Flu week: herd immunity

Vaccinations are one of the wonders of the modern world.  Most people think primarily of the first order benefits- I got a vaccination, therefor I don’t get sick.  Hurray!  Then there are the second order benefits- I got a vaccination, therefor I don’t get sick, therefor I can’t infect anyone else.  Hurray!    If enough people are vaccinated, this culminates in  a third order effect, herd immunity.

Most diseases are only infectious for a short period of time.  If they don’t infect at least one other person while you’re contagious, that line dies out.*  If a disease’s average transmission rate falls below one because there are so few infectable individuals, it will be impossible for the disease to sustain itself.  This is called herd immunity, and it means even vulnerable people (such as those with compromised immune systems) are safe.  If the population is “the entire world”, you can eradicate a disease entirely  This is what we did with smallpox.

This is why refusing to vaccinate your child didn’t have many consequences for the early adopters.  As long as vaccination levels in your local population (e.g. school) were high enough to provide herd immunity, and you didn’t travel to an area where the disease was endemic, you were safe.  But when enough people in the same population forego vaccines, the disease is able to get a foothold, with disastrous consequences.

The idea that vaccines cause autism is conclusively disproven, but I don’t find it unimaginable that some vaccines have some subtle negative side effects, or rarely trigger massive negative reactions  in unpredictable individuals.  But the cost of the vaccine only exceeds the cost of not getting the vaccine when everyone else is getting vaccinated.  If you’re in a population without herd immunity, the MMR vaccine is waaaay better for you than measles or mumps.**

This concept can extend beyond vaccinations to anything that lowers transmission rate, including hand washing, face masks, condoms, and HIV pre-exposure prophylaxis.  This why “what makes sense for an individual?” and “what is best for the population?” often have very different answers.

 

*You might be asking “But won’t they run out of people eventually?  How does any disease persist?”.  That is the subject of my undergraduate thesis, and also decades of work by hundreds if not thousands of brilliant people.  We have only a fraction of the answer.

**Rubella is actually not very dangerous at all, except for being absolutely devastating to the fetus if the mother catches it in a certain stage of pregnancy.  We vaccinate for it to protect those fetuses, not the vaccine recipients.

Flu week: why the flu is special.

Your immune system is faster to respond to pathogens similar to those that have infected you previously than it is to respond to completely novel pathogens, because it holds a memory of past infections.  I have read many descriptions of this process and they always read like magic to me.  I don’t know if I’m dense for not getting it, or if I correctly recognize the explanations as oversimplified.  Immunizations are designed to give your immune system that memory without the negative effects of an actual infection.  The common ways to do this are to kill the pathogen before it’s injected, or to use a weakened form of the pathogen that can reproduce but has fewer side effects.

The magic that allows the immune system to recognize pathogens is generally based on recognizing surface proteins.  If a pathogen’s surface proteins change too much, the past immunity is useless.  This is why it is so hard to fight HIV: it mutates so rapidly that the immune system can’t keep up.  It is also why flu immunity (natural or induced) rarely carries over from year to year: the virus’s surface proteins vary too much.

Variability can come from many sources.  One is a spontaneous mutation within a viral particle.  Another is when two similar viruses co-infect the same cell and exchange genetic material.    All viruses follow the same very basic pattern: they infect a cell with their own genetic material (either DNA or RNA), hijack the cellular machinery to copy that genetic material and to produce the proteins those genes encode for, and package up the DNA or RNA in those proteins into a new viral particle and escape the cell.  While the DNA/RNA is floating around, it may cross over.  In order to exchange alleles, two strands have to line up at equivalent points to cross over (e.g. the same position on the same gene).  If the DNA/RNA is circular, they must cross over twice, at equivalent positions, or the DNA/RNA strand is nonviable.  This is statistically very rare, but a single host cell can produce millions of new viral particles, so it still happens enough to be a concern.

The flu is special.  Most viruses have one long strand of DNA or RNA, which may be linear or circular.  Influenza has 8 strands, each of which carry one gene.  They are not actually chromosomes, but for our purposes they’re pretty equivalent.  When a flu particle is manufactured, the assembly machinery grabs 8 strands and packages them up.  If memory serves, the grab is random, but that gives only a (1/8)^8 chance of given viral package being viable, so I suspect I am wrong.

Either way, when a cell is co-infected by two different strains of flu, the viral assemblers will naturally mix and match from all available strains.  This makes it much easier to exchange genes between  different flu strains.

Tomorrow: it gets worse.

medical measurements

A lot of our medical metrics are really terrible.  For example, cancer interventions are generally evaluated by n-year survival rate.  The problem is that the count starts at diagnosis, so you can raise your “survival rate” just by catching it earlier, by, say, widespread testing of people with no symptoms.  And in doing so you’ll catch a bunch of cases that get the same name (such as breast cancer) but would never have been caught by a symptom-driven search because they were never going to cause problems.  And this metric heplfully ignores any of the costs of testing, which can include cancer.  This is one reason the US has a higher cancer survival than Europe- we test much more aggressively.

