Vaccine resistance against pertussis (whooping cough)

This falls under the bad news category.

One thing to note, it has taken a long time for a vaccine resistant strain to show up. Vaccines don’t act as selection pressures in the same manner that antibiotics and antivirals do. Antibiotics act as immediate threats to survival, selecting for the mutants in a population that can survive in the presence of an antibiotic. Vaccines functionally increase the number of infectious particles needed to overcome immunity.

Think of it this way, once you start a course of antibiotics, you already have billions upon billions of pertussis bacteria playing pinochle in your snout, pleural cavity (where your lungs are) and elsewhere, and you have probably exposed everybody that lives with you and a majority of people that work or go to school with you. If they have not been vaccinated, or have not received a booster in the last decade or so, they will be infected.

If a person has been vaccinated and has strong immunity from the vaccine, only the bacteria that are already mutated in a manner to evade the vaccine have much of a chance of successfully starting an infection. Some bacteria are better than others at infecting a host, and a smaller number of bacteria are needed to kick off an infection. This is called an infectious dose. The infectious dose of pertussis is probably pretty low, since it is so easily transmitted (susceptible coworkers are 70-90% likely to catch whooping cough, and since kids have terrible hygiene, its even higher for them. Since we don’t know what that dose is, let’s just call it X. If the mutation to evade a vaccine is only present in one out of a million bacteria (a very generous guess), the infectious dose for a vaccinated individual is one million times X. This makes it a lot harder for a vaccine evading strain of a bacteria like pertussis to get started than an antibiotic resistant strain. Luckily, when antibiotic resistant strains show up, they don’t tend to spread very well, probably because the level of vaccination is decently high.


Science Tidbits for July 17, 2012

Right. I’ll get to the science stuff in a minute. There’s a meteorite that hit the ground near here. I want to check it out. It won’t take long.

If you are teaching an astronomy class, I have a challenge for you. Introduce your students to minority astronomers. Neil deGrasse Tyson isn’t the only black astronomer! When I teach introductory biology I make sure to teach about women that are scientists and at the end of the semester, I often give a bonus point on the final if students can name a single female scientist that isn’t Marie Curie. Some can, some can’t.

Via Boing Boing, a heartwarming discussion of how your bellybutton is a special place for bacteria. OK, so it isn’t heartwarming, but what class from high school biology on up doesn’t involve sampling skin bacteria and growing them on petri dishes. It becomes slightly more intensive when you get into actually identifying all the bacteria present, but this is probably something that upper level courses might consider, if they have the required technology and resources.

Speaking of bacteria, and why not, since we are just walking, talking bacteria hosts and vectors, is this neat little bit on how certain bacteria have distinct smells. A well stocked lab with good safety controls could easily show off some of these lovely little bugs and remind students to use all their senses when making observations.

This piece actually reminds me of something I came across years ago about the naming of several short chain fatty acids (which happened to tie into my dissertation, another story for another day) and guess what, thank the interwebs, it still exists! If you are teaching a primary, secondary or introductory chemistry course, this would be a neat little thing to toss into a lab. It would only take a few minutes, perhaps while something else is going on, but having some samplers of things like butyric acid and a bit of rancid butter to compare it with would be a neat sensory lab. I’m not sure how you get a goat to compare caproic (hexanoic) acid with, but maybe some goat hair would do?

Worrying response to fatal shark attacks off the coast of Australia. While five fatal attacks in ten months sounds like it should be a definite concern, is it a trend marking a change in behavior? I’m not so sure.

If you look at the number of fatal attacks for all of Australia for the last decade, there is no clear trend that can be discerned. It is highly disturbing that there are now calls for a hunt for the shark responsible for the most recent attack. Attempting to hunt down the one large great white shark in an ocean that attacked a person is simply not a feasible idea. Great white sharks can roam dozens of miles in a day and can migrate thousands of miles seasonally. Without clear identification of the shark, checking stomach contents of a killed shark would be the only way to determine if you had caught and killed the right shark.

Revenge hunts won’t convince other sharks not to attack. People watching for sharks in the vicinity of beaches is a good preventative, but is not any more functional with a long coastline.

