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

June 5, 2017

Open Thread, 06/05/2017

Filed under: Blog,Open Thread — Razib Khan @ 11:08 am

Just a plug for Elements of Evolutionary Genetics by Charlesworth & Charlesworth. These are two great evolutionary geneticists, and we’re lucky to have a “core dump” from them on hand.

The curious thing is that there is so much science that is tacit and implicit, that the passing of each generation of scholars means that hidden reaches of knowledge are passing away. This is the flip side of the idea of progress being made through the death of older scholars and the acceptance of novel (and more right) paradigms.

Both Charlesworths are authors on a new paper (along with Nick Barton) in The Proceedings of the Royal Society, The sources of adaptive variation. Here’s the abstract:

The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today’s understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.

Another riposte to the EES. Entirely unsurprising that these authors and this venue would offer criticism to a reframing of the field of evolutionary biology. But it gets to the heart of the reality that this is going to be an argument that will be resolved through publication of new papers, not books or long popular science articles. The footprint of the EES in evolutionary biology popular science field is heavier than within evolutionary biology itself.

The prominent medical genomicist Dan MacArthur stated yesterday:

Not to be churlish, but let me clarify judging by the numbers of people Dan followed there were conservatives and libertarians he followed, he just didn’t, and doesn’t, know who they are. Also, there were several people he followed with center-right or libertarian views as a point of fact. I know because because I’m open about my right-wing views, and these people feel and felt comfortable telling me that they don’t agree with the vocal Left-liberalism which is pervasive in the political atmosphere on science twitter. Though most science twitter people don’t post much about politics, if they do, a substantial proportion are “social justice” oriented. That’s tolerable for most people because most scientists are on the Left side of the political spectrum.

My tendency to post right-wing political stuff into the feeds of scientists is annoying for many (or as some would say “problematic), but I don’t care. I know I speak for a substantial minority in the aggregate, and in some cases the majority (in terms of the latter, what I mean is that though most scientists are liberal, most are not on that far Left, though they may fear being attacked by the far Left and so are careful not to enter into any public dissent when that contingent starts to get a little out of control).

In a curious inversion with the norm I guess, my Twitter timeline is balanced politically. If anything, it’s more liberal than not. I don’t know what it would be to be in a political silo. I hear it feels good.

Detecting polygenic adaptation in admixture graphs. Educational attainment and unibrows. Yeah. One thing: “An open question in human evolution is the importance of polygenic adaptation.” This is literally true, but I think it is pretty obvious that the latest work is suggesting there has been a lot of it.

Widespread signatures of negative selection in the genetic architecture of human complex traits.

The Genomic Health Of Ancient Hominins.

May 14, 2017

Open Thread, 05/14/2017

Filed under: Blog,Open Thread — Razib Khan @ 2:31 pm

I’ve been working on some issues related to the website. Of most relevance for readers, https:// formatting should now no longer be broken. Also, please mention it if you get a 503 in the comments. Some people probably still get them, but they should be rare (I can track hourly hits, and there hasn’t been a systemwide drop in traffic since April 22nd; basically I have a script running which pings the site for 503s and reboots Varnish if it gets them).

I also know that the MySQL database locks up sometimes. There is a script to restart it but looks like it can take at least one minute. I had one that ran more consistently but it doesn’t seem to be working.

There has only been one update on my newsletter, but if the site goes down it’s probably best just to sign up for that if you care (when it goes down for a while people email me, which is fine, but responding to emails can get tedious).

When people ask me about textbooks on population genetics, I can rattle off many because I own many and have a sense of all of them. In contrast, for evolution the only text I have is Futumya’s. Does anyone have experience with the Ridley or Bergstrom and Dugatkin texts?

Science is by its nature subject to silos. That’s unfortunate, but it’s true. Evolutionary geneticists don’t really know too much more about paleontology than the average person. I have a pretty good grasp of what’s going on human population genomics, and perhaps mammalian population genomics, but outside of that not so much.

Speaking of Lee Dugatkin, his new book, How to Tame a Fox (and Build a Dog) is out. I don’t have time to read it now, but as I have said he’s a good writer.

As some of you may know I’m taking a one week sabbatical from social media (I’ll be back on Thursday), which consists of Twitter and Facebook. That means that there are things that need to be said which need an outlet. So I put up a post on Henry Wallace over at Secular Right. An op-ed in The New York Times by Wallace’s grandson hailing is grandfather’s prophetic prediction of American fascism doesn’t mention that he was notorious for not understanding the threat of Communism in his time (and literally being deceived by Potemkin villages in 1944).Also, Brown Pundits might make a comeback as a group blog soon (also, I’m not missing it to be honest).

If you subscribe to my total content RSS feed I do try and push stuff on other blogs/publications into that.

I may start writing again outside of the purviews of this weblog. But, I think more and more it is critical to control your own means of production. Much of the web-only content at high profile sites like The New Republic from the 2000s is not accessible because of reconstitutions of their archives.

