If you visit AoBBlog you’ll see a Bibliographies option on the menu bar, and dropping down from that four options. Three of these are shared collections and Pollination is curated by David Frost, the managing editor of the Annals of Botany. These are all administered at Mendeley. I’ve set up Arabidopsis, Ecology and Nutrition as shared collections so that when people who know more about Arabidopsis etc. than me sign up, they can keep the bibliography up-to-date. The reason you can see it on the website and not have to guess which AoB staff member is keeping the collection on Mendeley is that Mendeley now has an API, allowing me to pull data out of the site. There’s also a WordPress plugin for Mendeley and that’s how I’ve been able to put something quickly on the web rather than try to delve into JSON myself.

So why care?

About a year ago I put together a list of archaeology articles in PLoS ONE for someone. Recently Martin Rundkvist has also had a look at Archaeology in PLoS ONE. Now if I’d thought to make the PLoS papers I’d found a collection, then I could create a page for the bibliography, or else just drop it in below. Being able to add papers to Mendeley with one click and using the API would mean that you’d be getting the latest version whenever you visited the page, rather than the mid-2010 version. Handling shared collections is a bit more problematic at the moment, but in the near future a small group of people could make their references public on a collaborative project.

There are some problems. The API is new, and it’s not possible to pull all the data out of Mendeley yet. Page numbers are the most obvious missing data. There’s also a limited query rate, 150 queries an hour. This may rise in the future but for now it means you’ll have to cache results. It’s awkward but it’s not inherently a bad thing. Cached data are usually much faster, and it’s not like references will need much updating once they’re in a cache. A paper isn’t going to cease being published in Antiquity in 2003 and be published in AJA 2005, unless you’ve entered the data incorrectly. Tags and related papers are the attributes that are most likely to change and even these could often be updated on a weekly or monthly basis.

I’ll concede merely listing papers, even if it’s an automatically updated list, might not sound that exciting, so try this.

WordPress allows you to set up custom content types, and one of those types could be references. When the API is fully working you’ll be able to use it to populate you database with references from Mendeley. Mendeley in turn works with Zotero and CiteULike, so you could use these services to update your WordPress bibliographic database through Mendeley. Additionally these references need not be yours, they could be your contacts so you’re getting help from your personal research network. You can then write a plugin that will work using shortcodes so you can include references in posts or pages in a format like [ref-JonesH2009a]. The plugin formats the short code into the reference style that you want and includes the bibliography formatted in the right style at the bottom of the post. Then you can use Anthologize to render it into the format you want. It could turn WordPress into a social academic research environment. To take it further, you can make the blog private for members for collaborative research, or practice open research, however you want to do it. All of this would be accessible from anywhere with an internet connection.

It’s not possible yet, but it could be less than a year away. Personally, I think a tool where I can write drafts and which can ask me “Have you considered these additional papers?” when I add a citation would be extremely useful.

As a reality check I don’t yet have the skills with JSON or AJAX to write all of such a plugin myself but it’s not beyond my ability to learn given enough time.

I’m not planning to blog a lot on the Astronomical Orientation of Ancient Greek Temples as is openly accessible. Your comments are going to carry a lot more weight there than here. But I’ll try and keep track of what other people are saying elsewhere. I’m expecting this to be the first paper of a developing argument, so I’ll need to see what people identify as problems and address them. There’s two comments in the Times today which I think neatly highlight one of the issues. One is from Efrosyni Boutsikas and the other from Mary Beard.

Boutsikas’ objection is interesting. I wanted a comparison data set to examine for Greece and the only one I know of that’s published is Retallack’s in Antiquity. To be honest it’s not entirely fair to use Retallack’s data as he wasn’t that concerned with astronomy. Instead he was looking at geomorphology, and I think he has some really interesting results. Now Boutsikas has her own survey, which she did specifically with archaeoastronomy in mind. That’s why I’m interested when she says of 107 temples in Greece only 58% faced east. That might cause me some problems and here’s why.

