There is a decent amount of coverage about how the key study linking vaccination to autism was outright fraud. There should be more coverage. This needs to be shouted from the rooftops. Out of all the arenas of public thought, public health is one of the least forgiving and highest payoff areas where we can apply scientific thought. It is hard to understand the statistics of populations, as an individual. It is hard, rigorous, time consuming, invasive, and difficult work. This misinformation led to a decade-long public health scare. Scared and upset parents latched onto it and went off on a wrong path that will take at least as long to correct as it did to get there.

This is important: If we get our epidemiology right, then over time – many more people live healthy lives. If we get it wrong – if we instead indulge in undisciplined and magical thinking – if we fail to check and double check and check again – then unnecessary plagues ravage the land and literally thousands more people suffer and die. It was true with the HIV / AIDs epidemic, it is true with stem cell research, and it’s true in many others.

I encourage every sensible, thinking adult to google around and familiarize themselves with this information. Seriously. I’ll wait. I’ve sat through enough ranty conversations about the evils of vaccines to demand a little payback. How this technology, which is on the short list of truly incredible life-saving scientific tools we’ve ever developed, ought to be pitched because “scientific study,” showed something or other, and did we mention the autistic kids?

The table at the bottom of that review is killer. Out of 12 children in the study, every single one included false data. And this was not mere omission or oversight. The lead author was paid for his work – paid more than 400,000 pounds for work on a lawsuit claiming that vaccines were linked to autism and other disorders.

That author should be charged with, at least, negligent homicide. At least in part, because of his work, we’ve got whooping cough and typhoid fever breaking out in California. Scared parents were misled into not protecting their children – and by doing so they endangered those kids and others. Potentially well meaning but misinformed people then used the old “argument from authority” to go further even than the study.

It’s worth pointing out that one of the standard harangues about climate change applies here. Look, look, say the doubters: Science was wrong! You made a mistake – ha ha – how can we ever trust you? I’m sure that in short order, it’ll be “autism-gate.”

The distinction here is that this is how the system is supposed to work. Some bad data got in, and after the bad information got in – scientists kept working. Eventually the error was pointed out, retracted, and is being broadly corrected. The truth won out, but it took time, effort, and a lot of courage to do so. The truth did not win by argument from authority – by prayer – or by any other form of wishful thinking. We extract knowledge from the world slowly, painfully, through rigorous thought and yes – by finding and correcting mistakes and outright lies.

Hopefully, a ten year public health scare is over. Hopefully we can get back on the right path to actually helping parents whose kids have mysterious behaviors including autism – and hopefully we can do it while continuing to beat back diseases from the dark ages, using the only tools that have ever worked effectively against them.

There’s a lot of back and forth in the news about the appropriate size, shape, and funding sources for government. At least … that’s what I see when I choose to pretend that people are talking and thinking about what’s good for the nation rather than just yelling at each other and vying for power.

In any event, I have an idealized recollection of Minnesota’s snow removal laws from when I lived in Saint Paul. They went something like this:

* The city is responsible for keeping the streets clear. They also cut out around fire hydrants and so on. That’s tax funded.
* Property owners are responsible for keeping their sidewalks clear and safe.
* You have 12 hours after the snow stops to make that happen.
* After 12 hours, the city sends around crews. If the crews clear your sidewalks, you pay a moderate fine. It’s more than what you would have to pay someone to come and shovel for you (to discourage people from using the city as their snow service) – but not crippling.
* If you push your snow into the streets, you pay a fairly massive fine. I remember it being $700 per incident.

In my opinion, this setup strikes a nice balance. You’ve got a taxpayer funded system for shared infrastructure, an insistence on personal responsibility, and a safety net because – at the end of the day – you need to have clear sidewalks.

Maybe we could do something similar with health care?

Each year, I do a couple of these year-in-review posts. I find that they’re a good way to review where I’ve been and to try to guess where I might be going. Here is the first sentence from the first post of each month in 2010:

Previously:

* 2004
* 2005
* 2006
* 2007
* 2008
* 2009

January: Welcome to the future, again.

February: We’re in the ‘Blanchard’ or ‘Terre Noir’ neighborhood, perhaps a mile north of Cite Soleil – in Port au Prince. The clinic building where we are working survived the earthquake in remarkably good shape. It’s in a walled compound that also contains a 1,000+ seat church and a small school. The school is basically a loss, and the church has a large crack from floor to ceiling on the two side walls. The tower that holds both the satellite dish and the water tank is badly damaged, but standing. We suspect that re-filling the water tank would push it over the edge.

