to intensify in southern Africa. Growing epidemics are under way in Eastern Europe and in Central and East Asia. Five years ago, one in 10 new infections were in Asia. Today the number is one in four or five.

China, Papua New Guinea and Vietnam are facing significant increases. There are also alarming signs that Pakistan and Indonesia could be on the verge of serious epidemics, the report said.

Intravenous drug use and commercial sex are fueling the epidemic in Asia, where few countries are doing enough to inform people about the danger of such behavior, the report warned.

Worldwide, less than one in five people at risk of becoming infected with HIV has access to basic prevention services. Of people living with HIV only one in 10 has been tested and knows that he or she is infected.

That last part is critical. Great strides have been made, but it's not a time to rest on our laurels. Condoms and education have done so much--now we need to work to extend those services into areas where they aren't currently available. We also need to work to have more of those who are at-risk get themselves tested. This is a bit trickier, as there's not only the problem with lack of access to resources, but also stigma that comes from finding out one is HIV-positive. The latter can cause even those who may have access to tests to not take advantage of that--they'd rather not know their status, and thus don't get treatment, and potentially infect others. It's relatively easy to provide supplies; it's much more difficult to provide a shift in the cultural attitudes that will allow HIV+ patients to live a full life even after diagnosis.

U of Iowa faculty petition against ID released

2005-11-20T13:45:00.000-06:00

...and has spawned some press coverage, here in the Ames Tribune and
here in the Cedar Rapids Gazette, making us the first state to have faculty from all Regent universities speak out against intelligent design. I'll briefly address some of the comments.

In the first article, U of I physics professor (and signer of the DI's "Scientific dissent from Darwinism" petition) Fred Skiff elaborates one giant strawman:

"It's part of science to consider what blinders you might be wearing," Skiff said. "Materialists put conditions on science that things can only exist if they satisfy materialism. I think that is a mistake."

He said scientists need to be open to the possibility of God and the idea that the world could be "bigger than their imagination."

"They say that can't be true because it doesn't fit into their conception of the world," he said. "That's not science' that's metaphysics. It's not looking at the world around you. It's closing your eyes and saying that 'Nothing can exist except for things that can fit into my theory.'"

Skiff is using a typical Discovery Institute tactic here, equating accepting evolution with an atheistsic worldview. Too bad it's just wrong. Many scientists are, indeed, "open to the possibility of God." Many even consider themselves evangelic Christians. (Check out the "clergy letter project", where over 9,000 Christian clergy have signed seeking to "preserve the integrity of the science curriculum by affirming the teaching of the theory of evolution as a core component of human knowledge.") But they realize God just ain't something you can investigate scientifically. Additionally, even most scientists who are atheists would admit that there may be more out there--but that's not a question of science, it's a question of personal philosophy. Skiff and others try to conflate the two, despite the fact that science is a field where two people can have polar opposite personal philosophies, and yet still reach the same scientific conclusion using a materialistic *methodological* philosophy. This happens every day, and I'd assume that Skiff's own research also investigates only naturalistic phenomena.

Skiff said he believed the statement is intimidating to he and his colleagues who are open to intelligent design because it institutes the philosophy of materialism as the definition of science.
"They are saying that anyone who doesn't have our point of view isn't a legitimate scientist," he said. "That's coming on pretty strong."

That's just baloney. I don't know Dr. Skiff, and have only seen him once (and was thoroughly unimpressed, described here). He may very well be an excellent physicist, and I don't doubt for a minute he's a "legitimate scientist." I just think he's letting his religious views cloud his judgement in this matter. You can read the petitions for yourself: U of Iowa's; Iowa State's; and U of Northern Iowa's. Nowhere does it say that people who support ID aren't "legitimate scientists." The fact that he (and so many other) ID supporters feel that way is simply their own paranoia.

Speaking of which, from the Gazette article:

He [Casey Luskin of the Discovery Institute] criticized the ISU statement signed by professors opposing intelligent design as a slap at Gonzalez’ academic freedom.

‘‘This is a wonderful development,’’ he said. ‘‘It shows that people opposed to intelligent design are no longer acting like McCarthyites.’’

Again, you can read the ISU statement for yourself. Nowhere is Gonzalez targeted, and nowhere does anyone say Gonzalez can't research ID (not that he is, anyway). It simply says that it ain't science.

Also in the Gazette article:

Gonzalez said Avalos and a few other intelligent design critics have created a hostile environment for him at ISU by circulating the statement and speaking out in the media. But Gonzalez said he thinks many ISU faculty silently support teaching intelligent design as science.

‘‘It would be nice if someone took a poll to find out what the real opinions are,’’ he said.

Gonzalez said intelligent design is still too controversial to teach in high school, except as part of what he regards as the controversy over evolution. He also wouldn’t mandate that anyone teach it either. Partly, he said, because few teachers really understand it.

I find the irony here delicious. He acknowledges that few teachers understand ID. I'd wager this applies to most of the general public as well--they know ID as simply the "goddidit" argument, without a deeper understanding of exactly what ID says. Yet, Gonzalez thinks that many of these same people would "silently support" teaching ID. Does he think the faculty in general are more educated on the issue than secondary school teachers? I doubt it. One professor at ISU whose field is veterinary medicine, when the statement reached his/her department, even remarked that ID was something "for physicists to grapple with." !! They don't realize this is something ID advocates are trying to get into *every* department, by undermining the very nature of science.
Finally,

Officials at the Iowa Department of Education know of no school districts in the state teaching about intelligent design, department spokeswoman Kathi Slaughter said.

In my opinion, this is the way it should be. Though I think the whole "debate" is largely a waste of time and effort (since there *is* no real "challenge to evolution,") at least here in Iowa it's largely being carried out at the university level, rather than in our secondary schools. Maybe we'll succeed at other states' expense, making Iowa a state of science. Once again, if you're in Iowa and are interested in getting involved, check out our website, or email us at iowascience AT gmail DOT com.

Edited to add: bummer, as noted in the comments, Missouri beat us to the punch.

Edited again to add: I see Dembski is claiming " ID proponents were bypassed" when we circulated this. Not true at all--I don't even know who on the faculty is an "ID proponent" besides the already-mentioned Fred Skiff (and I can't say how it was circulated within the physics department, if it went there at all). It was mostly passed along through word-of-mouth, and generally sent to entire departments or colleges at a time. The idea that we were bypassing certain people on a faculty this large is a joke.

New malaria vaccine shows promise

2005-11-18T10:24:00.000-06:00

Malaria is one of the world's leading infectious killers. World-wide, almost 40% of the world's population is at risk of acquiring this disease--many of them in poor countries with limited resources to control the disease. Each year, malaria causes 300-500 million infections, and up to 3 million deaths--about 5000 Africans die of the disease every day; one child succumbs every 30 seconds. Mosquito-borne, simple devices (such as mosquito nets over beds) have been shown to drastically decrease the incidence of disease. Though these only cost a few dollars each, many in developing countries lack the resources to purchase them. Additionally, evolution, as we often see, has caused both the parasites that cause the disease (one of four species of Plasmodium) and the mosquitoes that transmit it (Anopheles species) to become resistant to our efforts to stop them. The parasites have developed high levels of resistance to many of the anti-malarial drugs, and many insecticides are of little use in controlling the mosquito population due to a similar phenomenon.

