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

November 30, 2016

Endings &Amp; New Beginnings

Filed under: Last Post,Miscellaneous — Razib Khan @ 9:37 pm
It's been exactly three years since I moved on from Discover. Change is timeless. So I thought it would be a good time to announce the move to another project today. Until further notice this is my last post as a blogger at Unz Review. Just as when I left Discover, this shouldn’t impact regular...

Endings & new beginnings

Filed under: Last Post,Miscellaneous — Razib Khan @ 9:01 pm

Screenshot 2016-11-27 20.15.36It’s been exactly three years since I moved on from Discover. Change is timeless. So I thought it would be a good time to announce the move to another project today.

Until further notice this is my last post as a blogger at Unz Review. Just as when I left Discover, this shouldn’t impact regular readers very much in terms of substance and content. As always you can follow me through my RSS feed, http://feeds.feedburner.com/RazibKhansTotalFeed, Twitter, http://twitter.com/razibkhan, and of course, my website, http://www.razib.com (I’m surprised how many people bookmark that website, as I got some emails when I changed the formatting).

Screenshot 2016-11-29 15.20.38The new site where I will host my content is not up yet, but it should be live within less than two weeks as engineers and designers work to get the final pieces in place (~2 weeks is within 95% confidence interval of the expected value, obviously hope it will be closer to now than not). If you want to be notified by email when the site goes live, subscribe to my newsletter. I probably won’t send out an email more than once a month, but I realize that not everyone uses RSS or Twitter, so it is probably best to start collecting a list of addresses for those who follow my work and would prefer to be contacted that way. If you are old school and just want to bookmark and check the site to see when it goes live, this will work:

http://gnxp.nofe.me

If you have a blog, please update your link to: http://gnxp.nofe.me. It will help me with getting some PageRank (I’m also going to point the front page of http://gnxp.com to the new site).

There will be some changes and flux. I’m starting “my own thing” over at N of Everyone, where I’m working with some friends to develop a new way of disseminating science to the masses. That is, I’m not just going to be a blogger, but am taking an active role in running the shop. A few of the big ideas motivating this move can be found in the piece I coauthored with David Mittleman from a few years back, Dragging scientific publishing into the 21st century. So expect the newest iteration of Gene Expression to be somewhat more experimental in terms of playing around with feature set and evolving more over time.

Also, honestly I’m not sure that Twitter will be around in its current form in another five years, so the Gene Expression at N of Everyone is going to be my attempt to create an independent platform so that I can communicate to who I want to communicate without relying on intermediaries…indefinitely (as long as I’m interesting in doing this, my professional path is definitely going to remain in science so I can express my opinions honestly without having to toe party lines).

Addendum: I’ll be moderating comments here for a bit as long as stray threads continue as long as Ron lets me continue with my permissions, but eventually I’ll stop checking.

Razib Khan at the Center of Eurasia

Filed under: Genomics,science — Razib Khan @ 6:41 am
The Eurogenes blog is running a fundraiser. I chipped in mostly to support his continued blogging. I don't agree with everything he posts, but the site is a good and valuable resource. "Genome blogging" hasn't gotten as far as I'd have thought it would have in 2010, mostly because the initial burst of enthusiasm wasn't...

November 29, 2016

Tad Williams’ Revisits Osten Ard

Filed under: Fantasy,Miscellaneous — Razib Khan @ 11:30 am
Tad Williams has a new book set in Osten Ard, The Heart of What Was Lost. At only 224 pages it seems more like a novella compared to what he produced for his original series. The last of that of that trilogy, Memory, Sorrow, and Thorn, To Green Angel Tower, weighed in at more than...

November 28, 2016

Genomics Is Not Magic, There Is No Magic

Filed under: Genetics,science — Razib Khan @ 3:26 am
MIT Technology Review has an article up, Do Your Family Members Have a Right to Your Genetic Code?, which is now part of the genomics-human-interest-piece genre you see regularly. Here you have the exemplar of this sort of narrative: what do you do when one twin gets a test and the other does not, and...