March: Man, times were – I would post seriously every day and twice or three times on a good day. Now, I’m lucky to settle in and write something substantive once a week.

April: Okay, here’s sorta how my week has felt: (picture) You can guess that I’m *not* the lion in this picture. At least it’s Friday and I get to go home.

May: So, we’re boiling water for tooth brushing here. Apparently a 10 foot wide water pipe burst just west of town – and now we’ve got pond water (backup supply) coming out the pipes.

June: Indulged, this past weekend, in the now four year old tradition of renting a cabin in the woods with a dozen or so friends. The stated purpose of the weekend is to work on the arts and crafts projects that we push to the side on any particular day in our “real” lives. The subtitle might be “if we’re so successful, why don’t we live more like this?”

July: I spent last Sunday in Detroit. Now when I say “in Detroit,” I don’t mean “chillin’ with my rich friends in Ann Arbor,” nor do I even mean “hey, I’m from Bloomfield Hills!” I mean my grandfather’s house in Highland Park.

August: Okay, those of you who asked if I had run into scammers on EBay? I said, “no?” I would like to change my answer.

September: With the somewhat overhyped passage of hurricane Earl, the lawn got some much needed rain – but things are otherwise stable.

October: Jen and I just got back from Ohio, where we attended the wedding of C to E.

November: My law of idiot inclusion: Any sufficiently large group of people will include some truly awful idiots.

December: I contribute, from time to time, to Freethought Rhode Island, an atheist radio show.

While I was installing my new car stereo, I had an experience that I thought was sort of cool.

First, context: It turns out that my car dashboard just pops right out. It’s got little plastic tabs that hold it in place, but if you use a “small pry tool,” (according to various websites) it’s simple to loosen. The tool looks sort of like a double-wide flat head screwdriver, with the tip of the bit smoothly bent to about 90 degrees.

While I’m disorganized about exactly where my stuff is at any given point, I do have a great feel for what stuff I own. I was pretty sure that I did not own one of these, and so I started looking for alternatives. Some websites recommended using a screwdriver, while others suggested a plastic putty knife. Both sorts are filled with comments on the order of “imbecile! The scratching! The ruining! Unprofessional HACK! Hire a professional, like MEEEEEE! Also: marketing).

Anyway, as I was weighing my options, I remembered that I had recently received my grandfather’s toolbox, and that it was sitting un-opened in the basement. Figuring, “hey, grandpa loved to work on cars,” I went down there and opened it up. On top of everything else, there was the exact tool I needed.

Thanks, grandpa.

I have declared this toolbox to be magical. When all seems bleakest, I will open it and find the exact tool I need, waiting for me.

There have been a few studies measuring happiness in various activities. The best ones pester the subjects to report their instantaneous happiness at random times throughout the study. “What are you doing right now, and how happy are you?”

If I were to participate in one of those studies, I suspect that it would find that some of the happiest times in my life are when I’m cooking or preserving food. We participate in the Cape Ann Fresh Catch community supported fishery, as well as two different CSAs. The afternoon that I bring home that box of veggies, or the ocean fresh fish, usually turn into a peaceful ritual of cleaning, packing, boiling, freezing, and so on. Similarly, people who have been over to my house know that I love the puttering around in the kitchen, trying to find a meal hidden in the ingredients that we happen to have at hand.

I used to do a lot more boiling-water-bath canning, but it’s something of a pain to get the water bath up to temperature. Since I’ve discovered freezing, and installed a chest freezer in the basement, I don’t do so much of it anymore.

I also used to go for huge batches – imagining somehow that I was stocking up for winter. In my situation, stocking up for winter would require almost full time work in the summer and fall. It’s not a good use of my time. In addition, it basically guarantees that a lot of the food will go un-eaten. If you were measuring my happiness – it hits a local low when I realize that something that I preserved has been allowed to go bad by sitting on the shelf.

So now with most recipes I just make a few pints at a time, and I open them at the drop of a hat. Food is for eating. It’s the same with the wine. Wine is for drinking, doubly so with the homemade stuff. The question that comes to mind when I find myself worrying about the supply of my pickles, relishes, or whatever is “what are you saving it for?” What better place than here? What better place than now?