Tara C. Smith describes using zombies to teach about diseases, pandemics and other public health issues. How cool is that? What an excellent opportunity for discussion and fostering an active learning environment!

More joy from the Philipines, sea turtles saved from poacher’s nets. This probably should be viewed in the context of a larger dispute over territorial waters claimed by both China (where the poachers were from) and the Philipines, as noted in the link.

Lemurs are facing some serious threats and may be at risk of extinction.

Apparently moon dust is bad for you. Well, I could have told you that! Sharp pieces of regolith could get in your eyes and scratch your cornea or irritate your airways, not unlike inhaling ground glass. Here is the paper for specifics.

E. coli strain 0157 is a very nasty bug, and since there is no good reason to assume that the Germantown, Ohio outbreak came from meat (a recent outbreak was linked to feral hogs foraging in fields being used to produce vegetables), it will be interesting to see if a source is found. I’ll be keeping my eyes on the MMWR. In fact, students in any microbiology, disease ecology or public health course dealing with epidemiology should be asked to read and present reports from the MMWR as part of their course in order to see how the things they are studying are reflected in the real world.

There is a belief that lies can be detected via body language hint of looking up to the left. Apparently (surprise), it isn’t true, or at least is unreliable. Just like so many other lie detection tools.

The placebo effect is a very important concept to understand when examining any claim that a drug, intervention, device, whatever, has a positive effect. Well designed clinical trials can help researchers separate false effects from real ones (which is why alternative medicine seems powerful in small trials with poor statistical power, but when examined in large randomized double blind trials, the effect is no different from placebo. Hope plus effective treatment is very powerful. Hope plus nothing may make a person feel good in the short term, but in the long run can lead to dangerous delays in treatment.

People are less familiar with the nocebo effect, wherein something has a negative effect, even if there is nothing there.

In one study, 44 percent of lactose-intolerant people reported gastrointestinal problems after taking a fake lactose tablet. (Impressively, a quarter of people without lactose intolerance also reported digestive troubles after taking the tablet.) And in a somewhat cruel prostate drug study, one group of subjects was told that sexual dysfunction was a possible side effect, while the other group wasn’t. The better-informed group reported sexual side effects at a rate of 44 percent, compared to only 15 percent in the blissfully ignorant group.

People can actually make themselves more likely to experience side effects by simply knowing about them. Medical and nursing students would be well served by reading and discussing how this affects their interactions with patients and communicating risks of treatments. There is a fine line between communicating and providing informed consent and negatively influencing a patient’s treatment.

Undergraduate students in psychology or communication courses would also benefit from class discussions about interactions and how they affect both patient expectations and patient compliance (the linchpin of slowing the development and spread of antibiotic resistance).

It can be difficult to express the sheer diversity of ferns, but this SA blog post does that in spades. Don’t just show your students a fern from the florist. Show them the wild variety of these ancient plants and toss in some examples of ferns from the fossil record. If you can afford it, add some to your personal or department fossil collection.

Mixing live virus vaccines that can mix genes is causing problems in chicken farms. Could this happen in humans? Except for the oral polio vaccine, no, because our live virus vaccines that are given simultaneously can’t mix genes. The oral polio vaccine can recombine, but this is uncommon, and the oral vaccine is only used where polio is still a common disease. Is this virus a risk to people? No, people can’t catch this particular virus. If this sounds like the flu strains swapping genes, it should.

I love cats and cats go so well with science. Cats aren’t just something that students are familiar with, but they have some great features that make them good teaching tools. For example, calico and tortoiseshell cats are almost always female because the mix of alleles that cause a tricolor cat can only occur in a cat with two X chromosomes. A male cat that is calico is going to be the feline equivalent of Klinefelter’s syndrome. If it is as common in cats as it is in people, an assumption for which I have absolutely no evidence, then only 1 in 500 to 1 in 1000 male cats would be feline Klinefelter’s, even before the color pattern is determined.