Hipster Video Gaming

Filed under: Miscellaneous,video games — Razib Khan @ 12:50 am
I began playing video games as a child after the crash of 1983. At the time I wasn't aware of the tumult in the culture and the technology scene that that had caused. Video games were just fun, not the it thing I suppose. Perhaps as an analogy it would be like getting online in...

November 27, 2016

Top Books Purchased Through This Site

Filed under: Books,Miscellaneous — Razib Khan @ 6:13 pm
So I have an Amazon referrer account. I've had one since 2003. Pretty much I use it to get money when people buy books (or other items) through links here. It's a non-trivial, though not princely, sum of money. Especially since it's passive. These are books I've read and want to talk about anyhow (usually...

Top books purchased through this site

Filed under: Books,Miscellaneous — Razib Khan @ 4:54 pm

51OftfuYlSL._SX316_BO1,204,203,200_So I have an Amazon referrer account. I’ve had one since 2003. Pretty much I use it to get money when people buy books (or other items) through links here. It’s a non-trivial, though not princely, sum of money. Especially since it’s passive. These are books I’ve read and want to talk about anyhow (usually around Christmas someone follows a book link, and ends up purchasing a computer or two, which is a way of “supporting my work” that I can get behind).

But one of the more interesting side effects is that I can see what my readers are buying (or if they are). For example, it heartens me when I see someone purchase Principles of Population Genetics. That means “I’m making a difference,” as I doubt that these are advanced undergraduates or graduate students. An interesting aspect is that I can see what interests people in terms of “clickbait”, before clickbait was a thing. Bobbi S. Low’s Why Sex Matters routinely gets a lot of clicks because of the title, despite the fact that I don’t flog it. In contrast, In Gods We Trust gets a lot of clicks because I tell people to read it to understand my thinking on religious phenomena.

51gYdVvOoQL._SX379_BO1,204,203,200_As the year ends I like to tally books people have ordered. It turns out that the most purchased book through this website for the year leading into December is The Monkey’s Voyage: How Improbable Journeys Shaped the History of Life. For Kindle, it’s Congo: The Epic History of a People.

Another category is conversion rate. In relation to number of clicks what proportion purchase. Tops for the books in that category is Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. My personal experience is that for technical books many people still prefer print for physicality and rendering of figures and graphs. For Kindle the highest conversion was Intelligence: All That Matters and Longitude: The True Story of a Lone Genius Who Solved the Greatest Scientific Problem of His Time. I think there was a “daily deal” or something at one point, and that prompted many purchases of the latter.

1846077Finally, there are books I see which I didn’t recommend, and didn’t know about. An intriguing one off this list is Barry Cunliffe’s By Steppe, Desert, and Ocean: The Birth of Eurasia. The main issue I’ve had with Cunliffe’s work of late is that he doesn’t seem to be reading enough of the Reich/Willerslev duopoly’s papers. Not that everyone has time to engage in such primary literature diving, but at this point you’re remiss if you write about archaeology and don’t include genetics. Unfortunately a search inside doesn’t indicate that By Steppe, Desert, and Ocean is DNA-heavy, but sometimes you take history and archaeology on its own terms and integrate them into your overall model of the world, rather than having someone else do that for you….

Top books purchased through this site

Filed under: Books,Miscellaneous — Razib Khan @ 4:54 pm

51OftfuYlSL._SX316_BO1,204,203,200_So I have an Amazon referrer account. I’ve had one since 2003. Pretty much I use it to get money when people buy books (or other items) through links here. It’s a non-trivial, though not princely, sum of money. Especially since it’s passive. These are books I’ve read and want to talk about anyhow (usually around Christmas someone follows a book link, and ends up purchasing a computer or two, which is a way of “supporting my work” that I can get behind).

But one of the more interesting side effects is that I can see what my readers are buying (or if they are). For example, it heartens me when I see someone purchase Principles of Population Genetics. That means “I’m making a difference,” as I doubt that these are advanced undergraduates or graduate students. An interesting aspect is that I can see what interests people in terms of “clickbait”, before clickbait was a thing. Bobbi S. Low’s Why Sex Matters routinely gets a lot of clicks because of the title, despite the fact that I don’t flog it. In contrast, In Gods We Trust gets a lot of clicks because I tell people to read it to understand my thinking on religious phenomena.

