How Blaze Pizza could really be more like Starbucks

pizzaI don’t want to disappoint my low-carb readers, but now and then I eat pizza. Especially when you have little kids pizza is a really good choice, since it tastes good, and even liminal toddler savages can consume it (it’s soft, it’s easy to grasp onto, and the mess isn’t that big of a deal). I probably should do more reading on food, since food is important, and I spend more than the typical American in terms of total budget (yes, I definitely lean SWPL in this domain). The family has an edition of On Food and Cooking which I used to thumb through, but I probably haven’t touched it in 5 years. Do any readers know if Pizza: A Global History is good? It’s part of a series.

My pizza preferences aren’t too sophisticated (though if you say that you like “Chicago style” you are dead to me). Usually I avoid the chains, because there’s often a good local joint. But of late I have been going toward a chain, Blaze Pizza. I really love the fact that you can order a specific pizza tailored to your preferences online, and then go and pick it up. And I’m not the only one, a 2015 survthough uey has Blaze up to the #2 “fast casual” brand. I asserted to my wife that Blaze is obviously trying to be the Chipotle of pizza, and apparently I’m not the only one making the obvious analogy. But the CEO of Blaze has higher ambitions. He wants the chain to be the “Starbucks of fast casual.” Good luck on that! (I think Starbucks is fundamentally a different beast as a Third Place, which an eatery like Blaze is never likely to be).

But here’s the reason I’m putting up this post: Blaze’s online ordering system has a major problem, and that is what they expect you to do when you pick up. Specifically, I make an online order, and then it tells me I need to pick it up at a specific time. They have everything set up, and they put it into the grill when you arrive. But, you are supposed to go up the cashier and tell them you’re an online order, and most of the time a lot of the other customers in line make it really hard for you to get the cashier’s attention. Half the time the cashiers themselves seem to wonder if you are trying to cut ahead in line. Perhaps it’s an feature of my local Blaze, but where you pick up pizza and where you pay the cashier are so close that it’s hard to differentiate myself. So yesterday it said I could pick up the pizza at 6:05. But they didn’t put it into the grill until 6:15 because 1) there was a woman who decided to harangue the cashier about the fact that they didn’t have specified quantities of how much pesto drizzle they had (she liked a “medium” amount) 2) even after she was done the cashier didn’t realize I was waiting for an online order even though I kept trying to make eye contact (I could have shouted “online order” but that would have entailed me cutting in on conversations that were going on).

If you aspire to be the Starbucks of a sector, you need to fix a problem this basic. The convenience of online disappears when there’s such an annoying rate-limiting step. If you want a frictionless experience, and I found that most of it is really smooth, you need to work just a little bit harder.

Your genes are what you eat

selecBy now you have read about the new paper in Science, Greenlandic Inuit show genetic signatures of diet and climate adaptation. Carl Zimmer has an excellent treatment in The New York Times, Inuit Study Adds Twist to Omega-3 Fatty Acids’ Health Story. The backstory here is that for decades people have been told to take fish oils because of their possible protective role against heart disease. Apparently some of these recommendations were based on observing the dietary habits of indigenous peoples of the Arctic and their health outcomes. Unfortunately studies which attempt to gauge the impact of these recommendations on Western populations have come back mixed at best. I myself stopped taking fish oils years ago after a review of the literature and asking around. Well, it turns out that there may have been a confound that the populations of the Arctic are adapted to their particular diet.

The figure to the right gets at the heart of the result. Greenland Inuit (they selected for individuals with less than 5% European ancestry), Europeans, and Chinese, exhibit a particular genome-wide pattern of relatedness, which you can see at the bottom. Looking at their results the authors found that there is gene flow from a Greenland-like population to the Chinese at some point over the last 20,000 years. This seems plausible. Additionally, I recall that Greenland natives and Europeans share Ancestral North Eurasian heritage. This is not a population genomics paper focused on phylogenomics, so these details aren’t too important. The takeaway is that on a set of derived alleles around the fatty acid desaturase genes the populations of Greenland seem fixed for variants which are very different from the major alleles in both Chinese and Europeans. These genes are very extreme in terms of their results on the population branch statistic (PBS), which measures deviations in allele frequency against reference groups.

