Razib Khan One-stop-shopping for all of my content

March 31, 2012

It was a good decade (UPDATE)

Filed under: Blog,The End — Razib Khan @ 11:48 pm

Update:  Actually, I was going to put up a post “10 years in blogging.” But right now I don’t have the time, seriously. 10 years is a LONG time though, so I now feel more comfortable talking about events “offline” which date to over half a decade in the past. One thing to note is that my current style of comment moderation crystallized in the mid-2000s because of various time constraints. The fact that I was going to school full time, or had a 65 hour a week job as my firm was coming up to a software release date, and, was in a long distance relationship, was not anyone’s business (did I mention I had freelance web development projects on the side, and was developing a content management system for a client as well?). But it certainly inculcated in me a lack of patience for bullshit. I was cranking out blog posts on Sundays, and in the hour I had after dinner & and my freelance project and before sleep. I recall in the fall of 2006 amusingly some moron left a comment about how I must have a lot of time, since I was posting on Friday evening. ...

What turns a blue-eyed girl brown?

Filed under: Uncategorized — Razib Khan @ 10:54 pm

I’m questing about for some answers. My daughter is now two months old, and to the left is an image of her eye. As you can see, they are blue. I was not particularly surprised that she was born with blue eyes. Her mother is of Northern European heritage. But, I’ve had both of us genotyped. My daughter is a heterozygote on the HERC2-OCA2 locus, which means that she has a 5% chance of blue eyes, 35% green/hazel, and 60% chance of brown, assuming a European genetic background. Obviously half her ancestry is non-European, so that does not hold (though for gene nerds, I am a homozygote for the “European” alleles of SLC24A5, as are many South Asians).

My question here is simple: of the half-browns with one Northern European parent,  what color were their eyes at birth, and what colors did they change to over time, if they changed at all? I have a friend who is half Bengali and Irish, and he and his brother have green eyes, and were born with green eyes. My friend Jason Goldman has the same genotype as my daughter on the  HERC2-OCA2 locus, but his baby blues disappeared after 2 weeks.

What I want in the comments are details about eye color and transitions, as well as parental ethnicity (I am not too surprised, for example, that one of Nikki Haley’s children has blue eyes as an adolescent).

If you are curious as to why I’m so curious. First, I’m a brown guy who is running around with a little baby with blue eyes. Second, people know of my fixation on genetics. So naturally questions will ensue.

(for further information, her hair color is medium brown; mine is black, her mother’s is blond).

When little differences matter a great deal

Filed under: Altruism,Anthroplogy — Razib Khan @ 10:37 pm

In the comment below Clark alludes to the fact that Jonathan Haidt kept reiterating that even if there were differences between populations due to recent evolution, if it was due to selection on standing variation upon quantitative traits then the between group variation would be dwarfed by within group variation. He didn’t quite say it like that, but I’m sure that’s what he meant. For example, there is now evidence that alleles which can explain the small height difference between Northern and Southern Europeans have been subject to natural selection. Most of the variation obviously remains within the groups; you can’t guess that someone is Italian or Dutch just based on their height. There are many tall Italians, and many short Dutch. But on average there are differences between the groups which can be attributed to genes, and those genes seem to have been targets of selection.

This is good as fair as it goes…but small average differences may not necessarily be marginal. That is because sometimes you select from the tails of a distribution. For example, if you want to ascertain which population will produce more N.B.A. players, ...

Jonah Lehrer, science fiction writer

Filed under: Anthroplogy,Creativity,Culture — Razib Khan @ 9:46 pm

He’s back, and he’s out with a new book, Imagine: How Creativity Works. I am talking of course about Jonah Lehrer, the enfant terrible of cognitive neuroscience. OK, perhaps more Wunderkind. In any case, I was struck by this post on his weblog, The Cost Of Creativity:

There is a serious complication to this triumphant narrative of cliff edges and innovation, however. Because our lifestyle has become so expensive to maintain, every new resource now becomes exhausted at a faster rate. This means that the cycle of innovations has to constantly accelerate, with each breakthrough providing a shorter reprieve. The end result is that our creativity isn’t just increasing the pace of life; it is also increasing the pace at which life changes. “It’s like being on a treadmill that keeps on getting faster,” West says. “We used to get a big revolution every few thousand years. And then it took us a century to go from the steam engine to the internal-­combustion engine. Now we’re down to about 15 years between big innovations. What this means is that, for the first time ever, people are living through multiple revolutions.”

