Archive for November, 2012

Can your genes be patented?

By Razib Khan | November 30, 2012 9:30 pm

Court to Decide if Human Genes Can Be Patented. So it seems a group of middle aged to very aged lawyers will decide the decades long Myriad Genetics saga. My position on this issue is simple: if you are going to award patents, they must be awarded to acts of engineering, not discoveries of science. See Genomics Law Report for more well informed commentary.

CATEGORIZED UNDER: Personal Genomics

Open Thread, 11-29-2012

By Razib Khan | November 29, 2012 3:37 am

Update: You can leave comments now. But, you are forced to register with no third party login option. I know many of you don’t like the last, because you are emailing me about it. If the quantity of responses (<5, vs. the usually of ~50 for an “open thread”) on this thread is a measure I suspect that I’ll have to switch web-discussion mostly to Twitter or Facebook. I balk at registering to comment personally, so I totally understand.

As you may have noticed there are some issues with Discover Blog‘s transition to a new system. But once comments work again, feel free to post here. I’m busy with some other things right now besides the blog, so I’m going to take the current technical issues as an excuse to not post for a few days.

CATEGORIZED UNDER: Administration
MORE ABOUT: Open Thread

There are no shortcuts to knowledge

By Razib Khan | November 26, 2012 2:53 am

As many of you know, right before the election I made a $50 bet with Hank Campbell that Nate Silver would get at least 48 out of 50 states correct for the 2008 presidential election. I also got one of Hank’s readers to sign on to the same bet. Additionally, a few readers and Twitter followers got in on the wager; they were bullish on Romney’s prospects, and I was not (more honestly, I was moderately sure they were self-delusional, and willing to take their money to make them more cautious about their self-delusional biases in the future). But there’s a major precondition that needs to be stated here: I hedged.

Last February a friend told me he was 100% confident that Barack Hussein Obama would be reelected. This prompted me to ask for favorable terms on a bet. The logic was simple, if he was 100% confident, then it shouldn’t be a major issue for him, because he was collecting anyhow. As it happens he gave me 5 to 1 odds, so that I would collect $5 for every $1 he might collect. I told him beforehand that I actually thought that Obama had a 60-70% chance of winning, so I went into the wager assuming I’d be out a modest amount of money. But that was no concern. My goal was now to convince those who were irrationally supportive of Romney to take the other side of the bet. For whatever reason people have an inordinate bias toward their hoped-for-candidate in terms of who they think will win, as opposed to who they wish to win. The future ought gets confused with the future is.* I got people to take the other side, which means that I was going to make money no matter who won.

At this point one might wonder about my comment that I suspected that those who were bullish on Romney were delusional. It’s rather strong, and my reasoning is actually rather strange. Overall I accepted the polling averages. A few years back I was an economic determinist in election outcomes, but Nate Silver had convinced me that the sample size was too small to get a good sense of the real proportion of variation being predicted here. In short, the economy matters, but I stepped back from the supposition that it was determinative (as it happens, purely economic models that were excellent at predicting past elections face-planted this time). So that’s why I relied on the polls. Though I leaned on Nate Silver, I didn’t think he was particularly oracular, and I’d say that I’m mildly skeptical of the excessive faith some put in his particular person. When I put a link up to Colby Cosh’s mild take-down of Silvermania I received a few moderately belligerent comments. This despite the fact that I was willing to put money on Silver’s prediction.

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CATEGORIZED UNDER: Science

Are you “Driftless”?

By Razib Khan | November 25, 2012 11:22 pm

GeoCurrents on the political anomaly of the “Driftless” zone of the upper Mississippi (via GLPiggy). The anomaly has to do with the fact that this area is very white, very rural, and not in the orbit of a larger cosmopolitan urban area (e.g., “Greater Boston,” which extends into New Hampshire). The post goes into much greater detail, but concludes with a request for more information. This is the area where local knowledge might be helpful.

