Thursday, August 24, 2006

My garden likes yogurt

You must read this. If you are a layman, read it for the perfect explanation of commensal bacteria and how not to screw them up. If you are a colleague, read it for the above to share with laymen. Read it. And take responsibility for your personal not-contributing-to-antimicrobial-resistance.

Tuesday, August 22, 2006

The doors (or gates) of the AIDS fight

Surprisingly, some people have realized that fighting AIDS is not just fighting disease. We can have the best medicine available to us, but people have to take it. People can take their medicine, but they also have to eat. They have to be able to walk safely to the clinic for their checkups. They have to be able to receive treatment for other illnesses. They have to be free to live, work, and be people. We can't just give them some drugs and hope the problem will go away.

Is that what the Gates Foundation is doing, though? Yes, their AIDS efforts are focusing on antiretroviral therapy. They also fund education programs. And nutrition efforts. Community-based programs. People like to describe them as a giant band-aid, throwing money at a problem that money can't fix. Well, I'm reminded of the bumper sticker: 'Money can't buy happiness, but neither can poverty.' Money can't fix the AIDS pandemic. Drugs can't fix it. Politically charged statements by ex-presidents can't fix it. Devout reliance on either abstinence training or condoms can't fix it. But ignoring the problem can't, either, nor can fighting about it. If we all take a step in the same direction from our different starting points, maybe we'll end up at the finish line together.

Friday, August 18, 2006

Good idea, Luke

I wasn't tagged but I felt like doing this. (Ditto)

1. Grab the nearest book

2. Open the book to page 123

3. Find the fifth sentence.

4. Post the text of the next 3 sentences on your blog along with these instructions

5. Don't you dare dig for that "cool" or "intellectual" book in your closet! I know you were thinking about it! Just pick up whatever is closest.

6. Tag three people.

The appropriate measure of association depends on the study design and its corresponding measure of disease frequency.
From Veterinary Epidemiologic Research by Dohoo et. al.

Wednesday, August 16, 2006

A little evolution lesson

All Things Considered this afternoon had a brief story about MRSA (methicillin-resistant Staph aureus), so here's a brief response:

The story discussed the fact that MRSA seems to be present in community-acquired skin infections on a more regular basis. Rather than sticking to ICU's and drug-using groups, it's been diagnosed in suburbia. However, while the strain in the hospitals is famously pan-resistant, the community-acquired strain is susceptible to the old drugs that are hardly ever useful anymore.

The narrator seemed suprised by this. I am not.

If you hit a group of bacteria with 3rd and 4th generation antimicrobials, the resistance to those drugs will become predominant thanks to selection pressure. If you don't challenge them with the old stuff (penicillin et. al.), that selection pressure is not there; hence, resistance to those strains (if it is independent of other resistance factors) gives no special advantage and may very well go away.

How many suburban kids are getting straight penicillin these days?

Submitted without comment

I couldn't help it.

The Onion usually makes me laugh, but this is too true to be funny. Or not. Okay, it's hilarious.

Tuesday, August 15, 2006

Je prefiere

My sister sent me to this site, after reading Blink. It's supposed to identify your initial prejudices. Yep, probably works. There were some surprises for me, but mostly it was my complete failure to line up with most of the automatic preferences they were obviously expecting. A few came out (I seem to associate African Americans with weapons and careers with men), but mostly I was neutral and in a few I broke the expected paradigm (a preference for Judaism over other religions, for example, and an association between Native Americans and American things). Or was I?

As I took these tests, I would routinely catch myself. I had a lot of the preferences they expected to see. I was just fast enough to hide them. That is far more disturbing to me than the results they gave me. I was proud to score such that I was unprejudiced and open-minded, but I know at some level that those scores are false. I am prejudiced. Maybe it's buried deeper in me than in other people, maybe I hide it better, but the prejudice is there. And that hurts.

Friday, August 11, 2006

How I spend the first hour at work every day

This is really just to get them all in one place away from my laptop, but here's my morning 'trawl', to use snark-speak (updated 1/11/08, and I've discovered Foxmarks, but people ask):
Sluggy Freelance - mad science and relationships
Irregular Webcomic! - spoofs and creative Lego use
Get Fuzzy - like Garfield crossed with Boondocks
PvPonline - geek culture and daily funny
Doonesbury - call me a political geek
Evil Inc. - superhero Dilbert
Schlock Mercenary - sci fi
Arthur, King of Time and Space - yeah, I was really into Arthuriana for a while
Narbonic - mad science at its best (over, but in re-runs with director's commentary)
Skin Horse - new from the author of Narbonic
Bunny the Book of Random - really, just randomness with bunnies
Political comics from NYT
Anywhere But Here - relationships (or lack thereof) with bizarrity
Questionable Content - relationships with sarcasm and indie rock
Ozy and Millie - grade school, multiculturalism, political sarcasm, hard to describe
Count Your Sheep - sweet and silly
XKCD - science humor, always ROFL
The Order of the Stick - fantasy/geek culture
Girl Genius Online Comics! - fantasy/mad science at its best (new)
Looking For Group - fantasy, but heading for "you lost me status"
Gunnerkrigg Court - fantasy without the funny
Full Frontal Nerdity - geek culture
The Non-Adventures of Wonderella - very wicked superhero
Piled Higher and Deeper - I am a grad student
Home Star Runner - my first love (webcomics-wise)
Todd and Penguin - Hobbes without the introspection
chopping block - sick and wrong, but funny
Crap I Drew on My Lunch Break - funny slice-of-life/autobiographical
Platinum Grit - Australian mad science
The Broken Mirror - hasn't updated enough times to know
You had me and you lost me (more snark-speak)
Dominic Deegan: Oracle For Hire - fantasy
Shortpacked! - geek culture
Defunct/not updating
Home on the Strange - relationships (now over)
Casey and Andy - mad science
Gossamer Commons - fantasy
The Pet Professional - strange taste for a vet, but really . . .
girl/robot - sci fi and cynicism

