Everything you wanted to know about microbiology and epidemiology, but were afraid to ask

Hey Doc - You keep writin', I'll keep readin'. All areas of what you do are interesting, so I would not presume to target anything in particular. Maybe what you do as a mom to protect the kids, and what we can do as parents to protect / prevent things with our families. Not-So-Old Wives Tales From Tara perhaps? My $.02

This could probably be called part of the "deep background" of microbiology, but I'd be interested in seeing a short history of the work (from what I understand it was principally done by Lynn Margulis) which underlies the discovery of the incorporation of free-living bacteria into the eukaryotic cell as mitochondria (animal) and chloroplasts (plant).

Traditionally, an avid student had to wade through the coursework for a B.S. degree, and do well, in order to make it into grad school, where the really cool stuff and very clever thinking got revealed.

That tradition sucks.

So, are you sucky-tradition killers? Then hooray for you, and it's about damn time.

So, is there something that you'd like to have explained?
Yeah - what's it going to take for people to stop thinking of "microbiology" as "the study of small living things that cause medical problems"? :-)
I'm an undergrad - hopefully for only one more semester - doing my best to study applied/environmental/industrial microbiology in an institution where the curriculum requires, for example, "Immunology" no matter what, but where "Ecology of Microorganisms" is not only an elective, but one that it seems impossible to get them to actually offer[1]. The implication that microbiology is obligately medical kind of annoys me, in a 'serious pet peeve' sort of way. It's doubly annoying considering that a large proportion of the faculty seems to have real expertise in environmental and industrial microbiology.
Our "Medical Microbiology" text has a whole section on spider bites and such. Spiders are "micro"? (and don't get me started on parasites - tapeworms are HUGE...). And, DAGNABBIT, "Food Microbiology" does NOT mean "spinach"!
It annoyed me so much I started blogging (rather sloppily I'm afraid, but hopefully I'll get better with time) what I'm doing just so there'd be SOME evidence online that there is more to microbiology than looking at close-ups of chancres and the like. I sometimes feel like I'm the only student in the world who is studying microbiology but isn't (and doesn't want to be) a pre-med, pharmacy, or dentistry student.
Of course, with a blog name like "Aetiology", I kind of suspect you're probably not the most sympathetic shoulder to whine at. :-)
(For the record, I actually have no problem with medical microbiology, I just hate that the focus on it seems to effectively drown out all other microbiology topics, despite the fact that "only a minority of microorganisms are pathogenic[2]".
[1] It's in the college catalog, but it sounds like it hasn't actually been offered in quite a while. Also, if I want to know about Fungi, I can take "Medical Mycology", but there is no other class on the subject available...
[2] From the textbook from my general microbiology class (Tortora, Funke, and Case, 1998 - "Microbiology - An Introduction", sixth edition [yes, I've been an undergrad for far too long...]). Which, incidentally, starts with three or so paragraphs explaining that microbes are vital to environmental processes and useful for commercial applications and food and so on - then proceeds to go about 710 pages talking about diseases. 30 pages of "oh, and there's some biotechnological stuff that isn't about diseases, too" is crammed into the end as an afterthought. Do microbiology textbooks still do this?

Ah yes, infectious vs contagious. It's those subtle little colorings that get you. Kinda like communicable vs transmissible.

Boy, that Hank guy sure was a hoot. Is he the front-runner to fill Dr. Gerberding's spot at CDC?

Sticking up for the epi side, I think ecological fallacy would make an interesting educational post.

Maybe what some of the basic mathematical models are for the probability of catching a disease? That is, why one group is more likely to catch a disease than another group, assuming negligible genetic differences in disease resistance. It should depend on the number of distinct individuals you come into contact with, and the number of encounters you have with each. I can come up with naive a priori models based on probability, but I'm sure there are subtle -- maybe profound? -- differences that come up when you actually check them against the real world.

I guess there is quite some amount of basic stuff hidden in scienceblogs already. The problem is to find it. Thus, a special "basic" label and a link to a "basics" channel on the homepage would help a lot. In addition there is a lot of basics in the internet which however is hard to distiguish from crap sites. Thus, I would appreciate a list of links to trustworthy sites peer-reviewed by sciencebloggers.

One concern: I like scienceblogs because it relates to current events and developments in science and other fields. Thus, I wouldn't appreciate too much if it evolved into some kind of an educational textbook like resource. I must admit though that those basics presented on scienceblogs, especially here and at Pharyngula, are always interesting, well written and comprehensible.

Off topic: Since the amount of information on scienceblogs seems to increase exponentally it is getting harder to follow it, especially if one uses the 24 hours link to enter.

Despite my medical background which is somewhat out of date, I think a post (or series) outlining and defining the various types of infectious agents would be useful. From prions, through viruses, up through the bacteria, yeasts, and mycotic agents. I tend to get particularly confused in the area of the relatively recently discovered critters like PPLO, Chlamydia, etc.

I'll also second sparc's idea of creating a Science Blogs channel for Basics.

SMC said:

Spiders are "micro"? (and don't get me started on parasites - tapeworms are HUGE...). And, DAGNABBIT, "Food Microbiology" does NOT mean "spinach"!

but SMC, if you want to understand the 'Ecology of Microorganisms' you must study the habitats of microorganisms - which include spiders, tapeworms, and spinach, among other things.

Identifying techniques and vaccine production.

