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 as a human and humanist endeavor

Science is grounded in the concept that we, as humans, can examine and understand the world around us. This is practically one of the roots of humanism as a philosophy. We don’t need supernatural causes to explain our surroundings. As Douglas Adams said, or perhaps wrote, “Isn’t it enough to see that a garden is beautiful without having to believe that there are fairies at the bottom of it too?”

In fact, the supernatural and science don’t play well together. A natural world can be studied, examined, and perhaps most importantly, quantified. We can’t be absolutely certain that a result from an experiment is a good representation of reality, but the better designed an experiment is, the closer to 100% we can get. Hence, the incredible excitement from particle physicists that a candidate for the Higg’s boson had been found and that the statistics showed that their results were valid to five sigma (five standard deviations). The scientific method would not work if capricious sprites and malevolent gremlins were playing in the results.

To put it simply, if you don’t start out with the concept that a human can understand the world through human endeavor, science would be a waste of time.

Science is often criticized by many religious or spiritual individuals for rejecting the supernatural, and is mired in a dull, naturalistic world. Again, the problem is that the supernatural, when we try to detect it, provides no good evidence that it is there. If it did, curiously, it would cease being supernatural and become natural.

Stephen J. Gould described this as non-overlapping magesteria (NOMA), wherein the natural and supernatural, the scientific and the religious, operated in two separate and distinct areas. Think of it like a Venn diagram, where the two circles don’t overlap. Sadly, this isn’t exactly a good explanation of how religion and science intersect. Instead, I prefer my own mental model of mutually exclusive magesteria (MEMA).

In the classroom, it is by far best for a teacher to rely on the NOMA model. Avoid getting yourself into a position where you support one religion over another, or your interpretation of religion over another. Just rely on what the evidence is and know that there are organizations that will back you up if you come up on a group that wants to pick a fight over evolution, stem cells or climate change.

However, where science has looked, the supernatural has given way. Many religions and denominations of religions accept this and shroud their position in mystery, holding to claims that they have answers to different kinds of questions. Others refuse to accept the evidence that they are wrong, and refuse to adapt. Failure to adapt to a changing environment tends to be the first step on a path to extinction.

The Earth is not the center of the universe. Zeus/Thor/Baal does not throw lightning from Olympus/Asgard/Bali Hai (that last one was a joke). Humans are primates, vertebrates and mammals. Humans can understand the world without resorting to ad hoc or post hoc claims of the supernatural.

There are no fairies at the bottom of the garden, but the garden is just as wonderful a place.

 

Chick-Fil-A supporters aren’t necessarily bigots

I had posted this on google+ and fezbook back during the height of the Chick-Fil-A debacle, and decided that I liked it enough to post it here, with some links and a little bit added on at the end.

I recently read a web piece calling for restraint from those criticizing Chick-Fil-A, pointing out that doing so does not automatically mean that the supporter is a bigot or a homophobe. That is fair. Most of us recognize that being called a bigot is a bad thing. When somebody says something critical of you, the human thing to do is to react defensively, not to examine the situation and ask if the comment was fair. Here are the alternatives that I can think of.

If you are choosing to support Chick-Fil-A and are unaware of their anti-LGBT stance, and having provided 5 million dollars to a variety of groups, some listed by the SPLC as hate groups, then you are ignorant. I can understand that. A few years ago, I didn’t realize that CFA knowingly gives money to groups that support laws in Uganda that would make being gay a death penalty crime, with a very weak standard of evidence to boot. I didn’t realize that completely legal discrimination in the US against people that I consider good friends and family members was being funded by my patronage. I was ignorant, but I got better.

Perhaps you simply don’t care about the social effect that discrimination has. If so, you need to work on your empathy and see beyond yourself and recognize that somebody in your family is being harmed. Friends and coworkers are being harmed. Your students are being harmed. Even if you teach at a conservative, religious school, some of your students are gay. In the city that I live in, the social normalization of homophobia has led directly to the bullying of children to the point that they choose suicide rather than spending another day dealing with the emotional pain it causes. You can be apathetic and disinterested and be neither a bigot or a homophobe.