And of course, relying on Twitter or YouTube as sole distribution channels has problems. Twitter as a solo-play is I think probably not going to work. I think it could work if they kept their ambitions and aims in check, but the combination of the public stock markets and the egos of their executives means that they’ll swing for the fences. Probably they will get acquired in the next 5 years, after which who knows what the new owners will do? Just because the name Twitter will be around in 2030 doesn’t mean you’ll recognize it (go check out MySpace some time).

As far YouTube is concerned, I think for now YouTube’s content is safe, but people who are trying to make a living off it have been whipsawed by changes in policies in advertising revenues. Diversification is key.

Over at Secular Right Dain has a post up, Anti-SJW Sentiment in China. The full article is fascinating, The curious rise of the ‘white left’ as a Chinese internet insult. I will say that amoral atomization often gives way to moral revivals, so don’t expect China’s John Galt moment to last too long.

A note on comments. I notice that some people say things like “I don’t want to presume….” That’s good. One of the most annoying things about having a blog with a reasonable amount of content is that socially deficient individuals think they can start drawing conclusions about your life or situation from what you make visible. For most of this blog’s history I actually hid much of my non-blog life. When my daughter was born and I wanted to talk about her genetics obviously I had to put a bit more into the public. But it’s always good not to infer too much about people who you read. They tell you on a need-to-know basis unless their lives are their brand (here’s an example, an anonymous regular commenter once left comments talking about aspects of my personal life I’d rather not have in comments; this person remains carefully anonymous themselves. This is the kind of shit I never forget and why I have some contempt for many, though not all, commenters).

A problem as a person who is not liberal on the internet that I encounter is “lib-splaining.” Basically, since I am not liberal and they are liberal (or to the Left of center for Europeans), the prior assumption is that they can explain to me how evolution, genetics, Islam, or many aspects of history work. If they are not stupid, they immediately realize the error of their ways, though the Dunning-Kruger effect is something I confront in that the duller the person the more difficult it is to explain to them that I’m not as ignorant as they might think (this is one of the things that annoys me about Twitter).

A major dynamic that many people of any ideology seem to have is a narrowness of view that occludes many major patterns for me. One problem is that few people know much history beyond a narrow subset of regions or periods. For the stereotypical conservative one might encounter assertions such as “America is the greatest nation in the history of the world” (what does that even mean?). The reasons offered for this tend to be…well, problematic. E.g., America is always on the side of freedom. Arguably, even if tendentiously, this was not even true of the Founding! (the revolutionary side was diverse, I would suggest that the New England partisans were people who we moderns would easily identify with, but the grandees of the Tidewater less so).

For liberals the problem tends to crop up when they are speaking cross-culturally. It usually turns out that these people only know a shallow sketch of even Western history, and no non-Western history, so they don’t have any basis to make any comparisons. Part of this is the abomination which is post-colonial theory, which has replaced the need for facts with a broad-overarching Manichean vision of the world.

One place I wish everyone would start out with is to study the history of China. There are several reasons why this is important. First, much of the human past is a history of China. One can not understand the history of the world without the history of China. One can not understand Japan, Korea, and Vietnam, without understanding China. Second, one can not understanding today’s China without understanding the China of the past, and one can not understand the 21st century without understanding China.

I will make some concrete recommendations. In sequence of order chronologically, The Early Chinese Empires: Qin and Han, China between Empires: The Northern and Southern Dynasties, China’s Cosmopolitan Empire: The Tang Dynasty, The Age of Confucian Rule: The Song Transformation of China, The Troubled Empire: China in the Yuan and Ming Dynasties, and China’s Last Empire: The Great Qing. I think all these books are both scholarly, and accessible to the lay audience. The Han dynasty surveys usually distill what you need to know from the earlier periods, so that is more purely academic (and the Shang dynasty is really the purview of archeology and not history).

Some of you may want a gentler introduction. John Keay’s China: A History would fit the bill. But please don’t stop at Keay. It is more a primer, and won’t give you much depth. John King Fairbanks’ China: A New History is good for depth, but it focuses way too much on recent events. I have a soft spot for A History of Chinese Civilization by Jaques Gernet, but it’s not that easy to always find a copy that is not priced outrageously (I read it as an undergrad via a library copy).

It is hard to ignore when one reads Chinese history that there are both clear similarities and obvious differences in relation to the West. For example, the analogy between the Kangxi Emperor and Marcus Aurelius jumps out at you, despite 1,500 years of space and the geographical-cultural chasm (one could argue that Marcus Aurelius is a bit idealized, while we know a great deal about the Kangxi Emperor from documents). A contrast is the role of religion in Chinese history. Though religion is important, the dominant recurring theme of subjugation of religious passions and concerns to that of public order and life was a revelation to Enlightenment intellectuals, who saw in China a “better way.”

Which brings me to a thought, would readers be interested in a “book club” format? I’ve had friends do this before on their blogs, and it’s worked out. But we’d need enough buy in. I’d put up a post once a week, perhaps every Sunday, and others would jump in.

Accumulation And Functional Architecture Of Deleterious Genetic Variants During The Extinction Of Wrangel Island Mammoths. If this was going to happen, it was going to happen to this population.