51gYdVvOoQL._SX379_BO1,204,203,200_As the year ends I like to tally books people have ordered. It turns out that the most purchased book through this website for the year leading into December is The Monkey’s Voyage: How Improbable Journeys Shaped the History of Life. For Kindle, it’s Congo: The Epic History of a People.

Another category is conversion rate. In relation to number of clicks what proportion purchase. Tops for the books in that category is Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. My personal experience is that for technical books many people still prefer print for physicality and rendering of figures and graphs. For Kindle the highest conversion was Intelligence: All That Matters and Longitude: The True Story of a Lone Genius Who Solved the Greatest Scientific Problem of His Time. I think there was a “daily deal” or something at one point, and that prompted many purchases of the latter.

1846077Finally, there are books I see which I didn’t recommend, and didn’t know about. An intriguing one off this list is Barry Cunliffe’s By Steppe, Desert, and Ocean: The Birth of Eurasia. The main issue I’ve had with Cunliffe’s work of late is that he doesn’t seem to be reading enough of the Reich/Willerslev duopoly’s papers. Not that everyone has time to engage in such primary literature diving, but at this point you’re remiss if you write about archaeology and don’t include genetics. Unfortunately a search inside doesn’t indicate that By Steppe, Desert, and Ocean is DNA-heavy, but sometimes you take history and archaeology on its own terms and integrate them into your overall model of the world, rather than having someone else do that for you….

Top books purchased through this site

Filed under: Books,Miscellaneous — Razib Khan @ 4:54 pm

51OftfuYlSL._SX316_BO1,204,203,200_So I have an Amazon referrer account. I’ve had one since 2003. Pretty much I use it to get money when people buy books (or other items) through links here. It’s a non-trivial, though not princely, sum of money. Especially since it’s passive. These are books I’ve read and want to talk about anyhow (usually around Christmas someone follows a book link, and ends up purchasing a computer or two, which is a way of “supporting my work” that I can get behind).

But one of the more interesting side effects is that I can see what my readers are buying (or if they are). For example, it heartens me when I see someone purchase Principles of Population Genetics. That means “I’m making a difference,” as I doubt that these are advanced undergraduates or graduate students. An interesting aspect is that I can see what interests people in terms of “clickbait”, before clickbait was a thing. Bobbi S. Low’s Why Sex Matters routinely gets a lot of clicks because of the title, despite the fact that I don’t flog it. In contrast, In Gods We Trust gets a lot of clicks because I tell people to read it to understand my thinking on religious phenomena.

51gYdVvOoQL._SX379_BO1,204,203,200_As the year ends I like to tally books people have ordered. It turns out that the most purchased book through this website for the year leading into December is The Monkey’s Voyage: How Improbable Journeys Shaped the History of Life. For Kindle, it’s Congo: The Epic History of a People.

Another category is conversion rate. In relation to number of clicks what proportion purchase. Tops for the books in that category is Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. My personal experience is that for technical books many people still prefer print for physicality and rendering of figures and graphs. For Kindle the highest conversion was Intelligence: All That Matters and Longitude: The True Story of a Lone Genius Who Solved the Greatest Scientific Problem of His Time. I think there was a “daily deal” or something at one point, and that prompted many purchases of the latter.

1846077Finally, there are books I see which I didn’t recommend, and didn’t know about. An intriguing one off this list is Barry Cunliffe’s By Steppe, Desert, and Ocean: The Birth of Eurasia. The main issue I’ve had with Cunliffe’s work of late is that he doesn’t seem to be reading enough of the Reich/Willerslev duopoly’s papers. Not that everyone has time to engage in such primary literature diving, but at this point you’re remiss if you write about archaeology and don’t include genetics. Unfortunately a search inside doesn’t indicate that By Steppe, Desert, and Ocean is DNA-heavy, but sometimes you take history and archaeology on its own terms and integrate them into your overall model of the world, rather than having someone else do that for you….