Needless to say, such revolutions aren’t fun. They’re unsettling ...

Jonathan Haidt & Robert Wright: crazy delicious

Filed under: Evolutionary Psychology,Jonathan Haidt — Razib Khan @ 4:21 pm

Last night I listened to a very long discussion between Robert Wright, author of The Moral Animal, and Jonathan Haidt, author of The Righteous Mind: Why Good People Are Divided by Politics and Religion. If you have been reading my weblog for years there may not be much new, but if you haven’t, then you’ll encounter a lot of novel information, in particular from Jonathan Haidt. I was intrigued by Haidt’s references to evolutionary and anthropology, and I immediately noticed on Twitter that of the 17 people he follows, two are John Hawks and Paul Bloom. John is a friend, and Paul Bloom has been highly influential in my own thinking about cognitive psychology (see Descarte’s Baby). Additionally, many of the other “shout outs” which Haidt makes are familiar to me as well (e.g., Scott Atran, the neo-functionalism of David Sloan Wilson, etc.).

In lieu of a conventional blog post here a list of comments, reacting mostly to Haidt’s various assertions.


- The biggest “bombshell” that Haidt drops is his empirical finding that when people of a given political ideology, going from very liberal to very conservative, are asked to model the opinions of other people ...

Post-Neolithic revenge of the foragers

Filed under: anthropology,Culture,Farmers vs. Foragers,History — Razib Khan @ 10:18 am

If I have something to share, why not share it? Over the past few weeks I’ve been ruminating on some of the possible intersections between historical population genetics and anthropology, especially in light of the discussion that I’ve had in the past with Robin Hanson about ‘farmers vs. foragers’. Entering into the record that such a dichotomy is too stark, and only marginally useful (i.e., I think it is important to separate farmers and foragers in to their own sub-classes, as some farmer types may share more with some forager types, and so forth), it may be that after the first wave of the Neolithic expansion the descendants of the foragers “bounced back” in many regions of the world. It does seem that ancient European hunter-gatherers have left modern descendants. They were not totally swamped out. Using autosomal patterns some genome bloggers have inferred the same pattern, and perhaps even a counter-reaction by “Mesolithic” populations which adopted some aspects of the “Neolithic” cultural toolkit.

But here let me come back to the Turks. Are they the descendants of farmers who expanded out of the valleys of eastern ...

Cultural Folkways in Flux

Filed under: American historical "dark matter",Culture — Razib Khan @ 9:43 am

A fascinating post over at The Crux, Votes and Vowels: A Changing Accent Shows How Language Parallels Politics. Here’s the section which I might quibble with though:

Labov points out that the residents of the Inland North have long-standing differences with their neighbors to the south, who speak what’s known as the Midland dialect. The two groups originated from distinct groups of settlers; the Inland Northerners migrated west from New England, while the Midlanders originated in Pennsylvania via the Appalachian region. Historically, the two settlement streams typically found themselves with sharply diverging political views and voting habits, with the northerners aligning much more closely with agenerally being more liberal ideology.

But first, here is a map of the dialects in question:

 


Now compare to a map of Yankee settlement in the mid-19th century:

I do not object to the argument that old historical patterns in the USA redound down to the present in surprising and often cryptic ways. I refer to this as the “dark matter” of American history; deep structural patterns which shape the cultural geography of the ...

Revenge of the herders

Filed under: Anthroplogy,Turks — Razib Khan @ 2:29 am

Let me make something explicit: I believe that the model outlined in First Farmers is too simple, and that extant patters of linguistic and genetic variation need to accept the likelihood of multiple population reorganizations across vast swaths of Eurasia within the last 10,000 years. The classic case in point are the Turks. Because of their exotic character vis-a-vis the populations which they displaced and assimilated we can peg rather easily their expansion. Between 0 and 1000 AD they began to make themselves felt across a broad expanse of Eurasia from the eastern fringes of Europe to the western fringes of China, and south toward the world of Islam. Between 1000 and 1800 the Turkic peoples took over much of Eurasia for various periods of time (e.g., the Ottomans, Safavids, and Mughals, were Turkic, while the Golden Horde which imposed the Tatar Yoke were mostly Turkic, not Mongol). It is notable to me that Turkic peoples contributed ~10 percent to the genetic ancestry of modern Anatolians. This is a significant achievement, because Anatolia has been a densely populated seat of agricultural civilization for almost the whole history of agriculture! ...