Or take infant mortality, which is defined as [deaths shortly after a live birth]/[total number of live births]. This measure actually has two problems, if you’re trying to decide where you should have your baby.  One is that while Europe’s infant mortality rate is much lower than the US, the survival rate for a birth during any given week of pregnancy is higher in the US.  Europe’s advantage is that it has fewer premature births.  We don’t know why.  It’s certainly possible that this is another example of the USA’s sympathy-based aid distribution, which drives us to spend ungodly amounts of money on rare but high profile cases and neglect basic care that everyone would benefit from (like pre-natal care).  Or non-medical but still government-spending-driven interventions, like financial aid.  Or government-controlled-but-non-spending-policies, like pesticide usage or maternity leave.  Or non-government factors, like cultural norms and likelihood of close social bonds.  
 
Additionally, the definition of live birth is surprisingly malleable.  The US is much more into heroic intervention/batshit crazy belief that a 20 week old fetus is a person/tax deductions for babies that live for 12 hours, and events that would have been scored as miscarriages or stillbirths in Europe are counted as live births followed by rapid death here.   Theoretically there are statistical models that could give you comparable numbers for cancer survival, and backing out the effect of more premature births in the US is trivial, but there are no numbers that can tell us the magnitude of this discrepancy.
 
So if you’re an individual deciding where to live based on infant mortality, where do you go?  If G-d gives you a signed piece of paper saying you will go into labor at week N, you go to the US, no matter what N is.  Without that certainty?  My best guess is that sufficient money will buy you the advantages of Europe while living in the US, but the reverse is not true.  So this is another case where the rich are better off in the US and the poor in Europe.
 
So much comes down to what the number is used for. The fact that the infant mortality metric is driven by so many things beyond the medical system in front of you during birth makes it almost useless for individuals choosing where to give birth*.  But all those external factors actually make it more useful for large organizations trying to evaluate the health of a country as whole.  
 
The same thing is true of BMI.  As a quick and dirty metric to evaluate the change in a country’s average fat % over time, it’s not terrible.  It diminishes the risk of scoring an increase in average height- almost always a sign of improved health- as negative.  If your current population is of the same genetic stock as the previous, individual variation in ideal body composition will come out in the wash.  BF% is of course a much better metric, but it’s a billion times harder to measure, and given a fixed amount of money for a study, it’s entirely possible the wider sampling allowed by the cheaper metric leads to more informative results.  But BMI is completely and utterly <i>useless</i> as an assessment of an individuals health.  Genetic and epigenetic variation is simply too high.  When you are an individual (or their doctor), the time to measure BF%, or actual metrics of health like activity level and blood pressure, will always be worth it.
 
Further reading:

Being happy without being Neo

I trained very seriously in martial arts for almost two years.  I quit a year and a half ago for various reasons, some of which will become obvious later in this post.  Last week I casually sparred with an old training partner. I went in knowing he would, by any objective measure, be the winner of a fight between us. He’s bigger, preternaturally talented, won every fight back when I was training actively, and has been training very seriously since. But I didn’t care, and the sparing exceeded my expectations- I got a few shots in, I took hits well, and it turns out most of his growth in the last 1.5 years was in control and teaching, so in many ways I actually felt like my actions had a bigger impact on the outcome of our fight than I did before. It was a huge success.

Off the mat, a bystander (not affiliated with my old dojo), complimented me, which was kind of him. I forget exactly what I said, but I referred to my friend as “better.”. The bystander cut me off.

“Don’t say that. If you think it it will always be true.”

Ugh.

I know this is well meant. And I know that perception can affect outcome. But American martial arts have such a strain of bullshit around this that I want to wash myself of the whole thing. There’s no shame in being worse at something than someone. There’s no shame in being worse than a particular person at a lot of different things. It would, in fact, not be the end of the world if my own pessimism led me to perform slightly worse at a hobby I no longer pursue, whose benefits were never skill acquisition.

I resent the suggestion that I could be a ninja if only I just imagined it. Or as my ex-dojo would say, committed to it. It was used to excuse people who hit way too hard or otherwise violated safety norms- “it only hurts so much because you’re afraid of it.” It may be true that it would hurt slightly less if I had less fear- but that’s not the same as saying it wouldn’t hurt, or that the pain/physical risk would be low enough to be acceptable to me.

Top Dog says that people work harder (and learn more) when put in competitions where victory is imaginable, but far from certain. I suspect that people who say these things are trying to induce me to work harder by suggesting victory is achievable. It doesn’t work on me in this case, because I’m convinced I have logic on my side. Even if I’m wrong, their attempts to negate the belief reinforce it, in mechanisms very similar to the one they claim is holding me back. It is, at best, trying to tear down the master’s house with the master’s tools.

What I would prefer is to find ways to be able to give my all (or whatever amount of effort and attention I deem optimal) regardless of my perceived chance of success. That strikes me as a much more worthy, and sustainable, endeavor.

