Lactose intolerance around the world

Most of us in the western world take drinking milk for granted, but the ability to digest lactose into adulthood is actually relatively uncommon from a global perspective. It comes from a genetic mutation called lactase persistence, which evolved independently in a few parts of the world in the last 5,000 years, probably as an adaptation to widespread dairying following the Neolithic (or Secondary Products?) Revolution. This makes it one of the clearest examples of gene–culture coevolution we know of, and therefore of great interest to evolutionary anthropologists (Ségurel and Bon 2017).

Trowelblazers on Wikipedia: Margaret Ursula Jones

Wikipedia is the world’s most widely read reference work but it has a well known systematic bias towards the interests of affluent, Western, young geeky men: more articles on pokemon than poets, and so on. A couple of months ago I thought I’d try and do a little bit to reverse it by improving the coverage of women archaeologists (Trowelblazers – cribbing the name from the fantastic blog that I also cribbed most of my source material from!)

Does archaeology have a reproducibility crisis?

The reproducibility crisis! It’s shaking the very foundations of the ivory tower. Reportedly the psychology wing is already in rubble. Medical researchers are having to glue their microscopes to their benches. But down in our dusty corner of the basement, the archaeologists don’t appear to have even noticed. Why not?

#ChromeScience: Dave Hughes on Chromebooks for science and teaching

I’ve written a little bit before about using Chromebooks and the Google ecosystem for research, specifically using RStudio Server on a Google Cloud Compute instance. Dan Hughes has beat me to a more comprehensive guide, with a series on using Chromebooks to teach and manage a proper science science lab.

Edge Annual Question 2016

This years Edge Annual Question asked their assorted eminent scholars to pick the most interesting scientific news from the last few years. The result is a nice set of short posts recapping some recent discoveries. Here’s a round-up of archaeology/anthropology related responses:

Say Hello to Hugo

Hello, Hugo! If you’ve noticed the blog looks very different to how it did yesterday, it’s because I’ve migrated it from Wordpress to Hugo – a lovely little static website generator. This simplifies things greatly for me behind the scenes, and means I can integrate the blog with the other bits I put under this domain. It’s something I’ve been meaning to do for a while: Wordpress is an unwieldy beast.

RStudio Server on a Google Compute Engine instance

RStudio Server running on a Compute Engine instance

RStudio Server running on a Compute Engine instance

When I started my PhD I decided to make my trusty fieldwork laptop – a Google Chromebook – my main work computer and try to do all my research in the cloud. It’s an interesting, ongoing challenge (a blog post for another day), but one thing I realised very early on was that I’d have to do any serious “lab work” (which for me is sitting at my desk playing with computational models) on a remote machine. You can install another Linux distro alongside ChromeOS easily and relatively seamlessly with crouton, giving you a traditional desktop environment to work with locally, but given Chromebooks’ underwhelming hardware, developing even simple models on them is a non-starter.

After a while using a university server, this year I moved all my lab work to Google’s Compute Engine. Like other cloud hosting platforms (Amazon Web Services, Rackspace, etc.) it’s mainly for providing the infrastructure for web applications. But I’ve found them ideal for research too. Relatively inexpensive, you get complete control over a virtual machine, which is securely stored in the cloud, but can also be made, unmade and played with at the click of a button, and if you have a big processing job you can just create a more powerful instance for it (or three). For Chromebook users, Compute Engine instances are easily accessed through a web-based ssh client.

My “Google Lab” became a hundred times more useful when I discovered RStudio Server. I do most of my work in R, so I already knew that RStudio was a near-essential IDE for the language. What came as a wonderful surprise was that there’s a server edition offering a polished, browser-based interface almost identical to the desktop version (for free!) Considering that even big companies’ attempts to bring desktop software to the cloud still deliver either limited functionality “lite” versions or lazy streaming clients (I’m looking at you, Adobe), RStudio really can’t get enough credit for this.

Setting up RStudio Server on a Compute Engine instance is mostly straightforward, but I ran into a few quirks along the way, so hopefully this brief guide will save some people the same head-scratching. I’ll assume you’ve already set up an instance with the operating system of your choice and figured out how to ssh into it. If not, you can follow Google’s quickstart guide (don’t bother installing Apache, unless you want a web server.) But I won’t assume any further familiarity with Compute Engine or Linux servers in general.

My instance is currently based on the stock Debian jessie image, which is what all the commands below will apply to. I’ll try to indicate how to do the same thing on other Linux distributions – but if you opt for Windows, you’re on your own!

Excavating at Kharaneh IV

I wrote a brief guest post for the Kharaneh IV blog, an Epipalaeolithic site in Jordan where I’ve been working the last few weeks:

Popular anthropology? Jared Diamond is the best we've got

Part 2 of Alex Posecznick’s delightful series on anthropologists as scholarly hipsters for Savage Minds sums up for me the problem of why the discipline can’t seem to produce public intellectuals of the calibre of Richard Dawkins, Brian Cox or, case in point, Jared Diamond (emphasis added):

Genetic Astrology

(Via John Hawks) Genetic Astrology chronicles the saga of Alistair Moffat’s shameful attempt to use libel law to silence scientific criticism of his genetic ancestry testing company BritainsDNA:

A Genetic Atlas of Human History

Hellenthal et al. introduced a new method for detecting and dating genetic admixture events in Science last week. The ins-and-outs of their analysis is, honestly, way over my head; but I do appreciate the paper’s companion website, featuring an interactive map of admixture events for 95 populations around the world.

Not so civilised

The way the word ‘civilisation’ is bandied about in popular writing about ancient history has always bugged me. Most archaeologists must be well aware of how problematic a concept it is, but when it comes to writing for a non-specialist audience, phrases like “the earliest civilisations” are suddenly back in fashion. I suppose the reasoning is that ‘civilisation’ is a more widely understood term than ‘complex society’ or ‘urban state’, but is it? Yes, most people will have heard the word before, and the same can’t be said about the current jargon. But it’s as slippery as Service’s greasy ladder and I doubt many’s understanding of it will particularly resemble the way it’s used in archaeology. So naturally when people encounter ‘civilisation’ used in the unfamiliar context of describing a historical development, they assume that the term must have a specialist definition that’s being applied. Since it doesn’t and isn’t, trying to swap in a familiar term ends up causing more confusion than it solves. Better to stick with the jargon, and realise that if you’re going to use unfamiliar concepts there’s really no way around explaining them.

Someone led up exactly this garden path recently posted in /r/AskHistorians, asking “What is the working definition of civilization that has been used to named ‘the first civilization’?” Which finally gave me a chance to pontificate on why ‘civilisation’ is meaningless in archaeology:

Little Red Riding Hood and the Second Wave Phylomemeticists

Jamie Tehrani has a very imaginative paper in PLOS ONE on The Phylogenetics of Little Red Riding Hood: