Nate Silver has an important post, Herman Cain and the Hubris of Experts. It’s not really about Herman Cain. Rather, it’s about the reality that pundits tend to underestimate uncertainty and complexity. Saying you don’t know isn’t as satisfying as making a definitive categorical assertion. This manifests particularly in the domains of sports and politics because there are clear and distinct criteria to assess predictive power. Politicians win or lose elections, while teams win or lose games. And yet despite the long history of minimal value-add on the part of pundits they persist in both domains. Why? I think it’s pretty obviously a cognitive bias toward storytelling. Similarly, in the 1930s the Alfred Cowles concluded that financial newsletters didn’t help their readers “beat the market,” but he also assumed these newsletters would persist. There was a psychological need for them.

The key here is to change the attitude of the pundit class. The populace will always have a preference for stories with plausible and clean conclusions over radical uncertainty. Not surprisingly many professional pundits reacted with hostility to Silver’s observation that they’re quite often wrong. I don’t venture into political punditry often, but when the Democrats passed health care reform I predicted that Mitt Romney would have no shot to win the the Republican nomination. The facts in this case seemed so clear. Romney was going to be walloped over and over again over his record on health care reform when he was governor. I was wrong. Romney may not win, but obviously he’s a contender. My logic was simple and crisp, but the logic was wrong. That’s why you let reality play out. If what was “on paper” determined national elections, then we’d be talking about President Hillary Clinton.

Of course political journalists that engage in analysis still have a role to play. Don’t newspapers have horoscopes and style sections?

A few weeks ago over at Slate Dave Weigel stated that “Electing Mitt Romney in 2012 would mean electing, for the first time, a president whose religion is not part of orthodox Christianity.” I tweeted to Weigel that this was just plain wrong. There have been plenty of presidents who rejected orthodox Christianity, the last one being William Howard Taft, a Unitarian who rejected the Trinity. And now Jeffrey Goldberg is saying the same thing in Bloomberg View:

But theological honesty demands that we recognize that. Romney would be the first president to be so far outside the Christian denominational mainstream.

There is much in Mormonism that stands in opposition to Christian doctrine, including the belief that the Book of Mormon completes the Christian Bible. Christianity had an established creed about 1,500 years before Joseph Smith appeared in upstate New York with a new truth, codified in the Book of Mormon, which he said was revealed to him by an angel named Moroni.

“The Nicene Creed and the Apostles’ Creed settled the basic ideas of Christianity,” said Michael Cromartie, an evangelical who is vice president of the Ethics and Public Policy Center in Washington. “The canon was closed, and then Joseph Smith comes along and says that there’s a new book, an extra-biblical addition to the agreed-upon canon.”

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I don’t have time for this, but I’m sure some readers do. 1000 Genomes has put a tutorial up. Breakdown:

1. Description of the 1000 Genomes Data, Gabor Marth pdf|pptx

2. How to access the Data, Paul Flicek pdf|pptx

3. Lessons in variant calling and genotyping, Hyun Min Kang pdf|pptx

4. Structural Variants, Ryan Mills pdf|pptx

5. Imputation in GWAS studies, Bryan Howie pdf|pptx

 

All Slides in PDF

Follow up to the previous post, (Via Ed), Fetal gene screening comes to market:

Until last week, scrutinizing a fetus’s DNA for indications of genetic abnormalities meant tapping into the mother’s womb with a needle. Now there’s a test that can do it using a small sample of the mother’s blood. MaterniT21, a Down’s syndrome test that Sequenom of San Diego, California, launched in major centres across the United States on 17 October, is the first of several such tests expected on the market in the next year. It signals the arrival of a long-anticipated era of non-invasive prenatal genetic screening, with its attendant benefits and ethical complications….

In the “news your can use” section of their press release:

The out-of-pocket cost of the test for insured patients will be no more than $235. Sequenom CMM will initially operate as an out-of-network provider to ensure eligible patients will have coverage for the test. While negotiating to ensure coverage by most major private insurance programs, the reimbursement for the test is expected to be similar to that of current invasive procedures like amniocentesis or CVS.

A friend pointed me to the heated comment section of this article in Nature, Rebuilding the genome of a hidden ethnicity. The issue is that Nature originally stated that the Taino, the native people of Puerto Rico, were extinct. That resulted in an avalanche of angry comments, which one of the researchers, Carlos Bustamante, felt he had to address. Eventually Nature updated their text:

CORRECTED: This article originally stated that the Taíno were extinct, which is incorrect. Nature apologizes for the offence caused, and has corrected the text to better explain the research project described.

