Endings & beginnings

By Razib Khan | November 30, 2013 10:32 pm

Update: Comments enabled now!

Until further notice this is my last post as a blogger at Discover Magazine. This shouldn’t impact regular readers. As always you can follow me by going to:

My feed, http://feeds.feedburner.com/RazibKhansTotalFeed

My Twitter, https://twitter.com/razibkhan

And of course, my website, http://www.razib.com

From December 1st, 2013, I will be blogging at Ron Unz’s new website, The Unz Review, at a familar subdomain http://www.unz.com/gnxp (feed, http://www.unz.com/gnxp/feed/).

I’m excited to explore this new opportunity. Ron is still nailing down the details of look, style, and functionality, so expect some changes on my Gene Expression sub-site. To make a long story short Ron wanted to beef up his science coverage, and I was amenable. At least when it comes to my particular bailiwick. Ron has merged my archives from the old Gene Expression website with the content generated at ScienceBlogs and Discover, so no matter where I go, or if I stop blogging due to other obligations, those archives will remain as a coherent whole.

I want to emphasize that my time at Discover was incredible. I want to give special thanks to Tasha Eichenseher, Amos Zeeberg, and Sheril Kirshenbaum. As it happens none of these individuals are associated with Discover at this point (Tasha is leaving as well), but they were instrumental in allowing me to either be here (in Sheril’s case) or focus on writing (in Tasha and Amos’ case). I assume you’ll be somewhat surprised that I mention Sheril, but I feel like I have to give special thanks to her because I’m 99% sure that it was her “good word” which allowed me to catch the eye of an outfit as respectable as Discover. Unlike a blogger as writerly as Ed Yong, or Sheril herself, I’ve always been more data nerd-cum-verbal pugilist. So this leads me to praise the great management skills of the two web editors I’ve had while being a blogger at Discover. They’ve let “Razib be Razib,” by and large letting me do my thing (though yes, in the interests of professionalism I’ve moved most of the more “direct” verbal volleys to Twitter). I really can’t thank anyone else at Discover because I barely knew they existed, which, in light of recent events, seems like a good thing. Overall I give Discover a good grade in terms of understanding how blogging should be run, with a light hand. This, despite the fact that I often put up posts which rubbed many “right-thinking-people” the wrong way, and scoured the comment threads acidly.

There’s really not much else to say. Aside from a new domain, don’t expect many changes.

CATEGORIZED UNDER: Administration
MORE ABOUT: Farewell post

The total information world

By Razib Khan | November 28, 2013 3:46 pm

Credit: Cryteria

Credit: Cryteria

Happy Thanksgiving (if you are an American)!

It’s been a busy few days in the world of personal genomics. By coincidence I have a coauthored comment in Genome Biology out, Rumors of the death of consumer genomics are greatly exaggerated (it was written and submitted a while back). If you haven’t, please read the FDA’s letter, and 23andMe’s response, as much as there is one right now. Since Slate ran my piece on Monday a lot of people have offered smart, and more well informed, takes. On the one hand you have someone like Alex Tabarrok, with “Our DNA, Our Selves”, which is close to a libertarian cri de coeur. Then you have cases like Christine Gorman, “FDA Was Right to Block 23andMe”. It will be no surprise that I am much closer to Tabarrok than I am to Gorman (she doesn’t even seem to be aware that 23andMe offers a genotyping, not sequencing, service, though fuzziness on the details doesn’t discourage strong opinions from her). An interesting aspect is that many who are not deeply in the technical weeds of the issue are exhibiting politicized responses. I’ve noticed this on Facebook, where some seem to think that 23andMe and the Tea Party have something to do with each other, and the Obama administration and the FDA are basically stand-ins. In other words, some liberals are seeing this dispute as one of those attempts to evade government regulation, something they support on prior grounds. Though Tabarrok is more well informed than the average person (his wife is a biologist), there are others from the right-wing who are taking 23andMe’s side on normative grounds as well. Ultimately I’m not interested in this this argument, because it’s not going to have any significant lasting power. No one will remember in 20 years. As I implied in my Slate piece 23andMe the company now is less interesting than personal genomics the industry sector in the future. Over the long term I’m optimistic that it will evolve into a field which impacts our lives broadly. Nothing the United States government can do will change that.

