The boss pointed me to this new series, Portlandia. I lived in Southeast near the Hawthorne neighborhood in 2002, so the following video brings back some funny memories….

Read More

About four years ago blogger emeritus RPM of evolgen brought into sharp relief an issue which has nagged me:

Caucasian, literally, refers to people native to the Caucasus, but it has become interchangeable with any number of ‘White’ populations, most of wh1om trace their ancestry to Europe. One gets the feeling that the term ‘White’ fell out of favor and was replaced by ‘Caucasian’ much like ‘Black’ was replaced by ‘African-American’. But the roots of such terminology are a bit disturbing; it was postulated that the natives of the Caucasus exhibited the idealized physical appearance so the Caucasus were believed to be the birthplace of mankind. The logic behind this idea — the assumption that Whites exhibit the best physical appearance — is implicitly racist. Additionally, we now know our species first appeared in Africa, so the biology isn’t any good either. The connotations of the term Caucasian along with the geographical absurdity of using that term to describe all Europeans or Whites are the two main reasons we should abandon the term.

Up until the late 1990s I had thought of people from the Caucasus mountains when I heard the term, but then I began to reorient my assumption because of its colloquial usage. But as it became more and more popular I got more irritated, because it became obvious that the type of people who now were using the term likely did not know where the Caucasus mountains were. With Ngram Viewer you can check the patterns of popularity over time:

Read More

Google is in the news, with Larry Page’s ascension. Generally when I hear people compare Larry Page and Sergey Brin it is Page who is described as the “Big Think” guy. But these guys didn’t always think big. Stupid Business Decisions: Excite Rejects Google’s Asking Price:

In 1999, Larry Page and Sergey Brin, the founders of Google (GOOG), decided that their creation was interfering with their studies and offered it to a slew of companies (including the defunct Alta Vista, which passed, and Yahoo (YHOO), which also passed, but had a strong enough product that they were able to stay afloat with their own technology). An offer was then made to Excite’s George Bell, who deemed the asking price of $1 million too high. Vinod Khosla of Kleiner Perkins went back for another attempt — this time for $750,000 — and was thrown out of Bell’s office.

George Bell still seems to be around. I guess when you achieve a certain level of success truly stupid decisions don’t matter. Whatever happened to “skin in the game”? But notice that Page and Brin actually thought about selling their idea for $1 million dollars in 1999! Bell wasn’t the only one who was lacking vision and genuine perspective. It should remind us that genuine innovation is by its nature hard to predict.

Also, Kambiz Kamrani is back blogging at Anthropology.net. Too bad he won’t be blogging chicken genetics! And another interesting blog, For what they were… we are.

Posts within the RSS feed will now be truncated. Since I occasionally write longer pieces, it is likely you’ll now have to “click through” to read the full post. If the ending of a post mystifies you, there is a good chance that it’s due to truncation, and not my being on some medications.

Finally, I feel guilty putting this post up without a great deal of content, so I’ll throw a thought out there triggered by discussion below on phenotypes in the Middle East: how many alleles which code for particular traits arose in the genetic background of population A only to move to fixation in population B? Lactase persistence in Europe may be a classic case of this, originating in Central Eurasian populations and later spreading to the Northwest European fringe, where the favored variant rose to near fixation. Here’s another possibility: the allele which codes for blue eyes in West Eurasian populations may have arisen outside of Europe, and moved into Europe through gene flow, and then been driven to fixation in the new environment. Often when people see someone with light eyes who is not European the presupposition is there has been European admixture, but it may be that a low proportion of individuals with the light eye variant around HERC-OCA2 has been the norm in Western Eurasia outside of Europe for a long time. Only in the European population did selection, or perhaps drift through population bottlenecks, recently drive the variant to near fixation around the Baltic. Anyway, I think that’s a plausible model,though someone who has looked at the haplotype in detail could no doubt disabuse me of the notion. I am inspired here by the ‘speed up’ model of human evolution, where large populations result in a greater mutational background from which natural selection can draw. Presumably with agriculture Middle Eastern populations exploded rather rapidly ~10,000 years ago vis-a-vis other groups in Western Eurasia. I now believe that a substantial proportion of the ancestry of modern Europeans and South Asians derives from a demographic expansion rooted in the Middle East (in combination with native substrate). Many of the traits diagnostic to Europeans and South Asians, and genetic alleles diagnostic to both groups, may then drive from the Middle Eastern newcomers, and not be due to deep local ancestry. This may be what occurred with R1b1b2.

