Archive for May, 2011

Let a thousand Thiel fellows bloom!

By Razib Khan | May 25, 2011 11:34 pm

Now that the Thiel Fellows have been announced the media has been pouncing. If you don’t know, Peter Thiel is giving a bunch of bright-young-things some money to drop out of college (or not go to college). Here are the details:

As the first members of the 20 Under 20 Thiel Fellowship, the Fellows will pursue innovative scientific and technical projects, learn entrepreneurship, and begin to build the technology companies of tomorrow. During their two-year tenure, each Fellow will receive $100,000 from the Thiel Foundation as well as mentorship from the Foundation’s network of tech entrepreneurs and innovators. The project areas for this class of fellows include biotech, career development, economics and finance, education, energy, information technology, mobility, robotics, and space.

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CATEGORIZED UNDER: Culture, Psychology

AIBioTech Sports X Factor is not worth the money

By Razib Khan | May 25, 2011 4:38 pm

Last week I posted Don’t buy AIBioTech Sports X Factor kit! I laid out my rationale explicitly:

I’ve been pretty vocal about the impending specter of genetic paternalism in relation to personal genomics, which I believe to be futile in the long term, and likely to squelch innovation in the United States in the short term. Like any new product category there’s a lot of hype and confusion in the area of personal genomics, but I think it’s important that we allow some mistakes and misfires to occur. Innovation and creativity isn’t failure-free.

With that said, I also think it is incumbent upon the personal genomics community, if there is such a thing, to “police” the flow of information. I have seen references in the media to a new personal genomics kit, Sports X Factor, selling for $180, from AIBioTech. My initial intent was to ignore this, as there is real science and tech to be covered. This is just another case of a biotech firm trying to leverage public confusion and gullibility into revenue. But if I think such a thing, I should make my opinion known, shouldn’t I?….

My intent was to come up high on Google searches for the firm and product which they’re selling. I don’t want to drive the firm out of business or anything like that, and I’m not a lawyer so I don’t know if I think what they are selling with Sports X Factor kit is technically fraudulent (though I don’t think it is). But I wouldn’t recommend this to my friends. $180 is not a trivial sum in my world. Unlike some I don’t think genetic information is horrible or incredibly precious information which only “professionals” should have access to. I just don’t think that the price is right. Too many of the media stories have a tendency to focus on the terror of people finding out about their genetic predispositions, but I think the truth of Sports X Factor kit is more banal: it is just not a product with results worth the money you are shelling out. Standard economics, not bioethics.

Today I got this strange comment from someone who works for AIBioTech, the firm which produces Sports X Factor, defending the product:

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CATEGORIZED UNDER: Personal Genomics

The rise of real meat factories

By Razib Khan | May 25, 2011 11:17 am

I’ve been taking about ‘meat things’ for nearly 10 years, so I was really excited by the new Michael Specter piece in The New Yorker about artificially grown meat, Test-tube Burgers. You can’t read most of it online, so I want to copy this small section:

…One study, completed last year by researchers at Oxford and the University of Amsterdam, reported that the production of cultured meat could consume roughly half the energy and occupy just two percent of the land now devoted to the world’s meat industry….

I say real factories because we are all aware I assume by this point of the nature of ‘factory farming’. But mass production of animal stock is an ad hoc kludge. Domesticated animals have been bred for meat production, but they remain organisms with all the range of activities and ends which the term ‘organism’ entails. Raising raw tissue in cultures may seem ‘yucky,’ a point Specter covers in assessing the reaction of some environmentalists and animal-rights activists who don’t seem as excited by the shift from conventional livestock raising to growing tissue as one would expect if they ran the numbers, but it is probably inevitable if it is feasible. The article makes the point that most of the focus on this area seems to be in the Netherlands, but thank god the Chinese are paying attention to this!