Yet tunneling down to the level of 23andMe’s specific issues with the regulatory process, there is the reality that it has to deal with the US government and the FDA, no matter what the details of its science are. It’s a profit-making firm. Matt Herper has a judicious take on this, 23andStupid: Is 23andMe Self-Destructing? I don’t have any “inside” information, so I’m not going to offer the hypothesis that this is part of some grand master plan by Anne Wojcicki. I hope it is, but that’s because I want 23andMe to continue to subsidize genotyping services (I’ve heard that though 23andMe owns the machines, the typing is done by LabCorp. And last I checked the $99 upfront cost is a major loss leader; they’re paying you to get typed). I’m afraid that they goofed here, and miscalculated. As I said above, it won’t make a major difference in the long run, but I have many friends who were waiting until this Christmas to purchase kits from 23andMe.

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CATEGORIZED UNDER: Personal Genomics
MORE ABOUT: Personal genomics

The FDA and 23andMe

By Razib Khan | November 25, 2013 12:30 pm

napFirst, download your 23andMe raw results now if you have them. If you don’t know what’s going on, the FDA has finally started to move aggressively against the firm. Unfortunately this is not surprising, as this was foreshadowed years ago. And, 23andMe has been moving aggressively to emphasize its medical, as opposed to genealogical, services over the past year. But this isn’t the story of one firm. This is the story of government response to very important structural shifts occurring in the medical delivery system of the United States. The government could potentially bankrupt 23andMe, but taking a step back that would still be like the RIAA managing to take down Napster. The information is coming, and if there’s one thing that can overpower state planning it is consumer demand. Unless the US government wants to ban their citizens from receiving their own genetic data they’re just putting off the inevitable outsourcing of various interpretation services. Engagement would probably be the better long term bet, but I don’t see that happening.

CATEGORIZED UNDER: Personal Genomics
MORE ABOUT: Personal genomics

Open Thread, 11/24/13

By Razib Khan | November 24, 2013 4:21 am

23andMe

One of the stranger call-ins on my interview with Kathleen Dunn last month was when a woman who proudly declared that she was a math major in college asserted that 23andMe had told her she wasn’t at risk for many diseases which now in her 60s she had developed. I didn’t want to be too pointed about it, but if you are in your 60s you are at risk for developing many illnesses no matter what your “genetic risk.” This is clear from 23andMe’s statistics, which display high baseline risks for many common diseases. From reading comments on 23andMe discussion forums it seems that perceived false negatives are going to be a much bigger issue than false positives over the long run. If the tests are “wrong” in a direction which leaves you in a better state than predicted you might feel like you’ve dodged a bullet. On other hand if the tests are “wrong” in a direction which gave you false comfort, or add insult to injury when you’ve developed a debilitating disease, then you feel much more burned.

I don’t really recommend blogs too much anymore. But please check out The Stage and Social Evolution Forum.

CATEGORIZED UNDER: Blog
MORE ABOUT: Open Thread

Our ancestors are part us…or the other way around?

By Razib Khan | November 20, 2013 1:34 pm

Keeping a close watch on media representations of the new Nature paper on the ancient Siberian genome. Here’s The New York Times, 24,000-Year-Old Body Is Kin to Both Europeans and American Indians. I don’t have a problem with the title, but the roll-out isn’t totally accurate in what it will connote to the audience in my opinion:

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CATEGORIZED UNDER: Archaeology
MORE ABOUT: Siberian boy

The long First Age of mankind

By Razib Khan | November 20, 2013 12:22 pm

OldSiberian

“What it begins to suggest is that we’re looking at a ‘Lord of the Rings’-type world – that there were many hominid populations,” says Mark Thomas, an evolutionary geneticist at University College London who was at the meeting but was not involved in the work.

Mark Thomas, as reported by Nature

This is in reference to the ancient DNA meeting where David Reich reported that the Denisovans, an exotic archaic population which contributed ~5-10 percent of the ancestry of Papuans, was itself a synthesis of Neandertals and a mysterious group currently unknown. This is not surprising, as the broad outlines of these results were presented at ASHG 2012, though no doubt they’re moving closer to publication. But for this post I want to shift the focus to a different time and place, after the ancient admixture with archaic lineages, and to the reticulation present within our own.