What’s going to kill us all next?

Final paper for my class on emerging diseases:

The longer I spend studying emerging diseases, officially or recreationally, the more I am convinced that hype will be the death of us. Forget bird flu, mad cow, super bugs, frankenfoods, or whatever clever nickname the media comes up with next. We’re actually all going to drown in a sea of clever nicknames.

In all seriousness, science is in more peril of death through over-hyped politicians than the average American is through disease emergence. Fear-mongering among infectious disease researchers, each looking for more government grants and pharmaceutical studies, is an emerging threat. As the case of Thomas Butler forebodes, infectious disease research is becoming both more lucrative and more fraught with danger. (Disclaimer: my MS is being funded by a USDA grant thanks to the surge in funding available in biosecurity.)

For US science, the only real solution is science education. If politicians were not scientifically illiterate (to a great degree), scare tactics would be useless. If federal officials understood the process of scientific research, they would be able to create meaningful and useful processes for control. If the public was familiar with basic scientific concepts, the media would not be able to (or have to) dumb down infectious disease news to Chicken Little and See No Evil.

That is the American (and, to some extent, European) reality. The situation in the developing world is much closer to horror than hype. With the near complete lack of diagnostic capabilities, government interest, control or surveillance, the majority of the global population is living in a time bomb waiting to explode. If the developed world is at risk, it is from the incubation potential in the developing world.

Where are we going? If things continue as they do, with funding pledged but not delivered, with isolationism and protectionism, with ignorance and complacency, the future does not look bright. The systems we are building with social, economic, and technological inequity will not protect us; they will eventually be broken down by the transboundary nature of the most serious infectious diseases. Unless changes are made, pandemics will become a regular but unpredictable reality.

What changes could protect us? Giving teeth to the only organizations with a presence in international disease control (WHO, OIE, FAO) would be a good start; the voluntary nature of the current system is unsupportable when diseases are mandatory. Fully funding even a tenth of the surveillance programs in existence would also be a strong step forward; the protections we have in place won’t work without supplies and staff. The most important move we could make, though, is to encourage education. Strong scientific education in the developed world would most likely result in a public that cares about funding disease research and control. Health education in the developing world could make a dent in the behaviors that breed epidemics. As the world understands infectious diseases better, infectious diseases have fewer chances to emerge and spread.

Tuesday, August 08, 2006

The Emergence of Mycobacterium bovis and its Effect on Human Health

A summary I wrote up for my class on emerging diseases:

The Pathogen

Mycobacterium bovis is the member of the Tuberculosis complex most removed, evolutionarily, from Mycobacterium tuberculosis, which is considered to be close to the ancestor organism1. It is a slow-growing bacteria that causes caseous abscesses, primarily in lungs and secondarily in lymph nodes, liver, spleen, and mammary glands2.


M. bovis is primarily transmitted by aerosol droplets, but can also be present in milk, urine, feces, and, rarely, reproductive fluids3. Pasteurization is sufficient to kill the organism, as is prolonged exposure to the elements3. Human to human transmission is possible, but less efficient than animal to animal and animal to human transmission4. Risks for infection are family cattle ownership, work with animals, and consumption of raw milk and raw or poorly-cooked meat4.

Host Species

Unlike M. tuberculosis, M. bovis is a pathogen of a variety of species. Besides humans, it can be identified in cattle, badgers, bison, buffalo, and deer, among others3. The pathogen is endemic in a variety of areas, including the wild cervids of Minnesota5 and Michigan6, badgers in the UK7, and possums in New Zealand8.


Primary diagnosis of TB in cattle and deer is through intradermal testing, which has the advantage of being cheap, easy, and laboratory-free9. This does not identify the strain of Mycobacterium involved and it is time-intensive. Other methods, including immunologic assays, are able to diagnose species, but they are more expensive and require laboratory capabilities beyond the ability of many developing countries. Because of these problems, the prevalence of M. bovis in most of the world is unknown.


In the developed world, human outbreaks of M. bovis occur primarily through raw-milk products such as soft cheeses10. At risk, however, are the immunosuppressed, especially from multi-drug resistant strains2. Epizootics have the potential to spread to humans, especially in animal keepers and meat industry workers2. In the developing world, especially Africa, food hygiene and close animal contact are the primary risk factors for infection4.