CATEGORIZED UNDER: Biology
MORE ABOUT: Lab Meat, Meat Things

Biology to the masses

By Razib Khan | May 25, 2011 9:17 am

Josh Roseneau, when he’s taking time off from the evolution-creation wars, is poking around his own genome. Some sage advice:

On DNA Day, 23 and Me had a sale on their personal genomics service. They’d do their standard scan of your genome for free, as long as you paid for a year’s worth of their online subscription service.

For the price (nearly free up front, and a modest cost for the online community provided), my wife and I jumped on the deal. Since I got the results back two weeks ago, I’ve been exploring not only the services and information provided by 23 and Me, but the various other tools that individuals have started producing to help analyze and investigate this insight into my ubiquitous but invisible DNA.

My genome, for instance, revealed a genetic predisposition towards late-onset Alzheimers. The odds of getting Alzheimers are still quite small, but elevated because of this particular mutation to the APOE4 gene. This wasn’t a total surprise, given my family history, and as a healthy, young guy with a background in biology and biostatistics, it wasn’t hard for me to put that information into a context and move on. Down the road, I’ll probably keep an eye out for new research on Alzheimers medicines and look into tools for early detection, but I’m not going to kill myself if I forget my keys. (Thanks to the federal Genetic Information Nondiscrimination Act and the Affordable Care Act’s prohibition on “pre-existing conditions” – not to mention the inherent uncertainties in translating this genetic result to a specific outcome – I’m not especially worried about discussing that result in public)

We need to demystify DNA. It’s pretty obvious to me that people perceive genetics to be in the domain of magic, when in reality it manifests itself in the banal realities of correlations within the family, which we’re intuitively aware of. But Josh’s post is more than just personal, he reviews the book Biopunk: DIY Scientists Hack the Software of Life:

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CATEGORIZED UNDER: Biology, Biotech, Personal Genomics

Against the "Thinking Machines"

By Razib Khan | May 25, 2011 1:08 am

Steve Hsu points me to this essay which discusses ‘high-frequency trading’, How to Make Money in Microseconds. This might elicit a takfir from my friends at the Singularity Institute, but that piece makes me less ill-disposed to a Butlerian Jihad. A lot of this stuff on the margins and frontiers of finance reminds me of intragenomic conflict or cancer; entities and phenomena which are generally proposed to serve as means toward particular ends develop their own internal logic and ends through a co-evolutionary “arms race” in their own domains.

CATEGORIZED UNDER: Economics
MORE ABOUT: Finance

Is the University of California putting politics before science?

By Razib Khan | May 25, 2011 12:54 am

Kennewick Man produced a cottage industry of journalism ~10 years ago, thanks to the political controversy around the science. Today the stakes are different. Consider this from John Hawks, “Agriculture, population expansion and mtDNA variation”:

I am less sanguine about their results for Europe. They show a gradual period of growth associated in time with the Younger Dryas (around 12,000 years ago), which could make sense in the archaeology. But I am not convinced that the “European” haplogroups here are really European to that time depth. We know that the Neolithic and post-Neolithic saw some large-scale shifts in the frequencies of mtDNA haplogroups in Central and Western Europe. Some Upper Paleolithic Europeans probably contributed mtDNA to this later population, but I have no confidence that the proportion was great enough to accurately infer the demography of that pre-Neolithic population. (This is also a problem with the current paper in Current Anthropology by Peter Rowley-Conwy. I’ll discuss this sometime soon.)

The next frontier in reconstructing the population history of Europe will be ancient DNA. A good sample of Neolithic and pre-Neolithic whole mtDNA genomes would settle this question and allow inferences about the kind of demographic recovery Europe underwent after the Last Glacial Maximum….

An open letter to Science highlights the same issue with Native Americans, Unexamined Bodies of Evidence:

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CATEGORIZED UNDER: Anthroplogy
MORE ABOUT: paleontology

Iran, Iraq, Syria, Turkey

By Razib Khan | May 24, 2011 10:38 am

Since most international migration is apparently between “developing nations”, I thought the Iran-Iraq-Turkey-Syria border would be interesting to look at in terms of differences in economic and social indices.