Top books purchased through this site

Filed under: Books,Miscellaneous — Razib Khan @ 4:54 pm

51OftfuYlSL._SX316_BO1,204,203,200_So I have an Amazon referrer account. I’ve had one since 2003. Pretty much I use it to get money when people buy books (or other items) through links here. It’s a non-trivial, though not princely, sum of money. Especially since it’s passive. These are books I’ve read and want to talk about anyhow (usually around Christmas someone follows a book link, and ends up purchasing a computer or two, which is a way of “supporting my work” that I can get behind).

But one of the more interesting side effects is that I can see what my readers are buying (or if they are). For example, it heartens me when I see someone purchase Principles of Population Genetics. That means “I’m making a difference,” as I doubt that these are advanced undergraduates or graduate students. An interesting aspect is that I can see what interests people in terms of “clickbait”, before clickbait was a thing. Bobbi S. Low’s Why Sex Matters routinely gets a lot of clicks because of the title, despite the fact that I don’t flog it. In contrast, In Gods We Trust gets a lot of clicks because I tell people to read it to understand my thinking on religious phenomena.

51gYdVvOoQL._SX379_BO1,204,203,200_As the year ends I like to tally books people have ordered. It turns out that the most purchased book through this website for the year leading into December is The Monkey’s Voyage: How Improbable Journeys Shaped the History of Life. For Kindle, it’s Congo: The Epic History of a People.

Another category is conversion rate. In relation to number of clicks what proportion purchase. Tops for the books in that category is Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools. My personal experience is that for technical books many people still prefer print for physicality and rendering of figures and graphs. For Kindle the highest conversion was Intelligence: All That Matters and Longitude: The True Story of a Lone Genius Who Solved the Greatest Scientific Problem of His Time. I think there was a “daily deal” or something at one point, and that prompted many purchases of the latter.

1846077Finally, there are books I see which I didn’t recommend, and didn’t know about. An intriguing one off this list is Barry Cunliffe’s By Steppe, Desert, and Ocean: The Birth of Eurasia. The main issue I’ve had with Cunliffe’s work of late is that he doesn’t seem to be reading enough of the Reich/Willerslev duopoly’s papers. Not that everyone has time to engage in such primary literature diving, but at this point you’re remiss if you write about archaeology and don’t include genetics. Unfortunately a search inside doesn’t indicate that By Steppe, Desert, and Ocean is DNA-heavy, but sometimes you take history and archaeology on its own terms and integrate them into your overall model of the world, rather than having someone else do that for you….

Open Thread, 11/27/2016

Filed under: Miscellaneous,Open Thread — Razib Khan @ 1:18 am
I spruced up my personal website recently. It was getting sort of cluttered. Also, the new theme should look better on mobile. Not sure how long Twitter will be around, but as long as it's around, make sure to follow me. Got my copy of The Atheist Muslim: A Journey from Religion to Reason. I'm...

Open Thread, 11/27/2016

Filed under: Miscellaneous,Open Thread — Razib Khan @ 12:26 am

510bcY7t15LI spruced up my personal website recently. It was getting sort of cluttered. Also, the new theme should look better on mobile.

Not sure how long Twitter will be around, but as long as it’s around, make sure to follow me.

Screenshot 2016-11-27 00.59.01Got my copy of The Atheist Muslim: A Journey from Religion to Reason. I’m personally opposed to a term like “atheist Muslim,” because a Muslim by definition to me is not atheist. But the author, Ali Rizvi, is an interesting fellow.

Going to try and get to Land of Promise: An Economic History of the United States before Christmas. Don’t know if I’ll get to it, but it’s been on my “to-read” list for a while.

Has anyone ever thought that the novel Musashi was somewhat reminiscent of Cúchulainn? No idea why I think this, but it’s always been on my mind…

I think someone keeps asking about South Asian genetic signatures in Southeast Asia, and I keep forgetting to respond to them. I think there was old (say Iron Age) gene flow from South Asia to various parts of Southeast Asia (basically the cores of Hindu-Buddhist archaic semi-historical polities such as Angkor era Cambodia), and, also more recent gene flow due to colonialism era migration mediated by Europeans. Also, I suspect there was more gene flow from early Holocene Southeast Asia into South Asia than we currently comprehend.