So why are calico cats important? Find me an introductory biology text that doesn’t have a picture of a tricolor cat in the section about X chromosome interaction. They give us a visible examples of the mosaics formed during development as one X chromosome or another is inactivated, and only the color gene on the active chromosome is expressed. The presence of two active X chromosomes in a cell is probably toxic on some level to the animal. This likely has to do with the effect that the dosage of genes on a single chromosome being just right, while two is too much. More on cats in the classroom and the effects of aneuploidy on cells in the future, just not simultaneously.

Gorgeous video of a variety of insects getting a tasty, nutrient rich snack of pollen. Don’t worry, the flower will probably benefit by having a little bit (just enough) pollen finding its way to a stigma and then on to an ovary. (via @BugGirl on the twitter machines)

And here is another video of a critically endangered Lord Howe Island stick insect emerging from its egg. Wow. How nice it must be to not have a hard exoskeleton immediately upon hatching! More info here.

Lord Howe Island Stick Insect hatching from Zoos Victoria on Vimeo.

Keep an eye out for baby spiders doing their best impersonation of beloved literary characters!

Auroras are pretty neat. Maybe I’ll get a chance to see one some time. I just hope it doesn’t come with a solar flare powerful enough to be visible in Central Kentucky. Phil Plait not only has coverage of the most recent flare, but like he suggests, check out his related links for far more information than I could possibly impart. Just don’t forget to enjoy this video of the aurora from the BBC.

Enjoy this 360 panorama view of the inside of the Large Hadron Collider.


There are now suspects in the vandalism of a fossil bed in Alberta. I hope they get put away for geologic time.

Edinburgh’s Legionaires’ outbreak is continuing, with the total reported cases topping 100.

Ever wonder how creationists respond to major news items regarding evolution, say, regarding fossil dinosaurs with type 1 feathers? Check it out at Playing Chess with Pigeons.

And if you are on Twitter, Follow me!

Further, if you are on twitter, follow Joanne Manaster @sciencegoddess for some great science information and teaching goodies like this!

Science Tidbits for July 3, 2012

The Skeptic Society has an educational resource page, and you should check it out. If you can, you should support it.

On with the show!

Light microscopy at its ultimate, the shadow of a single atom. That is light microscopy, which we typically say is only able to resolve images no larger than a small bacteria or particularly large virus, so I think WOW is appropriate. This was accomplished by holding a single atom in place in vacuum via some pretty cool electrical physics, shining light on the atom, and then using an extremely high resolution sensor to record the shadow cast. This could lead to some pretty amazing images being made of very delicate structures.

There is currently an outbreak of Legionaire’s in Edinburgh, Scotland. Legionaire’s is a fascinating disease, and it is amazing that there aren’t more outbreaks considering how widespread the causative organism is. Legionaires’ disease is a serious bacterial pneumonia caused by the legionella bacteria, and makes for a great disease to examine for class discussions. Legionella appear to live at least part-time in freshwater protozoa such as acanthameoba when they aren’t infecting humans, making them doubly interesting.

Topics can range from the history of the disease, from when it was discovered during an outbreak at an American Legion conference in  Philadelphia, to how human activity has produced niches for the legionella to thrive (fountains, cooling towers at power plants and factories, air conditioning catch pools), and how weather and climate can affect disease spread (cases increase after storms). This pathogen is especially important as many nations have an aging population, and the elderly are particularly at risk for Legionaires’ disease.

Linkity linkity link

Moth eyes inspire nano level structures that enhance xray imaging.
The Gaurdian has a video explaining what the Higgs boson is in laymans terms, which are just right for me.
More on the wonderful tiny phorid flies that were featured yesterday.
I find the concepts within evolutionary medicine to be fascinating, if not always useful… Science Based Medicine has a good examination of the topic. Make sure you read the comments, especially Drs. Gorski and Crislip.

Toxic Tuesday – Arsenic and old peppermints

Imagine popping a nice sweet into your mouth. It should be a pretty safe treat, right?

Not in Bradford, England, back in October of 1858.

Due to a mistake made by an assistant at a chemist’s shop, arsenic trioxide was sold instead of a filler called “daft.” The resulting batch of candies contained twice the lethal dose of arsenic in each candy.

Within days 25 people died, while at least 90 adults and 50 children became extremely ill. Counted among the stricken was Humbug Willie himself, who became sick from handling his own candies.