The details are somewhat gnarly. The authors look at several groups of genes, before zeroing in on the FADS group, and they also look at several variants within FADS, as well as various phenotypes. It turns out some markers make the Inuit differ in height and weight, and the height result also applies to Europeans (the frequency is far lower, so that may be why it wasn’t picked up in earlier GWAS).

But I want to focus on a major top-line result. First, here is Rasmus Nielsen in Carl’s piece, “The same diet may have different effects on different people.” And from the paper itself: “In addition to the associations with height, we also found known associations with low fasting serum levels of insulin, total cholesterol, and LDL cholesterol for European carriers of low-frequency–derived alleles of FADS1 variation, suggesting that there may be a protective effect of these variants on cardiometabolic phenotypes.” The implications of this study are commonsense, but they’re also very deep, as they confirm a deep intuition that the same dietary regime may not have the same outcome in all humans. As the authors note in the piece many of alleles at high frequency in Greenlanders are also at high frequency in American native populations in general. Looking at the time depth of the selection event it seems likely that a lot of change occurred in Beringia or Siberian, so for New World groups this may be an ancestral suite of characteristics. But perhaps even more interesting is that many populations have high minor allele frequencies of these alleles. I looked at one marker in the 1000 Genomes data set, and the range is wide. Many Eurasian populations have the “Greenland” variant at ~10% frequency, so ~1% might be homozygote for that genotype.

5169qqIjeZL._SX309_BO1,204,203,200_What that means is that studies in small populations like the natives of Greenland may still have wide-ranging implications. There are literally hundreds of millions of people with these alleles. Though one might suggestion caution about extrapolating results out-of-population, some of the phenotypes are replicated already in Europeans who have the variant.

This study can’t be understood in isolation. It allows for broader generalizations. Ten years ago I read Why Some Like It Hot: Food, Genes, and Cultural Diversity. This was really a pre-genomic era book, drawing on an older body of work. But it is very interesting, and reports on a wide range of studies and the author’s own experiences. Much of it won’t be a surprise to many, but others would still benefit from its comparative method. Today we know a lot more about population-level variation, and what it might tell us about individual-level variation. It’s going to be fun times ahead, as I suspect that the intersection of diet, nutrition, genomics, and quantified-self is going to be a very big deal in the near future.How and what we eat is important. The diet industry is nearly a one hundred billion dollar market.

Read/write world genomics?

I have a post up at the new GSA blog, Read/write access to your genomes? Using the past to jump to the future. One thing I would say: I didn’t get into human germline modification because I don’t think it’s going to be a major issue in the near term. And, I think it’s more of a bioethical aspect of the technology of genetic engineering than a scientific one. I’m pretty sure we’ll have the technology, but we’ll cross that bridge when we get to it. Also, special thanks to Yaniv Erhlic for writing A vision for ubiquitous sequencing. It really has gotten me thinking….

ASHG 2015 abstracts of interest

The abstracts can be found here. Will be updating this post repeatedly….

 Genome-wide data on 34 ancient Anatolians identifies the founding population of the European Neolithic.

I. Lazaridis 1,2 ; D. Fernandes ; N. Rohland1,2 ; S. Mallick 1,2,4 ; K. Stewardson 1,4 ; S. Alpaslan ; N. Patterson ; R. Pinhasi* ; D. Reich* 1,2,4 

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1) Department of Genetics, Harvard Medical School, Boston, MA USA; 2) Broad Institute of MIT and Harvard, Cambridge, MA USA; 3) Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland; 4) Howard Hughes Medical Institute, Harvard Medical School, Boston, MA USA; 5) Independent physical anthropologist, Netherlands. 