Blatant hypocrisy: Milo Yiannopouos now part of demonstration to cancel a graduation speaker. The fundamental issue, which I alluded to earlier this week, is that it may not be that the center can hold. Once the far Left began utilizing tools of speech suppression, which has been the norm throughout human history, it wasn’t going to be limited to them. Old fashioned liberals, generally older white men, are exactly correct about what will happen. It doesn’t matter, because norm-based group are so segregated the campus Left won’t back down and put away the ticking time bombs it’s been blackmailing the administration of universities with. Perhaps they know that everyone is going to jump off the cliff together, but it doesn’t matter.

Inferring Genetic Interactions From Comparative Fitness Data. There were some. Interactions that is.

One may have noticed that I’ve switched over to linking to biorxiv more and more. I also am forgetting to say “preprint” instead of “paper.” I think this presages a shift toward post-publication review. The future is finally almost here.

Phenotypic heterogeneity promotes adaptive evolution.

Also, Scireader seems back up.

This is the week you should be reading the Bell Beaker blog.

Coalescent theory. Do you know what it is? If not, you probably should if you are interested in population genetics.

May 7, 2017

Open Thread, May 7th 2017

Filed under: Blog,Open Thread — Razib Khan @ 7:18 pm

I read some of Wendy Doniger’s translation of the The Rig Veda. It’s about ~10% of the hymns in the whole work, but the author claims they’re the more important and evocative ones. There is a reasonable amount of commentary as well.

Two things so far. First, little similarities between Indo-European mythologies I was not aware of, such as the relationship between Indra and his father and Zeus and his father. Second, the Vedic Aryans were truly barbarians. I do not say that in a pejorative sense, but simply descriptive in that these are people who are outside of the gates of civilization. They were most def most total bros.

Reading some of Richard Haier’s The Neuroscience of Intelligence (I got a review copy, though I forgot I’d gotten a Kindle edition earlier). It is a short work, and though I haven’t gotten much through it it reminds me somewhat of Stuart Ritchie’s Intelligence: All that Matters. The main difference is that there is more of a focus on neuroscience.

Psychometrics, like the cognitive anthropology of religion, is a field I take some interest in, but mostly I’ve gotten what I want out of it and do not follow it closely anymore. That being said, I thought I would bring up an issue in relation to intelligence tests.

It is common to assert among many, including many biologists I know, that intelligence testing only measures how well you can take a test. This is false. It is well known that intelligence testing robustly predicts later academic performance to a reasonable degree of correlation. Of course a correlation of 0.50 can be highly significant, and also have lots of exceptions. But that is not a rebuttal, because no psychometrician would assert that their instrument is a perfect predictor, in large part because they also agree that academic performance has other major dimensions, such as conscientiousness, which are not accounted for by these tests.

Probably the major issue that highly educated people do not account for is range restriction. The issue is simple, but often overlooked. One of the professors I TAed for once explained to a class his graduate school did a survey and the correspondence between GRE score and grades to later scientific achievement was low to nonexistent. I asked him what university he went to. He said Stanford, and I immediately pointed out to him that Stanford graduate students are not a typical sample. He grasped what I was getting at because as a biologist he understands range restriction in other contexts, and we did not engage in a debate on this issue any further.

An interesting chart from the book, derived from the Study of Mathematically Precocious Youth, illustrates that standardized tests are highly predictive, even when you move many sigmas from the mean. Below are results for mathematically gifted 13 year olds and their outcomes as a function of their result on the math SAT at that age:

Remember that a math score of 450 for a 13 year old is not that bad. So the kids in the 700 range are truly exceptional.

To me the regional differences in voting in France are fascinating. I suppose I’ll get the raw data and look at some point myself. More rural de-industrialized areas went for Le Pen, as did the far south, which has long had tensions with its Muslim population (and where the pied-noir population tended to settle; randomly I just found out that the actress Eva Green has a Sephardic Jewish pied-noir mother).

For a while several readers have complained that the archives are incomplete. There are two reasons for this.

One reason is that they were from RSS feeds and so in some cases the source website did not show the whole post. This leads to a cutting off of most of the content. The second reason is that about six months ago I mistakenly removed several years of posts on the aggregator website, so there was a major gap between 2013 and later.

Thankfully Ron Unz’s IT guy had formatted a version of the websites that put them into MySQL files. Because of different versions of WordPress it has taken about a week tinkering here and there, but the full archives are now online (see to the right). Please note that some of the older ones are going to be wonky because of CMS changes (e.g., going from blogger to movable type to blogger to WordPress).

Aside from reader demand one reason I set the archives up is that my archives are pretty valuable for Google. The archives went live overnight and Google has already been hitting them as Analytics tells me that organic search has shot way up.