Malaria is an ancient disease. Descriptions of malarial symptoms exist in Chinese literature dating back almost 5000 years. The name itself comes from 16th century Italy, meaning "bad air" (the assumed cause at that time). The disease used to be rampant in the United States. During the U.S. Civil war, troops on both sides stationed in the south suffered more than a million cases of the disease. Indeed, malaria was endemic in the southern United States until the 1940s, and continues to be a problem in the U.S. due to "imported" cases. Despite this huge burden of disease, to date, there has been no successful malaria vaccine. This is largely due to problems that arise in trying to target an organism with an extremely complex life cycle (see image, left). 1. Sporozoites in salivary gland. 2. Oöcysts in stomach wall. 3. Male and female gametocytes. 4. Liver phase. 5. Release of merozoites from liver. These enter red cells where both sexual and asexual cycles continue. As you can see, it's a bit of a mess, with different protozoal antigens being expressed at different times throughout the life cycle. What do you target? Which are the most important for immunity?

A new study may have cracked that question. Led by Pierre Druilhe of the Pasteur Institute (link to journal article), investigators focused on a malaria protein--merozoite surface protein 3 (MSP-3)--that prior research had identified as the focus of the immune systems of adults who had proven resistant to the disease.

The team injected an MSP-3-based vaccine into 30 European volunteers who had never had malaria, readministering it after one month and again after four months. Blood samples were taken one month after each injection. These blood samples were then compared to French blood samples from individuals with no immunity to malaria and African blood samples from people with immunity.

Nearly every vaccinated sample produced an immune response to malaria when it was introduced in vitro and 77 percent produced anti-MSP-3 antibodies. Plus, these antibodies proved to be as good at killing the parasite as those from immune adults and, in some cases, better, destroying up to twice as much. "This type of immune response, characteristic of immune adults living in malaria-endemic regions, requires under natural conditions 10 to 15 years of daily exposure to billions of infected red blood cells," Druilhe notes.

They didn't challenge the volunteers with Plasmodium infection to put the nail in the coffin, but they did test it in humanized mice, where it was highly effective. Additionally, they tested the blood of immunized volunteers a year after vaccination, and it still was effective in neutralizing the pathogen. A long-lasting vaccine would be critical, since as mentioned above, resources in these countries are scarce, and frequent boosters would be unlikely.

Malaria vaccine research has also recently been given a "booster" of its own, in the form of a $258 million pledge by the Bill and Melinda Gates Foundation. About 40% of that donation is earmarked for vaccine research. However, while the news seems to be positive in the fight against malaria, we want to use caution. I recently linked a discussion on the evolution of avian influenza virulence. Similarly, a group of scientists published a paper last year suggesting that inadequate vaccines could increase malarial virulence:

Vaccines are designed to protect people by boosting the immune system to kill parasites but, unless a malaria vaccine leads to the death of every single parasite, the ones that survive are likely to be the nastiest.

Initially, the Edinburgh researchers directly injected two groups of mice with infectious parasites - "immunised" mice, which had been exposed to Plasmodium and then treated with the anti-malarial drug, mefloquine, and "naive" mice, which had not. They then transferred parasites via a syringe from host to host 20 times. The parasites thus evolved in the immune or non-immune environments. The parasites that evolved in the immunised mice were more virulent than parasites evolved in the naive mice. Infection was not as severe after transmission through mosquitoes, but the effect was still there. In other words, immunity accelerates the evolution of virulence in malaria, even after mosquito transmission, making them more dangerous to their non-immunised hosts.

Dr. Mackinnon said: "How does immune selection create more virulent pathogens? One possibility is that many parasites die in immunised hosts but those that win "the race to the syringe" - or the mosquito - are probably genetically equipped to stay ahead of the advancing immune system. Since the virulent strains showed no problems transmitting infection to new hosts, it's likely that such strains would spread throughout an immunised population.

This echoes a 2001 warning in Nature magazine by 2 of the same authors, where they emphasize infection-blocking vaccines, rather than vaccines that target the agent once infection has been established. The Druilhe article doesn't cite either of these studies, so I don't know if that's a concern they'd considered or not. However, since they identified this antigen by screening those in Africa who'd been repeatedly exposed *naturally* and were already immune, it seems likely that any increase in virulence due to partial immunity would have already occurred. Overall, this is some much-needed good news in the fight against this devastating infection.

The ethics of avian flu response

2005-11-17T11:06:00.000-06:00

Josh Braun (a "a card-carrying bioethicist") at Sciencegate, the official editorial blog of Seed Magazine, has posed a number of interesting questions regarding 10 topics in pandemic flu response and preparedness. Topics include many that I've considered, but don't have any definitive answers to, such as:

Is the mainstream media scare-mongering? Or is it providing a public service? If there is an eventual backlash in public support for pandemic preparedness that results in hundreds or millions of bird flu deaths, who is to blame?

and

...do developed nations have the right to stockpile antiviral medications for treating their populations at large in the event of avian flu, when the drugs are best indicated for the control of new avian flu outbreaks - outbreaks that are far more likely to occur in developing nations?

Lots of food for thought over there. I hope our leaders are having similar "what if/what's the right thing to do" brainstorming sessions.

Video time capsule

2005-11-17T10:00:00.000-06:00

I first ran across the thylacine (aka "Tasmanian tiger" or "Tasmanian wolf") when I was preparing to teach a summer course on vertebrate zoology for a local Catholic college during grad school. While I'd had a decent amount of organismal biology and zoology as a college undergrad, I was a bit rusty from a few years of only studying organisms lacking nuclei, so I was looking for a quick refresher as well as some interesting topics for final paper assignments for the course. Just announced around that time was a "breakthrough" in the attempt to clone the thylacine, so I introduced that to the class in a discussion of geographic isolation, and had a nice discussion of both the molecular techniques and the ethics of a Jurassic Park-type scenario.

For those of you unfamiliar with this animal, it was, like many Australian mammals, a strange critter. Though it looks like a dog or hyena (hence the nickname "wolf"), it's a marsupial. Thousands of years ago, they were main predators in Australia, until dingoes pushed them out. They stuck around longer in Tasmania, until settlers in the 1800s worked to seal their fate. The Tasmanian government began to offer a bounty for the thylacine in 1888; at least 2,268 were brought in for the reward between 1888 and 1914. Infectious disease seems to have decimated them further; an outbreak thought to be distemper (likely brought by introduced dogs) occurred in wild thylacines in 1910.

In 1936, the Tasmanian government reversed their stance and granted the thylacine protected status, but it was too little, too late: the thylacine was already gone. The last captive thylacine died in captivity that same year. The last recorded kill of a wild thylacine was recorded in 1930, and the last one captured live was caught in 1933, but died the same year in the Hobart zoo. Since then, the animal has become somewhat of a legend. A sighting was reported in western Australia in the 1980s, but has not been confirmed, and it is assumed to be extinct. However, as mentioned above, attempts have been made in recent years to clone the animal. At least 3 different animals are known to be preserved in ethanol in collections in Australia, and DNA has been extracted. Currently, it seems that the cloning project has been put on hold, but genome wiz Craig Venter has offered assistance and possible collaboration--so this may gain more steam in the future. Only time will tell if we'll ever see a live thylacine.