It has hitherto been difficult to obtain genome-wide data from the Near East. By targeting the inner ear region of the petrous bone for extraction [Pinhasi et al., PLoS One 2015] and using a genome-wide capture technology [Haak et al., Nature, 2015] we achieved unprecedented success in obtaining genome-wide data on more than 1.2 million single nucleotide polymorphism targets from 34 Neolithic individuals from Northwestern Anatolia (~6,300 years BCE), including 18 at greater than 1× coverage.  Our analysis reveals a homogeneous population that is genetically a plausible source for the first farmers of Europe in the sense of (i) having a high frequency of Y-chromosome haplogroup G2a, and (ii) low Fst distances from early farmers of Germany (0.004 ± 0.0004) and Spain (0.014 ± 0.0009). Model-free principal components and model-based admixture analyses confirm a strong genetic relationship between Anatolian and European farmers. We model early European farmers as mixtures of Neolithic Anatolians and Mesolithic European hunter-gatherers, revealing very limited admixture with indigenous hunter-gatherers during the initial spread of Neolithic farmers into Europe. Our results therefore provide an overwhelming support to the migration of Near Eastern/Anatolian farmers into southeast and Central Europe around 7,000-6,500 BCE [Ammerman & Cavalli Sforza, 1984, Pinhasi et al., PLoS Biology, 2005]. Our results also show differences between early Anatolians and all present-day populations from the Near East, Anatolia, and Caucasus, showing that the early Anatolian farmers, just as their European relatives, were later demographically replaced to a substantial degree.

Ancient European haplotype enrichment in modern Eurasian populations.

D. Harris ; T. O’Connor 

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1) Graduate Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD; 2) Institute for Genome Sciences, Program in Personalized and Genomic Medicine, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD. 

The diversification of modern European populations is a fascinating puzzle that has recently advanced due to the sequencing of ancient European genomes. We analyzed 732 modern West Eurasian individuals using three ancient samples coming from the Lazardis et al. Human Origins Array dataset. Specifically, we determined ancient European haplotype enrichment by calculating pairwise differences (PWD) between each ancient European individual and modern Western Eurasian individuals in 50 SNP blocks. Modern Western Eurasians had the fewest PWD across all population groups with the farming Stuttgart individual and had the most PWD with the Loschbour and Motala12 hunter-gatherer individuals confirming Lazardis et al. observation that modern Europeans are more similarly related to ancient individuals coming from a farming community. We selected SNP blocks, for gene ontology enrichment analysis through the use of GORILLA, based on 1) the 10% of regions with greatest differences of PWD between groups, and 2) the 10% of those regions from the first criterion that most closely correlated with the geography of those groups. Most SNP blocks positively correlated to PC1 (latitude) and PC2 (longitude), therefore we focused on outliers that negatively correlated to biogeography. For SNP blocks that negatively correlated to PC1; “regulation of chondrocyte development”, “androsterone dehydrogenase activity”, and “antigen processing and presentation of endogenous peptide antigen” had the highest enrichment score in the comparison of the Stuttgart, Loschbour, and Motala12 individuals, respectively. Interestingly, the “alpha-beta T cell receptor complex” and “interleukin-17 receptor activity” (including CD3D,E,G and IL17RC,E) were enriched in the Loschbour and Motala12 comparisons of SNP blocks that were positively correlated to PC2. In addition, the Stuttgart individual had the lowest PWD disparity between all modern populations for the SNP blocks that contain the IL17R and CD3 genes, which potentially indicates selection acting on these immune system haplotypes from the Stuttgart individual consistent with the Stuttgart farmer and modern Europeans’ continual close interaction with animals and zoonotic disease exposure. In conclusion, our approach of calculating PWD in small SNP blocks supported prior conclusions made by Lazardis et al. and illuminated small genomic haplotypes that are of importance to the evolution of modern West Eurasian populations.

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Open Thread, 9/13/2015

ShowCoverVarieties of evolution

Years ago I remember Joe Thornton asking me if I wanted to be an evolutionary biologist, and I didn’t have a really good answer. Yes, I have degrees in biology and biochemistry, but it seemed weird to make your living studying evolution. It had long been a hobby of mine, back to the descriptive paleontology days, and in my adulthood more in the domain of theory undergirded by genetics. But it had always been an avocation until I decided to go to graduate school. At this point I’m focused on mammalian genomics professionally, with an obvious interest in domestication. But sometimes you get too narrowly focused, and it’s important to take a step back, and evaluate. Some hot chains to explore different peaks if you will.