I went poking around old county level presidential election maps, and I can’t see the Driftless blue-zone being a shadow or ghost of any past pattern. But, I did stumble upon again the 1856 presidential election map by county…can there be a better illustration of the “Greater Yankeedom” (the red are Republican voting counties, the first year that the Republicans were a substantial national party):

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CATEGORIZED UNDER: Politics
MORE ABOUT: Politics

Going short and going long in terms of blog traffic

By Razib Khan | November 25, 2012 11:59 am

Arnold Kling took a break from blogging, but is coming back. But under an explicit set of personal guidelines. About This Blog:

I decided to go with my own blog, rather than return to EconLog, because I want to have total control over the blog content. I want to model a very particular style of discourse, as indicated by the tag line “taking the most charitable view of those who disagree.” In June, I wrote

Suppose we look at writing on issues where people tend to hold strong opinions that fit with their ideology. Such writing can

(a) attempt to open the minds of people on the opposite side as the author
(b) attempt to open minds of people on the same side as the author
(c) attempt to close minds of people on the same side as the author

So, think about it. Wouldn’t you classify most op-eds and blog posts as (c)? Isn’t that sort of pathetic?

My goal is to avoid (c). I will try to keep the posts here free of put-downs, snark, cheap shots, straw-man arguments, and taking the least charitable interpretation of what others say. So, if what you most enjoyed about my past blogging efforts were the put-downs, be prepared for disappointment with this incarnation.

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CATEGORIZED UNDER: Politics
MORE ABOUT: Arnold Kling, Politics

Prop 37 vs. Obama (by county)

By Razib Khan | November 22, 2012 11:12 pm

Following up my request a reader crunched the numbers (here is his data table) to show the association between supporting supporting Proposition 37 and voting for Barack Obama by county in California:

From what I know this issue really polarized people in highly educated liberal enclaves in the state of California. Many of my Left non-scientist friends supported the measure because of an anti-corporate animus. But, another issue that sometimes came up was transparency and fair play, in a “teach the controversy” fashion. My own contention is on the scientific point there is no controversy.

CATEGORIZED UNDER: Politics
MORE ABOUT: Politics

Open Thread, 11-22-2012

By Razib Khan | November 22, 2012 1:11 am

If you aren’t too stuffed, ask! I plan to get my simultaneous review of The Signal and the Noise: Why So Many Predictions Fail-but Some Don’t and Uncontrolled: The Surprising Payoff of Trial-and-Error for Business, Politics, and Society up over the holiday weekend, but I’m going to be focused on other things besides the blog obviously. That being said, to be frank I don’t personally feel that the regular reader of this weblog would get much value from The Signal and the Noise (Nate Silver interviews Robin Hanson. I didn’t need to read his book to be aware of Robin Hanson’s ideas, he quite freely shares them to all curiosity seekers on the internet and in person).  Uncontrolled adds more value in my opinion because experiments in social science are more difficult, and probably more genuinely ground-breaking (if less sexy), than statistical inference.

CATEGORIZED UNDER: Uncategorized
MORE ABOUT: Open Thread

Back to crunching personal genomic data

By Razib Khan | November 22, 2012 12:54 am

Many months ago I told some of my friends that I’d run analyses of their 23andMe data, and report it back to them. A year ago I made the same promise to some of my readers. But life got in the way, and I’ve been very busy. I’m working on scripts to make the whole process efficient for me (if you want to know, I’m trying to get the output to be easy to merge many runs with CLUMPP and then produce DISTRUCT type outputs; I’ve done this with other Admixture outputs, but for various reasons the labeling gets messed up with my ‘personal’ project). But I’ve decided to at least start pushing some of the results live. I won’t be putting it in this space, probably razib.com. But I thought I would get your attention first. I know a lot of ID’s are missing, but I’ll add them later when I can find anything. And yes, I need to get back to African Ancestry too (that site was infested with a backdoor, so I had to yank it). This is all rather basic stuff, but I just don’t have the time to do things in a manual fashion, and the scripts I have for population sets don’t transfer over when I want to give individual friend results as well as population results.