The real secret history of the Mongols?

Filed under: Anthroplogy,Human Genetics — Razib Khan @ 2:14 am

Thank god for steppe hyper-patriarchy; it’s a model which we can test. Dienekes points me to a paper, The Y-chromosome C3* star-cluster attributed to Genghis Khan’s descendants is present at high frequency in the Kerey clan from Kazakhstan, which is notable for increasing sample coverage of the distribution of “Genghis Khan haplotype.” As you might recall in 2003 a paper reported that a particular Y-chromosomal phylogeny was extremely common in Central Eurasia, and, that it had expanded rather rapidly starting approximately ~1,000 years ago. The natural supposition was that this was connected to the rise of Genghis Khan, from whom male-line descent in particular has become a matter of pride and prestige across the former domains under his rule. Subsequent researchers have supported this finding insofar as the distribution of the haplotype does tend to drop off among the “Western Mongols,” who were for various reasons marginal during the time of Genghis Khan, and whose ruling class were subsequently diminished in part due to their lack of a Genghiside pedigree.

 

The new paper above presents the novel result that the Kereys of Kazakhstan have the highest ...

March 30, 2012

Nature Precedings closes up shop

Here’s the announcement:

As of April 3rd 2012, we will cease to accept submissions to Nature Precedings. Nature Precedings will then be archived, and the archive will be maintained by NPG, while all hosted content will remain freely accessible to all.

Looking forward, NPG remains committed to exploring ways to help researchers, funders, and institutions manage data and best practices in data management, and we plan to introduce new services in this area.

We have truly valued your contributions as authors and users to Nature Precedings and hope that you will actively participate in this research and development with us.”

This comes on the heels of Dr. Joseph Pickrell’s first author submission of a preprint. Correlation? Yes. Coincidence? I’ll let you decide.

In other news the existence and flourishing of arXiv puts a whole different spin on “physics envy.” And, just to reiterate, if I post about a paper, and you don’t have access email me and I will send you the paper.

March 29, 2012

How Game of Thrones Should Have Ended

Filed under: Culture,Fiction — Razib Khan @ 10:04 pm

I haven’t watched most of the films (or video games, or T.V. shows) being parodied by How It Should Have Ended. But I have read A Game of Thrones. So I’m confused as to why this struck me as rather unfunny, in comparison to most of the others where I have to educate myself on what’s being parodied….

March 28, 2012

How culture crashes clines

Filed under: Afghanistan,Anthroplogy,Human Genetics,Pashtun — Razib Khan @ 11:14 pm

The USA has been in Afghanistan for over 10 years now. Like many Americans my own personal preference is that we get out as soon as possible. Because of American involvement we see terms like “Pashtun” bandied about in the media, but there is little further exploration. But politics and international relations are the not focus of this post, at least not politics and international relations in our time. A new paper in PLoS ONE examines the Y-chromosomal patterns as they partition across ethnic groups in Afghanistan. By this, we mean the direct paternal lineage of Afghan men. Additionally, the authors place the results in a broader Eurasian context. The results are not surprising, though they add greater precision and power to our picture because of their sample size. The main downside is that they did not include mtDNA (maternal lineage) or autosomal analysis (the total ancestry, not just the paternal or maternal line).

 

At this point most Americans should in theory have a general sense of Afghan ethnography. But let’s go over it again. First and foremost you have Pashtuns, who are a broad coalition of tribes who are ...

March 27, 2012

Targaryen genetic load

Filed under: A Song of Ice and Fire,Genetics — Razib Khan @ 10:57 am

I have to point you to this post on royal inbreeding in A Song of Ice and Fire. They reference my post on the Habsburgs. Well done! In any case, one possibility is that the Targaryen lineage may have purged their genetic load through inbreeding. The basic logic is that all the recessive traits are going to be “exposed” every generation, resulting in a far stronger selection coefficient against those alleles than would be the case in a outbreed population (where most deleterious variants with recessive expression are masked by being present heterozygote genotypes).

March 26, 2012

How income, class, religion, etc. relate to political party

Filed under: data,Data Analysis,Demographics,GSS,Politics — Razib Khan @ 9:11 pm

Update: There was a major coding error. I’ve rerun the analysis. No qualitative change.