This is important. I am frankly disturbed how social media drives much of the traffic to this website. Facebook is pretty opaque; you don’t know who the referral is from and what they’re saying. Twitter, I’m not sure Twitter will be around much longer (I think most of the Twitter referral is at least from me).The days of getting links from other blogs are pretty much gone from what I can tell (and to be honest, I don’t link to other blogs much because I don’t read other blogs much anymore)

Google is in many ways a monopoly, but it’s another pipeline to get traffic and have some visibility. More is better.

In the near future I think a lot of ‘media’ is going to disaggregate. We’ve seen many prominent bloggers become the media or join the media. That’s fine, but at some point in the next decade or so I wonder if the media landscape will thin out even more than it has today.

Scientific blogging is in many ways on a downswing. Many scientists go straight to Twitter. There are problems with this. In relation to the epistasis paper in  Science I mentioned earlier, here is a bloggy behind the scenes from the first author. The authors tweets are much harder to follow and may not be around years from now.

You have probably heard about the controversy around Rebeca Tuvel, This Is What a Modern-Day Witch Hunt Looks Like. The problem is with the “academics.” The rank-and-file students are much more tolerant. And it’s not all of the academia. Frankly it is those fields populated by style, posing, and signaling, rather than substance. I think this will take care of itself. These people burn witches for fun and profit. Once it’s less fun, and there’s no profit, they’ll move on.

Is there any reason the public funds should support this behavior:

Others went further and supported Tuvel in private while actually attacking her in public. In private messages, these people apologized for what she must be going through, while in public they fanned the flames of hatred and bile on social media. The question is, why did so many scholars, especially feminists, express one sentiment behind closed doors and another out in the open? Why were so many others afraid to say anything in public?

The worst thing for Tuvel is that she now truly knows what craven cretins her colleagues and peers are.

Just curious if readers are finding many 503’s? I think I finally tweaked the varnish restart script appropriately so that this doesn’t happen much, though I’m worried about comments.

Just a quick shout out to those who are using Amazon link to buy stuff. Looks like more people are using this option. There was one Christmas someone bought an expensive gaming computer and I got $480 total (not just because of the computer). I wouldn’t mind if revenues got that high!

King James asserted that “No Bishop, No King.” I think this was wrong. But what follows from what? That is the question. What if we all agree that truth is not the goal, but social harmony is. What follows from that?  I have some ideas. More for later….

Hope the Wonder Woman movie isn’t ruined by DC’s kiss of death.

May 5, 2017

BaneCat is back!

Filed under: BaneCat,Blog,Culture — Razib Khan @ 9:39 pm

May 1, 2017

Open Thread, 05/01/2017

Filed under: Blog,Open Thread — Razib Khan @ 6:24 pm

The survey suggests that 14% of my readers (or at least 14% of the 425 people who responded to the survey) consider themselves geneticists in some fashion. Above you see all the types of geneticists read this weblog. Remember that people can, and did, check more than one box. Not surprisingly, 75% of people who said they are “genomicists” also stated they were “computational biologists.”

In terms of knowledge, only 50% of geneticists who read this weblog could recall Hamilton’s Rule or the rate of substitution in a neutral model. Somewhat surprising to me, but only one out of three geneticists reading consider themselves a population geneticist so it is not entirely unreasonable.

If you have read me for a long time you know I’m a fan of alternative history, and alternative history fiction (some of you have followed me from USENET from those groups).

Though I think Harry Turtldove has gotten a little hackish recently (too much quantity, not enough quality), his older stuff is good. Agent of Byzantium in particular is good, not taking the easy way out of later books, which basically dress up events from our timeline in somewhat different garb. For the mainstream science fiction reader Years of Rice and Salt is probably what they are most familiar with, though I think it’s a little overrated. The Uchronia website has a good list of books and works, but I thought I’d pass something else along I found on Twitter, Clash of Eagles, which is volume 1 of a trilogy. Too bad I don’t have much time to read fiction…it looks like there’s some really good work being produced today.

A question in the comments below, isn’t 2007’s Principles of Population Genetics a bit on the old side? I don’t think this is a big issue. But if you want a more recent book, 2013’s An Introduction to Population Genetics: Theory and Applications is more what you are looking for I guess. Here is the publisher introduction:

“A text for a one-semester course in population genetics. It introduces students to classical population genetics (in terms of allele and haplotype frequencies) and modern population genetics (in terms of coalescent theory). It presents numerous applications of population genetic methods to practical problems, including testing for natural selection, detecting genetic hitchhiking and inferring the history of populations.

Basically the reason this book exists, in my opinion, is that older works don’t explore in much detail genomic applications of population genetic theory. And that’s the main reason you would be unsatisfied with an older work, because it doesn’t grapple with genome-wide data, because that was not a major concern when population genetics was being developed as a field. Even a book that was published in 2007 just isn’t really going to be up to date when it comes to genomics, because 2017 is so much further along.

But ultimately genomics isn’t really necessary to understand population genetics. Kimura and Crow’s Introduction to Population Genetics Theory, written in the late 1960s, would be more than sufficient I would think (though I do have to say that An Introduction to Population Genetics is very good about integrating a coalescent framework into one’s thinking, which is obviously not the case with older texts).