516FJKA926L._SY344_BO1,204,203,200_On Twitter I got into a discussion with Nathaniel Comfort about his review of Richard Dawkin’s latest book, Brief Candle in the Dark: My Life in Science. Broadly Nathaniel takes the perspective that Dawkin’s views on evolutionary biology are somewhat anachronistic, that they’ve become frozen in the 1970s, when he was beginning his career as a science communicator, and still primarily focused on research. Comfort’s contention is that things have changed, but that Dawkins has stood in place. Specifically he seemed to suggest that the rise of genomics has changed how we view evolution. This I am skeptical of. Evolutionary biology pre-dates genetics, and genetics pre-dates our understanding of DNA as its concrete substrate. Genomics changes a great deal (as Graham Coop observed genomics makes a big difference in understanding the molecular dynamics of evolutionary process, but says less about the details of phenotype). But I’m not convinced that it has revolutionized our understanding of evolution. Rather, it has had an evolutionary effect on the broadest scale. There are a diversity of opinions on a variety of topics, and Richard Dawkins’ views are not necessarily “orthodox” on all counts, but, he’s not an out of touch dinosaur. There are serious active researchers who would defend his oeuvre (here’s something I found out, a sequence of advisers and students, Richard Dawkins → Alan Grafen → Laurence Hurst → Gil McVean). In fact, I would contend Dawkins is closer to the “center” of opinion among evolutionary biologists than the “extended synthesis” crowd, who many feel are a touch self-aggrandizing.

But, I do think “dissenting views” are interesting, and illuminating. One think I’m going to endeavor to do in the next few months is get around to reading James Shapiro’s Evolution: A View from the 21st Century. I purchased it when Jerry Coyne mentioned that for a limited time it was free on the Kindle, but it’s sat there ever since.

Commenter’s policy

I continue to have problems with commenters not understanding the ground rules, and becoming enraged when I tell them they aren’t very smart. This has been a bigger issue since I moved to Unz Review. I suspect part of this is that my policy is somewhat of a shock set against Ron’s radical libertarianism in this regard, and the general liberality of most of the other bloggers here. But I need to keep reiterating the framework. It’s something I’ve come to feel works for me, and I’ve evolved organically toward it over 13 years of blogging.

There are two general things to consider. How comments relate to me. And how they relate to you (commenters). First, me. I don’t talk about my non-blog life in detail here because it’s not important, nor is it really any of your business. But I’m a person who is in graduate school (which often involves me being a teaching assistant as well as doing research in the lab), does a fair amount of consulting work in genomics, and, has a family (small children) and a wide circle of friends. An issue of side interest to some of you is that one reason I didn’t want to dwell on what happened with The New York Times is that I’m just very busy, and most of my professional focus isn’t on writing at all. I had other things to do and so didn’t really have the marginal time to be sad about missing out on an opportunity that literally fell into my lap, and was never going to be a major income source. I know it’s unhealthy, and I worry about it, but one way I “get shit done” (as David Mittleman would say) is that I don’t sleep as much as I should. This means I’m cranky, and my time is precious. Every comment I read has an opportunity cost.

So how do I justify reading and allowing comments? It’s important that the commenters add genuine value. That means new ideas and concepts which I find interesting. Unfortunately there are several classes of commenters who don’t fall into these categories. First, there are those of low intelligence. There’s not much to say here, and the whole situation is unfortunate for everyone involved in any intellectual enterprise. Second, there are the class of commenters whose priors are so different that there’s no point in having a discussion. For example, if a commenter is a Creationist, even if they are intelligent, there’s really not going to be a fruitful exchange. So I don’t post Creationist comments (I get one about once a month). Of course Creationism is an extreme case. Consider this comment. The individual is well informed and intelligent, but unfortunately I’m going to ignore the whole comment because I disagree with one of the axioms which you have to hold to make the comment worth reading in its entirety (that scripture/text are in a deep way determinative of a religion). My disagreement here is predicated on my reading of a particular domain of scholarly literature, and I came to this conclusion after holding the position of the commenter before changing my views. I understand many people disagree with me, so I often post these comments, though I generally respond as I did, that I simply don’t accept the premise of the argument and so it’s pointless to continue. Unfortunately, the next stage for many commenters is anger and accusation that I’m stupid or ignorant. Rather than taking disagreement at what it is these commenters begin to hector me after I don’t recognize their self-evident genius, at which point I have to ban them (I’m not saying this has happened with this commenter, just that it often does when I dismiss someone’s axioms and so render their own logical/analytic enterprise moot in relation to me).

