SciReader, more bookmarks you might not get to….

scireaderThe Pritchard Lab at Stanford is beta testing a new tool to help you sort through the tsunami of publications coming at you, SciReader. Registration is easy enough, and I just imported my library from PubChase, which does something very similar. Right now the recommendations from SciReader aren’t really relevant, despite the fact that I’ve put in topics, authors, and a rather large PubChase library. So I assume it’s waiting me to “like” more papers. Fair enough. (or there might be a latency in relation to how soon the engine responds)

pubBut one thing that has come to mind is what I use these tools for. If you look at who I it generally does not go above 300 (I prune inactive/dormant accounts as I add people), and the list is heavily skewed toward those with a disciplinary focus similar to mine (evolutionary genomics, broadly). I’ve noticed that PubChase is usually a day to a week behind Twitter in pointing me to papers of specific interest to me.* So why are these tools even useful? First, it’s a good way to have a personal library that one can use for references. But second, it also points me to papers which are of interest, but somewhat just outside of my core domain of focus. Basically they make sure I don’t get too snug on my optimum adaptive peak, and ignore goings on outside the ghetto.

Update: Jonathan Pritchard leaves a comment, which I think is very clarifying as to why a prominent research lab is developing a tool which seems more up the alley of the private sector:

Hi Razib

Thanks for this shout-out!

To clarify about the recommendations, right now we have these running overnight, so you should get recommendations tomorrow. (In the near future we will hopefully provide these within a few minutes, but we need to rewire some code for this.)

I hope that as we develop the site further, SciReader will be a more tunable and more flexible recommendation system than the other current systems. You mentioned Twitter–I agree that this is a great source of papers. We are now scraping Twitter for papers that are being discussed on Twitter. Right now we present this as a separate Twitter summary, and we will also be incorporating this into the recommendations.

One of our long-term goals is to encourage the community to adopt post-publication recommendation and peer-review in a unified platform:
http://genomesunzipped.org/2011/07/why-publish-science-in-peer-reviewed-journals.php
although we have not yet implemented much in that direction. These functions (finding and discussing papers) should really be core activities for all scientists, so I think there’s value in having a variety of tools in this space trying to figure out how to really make this work.

Finally, this is currently a beta release and we very much welcome bug reports and suggestions on how to make this tool more useful.

cheers
Jonathan

* Google Scholar now as a recommendation service, and though it’s less frequent in telling me to notice a new paper, they tend to be very laser targeted.

Liberal science denialism at the ballot box

Golden Rice
Golden Rice
The two major issues where liberals in the United States get tagged as “denialist” or “anti-science” is on vaccination and GMO. A major problem with this thesis though is that in aggregate the social science doesn’t support this. I’ve used the GSS to check on GMO attitudes, and education/intelligence (or lack of) are the strongest predictors of skepticism, not ideology. And the best social science doesn’t seem to indicate strong political valence to anti-vaccination sentiment at the grassroots.

But sometimes looking at aggregates misses the important dynamics. I’d argue that the reason people keep thinking that there is a correlation between anti-vaccination opinions and anti-GMO opinions and the Left is that the the most vocal elite expositors of these positions hail from the cultural Left. Policy positions that start out non-ideological can quickly become polarized when elites lead in a particular direction.

The state of Oregon had a ballot measure on genetically modified organisms and labeling. Oregon also legalized marijuana. We have county-by-county results for both, as well as results for the governor’s race. I brought them together and generated some scatter plots. As you can see below:

1) There is a strong correlation on the county level for support for legalization of marijuana and GMO labeling (R2 is just the square of the correlation, and explains proportion of variation in Y explainable by variation in X).

2) There is a strong correlation on the county level for support for Democratic candidates and GMO labeling.

I am aware that not all of those who support GMO labeling are denalists. Some of them are . But my personal experience with those who support GMO labeling (there was a measure in California a few years back) is that their rationales are inchoate, and often not “reality based” (i.e., they are more about fear than anything else). Though there is no strong political valence on the grassroots at this point, I predict that if GMO labeling keeps coming up over and over, and it becomes a social movement, you’ll see it become Left-tinged as people like Michael Pollan start polarizing opinions. Of course in some places, such as Europe, the anti-GMO position has swept society to become the dominant one.