Anyhoo, the point of all this background was to introduce some video clips of captive thylacines I recently ran across: found here. They don't have any sound, but they're still a haunting reminder of what we've lost, possibly forever.

Tangled bank #41

2005-11-16T09:25:00.000-06:00

Apparently it's been 2 weeks already--time flew, and I forgot to submit anything for this one. Nevertheless, lots of good stuff to read over at Flags and Lollipops. My highlights: over at Thinking for Food, Bughunter discusses his bout with pertussis (whooping cough) as an adult, a first-hand account of why new vaccine recommendations for pertussis are coming. Ruminating Dude discusses dangers besides "bird flu," featuring MRSA. And the invasive species weblog discusses giant, frog-eating hamsters and tex-mex frogs.

Human H5N1 cases confirmed in China

2005-11-16T08:55:00.000-06:00

China confirms three human cases of bird flu

China reported its first three confirmed human cases of bird flu Wednesday as the government raced to vaccinate billions of chickens, ducks and other poultry in a massive effort to stop the spread of the virus.

The World Health Organization said two of those cases were fatal.

The Health Ministry confirmed two human cases in the central province of Hunan and one in the eastern province of Anhui, the official Xinhua News Agency reported. Both areas reported outbreaks in poultry in the past month.

The fatalities were a 12-year-old girl in Hunan and a 24-year-old female poultry worker in Anhui, said Roy Wadia, a WHO spokesman in Beijing.

Not too shocking, considering the large poultry outbreaks that had been seen there. In the meantime, China is planning to vaccinate billions of birds against H5N1, in an effort to reduce both bird and human cases.

More bacteria discovered using metagenomics strategy

2005-11-16T08:00:00.000-06:00

I know, everyone's so sick of all the new "omics"es. But "metagenomics" is one that I don't see going away anytime soon. At its core, metagenomics is a way of looking at organisms in concert as a complex ecology, rather than as an individual, as genomic analysis has traditionally been done. Rather than isolating 10 different species of bacteria from, say, a gram of soil and analyzing them all separately, a metagenomics strategy would investigate all the organisms in the soil (or in sea water, dental plaque, or even human feces). A huge advantage to this approach is that we can get sequence data even from organisms that we're unable to culture; as such, it's not surprising that huge numbers of novel microbes are found whenever researchers tackle a new area using this strategy. Also, as you may expect, one focus of this research in humans is to discover causes and/or cofactors of diseases.

One of these diseases is bacterial vaginosis, one of the most common infections among women. Despite this distinction, scientists and doctors know little about the causes of bacterial vaginosis (BV), a usually benign disease that is also linked to serious health problems including pelvic inflammatory disease, an increase in the viral load of HIV from infected women and a two-fold increase in risk for pre-term labor and delivery. A study in the Nov. 3rd issue of the New England Journal of Medicine seeks to shed some light on this mystery.

Previous studies of this disease have been based on culture of bacterial organisms. However, this has a fatal flaw: we know that many of the bacteria that live within our bodies are not amenable to culture by traditional means. Therefore, investigators used a strategy targeting the bacterial 16sRNA gene. This is a gene present in all bacterial species that has been widely used for species identification. Their results?

Women without bacterial vaginosis had 1 to 6 vaginal bacterial species (phylotypes) in each sample (mean, 3.3), as detected by broad-range PCR of 16S rDNA, and lactobacillus species were the predominant bacteria noted (83 to 100 percent of clones). Women with bacterial vaginosis had greater bacterial diversity (P<0.001),>with 9 to 17 phylotypes (mean, 12.6) detected per sample and newly recognized species present in 32 to 89 percent of clones per sample library (mean, 58 percent). Thirty-five unique bacterial species were detected in the women with bacterial vaginosis, including several species with no close cultivated relatives. Bacterium-specific PCR assays showed that several bacteria that had not been previously described were highly prevalent in subjects with bacterial vaginosis but rare in healthy controls. FISH confirmed that newly recognized bacteria detected by PCR corresponded to specific bacterial morphotypes visible in vaginal fluid.

So, the women with BV not only had a greater diversity of bacteria, but they were also more likely to be colonized with these previously unknown species of bacteria. Obviously, if we don't even have a clue as to what these bacteria are, we don't know the best way to treat them. It still amazes me at times to contemplate how little we know about the organisms we are most intimately associated with.

Cow tipping debunked

2005-11-15T12:23:00.000-06:00

I grew up in the middle of vast swaths of northwestern Ohio farmland. My dad, the youngest of 13 kids, was raised on a farm, most of my uncles still farm to some extent, and collecting eggs and shearing sheep was something I got to do regularly as a kid on visits to Grandma's house. But I'd honestly never heard of "cow tipping" until I went to Swanky East Coast College (TM) and got asked if that was a pasttime I and my rural friends engaged in. (Obviously, it wasn't). Well, now researchers at the University of British Columbia have data to show that it's likely that all these tipping stories are simply myths.

Ms Boechler, now a trainee forensics analyst for the Royal Canadian Mounted Corps, concluded in her initial report that a cow standing with its legs straight would require five people to exert the required force to bowl it over.

A cow of 1.45 metres in height pushed at an angle of 23.4 degrees relative to the ground would require 2,910 Newtons of force, equivalent to 4.43 people, she wrote.

Dr Lillie, Ms Boechler’s supervisor, revised the calculations so that two people could exert the required amount of force to tip a static cow, but only if it did not react.

“The static physics of the issue say . . . two people might be able to tip a cow,” she said. “But the cow would have to be tipped quickly — the cow’s centre of mass would have to be pushed over its hoof before the cow could react.”

***

Another problem is that cows, unlike horses, do not sleep on their feet — they doze. Ms Boechler said that cows are easily disturbed. “I have personally heard of people trying but failing because they are either using too few people or being too loud.

“Most of these ‘athletes’ are intoxicated.”

I've not been around cows much--Grandma had them occasionally on the farm, but it was mostly sheep and chickens (and poor, tortured barn cats. Think Elmyra on Tiny Toons, then multiply it by about 10 because I had way too many cousins). Anyway, we now live on a farm and currently have about 15 cows quite literally in our backyard--and yeah, they are *not* heavy sleepers. The second I let my dogs out in the morning, all the cows are running away from the fence, despite the fact that neither my door nor my dogs are very noisy. I guess it's good to know that our bovine friends are (well, mostly) safe from the shenanigans of intoxicated frat boys throughout the country.

(Hat tip to SciAm Observations for the link to the study)

Doesn't look too bad for 175 years old...

2005-11-15T11:28:00.000-06:00

Happy birthday, Harriet!

Harriet the tortoise, quite possibly the oldest living animal on Earth, celebrated her 175th birthday on Tuesday -- with a pink hibiscus flower cake at her retirement home in northern Australia.
Australia Zoo, where Harriet has spent the past 17 years, claims the Giant Galapagos Land Tortoise was collected by British scientist Charles Darwin in 1835.

More pictures of Harriet eating.

