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.


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.

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!

Short Break

Taking a couple of days off from blogging to take care of my fuzzy writing partner. No, Carla isn’t fuzzy. I mean my cat, June.

June is OK, but she gave us a bit of a scare over the weekend. We had just gotten our three cats (we hold to the no more than n+1 cats rule, where n = number of people in a house) back from having their teeth cleaned, and while June now has wonderfully clean chompers, the next morning, Carla noticed that June was a little blue.

A little bit blue meaning cyanotic. Her nose, gums, tongue and ears weren’t pink, the way they should have been, but had taken on a grey color. That falls into a category of what I consider “bad things.” We took her right back to the vet (who we really like) and she got the VIP treatment.

We still don’t know what the cause of the cyanosis was, but after a day in an oxygen tent, several tests, and a couple days of careful observation and sequestration from the other two cats, she is mostly back to her old self. Regular blog updates should resume tomorrow.


To my American readers, Happy 4th. To everybody else, Happy Higgs Boson, especially India.

Keep your pets safe and comfortable this holiday weekend. The 4th of July is said to be the day with the most lost pet reports.

Want to know what makes different fireworks different colors? Consult this friendly guide from Gizmodo!

Be careful with fireworks. Only you can prevent losing a thumb or eye. And in the immortal words of Ben Stern, “Don’t be stupid, you moron.” Oh, and the guy at the end has some adult words for adult ears. (That should guarantee kids listen to it)

Eugenie Scott – Why Creationism isn’t Science

I’m a big fan of Eugenie Scott and the National Center for Science Education‘s (NCSE) work to keep science education free from creationism. – Via

The NCSE is branching out to fight climate denialism as well, which is a good move. They are well placed for such a move since climate denailists tend to use many of the same rhetorical tactics as creationists. The Skeptical Teacher has a video from Mark McCaffrey, the NCSE’s climate expert. BTW, they are currently looking for a second climate expert to round out their team.

Fun science stuff, tidbits tomorrow

I had a very long day doing hard labor, so have some fun with these and I’ll put science news tidbits up in the morning (good thing that on Earth, its always morning somewhere).

Close your eyes and listen to the annoyed cat in this first video.

Is it saying anything? Can you make out specific words? Now play it back and watch the video. It all makes perfect sense with subtitles! If you want to really test this, play it a third time, eyes closed. Did you “understand” the cat now that you are primed to decode certain words?

This is an example of paredolia, specifically, audio paredolia. Your brain is very good at finding patterns, even where they aren’t really there, and if you prime it to pick up a pattern, it can be extremely hard not to notice it later on. We see faces in blobs, shapes in clouds or craters, and we think that certain cats are secretly pirates.

I have also had half of a class close their eyes and just listen, and the other half watch and listen and then poll the students to see if they could understand the cat. Its a great way to show how suggestible the mind is.

Want to show what calories look like? Just ask Dr. Bunhead.

Now aren’t you glad that your body releases that energy in little packets of ATP instead of all at once?

They laryngeal nerve is an excellent example of something you would expect from evolution, but not intelligent design. It runs from the brain, around the aorta and back up to the larynx. It works well for fish, but when you remodel the body a bit, a vital nerve that can’t be cut running around a vital artery that can’t be cut, with both developing early in the embryo means you are stuck with a minor tangle. Take that and apply it to a giraffe…

(giraffe autopsy, not for the squeemish)

Site redesign

I’m trying out a few new themes, so if things look bad, hopefully they will get better.

I’m pretty happy with this, so there should only be a few more minor changes over the next day or two.

Of Noses and Nerves

So I have had nosebleeds since college. For no reason at all, I would just start gushing. It was like I was a character in an anime, confronted with a lust-inspiring image (nosebleeds are very weakly connected to high blood pressure (which I don’t have) and probably not at all to sexual arousal). This isn’t usually a problem as I can just pinch my nose closed and after a couple of minutes, the bleeding stops. The bleed occurs in the front of my nose, so it is an anterior nosebleed. If it happened deeper in the nose, it would be a posterior nosebleed, and pinching wouldn’t help. If either type of nosebleed won’t stop, go to see a doctor. In fact, posterior nosebleeds often require some kind of hospital visit, and likely will need admission. These can be very serious, especially in the elderly. A neat little micro tidbit for you, and one that med students need to be aware of is that the iron in blood, if it is freed from dying cells, is like bacterial fertilizer. Iron is one of those nutrients that is rate limiting for bacterial growth. Your body does a good job keeping iron sequestered, and it has been suggested that this was an early evolutionary step to keep iron away from potentially unfriendly bacteria.

I had put up with this situation for long enough and made an appointment to get something done about it. I was pretty sure about what I could expect, some form of cauterization of the suspect tissue.

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