While I’m on the subject, I am also tired of medium-to-large men telling me any strength differential can be overcome by sufficient skill. It’s technically true for a broad enough definition of the word “skill”

[here, skill is defined as bringing a gun to a sword fight]

but it still lowers my estimation of what the speaker could teach me.

Book Review: Top Dog

A popular science writer has two choices: be vague when explaining the specific experiments behind their explanations, thus leaving themselves open to criticism about not sufficiently proving their supposition, or be exhaustive, which is boring.  It is impossible to be both truly rigorous and readable by mainstream publishing standards.

Reading Top Dog, I had an urge to make myself feel smart/assert dominance by criticizing their science.  Those of you who follow me on twitter got a taste of that.  But I stopped because I realized the criticism was a net drain on the universe.  While every study and experiment they cited could be criticized, that  is the nature of research: you can only prove so much in any given run.  You have to draw conclusions from the body of applicable research as a whole.  And in that context, I think it’s a pretty good book.  It explained  biochemistry in a way I found understandable but rigorous,* and I think their overall conclusions  are merited and well supported.  Some of them will be proven incorrect tomorrow, but that is the nature of science.

If you are looking for science writing for the sake of science writing, I would recommend the authors’ previous work, Nurture Shock.  But if you are looking for something specifically on the science of competition and, more broadly, stress, seriously consider Top Dog.

* This is a compliment.  I nearly ran on stage last week when a play’s key plot point depended on a faulty understanding of sickle cell anemia.

Systems vs. Goals

Scott Adams talks a lot about goals vs. systems.  I’m reading this in his latest book How to Fail at Almost Everything but he’s also blogged about it.  His main point is that if you have a goal, you’ve set yourself up to never feel successful.  You’re failing for the time between setting the goal and achieving it, and then once you’ve achieved it, it’s no longer a goal.  You have one, brief transition point to feel like a success.

We could get bogged down here in things like the definition of goal, system, and success, or the fact that meeting goals can pay dividends besides a vague feeling of success, but for now I want to accept this paradigm as useful and apply it to my work at the crisis chat.  Because it would be really, really easy to feel like a failure as a chat specialist.  People are constantly being sad at you, many of their problems are unsolvable and even if you know the solution you can’t make them do it, you never see your most successful chatters again, and you’re operating almost blind.*

If we had a personal goal of “this person feels X better” for each chat, we’d constantly feel like failures.  And the pressure to make them Feel Better would probably make us worse listeners and more proactive fixers.   Instead, we have a system of “listen, reflect, identify, give them space to identify their own solutions.”   I do go off book, and especially with teenagers I often end up giving specific ideas, but they’re presented as examples to provoke brain storming, not commands.

Obviously it’s dangerous to worship a system regardless of results.   But in this case, I think we’ve chosen a really great system that supports our desired results.  I was really worried crisis chat would be too stressful for me because I wouldn’t be allowed/able to fix people’s problems. **   Now I’m trying to figure how can I/should I hold onto this while practicing psychiatry.

*You would be amazing how many people mention that they’re in really great therapy for a diagnosed issue 30 minutes in.  This is why you ask about their current support network before offering suggestions.

**I feel really blessed that several friends very delicately brought up the same concern.  Because they knew me, and they wanted to make sure I had taken this into consideration before committing myself, but they didn’t push it when I said their concerns were valid and I wanted to do it anyway.

Reason #28348 to hate open offices

I’m going to discuss some gender-based psychology research.  Before I begin, I would like to give my standard disclaimer: any such research is measured at the aggregate level.  Individual variation is very high, so even very strong trends don’t tell you much about how any particular person will behave, or why.  I’m not going to speculate as to the relative importance of environment and biology, because it doesn’t matter for these purposes.

Top Dog talks about some very interesting research into group dynamics.  According to the studies they cite, working in dyads requires a very different set of skills than working in groups, to the point that techniques that are beneficial for one can be detrimental in the other.  The most productive way to interact with a group is as a team: with each person taking a specialized role, which includes letting some people be more valuable than others.  Dyads function best if both people are pretty equal.  Treating a group of 5 as 4 individual dyads and managing the relationships as such is exhausting and slows down the group considerably.

It turns out that women are better than men in dyads, and men are better than women in teams.  Men in dyads are more likely to waste energy competing with one another, women in groups are more likely to waste energy signalling a lack of competition.  The reasons for this are undoubtedly a complicated mix of biology and environment we do not possible have time to get into.  But assuming that it is true, in this culture, right now, what are some implications?
I work in an open office.  And I am acutely aware that one of the reasons it slows me down is that I can’t just have a 1:1 conversation.  I have to think about who might overhear us, and how this will sound to them, and prepare if they jump in… and it’s exhausting.  I wonder if this has the same underlying causes as women’s difficulties in groups.
The counter argument to this is that when I am in groups, I am all about specialization and hierarchy. But I am self conscious about that, and do hold back because I’m afraid of what other people will think of me.  Which is not necessarily irrational: it’s entirely possible the women reason react different in groups is that people (gender deliberately unspecified) react differently to them.
I would really love to see some hard data on whether men and women react to open offices differently.