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Friday, December 29, 2017

A brief history of anti-vaccinationism

Vaccination is taking a "dead" or "deactivated" virus and exposing a person to it in order to achieve immunity.  Before there was vaccination, there was inoculation*.  Inoculation is exposing someone to a live disease in an effort to cause a mild form of the disease, which would hopefully induce immunity but be less destructive than the full-blown disease.

People inoculated children for smallpox by placing infectious pox scrapings into small skin cuts.  This more commonly resulted in a milder case of the illness than acquiring it naturally, although it did carry a risk that the illness could become severe and fatal (there was a ~2% risk of death after inoculation vs ~20% after natural infection).  Some argued that the lower risk of dying did not justify the possible risk of causing a fatal illness by inoculation.  Benjamin Franklin's son died of smallpox before he could be inoculated in 1736, and he later wrote about inoculation:



In 1796, Edward Jenner vaccinated a boy with cowpox and then exposed him multiple times to smallpox, proving that this provided protection from the disease without having to cause the disease itself.  Vaccination with cowpox became recommended over inoculation as the cowpox disease was much less severe in humans and did not carry a 2% mortality rate.


This is a cartoon from 1802 by James Gillray criticizing Jenner's method of vaccination.  Some critics of vaccination argued that the science wasn't correct--at the time the germ theory of disease was not universally accepted, and so the reasons vaccination would work were suspect.  Some argued that the practice could spread syphilis, or that it did not work as well as it needed to.  Others believed that vaccination circumvented the "natural" order and that suffering from smallpox would be morally superior to avoiding that fate.  Complicating the issue of whether everyone should be vaccinated was mandatory vaccination programs that started in the late 1800s, which led some to argue that for the sake of personal freedom it shouldn't be the case that everyone must be vaccinated.  Because of its efficacy and safety compared to the prior option of inoculation, vaccination did become very widely used during this time, although many mandatory programs were made voluntary.

In 1974, a small case study of 36 children who developed neurological disorders (seizures, coma) after the DTP (diphtheria, tetanus, and pertussis combined) vaccine was published.  Concern developed that the vaccination, especially the pertussis component, was responsible for severe permanent neurological reactions.  Documentaries and books were published declaring the vaccine unsafe.  Large scale studies were performed which did not bear this out; however, public opinion against the vaccine turned.  Nonpermanent reactions like swelling at the injection site or even scary febrile seizures were associated with vaccination, and so an effort was made to make the vaccine safer by using parts of the pertussis bacteria (an acellular vaccine) instead of the whole bacteria.  In the 1990s an acellular pertussis vaccine was developed, and today the vaccines commonly used in the U.S. are DTaP or TdaP, which produce fewer minor reactions of which the whole cell pertussis vaccine was guilty.

In 1998, just in time for the DTP anxiety to blow over, Andrew Wakefield published a study claiming a link between the MMR (measles, mumps, and rubella) vaccine and autism.  It eventually came out that he had acquired his study subjects unethically, made up much of his data, and had a financial incentive to obtain results that would show vaccines harmed children.  His study was retracted from the medical journal that originally published it.

In 2005, Dan Olmsted wrote an article claiming that the Amish community did not vaccinate and that they were never diagnosed with autism.  As it turns out, the Amish do vaccinate their children and sometimes are diagnosed with autism.

Also in 2005, Robert F Kennedy Jr wrote an article for Rolling Stone outlining the government's conspiracy to hide findings that thimerosal, a preservative and ingredient in vaccines, had caused autism.  The article misrepresented the removal of thimerosal from vaccines in 2001, an action taken to improve public support for vaccines because thimerosal contains mercury.  Although no evidence showed that the thimerosal containing vaccines had caused harm, it was thought that concerns would be allayed by removing this preservative from all pediatric vaccinations except for some flu vaccines.  Instead, this action was treated as evidence that vaccines caused harm and needed to be changed to become safer.

In case you thought criticism of vaccines left the cartoon medium two centuries ago,
here is the illustration that accompanies RFK Jr's article in Rolling Stone by Ed Sorel.
Click on the picture to see it full-size on the website.
In 2007, Jenny McCarthy announced on Oprah that her son had been diagnosed with autism and that she believed vaccines had triggered the condition.  She became an advocate for finding treatments for autism, including some therapies that were much more likely to cause harm than benefit, like chelation therapy for presumed mercury poisoning.

Also in 2007, Dr. Bob Sears published The Vaccine Book, which suggested an "alternative vaccine schedule" based on the fear that some people had that vaccines were given "too many, too soon."  The schedule was not in any way based on science or studies suggesting the alternative schedule would be safer, and was more likely to leave kids unprotected from vaccine-preventable diseases.