SMC,

I understand your frustration. I have been looking at grad schools for microbial ecology and have not found any (within my search radius) that even more than one professor doing that type of research. None had any departments at all. All the micro departments seem to specialize in a segment like medical, vet, water quality, etc. Since my goal is to teach at a CC I have decided to get a masters of science teaching in biology at the school I go to now. There are some good micro people there and I will be able to take whatever micro courses they offer.
If you are going to go to grad school and don't mind where you go I'm sure you can find a school that will satisfy your interests. Good luck.

SMC and KevnC: I got my PhD in microbiology - but I didn't work on a medical problem. My former university was great in this regard- I highly recommend the University of Washington - there's lots of great environmental micro going on - in many different departments.

llewelly:"[...]the habitats of microorganisms - which include spiders, tapeworms, and spinach[...]"
Yes, but the aforementioned subjects are not in the textbook as examples of habitats of microbes (well, the "spinach" example might be, but if it is, I'll guarantee it's just a mention that if someone with E.coli doesn't wash their hands, you can get the disease that way - not a real discussion of how E.coli lives when not causing diarrhea...). The "Spider bites" stuff in the text appears to be talking about the bites (e.g. venom), not even "infections you can aquire secondary to a spider bite".
I should emphasize (in case it's not obvious) that this is a mostly good-natured rant, and I actually do think pathogens are kind of interesting as well (and an obviously important category of microbiology to include in any well-rounded microbiology curriculum). Further, the pathogenic microbiology instructor has already explained that he's going to focus on bacteria and fungi (which is to say, actual MICROorganisms), as there are separate whole classes devoted to parasitology and entomology and such available in the curriculum.
It just bugs me that it's so much harder to find non-medical microbiology discussions (though I very much enjoyed Blog around the Clock's discussion of circadian rhythms in prokaryotes not too long ago)
KevinC: I'm lucky in this regard, in that although the institution I'm going to doesn't seem to recognize non-medical microbiology as more than an obscure oddity, there are actually several professors doing non-medical microbiology research. Given that the college is one of the lowest-paying in the entire country, though, I'm beginning to wonder if they're only clustered there because most of the higher-paying institutions didn't want non-medical microbiologists (or conversely that medical specialists expected more money than the institution here was willing to pay out). Although I can't seem to get much "formal" instruction in my interests, I am at least managing to pry a lot of useful learning out of the situation outside of class time and hopefully get a little undergraduate research done.
KevinC and Sandra Porter: Unfortunately, my situation is quite restricted. I'm 37, married (to someone who already has a Ph.D. [geology] and therefore has by far the most right to determine where we live and work), and I can't really just pack up and go to college anywhere I want. I'm where I am mainly because it's really my only option at the moment. The good news is, it seems likely we'll be relocating soon (which is why I need to graduate this summer with my 20-year "4-year" degree...) and so far the most likely area appears to be Maryland. I heard a rumor that there might be a college or two there that might know something about microbiology. :-) ) My grades are quite good, and I suspect that when I get around to taking the GRE's I'll do reasonably well, so hopefully getting an RA or TA for graduate school won't be too much of a problem.

SMC - University of Maryland is great! Rita Colwell is there! She's a fantastic scientist, a marine microbiologist, and was the head of the National Science Foundation.

One thing about medical microbiology vs. environmental, is that whatever you learn about medical microbes, will probably hold true for the others as well. All species of procaryotes, really do have quite a bit in common. If you learn something about E. coli, it's likely to be true for Rhizobium or Pseudomonas, too. Archeabacteria are pretty different, but even they need to do the same things that other bacteria need to do to live.

With the DOE funding the genomes to life projects, all kinds of bacteria are getting attention these days.

Good luck with pursuing your dreams!

I like the Sparc idea of a Basics links list.

One specific thing: Why is the tetanus vaccine called a toxoid? Are the others in the DTaP also toxoids? How is a toxoid different from other vaccines?

Toxoid is the non-toxic form of the toxin.

How about explaining the concepts of bias and confounding in epidemiology?

Toxoids are inactivated toxins. Vaccines are for viral diseases and are killed or attenuated viral particles. Although, I think they are trying to take viruses and remove the disease causing characteristics without altering the recognition sites for the host defenses. Killed viral vaccines aren't as effective as attenuated vaccines, but attnenuated run the risk of causing illness.

Vaccines can protect from both bacterial and viral disease not just viral disease.

In the case of DTaP, the vaccine use the tetanus and diphtheria toxoid and antigenic fragment/protein of Bordetella pertussis.

Regarding basic concepts in Epidemiology: I think that one of the basic points (and something that is often overlooked) is the difference between attributable risk and relative risk. RR is often seen in the press and can be alarmingly high in certain instances - but this is often just an artifact of a low background incidence. AR is a better metric for understanding the impact on the public's health but is often not reported. Just a suggestion. Keep up the good work, I enjoy the blog.

If you're thinking basic epidemiology you could start with rates. Then maybe a follow up post to go into the differences between commonly used (and misunderstood) terms such as attack rate, case fatality rate, age-adjustment etc.

Hey, I'm an undergraduate in college and i'm interested in a field in science. I don't know much about the types of fields in science so if you could please answer all the fields in science I will really appreciate it. I also have an other question.Has everything been discovered about microbiology?

I am still in grade nine, and i want to know, is it very hard to become a microbiologist. I really want to be a microbiologist. please help.