The aftermath of this accidental mass poisoning led to a requirement that arsenic include a coloring agent so that it would not be mistaken for other chemicals, as well as tighter regulation of arsenicals (chemicals containing arsenic). In the US, problematic patent medicines and disease outbreaks from food led to the passage of the Pure Food and Drug Act, which created the Food and Drug Administration.

This case reminds me of one of the truisms of toxicology, that laws regulating poisons are written in blood. (Laws regulating poisson are written in fish-hooks)

Science Tidbits for June 26, 2012

Two quick news items for today and one video.

First up, more information on the effect that the 2009 H1N1 pandemic virus had. The H1N1 “swine” flu inflicted a particularly severe toll based on an interesting application of a couple concepts from the world of epidemiology and public health.

There are multiple ways to describe the death rates of a disease, one of which is simply the number of people that die from the disease. This simple measurement of mortality doesn’t tell us everything. Influenza typically kills a mix of the very young and very old. The 2009 H1N1 pandemic flu killed far more young people than the seasonal flu normally does, which changes the effect on society.

The concept to stress here is that of patient or person years. Functionally, every person that lives one year lives a person year. If you have fifty people that live one year, you can express this as fifty person years. If they are patients, you would say that there were fifty patient years.

A good way to bring this to the classroom is to compare one young person and one older person. Let’s say that the young person can expect to live sixty more years, while the older person can expect to live twenty more years. If both people die from the same disease, at the same time, the young person lost more years than the older person. Sure, if either one of them had survived the disease, either could have been hit by a bus the very next day, but statistically, the death of the younger person was a greater loss of potential years of life. If we have a very large population, with perhaps tens of thousands of young people and old people falling into our patient group. For every young person that dies, three older people have to die to add up to the same number of patient years.

It sounds like a very cold and callous way to look at the lives and deaths of real people, but this system is used to determine what level of risk is acceptable for a medication. How many patient years are saved from the treatment and how many are lost from side effects? How severe was an outbreak? How useful was a new safety technology installed in automobiles? Many concepts in public health take an impersonal look at an issue because of the sheer number of people involved.

This can lead to a great discussion of the differences between patient and population centered medicine, if that is in the scope of the class you are teaching.

The second tidbit is a quick explanation of a piece that was in the news a couple of weeks ago. A woman eating parboiled squid bit into what appeared to be a tasty piece of meat, but was in reality a reproductive organ of the male meal. This can either be passed along to students asking if it was real, or be used in a zoology course when discussing the reproductive strategies of a variety of invertebrates.

Finally, a video that I have used in teaching about the process of mitosis.

I have shown the video as is to a course, muted it and described the steps in the video, pausing to point out specific features, and have included it as a link on a course website (both Moodle and Blackboard). However you approach the multimodal classroom, videos like this can be very useful in helping students understand how something like mitosis works, and can be used at multiple levels of difficulty, from simply learning the phases of mitosis in order to beginning to understand the function of spindle fibers.

Teach on.

Science Tidbits for June 25, 2012

First things first, the Houston Museum of Natural History (@HMNS) is running a fundraiser, calling on donors to “adopt” a prehistoric pet. Depending on the donation, you can adopt a different animal and can receive a variety of thank you gifts including drawings or replicas of your pet, certificates, or tickets to the museum, but most importantly, the knowledge that you are helping a home of public learning and science advocacy. If I get the job I’m hoping for, I might just adopt a triceratops. I hope it stays small. I hear they can get rather big…

Now on with the Science!

For the last week, I have been posting “science tidbits” as my own take on teaching tidbits. The idea behind a “tidbit” is that you can drop it right into a lesson plan in order to enrich the lesson, make it more relevant to students, or to tie it into current events. I try to mix in ideas about how to use them in the classroom and if you have an idea, please share it in the comments.

When you think of sharks, you usually think of fast predators, moving just under the waves, carefully stalking its prey… The Greenland shark fits all of those ideas except for “fast.” Scientists knew that the greenland shark ate seals from examination of stomach contents, but figured that they scavenged dead seals. Seals are really fast, so a shark that swims at a speed slower than a mile per hour is an unlikely predator. There is a new hypothesis, though…

“Arctic seals sleep in water to avoid predation by polar bears (Ursus maritimus), which may leave them vulnerable to this cryptic slow-swimming predator,” wrote the authors of a recent study on Greenland sharks’ speed, published in the Journal of Experimental Marine Biology and Ecology.