Image Credit: George Baird.

1) First, a post from the past: Neandertal & H. sapiens sapiens interbreeding.

Read More

WORDSUM is a variable in the General Social Survey. It is a 10 word vocabulary test. A score of 10 is perfect. A score of 0 means you didn’t know any of the vocabulary words. WORDSUM has a correlation of 0.71 with general intelligence. In other words, variation of WORDSUM can explain 50% of the variation of general intelligence. To the left is a distribution of WORDSUM results from the 2000s. As you can see, a score of 7 is modal. In the treatment below I will label 0-4 “Dumb,” 5-7 “Not Dumb,” and 8-10 “Smart.” Who says I’m not charitable? You also probably know that general intelligence has some correlation with income and wealth. But to what extent? One way you can look at this is inspecting the SEI variable in the GSS, which combines both monetary and non-monetary status and achievement, and see how it relates to WORDSUM. The correlation is 0.38. It’s there, but not that strong.

To further explore the issue I want to focus on two GSS variables, WEALTH and INCOME. WEALTH was asked in 2006, and it has a lot of categories of interest. INCOME has been asked a since 1974, but unfortunately its highest category is $25,000 and more, so there’s not much information at the non-low end of the scale (at least in current dollar values).

Below you see WEALTH crossed with WORDSUM. I’ve presented columns and rows adding up to 100%. Then you see INCOME crossed with WORDSUM. I’ve just created two categories, low, and non-low (less than $25,000 and more). Additionally, since the sample sizes were large I constrained to those 50 years and older for INCOME.

Read More

Long time readers know well my fascination with quantitative history. In particular, cliometrics and cliodynamics. These are fields which attempt to measure and model human historical phenomena and processes. Cliometrics is a well established field, insofar as it is a subset of economic history. But cliodynamics is new on the scene. At the heart of cliodynamics is the quantitative ecologist Peter Turchin. I highly recommend his readable series of books, Historical Dynamics, War and Peace and War, and Secular Cycles. Also, see my reviews of the first two books.

With that, I am rather excited by the debut of Cliodynamics: The Journal of Theoretical and Mathematical History. Here’s the description of the brief of the field and the journal:

‘Cliodynamics’ is a transdisciplinary area of research integrating historical macrosociology, economic history/cliometrics, mathematical modeling of long-term social processes, and the construction and analysis of historical databases. Cliodynamics: The Journal of Theoretical and Mathematical History is an international peer-reviewed web-based/free-access journal that will publish original articles advancing the state of theoretical knowledge in this discipline. ‘Theory’ in the broadest sense includes general principles that explain the functioning and dynamics of historical societies and models, usually formulated as mathematical equations or computer algorithms. It also has empirical content that deals with discovering general empirical patterns, determining empirical adequacy of key assumptions made by models, and testing theoretical predictions with the data from actual historical societies. A mature, or ‘developed theory,’ thus, integrates models with data; the main goal of Cliodynamics is to facilitate progress towards such theory in history.

