Archive for May, 2011

Amongst the believers

By Razib Khan | May 31, 2011 10:17 pm

I don’t post Creationist related stuff often, but Harun Yahya always brings out the funny in people. So check this out, In France, a Muslim offensive against evolution. First, some standard dullness:

Dressed in a traditional black robe decorated with rhinestones and a white veil that she wears “only” when she comes to the mosque, Maroua admits that she has always wondered about “the dinosaurs and the origin of man…but at school, it cannot be refuted: we’re taught that man descended from monkeys. At home and in the Koran, [we’re taught] that we descended from Adam and Eve, and that God created all living beings.”

Ali Sadun Engin, Yahya’s representative in the current tour of French mosques, seems to have convinced the young girl. “I find his explanations logical,” she says. The proof for creationism is demonstrated with some perfunctory presentations of fossils, including bear, crocodile, and tortoise skulls, and can be summarized in a few brief sentences: “If fish left the water to walk, if dinosaurs were transformed into birds, then we should discover fossils of these beings in transition. However this is not the case. Science thus shows one sole truth: creation as we know it from the Koran.”….

But it starts to get really weird:

Read More

CATEGORIZED UNDER: Creationism
MORE ABOUT: Creationism

Mediterranean men on the move

By Razib Khan | May 31, 2011 3:06 pm

ResearchBlogging.orgSeriously, sometimes history matches fiction a lot more than we’d have expected, or wished. In the early 2000s the Oxford geneticist Bryan Sykes observed a pattern of discordance between the spatial distribution of male mediated ancestry on the nonrecombinant Y chromosome (NRY) and female mediated ancestry in the mitochondrial DNA (mtDNA). To explains this he offered a somewhat sensationalist narrative to the press about possible repeated instances of male genocide against lineage groups who lost in conflicts.

Here is a portion of the book of Numbers in the Bible:

15 – And Moses said unto them, Have ye saved all the women alive?

16 – Behold, these caused the children of Israel, through the counsel of Balaam, to commit trespass against the LORD in the matter of Peor, and there was a plague among the congregation of the LORD.

17 – Now therefore kill every male among the little ones, and kill every woman that hath known man by lying with him.

18 – But all the women children, that have not known a man by lying with him, keep alive for yourselves.

Then there is the rape of the Sabine women. The ethnogenesis of the mestizo and mulatto populations of the New World in large part was the union between non-European women and European men. These are hard brutal myths and hard brutal facts. But do they reflect an essential aspect of the dynamics which have shaped our species’ past?

I’m not willing quite yet to add a confident weight upon this possibility, but this seems to be part at least part of the picture. You see a major disjunction on male and female lineages among South Asians for example. A new paper in PNAS adds weight to this possibility, albeit only incrementally. Ancient DNA reveals male diffusion through the Neolithic Mediterranean route:

Read More

CATEGORIZED UNDER: Anthroplogy, Genetics, Genomics

Ban them! (including ancestry analysis)

By Razib Khan | May 31, 2011 10:05 am

Direct-to-Consumer Genetic Tests Neither Accurate in Their Predictions nor Beneficial to Individuals, Study Suggests:

Direct-to-consumer (DTC) genetic tests give inaccurate predictions of disease risks and many European geneticists believe that some of them should be banned, the annual conference of the European Society of Human Genetics heard May 31….

Here’s the abstract for the talk which argued that DTC companies don’t give the best disease risk estimates:

Objective: Direct-to-consumer (DTC) companies predict risks of common complex diseases on the basis of genetic markers. Given the low number of markers involved and their small effect sizes, it is unclear whether high-risk groups can be identified. We investigated the risk distributions generated by two DTC companies for 8 diseases.

Methods: We simulated genotype data for 100,000 individuals based on published genotype frequencies. Predicted risks were obtained using the formulas and risk data provided by the companies.

Results: The table presents observed and trimmed ranges of predicted risks. The two companies used different formulas to calculate risks. One company predicted risks higher than 100% for 5 out of 8 diseases, which for AMD concerned 1 in 200 individuals. Observed ranges were smaller for the second company, except for Type 1 Diabetes. Predicted risks higher than 50% were frequently observed for company 1, but were exceptions for company 2. When predicted risks of company 1 were calculated using the formulas of company 2, observed ranges were substantially smaller.

Since I don’t put much stock in the small effect disease risk predictions currently, I am not surprised. But I’d be curious to look at the guts of their results. This was presented at conference, so some caution has to enter into the picture. The main issue I’d always want to emphasize with critiques of the lack of efficacy of DTC is that they need to be evaluated against the baseline of the limits to the efficacy of medical professionals and medicine in general. Genomics and DNA doesn’t make something magical, whether for good or ill.