Where does this fit into a lesson? Any discussion of a food web in the Arctic would include polar bears as an apex predator, and adding the greenland shark into the mix stresses the diversity of the environment and the importance of what happens beneath the ice. You could also describe the shark, where it is found, how fast (or slow) it is, and ask students to come up with ideas about what an animal like this would eat.

Beyond that, the greenland shark isn’t the best known or best studied of sharks, which can make it an interesting creature for an “internet” scavenger hunt, where students hunt for information about the slowest shark, or smallest deer or a venomous mammal, or a good topic for a short group presentation on lesser known organisms.

Making the tidbits again, a chance to talk about zoonotic diseases. Koala bears are one of the cutest animals on the planet. Who doesn’t love them?

Wild koala numbers started dropping last decade, and researchers asked the obvious question, why? (Brainstorm opportunity) It turns out that there are three different organisms attacking koalas, one of which is a retrovirus that is attacking their immune system. The other two are different strains of the Chlamydia, Chlamydia pecorum and Chlamydia pneumoniae, and at least the C. pneumoniae strain can infect humans.

Unfortunately, C. pneumoniae can be transmitted to humans. Koala’s incredible cuteness works on the disease’s behalf. People enjoy picking them up, but like many tree-dwelling animals, koalas don’t much care where they urinate. If an infected koala urinates on a person, they can possibly transmit the strain of chlamydia to the human.

It is frighteningly easy to pick up diseases from animals, wild or domestic, so being aware of these risks is a good idea. Another opportunity for discussion comes in with what people can do to help the koalas. There is a vaccine that appears to work for the retrovirus, but the only treatment for chlamydia sp. is antibiotics. This can quickly lead to a secondary discussion of antibiotic resistance, as there is nothing to prevent reinfection or to prevent resistance from arising. Since humans can be infected with C. pneumoniae, it would be a very bad thing to encourage the bacteria to develop resistance in the wild as it would limit which antibiotics could be used to treat infected humans. This closely mirrors discussions of the use of antibiotics in livestock.

The opportunities for dropping this topic into lessons about infectious diseases, antibiotic resistance, ecology… are endless. Its a good topic for high school on, with advanced undergraduate and any graduate student delving deeper, perhaps presenting short talks on the topic.

The concept of a “living fossil” is a messy one. It suggests that an organism is completely changeless over millions of years, which can be very misleading. Many so called living fossils closely resemble their ancient relatives, while others have undergone morphological changes. The coelacanth isn’t just a single species of lobe finned fish, but is a large group of both modern and extinct species with many morphological differences and falls into several species. Beyond that, they are no longer thought to be the group most likely to have given rise to land dwelling tetrapods.

This isn’t just a good discussion topic, but can be a good topic for small group discussions in high school and undergraduate courses. Give students a list of misconceptions about evolution (a very long list can be found here) and have them examine and present the science behind them. This has great risks and great rewards. Students teaching each other can be one of the most effective ways to learn, and breaking down bad ideas is an important step in the process of learning evidence based science. Remember what Chuck said,

False facts are highly injurious to the progress of science, for they often endure long; but false views, if supported by some evidence, do little harm, for every one takes a salutary pleasure in proving their falseness.

-Charles Darwin

Giving students the tools to replace false facts with true ones is vital in teaching topics that are controversial in culture, but not among scientists. The talk origins database is one of the best ones you can offer for evolution, with Skeptical Science a great one for climate change (from real skeptics, not ones using the title for PR purposes). However, if you get a student that wants to present personal beliefs instead of what the evidence says, or if you pick a topic that is too broad or too narrow, it can end up as a mess.