But if you are hiding behind this book of sacred law or that one to justify bigotry, that doesn’t make you less of a bigot. Just that you have done exactly what people that have used the sacred to justify the profane institutions of misogyny, slavery and racism have done. History will pass you by and with the passage of time, chances are, you will be finding ways to act like this all never happened.

Addendum:

Chick-Fil-A had pretty impressive sales on August 1. That would suggest that this controversy has helped them, right? Well, that isn’t what all the evidence is saying. The brand’s image took a major hit once the company’s support of hate groups became well publicized. It will probably not recover any time soon, and while a core customer base has been strengthened, the larger customer base has become less enamored of cows that write like lolcats. The long term viability of the company has likely been affected, and only time will tell if it is for better or worse.

There is a consistent historical trend towards a more tolerant and fair society (but not one tolerant of intolerance), with racism becoming something that is frowned on in society, sexism is taking its last gasps, and just as social acceptance of those that wanted to prevent mixed race marriage sank to the depths, bigotry against members of the LGBT community (real or just assumed) will follow. It won’t be fast or easy, but it will happen.

And just as your personal “gaydar” may not always be reliable, just because somebody is eating Chick-Fil-A, they aren’t automatically a bigot. And the same goes for the employees of Chick-Fil-A. Right now, for many people, including some that may be in your classroom or on your campus, take the jobs that they can get, not necessarily the jobs that they want. Don’t make it harder on them.

Caturday’s common ancestor #2

PZ Myers is continuing to wage war against Caturday. OK, nudibranches are quite gorgeous, but not exactly cuddly. Those scavenged cnidocytes can make for a bad day for nudibranch snugglers. Think of slugs, but all dressed up and with a whole ocean for having fun (link to the video).

Continuing as a cat / non-cat accommodationist, how far apart are nudibranches (the specific one shown munching away at a Portuguese man o’ war in the video is a blue dragonGlaucus atlanticus)   and housecats (Felis catus / Felis domesticus)? This is a painful one. They are very far apart, as one would expect for members of different phylums.

Timetree didn’t recognize the species, but it knew the family Glaucidae, and here is the time to most recent common ancestor

782.7 Million Years Ago (or worse, as much as 910mya). Precambrian, late proterozoic… Um. Hey it isn’t as far back as cats and catnip, right?

I’m concerned that this cat / not cat is driving us away from what should be our real focus, which is that we shouldn’t trust those weird prokaryotes. No nucleus, no way. Cats have cells with nuclei, which is fine by me.

Science or Fiction, July 2012

About once a month, I get together with several friends and colleagues for the Lexington Skeptics meetup for dinner and conversation. The topics tend to run from recent science discoveries, pseudoscience controversies, scams and flim flam. Discussion sometimes ranges into religion and politics, but is always polite.

Many people find their way to “scientific skepticism” by way of podcasts like The Skeptic’s Guide to the Universe (SGU) and one of my favorite parts of the SGU podcast (which you should be listening to) is the Science or Fiction segment.

Briefly, the host, Steve Novella asks the co-hosts and guests to pick one fake story from a set of three or four. The others are true, at least in a technical sense. If a true story is turned into a false one and the detail changed is a number, the number is changed to an unreasonably high or low number.

Tonight’s Science or Fiction was a fun one, and led to a discussion of why certain things were possible or not. Read over the following three items, try to pick out the fictional news piece and then click through (or just don’t scroll past the science cat).

  1. Milk thistle slowed the progression of Hepatitis C infection in a placebo controlled clinical trial.
  2. Bacteria are being used to grow spider silk with the tensile strength of black widow spider silk.
  3. Injuries from laser hair removal have led to calls for regulation in Britain.

Continue reading

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.

Updates:

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!

Site updates

After bringing this blog back from the dead (castle tower, driving rain, lightning not included) I realized that several of my old links were out of date and many science related blogs I read on a regular basis and rely on for content weren’t on the list, I had some work to do. It is much better now, and should be where I want it in the very near future. Also coming soon are updated Comment Policy and About Me pages. Hurrah!