This gets to the fact that ultimately I am the judge of what’s useful/edifying for a comment thread. Commenters sometimes seem to think that the threads exist to show off their erudition or filibustering capabilities. In other cases people get into juvenile debates where they really seem to believe winning an argument on the internet is something that does anything. The aim of discussion in my opinion is less about convincing your interlocutor, and more about fleshing out and dissecting your own opinions. On a related matter, often commenters want to talk about their own hobby-horses, or move the discussion into a topic of their preference or choosing. This is tolerable, but I have my limits, and I particularly am harsh on monomaniacal individuals (well, except perhaps the guy who kept going back to the lack of female pubic hair today; that guy was just funny). Some commenters think that I’ve been caught or I’m trying to hide something when I don’t want to talk about what they want to talk about. Actually, I just don’t want to talk about what they want to talk about.

Finally, there is the whole issue of commenters who are insulting and/or awesome. Let me start with the awesome ones. They are awesome in their own eyes. These the individuals who are supposedly incredibly smart, despite me judging them to be rather dull. That might simply be due to the fact that I’m dull. But that makes me wonder: why is that they are reading me, and I’m not reading them? These are people who are reading what I have to say, and then proactively leaving a comment on what I have to say, who then throw a fit when I tell them to please not comment in the future. Despite them invariably telling me I’m a loser, and explaining at length how awesome they are (sometimes for paragraph after paragraph!), I suspect that something related to ego is going on here (yes, they accuse me of ego, which is fine, I have a big enough ego that I really don’t give a shit what they think). And last but not least there are the insulting/presumptuous types. These two tendencies go together; the correlation is very high. Being told I’m stupid isn’t really an insult, it’s more a descriptive hypothesis. I could be stupid, in which case I invite you never to read me or comment here. But sometimes people leave weird creepy comments about my race/personal history/background that they have no knowledge of. For example, the commenters who leave statements of the form “you were obviously raised abroad, so you can’t understand Americans….”, or something of that variant. Or, “your mentality is obviously South Asian….” A lot of these are in the what?/not even wrong category. I’m sure they have their own logic, but the statements are often difficult to parse, and usually presuppose facts which are false (e.g., I was raised abroad [my formative years were spent in the inter-Montane West], I want to marry a white woman but never will [box already checked, hope your head doesn’t explode], I’m a Muslim [no], I’m pro-life [no], etc.).

In conclusion, if I ban you or don’t post your comment, perhaps you should be insulted and angered. But rather than leaving a bizarre and self-indulgent comment and wasting your own time (after all, you’re an awesome mind and your time is precious!) you should just move on. A few of the readers here on this blog have become friends, but in general I’m not here to make friends, those I already have are sufficient. I’m here to extract interesting information out of you if you want to engage.

linear-300x300Humanity as a plesiomorphy

So, Homo naledi. About two years ago I randomly happened to be in town when Lee Berger gave a talk in Washington D.C. So I’ve known since then what he’s been sitting on. People are asking me: so what? I’m an aspiring evolutionary geneticist, not a paleontologist, so why should my opinion even count? But here’s what I’d say: the likelihood of conscious deposition of these individuals who morphologically are very different from modern humans makes us reconsider what “human” is. My own opinion on this changed when Luke Jostins crunched the data and showed that the cranial capacities of all hominin lineages seem to have been increasing over the past 2 million years. Relevance? I don’t think that “behavioral modernity” was a contingent fluke. Rather, I think that once our own lineage reached a particular point in evolutionary development ~2 million years ago some sort of adaptive ratchet kicked in, and humanity was inevitable. The Neanderthal Parallax then could be understood as alternative history in a fundamental sense. Being “behaviorally modern” is not a derived character of our particular lineage of Homo sapiens. Its potential at the base of our line, as far back as the australopiths.

51yuNuckdiL._SY344_BO1,204,203,200_Human evolution

In light of the recent discovery, a friend asked me what I should read about to understand human evolution. Unfortunately, that’s like asking what you should read about to understand physics as quantum mechanics was being developed. Things are just changing so fast. I would say that one book I read a few years ago has struck me as very useful when it comes to the paleoanthropology, The Humans Who Went Extinct. In particular the author focuses on the role of the Gravettian culture in developing the toolkit which allowed modern humans to conquer Northern Eurasia and ultimately push beyond Beringia. And, I have to say that Richard Klein’s The Dawn of Human Culture is still very interesting and important. It basically tells you what the dominance of an “Out of Africa” and total replacement framework had led many to conclude: that modern humans were a nearly a saltation that occurred 50,000 years ago. That modern humans were in fact the humans, the only ones with speech, and therefore culture.