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CATEGORIZED UNDER: Anthroplogy, Archaeology
MORE ABOUT: Siberians

Open Thread, 11/17/2013

By Razib Khan | November 17, 2013 7:22 pm

Finished J. P. Mallory’s The Origins of the Irish. Good book, but it was as illuminating as to the origins of the Irish as Danel Dennett’s Consciousness Explained was in explaining consciousness.

CATEGORIZED UNDER: Administration
MORE ABOUT: Open Thread

The color of life as a coincidence

By Razib Khan | November 13, 2013 2:35 am

Credit: Eric Hunt

Credit: Eric Hunt

I do love me some sprouts! Greens, bitters, strong flavors of all sorts. I’ve always been like this. Some of this is surely environment. My family comes from a part of South Asia known for its love of bracing and bold sensation. But perhaps I was born this way? There’s a fair amount of evidence that taste has a substantial genetic component. This does not mean genes determine what one tastes, but it certainly opens the door for passive gene-environment correlations. If you do not find a flavor offensive, you are much more likely to explore it depths, and cultivate your palette.

220px-Durio_kutej_F_070203_ime

Dost thou dare?
Credit: W.A. Djatmiko

And of course I’m not the only one with a deep interest in such questions. With the marginal income available to us many Americans have become “foodies,” searching for flavor bursts and novelties which their ancestors might never have been able to comprehend. More deeply in a philosophical sense the question of qualia reemerges if there is a predictable degree of inter-subjectivity in taste perception (OK, qualia is always there, though scientific sorts tend to view it as intractable in a fundamental sense).

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Is that white supremacist part black?

By Razib Khan | November 12, 2013 11:45 am

Goebbels, Nordic superman! Credit: Bundesarchiv, Bild

Goebbels, Nordic superman! 
Credit:, Bundesarchiv, Bild

Many of you probably know about Dave Chappelle’s black white supremacist sketch (NSFW video!), though fewer are aware of Leo Felton, a white supremacist (ex, after he was outed) with a black father (a less tragic outcome than Dan Burros, the Jewish American Nazi). I know, these sound like they’re out of South Park episodes, though the last two are actually not fictional. But now the media is exploding with news that a DNA test has suggested that a notorious white supremacist is 14 percent black. The same one who was recently profiled in The New York Times promoting a separatist racial vision in a small North Dakota town. I’ll be honest and admit that I don’t think that these results will hold up. (though personally I would think it was rich and very funny if they did, just like everyone else).

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CATEGORIZED UNDER: Race
MORE ABOUT: Craig Cobb, Race

Isn’t he special!

By Razib Khan | November 12, 2013 5:50 am

Credit: Marrabbio2

Credit: Marrabbio2

There’s a nice letter in Nature right now with an understated title, Mating advantage for rare males in wild guppy populations. But if you dig deeper you see some moderately grand claims being made. The key issue is that the authors seem to be implying that negative frequency dependent selection (NFDS) is a major factor in maintaining genetic diversity in populations. A reductio ad absurdum of the problem might be to ask why a superior and ideally fit morph does not dominate the whole planet? A more elaborated question lay at the heart of Charles Darwin’s The Origin of Species. Fundamentally: why diversity? There have been many answers posited (e.g., see W. D. Hamilton’s ideas in regards to sex, Narrow Roads of Gene Land). We needn’t try to tackle the whole problem here, no matter what needs to be written in grant applications. Guppies are sufficient and interesting in and of themselves.

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CATEGORIZED UNDER: Ecological genetics

bioRxiv is here

By Razib Khan | November 12, 2013 3:45 am

bioRxivFor years many in the biological sciences community have been jealous of the exist of arXiv. This preprint server allows researchers to distribute their work widely to all comers. On occasion when when there have been debates about mimicking arXiv for biology there has been skepticism about the nature of the outcomes (my own rejoinder is that fields where a preprint culture is the norm, such as economics and physics, don’t seem to be doing badly). Now we’ll see if the end is nigh in biological science due to preprints; bioRxiv is live (sponsored by CSHL). The first paper, The Population Genetic Signature of Polygenic Local Adaptation. There’s not much up yet, but there will be.