The results in tabular format are here. And all individual results are here. In terms of the tech details, ~140,000 SNPs, ~3000 total individuals in the data set, at K = 11. I will probably be reporting K = 12 to K = 25 from now on (I’m just going to get 10> replicates and merge them).

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CATEGORIZED UNDER: Personal Genomics
MORE ABOUT: Personal genomics

A very special Thanksgiving to one and all!

By Razib Khan | November 21, 2012 7:40 pm
CATEGORIZED UNDER: Uncategorized
MORE ABOUT: My Girl

Obama on the age of the earth

By Razib Khan | November 21, 2012 5:29 am

Jump to 9:00.

CATEGORIZED UNDER: Creationism
MORE ABOUT: Creationism

The crowds knows better than you?

By Razib Khan | November 21, 2012 5:23 am

Justin Wolfers & Betsy Stevenson have a piece up in Bloomberg, Crowds Are This Election’s Real Winners. In The Signal and the Noise Nate Silver has a chapter on Wolfers’ belief that prediction markets are superior to the sort of quantitative analysis that is his stock & trade. The belief isn’t based on an intuition. One of Wolfers’ graduate students produced a paper showing that Intrade was actually better than FiveThirtyEight in 2008. Silver demurs in the chapter because he suggests that the model which Wolfers and his student lay out in the paper had some modifications which allowed for one to judge Intrade’s performance superior. I’m willing to accept Silver’s assertion here because I’ve seen enough economic models which are modulated just enough to produce elegant and clean results. That being said, the general tone of the chapter is such that in his heart Silver seems to agree that Wolfers is fundamentally correct in the long term. Prediction markets, when done right, are more powerful than any analytic an individual could cook up.

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CATEGORIZED UNDER: philosophy
MORE ABOUT: Philosophy

Iterating science, supercharged

By Razib Khan | November 20, 2012 7:17 pm

Science is about “updating” with new information. But people are attached to their propositions, and shifts in paradigms can take a very long time, often dependent more on human lifespans than the constellation of the data. But please see this post by Luke Jostins’ over at Genomes Unzipped. He has “updated” his own view of his recent Nature paper on inflammatory bowel disease. This is rather awesome, because yes, there was some talk about the balancing selection aspect of the paper at ASHG, and now Luke has gone and amended his own position.

The reality is that emotions are a big deal in science. But in theory we simply look at the evidence. Bridging that gap, and shifting the balance to the latter, is very important in keeping the enterprise honest, fruitful, and attractive to young scholars. I’m hoping that the more rapid dissemination of information via projects like Haldane’s Sieve will aid in the rate of iteration.

CATEGORIZED UNDER: Science
MORE ABOUT: Science

The Kindle price

By Razib Khan | November 20, 2012 7:11 pm

I’ve had a Kindle for a few years now. I read a lot on it. And yet I observed something recently: I’ve stopped going to the library much. This is a big deal for me…probably since the age of 7 I’ve clocked in at least one visit to the public library per week in my life. I never turn books in past due because of the frequency with which I patronize the public or university libraries which I’ve had access to in life. Until recently. Now on occasion books go overdue, because I don’t go very often.

In the short term the Kindle has been a boon. But I’m not sure if it’s good for us in the long term. I’d rather pay more for a device which allowed for easier usage of different formats, as well as looser distribution policies.

CATEGORIZED UNDER: Technology
MORE ABOUT: Kindle

Mine eyes have seen the glory; we are as gods!

By Razib Khan | November 20, 2012 6:52 pm

Earlier today Erick Erickson of RedState put up a long and meandering post titled “I Believe and Am Thankful”. As you might infer from the title it elaborates Erickson’s own theological position, and his stance toward the expression of faith in the public square. Because I am an atheist I disagree with many aspects of his position, and because I am not a liberal I agree with other elements of his argument. But there was one portion of which alarmed me a great deal, because I believe it displays an epistemological superificiality which is all too common. Erickson’s first paragraph is:

Marco Rubio is getting beaten up by the press for not decisively and convincingly saying he thinks the world is billions of years old. It has become the new litmus test in the media. Believing what was believed to be literally true for a few thousand years is now nutty. Christian homeschool kids, often taught that the world is not as old as some believe and who routinely kick the rear ends of the ivy prep kids in academics, are considered stupid.