2978777Ten years after first reading it I appreciate Adam K Webb’s Beyond the Global Culture War more. Why? Probably because universal liberal democracy seems less assured as the final stationary state of society in all places now than it did then. It’s an interesting book in part because it attacks the global cultural element with which it is probably easiest to identify me with.

November 26, 2016

The Species Barriers Between Neanderthals and Anatomically Modern Humans

Filed under: Genetics,Neanderthals,science — Razib Khan @ 11:55 pm
A new paper in The American Journal of Humans Genetics, The Divergence of Neandertal and Modern Human Y Chromosomes, reports on possible reasons why we don't see Y chromosomes in modern humans from this archaic lineage, despite exhibiting detectable levels of autosomal admixture. As you might recall the clear lack of deep branching Y and...

Afro-Asiatic and Eurasian Backflow

Filed under: Africa,Genetics,science — Razib Khan @ 11:55 pm
If you follow Y genealogy you know that the distribution of R1ba2 exhibits a peculiar pattern. R1b is the most common haplgroup in Western Eurasia, and shares a deep common ancestry with R1a. It seems to have risen to high frequencies in Europe only during the Bronze Age, though has been found in earlier periods....

The species barriers between Neanderthals and anatomically modern humans

Filed under: Genetics,Neanderthals,science — Razib Khan @ 3:30 pm

gr2A new paper in The American Journal of Humans Genetics, The Divergence of Neandertal and Modern Human Y Chromosomes, reports on possible reasons why we don’t see Y chromosomes in modern humans from this archaic lineage, despite exhibiting detectable levels of autosomal admixture. As you might recall the clear lack of deep branching Y and mtDNA lineages was long one of the major genetic rationales for why gene flow between Neanderthals and modern humans was presumably not very significant. This, despite suggestive evidence from morphological analysis as well as inferences from autosomal data. The problem is that it is harder to do the sort of clean phylogenetic reconstruction via a coalescent model utilizing autosomal data (which recombines, as opposed to the Y and mtDNA, which do not for the regions of interest), so ancient genome sequences were really what was needed to convince most people with these sorts of markers.

This makes us ask: why are Neanderthal Y and mtDNA lineages not found in modern humans which exhibit indications of gene flow from other hominin lineages? After all, the lack of these really led many people off on the wrong track for years. I recall in 2008 going to a talk by Svante Paabo who reported that the Neanderthal mtDNA he had sequenced was definitely very different from anything in the current databases for our species, which confirmed his assumption that there was no admixture into modern populations (Paabo changed his tune very soon after due to the whole genome sequencing obviously). One simple explanation is that because effective population sizes of Y and mtDNA are smaller than autosomal regions of the genome they’ll be more strongly subject to drift, and exhibit higher extinction rates. In other words, it wouldn’t be that surprising of all Neanderthal Y and mtDNA went extinct after admixture because they were a small minority, and most lineages went extinct in any case. Researchers who work in non-human phylogeography who relied on mtDNA in particular can tell of many stories of being led astray by looking at one informative locus.

But chance may not be what is at work here. Buried in the discussion of the paper:

…polypeptides from several Y-chromosome genes act as male-specific minor histocompatibility (H-Y) antigens that can elicit a maternal immune response during gestation. Such effects could be important drivers of secondary recurrent miscarriages30 and might play a role in the fraternal birth order effect of male sexual orientation.31 Interestingly, all three genes with potentially functional missense differences between the Neandertal and modern humans sequences are H-Y genes, including KDM5D, the first H-Y gene characterized…It is tempting to speculate that some of these mutations might have led to genetic incompatibilities between modern humans and Neandertals and to the consequent loss of Neandertal Y chromosomes in modern human populations. Indeed, reduced fertility or viability of hybrid offspring with Neandertal Y chromosomes is fully consistent with Haldane’s rule, which states that “when in the [first generation] offspring of two different animal races one sex is absent, rare, or sterile, that sex is the [heterogametic] sex.”