CATEGORIZED UNDER: Science
MORE ABOUT: bioRxiv

Vaccination, and social information networks

By Razib Khan | November 12, 2013 3:34 am

Preventable

If you have not read Julia Ioffe’s story about getting whooping cough at the age of 31 (also see follow up), you might want to. Here’s some further context, Vaccine Refusals Fueled California’s Whooping Cough Epidemic. This topic has been covered and dissected in great detail by many writers and scientists, so I won’t repeat what you already know in regards to herd immunity. There’s no point in preaching to the choir.

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CATEGORIZED UNDER: Medicine

Open Thread, 11/10/2013

By Razib Khan | November 10, 2013 1:35 pm

Change is the only constant.

CATEGORIZED UNDER: Administration
MORE ABOUT: Open Thread

Selection happens; but where, when, and why?

By Razib Khan | November 8, 2013 3:49 am
Distribution of SLC452 variation at SNP rs1426654. Credit, HGDP Browser

Distribution of SLC452 variation at SNP rs1426654. Credit, HGDP Browser

Nina Davuluri, Miss America 2014, Credit: Andy Jones

Nina Davuluri, Miss America 2014, Credit: Andy Jones

One of the secondary issues which cropped up with Nina Davuluri winning Miss America is that it seems implausible that someone with her complexion would be able to win any Indian beauty contest. A quick skim of Google images “Miss India” will make clear the reality that I’m alluding to. The Indian beauty ideal, especially for females, is skewed to the lighter end of the complexion distribution of native South Asians. Nina Davuluri herself is not particularly dark skinned if you compared her to the average South Asian; in fact she is likely at the median. But it would be surprising to see a woman who looks like her held up as conventionally beautiful in the mainstream Indian media. When I’ve pointed this peculiar aspect out to Indians* some of them of will submit that there are dark skinned female celebrities, but when I look up the actresses in question they are invariably not very dark skinned, though perhaps by comparison to what is the norm in that industry they may be. But whatever the cultural reality is, the fraught relationship of color variation to aesthetic variation prompts us to ask, why are South Asians so diverse in their complexions in the first place? A new paper in PLoS Genetics, The Light Skin Allele of SLC24A5 in South Asians and Europeans Shares Identity by Descent, explores this genetic question in depth.

Much of the low hanging fruit in this area was picked years ago. A few large effect genetic variants which are known to be polymorphic across many populations in Western Eurasia segregate within South Asian populations. What this means in plainer language is that a few genes which cause major changes in phenotype are floating around in alternative flavors even within families among people of Indian subcontinental origin. Ergo, you can see huge differences between full siblings in complexion (African Americans, as an admixed population, are analogous). While loss of pigmentation in eastern and western Eurasia seems to be a case of convergent evolution (different mutations in overlapping sets of genes), the H. sapiens sapiens ancestral condition of darker skin is well conserved from Melanesia to Africa.

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CATEGORIZED UNDER: Anthroplogy, Genetics, Genomics
MORE ABOUT: Pigmentation

The future always advances

By Razib Khan | November 7, 2013 2:56 am

The last week has seen a lot of chatter about the slapping down of the diagnostic patent by Sequenom, Judge Invalidates Patent for a Down Syndrome Test:

A federal judge has invalidated the central patent underlying a noninvasive method of detecting Down syndrome in fetuses without the risk of inducing a miscarriage.

The ruling is a blow to Sequenom, a California company that introduced the first such noninvasive test in 2011 and has been trying to lock out competitors in a fast-growing market by claiming they infringe on the patent.

Sequenom’s stock fell 23 percent on Thursday, to $1.92.

The judge, Susan Illston of the United States District Court in Northern California, issued a ruling on Wednesday that the patent was invalid because it covered a natural phenomenon — the presence of DNA from the fetus in the mother’s blood.

The existence of intellectual property is a utilitarian one. That is, these are institutions which are meant to further the cause of creativity and innovation. Is there going to be an abandonment in this domain of the push toward technological innovation? Coincidentally in the last week of October Sequenom put out a press release which heralded some advances in its panel:

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CATEGORIZED UNDER: Personal Genomics

Open Thread, 11/3/2013

By Razib Khan | November 3, 2013 12:34 pm

Origins-of-the-Irish1After reading Ancestral Journeys, I decided to get J. P. Mallory’s The Origins of the Irish. A bit on the academic side for some, but definitely a good dive into the literature. Mallory is well aware of the latest genetic research, so this is as up-to-date as it gets. It’s a good case study in how multidisciplinary prehistoric studies should be done.