There are two components to my reaction. One is rather general and abstract, while the other is specific. I will begin with the abstract. The fact is that you would be foolish to accept what people believed for “thousands of years” in many domains of natural science. When it comes to the ancients or the moderns in science always listen to the moderns. They are not always right, but overall they are surely more right, and less prone to miss the mark. In fact, you may have to be careful about paying too much attention to science which is a generation old, so fast does the “state of the art” in terms of knowledge shift. That was part of my critique of Richard Lewontin. A great evolutionary biologist of the 1960s, today Lewontin seems far behind the times, tackling issues near and dear to the 1970s, when we live in the post-genomic era.

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CATEGORIZED UNDER: Creationism
MORE ABOUT: Creationism

Being pro-life and pre-implantation diagnosis

By Razib Khan | November 20, 2012 12:58 am

The recent controversy over Peter Singer and Fordhman got me thinking about the logical implications of a consistent ethos. Singer certainly has a consistent ethos. Or at least he tries to work out the logical implications of his axioms, no matter where that goes. I don’t agree with Peter Singer’s utilitarianism because I am skeptical of his extreme ethical reductionism, but it’s clarifying at least.

But that got me to thinking about the implications of being pro-life in the 21st century, as biotechnology becomes more and more a part of our lives. From what I gather the standard pro-life position is that life begins at conception, where you have the potential for a human being. One aspect of this has always disturbed me: it is likely that more than 50% of conceptions miscarry, without anyone being the wiser. Most karyotype abnormalities, for example, miscarry. If these are human lives, does this mean that the majority of humans die even before they are born? How can we fix this tragedy?

In the pre-modern age there wouldn’t be a tragedy to fix. Saving these humans would be beyond our power. But today there are ways we may reduce the harm. First, one could fertilize a range of eggs, and then screen them for genetic abnormalities. Only the ones who pass a quality control threshold would be implanted, to minimize miscarriage risk.* The others could be put in ‘stasis,’ until the point where medical technology has advanced to the point that ailments can be fixed by genetic re-engineering at the zygotic stage.

And that is my attempt to think like a pro-life Peter Singer.

* In the future artificial wombs are definitely the way to go, as the developing fetus could be closely monitored.

CATEGORIZED UNDER: philosophy
MORE ABOUT: Philosophy

San Francisco supported Proposition 37!

By Razib Khan | November 20, 2012 12:15 am

A few weeks ago I alluded to the controversy around proposition 37. This was the GMO labeling law proposal. Many life scientists in California opposed this law. One aspect of this issue is that it is an area where the Left may be stated to be “anti-science.” This is why this was highlighted in Science Left Behind. But there’s a problem with this narrative: the survey data for it is weak. There are broad suggestive patterns…but the reality is that the strongest predictor of skepticism of genetically modified organisms is lower socioeconomic status. The GSS has a variable, EATGM. Here are the results by ideology:

Liberal Moderate Conservative
Don’t care whether or not food has been genetically modified 15 16 17
Willing to eat but would prefer unmodified foods 55 53 52
Will not eat genetically modified food 30 30 31

 

I would caution that the sample size is small. But, if you dig deeper into the survey data you can find evidence that conservatives are more unalloyed in their support of biotech.

And yet with all this said, today I noticed that the California proposition 37 results are rather stark in their geographic distribution. The measure failed statewide, but 2/3 of the people in San Francisco and Santa Cruz counties supported it, as did 60% of the people in Marin (interestingly, only a little over 50% supported it in San Mateo and Santa Clara). I couldn’t find a tabular list with the results by county, but there are interactive maps. If someone was industrious (and had more time than I do) they would go and collect the data from the maps, and do a loess of “support proposition 37” vs. “support Obama.”