The other risk/landmine is that you absolutely should avoid discussing religion in a public school classroom, and if you are teaching at a religiously affiliated private college (or even a public institution), you need to be careful to make sure that your administration backs you up. Creationist organisations can put a tremendous amount of pressure on a college and the list of educators that have lost their positions due to the controversy that they can bring to bear is very long and grows longer every year. Be careful to stay within the boundaries of science. No matter what you think of NOMA personally, it is a good guideline for the classroom. If you limit discussion topics to things like living fossils, missing links, the existence of transitional fossils, or why gaps in the fossil record are not only expected but are not a problem for evolution, you should be fine. If you need advice, talk to the NCSE (link above).

If you are using the previous tidbit, or are sending students to use the internet for sources, this is a good read for you and for more advanced students. Lots of material on the internet is accurate, but lots of it is simply junk. If students are doing a presentation, go over their sources with them, and look to make sure that they are reliable.

And one for the teachers, when you are teaching a difficult concept, one that students typically respond to by saying that they will never use it… you need to respond immediately with real world uses, or defuse it before it starts. That can be easy for me. Not understanding evolution kills people via a bad understanding of antibiotic resistance, genetic and evolutionary causes of medical problems, etc. Students can grasp the importance of medicine, poisons, venoms, cancer. But not everything is so easy. Tidbits help a lot. That is the purpose of sharing them and always looking for new ones.

Teach on.

Science tidbits June 18, 2012

Science tidbits for this, the 18th of June, 2012

You got your dolphin on my octopus! You got your octopus on my dolphin!


1) Raw milk is not “safe” 2) Blogs are a great way for students to write about science for a broad audience.

– In the last seminar class I taught, I wanted to include a blog writing assignment, where students would write up a post on their seminar topic for popular consumption. I still would like to try it, perhaps for an honors class. Beyond that, this is an outstanding topic for discussion of personal risk and how public health decisions are made. While a single person may have very low risk from drinking raw milk, the probability that a single person or multiple people in a population will be affected becomes extremely likely. Blessed are the cheesemakers.


“Wildlife rangers were forced to shoot dead the [lion] cubs’ mother after it was spotted in Nairobi’s Karen suburb” – I stayed for a week in Karen with family while my wife was gathering data for her dissertation, and photographed lions enjoying the remains of an antelope in the nature reserve with Nairobi’s skyline in the distance. Turns out, this isn’t an isolated experience. Lions sometimes find their way into Karen and get stuck in the compounds (think of a cul-de-sac, with tall fences around each home with a locked gate, and at the entry to the cul-de-sac is another locked gate, sometimes manned by a guard), which means that nobody can come or go until the lion leaves.


Poor itty bitty spider got the fungal rot, down came the rain, washed the spores about. Cordyceps is a genus of sac fungi that parasitize arthropods. While parasites tend to give people the willies, as do spiders, Cordyceps is a fascinating group that challenges what students think about when they hear “fungus.”


Via Jerry Coyne,  a good read about gill slits, and how they fit into vertebrate development. This can also help you answer questions from students about what a gill slit is and how it fits into the evidence for evolution from a common ancestor.


Bonobos (the nice chimps) have now been sequenced! 1.3% diff from us, 0.4% diff from Pan troglodytes. I wouldn’t introduce the sexual habits of Bonobos to elementary or middle school students… and I would be hesitant to discuss it with high school students unless I knew that my administration had my back. For undergraduates, most can handle a discussion of the variety of sexual habits of animals, and it can lead to a better understanding that what they think is natural is not always reflected in reality.


Gender roles in nature, with cartoons for those that need pictures. This is another good topic for advanced high school students and undergraduates, when discussing reproductive strategies, sexual selection and evolution. Try showing pictures of male and female birds and discussing how the bright colors of males are important for multiple reasons, including attracting a mate and perhaps even displaying the health of the bird (no parasites, good nutrition, etc). Then show them a picture of male and female seahorses and ask them which they think is which (males tend to be dull and females brightly colored). As you describe how the seahorses rear their young, see if you can start a discussion on how the individuals competing for the attention of a mate are the ones investing resources in their appearance, and that this is not always the male.


Evolution as chemical warfare. Mouse eats seed. Plants that poison seeds selected for. Now for mice to evolve immunity. If you are looking for a way to introduce the Red Queen Hypothesis, this is perfect.