As is often the case a 10 minute post using the General Social Survey is getting a lot of attention. Apparently circa 1997 web interfaces are so intimidating to people that extracting a little data goes a long way. Instead of talking and commenting I thought as an exercise I would go further, and also be precise about my methodology so that people could replicate it (hint: this is a chance for readers to follow up and figure something out on their own, instead of tossing out an opinion I don’t care about).

 

Just like below I limited the sample to non-Hispanic whites after the year 2000. Here’s how I did it: YEAR(2000-*), RACE(1), HISPANIC(1)

Next I want to compare income, with 1986 values as a base, with party identification. To increase sample sizes I combined all Democrats and Republicans into one class; the social science points to the reality that the vast majority of independents who “lean” in one direction are actually usually reliable voters for that party. So I feel no guilt about this. I suppose Americans simply like the conceit of being independent? I know I do. ...

The evolution of the human face

The face is an important aspect of our phenotype. So important that facial recognition is one of many innate reflexive cognitive competencies. By this, I mean that you can recognize a face in a gestalt manner, just like you can recognize a set of three marbles. You don’t have to think about it in a step-by-step fashion. Particular types of brain injuries can actually result in disablement of this faculty, and a minority of humans seem to lack it altogether at birth (prosopagnosia). That’s why I’ve long been interested in the genetic architecture and evolution of craniofacial traits. I long ago knew the potential range of pigmentation phenotypes for my daughter because both her parents have been genotyped, but when it comes to facial features we’re stuck with the old ‘blending inheritance’ heuristic. The most obvious importance of teasing apart the genetic architecture of craniofacial traits is forensics. It might not put the sketch artist out of a job, but it would be an excellent supplement to problematic eye witness reports.

But it isn’t just forensics. The issue has evolutionary relevance. It looks like that in terms of morphology our own lineage has had a lot of diversity up until recently. I’m thinking in particular of the ‘archaic’ looking humans recently discovered in China and Nigeria, who seem to have persisted down into the Holocene. More generally, humans as a whole have become more gracile over the last 10,000 years. Why? There are two extreme answers we can look to. First, gracile humans have replaced robust humans. Second, natural selection for gracility has resulted in the in situ evolution of many populations over the last ~10,000 years. An interesting aspect of this is that it looks as if many salient traits have been targets of selection, and therefore evolution and population differentiation.

Here the top 10 SNPs which deviate from the overall phylogenetic tree of population relationships in the HGDP data set:

 

SNP Chr Nearest gene Phenotype
rs1834640 15 SLC24A5 skin pigmentation
rs260690 2 EDAR hair morphology
rs10882168 10 CYP26A1/FER1L3 ?
rs4918664 10 CYP26A1/FER1L3 ?
rs2250072 15 SLC24A5 skin pigmentation
rs6583859 10 CYP26A1/FER1L3 ?
rs2384319 2 KIF3C ?
rs6500380 16 LONP2 ?
rs4497887 2 CNTNAP5 ?
rs9809818 3 FOXP1 ?

There are two things I want to say off the bat. First, a given SNP likely has many phenotypic effects. So the trait that we “see” in terms of its effect may not be the same trait that natural selection “sees.” Second, it is not a surprise that out of the traits that a given variant may affect the physically salient ones stand out; sometimes you do go looking where the light is shining on a dark street. We know that the lighter complexion of East and West Eurasians seems to be due to independent evolutionary events. In other words, they aren’t derived from common ancestry. When it comes to hair form the EDAR locus seems to be responsible for the distinctive characteristics of East Asians, and has been under recent selection.

What does all this have to do with craniofacial traits? Simple: the coarse and “skin deep” traits that physical anthropologists used decades ago to classify human beings have been rather informative to a first approximation of both details of phylogeny and natural selection. I see no reason why craniofacial traits should be any different. Humans have become more gracile, and some human populations seem to have been changing rather rapidly. I am highly skeptical that this is a neutral process. We care a great deal about facial features, and deviation from the norm can be arresting. If there has been change it is either due to population replacement, or selection (it could be a correlated response, or direct selection).