There are other articles, interviews, celebrities, etc. that likely reached a wide audience and influenced thousands of people to be suspicious of vaccines, but these are the biggest ones that I am aware of.

I've heard people blame mainly Wakefield and McCarthy for being the originators of the current anti-vaccine movement, but anti-vaccination feelings have been around for two centuries (longer if you count anti-inoculation sentiments).  Without their superstars anti-vaccinationism would likely still have legs--there's just something that bothers people about it.  For two hundred years people have argued that vaccination was unnatural, unsafe, and unscientific.  And for almost two hundred years it has been large governments and organizations--those who have the power to do great things and also, the power to limit freedoms and take advantage of the public--who organize mass vaccinations.  Arguments against vaccination will likely continue regardless of who has their medical license revoked.

Here is a pet peeve of mine: McCarthy's prior employment as a Playboy model is frequently cited as proof that she is dumb and uneducated, and many people claim that they would never be as dumb and uneducated as to follow her. However, in speaking about her son she comes across as a very caring mother who wants the best for her child, and gets her point across very clearly in every interview.    In the discussion section of the 1974 article about complications after the DTP vaccine, the authors state, "It could be argued that any illness in infancy will bear a temporal relation coincidentally to such events as teething and inoculation," and this temporal relation in early childhood of developmental or health problems being diagnosed after vaccination is cited over and over in current anti-vaccination stories.  Patting yourself on the back because you don't believe someone who once took naked pictures doesn't make you smart, it makes you a snob, and it makes you vulnerable for making the same mistake everyone else does when it's not a Playboy model but non-Playboy model Ms. Smith giving the same story.  Jenny McCarthy isn't wrong because she took naked pictures, she's wrong because noticing symptoms of a neurological problem after vaccination does not prove causation.  The evidence shows vaccination is safe.

*Nowadays, people use "inoculate" to mean "inject," so the terms can be a little interchangeable.

Friday, December 22, 2017

2017 Christmas cookies

OK, look, here's the thing.  I read food blogs.  I know you're supposed to take a beautiful picture of your food, talk about some special memory you have of eating that food, and then post the recipe.  But my best camera is currently on my iPhone, and it's the middle of winter so the "golden hour" happens for about 5 minutes at 3 PM or something?  My food pictures more closely resemble dimly lit meals for one than aspirational designs.  You know the ones that make you think, "I could cook that, then invite all my friends, and we would have a charming and festive soiree!"  I can't take pictures like that.  

My second this-can't-be-a-food-blog problem is that I don't think I can adequately describe the fun time we have every year with good friends we've been baking cookies with for the past decade.  

So anyway, here are the cookies we made this year.  They're all vegan because our friends are vegan.  I increase the amount of vanilla extract from the original amount used in any recipe.  I didn't feel like dealing with fancy salt this year so I skipped sprinkling fancy salt on top of any cookies.  And I usually mix the dough one day a few weeks to a month out from cookie o'clock, and then freeze everything, and then on the day of cookie baking I thaw the dough for making cut-out sugar cookies in the fridge but cook the other cookies from frozen.  I usually hover around the oven during the duration of cooking, so I don't have good times for how long the cookies should really stay in.  For all the cookies, you probably need more than ten minutes, but less than twenty.  

 NYT Chocolate Chip Cookies but vegan and various shortcuts




2 cups minus 2 tablespoons (8 1/2 ounces) cake flour
1 2/3 cups (8 1/2 ounces) bread flour
1 1/4 teaspoons baking soda
1 1/2 teaspoons baking powder
1 1/2 teaspoons coarse salt
2 1/2 sticks (1 1/4 cups) vegan margarine (I used Earth Balance this year)
1 1/4 cups (10 ounces) light brown sugar
1 cup plus 2 tablespoons (8 ounces) granulated sugar
6 Tbsp applesauce
1 Tbsp natural vanilla extract

1 1/4 pounds chocolate chips (I usually just add chocolate chips until it seems an appropriate amount of chips are in the cookie dough, which I think is close to this amount recommended by the original recipe.)