The second presentation covered in the ScienceDaily release is kind of more disturbing to me. Here’s the abstract:

Read More

The mess that is mouse

By Razib Khan | May 31, 2011 3:20 am

Recently an evolutionary geneticist told me that his colleagues who worked with mice really didn’t have their stuff together. Actually, his language was a touch more colorful than that. But the gist of the argument seemed plausible enough to me. I tend to avoid reading papers using the mouse as a model organism in genetics because I recall getting confused by the pedigrees and various strain acronyms and abbreviations (nonstandard acronyms and abbreviations have also been a problem for me whenever I try to read developmental genetics). If I want to look at the genetics of a mammal besides a human being I often like to focus on dogs. The breeds of dogs actually mean something to me. There’s only so many skinned mouse hides I want to stare at.

ResearchBlogging.orgWith all that said there is a huge scientific complex devoted to the mouse. If the house of mouse is a mess, then someone needs to do cleaning at some point. A new paper in Nature Genetics starts the process, using SNPs and variable intensity oligonucleotides (VINOs) to assess the relationships between distinct lab strains as well as wild subspecies. Ignorant as I am of the biology of the mouse I was vaguely aware that like elegans much of the laboratory stock derives from a very small founding population. In psychology there’s the problem of the outlook and dispositions of Western university students getting extrapolated to the whole species of man, so I have wondered about this problem for some of the model organisms now then. If you’re studying very general biological processes this shouldn’t be that big of an issue, but for evolution obviously characterizing the nature of variation is of the essence.

The paper title & the abstract, Subspecific origin and haplotype diversity in the laboratory mouse:

Read More

CATEGORIZED UNDER: Genetics, Human Genetics

Hope before the fall

By Razib Khan | May 30, 2011 11:08 pm

I think it is pretty irrational to bet on the Mavericks against the Heat in the NBA Finals. And since my Celtics lost I haven’t been following what’s going on closely, but I hope Jason Kidd gets his ring. He’s had some ups and downs, but I do remember being amazed by him when he was a freshman at Cal (though watching tape of Magic it was clear that he had the same panache when it came to assists):

CATEGORIZED UNDER: Sports
MORE ABOUT: Jason Kidd, NBA

Incredible human journeys (and more)

By Razib Khan | May 30, 2011 9:29 pm

A reader pointed out that the BBC series The Incredible Human Journey is online on YouTube thanks to the WhyEvolutionIsTrue channel. You can find all the episodes here. I’ve embedded episode 1 below. For what it’s worth I am no longer am confident that we should start these sorts of narratives like the presenter does, by suggesting that “a handful of African families could become a whole world of people.” I suspect that the emergence of modern humans is not so neat & tidy.

CATEGORIZED UNDER: Human Evolution, Human Genetics

The rise and fall of societies in Greenland

By Razib Khan | May 30, 2011 9:10 pm

I have no idea when the paper will be on PNAS‘s website, so I thought I would at least point to the ScienceDaily release, Climate Played Big Role in Vikings’ Disappearance from Greenland:

Greenland’s early Viking settlers were subjected to rapidly changing climate. Temperatures plunged several degrees in a span of decades, according to research from Brown University. A reconstruction of 5,600 years of climate history from lakes near the Norse settlement in western Greenland also shows how climate affected the Dorset and Saqqaq cultures…..

The Dorset were the non-European population which preceded the Inuit, and the Saqqaq preceded them. Last year Nature published a paper based on 350,000 SNPs from an ancient Saqqaq male which showed that he was related to modern Siberian peoples, and not to the later Inuit. That’s at least a very clear argument for why we should be very cautious about extrapolating from the genetic patterns of the present back to the past (and to be fair, poking around Google Books it seems that the archaeologists were skeptical of continuity between Saqqaq and Dorset cultures on empirical grounds, even if their theoretical disposition tended toward establishing an evolutionary relationship between the two).

One major issue which always seems to crop up when it comes to climate & culture is that Greenland seems to be the favorite example of a given pet theory for the rise & fall of societies. This is because in Greenland’s case it’s obviously really on the margin of habitability, so a slight shift in the climatic regime may drive a population to extinction. I hope that the paper has a sophisticated accounting of this possibility though, because it is kind of useless to talk about an exogenous factor like climate without also considering the contextual issues. Some historians argue that one reason the Norse of Greenland “died out” is that at the end of the day they didn’t need to adapt, they could evacuate to nearby Iceland, which is what some scholars argued occurred in the early 1400s. The church records clearly indicate that there were marriages between Greenlanders and Icelanders during that period.