It is with that preamble that I offer up Mark Shriver’s abstract at the Modern Human Genetic Variation symposium:

The genes determining normal-range variation in human faces are arguably some of the most intrinsically interesting and fastest evolving. However, so far, little work has been focused on discovering these genes. Working under the hypothesis that genes causing Mendelian craniofacial dysmorphologies also may be important in determining normal-range facial-feature variation, and that those genes associated with population differences in facial features should have experienced greater levels of evolution (change in allele frequency), we have taken an admixture mapping/selection scan approach to identifying and studying the genes directly affecting facial features. We have applied the methods of automated quasi-landmark analyses, partial least squares regression, and individual genomic ancestry estimates to explore the distribution of facial features across two groups of human populations — West Africans and Europeans. Using three samples of admixed subjects (American; N=159, Brazilian; N=197, and Cape Verdean; N=248) we have modeled facial variation in the parental populations and compared the extent to which estimates of ancestry from the face compare to genomic-ancestry estimates. We also have tested six selection-nominated craniofacial candidate genes for functional effects on facial features using admixture mapping. In objective tests, two of these six genes (FGFR1 and TRPS1) show significant effects on facial features. In addition, human-observer ratings of the similarity between subjects and allele-specific facial morphs show the same effects for these two genes. Additionally, exaggerated allele-specific morphs based on normal-range variation in these genes recapitulates the syndromic facies of the craniofacial dysmorphologies with which they are associated.

I asked Mark about the nature of these genes and the traits. The paper is coming soon, but he told me that he does not think that the genetic architecture of craniofacial traits is going be as simple or easy to characterize as pigmentation genes. On the other hand, he’s reportedly capturing 35% of the African vs. European difference with his marker set, so that’s not trivial, and some of the individual loci have a strong enough effect that it’s visible by eye! Also, given the preserved extant diversity within populations (pigmentation genes are often disjoint across Africans and Europeans) he believes that the selection events are recent.

March 25, 2012

The agricultural “express train”

Filed under: Agriculture,Anthroplogy — Razib Khan @ 10:25 pm

One model for the spread of the agricultural way of life into Europe is of inexorable “demic diffusion” via a “wave of advance” of farming populations met by a land surplus. Conceptually and analytically it’s an elegant model. It’s also fundamentally methodologically individualistic, and so in keeping with the spirit of the age. There’s no need to appeal to higher order social structure or organization, farmers who have a specific cultural toolkit drive the dynamic through endogenous growth in pre-state cultures through the production of large families. This growth washes over the frontier of the advance, and the original locus of the demographic pulse synthesizes across a transect with the indigenous substrate. In the early aughts historical geneticists Bryan Sykes and L. L. Cavalli-Sforza sparred over whether demic diffusion was useful or not as a conceptual framework. Sykes reported chromosomal results which implied that 75 percent of the ancestry of Europeans derives from Pleistocene hunter-gatherers. Cavalli-Sforza’s riposte was that the original model did not specify a particular Paleolithic-Neolithic ratio, but rather characterized a dynamic which emphasized the necessity of migration as a mediator for cultural changes (the two perspectives are outlined in Seven Daughters of Eve and A Genetic and Cultural Odyssey).

 

In the end the debate did seem semantic quibbling. And today it also is likely outmoded and irrelevant. There is a high probability that the basic fundamental assumptions of the original diffusionist model, whether cultural or genetic, were pushed too far. It neglected the profound discontinuities introduced into the equation by the protean tendencies of human culture. Empirically there is evidence of this in works such as Lawrence Keeley’s War Before Civilization of this in the European context. As farmers impinged upon the territories of Mesolithic populations which utilized marine resources the advance of agriculture often stalled, and there are archaeological remains which are suggestive of violent conflict across Northern Europe’s maritime fringe. Additionally, when humans advance into “virgin” territory the landscape can often seem “patchy.” Instead of a spatially uniform wave of advance one almost certainly saw farmers race up favorable valleys and avoid zones of decreased fertility. In the United States the Far West was understood to be more amenable to agricultural techniques than the Great Plains in the 19th century, so one notes a “leap frog” to California and Oregon in the decades before the Civil War, leaving the intervening lands to native populations (at least temporarily).

It is with this in mind that we must take in results being published more recently which suggest a more confused and irregular shift of peoples and cultures in Neolithic Europe. For example, at the symposium on Modern Human Genetic Variation Mattias Jakobsson is reporting on results of ancient DNA from ~5,000 year old samples from Scandinavia. The individual who was a farmer resembles Southern Europeans, while the two hunter-gatherers resemble modern Northern Europeans. Jakobsson observes that most modern European populations span the gamut between the two extremes. A few years ago a paper came out which reported that the mtDNA lineages of LBK individuals from Central Europe (the earliest farming culture) resembled Near Easterners more than modern Europeans. A similar discontinuity seems evident in France. At this point I think there are enough data to force us to move past an simple Neolithic demic diffusion wave of advance, and any model which posits pure cultural diffusion or total replacement of the indigenous populations. We should be careful about making grand pronouncements for the next few years, because the outlines will be clear and pegged down within 5 years due to the impending surfeit of ancient DNA studies.