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CATEGORIZED UNDER: Data Analysis

Giant enjoying eating humans

By Razib Khan | May 23, 2011 11:24 am

(the baby is laughing slow-mo)

CATEGORIZED UNDER: Blog
MORE ABOUT: Baby

Proper methods and false results

By Razib Khan | May 23, 2011 12:07 am

ResearchBlogging.orgThe Pith: Honorable intent and punctilious adherence to proper form and method does not guarantee a set of results which flesh out a genuine phenomenon. Much of science is tragic.

Most of the time I point to and review papers on this weblog which excite me. But in the interests of “balance” and dampening the bias toward material I find interesting and salient I thought it would be interesting to look at a paper which I thought wasn’t too interesting. It’s in the Journal of Human Genetics, part of the Nature Publishing Group empire. Also, it is open access, so you can read it yourself and make your own individual judgments.

The Soliga, an isolated tribe from Southern India: genetic diversity and phylogenetic affinities:

India’s role in the dispersal of modern humans can be explored by investigating its oldest inhabitants: the tribal people. The Soliga people of the Biligiri Rangana Hills, a tribal community in Southern India, could be among the country’s first settlers. This forest-bound, Dravidian speaking group, lives isolated, practicing subsistence-level agriculture under primitive conditions. The aim of this study is to examine the phylogenetic relationships of the Soligas in relation to 29 worldwide, geographically targeted, reference populations. For this purpose, we employed a battery of 15 hypervariable autosomal short tandem repeat loci as markers. The Soliga tribe was found to be remarkably different from other Indian populations including other southern Dravidian-speaking tribes. In contrast, the Soliga people exhibited genetic affinity to two Australian aboriginal populations. This genetic similarity could be attributed to the ‘Out of Africa’ migratory wave(s) along the southern coast of India that eventually reached Australia. Alternatively, the observed genetic affinity may be explained by more recent migrations from the Indian subcontinent into Australia.

To be blunt about it I think the researchers here just randomly stumbled onto a weird result which happened to align with some plausible preconceptions. This happens all the time, and is responsible for the unfortunate confirmation bias which plagues science. Researchers know very well what the expected results are, and may unconsciously or consciously sift through their data for a set of facts which align well with their theoretical preconceptions. In this case it isn’t quite so bald, as there are no orthodoxies, but a set of alternative hypotheses which go back a century or so.

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CATEGORIZED UNDER: Anthroplogy, Genetics, Genomics

1493: Uncovering the New World Columbus Created

By Razib Khan | May 23, 2011 12:05 am

For obvious reasons I don’t usually post about material I haven’t read, but Tyler Cowen points me to the fact that Charles C. Mann has a new book coming out this summer. If you haven’t, I would highly recommend his previous book, 1491: New Revelations of the Americas Before Columbus. I think it is correct that Mann probably skewed his narrative a bit too much to the revisionist side, but it is a genuinely revelatory work.* I was aware of the broad outlines already, so it wasn’t surprising, but he marshals the data in a fascinating and engaging manner. The new book is apparently a sequel of sorts, 1493: Uncovering the New World Columbus Created. Cowen says “I am spellbound reading it, it will be one of the best books of this year, and, although I know this area somewhat, I am learning fascinating information on literally every page.” I suspect that what occurred in the New World after 1492 is actually an amplified version of what occurred across much of the Old World over the past 10,000 years, with the rise of massive agglomerations of humanity due to agriculture.

In other news, malnourished children apparently had mortality rates of 40% due to measles!.

* There is a lot of politics you have to navigate on this topic, from all directions.