I think I figured out the way to resolve the 503 error problem (more precisely, I figured out how to set up the script that checks for 503 errors and restarts varnish if it’s giving 503 errors). I’m also working on restoring the full archives of my content (have to get the MySQL tables working in my database for this weblog).

Lee Alan Dugatkin’s How to Tame a Fox (and Build a Dog): Visionary Scientists and a Siberian Tale of Jump-Started Evolution is out. I’ve enjoyed three of the author’s books, The Imitation Factor: Evolution Beyond The Gene, The Altruism Equation: Seven Scientists Search for the Origins of Goodness, and Game Theory and Animal Behavior. He’s a great writer, and an accomplished scientist, so I’m sure How to Tame a Fox (and Build a Dog) will be good.

King James asserted “No bishop, no king.” I would say, “no science, no liberal democracy.” Not that I think science is the root cause of liberal democracy, I think the two emerge from a particular view of the world and how to engage it and talk about it. The decline in scientific discourse then won’t cause the decline of liberal democracy, but will signal the diminishing of the fuel which fires both. More on that later.

I said this on Twitter because I think this might be a serious idea:

People are saying I should read something “out of the norm.” I used to do that more often in the past. For example, I read The World Beyond the Hill – Science Fiction and the Quest for Transcendence. Though I guess it was literary analysis and history of a genre which I found interesting. But what specific books should I read? I’ll pick one and get back to you with my opinions….

The Evolution Of Covert Signaling. Rule-of-thumb, if it has Richard McElreath on the author list, it’s worth reading.

My request for readers to buy things from Amazon through the links on this website has been modestly successful. I didn’t make a “record” amount of money, but I did notice more “random” things than usual, which suggests to me that I pushed more revenue through that avenue than would be otherwise expected.

If winning is all that matters, then there are no rules in the game.

Now and then I wonder why I’m still blogging all these years later. I don’t make much income off it. If I wanted to be “famous” I would have been much more careful about what I said over the years. Part of it is that I get some interesting comments from readers who aren’t stupid, unlike most humans, who are basically the literal definition of vacuous. But part of it is that I don’t quite see anyone else saying some of the things I say or occupying the same space. So here I am. For now. If someone else is occupying the same space…, tell me and I’ll perhaps retire.

April 26, 2017

Why do you read me and who are you

Filed under: Blog,Unlurk — Razib Khan @ 8:20 pm

The first time I tried to get through Scott Atran’s In Gods We Trust: The Evolutionary Landscape of Religion, I gave up because it seemed so pretentious and impenetrable. My curiosity was piqued by the fact that the subtitle alluded to evolution, and I was interested in evolutionary psychology. But though In Gods We Trust does talk somewhat about the evolutionary origins of religion, fundamentally it’s a work of cognitive anthropology.

Because I did not know about this field, its lexicon struck me as totally opaque, and there seemed something almost Post-Modern and French about Atran’s prose. Actually though this perception made some sense, Atran, Dan Sperber, Pascal Boyer, and Larry Hirschfeld actually came up with the naturalistic paradigm in anthropology while meeting at Sperber’s home in Paris in the early 1980s.

I did end up reading In Gods We Trust front to back a year after I initially tackled it, along with some other books on religion from this perspective (e.g., Religion Explained by Pascal Boyer). Up until 2007 or so I would write extensively on cognitive anthropology and religion, but I got what I wanted to in terms of insight after period and do not write much on this topic (in 2006 I actually got invited to a conference with a press pass on the topic of religion and evolution, my interests had become so well known in this domain).

So I was surprised to see this comment:

I’ll give it a go. I tried starting with Principles of Population Genetics but found it heavy going (Ive only been reading here for a few years and mainly got into it for the posts about religion, but the genetics stuff is quite interesting)

I suppose I still write about religion enough that that might hook some people. Though honestly I don’t have anything original to say…it’s just that much of mainstream commentary strikes me as totally dumb and uninformed.

But that prompts me. Consider this an “unlurk” thread. Two questions:

1) Why do you read me? (and implicitly, what should I write about more?)

2) Tell me anything about yourself that you think would be of interest to me or other readers (some of you are not anonymous, so I know those who are lawyers in Colorado or engineers in Australia; that sort of thing)

April 23, 2017

LaTeX notes

Filed under: Blog,LaTeX — Razib Khan @ 11:40 pm

I recently installed a plugin that will allow me to render LaTeX. Mostly this is because I’ve long avoided writing out equations because it’s awkward in HTML, and it gets unintelligible quickly. This will allow me to explore population genetics in its “natural language” a little easier.

But I just noticed on my RSS feed view the LaTeX is not rendering for whatever reason. Where there should be equations or LaTeX rendered text there is a blank space. This is unfortunate, but I don’t know what to do about it. So just click through if you want the equations. If you are willing to “hum through” those portions it shouldn’t matter. The equations aren’t going to take up much of any post.

Also, Donald Knuth is a god. Probably he’ll think that’s blasphemous because he’s a Lutheran and all, but The Art of Computer Programming beats the Bible in my book!