First we need three variables. n is the number of temples. That’s 107. p is the probability and event will happen, and q the probability it won’t. p+q = 1 because something has to either happen or not happen. So what value is p? It depends on what Boutsikas means by east. If she means the eastern half of the horizon, then p is 0.5 and so is q. By pure chance we’d expect np temples to face east. That’s 53.5. In her survey 62 temples faced east. That’s more than chance, so I’m right yes? Not so fast.

There’s never going to be exactly 53.5 temples facing east. Around 19 times out of twenty 20 there’ll be 53.5 plus or minus two standard deviations. If you want the chance of a false positive to be lower than 1 in a 100, then you need 53.5 plus or minus three standard deviations. The standard deviation (σ) for this kind of distribution is calculated by the formula:

If we want the one in twenty confidence that means

So 19 times out of 20 you might expect to find between 43.1 and 63.9 temples facing east. The result of 62 is inside this range, so there’s nothing significant. How do I explain that? I’m not sure I can. I can’t say what time period her temples come from. If she’s looked at Bronze Age sites and Roman sites in Greece then we’re not comparing like with like and it’s possible that when we compare temples built in the archaic and classical periods as they were in Sicily then we’ll have more of a match. Another possibility is that I’m simply wrong.

But this depends on Boutsikas meaning eastern half of the horizon when she says east. I use different definitions of east for different tests and make clear which are which in the paper because it makes a difference. If Boutsikas has put her temples into four categories, north, east, south and west, then east means eastern quarter of the sky and the equations turn out differently.

If east is the eastern quarter then 19 times out of twenty at most we would expect at most 35.71 temples. By chance there’s be over 40.19 temples in the sample less than 1 time out of 100. 62 temples would be over seven standard deviations away from the expected result. If that’s by chance it’s an amazing freak result. It means I can’t respond to Boutsikas’s claims until I can see the data to analyse, so I know what east means. She might have proven my paper wrong, or else proven it very right. How can that be when only just over half of the temples face east?

Imagine you’re at a casino. Someone is spinning the roulette wheel. Half the time it lands on the numbers 0–9 and the other half it lands on another number. It doesn’t matter than you can’t predict exactly where the next ball will land. In the long term that casino will lose money because something is affecting the wheel. This isn’t about having a hard and fast law for astronomical alignments. It’s about whether or not a significant number of temples are aligned to the sun. If you’re going say that there is or isn’t a significant number, first you have to know what a significant number would look like. Typically in the social sciences that would np +/- 2σ. I prefer np +/- 3σ because I’m making claims which people might not be comfortable with, so it’s reasonable I should provide stronger evidence.

If I am right that doesn’t mean Boutsikas’ and Retallack’s surveys can be junked. In fact it means the opposite. In Retallack’s case he’s showing there’s a clear correlation between the dedication of a temple and the soil type it’s built in. Now if there’s a general rule that Greek temples face east, the temples which don’t become more interesting because then you can ask “What’s special about those temples? Why were they built that way?” It’s the same for Boutsikas’ data. If there’s nothing special about the alignments then temples which don’t face east are nothing special. If, using this method, her data shows a tendency for eastern alignments then she has a data set with plenty of interesting temples that could tell us something about Greek religion. For instance it could highlight where a local cult was doing something special that you wouldn’t find elsewhere in Greece.

Clearly Boutsikas’ objection is serious and I’ll need to consider it carefully, but in this case it could be a case of cross-wired. I don’t think she’d seen my article when she talked to the Times because I hadn’t emailed it to her till last night. We’ve both been working on similar topics and so could have come to the same conclusions. If we been talking with each other then there could have been a bit of friction if we saw our ideas in each other’s theses. She’s been put on the spot reacting to a paper which she probably hasn’t read, but she’s clearly an expert in the subject because of her own research. She’ll go where her research takes her and I’ll go with mine. The reporter has picked up on that confusion. Does that leave him in the dog house? Definitely not.