CATEGORIZED UNDER: Anthroplogy

Camping's Wager

By Razib Khan | May 22, 2011 3:29 pm

I’ve had to deal with vulgar* expositions of Pascal’s Wager my whole life from friends and family. The basic logic is “you have nothing to lose and everything to gain!” There are many ways to critique this “argument”, but the bizarre media circus around Harold Camping’s prediction of apocalypse illustrates an extreme case of one the major issues with the wager: people turned their lives upside down based on their sincere belief. If they were right, they would be “Raptured.” If they were wrong, what did they have to lose? Well, it turns out a lot. Their life savings, their jobs, their self-respect. It reminds me of the logics which you encountered after the Branch Dravidians fiasco. Some members of this cult were faced with the choice: follow the Messiah, or follow the false Messiah. They struggled with the possibility that if they turned their back on David Koresh they were turning their back on the Messiah. But of course this really wasn’t a 50/50 proposition. The risks, as we now know, of continuing to follow Davis Koresh were actually rather high. Belief was not without cost.

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CATEGORIZED UNDER: Religion

Facebook finally plateaus in 2011!

By Razib Khan | May 22, 2011 3:02 pm

I’ve been using Google Trends to track the rise of Facebook and the fall of MySpace for years. To my surprise Facebook has kept ascending up the Google search traffic for years past when I thought it would hit diminishing marginal returns of mind-share (I assumed it would level off in 2008). But it looks like it has finally reached a “mature” phase in 2011. First, let’s compare Facebook, Myspace, and Google in 2008. The following is search traffic on Google for the whole world….

Now for the past 12 months….

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CATEGORIZED UNDER: Technology
MORE ABOUT: Facebook

Kissing and cancer

By Razib Khan | May 21, 2011 11:39 pm

I recently listened to Paul Ewald talk about how a lot of cancer is due to infection on the radio show To the Best of Our Knowledge. That wasn’t too surprising, Ewald has been making the case for a connection between infection and lots of diseases for a while. What jumped out at me is his claim that kissing can spread some of the viruses. Here’s something he told Discover a few years back:

D: How do we get infected with these dangerous pathogens?

PE: Two of the most powerful examples are sexual transmission and kissing transmission, and by that I mean juicy kissing, not just a peck on the cheek. If you think about these modes of transmission, in which it might be a decade before a person has another partner, you realize that rapidly replicating is not very valuable—the winning strategy for the microbe would be to keep a low profile, requiring persistent infections for years. So we would expect that disproportionately, the sexually transmitted pathogens would be involved in causing cancer, or chronic diseases in general. You can test this. Just look at the pathogens that are accepted as causing cancer—Epstein-Barr virus, Kaposi’s sarcoma–associated herpesvirus, human T lymphotropic virus 1—and find out whether they’re transmitted this way. They almost all are. A random sample would yield maybe 15 to 20 percent of pathogens associated with cancer being sexually transmitted, yet the figure is almost 100 percent. When you look at viruses alone, it is 100 percent.

If a lot of kissing and number of sexual partners is predictive of risk of cancer, my immediate thought is that this naturally explains a lot of the cancer that  runs in families. Families can pass on genes and cultural norms which would favor or disfavor certain behaviors.

CATEGORIZED UNDER: Health
MORE ABOUT: Cancer, Disease

A map of genome blogging participants

By Razib Khan | May 21, 2011 12:02 pm

Both Eurogenes and Harappa now have map interfaces where you can drop in the origin of your location if you’re a participant. If you have submitted your data you should add your information in. We’re at a point where data is relatively plentiful, at least before the tsunami of whole genomes, so visualization and representation is of the essence.

Here’s HAP:

CATEGORIZED UNDER: Genomics, Personal Genomics
MORE ABOUT: Genome Blogging

Where people use their information appliances

By Razib Khan | May 21, 2011 11:58 am

In the U.S., Tablets are TV Buddies while eReaders Make Great Bedfellows:

Fast Company has a write up of the survey, concluding:

What can we learn from this data? Smart gadgets are pervasive. They’re already changing long-held habits, and doing so very fast. If you’re a content creator on almost any platform, you’ll need to be aware of how your audience’s attention is changing, and if you’re a marketer then think of the plethora of new ways to appeal to the public through their emerging habits.