Open Thread, 3/23/2017

Filed under: Blog,Open Thread — Razib Khan @ 10:48 am

The reader survey now N > 300. I assume it will stabilize in the next few weeks in the 400s.

So far the biggest surprise that I’ve noticed is the ratio of married to divorced; 14o to 9. But, this aligns with research that college educated people do not get divorced at a high rate, and more than 50% of my readership has completed graduate educations, so the sample is probably even more biased.

In France it is Marcon vs. Le Pen for the second round it seems. It seems likely Marcon will win the second round…but I do wonder if some far Left voters will refuse to vote for a candidate is a pretty transparent avatar of the globalist elite.

I love California, but, In costly Bay Area, even six-figure salaries are considered ‘low income’:

San Francisco and San Mateo counties have the highest limits in the Bay Area — and among the highest such numbers in the country. A family of four with an income of $105,350 per year is considered “low income.” A $65,800 annual income is considered “very low” for a family the same size, and $39,500 is “extremely low.” The median income for those areas is $115,300.

The problem many, but not all, Lefties in this part of the country have is their rhetoric is always about making housing affordable, not making more housing (which would naturally lead to more affordability).

Stanford CS department updates introductory courses: Java is Gone.

I was a bit surprised how few readers had read Matt Ridley’s Genome: The Autobiography of a Species in 23 Chapters. I’d highly recommend it.

A new wave of GSS data is out. Might start some GSS blogging again.

Maybe moderate drinking isn’t so good for you after all:

But our latest research challenges this view. We found while moderate drinkers are healthier than relatively heavy drinkers or non-drinkers, they are also wealthier. When we control for the influence of wealth, then alcohol’s apparent health benefit is much reduced in women aged 50 years or older, and disappears completely in men of similar age.

People I know had long warned these were observational studies. But perhaps I run with a strange crowd….

Why the Menace of Mosquitoes Will Only Get Worse: Climate change is altering the environment in ways that increase the potential for viruses like Zika.

April 21, 2017

2017 Gene Expression reader survey

Filed under: 2017 Reader Survey,Blog — Razib Khan @ 6:22 am

Since I’m finally getting settled in here, I thought it was a good time to do a reader survey: https://www.surveymonkey.com/r/MW3YFZH.

So it’s open. You can only take it once, but it shouldn’t take more than a few minutes. There are 30 questions but the first 20 are mostly demographic and should go very quickly (e.g., your age, your sex, your race), and the last 10 are not difficult either (if you don’t know if you are a deontologist or consequentalist on ethics, don’t answer). Many are now of the form where you can answer more than one option.

I basically took the template of last year’s survey, made several changes, removing some questions and adding some. Also, I stole a few from Slate Star Codex.

You can read the non-text answers of the 2016 survey here.

In the middle of May I will the raw data (no-IP) and post it here so others can analyze if they want.

Addendum: Since I don’t know where else to put this, I have noticed an increase in referrals through my Amazon links. So that’s much appreciated. Obviously I’m not really getting paid much for blogging or doing the sysadmin activities, but it’s definitely going to covering overages from VPS traffic or anything like that. Remember, even if you don’t buy directly through the link I still get a referral if you are on Amazon during a session and buy something different.

Addendum 2: Forgot to mention. I’ve been doing reader surveys since 2004. The final tally of the number of people who fill the survey is always between 300 and 500, invariant of how much traffic I received (my traffic has varied about an order of magnitude over the years). It is curious to me that this “core readership” (as I perceive it) is about the same size as a Roman cohort.

April 17, 2017

Only half of the traffic on this website is a personal ‘computer’

Filed under: Blog,Metrics — Razib Khan @ 12:20 pm

I spend way too much time semi-competently managing the VPS this site is hosted on. But at least now I can look at Google Analytics. I’ve found some interesting things.

For example, 35% of the traffic on this site comes from phones, and 10% from tablets. That means that conventional computers are only somewhat more than half of the views. Additionally, 50% more of the Facebook shares are via the mobile Facebook app than the normal desktop version (I tend to get the most referrals from Twitter since I have a bigger Twitter following, but at some point I expect Facebook to surpass that as people realize I’m blogging again).

Probably going to make a few changes to make the site more mobile friendly since so many of you tend to read it on that device….

April 16, 2017

Open Thread, 4/16/2017

Filed under: Blog,Open Thread — Razib Khan @ 4:41 pm

Happy Easter. Spend most of the day figuring out how to restart Varnish. I don’t really know why there are so many database connection problems and caching…but I inherited the VPS. Might have to bone up on being a sysadmin more. Do any readers know if Varnish is really worth a modest site like mine?

Erdogan Claims Vast New Powers After Narrow Victory in Turkish Referendum. First, I have to say that The Future of Freedom: Illiberal Democracy at Home and Abroad is pretty relevant today. Second, Erdogan has shown many faces to the world over the past 15 years. I remember for example him telling people in post-Arab Spring Tunisia that in a free society atheism is a real option (to some criticism).