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Open Thread, November 16th, 2014

I’ve updated the raw data (csv, Excel) for the survey, which has nearly 340 respondents now. You can see the results so far here. Interestingly, 75 percent of readers claim to have read , vs. 65 percent who’ve read . More have read than or . Not surprising. What is surprising is the reader who claims to have read me for 20 years! I assume that this individual means 2 years. Most of the results align with what has always been the case since the beginning of the blog. Mostly male. Mostly atheist. Mostly white. Politically diverse. Socioeconomically skewed toward the higher income and more well-educated (~15% of readers do nothave a university degree).

Ideological profile of GNXP readers

Below I’ve take the survey results and plotted the scatter of results along two dimensions, and smoothed them out. No surprises, readers are about equally divided between libertarians, liberals, and conservatives, with a bias of numbers in that order. There are very few “populists,” understood to be people with Left economic views and Right social views. The good majority of readers are anti-interventionist, but there’s a small minority that is internationalist. There are very few “liberal internationalist” types among my readers. Rather, the tendency for this to correlate with economic, and to a lesser extent social, conservatism suggests these are probably non-libertarian conservatives in the readership.

Note: The charts’ titles have “conservatism” and “interventionism” in them because higher values on the x or y axis indicates higher values in this direction.

plot1plot2plot3

Beyond the cartoon in understanding the world

In The Atlantic Shadi Hamid has interesting article, The Roots of the Islamic State’s Appeal, which is basically a precis of his recent book . This is on my “to-read” list, so I’ll get to it at some point, though Hamid has been expressing his views for years now, so I don’t anticipate any new big picture analyses. Since my post on ISIS this summer he’s been pointing to some of my posts of interest to him now and then (e.g., ISIS’ Willing Executioners. I don’t always agree with Hamid, but he is a serious thinker. In contrast, most of the public discussion is performed in a manner where it is clear that the interlocutors have in mind only idealized cartoons. The sort of multiculturalist Left liberalism which fixates upon Islamophobia reduces Islamic civilization as an colonized adjunct to the Western experience. On the other side you have the type of intellectual whose comprehension of Islamic civilization does not extend much beyond the latest bombings. To truly grasp issue and affairs across geographic space and the vast spans of history requires some modicum of scholarly learning, which most who offer their opinion do not have. This is why I often dismiss readers who “explain” to me their understandings gleaned from a few books here and there, because if I agree their opinions are irrelevant, and if I disagree why exactly would I take the opinions of those far less informed than me on anything? Everyone has a right to their opinion. What concerns me is when the uninformed are on the ones who are influencing policy decisions.

More to the point in relation to Hamid’s piece, one of the implications is that this anti-Islamist phase in the Arab world is a correction, but that the arrow of history will probably lead to a second rise of Islamism and illiberalism. In other words, it will get worse before it gets better (if it gets better, Hamid seems to be skeptical of taking the Western arc of history as anything but a specific contingency). What immediately comes to mind then are the Copts. It seems clear that much of the Fertile Crescent excluding Israel and Lebanon will be cleansed of its ancient communities. The numbers work, insofar as these are minorities on the order of percents in populations of millions. But the Copts of Egypt number millions in a population of tens of millions. The second Islamist age in Egyptian politics and society will not be pretty for this minority, who will experience repression and exclusion as a matter of ideological commitment from the powers that be.

2014 Gene Expression reader survey

IMG_20141111_213014407Over the years I’ve realized that since I regularly verbally bludgeon readers people think I’m a severe and overly serious person. Apparently the headshot which I have on also seems a bit dickish (it was taken in Florence in 2010). To compensate for that I had a friend take this picture of me recently. I’m smiling. So I’m capable of that.

Second, it’s been a while since I posted a reader survey. I’ve been doing them every few years since 2005. I expect that since I moved to Unz Review there has been some change in the readership, but I also have the same people who have been following me across platforms (speaking of this issue, just ).