Basal Eurasians

It looks like ancient Anatolian genomes will answer a lot of questions. Hopefully. I’m going to ASHG 2015, and there are some posters there. So updates soon. I looked at some data…and it is weird that the LBK “First Farmer” has such strong affinity to Cypriots, as well as groups like Tunisian Jews. I got into a discussion on Twitter with Iosif Lazaridis, and he pointed out that there is less Basal Eurasians in modern Middle Eastern groups than in the past. I had thought before digging into the data myself that North Middle Eastern groups (e.g., Armenians) would have a lot of Basal Eurasian, but they don’t seem to have an inordinate proportion.

Rising Star Expedition announcement

If you care about human evolution, keep an eye out for reports on what happened in South Africa a few years ago. A massive cache of bones was discovered. I’ve been privy to a few preliminary findings, and the implications are explosive, revolutionary, all the hyperbolic language that I tend to avoid. This is a big deal, not just because of the results, but also because of the possibility that this will be an inflection point in how paleoanthropology is done. That is, rather than hoarding fossils the “sharing economy” of science will make itself felt within the individualistic and proprietary domain of the fossil hunters.

If I did the timing right the announcement should drop in a little over a day from when I post this. Keep track of Lee Berger and John Hawks’ Twitter.

The Basque culture is that of the First Farmers


There’s a new paper in PNAS, Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques. It is a nice complement to the earlier paper on an earlier Iberian Neolithic sample. These individuals all date to a later period, most ~5,000 years ago, and one ~3,500 years. Despite the media hype, the results of this paper were pretty much expected, and it’s the final nail in the coffin of the idea that the Basque language and culture are relics of Paleolithic Europe. Rather, it confirms the result that the Basque descend in large part from agriculturalists who brought the Neolithic revolution to Europe. The genetic result began to be clear as early as 2010, when PLOS BIOLOGY published A Predominantly Neolithic Origin for European Paternal Lineages. The interpretation of that paper was wrong in some of the specific detail. It is quite likely that the R1b haplogroup did not come with the first farmers, but that it was a later arrival. But, the authors were early in refuting the contention that the high frequency of this lineage among Basques was ipso facto evidence that it was a primal Paleolithic signature. In fact much of that work exhibited some circularity, with the premise that Basques were primal descendants of hunter-gatherers being the linchpin for archaeogenetic inferences which then came back around to pointing out that the intuited genetic distinctiveness of the Basques was further evidence of their uniqueness.

Screenshot - 09082015 - 10:30:26 AMThe admixture plot to the left reiterate a few things I’ve been asserting of late. First, the Spanish Basque are unique in having weaker signatures of being impacted by North African gene flow and the genetic signal associated with people from the Eurasian steppe than other groups in the Iberian peninsula. This isn’t a new finding. What is interesting though is that the authors confirm through a variety of methods that the Basque have Western European hunter-gatherer gene flow which post-dates the arrival of the first farmers. The earlier paper I allude to above suggested that the Iberian Cardial individual, which predates the oldest of these samples by ~2,500 years, had hunter-gatherer ancestry which exhibited affinities with a Hungarian, and not Spanish, sample. In other words, the first European farmers were themselves a compound population to begin with. Subsequent to their expansion all across Europe they seem to have absorbed local hunter-gatherer populations. This is the resurgence of hunter-gatherer ancestry over thousands of years that David Reich has mentioned before. This was a phenomenon across much of Europe, not just in the Iberian peninsula.

Which brings us to how we go about solving this puzzle. It seems that archaeologists and anthropologists have to start tackling the issue. One possibility is that the human geography of ancient Neolithic Europe was intercalated, with hunter-gatherer populations occupying zones between the expanding farmers which were not amenable to their agricultural practices. I suspect that the Pygmy example might be informative, as this group has had a long period of symbiotic coexistence with agriculturalists. Note also that the results from earlier work suggests that the fraction of hunter-gatherer ancestry increased even before the arrival of the Eurasian Steppe populations, which changed the character of Europe’s north, and to a lesser extent south.