The main problem in the developed world is due to latency. TB can be overlooked early in infections, due to the slow growth of the organism, and can be reactivated years after apparent clearance11. In the developing world, the problems are legion: cultural attitudes and habits that maximize pathogen spread, immunosuppression from HIV infection, lack of diagnostic capabilities, and overall complacency towards what is considered a livestock disease12.

Reference List

1. Hewinson RG, Vordermeier HM, Smith NH, et al. Recent advances in our knowledge of Mycobacterium bovis: A feeling for the organism. Vet Microbiol 2006;112:127-139.

2. Thoen CO, LoBue P, de Kantor I. The importance of Mycobacterium bovis as a zoonosis. Vet Microbiol 2006;112:339-345.

3. Neill SD, Skuce RA, Pollock JM. Tuberculosis--new light from an old window. J Appl Microbiol 2005;98(6):1261-1269.

4. Ayele WY, Neill SD, Zinsstag J, et al. Bovine tuberculosis: an old disease but a new threat to Africa. Int J Tuberc Lung Dis 2004;8(8):924-937.

5. Bovine Tuberculosis Surveillance. Available at:

6. About Bovine Tuberculosis. Available at:,1607,7-186-25804---,00.html.

7. Bovine TB-What is bovine tuberculosis? Available at:

8. Lake R, Hudson A, Cressey P. Risk Profile: Mycobacterium bovis in milk. In: Anonymous. Christchurch, NZ: Institute of Environmental Science & Research Limited, Christchurch Science Centre, 2002;1-31.

9. Palmer MV, Waters WR. Advances in bovine tuberculosis diagnosis and pathogenesis: what policy makers need to know. Vet Microbiol 2006;112(2-4):181-190.

10. Anonymous. Epidemiologic Notes and Reports Disseminated Mycobacterium bovis Infection from BCG Vaccination of a Patient with Acquired Immunodeficiency Syndrome. 1985;34(16):227-228.

11. Hancox M. Latency and the control of bovine TB in man and other animals. Respir Med 2003;97(9):1075-1077.

12. Cosivi O, Grange JM, Daborn CJ, et al. Zoonotic Tuberculosis due to Mycobacterium bovis in Developing Countries. Emerg Infect Dis 1998;4(1):59-71.

Wednesday, August 02, 2006

I don't want to think about it

A few things lately have brought the concept of complacency to the forefront of my mind:

The first is work-related. I'm taking my required summer-full-time-student class right now, Emerging Diseases. One of the factors for emergence, and especially re-emergence, of diseases is complacency towards the risk. For example, the first deaths thought to be due to West Nile Virus in New York City were birds noticed by a vet at the Brooklyn Zoo, but the officials pretty much patted her on the head and told her to go back to the fuzzy animals where she belonged. If you were in the US in the last 5 years, you probably know how that ended.

Today we were discussing the (lack of) government response to Hurricaine Katrina and its cause, which was a combination of complacency and politics as usual. There are myriad examples in public health (interesting fact from today: 1 in 4 middle-class suburbanites has genital herpes) of a disease or issue being ignored because, well, we can't be bothered to change. Grr.

And then there's the opposite of complacency towards disease. After hiding SARS and H5N1 infections from the world, allowing dangerous spread of dangerous diseases to avoid losing face, China has decided to fight back. Is beating 50,000 dogs to death going to stop rabies? Maybe. Is it the way to go? NOOOOO! Bad China! Bad! My instructor (a rabies control expert) mentioned that there was talk of trying to eradicate rabies in a developing country. China was an option, but she didn't think it was a good idea (I think in part because, as she said, she'd rather go to Tanzania). Are they trying to show their fitness for an eradication campaign? 'Cause if they are, don't suggest eradicating AIDS to the Chinese government.

The second thing that got me thinking about complacency was a weekly email devotion that arrived today. At first I was a little wary of the opening citation, Lebanon weeping etc., but the commentary was amazing. Really, part of the problem in the Middle East is complacency in the citizens, a refusal to step up and say that they want peace, a self-denial of the extremism that is running their respective countries. If the people who are being bombed etc. were to raise their hands and say they want peace, would terrorism go away? Of course not. Would it lose its mandate in Lebanon, Syria, Palestine, Israel, Iran, or any country being ruled by violence? Maybe. Would something change? Definitely.

Complacency extends far beyond war and disease. In a fair amount of cases of poverty and dispossession, the poor are complacent because 'what can they do?' while the non-poor are complacent because they're not struggling. In those cases, development workers need to educate the poor and non-poor alike if they hope to effect change.

The third thing to get me on the issue of complacency is my mother having breast cancer. She was diagnosed yesterday, after a routine mammogram sent her to biopsy-world. No, she wasn't complacent. I want to be. Really, I want to be able to ignore how serious this whole situation is. I want to pretend a double mastectomy is a minor procedure with no risks. I want to believe her prognosis is excellent. I want to go on trusting my mom to be there. I want to be complacent. I can't be. Curse you, medical training!

I deplore complacency that allows disease and war and poverty to spread, but I think I'm starting to understand it.