Evolution of resistance--bacteria win again

2005-11-15T02:33:00.000-06:00

Resistance to antibiotics has been a concern of scientists almost since their widespread use began. In a 1945 interview with the New York Times, Alexander Fleming himself warned that the misuse of penicillin could lead to selection of resistant forms of bacteria, and indeed, he’d already derived such strains in the lab by varying doses of penicillin the bacteria were subjected to. A short 5 years later, several hospitals had reported that a majority of their Staph isolates were, as predicted, resistant to penicillin. This decline in effectiveness has led to a search for new sources and kinds of antimicrobial agents. One strategy involves going back to a decades-old approach researched by Soviet scientists: phage therapy. Here, they pit one microbe directly against another, using viruses called bacteriophage to infect, and kill, pathogenic bacteria. Vincent Fischetti at the Rockefeller University has used this successfully to kill anthrax, Streptococcus pyogenes, and others. Another novel source of antibiotics has come from our own innate immune system, one of our initial defenses against microbial invaders.

An enormous variety of organisms produce compounds called cationic antimicrobial peptides. A component of our own innate immune system, these are fairly short strings of amino acids (less than 100 a.a.’s) that have a net positive charge. It is thought that these peptides work primarily by disrupting the integrity of the bacterial cell wall, essentially poking holes in the wall, causing death of the cell. Since the peptides are targeted at the bacterial cell wall structure, it was thought that resistance would require a fundamental change in membrane structure, making it an exceedingly rare event. Therefore, these antimicrobial peptides might make an excellent weapon in the fight against multiply drug-resistant bacteria. Additionally, the remarkable diversity of these peptides, combined with the presence of multiple types of peptides with different mechanisms of action present at the infection site, rendered unlikely the evolution of resistance to these molecules (or so the common thinking went). However, evolutionary biologists have pointed out that therapeutic use of these peptides would differ from natural exposure: concentration would be significantly higher, and a larger number of microbes would be exposed. Additionally, resistance to these peptides has been detailed in a few instances. For example, resistance to antimicrobial peptides has been shown to be essential for virulence in Staphylococcus aureus and Salmonella species, but we didn't *witness* that resistance develop--therefore, it might simply be that those species have physiological properties that render them naturally resistant to many of these peptides, and were never susceptible in the first place.

Antimicrobial resistance is always a problem—it can render antibiotics much less useful, and make deadly infections almost untreatable. But resistance to these peptides could make us all vulnerable. The peptides of our innate immune system are one of our first lines of defense against an immense variety of pathogens, and we don’t know what the outcome may be if we compromise this essential level of protection. But realistically, could such resistance evolve within the bacterial population?

Dr. Michael Zasloff of Georgetown University was originally a doubter. In this 2002 Nature article, he states in conclusion:

Studies both in the laboratory and in the clinic confirm that emergence of resistance against antimicrobial peptides is less probable than observed for conventional antibiotics, and provides the impetus to develop antimicrobial peptides, both natural and laboratory conceived, into therapeutically useful agents.

Certainly in the short term, resistance was unlikely to evolve for the reasons I mentioned above. However, if these peptides are used over an extended period of time, could the mutations necessary to confer resistance accumulate? This was the question asked in a new study by Dr. Zasloff along with colleagues Gabriel Perron and Graham Bell. Following publication of his 2002 paper where he called evolution of resistance to these peptides “improbable,” Bell challenged Zasloff to test this theory. Zasloff took him up on the offer, and they’ve published their results in Proceedings of the Royal Society.

They tested this using strains of E. coli and Pseudomonas fluorescens. They started out growing these bacteria with low concentrations of a peptide antibiotic called pexiganan, a derivative of a peptide originally isolated from a frog. (Carl Zimmer has an excellent post on this same topic here). The experimental design was quite simple. They grew the bacteria, took a portion of the growth, and added that to a new tube with fresh media. Gradually, they increased the concentration of pexiganan in the growth medium. In all, they did 100 serial transfers of the bacteria (correlating to ~500-600 generations of bacteria), and the end result were--voilà!--bacterial populations that were resistant to the peptides.

Creationists/ID advocates (such as chemist Phil Skell) often claim that “evolutionary theory contributes little to experimental biology,” or that “evolution has little to do with almost all research in biology and biotechnology”, etc. etc. And sure, the theory of evolution didn’t *directly* result in the discovery of peptide antibiotics. But advances in biotechnology do not exist in a vacuum, and we have seen what can occur from the misapplication of these types of technologies, unguided by an understanding of underlying evolutionary principles. Peptide antibiotics have not yet been used clinically to treat human infections, but imagine if they had gone into widespread use without a thought given to the evolution of resistance to these peptides. Imagine if they had gone into widespread use prior to an investigation of the relatedness of various peptides to those produced by humans. Imagine if, as a result of not considering these implications, we had lost an ancient protection against bacteria—-which *evolved* over millions of years of host-pathogen interaction--due to a mere advancement in biotechnology. While I enjoy proving the evolution-doubters wrong, I hope it never comes down to that kind of situation in order to do so, and I hope this example is instructive to those who claim that evolution isn't useful.

ID advocate Guillermo Gonzalez speaking in Lima, Ohio

2005-11-14T14:07:00.000-06:00

Okay, so the fact that I've already attended one of his talks here in Iowa, coupled with the fact that the one I'm mentioning is about 500 miles away from where I live may make me look like a stalker. But I swear, I'm not. I just found out that Gonzalez is giving a talk at a church in Lima, Ohio next Saturday, the 19th.

Professor Gonzalez will be speaking on the subject of Intelligent Design, how it makes the earth a privileged planet, and why Darwinian science from the steam engine era is no longer able to keep up in the information age.

I'm from that area, and I'm heading back there this weekend to throw a baby shower for my sister. So, I'll be about 20 minutes away from Lima with time to kill and might stop by. If anyone else is planning on heading there, drop me a line.

Edited to add: I just realized he's referred to as an "astrobiologist" on the church's website. Astrobiologist, my ass...he kept saying over and over how he's "not a biologist" at his UNI talk, and his research (according to his ISU website) is on "the late stages of stellar evolution through the use of spectroscopic observations. Recent work includes spectroscopic abundance analysis of post-AGB supergiants and RV Tau variables. He has also undertaken a study of the parent stars of the recently discovered extra-solar planetary systems. The results indicate that these stars have anomalous chemical abundances, suggesting some sort of unusual formation history." Maybe I'll start calling myself a biophysicist...I have more training in physics than Gonzalez appears to have in biology.

IA and ID in the WSJ; update on CfS

2005-11-14T11:29:00.000-06:00

Today's Wall Street Journal has an article on ID in college classrooms today.

AMES, Iowa -- With a magician's flourish, Thomas Ingebritsen pulled six mousetraps from a shopping bag and handed them out to students in his "God and Science" seminar. At his instruction, they removed one component -- either the spring, hammer or holding bar -- from each mousetrap. They then tested the traps, which all failed to snap.

"Is the mousetrap irreducibly complex?" the Iowa State University molecular biologist asked the class.

"Yes, definitely," said Jason Mueller, a junior biochemistry major wearing a cross around his neck.

That's the answer Mr. Ingebritsen was looking for. He was using the mousetrap to support the antievolution doctrine known as intelligent design. Like a mousetrap, the associate professor suggested, living cells are "irreducibly complex" -- they can't fulfill their functions without all of their parts. Hence, they could not have evolved bit by bit through natural selection but must have been devised by a creator.

"This is the closest to a science class on campus where anybody's going to talk about intelligent design," the fatherly looking associate professor told his class. "At least for now."