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CATEGORIZED UNDER: Agriculture, Politics
MORE ABOUT: Proposition 37

Richard Lewontin against the age

By Razib Khan | November 19, 2012 9:35 pm

Richard Lewontin’s fame rests in part on his pioneering role in the development of the field of molecular evolution, and secondarily due to his trenchant Left-wing politics. Several readers have already pointed me to his rather strange review of two new works in The New York Review of Books. The prose strikes me as viscous and meandering, but some of the assertions are rather peculiar. For example:

The other exception to random inheritance is not in the chromosomes, but in cellular particles called ribosomes that contain not DNA but a related molecule, RNA, which has heritable variation and is of basic importance to cell metabolism and the synthesis of proteins. Although the cells of both sexes have ribosomes, they are inherited exclusively through their incorporation in the mother’s egg cell rather than through the father’s sperm. Our ribosomes, then, provide us, both male and female, with a record of our maternal ancestry, uncontaminated by their male partners.

Harry Ostrer, who is a professor of genetics at Albert Einstein College of Medicine, and Raphael Falk, who is one of Israel’s most prominent geneticists, depend heavily on our ability to trace ancestry by looking at the DNA of Y chromosomes and ribosomes….

There is no mention of ribosomes in Legacy: A Genetic History of the Jewish People. I know, because I used Amazon’s ‘search inside’ feature. Rather, there’s a lot of reference to mitochondrial DNA and mtDNA, which is what Lewontin truly meant. Or at least I hope that’s what he meant. Because Lewontin is an eminent evolutionary biologist I assume they felt like they didn’t need a science editor, but perhaps they need to reconsider that.

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CATEGORIZED UNDER: Science
MORE ABOUT: Science

Why Marco Rubio waffled on the age of rocks (in numbers)

By Razib Khan | November 19, 2012 8:29 pm

If you have a pulse and follow “science news” you are aware that Marco Rubio gave a very equivocal answer to a very simple question about the age of the earth. As many have noted this is basically a way to call out Republican politicians for the fact that they have to satisfy the cultural signals of a segment of the American population which has a deep hostility to science which undercuts their naive reading of the Bible. To Mitt Romney’s credit he did not evade on this question, but gave a mainstream answer among the well educated. This sort of political pandering isn’t too surprising. Remember Hillary Clinton dismissing ‘elite economists’ when it came to her silly gas tax suspension idea? It’s a democracy, and that means you can get very far appealing to the populist sentiment.

More concretely, I want to address something Rod Dreher asserted at The American Conservative:

I wish one of these liberal journalists would go into a black or Latino church supper and ask people their thoughts about how the universe began. I’d bet that 99 percent of the people there would agree with Marco Rubio, even if most of them would vote for his opponent. People just don’t care about this stuff at the national political level. You’d better believe I’d fight over this issue if it came down to a matter of what was going to be taught in my local school. But I couldn’t possibly care less what the guy who lives in the White House thinks, unless he tries to impose it on the country.

When I hear the word “bet” I start thinking of laying down odds and stealing someone’s cash! But in this case I’ll assume Rod was being rhetorical. But let’s review the numbers, shall we?
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CATEGORIZED UNDER: Creationism
MORE ABOUT: Creationism

Skydiving + cats = ?

By Razib Khan | November 18, 2012 2:48 am
CATEGORIZED UNDER: Culture
MORE ABOUT: Cats

The archaeologist, James Fallows, and Neandertals

By Razib Khan | November 17, 2012 10:10 pm

A month ago I posted Don’t trust an archaeologist about genetics, don’t trust a geneticist about archaeology, in response to James Fallows at At 5% Neanderthal, You Are an Outlier. Fallows has now put up a follow up, The Neanderthal Defense Committee Swings Into Action, where he links to my response post. This prompted the original archaeologist in question to reach out to me via email. I am posting the letter, with their permission, below.

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CATEGORIZED UNDER: Anthroplogy, Genetics
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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!
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