  1. Whisk flours, baking soda, baking powder and salt in a bowl. Set aside.
  2. Using a mixer fitted with paddle attachment, cream margarine and sugars together until everything turns a lighter color, about 5 minutes. Add applesauce. Add vanilla. Reduce speed to low, add dry ingredients and mix until just combined. Add chocolate chips. Press plastic wrap against dough and refrigerate for 24 to 36 hours. Dough may be used in batches, and can be refrigerated for up to 72 hours. (This is the point at which I usually freeze the cookies, but if you don't the refrigeration step is supposed to be important in how the cookies turn out.)
  3. When ready to bake, preheat oven to 350 degrees. Line a baking sheet with parchment paper or a nonstick baking mat. Set aside.
  4. These cookies spread out as they bake into regular flat cookie shapes (as in picture above), so they can really be placed on the cookie sheet in any lump and they'll cook pretty well.  I usually use a large spoon to measure out a spoon-sized lump of cookie dough, which is smaller than the 3.5 oz mounds that are recommended by the original recipe.  Some of my cookie sheets are smaller, and I tend to put even smaller cookies on these, to avoid losing cookie off the edge of the sheet during spreading.  If the cookies spread out and run into each other though, they are still tasty.  This recipe makes a lot of cookies--I usually get at least three or four dozen.  I would check on them at ten minutes and then every 1-2 minutes after until they're just barely turning brown on the edges.  The original instructions, for those who would like to follow them, are below:
Scoop 6 3 1/2-ounce mounds of dough (the size of generous golf balls) onto baking sheet, making sure to turn horizontally any chocolate pieces that are poking up; it will make for a more attractive cookie. Bake until golden brown but still soft, 18 to 20 minutes. Transfer sheet to a wire rack for 10 minutes, then slip cookies onto another rack to cool a bit more. Repeat with remaining dough, or reserve dough, refrigerated, for baking remaining batches the next day. Eat warm, with a big napkin.

Yield: 1 1/2 dozen 5-inch cookies.

Bon Appetite's Chocolate-Pistachio Sables but vegan
and extra salt makes these better


2 1/2 cups all-purpose flour
1/2 cup unsweetened cocoa powder
3/4 tsp salt
1/4 tsp baking soda
1 1/4 cups (2 1/2 sticks) vegan margarine
1 1/4 cups light brown sugar
2 tsp vanilla extract
2 Tbsp applesauce
5 oz chocolate chips
1 cup chopped pistachios, usually originating from shelled salted and roasted pistachios meant for snacking, which are really annoying to de-shell and then chop, but this job is made better if you buy enough pistachios so you know you can eat a bunch during de-shelling and still have enough for cookies.
  1. Whisk flour, cocoa powder, salt, and baking soda in a bowl.
  2. Using an electric mixer on high speed, beat margarine and brown sugar until everything turns a lighter color, about 5 minutes.  Add vanilla.  Add applesauce.  Reduce speed to low and gradually add dry ingredients.  Mix just to combine.  Fold in chocolate and pistachios.
  3. Divide dough into 4 pieces.  Roll each piece into a log, pushing dough together if it feels crumbly.  Wrap in cling wrap and chill until firm, at least 4 hours. (This is where I usually freeze the dough.)
  4. Preheat oven to 350 degrees.  Cut logs into rounds and transfer to parchment-lined baking sheets, spacing 1/2" apart.  (These cookies do not do a lot of spreading, and look basically like they do when done as they do when you place them on the baking sheet.  The original instructions recommend 1/4" thick rounds but mine are thicker.  The original instructions also say to use a serrated knife to cut them--I used a dull table knife, which is probably why my rounds are a little flattened.)
  5. Bake cookies until set around edges and centers look dry, 10-12 minutes.  Transfer to wire racks and let cool.  (The pistachio chocolate cookies are the hardest because they are already dark, so I usually waited until they seemed to have *just* turned solid in the middle.  If they're still jiggly in the middle, it's too early.  If you can poke the middle of the cookie without worrying you're going to get hot dough stuck to your finger, then they're done.  Sometimes I tried to put chocolate chip cookies and pistachio chocolate cookies in at the same time, so I could time the dark cookies by the ones that change color, but the cook times weren't exactly the same.)

The original recipe says this will make 8 dozen cookies, but I usually get closer to 4 dozen, probably because I cut them a little thicker than recommended.

Best Cut-Out Sugar Cookies--my own recipe, although unknown better bakers than me invented cut out cookies in the first place


It's hard to find a good cut-out sugar cookie recipe, because the recipes that have cookies that hold their shape well usually don't taste very good, and the cookies that taste very good usually spread during baking and don't hold a shape very well.  This recipe is based off a few recipes that I combined and then veganized.  It makes a cookie dough that is easy to cut-out, holds its shape very well when baking, and also tastes good.  I'm pretty proud of it.  I wish I could link to the original recipes I borrowed from, but I wrote them down without labeling where they were from.  