Overshadowed by attacks on evolution in high-school science curricula, intelligent design is gaining a precarious and hotly contested foothold in American higher education. Intelligent-design courses have cropped up at the state universities of Minnesota, Georgia and New Mexico, as well as Iowa State, and at private institutions such as Wake Forest and Carnegie Mellon. Most of the courses, like Mr. Ingebritsen's, are small seminars that don't count for science credit. Many colleges have also hosted lectures by advocates of the doctrine

*groan*

At the end of the article, they present one of Ingebritsen's tactics:

On a brisk Thursday in October, following the mousetrap gambit, Mr. Ingebritsen displayed diagrams on an overhead projector of "irreducibly complex" structures such as bacterial flagellum, the motor that helps bacteria move about. The flagellum, he said, constitutes strong evidence for intelligent design.
One student, Mary West, disputed this conclusion. "These systems could have arisen through natural selection," the senior said, citing the pro-evolution textbook.

"That doesn't explain this system," Mr. Ingebritsen answered. "You're a scientist. How did the flagellum evolve? Do you have a compelling argument for how it came into being?"

Ms. West looked down, avoiding his eye. "Nope," she muttered. The textbook, "Finding Darwin's God," by Kenneth Miller, a biology professor at Brown University, asserts that a flagellum isn't irreducibly complex because it can function to some degree even without all of its parts. This suggests to evolutionists that the flagellum could have developed over time, adding parts that made it work better.

During a class break, Ms. West says that Mr. Ingebritsen often puts her on the spot. "He knows I'm not religious," she says. "In the beginning, we talked about our religious philosophy. Everyone else in the class is some sort of a Christian. I'm not." The course helps her understand "the arguments on the other side," she adds, but she would like to see Mr. Ingebritsen co-teach it with a proponent of evolution.

Ms. West and other honors students will have a chance to hear the opposing viewpoint next semester. Counter-programming against Mr. Ingebritsen, three faculty members are preparing a seminar titled: "The Nature of Science: Why the Overwhelming Consensus of Science is that Intelligent Design is not Good Science."

I think that's a *course,* not a one-time, hour-long seminar, if I'm not mistaken. Or at least, a similar one was/is in the works there. Additionally, for those of you who are in Iowa, there also will be a seminar on Feb. 2nd at ISU:

Why Intelligent Design Is Not Science - Robert M. Hazen
02 Feb 2006, 8:00 PM @ Sun Room, Memorial Union - Robert M. Hazen is the Clarence Robinson Professor of Earth Science at George Mason University, and a scientist at the Carnegie Institution of Washington's Geophysical Laboratory. He received his M.S. in geology from the Massachusetts Institute of Technology, and his Ph.D. in Earth Sciences from HarvardUniversity. Dr. Hazen is the author of over 240 articles and 16 books, including the most recent Genesis: The Scientific Quest for Life's Origin; Why Aren't Black Holes Black? and the best-selling Science Matters: Achieving Scientific Literacy, which he co-authored with James Trefil. Dr. Hazen has recorded the acclaimed lecture series, The Joy of Science, with the Teaching Company (www.Teach12.com), which provides a fresh and definitive overview of all the physical and biological sciences.

Finally, again for those of you in the Hawkeye State, the Iowa Citizens for Science group now has a website: http://www.iowascience.org. It's still a bit rough, but I'll be updating it with events like these as I find out about them, so keep an eye on it--and drop me an email (iowascience AT gmail DOT com) if you'd like me to add you to the email list for even quicker updates.

Prions popping up all over the place

2005-11-14T07:15:00.000-06:00

Just a few weeks back, I discussed new research showing that prions had been found in urine. Now, a new paper in Nature(Nature summary) shows that the prion protein has been found in the mammary glands of sheep affected with scrapie.

The inflamed mammary glands of sheep have been found to contain protein particles that cause scrapie, a sickness similar to mad cow disease. This suggests that the suspect proteins, called prions, may also be present in the milk of infected animals.

If prions exist in the milk of cows infected with both an inflammatory illness and mad cow disease, formally known as bovine spongiform encephalopathy (BSE), this raises concerns for human health. Consumption of prion-contaminated meat from cows with BSE is believed to cause the fatal variant Creutzfeldt-Jakob disease (vCJD) in people; so might contaminated milk.

Man, that just opens up a whole new can o' worms. Pasteurization, which works well against bacteria, likely wouldn't put a dent in prion contamination in milk. Those suckers can survive full-out burning and still remain infectious.

The good news, though: so far, no prions have been found directly in the milk (though researchers expect to find them there in the future). Concentrations of prion in the mammary tissue was many times lower than that found in the brain. Additionally, prion presence in the mammary glands was correlated with infection by the Maedi Visna virus, so some other kind of infection may be necessary in order to have prion in that tissue.

Which is better for surgery: soap or bacteria?

2005-11-10T06:55:00.000-06:00

That's the question asked by a University College London researcher, apparently.

Doctors might be better off washing their hands with yogurt instead of relying on antiseptic soap-scrubbing, according to a new discussion paper by a UCL (University College London) researcher.
Scientists should investigate whether saturating the skin with 'good' bacteria would offer better protection against deadly germs, says the paper. Professor Mark Spigelman, of the UCL Centre for Infectious Diseases and International Health, is calling for a study to be set up in hospital units in which antibiotics would be banned, to explore alternative health protection measures against MRSA.

Okay, I can go with that. Investigate novel ways to control pathogens. But pretty much after that, he loses me. From the article:

It must be remembered that after almost 40 years, MRSA has not become widespread except in hospitals where we use the most advanced antibiotics and most rigorous antiseptic measures. Why is this? More of the same does not seem to be working – new antibiotics and antibacterial soaps have not stopped MRSA.

Point taken, but community-acquired MRSA is becoming more common, as I mentioned here. While it remains a problem mostly of hospitals, it's spread beyond that.

Inappropriate use of antibiotics remains a major problem, despite our ever-growing understanding of how bacteria behave. For example, any student who has grown bacteria in a lab will know that they generally do not grow on top of one another. So when we wash our hands, we could actually be killing off harmless commensals to the extent that we leave space for other bacteria, such as MRSA strains, to settle.

"they generally do not grow on top of each other?" I hope he realizes that this happens because of dilution and streaking techniques--in other words, artifacts of how we grow them. (And what does he think colonies are, exactly, except bacteria "growing on top of each other?") Bacteria are happy to grow "on top of each other;" in fact, some of them depend on it. I hope he's head of a little thing called biofilms. But still, despite this, I agree with his assertion that by washing hands, we could be opening up space generally filled by non-pathogenic species for colonization with worse ones, such as MRSA.

Moving on,

Many bacteria that are pathogenic do lose their pathogenic islands or modify them when the need for them disappears. Perhaps here we have an explanation of why MRSA has never entered the community.

Hold on--it has entered the community. And sure, sometimes pathogenicity islands or resistance genes are lost, but often, they are not. Anyhoo, he elaborates on this but it seems he doesn't have a very strong grasp on bacterial evolution.

Next, to his suggestions. He says that what must happen is to build surgical hospitals which are antibiotic free and:

1. The hospitals must be stand-alone separate units.

2. The surgeons must not order, or use, antibiotics on any of their patients.

3. No antibiotics can be used in the hospital.

4. A transfer to a hospital where antibiotics are used must be the way to treat wound infections.

5. The surgeons and staff operating in these hospitals should not be permitted to enter or treat patients in hospitals where antibiotics are used.