Here is this the link for this year’s survey, http://www.surveygizmo.com/s3/1890211/Gene-Reader-Survey. There are 33 questions. Many of them pretty quick (e.g., age, sex, number of children). I’ll be posting an update, and the raw data (csv format) later.

Finally, old reader survey posts.

Update: Nearly 300 responses in. Past experience tells me that the numbers won’t go much more than 500, and that will take a long time. I’ve put the results so far in csv and excel format. I’ll keep the file name the same as I generate updated reports. No big surprises so far, as the respondents pretty much fit the profile of earlier results. Only major surprises to me are the high support levels for maintaining blue collar wages through government intervention, and, the overwhelming acceptance (~75%) of anthropogenic climate change given the somewhat libertarian bias of the readers.

Is Jonah Lehrer “one of the most gifted nonfiction writers of his generation”?

candle_in_the_dark_by_kyrille-d32dybqI wish Jonah Lehrer success in his life. I’ve told him so personally and privately, though that was easier for me than most since I don’t think of myself as a science writer, so his betrayal did not strike as close to home. When I read in 2006 I actually thought it was a pretty good book, but a friend who was a Ph.D. student in cognitive psychology told me to be very careful of Jonah, because he cut corners. A few years ago another friend recounted to me the story of how she recommended one of Jonah’s books for a book-club in her graduate program, and a colleague offered that though he found Jonah’s work interesting, whenever it touched something he knew about it seemed either superficial or error filled.

So we’ve established that heretofore Jonah has a history of not being exceedingly punctilious toward the source material, fabrication and plagiarism aside. A contrast might be with Carl Zimmer. Sorry to pick on Carl, but I’d have a heart attack if I found that he did something sensationalist I’d be so shocked. Rather, the issue is whether Jonah is “one of the most gifted nonfiction writers of his generation.” Is his storytelling ability and writing style so exceptional to warrant this appellation? Many people are expressing a lack of surprise. Jonah fits the expectation of a “boy genius” writer on paper. He looks the part, he speaks the part. I used to joke that he was the “boy king of cognitive neuroscience.” To be plain about it, Jonah is a young white male, so he’ll be given particular breaks in this world. I am generally averse to this kind of reductive thinking, but it is hard in this case to avoid concluding that there is something to this. He rose fast, he rose high, and he fell far. And now he’s back where few could ever aspire to be, all within a few years.

The issue is simple for me, and it has to do with numbers. Many, many, people want to be science writers. That’s why there are now professional programs to train you to do this. But very few make a good living in this area. One issue that immediately comes to mind is that you probably need some financial buffer to really take this risk as far as a career choice. It could be family money, or, it could be that your partner has a more conventional job which can allow for income smoothing over time. I also happen to know that Jonah had some powerful and influential mentors, so it wasn’t hard for him to become a public intellectual, and so bring to the table the requisite synergy that agents are looking for. Every now and then literary agents contact me, and one issue that comes up is that they want me to increase my public profile so that I will be able to push copies of anything I publish using my own resources of my own personal fame. I have not forged that path, rather, I’d like to think I’m a much more eccentric character who has tracked himself into much more exotic territory, career-wise. But back to the numbers, the vast majority of people who aspire to be science writers will not become science writers. Jonah was one of the few who had made it, and spectacularly so. He then flamed out, again, spectacularly so. Now he’s back, seemingly on his way to success. Is he such an exceptional talent that he deserves this? Are there no other Jonah Lehrers in the world who haven’t been given a chance and who happen not to have Jonah’s baggage? It is hard for me to believe that.