So work is closed this week. There may be some INBOX cleaning, here and there, but by and large this week is mine to refresh and recharge. In usual form, I’ve set myself a rather savage schedule of projects that have been sitting around for a while. Based on today’s efforts, I’m one for one – keeping pace with the unyielding demands of time. We’ll see how the snow helps out tomorrow.

My father in law sent me a car stereo. I’ve been wanting to play driving music directly from the iphone for a while now. Mostly, this is pride: burning 14 to 20 songs onto plastic, shackled to the whim of the licensing gods, does not suit. The bit and harness – they chafe. I was only briefly put off by the fact that Sony decided to name it “XPLOD”. As in “kaboom.” Once I got over that – I went ahead with the noble business of mounting it in my car.

I had never changed any component in my car before. I realize that as an American man in his mid thirty’s, this probably means that I’m some sort of communist. Anyway, I found many wonderful resources online. This stuff is totally fun. It’s a series of little puzzles that are totally solvable – provided that you don’t break the little plastic tabs or anything.

It turns out that in addition to the stereo itself, you need:

* A “dash kit” to mount the thing in your dashboard. Stereos are a standard size, but dashboards are not. The size standard is “DIN,” where the “D” stands for “Deutsches”. There, now you know.
* A “wiring harness” to adapt the Sony “standard” plug to my 1998 – 2002 “standard” plugs. Apparently the colors of the wires are standard – but the shapes of the plastic plugs are not.

I figured all that out, and had a contented evening soldering some wire splices.

There were a lot of fun little puzzles along the way to getting it working. The solution to the final puzzle (back and forth to the car, in the snow), was to wire the powered-antenna line (blue, FWIW) directly to 12V power. Apparently, little-known fact here, that line also TURNS ON THE SPEAKERS. I had been assuming that it meant “power for the mechanical antenna.” Like, how it’s labelled on the wire and in the book. I have no powered antenna, so I had just connected it to the blue wire on the stereo plug … further assuming that the stereo would do the right thing. No dice. That caused the system to work when using the radio – but to be silent (though superficially functional) for any other mode. The stereo was trying to deploy the antenna only when the tuner was on – and otherwise playing without powering the speakers.

For the record, it’s not the “powered antenna” line. That’s the “make the whole damn system work,” line.

Rasafracka.

Stole a couple of days with my spouse to get down to New York prior to the holidays. Cashed some Marriott points for a stay in a damn nice hotel. Took the Acela down on Wed, and the limoliner (bus) back on Friday.

In between, we walked our butts off. Saw the Rockettes, which was straight from the 30’s: “Girls in a line, kicking their legs up in the air.” Good times, but I had to suspend my thoroughly modern sensibilities – since I’m sure that whole feminist tracts could be (and have been) written about it. Saw the decorated window displays for the major stores – and the tree in Rockefeller center. It turns out that I totally have a thing for “empire” period architecture – of which Rockefeller Plaza is the stone-cold exemplar. Who knew? It’s the long vertical lines, and the belief in the triumph of humanity and knowledge over the forces of chaos, I think.

We also had lox on a bagel, Pickles, some authentic chinatown fare, and so on.

Today was a low key day of exchanging gifts, and then going to see Tron in 3d. My assessment is that Tron Legacy makes a great music video for Daft Punk – and it was a fine action movie. The fight scenes are good, and both the beefcake and the cheesecake are on full display. Great art, it ain’t … but I didn’t really go into it looking for great art – so all is well.

Check out Paul Krugman’s latest blog post for a decent holiday message. In fact, I’ll excerpt:

Nothing lasts forever, and there are times when I listen to the demagogues and fanatics, and fear that America as we know it is slipping away. But there is a basic decency to this nation. And in the end, I believe and hope, that decency will continue to prevail.

I find myself filled with a calm and abiding optimism today. I hope that it continues tomorrow. I hope that it continues much longer than that.

One last thought on the Warrior gene.

Based on a semi-casual survey of three SNPs from my 23 and me data, I do not carry this gene. Yet, when I started looking into this, my guess was that from experience, I have a strong built-in desire to punish the wrong-doers – and a little extra hit of the hot sauce sounds like a great way to do it.