CATEGORIZED UNDER: History

Zombie genome blogging

By Razib Khan | May 30, 2011 12:30 pm

Happy Memorial Day, if you’re American!

Dienekes has some very interesting posts up over at Dodecad, How to create Zombies from ADMIXTURE etc., and More Zombies: Ancestral North Indians and Ancestral South Indians reborn. If you are playing with ADMIXTURE this are going to be very useful in the future.

CATEGORIZED UNDER: Genomics
MORE ABOUT: Admixture, Zombies

Fun with Google Correlate

By Razib Khan | May 30, 2011 12:45 am

A few people have pointed me to Google Correlate. Google says that this tool is like “Google Trends in reverse.” You know I love Google Trends, so of course I’m going to poke around Google Correlate. The tool shows you the strongest correlations by query over time, as well as concentrations and correlations of the query by state. So here’s the distribution for “Jesus”:

If you know something about the United States, I assume you aren’t surprised. But how about something like “Krishna?”

Does this make sense to you? What’s up with New Jersey? As a proportion it has by far the greatest number of Indian Americans. (the #1 correlate is “Radha,” which makes sense)

How about something more obscure? OK, “Ludwig von Mises”:

Read More

CATEGORIZED UNDER: Technology
MORE ABOUT: Google Correlate

Less fear of the flu for asthmatics?

By Razib Khan | May 29, 2011 8:57 pm

One of the reasons I tend toward a bit of hypochondria is probably the fact that what for others are inconvenient minor ailments often trigger my asthma. So nice to see this, Why Does Flu Trigger Asthma?:

When children with asthma get the flu, they often land in the hospital gasping for air. Researchers at Children’s Hospital Boston have found a previously unknown biological pathway explaining why influenza induces asthma attacks. Studies in a mouse model, published online May 29 by the journal Nature Immunology, reveal that influenza activates a newly recognized group of immune cells called natural helper cells — presenting a completely new set of drug targets for asthma.

If activation of these cells, or their asthma-inducing secretions, could be blocked, asthmatic children could be more effectively protected when they get the flu and possibly other viral infections, says senior investigator Dale Umetsu, MD, PhD, of Children’s Division of Immunology.

Although most asthma is allergic in nature, attacks triggered by viral infection tend to be what put children in the hospital, reflecting the fact that this type of asthma isn’t well controlled by existing drugs.

For various reasons I’m moderately skeptical of incremental improvements in life expectancy in developed nations through drugs. But, I do think there are plenty of possibilities when it comes to reducing morbidity, and therefore increasing productivity of a life well lived.

CATEGORIZED UNDER: Health
MORE ABOUT: Asthma, Health

The housing bubble vs. the financial crisis

By Razib Khan | May 28, 2011 9:26 pm

In the mid-2000s many regular folks knew that something was weird in housing. Of course everyone was aware that there was a short term windfall to be made if you could flip. But there were normal discussions about the bubble, and when it would burst, or if the weird arguments by some economists and the real estate industry that there wasn’t a bubble were true. In contrast regular people weren’t aware of the possibility of a financial crisis. I recall saying stupid things about the “Great Moderation,” parroting what I’d heard smarter people who I assumed knew better say, in the summer of 2008. Or take a look at some of the comments when I mooted the possibility of a recession in mid-2007: “They’re practically glorified hiccups nowadays. I don’t get what the big deal is.”

With that in mind I looked at Google Trends for two queries, “housing bubble” and “financial crisis.” The top panel is search query, and the bottom panel is news query. The financial crisis query is what you’d expect:

The housing bubble query is more interesting:

Read More

CATEGORIZED UNDER: Economics
MORE ABOUT: Google Trends

Loose vs. tight societies

By Razib Khan | May 28, 2011 2:23 pm

ResearchBlogging.orgA new paper in Science, Differences Between Tight and Loose Cultures: A 33-Nation Study, is making the media rounds. Here’s NPR:

…The idea for this study really dates to the 1960s. Back then, an anthropologist decided to evaluate a few dozen obscure cultures and see if he could rank them on a scale from “tight” to “loose.” He defined tight cultures as having a lot of rules, which people violate at their peril. Loose cultures are more relaxed in their expectations, and more forgiving of people who deviate.

The Tightness Scale

“So for example, you might have been asked, how appropriate is it to curse in the bank or kiss in a public park, or eat or read a newspaper in a classroom? And we were able to derive scores of how constrained, in general situations, they are, versus how much they have latitude in different countries.”

“Some of the cultures that are quite tight in our sample include places like Singapore, Japan, Pakistan,” Gelfand says. “Whereas many loose societies include countries like New Zealand, the Netherlands, the United States.”