That is why I wish Jonah and his family success in the world, but I’d have hoped he would have moved on to another line of work, and allowed others to step into the glory and fame. There are many people in the trenches who I think could actually succeed in doing what he did. To me it’s a matter of just desserts. To become a writer who can buy a million dollar house is a once in a lifetime opportunity. Jonah blew it. It is now rightfully the turn of others. But perhaps Jonah is just so good, such an incredible talent, that they had to snap him up again, justice be damned! Honestly of that I’m skeptical. Despite his transgressions, my interactions personally with Jonah have been cordial. He seems cool. But just because he’s a good guy is not enough to warrant a second chance in his chosen career as a writer. There are many people out in the world who don’t have the privilege of choosing their careers. Perhaps Jonah needs to experience that more pedestrian life too.

A feline genome in full

10527267_10152223425537984_6323791029112781898_n
Best friends forever
As I mentioned yesterday I’m a contributor to a paper which made a big splash yesterday in PNAS, Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. It’s been pretty widely covered in the media. One thing that hasn’t gotten that much play because most people don’t work with whole genomes is that the feline reference genome needed some work, and the group at Washington Unviersity’s Genome Institute really pushed it much further along the way to being useful. Much respect to Wes Warren and his team. This is not an uncommon issue. We may live in the “post-genomic era,” but that really applies to humans and a few particular model organisms for now. For many lineages there is the requisite genome-of-the-week paper, a hastily assembled reference, and then the group goes onto greener pastures. To get a sense, the original “cat genome” paper had 1.9-fold coverage. That means you expect that each SNP will be sequenced ~2 times. The problem with this is that that’s an average, and with variation there will be lots of gaps (leaving aside repetitive regions which are hard to span normally). And, with a ~1% error rate it will be hard to be confident about whether the variation you see is “real” or just error. To get a sense of how much better this paper’s data is they got 58-fold coverage out of pooled samples (n=22) from a wide range of domestic cats from different lineages (as opposed to just Cinnamon the Abyssinian). They also got 7-fold coverage of the wildcat samples, essential for comparative purposes.

To get you some quick background, F. silvestris catus diverged from its wildcat ancestors 5,000 to 10,000 years ago. This is in contrast to the dog, which seems to have been domesticated at least 15,000 years ago. The mitochondrial profile of Egyptian cats ~2,500 years ago was already similar to what you see in Egypt today. Over the past few thousand years domestic cats have expanded across a wide range in Eurasia. Breeds are relatively new for domestic cats, and tend to be relatively inbred lineages developed over the past few hundred years at most. In contrast the feral cats exhibit population genetic diversity in the same range as humans.

Citation: Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication
Citation: Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

So what did this paper find? First, I think the biggest aspect, which has been picked up by the media, is that cats are subject to the “domestication syndrome” due to selection on development of neural crest cells. This is not entirely surprising. Domestic cats have a reputation as being marginally tame and lacking in the servile sycophantic affect of the dog. But in comparison to the wildcats F. silvestris catus is actually very tolerant of coexistence with humans. In addition, they exhibit behavioral patterns which are not found in wildcats, such as residing in colonies. The practical reason for this is pretty obvious, as cats residing within Neolithic villages would be living cheek-by-jowl in comparison with their ancestors.

In regards to selection, because there were numerous samples, comparisons could be made across lineages using a sliding window method. Areas with high Fst and sharply reduced heterozygosity are tells for selection events. Everyone has their particular genes of interest. What always makes a mark for me is how often I recognize genes which are targets of selection in domestic mammals, considering that that there are ~20,000 genes (granted, some of these selection events sweep across many genes, and the ones listed are often selected based on functional considerations). Evolutionary processes are substrate-neutral, but across a particular phylogenetic depth they tend to rework the same ‘raw material’ over and over again. As we expand the post-genomic empire outward it seems likely that animals and plants closely associated with humans will get the earliest treatment. And I think that will yield some very definite insights into the nature of genomic constraint and convergence conditional on being wrapped up in the same ‘ecosystem’.

What the internet can be to intellectual discourse

I’m having a discussion on Twitter about the value of journals, etc., in this age. You’ll hear more from me on that topic in the near future. But right now I want to tell a quick story about how novel distribution and communication channels speeds up everything. A few years back I had some discussions with Peter Ralph while he and Graham Coop were putting together their manuscript for The Geography of Recent Genetic Ancestry across Europe. Peter told me that once the manuscript was put on a preprint server he’d email me so I could check it out. What happened is that 1) the preprint went up 2) within one hour people were talking about it on Twitter 3) within two hours I had put up a blog post about it. Peter emailed me to laugh about the fact that he was about to tell me that the preprint was up when he saw that I had already written a blog post about it.