The origin of species is obviously one of the founding questions which arose with the emergence of evolutionary biology. Haldane’s rule dates to the 1920s. In mammals the heterogametic sex are males, so these the hybrids which will be selected against (or, they may be sterile). There’s been a lot of research of late on why Neanderthals went extinct, and whether there were speciation barriers in keeping with the biological species concept between our two lineages. This result suggests that there is going to be interesting stuffed coming out of the population genomics of ancient hominins in the near future….

The species barriers between Neanderthals and anatomically modern humans

Filed under: Genetics,Neanderthals,science — Razib Khan @ 3:30 pm

gr2A new paper in The American Journal of Humans Genetics, The Divergence of Neandertal and Modern Human Y Chromosomes, reports on possible reasons why we don’t see Y chromosomes in modern humans from this archaic lineage, despite exhibiting detectable levels of autosomal admixture. As you might recall the clear lack of deep branching Y and mtDNA lineages was long one of the major genetic rationales for why gene flow between Neanderthals and modern humans was presumably not very significant. This, despite suggestive evidence from morphological analysis as well as inferences from autosomal data. The problem is that it is harder to do the sort of clean phylogenetic reconstruction via a coalescent model utilizing autosomal data (which recombines, as opposed to the Y and mtDNA, which do not for the regions of interest), so ancient genome sequences were really what was needed to convince most people with these sorts of markers.

This makes us ask: why are Neanderthal Y and mtDNA lineages not found in modern humans which exhibit indications of gene flow from other hominin lineages? After all, the lack of these really led many people off on the wrong track for years. I recall in 2008 going to a talk by Svante Paabo who reported that the Neanderthal mtDNA he had sequenced was definitely very different from anything in the current databases for our species, which confirmed his assumption that there was no admixture into modern populations (Paabo changed his tune very soon after due to the whole genome sequencing obviously). One simple explanation is that because effective population sizes of Y and mtDNA are smaller than autosomal regions of the genome they’ll be more strongly subject to drift, and exhibit higher extinction rates. In other words, it wouldn’t be that surprising of all Neanderthal Y and mtDNA went extinct after admixture because they were a small minority, and most lineages went extinct in any case. Researchers who work in non-human phylogeography who relied on mtDNA in particular can tell of many stories of being led astray by looking at one informative locus.

But chance may not be what is at work here. Buried in the discussion of the paper:

…polypeptides from several Y-chromosome genes act as male-specific minor histocompatibility (H-Y) antigens that can elicit a maternal immune response during gestation. Such effects could be important drivers of secondary recurrent miscarriages30 and might play a role in the fraternal birth order effect of male sexual orientation.31 Interestingly, all three genes with potentially functional missense differences between the Neandertal and modern humans sequences are H-Y genes, including KDM5D, the first H-Y gene characterized…It is tempting to speculate that some of these mutations might have led to genetic incompatibilities between modern humans and Neandertals and to the consequent loss of Neandertal Y chromosomes in modern human populations. Indeed, reduced fertility or viability of hybrid offspring with Neandertal Y chromosomes is fully consistent with Haldane’s rule, which states that “when in the [first generation] offspring of two different animal races one sex is absent, rare, or sterile, that sex is the [heterogametic] sex.”

The origin of species is obviously one of the founding questions which arose with the emergence of evolutionary biology. Haldane’s rule dates to the 1920s. In mammals the heterogametic sex are males, so these the hybrids which will be selected against (or, they may be sterile). There’s been a lot of research of late on why Neanderthals went extinct, and whether there were speciation barriers in keeping with the biological species concept between our two lineages. This result suggests that there is going to be interesting stuffed coming out of the population genomics of ancient hominins in the near future….

November 20, 2016

Open Thread, 11/20/2016

Filed under: Miscellaneous,Open Thread — Razib Khan @ 4:33 pm

lsWent to Z & Y in San Francisco recently. Second time. Still have to give Mala in Houston better marks. A friend who has been to both agrees.

Been busy working recently. But obviously a lot is going on in science and non-science….

Open Thread, 11/20/2016

Filed under: Miscellaneous,Open Thread — Razib Khan @ 4:33 pm
Went to Z & Y in San Francisco recently. Second time. Still have to give Mala in Houston better marks. A friend who has been to both agrees. Been busy working recently. But obviously a lot is going on in science and non-science....

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