6. Continuity of care is something that must be sacrificed in this situation as it is for the patients' benefit.

First and most glaring--just because the surgeon may not be treating patients elsewhere where antibiotics are used, he can still be exposed to antibiotic-resistant bacteria. What Spigelman seems to be overlooking (multiple times) is that these *are* out there. Heck, they might be in your next sandwich, or on a doorknob you touched on your way to work.

He wraps up the article by suggesting that surgeons might dip their hands in a solution which contains "harmless bacteria," and even saturate the patients' wounds with it prior to surgery. That sounds like a hugely bad idea. One reason why many non-pathogenic bacteria don't cause disease is because they lack the ability to invade. Throw them on an open wound, and all sorts of bad things are bound to happen, even with "harmless" bacteria.

I'm all for "outside of the box" thinking, but it seems this one is a little bit too far out there to have any chance of success. Indeed, it sounds like it would endanger patients in several different ways.

Influenza ecology

2005-11-10T06:40:00.000-06:00

I briefly mentioned this NY Times article in this post on Tuesday. Joshua Rosenau has an ecologist's take on it in this post, which also complements nicely recent discussions on Ebola evolution and evolution of virulence in influenza viruses. But, y'know, all that evolution stuff is just a waste of time, according to some...

Yay Dover, boo Kansas

2005-11-09T10:49:00.000-06:00

Well, it was a split decision yesterday for those who want to keep good science taught in our schools. In Dover, PA, citizens voted in pro-science citizens for their school board, ousting many incumbents who'd supported the teaching of intelligent design (or outright young-earth creationism) in biology. (More info on The Questionable Authority). But in Kansas, as expected,

Risking the kind of nationwide ridicule it faced six years ago, the Kansas Board of Education approved new public-school science standards Tuesday that cast doubt on the theory of evolution.

The 6-4 vote was a victory for "intelligent design" advocates who helped draft the standards. Intelligent design holds that the universe is so complex that it must have been created by a higher power.

Critics of the new language charged that it was an attempt to inject God and creationism into public schools, in violation of the constitutional ban on state establishment of religion.

All six of those who voted for the new standards were Republicans. Two Republicans and two Democrats voted no.

They claim that this will get students to learn something other than the "dogma" of evolutionary theory, and will have the effect of "raising" the standards of education in Kansas. Yeah, we've heard that before: War is Peace. Freedom is Slavery. Ignorance is Strength, yada yada yada.

This ain't over, though. Any interested Kansans out there, please get in touch with members of Kansas Citizens for Science, who have been fighting this (and will continue to do so). We can still show them that not all of us in the Midwest are redneck, anti-science hicks.

Dramatic decrease in measles in Africa

2005-11-09T10:28:00.000-06:00

Wonder what the anti-vaccination crowd makes of this?

Measles cases and deaths fall by 60% in Africa since 1999

Largely due to the technical and financial support of the Measles Initiative and commitment from African governments, more than 200 million children in Africa have been vaccinated against measles and one million lives have been saved since 1999. Measles cases and deaths have dropped by 60%, thanks to improvements in routine and supplementary immunization activities in Africa.

This dramatic drop has occurred in only a few years, coinciding with a massive measles vaccination campaign throughout the African continent (discussed briefly in this post and in the article linked above). Typically, anti-vaccine folks say that the drop in infectious disease mortality that coincided with increase in vaccination rate was actually due to improvements in diet and sanitation (which, granted, can definitely do a lot to decrease infectious disease morbidity and mortality), but no notable improvements have been made in these areas over the past 5 years during the measles vaccine campaign. Think any of them will finally admit they're wrong?

Yeah, me either.

More info on (and more cases of) polio in Minnesota

2005-11-09T09:45:00.000-06:00

Yesterday's NY Times carried an article discussing the polio cases in an Amish settlement in Minnesota: 5 Cases of Polio in Amish Group Raise New Fears. I'd blogged about this previously (here and here). The article discusses more about the 8-month-old child who seems to be serving as a "polio Mary." She has an immune system deficiency, and doesn't seem to be clearing the virus. To date, there have been 5 cases in the Amish community there, and it's still uncertain how the child contracted the virus. Notes an official:

"If that child is a message in a bottle," said Bruce Aylward, coordinator of the global polio eradication initiative at the World Health Organization, "it has just washed up on shore."

The child is in isolation at an undisclosed hospital...hopefully this will allow the transmission to cease within the community. In a piece of good news, the article does mention that the polio outbreak caused at least one famer get his kids vaccinated against polio, measles, mumps and rubella, and said several others have done the same. It's a start, at least.

For those of you following the Dover trial...

2005-11-08T10:38:00.000-06:00

...The closing arguments are available. (Hat tip to PZ at Pharyngula). And man, are they good. Some highlights:

What I am about to say is not easy to say, and there is no way to say it subtly. Many of the witnesses for the defense did not tell the truth. They did not tell the truth at their depositions, and they have not told the truth in this courtroom. They are not telling the truth when they assert that only Intelligent Design, and not creationism were discussed at the June 2004 board meetings. They did not tell the truth when they place the "2000 years ago" statement [board member Bill Buckingham has been quoted as saying "2000 years ago, a man died on a cross; can't we take a stand for him now?"] at the meeting discussing the pledge [of allegiance] rather than at the June 14, 2004 meeting discussing the biology textbook. They did not tell the truth in their depositions, for for that matter to the citizens of Dover, about how the donations of Pandas books came about.

later,

This board's behavior mimics the Intelligent Design movement at large. The Dover board discussed teaching "creationism," then switched over to "Intelligent Design" to carry out the same objective and then pretended they were never talking about creationism. As we learned from Dr. Forrest's testimony, the Intelligent Design movement used the same sleight of hand in creating the Pandas textbook. They wrote it as a creationist book, then, after the Edwards decision outlawing the teaching of creationism, simply inserted the term "intelligent design" where "creationism" had been before. Dean Kenyon wrote the book at the same time he was advocating "creation science" as the sole scientific theory to evolution. But now, like the Dover board, the Intelligent Design movement pretends it was never talking about creationism.

and don't miss,

Professor Behe's testimony and his book Darwin's Black Box is really one extended insult to hard working scientists, and the scientific enterprise. For example, Professor Behe asserts in Darwin's Black Box that "the scientific literature has no answers to the question of the origin of the immune system" and "the complexity of the system dooms all Darwinian explanations to frustration." I showed Professor Behe more than 50 articles, as well as books on the evolution of the immune system. He had not read most of them, but he confidently, contemptuously dismissed them as inadequate. He testified that it is a waste of time to look for answers about how the immune system developed.

New TV shows on Ebola, influenza

2005-11-08T10:18:00.000-06:00

I thought PBS did a good job last week with their Rx for Survival: A Global Health Challenge National Geographic Channel is getting into the game.

SUNDAY, NOVEMBER 13

***WORLD PREMIERE** "MicroKillers: Ebola" at 9P et/pt
It's called "the death of a thousand cuts" because the deadly Ebola virus tears you apart from the inside. NGC explores the horrors of an Ebola infection and what could happen if the virus came to America.