Obviously not all aspects of the academic production process can be accelerated in this manner. But there are now steps in the reaction where there is very little friction, and the latency can be pretty much abolished. The internet introduced us to “Netscape time”, but it doesn’t seem that many aspects of science have changed much since the universal penetration of the internet….

The K14 paper, an author speaks

In the post below Martin Sikora, an author on the K14 ancient DNA paper, has responded. The whole thing is worth reading:

Hi Razib,

after reading your post it I thought it would not hurt to chime in with a bit of perspective from my side, as I don’t entirely agree with some of your criticisms. Some of the reactions to our paper have caught me a little by surprise, but in retrospect it probably reflects the complexity of the story, which is something I also struggled with (and still am!).

Part of the confusion seems to be that it is assumed that since we find that K14 somehow relates to all three European ancestral proposed by Lazaridis et al., that it necessarily also has contributed these components to modern Europeans. In your post you also seem to imply that, i.e we don’t “acknowledge the possibility that K14 did not leave modern descendants, and was part of an early population which did not end up flourishing”. I actually agree with the early population part, and we also acknowledge that in our suggested model in Figure 2, which does not have a K14-related population directly contributing to modern Europeans. What one can say with reasonable certainty though is that K14 does share substantial amount of ancestry with Mesolithic Hunter-gatherers (and therefore modern Europeans by extension), but at the same time appears less close to East Asians than all Western Eurasians, so things are complex. Therefore if you take the Lazaridis et al. model as a backbone, you need some extra gene flow to account for that, be it from Basal Eurasian into K14, or some sort of basal gene flow between East Asia and early West Eurasians, post-K14 but pre-ANE/HG split. While we don’t have the resolution to be sure, our results do suggest that K14 was close to or a already somewhat down the HG branch of the ANE/HG split, which implies that those proposed components would not only have to be already somewhat differentiated by 36 kya, but also already have had mixed to a certain extent.

Regarding your take on the PCA results, I would disagree and say that these are very much what you would expect for an individual of that age. K14 is after all ~36,000 years closer to the East Asia / West Eurasia split, so it lacks a substantial amount of drift on the European branch. It is nevertheless shifted towards Europe on PC1 from the origin as expected (a bit more so than MA1 actually). Pontus Skoglund had a nice recent paper in MBE that demonstrates the same effect (see Figure 9 in doi:10.1093/molbev/msu1920). As you say, using modern variation to infer affinities of ancient samples has limitations, and PCs are often hard to interpret. In the same spirit I would also not interpret the different admixture components in K14 as itself being admixed with all those components, but rather reflecting ancestral relationship with modern populations represented by these components. The same is obviously true for the “Middle East” component, but it still implies that K14 somehow relates ancestrally to those populations whereas all other HGs including MA1 do not.

Overall, I do think that migrations played an important role, e.g. I don’t think that “Basal Eurasian” came with K14 to Central Europe or was already present back then in another way, that seems pretty clear. I would also not say that our results are necessarily a refutation of the Lazaridis et al model, but I do think they show that it seems to have been already quite complicated in the Upper Paleolithic. If you need a new migration/component for every new individual, to me this questions at least to a some extent whether one can really talk about three or any other number of discrete ancestral populations for all modern Europeans. Personally I would expect ancient samples from the Caucasus or Central Asia to yet again spring some surprises. The cool thing is that we’ll probably know soon, since many groups are adding more and more samples to the picture.

Anyways, I just wanted to share my thoughts, hope this clears up things a bit.

Btw regrading your subsequent ANE post, I can confirm that those are the Kalash. Interesting also that the correspondingly the Kalash ADMIXTURE component shows up in MA1, but is almost absent in K14 (see our Figure S20).