Rather, let’s switch back to the question of clines and gradual shifts. The problem here may be the granularity of the archaeological data. It seems likely that the expansion of agriculture was more spatially patchy, and exhibited more starts and stops, then the samples we have allow us to infer with any confidence. The arrival of startlingly distinctive populations genetically and culturally across which likely rapidly traversed territory in a point-to-point fashion, and their subsequent extinction or assimilation into local substrate, is less surprising when we keep in mind the discontinuous nature of much of cultural change.

The upper class is more Republican

Filed under: data,Data Analysis,Demographics — Razib Khan @ 2:31 pm

A few months ago I listened to Frank Newport of Gallup tell Kai Ryssdal of Marketplace that upper class Americans tend to be Democrats. Ryssdal was skeptical, but Newport reiterated himself, and explained that’s just how the numbers shook out. This is important because Newport shows up every now and then to offer up numbers from Gallup to get a pulse of the American nation.

Frankly, Newport was just full of crap. I understand that Thomas Frank wrote an impressionistic book which is highly influential, What’s the Matter with Kansas, while more recently Charles Murray has come out with the argument in Coming Apart that the elites tend toward social liberalism. I’m of the opinion that Frank is just wrong on the face of it, but that’s OK because he’s an impressionistic journalist, and I don’t expect much from that set beyond what I might expect from a sports columnist for ESPN. Murray presents a somewhat different case, as outlined by Andrew Gelman, in that his “upper class” is modulated in a particular manner so as to fall within the purview of his framework. Neither of these qualifications apply to Frank Newport, who is purportedly presenting straightforward unadorned data.

When the “average person on the street” thinks upper class they think first and foremost money. This is not all they think about, but in the rank order of criteria this is certainly first on the list. We can argue till the cows come home as to whether a wealthy small business owner in Iowa who is a college drop out is more or less elite than a college professor in New York City who is bringing home a modest upper middle class income (very modest adjusting for cost of living). But to a first approximation when we look at aggregates we had better look at the bottom line of money. After that we can talk details. And the first approximation is incredibly easy to ascertain. Below is a table and chart which illustrate the proportion of non-Hispanic whites after 2000 who align with a particular party as a function of family income, with family income being indexed to a 1986 value (so presumably $80,000 hear means what $80,000 would buy in 1986, not the aughts).

 

Family Income Strong Dem Dem Lean Dem Ind Lean Rep Rep Strong Rep
Less than $20,000 12 15 12 24 9 15 12
$20-$40,000 12 15 10 18 11 19 15
$40-$80,000 11 14 10 13 11 24 18
More than $80,000 12 12 10 11 11 23 21

The results are straightforward: the more income a family has, the more likely they are to be Republican. There is a lot of nuance and geographical detail to be fleshed out in these results. But these facts are where we need to start.

Andrew Gelman has much more as usual. For example, this chart:

 

 

Why do I keep posting this stuff? Because facts matter. That’s my hope, my faith. Tell people facts, and they will open their eyes. Tell your friends, tell your family. Have whatever opinion you want to have, but start with the facts we know. Look up facts, calculate facts, analyze facts. They are there for us, we just need to go look. Google is your friend, Wikipedia is your friend. The General Social Survey is your friend.

The revival of the American city?

Filed under: Demographics,Urbanism — Razib Khan @ 1:37 pm

I’ve never watched Mad Men, but I really can’t help but hear all about the show. One thing that has struck me about the change from then, ~1960, to now, ~2010, is the alignment of quantitative demographic trends with impressionistic cultural ones. The 1970s were a disaster for the old urban order. Below are the top 10 cities by population in 1960 and 2010.