Finally, there’s the enigma of the Basque language. The authors of the above paper mention possible connections with Paleo-Sardinian, which predates Romance dialects on the island. And Sardinians, like Basques, exhibit strong signatures of farmer ancestry. In fact, Sardinians have more farmer ancestry than any other Europeans, likely due to marginal pre-Neolithic presence on the island. The genetic closeness of the farmer groups from Spain up into Germany in the early Neolithic indicates a rapid expansion from a small founding stock with roots in the Balkans and or Anatolia. This sort of expansion is highly likely to be accompanied by the spread of the common language and culture of these people, and in that way the Basque can actually give us some vague insight as to the cultural character of the first Neolithic people, not, the hunter-gatherers. These results reiterate that some of the ancestry of the Basques does derive from the people of Paleolithic history in a genetic sense. But perhaps more importantly, it points the likelihood that there was a massive cultural rupture between Ice Age and Neolithic Europe, and the Basque stand with the latter.

The need and the right for one’s own genetic data

Giant study poses DNA data-sharing dilemma:

Next month, the group is expected to release a project plan. Observers are eager to learn its answer to a key question: how much information about disease risk, especially genetic data, will the project share with participants?

That issue is the subject of much debate. Dishman and others say that participants should at least have the option to see all their personal data so that they can investigate their own health, just as he did. But some specialists in the field say that showing participants their data is irresponsible, because the information is challenging for people to interpret and its significance is often uncertain.

Most genetic variants linked to disease increase risk only slightly, yet people who discover that their genome holds such a variant might worry excessively or seek unnecessary medical tests. Or they might do nothing: the limited research on how people react suggests that, far from causing panic, information about common variants of small-to-moderate effect does not seem to motivate people to make recommended long-term behavioural changes to lessen risk. “Unless you give people the tools and the skills to deal with the raw data, I don’t see how you could give them the raw data,” says Brian Van Ness, a geneticist at the University of Minnesota in Minneapolis.

Years ago I had a short conversation with Mike Snyder where we discussed the fact that for human genomics to become useful there had to develop a culture of openness and ubiquity of data. That is, you need huge sample sizes and lots of information on those samples. Several years ago I elaborated some of my views with an essay in Genome Biology, co-written with my friend David Mittleman, Rumors of the death of consumer genomics are greatly exaggerated. The point is that the gains to genomics, and what is now being called “precision medicine”, is really going to occur when there is widespread adoption of sequencing and comfort among the populace with analyzing the intersection of the sequence data with phenotype data. That is, there are returns to scale. But all this sounds very “Brave New World” to people, and they are not comfortable with it. Yet. One way to make people more at ease is to give them some “ownership” of the process. They may never analyze their raw data, but they’ll have it, forever. Or, they may analyze it with third-party tools such as Promethease. Ultimately personal genomics needs to be personalized, and if you lock the data behind gates, that totally undermines the message.

Second, I think on normative grounds one can say that it is not ethical and right for researchers to withhold your own sequence when they are attempting to do research with your data. After all, they are making gains career wise with your own information, your raw data. It strikes me as unjust that they’d withhold that data because you might not do the right thing with it. That it’s up to them to decide when you can see information on your own body. There is perhaps a place for paternalism on some issues, but in the generality this is not one hill that I think many geneticists will die on. Those who stand athwart history are going to look foolish in hindsight.

Open Thread, 9/6/2015

51X30zMkuYL._SY344_BO1,204,203,200_After In God’s Path I noticed that Amazon recommended I check out Dividing the Spoils: The War for Alexander the Great’s Empire. So I bought it. Alexander to Actium is pretty far back in my history, so it seems appropriate to “catch-up” on the genesis of the Hellenistic era. But right now I’m back to A New History of Western Philosophy, which has been slow going…. I think part of the issue here is that it is always a slog to work your way through ideas which I feel are not relevant in any direct fashion today, but are of interest as intellectual history and backdrop. And I haven’t even gotten to The Shape of Ancient Thought and Warriors of the Cloisters.

This pre-print, Analyses of Eurasian wild and domestic pig genomes reveals long-term gene-flow during domestication, has now been published. It’s pretty interesting, as it suggests the complexity of animal domestication. Contrast this with how clear the process is in plants.

In other news, check out the demographics of those admitted to Harvard this year.