Are 90% of academic papers really never cited? Reviewing the literature on academic citations. It’s really a problem in the humanities:

Many academic articles are never cited, although I could not find any study with a result as high as 90%. Non-citation rates vary enormously by field. “Only” 12% of medicine articles are not cited, compared to about 82% (!) for the humanities. It’s 27% for natural sciences and 32% for social sciences (cite). For everything except humanities, those numbers are far from 90% but they are still high: One third of social science articles go uncited! Ten points for academia’s critics. Before we slash humanities departments, though, remember that much of their most prestigious research is published in books. On the other hand, at least in literature, many books are rarely cited too.

White supremacist who created stir at Stanislaus State seen punching woman at Berkeley protest. First, please note that this woman went to the protest to get “Nazi scalps” according to her social media. Second, the image of a white supremacist punching an anti-fascist woman is exactly what Sarah Haider told me was going to be a problem with contemporary Leftist valorization of violence: Left-wing organizations have proportionally many more women than right-wing militant organizations, which isn’t an asset in pitched physical combat.

Theresa May’s Conservatives are 21 points ahead of Labour in new poll. I think Scotland will leave the United Kingdom in the next 5 years.

Suzan Mazur interviews Richard Lewontin. I used to think Mazur was exceptional, and she still is, but only in her artlessness in pushing her agenda.

April 12, 2017

This website is wicked popular in Boston

Filed under: Blog,Blog stats — Razib Khan @ 1:22 pm
Traffic Feb 1 2017 to Apr 1 2017, top 10 cities
New York Boston
London New York
Sydney London
Los Angeles Los Angeles
Melbourne Chicago
Madrid Washington
Toronto San Francisco
Chicago Seattle
Washington Toronto
Brisbane Dallas

Weird pattern in terms of top cities that read this new version of GNXP. I’m comparing to the old blog over the same time…most of that is search engine traffic, so it’s not totally representative. The Australian overrepresentation is strange to me but it may be some Australian focused blog posts were promoted on some site down under. As search engine traffic increases on this website I’m assuming New York will be taking the top slot….

April 9, 2017

Open Thread, 4/9/2017

Filed under: Blog,Open Thread — Razib Khan @ 4:08 pm

Roger Lowenstein’s When Genius Failed: The Rise and Fall of Long-Term Capital Management was influential in turning me against naive market libertarianism. Market can correct for errors, but when that takes the whole global economy down…. (also, hedge fund guys are genuine assholes who don’t give a shit in many cases)

Why ISIS Declared War on Egypt’s Christians. An analogy here is made to Shia in Iraq. The analogy breaks down because the Shia Arabs of Iraq are about half the population. Coptic Christians are closer to 10%. Because Egypt has a large population there are probably more than 5 million Coptic Christians. Mass migrations as occurred with Iraqi Christian can’t work because there are too many of them.

California is getting so much power from solar that wholesale electricity prices are turning negative. Not surprising if you read Ramez Naam’s The Infinite Resource: The Power of Ideas on a Finite Planet.

Syria intervention: skeptical. The best of intentions….

Postdocs getting a pay raise, but many say it’s not nearly enough. I suspect what’s going to happen is that there will be fewer postdocs and they will get paid more.

To Be a Genius, Think Like a 94-Year-Old.

UC Berkeley Was Warned About Its Star Professor Years Before Sexual Harassment Lawsuit. Searle is rightly famous. His ideas may have merit even if he is a horrible person. And for all the moral panic about sexual assaults on campus between undergraduates, one thing you notice if you are in academia is there are a well known list of creepy professors who you hear about, but who are too famous and powerful to confront unless they really, really, step over the line, or, someone is willing to stake their reputation and career on a take-down.

An updated meta-analysis of the ego depletion effect. A big deal. Probably true.

This thread illustrates that New York City consists of four broad groups of people:

1) The affluent, from young finance professionals to the Upper East Side wealthy.

2) The transient. This includes young artists and creative types who live relatively cheap and have few expenses, and will probably move on as they mature, either into another field that pays better, or, to a region they can afford. It also includes immigrants who are just starting out in this country. By the second and third generation many of their children and grandchildren will be moving out of the city.

3) The permanent poor. See the Bronx.

The dynamic upper limit of human lifespan.

Pizza chains are making a desperate push to avoid posting calories on menus. Have you seen how many calories are in one slice?

Two issues with this blog. First, lots of problems with connecting to the MySQL database. A quick hack is that I wrote a script which checks if the database is down every 5 seconds and restarts it if it’s down. Also, lots of 503 errors, probably because of a caching problem. I’ll fix this, but if you have advice, appreciate.

Also, I’m loading the full archives of my content right now. It might be disorganized, but all of it should be searchable soon(ish).

April 8, 2017

On monetizing this website

Filed under: Blog,Monetization — Razib Khan @ 9:49 am

For ten years I have not given much thought to monetization of this weblog. Other people took care of that for me.

The upside of running my own ship is obvious in terms of control. The downside is I’m now my own sysadmin, and I’m not getting paid to do that (not to mention hosting, etc.).