The abstract from the paper is a little harder to parse:

Read More

CATEGORIZED UNDER: Anthroplogy, Culture, Social Science

Zanran Numerical Data Search

By Razib Khan | May 28, 2011 11:38 am

Via Kevin Drum, Zanran, “Your source for data & statistics – graphs, charts and tables.” I am just checking it out, but I think it will be of use to readers.

CATEGORIZED UNDER: Technology
MORE ABOUT: Zanran

Friday Fluff – May 27th, 2011

By Razib Khan | May 27, 2011 3:05 pm

FF3

1) First, a post from the past: Personality variation by region (USA).

Read More

CATEGORIZED UNDER: Blog
MORE ABOUT: Friday Fluff

Comments in the republic of Khan

By Razib Khan | May 27, 2011 12:09 pm

So today I received an email from regular commenter German Dziebel:

Razib, what’s your relationship with the Discover Magazine? Up until now I thought of your blog as more or less a public forum, rather than a private franchise. Please clarify, so we don’t bicker about ethics in public.

I have no idea what German precisely means by “public forum” or “private franchise,” though I have a general sense. Discover Magazine pays me to blog. I also have an editor who I consult now and then. For example when I discussed traffic patterns to this website I asked if that would be OK, since I know that sort of information is often material sites like to keep somewhat private. When Marnie Dunsmore threatened to sue me for “stealing her ideas” I shot an email to the editor to notify him of her strange accusations. But in general my communication with Discover Magazine is limited to technical issues, as well as some exchanges of ideas and topics to post on (this isn’t formal, the editor knows the kind of stories and papers I dig, and will send me an email or point a tweet my way).

I like it that way. It gives me time to blog. There’s a lot of interesting stuff in my “task stack” which I never get to because of the pressures of time. When I began blogging in 2002 I did so with an assurance I wouldn’t have to spend too much time on technical or administrative crap with my co-bloggers. That didn’t totally work out, but it is an ideal which I like to aim for. This post is a violation of that ideal. I’m engaging in meta blather about comments policy and what not when I could be blogging, finishing the coffee I’m drinking right now, or watching the episode of South Park which I haven’t watched yet.

If I had to condense my summary for how I run these comments, I’d say I run this place as if I’m Sulla during the period in his life when he was the dictator of the Roman Republic. Since most of you probably don’t get the allusion, I will elaborate….

Read More

CATEGORIZED UNDER: Administration, Blog

"Gross national happiness" in numbers

By Razib Khan | May 27, 2011 12:34 am

Bhutan famously espouses “gross national happiness”:

The term “gross national happiness” was coined in 1972 by Bhutan’s former King Jigme Singye Wangchuck, who has opened Bhutan to the age of modernization, soon after the demise of his father, King Jigme Dorji Wangchuk. He used the phrase to signal his commitment to building an economy that would serve Bhutan’s unique culture based on Buddhist spiritual values….

Apparently the nation has recent switched from absolute to constitutional monarchy:

Bhutan’s political system has developed from an absolute monarchy into a constitutional monarchy. In 1999, the fourth king of Bhutan created a body called the Lhengye Zhungtshog (Council of Ministers). The Druk Gyalpo (King of Druk Yul) is head of state. Executive power is exercised by the Lhengye Zhungtshog, the council of ministers. Legislative power was vested in both the government and the former Grand National Assembly.

On the 17th of December 2005, the 4th King, Jigme Singye Wangchuck, announced to a stunned nation that the first general elections would be held in 2008, and that he would abdicate the throne in favor of his eldest son, the crown prince….

From what I can tell the royal house of Bhutan seems genuinely sincere. More plainly paternalist than deiviously despotic.

Below are some Google Data trend lines comparing Bhutan to some of its smaller South Asian neighbors, as well as Sweden and Equatorial Guinea as comparisons at the high and low ends.

Read More

CATEGORIZED UNDER: Data Analysis
MORE ABOUT: Bhutan, Data, Economics

The revolution swallowing Powell's Books?

By Razib Khan | May 27, 2011 12:14 am

A friend asked me today if I thought that Powell’s would be around a year from now. I had no idea what he was referring to. By that, I don’t mean that I didn’t know he was referring to Powell’s Books of Portland. I mean that I had no idea that Powell’s was in any trouble. I thought of Powell’s as an institution which could weather any shocks, its huge selection and special experience giving it an edge over other independent booksellers (and even over Barnes & Noble and Borders). The main Powell’s store covers a full city block, 1.6 acres. The total inventory of the company is at 4 million books (new, used, etc.). The downtown Portland location can be overwhelming and all consuming. And I have many fond memories of the Powell’s in the Hawthorne District from when I lived in Portland in 2002. In fact, between 2000-2005 I purchased quite a few books at the main location, as well as at Powell’s Technical. Despite not living in Portland for most of that period, I regularly visited, and always made a point to get lost at Powell’s when I came through town.