***WORLD PREMIERE*** "MicroKillers: Super Flu" at 10P et/pt
Are we prepared for a global Asian bird flu epidemic? Follow a fictional traveler who unknowingly spreads the disease through casual social encounters. The horror and ease of infection are chilling reality checks.

I'm not even sure I have this channel, so I can't say how well they stick to the facts or go off into a more, erm, "creative" area to appease viewers. I see that the show just prior to the Ebola segment is:

Explorer: "Search for Adam" at 8P et/pt
Could we all be descendants of Adam? If he existed, who was he, where did he live, and what did he look like? The answers will surprise you.

Anyhoo, could be interesting viewing, if you can pull yourselves away from "Desperate Housewives" for a night.

More avian flu news

2005-11-08T09:34:00.000-06:00

I've been trying not to concentrate on this too much (there *are* lots of other interesting topics in the news!), but there have been a few updates I'd like to address. One, Vietnam has had another death due to H5N1, bringing the total there to 42 known deaths from the virus. Two, Roche has suspended shipments of Tamiflu to China (as they did previously with the U.S.) Third,

In Geneva, experts at the first major international coordination meeting on bird flu said a human flu pandemic was inevitable and urged countries to draw up plans.

Six months ago, fewer than 40 countries had a pandemic flu plan, said Dr. Mike Ryan, WHO’s director of epidemic and pandemic response. Now, 120 countries, or 60 percent of the WHO member states, have a plan, he said.

Hopefully US officials will be a bit more open to this than they have been in dealing with the U.N. A pandemic is, by definition, a worldwide event, and meeting to work out coordinated efforts across the globe is a great start. An article on the first day of the meeting can be found here.

Finally, Gina Kolata has an article in Today's NY Times regarding where the 1918 virus really came from, and whether we're looking in the wrong places for emergent avian viruses. Recommended reading.

Grand Rounds 2.07 debuts

2005-11-08T09:22:00.000-06:00

This week's Grand Rounds, a collection of medical-themed blogging, is up over at MSSP Nexus blog. Highlights: Information is free proposes a study examining marital separation and migraines; the Genetics and Public Health blog reports on a survey on public support for genetics; an interesting discussion of correlation vs. causation on Catallarchy; and Dr. Helen shares her personal story as a woman with a heart condition, and the difficulty of having it diagnosed in the first place. An excellent reminder at the end:

Women have been led to believe that breast cancer is the number one killer of women. This could not be further from the truth. Almost one half million women die each year from heart disease. Breast cancer kills only 40,000. The sad part is that half of all the women who have a heart attack each year die before they reach the hospital. I believe this is partly because women do not take symptoms of heart attacks seriously--they wait too long before going to the hospital and do not address heart issues with their doctors. Doctors are to blame at times; they buy into the myth that women are more likely to get breast cancer and that heart disease is for men. In order to change this, women must start asking their doctor to discuss heart disease prevention with them from an early age and to demand testing if they have symptoms. Hopefully, awareness of heart disease will infiltrate the public in much the same way breast cancer awareness did--but it will not begin until women decide that red dresses for heart disease are just as important or maybe more so (given the large number of women dying) than pink ribbons are for breast cancer.

Father speaks out against Michigan anti-thimerosal bill

2005-11-07T02:52:00.000-06:00

JP over at Support Vaccination.org shares a sad story about the death of 5-year-old Alana due to influenza. Her father sent this letter to Senator Hammerstrom, sponsor of the bill:

Senator, unfortunately I have had to live through the tragedy of losing my 5 year old daughter Alana to Influenza - a vaccine preventable disease.

On February 2nd of 2003, Alana had developed a low grade fever (100 degrees) but, spent much of the day playing with her siblings (eating ice cream, dancing, and watching movies). That evening Alana's fever went to 106 and was rushed to the hospital by ambulance. Within hours of arrival to the local hospital Alana died of complications of the flu - causing swelling to her brain. Unfortunately, Alana was never vaccinated with the Flu-Vaccine because we were never informed of the dangers of Influenza and our pediatrician had never suggested giving any of our children the Flu-Vaccine. However, I strongly believe that had Alana been vaccinated her chances of surviving the Flu would have greatly increased.

The Anti-thimerosal Vaccine Legislation is dangerous to our nation' health. It could result in children going unvaccinated because current U.S. manufacturing capacity cannot produce enough thimerosal-free vaccine each year to vaccinate children. The pediatric influenza deaths rates during 2003-2004 season (Alana being one of them) are a sharp reminder of the danger that vaccine-preventable diseases still pose to children and the need to ensure that every child is vaccinated. The one manufacturer of thimerosal-free influenza vaccine is moving to expand manufacturing capacity. Passing state laws outlawing thimerosal will not make manufacturing capacity increase faster, it will just mean that vaccine may not be available to vaccinate children in anti-thimerosal states.

This letter was sent in reference to Michigan Senate Bill 720 (more info here), apparently prohibiting "immunizing agents that contain more than 1 microgram of mercury or compounds of mercury." This seems to be in response to the thimerosal scare, and Alana's family is worried that it will result in a decrease in vaccination rates, with a subsequent rise in vaccine-preventable diseases.

I hadn't realized until now what Iowa was the first state in the nation to ban thimerosal in vaccines.

Iowa's anti-thimerosal action came four days before a panel of the federal advisory Institute of Medicine (IOM) issued its final report on thimerosal in vaccines. That May 18 report, which received widespread press attention, concluded that no evidence supported this conclusion. While the IOM report sought to resolve the controversy over thimerosal, Bernard says the debate is far from over. "The IOM report makes things more difficult for us in terms of convincing the wider medical community that this is a problem," she says. "We don't want the IOM to shut down the science or the debate so the legal system doesn't have anything to work with." Bernard says many new research efforts on thimerosal and autism were under way, including some funded by SAFE Minds.

(Emphasis mine) Doesn't this send off any alarm bells for anyone? The scientific community be damned, we're going to keep pushing doctors to believe our ideas, even against the weight of evidence? Worrying about the legal system instead of the scientific consensus?

I have a lot of sympathy for these parents. The article mentions one family that had to spend $30,000 in one year for care of their autistic child. As a parent, I cannot imagine how they must feel. But the evidence just isn't showing the link they want it to, and meanwhile, autism is still a huge problem in this country. How tragic that their efforts, instead of saving children, may cause more to suffer Alana's fate instead.

Back 'n' forth about evolution of virulence and avian flu

2005-11-07T01:26:00.000-06:00

There's been some interesting discussion over on SciAm Observations about the evolution of infectious diseases, and notably, influenza. It all started with editor John Rennie's post, discussing an article on H5N1 written by Wendy Orent, here:

Part I

Wendy Orent and evolutionary biologist Paul Ewald both replied in Part II and Part III, respectively:

Part II

Part III

Both discussed Rennie's mention of a critique of Orent's article on the public health blog, Effect Measure. The pseudomynous Revere from that blog then replied in Part IV:

Part IV

I've said before that I have a lot of interest in Ewald's work (and we touched on some of Ewald's claims about influenza virulence in the discussion in this thread). I also take issue with Ewald's claim that:

Being an expert on the molecular biology or epidemiology of influenza viruses does not translate into expert assessments of the future evolution of influenza viruses. One need only peruse the writings of such influenza experts to recognize that they generally fail to incorporate the most essential component of the evolutionary process into their arguments--they talk as though mutation and reassortment were the only processes relevant to the evolution of influenza viruses. To discuss evolutionary processes with any degree of expertise one must focus on natural selection. Mutations and reassortments generate the variation on which natural selection acts. But natural selection molds viral evolution.