Rank 1960 2010
1 New York New York
2 Chicago Los Angeles
3 Los Angeles Chicago
4 Philadelphia Houston
5 Detroit Philadelphia
6 Baltimore Phoenix
7 Houston San Antonio
8 Cleveland San Diego
9 Washington Dallas
10 St. Louis San Jose

The rise of the “Sun Belt”, housing bubble notwithstanding, is a real and awesome phenomenon. Below the fold I’ve taken some demographic trend data for the top 10 cities of 1960. The first two panels show raw population data. The second two panels show the decade-to-decade change in population in terms of multiples (i.e., 1.2 for 2010 means that the population in 2010 was 1.2 times that in 2000).

 

For me the biggest surprise is how much the trajectory of Chicago resembles stereotypical “Rust Belt” cities. Unlike New York City Chicago lost population in the aughts. In some ways New York City is sui generis. I went through the precipitous near collapse in the 1970s, just as the smaller cities of the Heartland, but over the past few decades it has refashioned itself, exhibiting a demographic vigor to match Los Angles on the West coast. A second surprise is Philadelphia’s robustness. Unlike the Midwestern cities it seems to have developed some “stabilizers.”

More starkly, observe the rate of change in the 1970s. We often reflect upon the cultural shifts in the 1960s, the first half of which are arguably part of the long 1950s. But chaos of the late 1960s bore fruit over the 1970s, and echoed down into the 1980s. Though the worst of the decline was over by the 1980s, a pall of decline still hung over much of the decade (e.g., “Japan Inc.”) due to the experiences of the 1970s, Ronald Reagan’s robust counter-narrative notwithstanding. And the great urban revival of the 1990s clearly leveled off in the last decade.

Source data.

No comments please, we’ve made it through peer review (?)

Filed under: science — Razib Khan @ 11:58 am

Recently Daniel MacArthur pointed to the vibrant discussion over at Genomes Unzipped on a moderately infamous paper from Science last year, Widespread RNA and DNA Sequence Differences in the Human Transcriptome, asserting that it is “exactly what open peer review should be like.”  This made me wonder, it’s been over five years since Chris Surridge asked why there was so much more commentary on a PLoS ONE paper, By Hook or by Crook? Morphometry, Competition and Cooperation in Rodent Sperm, on blogs than on the paper itself. Has anything changed? The most viewed paper on PLoS Biology, How Many Species Are There on Earth and in the Ocean?, has 9 comments for 45,000 article views. In contrast, Genomes Unzipped has 14 comments for likely far fewer page views. Additionally, if you find the post on the weblog the comments automatically load. Not so with the PLoS Biology paper, you have to click through (yes, I see how this can be a feature, not a bug, but in that case why even bother with comments if you provide an email address for correspondence?)


I’m not going to rehash Joseph Pickrell’s argument in Why publish science in peer-reviewed journals? Rather, I want to reiterate that the ultimate goal here is to figure out how the world works. To understand that you need to get a sense of the science, and if you aren’t a specialist simply consulting peer reviewed literature is not always sufficient or practicable. Recently a researcher was discussing the Science paper at issue above to some graduate students, reiterating Joseph Pickrell’s points. When someone was curious about further details the individual explaining the controversy specifically cited Pickrell’s earlier post on the topic in Genomes Unzipped to get an understanding of the broader issues of the critique. From what I know this person is not a major reader of science blogs. Rather, Pickrell’s post likely came up high on a search engine query, and to his mind was an appropriate reflection of the scientific consensus as he understood it. The question is why does the discussion not begin in the journals themselves? Why do curious people have to scour the internet? When a controversy or “big paper” emerges in a specific area outside of my detailed focus I know what I do: I simply load the appropriate science blogs which cover that topic. There I hope to get a sense of what the people in the field think. Peer review is not sufficient in many cases. Science is a production of humans, and so is fraught with politics, and reputations are thrown about to get a paper in “high impact” journals.

But is anything broken in the first place? Is this how it’s supposed to work, and how it’s going to work? Journals make a huge argument for their value. They charge academic libraries quite a mint (with honorable exceptions made for open access journals!). It seems that they should make at least a good faith effort at post-publication review and extension. Did you know that Nature has a comments feature? Have you ever seen a comment posted via this feature?

March 24, 2012

Panem ~ Bharat

Filed under: Futurism — Razib Khan @ 12:06 pm

Could any real country have an economy like Panem’s? Actually, yes. Not exactly analogous, but: More mobile phones than lavatories for a booming India. I would currently bet that a future like India writ-large is somewhat more likely than China or USA writ-large. Though I don’t think there are any overwhelming odds here.

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