One thing I notice about reading on the Kindle is that I’m more likely to finish books I begin front-to-back, because the device keeps my place. Flipping through the “book” is actually not as fluid, so in some ways I guess the Kindle is enforcing a retro-traditional reading style on me.

CATEGORIZED UNDER: Technology

Adam was African, but perhaps barely

By Razib Khan | May 20, 2011 11:36 pm

The figure to the left comes from a short paper in The American Journal of Human Genetics, A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa. The paper is interesting because of two factors: 1) they sequenced more of the Y chromosome 2) their African data set of individuals was very large, in excess of 2,000. The weird thing about the results is that it upends one of the truisms in human phylogenetics: that African Pygmies and Khoisan are basal to other human lineages. By this, I mean that they “split off” first (this is why people say these are the “oldest” human populations). This is not what these researchers found. Rather, the basal Y chromosomal haplogroups were concentrated in Central West Africa and Northwest Africa! The map below shows the distributions of the two most divergent Y chromosomal lineages, red being the outgroup, and green being the second most divergent:

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Don't buy AIBioTech Sports X Factor kit!

By Razib Khan | May 20, 2011 11:07 pm

I’ve been pretty vocal about the impending specter of genetic paternalism in relation to personal genomics, which I believe to be futile in the long term, and likely to squelch innovation in the United States in the short term. Like any new product category there’s a lot of hype and confusion in the area of personal genomics, but I think it’s important that we allow some mistakes and misfires to occur. Innovation and creativity isn’t failure-free.

With that said, I also think it is incumbent upon the personal genomics community, if there is such a thing, to “police” the flow of information. I have seen references in the media to a new personal genomics kit, Sports X Factor, selling for $180, from AIBioTech. My initial intent was to ignore this, as there is real science and tech to be covered. This is just another case of a biotech firm trying to leverage public confusion and gullibility into revenue. But if I think such a thing, I should make my opinion known, shouldn’t I?

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CATEGORIZED UNDER: Genetics, Genomics, Personal Genomics

Friday Fluff – May 20th, 2011

By Razib Khan | May 20, 2011 5:19 pm

FF3

1) First, a post from the past: Pentecostals are stupid? Unitarians are smart?.

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CATEGORIZED UNDER: Blog
MORE ABOUT: Friday Fluff

Organismic complexity is just duct tape

By Razib Khan | May 20, 2011 12:04 am

ResearchBlogging.orgThe Pith: Biological complexity may be a particular evolutionary path taken due to to random acts of nature, not because there is a selective advantage to complexity.

The title above basically describes the message of evolutionary biologist Mike Lynch from what I can gather. His basic argument is outlined in long form in The Origins of Genome Architecture, though the outline of the thesis is evident over 10 years back (see Preservation of Duplicate Genes by Complementary, Degenerative Mutations). Verbally I think the easiest way to explain Lynch’s framework is that in species with small effective population sizes the creativity of stochastic forces in generating non-adaptive structure and complexity tends to overwhelm the power of natural selection to prune this tendency toward baroque. I reviewed a paper last year which argued that Lynch’s observation of an inverse relation between effective population and genome size was an artifact, that once you controlled for phylogenetic history it disappeared. Suffice it to say this is an area of dispute and active research, so we shouldn’t take any individual’s word for it. This is science on the broadest canvas. Extraordinary general claims need to backed by a generation of publication I’d think.

Lynch is now a co-author on a new letter to Nature (which is open access, so read it!), Non-adaptive origins of interactome complexity. Imagine if you took biochemistry, specifically the nearly impenetrable language of protein interactions, and crossed it with evolutionary genomics. This is what you’d get.

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CATEGORIZED UNDER: Biology, Genomics

Kindle books outsell print books on Amazon

By Razib Khan | May 19, 2011 7:50 pm


Amazon: Kindle books outselling all print books
. This is more something I’d put on pinboard, but this requires noting more prominently. The figure itself isn’t important, but it is a marker for a silent transition occurring as we shift mediums.

CATEGORIZED UNDER: Technology
MORE ABOUT: Technology
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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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