The first issue has an article by Sergey Gavrilets, David G. Anderson, and Peter Turchin. Gavrilets is a familiar face. I know him from his work in evolutionary theory. The paper itself is a readable and plausible model of how “medium scale” societies rise and fall through conflict and consolidation. Basically the stage of human society described in Laurence Keely’s seminal War Before Civilization; after agriculture, but before major literate state systems. Their basic method is to take a mathematical model with a tractable number of plausible parameters and run simulations which give one a sense of how it changes dependent variables of interest. Polities were modeled as being circumscribed hexagons; so they had six neighbors (instead of four which would be the case if they were squares). The area modeled had an “edge,” and polities can exist in a flat hierarchical structure, or eventually aggregate so they exhibit rank order. Additionally, polities varied by economic productivity. Finally, there was a temporal aspect in that there was a potential conflict per generation where the probability of success was conditional upon the strength of the polity. Being more powerful increase the probability of victory, but does not guarantee it. Flukes do happen. The full model can be found in the paper, which is open access. The math isn’t totally opaque, so I’m really not going to distill it down. You can swallow it whole. Rather, let’s look at the list of parameters and statistics:

Read More

A few people have inquired of the PNAS paper On sharing genes with friends. I avoided comment in part because I’m skeptical of the findings. So much behavior genomics just hasn’t panned out over the long term, and is probably susceptible to the issues which fuel the “decline effect”. Statistical significance is a random variable too. The fundamental issue which I want to emphasize is this: many behavioral traits are highly heritable, insofar as the correlation between relatives of trait value is in direct proportion to their genetic correlation. But, just because a trait is heritable does not mean that you can affix the variation to a specific set of genes. That is because the character of genetic architecture varies, and it may be that for many behavioral traits with some biological basis the causal variants which are responsible for the range in trait values are distributed across thousands of genes, and so are of very small effect.

Carl Zimmer relayed the depth of skepticism in the scientific community yesterday, and today Dr. Daniel MacArthur reviewed the paper. Here are the top line reactions:

Read More

Today I received an email from an academic with whom I am acquainted about how to get a successful blog going. Obviously the main necessary condition is actually to keep plugging away.  Though that’s not sufficient. Jason Goldman has a post up, In the Wake of Science Online (#scio11): Supporting New Bloggers. I don’t believe in supporting new bloggers just because. They have to be good. But assuming that the goodness criterion is met, what next? Last spring when I was on vacation I noticed that Jason Goldman retweeted one of my posts on Jewish genetics. I knew Jason’s blog from ResearchBlogging. Additionally, he moved into the ScienceBlogs neighborhood just as I moved out. But the topicality of our weblogs are far enough apart that the retweet got my attention.

Read More

In science, like most things, one prefers simple over complex whenever possible. You keep adding variables until the explanatory juice starts hitting diminishing marginal returns. So cystic fibrosis is due to a mutation at one gene, and the disease expresses recessively at that locus. The reality is that one mutation accounts for ~65-70% of cystic fibrosis cases around the world, and there are nearly ~1,400 known mutations on the CFTR locus. How about skin color? Mutations on a dozen genes can probably explain ~90% of the variance in the trait value across the world between populations. In fact, one single mutation on one base pair can explain ~30-40% of the trait value difference between Europeans and Africans. This is a more complex story that cystic fibrosis; you have not just many mutations, but many mutations across many genes. But, the number of genes and mutations are manageable. You can keep track of most of them in your head (e.g., I can tell you that SLC24A5, SLC45A2, KITLG, and HERC2, can explain most of the trait value difference between Africans and Europeans without looking it up).

Now think about something like height. The only gene I can think of off the top of my head is HMGA2. With obesity I know FTO. The reason is that there’s a veritable alphabet soup of genes which pop out of the numerous studies focusing on these traits. But the reality is that it seems possible that there are many genes which harbor variants of small effect size which in totality account for the range of the trait value. Abstractly this isn’t really that much more complex than the models above. You can imagine it as a concrete instantiation of the central limit theorem. But in practice it does change things when you can’t focus on one gene, or a few genes, but have to understand that there exists a huge class of genetic causes which modulate the expression of the phenotype.

We’ve reached a stage where the mapping from genotype to phenotype is getting a bit on the baroque side. We have come to confront and wrestle with ‘genetic architecture.’ Here’s what Wikipedia says about this term:

Read More