So what gives? I’ve got a measurement that says I don’t carry the trait for – loosely – being willing to pay out-of-pocket to punish a wrongdoer. However, I’ve got experience and evidence that says that not only do I *feel* such urges – I will actually *do* so unless I actively monitor myself and nip those urges in the bud.

And so we come to the crux of it. There are some questions where the genes give clear, unambiguous answers. “Yes, this tissue came from that person.” “Yes, you have Huntington’s Disease.” For most others, particularly with regard to behavior and perception, the genes do little more than set the stage. I find a strong connection here with one of the interpretations of karma. I was born as a certain body, with certain proclivities and certain traits. I happen to be very lucky in that regard. I’ve got a healthy body, a decent mind, and so on. Other factors outside my control have helped as well. I was born to highly educated parents in a rich and powerful nation. Then we come to the things within my control, and my reaction to stressors and jackasses is one of them. While I do have certain reactions – they could be much worse.

Finding out that I don’t have this particular gene actually strengthens my compassion for folks who flip out and lose their temper on a regular basis. What would it be like to constantly be on a high tide of emotion? What would it be like to be unable to hold back tears? Maybe that’s why the driver in the next lane is honking frantically – or the person behind me at the retail checkout is huffing and bumping me.

What I take away from it is that – on the grand scheme of things – I probably have an easier time controlling this particular urge than other people do. However difficult it is to be me, I still probably have it easier than most.

For me, at least, that’s been a broad truth in this whole exploration. Everywhere I look, there are horrible conditions, situations, and proclivities that I do not share. Everywhere I look – I seem to have it pretty good, compared with what could have been.

I did a bulk import from LJ into chris.dwan.org last night. Apparently, if you have update notification turned on, you got about 2,000 notifications.

Apologies to anyone who I spammed. Shouldn’t happen again.

FWIW, I’m not planning to turn LJ off – I just want to centralize my blog activities onto a server that I control and can (for example) back up from time to time.

My friend found a solution for my question of what he terms the ‘manliness’ gene! I will briefly protest that neither are all belligerent hot-sauce administering warriors men, nor are all men warriors, and then move on.

The solution is to use some of that basic genetics knowledge that I should have remembered from the early 2000’s.

The key is that while we can’t use the SNPs to directly measure the trait in question, we can take advantage of the fact that they are located on that same relatively small chunk of DNA. These SNPs associate with this particular mutation, meaning merely that they tend to vary along with it. If we assume that the SNPs will vary – give or take – at the same rate as the tandem repeat, and if we can find someone who measured both the SNPs and the trait on a decent sized population, then we might be back in business. As he says: it wouldn't do for the block to be coherent *except for* the one variable little piece that actually matters.

Once again, we bang up against that annoying definition of “genes.” I’m now dragging in some other study about a different thing. This is, in the very small, why good scientists are so very thorough and paranoid about making declarative statements.

Anyway, here’s his answer:

This paper briefly describes some markers around MAOA: http://www.biomedcentral.com/1471-2156/6/46

You have SNP states at these MAOA markers described in the paper: rs3788862, rs6323, rs979605. Looking at Figure 1, right side:

marker    you   A1 A2 A3 A4
rs3788862 A/T   C  T  T  C
rs6323    G/C   A  C  A  C
rs979605  A/T   C  T  C  T
            ^      ^

So it looks to me like you have type A2 -- or at least, you share these SNPs with the A2 set of this sample of Swedish individuals. The chance of coming to this configuration by chance is on the order of 1/64 (not quite, since the sites aren't independent). And: "Only two common haplotype variants of the MAOA locus were found among individuals of northern European ancestry."

Trait association: "Two MAOA haplotypes, A1 and A3, both sharing identical alleles at the three first haplotype positions (CCA-) (Figure 1), were associated with a significant decrease in trbc-MAO activity" You are A2; so I presume you have higher trbc-MAO activity. Skimming the PNAS paper, I see that "individuals with the low activity form of MAOA proved more likely to administer hot sauce to their opponent." So I conclude that if you and Attila the Hun were in a hot-sauce-administering contest, you would lose.

My friends are clever. Until someone shows me a study involving more than 573 Swedes, I’ve got my answer. Of couse, that’s a mark of decent scientific thinking: I’ve found an acceptable answer based on the available information. I also have a decent grasp on where I might be wrong, and I retain a fair degree of curiosity about what else might be down this superficially simple rat-hole.