3 cups all purpose flour
1 tsp baking powder
1/2 tsp salt
1 cup (2 sticks) vegan margarine
1 cup sugar
4 tbsp applesauce
1 tbsp vanilla extract
2 tsp almond extract
  1. Whisk flour, baking powder, and salt in bowl
  2. Using electric mixer, beat margarine and sugar until everything turns a lighter color, about 5 minutes.  Add applesauce, vanilla extract, and almond extract.  Beat in dry ingredients until just combined.  Divide dough in half.  Flatten each half into a disk, wrap in plastic and chill 1 hour.  (This is when I usually freeze the dough.  In order to roll the dough out later, I put it in the refrigerator the night before using to thaw.)
  3. Preheat oven to 350 degrees.  Line baking sheets with parchment paper.  Sprinkle work surface and top of dough with a small amount of flour.  Roll out dough to 1/2 inch thickness.  Cut out cookies with cookie cutters.  Transfer to prepared sheets, spacing 1 inch apart.  Gather scraps and roll out on floured surface, and cut out more cookies.  Repeat until all dough is used.  
  4. Bake cookies, about 10-12 minutes.  I tried to catch them just before turning golden, when they seem pretty solid but are a nice even beige color even on the tips of stars, although they taste pretty good even when they turn a bit darker on the edges.  Transfer cookies to racks and cool completely.

Friday, December 15, 2017

Friday, December 1, 2017

Things spilled in roads




Friday, November 17, 2017

Herd Immunity

Herd immunity is cool.  It's like, science, but it's also an intuitive theory that you can understand without performing Bayesian estimations.


So, epidemiologists like to study the spread of disease.  They noticed that some diseases spread more easily than others.  (Forgive me for channeling Contagion.)  By looking at how fast diseases spread in a population, you can estimate how many people the average sick individual infects--this number is called R0 (pronounced "R-naught" by normal people and "Arrg-naut" by pirates).  That means that, on average, a sick person is capable of infecting R0 people during their illness.  R0 is different for every microbe, based on the microbe's properties.  The more and easier ways a microbe can be spread, the higher the R0.  For instance, if an illness can only be spread by a child sneezing directly into your mouth from less than six inches away, it will probably have a lower R0 than one that will spread to anyone touching a doorknob after the infected person for the next 12 hours.
Kate Winslet explaining R-nought in Contagion.


People hypothesized that if a proportion of the population were immune to a disease, transmission and then incidence would decrease.  If R0 is the number of people on average infected by an individual, it makes sense that if (R0-1)/R0 of the population were immune, the effective transmission rate would decrease to less than one person per sick person, and incidence of the disease would decrease as a result.  So if you on average infected four people with a cold (R0=4), then if at least (4-1)/4 or 3/4 or 75% of the population were immune, you would transmit your cold to fewer than one person on average.
With no one in a population immune and the R0>1, infections occur exponentially.  
This is usually what happens when an epidemic occurs--a large percentage of the population is susceptible to a disease, so the disease can spread rapidly through the population.  One example is the flu--because the virus mutates every year, the entire population is susceptible to it every year.  Its R0 is slightly above 1.
With 50% of the population immune, or [(R0-1)/R0=(2-1)/2], the effective R0 becomes 1.   
Only one person is infected by each sick person, and the transmission rate drops.  The incidence (number of people with a disease at any one time) of the disease also drops--instead of having eight sick people by the fourth generation, there is only one sick person.  The disease will still persist in the population at a stable level.  This is usually what happens when an endemic disease is present--the percentage of immune people in the population prevent the disease from spreading exponentially, but a susceptible population continuously transmits the disease so it persists in the population.  Many childhood diseases act this way--while adults have often achieved immunity by, well, getting the disease as children, newer members of humanity continue to enter the world non immune and susceptible to infection.  Adults who escaped infection as children are often protected by the immunity of other adults until they become schoolteachers or start hanging out with their own children.
With slightly more than 50% of the population immune, R0 is less than 1, and herd immunity is achieved. 
If slightly less than one person is infected by each sick person, transmission will eventually stop and the incidence of the disease will decrease until it reaches zero:  basically, the disease will die out of the population.  This doesn't mean that transmission can't happen at all--a few unlucky susceptible people can still be infected before the disease reaches a host that does not pass it on--but it does mean that it will fail to become either epidemic or endemic.  The population (herd) as a whole will not support the disease.

One way to achieve herd immunity is through vaccinations.  If you need >(R0-1)/R0 of the population immune, and a vaccine successfully immunizes E proportion of people who receive it, then the amount of people who need to be vaccinated is greater than:
Ta-da!
So, if a vaccine immunizes 90% of the people who receive it, and R0 is 2, then the number of people who need to be vaccinated to achieve herd immunity is ((2-1)/2)/.9=0.55, or >55% of the population.

Or, if you'd prefer a real-world example to my hypothetical illness, measles has an R0=12-18.  If both an initial and booster dose of the MMR vaccine is given, the effectiveness of the vaccine is 99%.  So,
((12-1)/12)/.99 or ((18-1)/18)/.99 = 92-95% of the population needs to be fully vaccinated to achieve herd immunity against measles.

Fine, P., Eames, K., Heymann, D. "'Herd Immunity': A Rough Guide," Vaccines. (2011) 52:911-916