I can't imagine that there are really influenza experts out there who don't realize the importance of natural selection. I agree that perhaps discussion of that factor of the equation gets overlooked and a disproportionate amount of time is given to discussion of what mutations might occur, but that's hardly the same as "failing to incorporate" selection into the models and discussions.

And this brings us to Ewald's main beef--that not all scientists agree with him that virulence can be predicted. His theory states that high virulence should only occur in an immobilized host--such as was the condition on the western front during WWI, which he claims enabled the Spanish flu to become so virulent. I've read many of Ewald's works on this (for those of you unfamiliar with his theory, the most comprehensive discussion is in 1994's Evolution of Infectious Diseases; other writings are listed here, and a freely available Emerging Infectious Diseases article on the topic is here). I think he has some excellent ideas, but I agree with Revere (though I'd say it in a much nicer way :) ) that Ewald's claims are "too sweeping." They're thought-provoking and he's done wonders advancing study into the evolution of infectious disease (and specifically, the evolution of virulence), but he seems to allow for no exceptions to his rule. This, IMO, is a mistake. We all know that biology is messy, and that it's tough (impossible?) to predict anything in this field with 100% certainty. Sure, we can say there are trends one way or another, and one outcome may be significantly more likely than another, but I certainly wouldn't want to bet the farm on the idea that we'll never have another monster influenza pandemic without something like WWI conditions to select for a highly virulent virus.

(Edited to add: Revere has some additional remarks on the exchange and the topic here).

Man, that's some stamina....

2005-11-05T00:32:00.000-06:00

Fossils copulating for 65 million years

Scientists in India say they have discovered two fossils fused together in sexual union for 65 million years.

The findings were published in the October edition of the Indian journal Current Science, which said it was the first time that sexual copulation had been discovered in a fossil state, according to the Press Trust of India news agency.

The fossils are tiny swarm cells, a stage in the development of the fungus myxomycetes, also known as slime molds. The cells reproduce by "fusing," Ranjeet Kar of the Birbal Sahni Institute of Palaeobotany in Lucknow reportedly told PTI. Once the cells fuse, long, threadlike appendages known as flagella, are lost, he said. Finding the fossils in a fused position and with their flagella shed, is evidence that the two cells were having sex, Kar said.

Journal article can be viewed here for those of you who are into slime mold porn. (Oh yeah, I know you're out there. Freaks.)

DarkSyde's Science Friday--little girls, HPV, and the vaccination controversy

2005-11-04T10:20:00.000-06:00

DailyKos diarist DarkSyde has a personal account detailing why the Religious Right's opposition to the HPV vaccine is nuts. PZ and I both blogged about this earlier this week, and DarkSyde's stories really bring it home.

Late for the Halloween party

2005-11-04T09:31:00.000-06:00

I saw this reported about a week ago via ProMed, but hadn't seen any of the "real" news outlets covering it yet. Now the BBC has an article about Vampire bats going attacking humans in Brazil:

Health authorities in northern Brazil are trying to cope with a wave of attacks on humans by vampire bats infected with the deadly rabies virus.

Rabies caused by bat bites has killed 23 people in the last two months.

There was a similar phenomenon last year in Brazil, with at least 22 dead from rabies due to vampire bat attacks. At least 23 are dead from this round.

Health authorities say they have treated more than 1,300 people for rabies after being attacked by vampire bats, almost always at night in their houses.

In the affected areas, people have been trying to fill gaps in the walls of their huts with banana leaves to stop the bats getting in.

Some experts have blamed the attacks on destruction of the rainforest, denying the bats of their natural habitat.

But others have suggested the vampire bat population may have grown rapidly, with the spread of cattle farming in the region providing an ample food supply.

Mass attacks on humans have occurred in other cattle regions in Latin America when the cattle are suddenly removed.

The bats drink the blood of other mammals while they are asleep. They are the main carriers of rabies in Brazil.

I don't know enough about vampire bats to even begin to speculate on the cause of the attacks, and whether deforestation or increased cattle populations is a greater cause of the human attacks. But just to stop any myths in their tracks: 1) vampire bats do not "suck" blood, Dracula-style; they make little cuts in the flesh with their teeth, and lap up the blood. 2) The vampire bats responsible for this outbreak are not large, nor are they aggressive. They attack when their "victim" is sleeping, and will fly off if frightened. Their biggest threat isn't from "draining blood," but from inoculating the victim with the rabies virus.

Aetiology

For Koufax Award voters...

Aetiology is moving!

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

New Grand Rounds!

Aflatoxin found in pet food

South African AIDS activists sue denialists

Two potential rotavirus vaccines tested

Not gotten enough PZ Myers at Pharyngula?

What a difference a molecule makes...

2005 Medical weblog awards--voting open

This view of life

Back from the net void...

Last grand rounds of '05

Population-based surveillance for MRSA

Those who do not learn from history...

Iowa Academy of Science supports Dover decision

Mike Argento weighs in

So, is it over?

Kitzmiller decision--required reading

New Grand Rounds

Victory!

Bill Maher and his anti-vaccination claims. Again.

Breakthroughs in progeria research

Persons of the year

Doonesbury does ID

Secret of surviving sepsis, say scientists

Avian flu in Malawi?

2005 Koufax nominations are open

Napoleon lice 'n' mites

Did Macbeth have mad cow?

New Ebola outbreak in African primates?

More than just a pretty face

Six years ago today

Everything old is new again

Whole hog analysis of emerging diseases

Synopsis of Maggiore's Primetime Live Appearance

ID rumblings in Muscatine, Iowa

Thai 5-year-old becomes 70th known H5N1 death

Science year in review

Is Indonesia even dumber than the United States?

State science standards are in

Institute of Medicine lays the smackdown on SpongeBob

What's causing the "Grisis Signis?"

U.S. unprepared for health disaser

On the more positive side

...what if?...

New Grand Rounds!

About your "poo print"

Emergence of epidemic Clostridium difficile

AMA Op-Ed: "loopy times," and what medical professionals can do

New Archaeopteryx fossil provides further insight into bird, dinosaur evolution

Are fruit bats a reservoir for Ebola?

You go, (Professor) girl!

Science blogs getting noticed by the big guns

"Face/off"...and back on again

Just following the cool kids...

Check out Tangled Bank #42

Berenstain Bears co-creator, Stan Berenstain, dies

Grand Rounds 2.10

Super-sized needles

It’s a small world, after all

China--being as forthcoming as they claim?

Back!

More microbial tools

Influenza series from LiveScience

Could arsenic poisoning have led to the development of Chilean mummification techniques?

Only in America...

Followup to "dragons and microbes" post

Flu and asymptomatic infections

Of dragons and microbes

Grand rounds 2.09

Other topics

40 million infected with AIDS; but, some good news

U of Iowa faculty petition against ID released

New malaria vaccine shows promise

The ethics of avian flu response

Video time capsule

Tangled bank #41

Human H5N1 cases confirmed in China