For over a decade I’ve also been an Amazon Associate. When I put up book reviews I link to Amazon, and if you buy the book I get a cut. But, another aspect of this is that the referral session stays active even if you use Amazon to purchase something else.

I’ve been rather passive about this so far, but now I’ve decided to put a link to my Amazon associates page on the top right. If you click through that link and buy something at Amazon I get a cut. This isn’t trivial when it comes to big ticket items. Anyway, I would appreciate if long time readers were conscious of this.

I know many of my readers buy from Amazon anyway, so it’s a way to support me generating this sort of content for “free” in the normal course of things.

April 5, 2017

What should I blog about in the next two weeks?

Filed under: Blog — Razib Khan @ 10:01 am

Any thoughts/suggestions? Only thing off limits would be anything too personal. I already asked on Twitter and got some responses so no need to be redundant unless you want to add to the weight of a preference.

Also, now that I finished Reformations* I’m finally reading Nick Bostrom’s Superintelligence front to back. But I have a lot of other Kindle books in the “stack”, and aside from those I’m going to tackle for personal/professional development (e.g., stuff on machine learning or Bayesian statistics) I have some latitude and am toying with listing books and giving readers some input in the arrangement/sequence.

* I’ll review the book at some point, but main quibble is that it was too heavy on ideas/theology, even though by the end the author admitted one should be cautious about focusing on this aspect.

November 24, 2013

Open Thread, 11/24/13

Filed under: Blog,Open Thread — Razib Khan @ 2:21 am


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

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

The post Open Thread, 11/24/13 appeared first on Gene Expression.

Open Thread, 11/24/13

Filed under: Blog,Open Thread — Razib Khan @ 2:21 am


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

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

The post Open Thread, 11/24/13 appeared first on Gene Expression.

January 3, 2013

The end of the blogroll

Filed under: Blog — Razib Khan @ 11:55 pm

One of the major annoyances with the redesign of this weblog was that its precipitous nature was such that many of the sidebar links, etc., were removed. But, it did make me admit a major point: blogrolls are pretty much dead. In the early years of the blogsophere they served as a way to share traffic and endorse sites of interest. But with the rise of RSS, and later Twitter and its confederates they went into decline. By the end I barely recalled which sites I had on my blogroll; most of them I followed in via RSS. So I’m not going to recreate one at this point. Rather, if you want to get a sampling of what I read and such, please see my Pinboard page (to which you can subscribe via RSS if it suits you). And of course you can follow me on Twitter, though that will include my banter with other people and such. A more likely avenue is to note which websites I link to in my posts…though I’m not a copious linker to other blogs at this point….

January 2, 2013

Andrew Sullivan goes independent

Filed under: Blog — Razib Khan @ 11:13 pm

You may have heard that Andrew Sullivan & compnay’s The Daily Dish is leaving The Daily Beast. This is making some waves in the blogosphere, with many of my thoughts being in line with Tyler Cowen‘s. I’ve followed Sullivan’s career since the mid-1990s when he was editing The New Republic, and I remember reading Virtually Normal in 1999. In 2000 I noticed he had is own independent website, and over the course of the decade he’s become a internet impresario of sorts. In those years Andrew Sullivan has linked to Gene Expression in one of its incarnations many times. The Daily Dish has also been one of the major boosters of another website with which I am involved, Secular Right. I was even solicited for my own reflections on the 10 year anniversary of Sullivan’s blog.

This is all on my mind because Sullivan et al. are now rolling out a $19.99 membership plan for all their original content & curation services. That’s a very small price (and the gate is very leaky). I can spend more in two visits to Panera Bread. The Daily Dish is certainly an essential part of my information ecosystem. But, the important point for me is that I am only a marginal consumer of the primary production of Andrew Sullivan and his confederates. I encounter as people share links on Facebook, via Twitter, and through referrals (my non-science friends and acquaintances in “real life” only encounter my blogging persona on Sullivan’s site). There’s just so much there that I assume I’ll encounter it through the sieve of the broader internet, in which Sullivan and company loom large. So what I’d be paying for is Andrew Sullivan’s role in the ecosystem, not Andrew Sullivan’s blog per se. It would be like paying for Twitter or Facebook, which I don’t pay for now.

$19.99 is a pittance. But if I give Andrew Sullivan his due, who else should I “tip.” How about Tyler Cowen? Or Maria Popova? I consume more of Tyler’s content directly than Andrew’s, and Maria’s even more indirectly and in a diffuse fashion. In terms of media consumption I’m currently a subscriber to The New York Times, contribute to Wikipedia, try and support bloggers who I read and have fund drives, and also have a Netflix account. This isn’t much. But it starts to add up. The content universe of the internet is vast for the infovore, especially for one who relies a great deal on intermediating technologies to sift and filter the stream of content.

Like Tyler I don’t really know where we’re going with all of this, and how people who generate content and take time to curate can be appropriately compensated for their time.

September 26, 2012

Open thread, 9-26-2012

Filed under: Blog — Razib Khan @ 10:00 pm

Be heard!

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