As I’ve suggested earlier prehistory looks to be a good deal more complex than we had previous thought, so expanding beyond single methodological perspectives is probably essential if we really care about truth.

In other news, a short piece in The New York Times refers to Salafis as ‘ultraconservative.’ I think this misleads most people about the nature of Salafism: it is a radical utopian system which recently arose out of Islam’s confrontation with Western derived modernity. It isn’t conserving anything. This aspect of Salafism explains why Saudi Arabia condones the bulldozing of Muhammed’s tomb and celebrates modern monumental architecture in Islam’s holy city.

CATEGORIZED UNDER: Culture
MORE ABOUT: Open Thread

The human genetic casserole

By Razib Khan | October 30, 2013 9:48 pm

HotdishI haven’t said much about this article in Science, Ancient DNA Links Native Americans With Europe, because it would be an understatement to say I’m digesting it. I would offer up a caution that using terms like “Europeans” and “East Asians” for populations which flourished ~25,000 years ago might be misleading. We are used to thinking of genetic distance in terms of space, but time is also a dimension to consider. Populations even without admixture or gene flow will have drifted in allele frequencies over so many generations.

But I have to admit that it seems more and more likely that most extant modern populations are combinations of lineages which diverged very early after the “Out of Africa” migration. We see this clearly with South Asians, and now Europeans and Native Americans. The Reich lab has also found evidence of admixture in in Australians. The closer we look, the more amalgamation we see between disparate lineages. Using the elements of the present to reconstruct the patterns of the past is going to be a more daunting task than most would have guessed.

CATEGORIZED UNDER: Archaeology
MORE ABOUT: Human History

Our forefathers were fierce & our foremothers were faithful

By Razib Khan | October 27, 2013 8:51 pm

Credit: Chineeb

Credit: Chineeb

One of the peculiarities of human historical genetics is that people can simultaneously accept the existence of aggressive polygynous males such as Genghis Khan, and promiscuous females who give rise to the idea that 1 out of 10 children have an incorrect assigned paternity. I’ve mentioned the cuckoldry myth before. It is a common evolutionary myth; I’ve heard many biologists quote the 1 out of 10 number, and have often made myself obnoxious by pointing to the contradictory literature in this area. This isn’t to say that cuckoldry doesn’t exist. There’s certainly an evolutionary reason so many males engage in “mate guarding.” But you don’t need a high frequency of a trait to allow it to be selectively constrained. If it’s deleterious, then it will be driven down in frequency rather quickly. Whenever you get outbreaks of males who are sanguine about providing resources for offspring who are not their biological issue, natural selection will kick in and guarantee that this generous spirit toward their cheating partners and the delinquent cads does not persist.

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CATEGORIZED UNDER: Evolution
MORE ABOUT: Cuckoldry

Open Thread, 10/27/2013

By Razib Khan | October 27, 2013 5:33 am

I’ll be on the Kathleen Dunn Show on Monday, 2 to 3 PM Central Standard Time. You’ll be able to listen to the show after it airs on the website. It will be about my piece in Slate.

AJjacketI recently read Ancestral Journeys: The Peopling of Europe from the First Venturers to the Vikings by Jean Manco. You can find more information at her website, but I pretty much would recommend this book to all my non-scientist readers. I’d recommend it to many of the scientists too, if you are rather weak on archaeology, because that’s where Manco’s knowledge is really impressive. It’s not a perfect book, and I don’t agree with all the details, but it’s a very detailed, dense, and fast read.

There was a question below in regards to the Fast Company profile of 23andMe and what they’re trying to do. A major ethical issue brought up is whether it is acceptable to type children and disclose possible disease risk later on in life. As an extreme case, what if you find out that your child is going to develop a life threatening disease by the time they’re 40? My own perspective as a parent is that I’d like to know, and I’d probably want to tell my child as soon as I think they can handle it. The reason is simple: you base your life decisions on various aspects of life expectancy. People put things off, or forgo consumption, all the time.

CATEGORIZED UNDER: Culture
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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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