Here’s Wikipedia on the Taino today:

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In my spare time today I went through much of Madagascar: A Short History. After reading it I’m even more convinced that people need to stop talking authoritatively about this island and its people. There’s a lot of interesting material in it, but ultimately the years before European contact remain very shadowy. I don’t know much new about this period. This brings me to why I’m putting this post up: I am going to try and see if I can estimate an average age of admixture for my two Malagasy individuals. Hold me to it. I’ll make time.

John McCarthy has died. Sadly I was expecting this, I was told that McCarthy was still teaching courses in 2008 by someone in Stanford’s computer science department, but he was in obvious bad health. One of the major downsides of the incredible information flow in the internet age is that you often hear through the grapevine that eminent so-and-so is ill, and have to prepare yourself years ahead for the inevitable. We all die, but it seems starker in the case of those individuals who have grasped upon a fragment of the sort of immortality given to Gilgamesh.

In the early to mid-2000s I had some conversations and arguments with McCarthy about the history of Islam and the politics of the Middle East (in hindsight I knew a lot more about the former than I did the latter). He followed Gene Expression now and then in the course of his meanderings around the web. Initially I did not make the connection that this was the John McCarthy, which was especially ironic in that I was playing at learning Lisp at that moment! Outside of his domains of almost godlike achievement I have to say that McCarthy was a relatively no-nonsense down to earth person from what little I could gather. He was curious about what he didn’t know, and if you weren’t aware that he was one of the most accomplished computer scientists in the world he didn’t seem too keen on cluing you in. My own overall impression was that he was a deep pragmatist and skeptic.

Dienekes points me to the fact that Ewen Callaway has the dirt on what’s going on with Ötzi:

To get a better grip on his ancestry and predisposition to disease, Albert Zink, head of the Institute for Mummies and the Iceman in Bolzano, and his team sequenced Ötzi’s 3 billion base pair nuclear genome from a shard of hip bone. Their sequence covers more than 90 percent of the Iceman’s genome. Their team also analysed DNA preserved in Ötzi’s stomach in hopes of revealing the microbes that colonized his gut.

Zink says his team is keeping most of the results of these studies under wraps, pending publication. They had hoped to have the paper out in time for last week’s Mummy Congress and a television special called Iceman Murder Mystery.

His team plans to use the sequence to determine Ötzi’s status for genetic variations linked to diseases in modern humans, particularly arthrosclerosis. A full nuclear genome will also paint a more detailed picture of the Iceman’s ancestry and his relationship to present-day humans. Zink’s team will ask whether Ötzi is an ancestor of people living in Central Europe today, or whether he and his kin died out and were replaced by migrants from elsewhere, such as the Middle East. To buff up this analysis, they are analysing DNA preserved in the skeletons of other ancient inhabitants of central Europe.

~90 percent of a genome is way more than you’d need for some basic analysis and inference of relationships to contemporary populations. So what’s the big deal? No idea, but this tardiness makes me turn the needle up in terms of assuming that they found some interesting stuff. If it’s what you’d expect, why recheck and beef up your analysis with as much support as you can find? Of course, I hope that they found some interesting stuff, so I shouldn’t trust my own judgments in this area. My own suspicion is that they have found extensive genetic turnover over the past 6,000 years in Western Europe, and they are using modern and ancient samples to flesh-out their model. The two dominant paternal haplogroups in Europe today, R1a and R1b, are suspiciously scarce in the ancient DNA samples.

Over the past few weeks I’ve been observing the response to Rick Scott’s suggestion that Florida public universities focus on STEM, rather than disciplines such as anthropology. You can start with John Hawks, and follow his links. More recently I notice a piece in Slate, America Needs Broadly Educated Citizens, Even Anthropologists. There several separate issues here. Superficial concerns of money going to your political antagonists, commonsense considerations of the best utilization of public educational resources, and broader reflections upon the nature of a ‘liberal’ education.

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Dienekes has some harsh words for the way some science is produced, focusing on the genome of Ötzi the Iceman as a case in point:

Yesterday, I twitted in exasperation that Otzi’s genome, which must have been available in at least some sort of draft form since at least the beginning of this year, has been under lock and key, presumably because of the need to make a big splash with the simultaneous Bolzano conference, TV special, likely imminent journal publication, and all the media stories that will follow.

What I don’t understand: how come no one is editing the Wikipedia entry ahead of time? I wonder in hindsight if there’s no there, there, though I hope I’m wrong about this. Going by the lack of media mention of ahead of the NOVA documentary I do suspect we’re seeing the calm before the embargo explosion.