Read More

CATEGORIZED UNDER: Culture
MORE ABOUT: Books, Powell's Books

The power of one (Nubian that is)

By Razib Khan | May 26, 2011 10:21 pm

Maju pointed me to a new paper on the genetics of Sudanese today. My interest was piqued, then not so much when I looked more closely. Genetic variation and population structure among Sudanese populations as indicated by the 15 Identifiler STR loci:

Background
There is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region.

Results
We report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE) was 0.9999981, and the combined match probability was 1 in 7.4 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia.

Conclusion
We show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.

The upside: nearly 500 individuals from a huge range of ethnic groups in Sudan. This is the level of population coverage you’d want. Most of the ethnic groups cover the sample size range from 10 to 50. The downside: only 15 microsatellite markers. About the same number as in the study which I critiqued earlier this week. This is just not a huge number. The authors did try very hard to prune the marker set to be ancestrally informative on this scale, but I think it’s pretty obvious that there are major shortcomings in their analysis. 15 STRs is probably useful for inter-continental genetic variation, but not for intra-continental differences. The paper is open access so you can read the whole thing, but I want to highlight a speculation which they offer based on their results:

Read More

CATEGORIZED UNDER: Anthroplogy, Genetics, Genomics

Toward evolutionary monism

By Razib Khan | May 26, 2011 4:00 pm

Is there any substantive difference between natural, sexual, and artificial selection? Or is it just semantic sugar, useful for humans in our own cognitive bookkeeping? I lean toward the latter proposition. To some extent I would think that this is an irrelevant issue, selection is selection, but I have encountered folks who seem surprised at analogies between “artificial” and “natural” selection quite regularly. Of course Charles Darwin famously elided the distinctions across the two categories in his original works in the 19th century (this was later a subject of controversy, insofar as Darwin’s conflation of the properties of artificial and natural selection may have misled him in terms of the weight of factors shaping evolution in the wild).

These are the questions which bubble to the fore of my mind when I encounter reports such as Elizabeth Pennisi’s in Science, On the Trail of Brain Domestication Genes:

Researchers have proposed that bonobos evolved domesticated behavior to encourage group living. By isolating a group of 40 putative brain domestication genes in the prefrontal cortex and comparing their expression in humans versus chimps and bonobos, researchers found that the activity of that gene group in bonobos was clearly “domesticated” compared with chimps, they reported at the Biology of Genomes meeting.

The full piece is gated, so here’s the relevant section in the details:

Read More

CATEGORIZED UNDER: Anthroplogy, Genetics, Genomics

Twitpic, all your photos are ours

By Razib Khan | May 26, 2011 2:25 pm

We’re in a brave new world when it comes to our conception of property. I’m on the skeptical side when it comes to the current aggregate long term utility of IP law (I think the value of property rights may be overwhelmed by the abuse which large corporations are inflicting upon the spirit of the laws). But I thought I’d pass on what everyone is talking about in relation to Twitpic, Why I abandoned Twitpic photo-sharing:

– 1. If someone wants to use my photo commercially, they need to ask Twitpic (but not me) and then credit Twitpic (but not me).

– 2. Twitpic can use or change my photos, in any, way without asking me first.

The financial rationale for this sort of behavior on the part of firms providing free services is pretty straightforward. If you want some level of control and ownership of what you produce, you’ll probably have to pay for services which grant you these liberties in the future, at least if you want to utilize the cloud.

For the record, I don’t mind if people somehow make money with my genotype. But I would be very skeptical of individuals who somehow assert exclusive ownership. When you grant exclusive rights to an idea, an abstraction, it isn’t surprising that individuals will begin to extract rents.

CATEGORIZED UNDER: Technology
NEW ON DISCOVER
OPEN
CITIZEN SCIENCE
ADVERTISEMENT

Discover's Newsletter

Sign up to get the latest science news delivered weekly right to your inbox!

Gene Expression

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!
ADVERTISEMENT

See More

ADVERTISEMENT

RSS Razib’s Pinboard

Edifying books

Collapse bottom bar
+

Login to your Account

X
E-mail address:
Password:
Remember me
Forgot your password?
No problem. Click here to have it e-mailed to you.

Not Registered Yet?

Register now for FREE. Registration only takes a few minutes to complete. Register now »