I’m really pleased with the way Mark Henderson has written this up. It’s not his job to preach my wonderfulness, it’s to report on how this research fits in with other research. Getting the quotes from Efrosyni Boutsikas was brilliant because it shows there’s currently two models which come to opposite conclusions. As we both publish more those models will get fleshed out and adapt. Which one will be accepted? Hers? Mine? Some kind of hybrid, or even neither? It’s not just about getting the right answer. At the moment we might not even agree on what the right answer will look like. Which brings me to Mary Beard’s piece.

I think it’s great commentary. I think she’s spot on when she rejects the idea of a modern astronomy in the ancient world. I would quibble with her rejecting astronomy for the rhythms of day and night. That sounds astronomical to me and there’s also evidence the seasons were important. I think she might be trying to emphasise the importance of cosmological features, in the sense of natural order, rather than strict observation. The only real puzzle is that she’s saying that there’s it’s obvious that Greek temples align east-west when in the column next to her Efrosyni Boutsikas is saying they obviously don’t. This is a bit of an interdisciplinary gap.

From the outside you might expect archaeologists and classicists to talk to each other. They’re dealing with the same people in the same time period. In reality this doesn’t always happen. A few years back the Roman Archaeology Conference, the big conference for Roman archaeologists held once every couple of years was scheduled opposite the Classical Association conference. The two sides don’t always talk to each other. In the past few years Boutsikas has been publishing on her work. Ioannis Liritzis and Helena Vassiliou have been arguing that Greek temples were aligned towards or away from aurorae or stars. This is having no impact amongst classicists. Equally I can’t just turn around and say “Greek temples tended to face east” because all the researchers who disagree could ask “How do you know?” It’s obvious doesn’t work as an academic response, even though I agree with Mary Beard. I don’t imagine that would be her response in an academic forum. But what she’s done is she’s very helpfully shown that if I want to talk to classicists then show why I think I have something to talk about.

That’s why I’ve had to write this paper. I want to write more, but the first question anyone can ask is “How do you know that’s not just a chance result?” That’s why I developed this method. I wanted something simple and effective. The reason I put it in PLoS One is that it also has to be accessible. I’m planning to write more articles for specialist journals, but people reading those will need access to my data and my methodology. That needs to be available to classicists, archaeologists, astronomers and anyone else with an interest.

You can read the original research for free and download it at PLoS One. If you leave comments there then they’ll be seen by everyone else who examines the paper. If you’d like to blog about the paper there’s a collection of photos from Sicily at Flickr with a Creative Commons licence.

Salt, A. (2009). The Astronomical Orientation of Ancient Greek Temples PLoS ONE, 4 (11) DOI: 10.1371/journal.pone.0007903

1. It’s fast.
   The paper was submitted on the 8th of September and I got the acceptance, subject to revisions on the 30th of September. I wouldn’t be quite so happy if it had been rejected, but you have to be prepared for that. The faster there’s a decision the quicker you can work on the revisions or else re-write for another journal. The rapid response means that I can cite the data in this paper in other papers immediately rather than delaying writing about further work.
2. It’s accessible.
   Research might be interdisciplinary, but not so many journals are. For this paper the alternatives would be publication in specialist archaeoastronomy, classics, archaeology or astronomy journals. I can do that and will do that in the future, but writing for those journals means writing for those specific audiences. If they’re subscription-based they also lock out a large proportion of the potential audience. If an astronomer is in a university without a classics department then it’s going to be hard for him to get a copy of the paper. Likewise many universities don’t carry archaeoastronomy journals. PLoS One gives me a platform to introduce the work and then I can publish tailored articles developing ideas in the specialist journals.
3. It opens conversation.
   You can comment on the paper. So too can anyone else. This is particularly handy for interdisciplinary work. I’m hoping the conversation doesn’t end with this one paper. The article-based metrics will included some of citation search. Hopefully in a couple of years people reading this paper will be able to see where they can find criticisms and developments in other papers. That’s amazingly useful for interdisciplinary work where subsequent papers could be in journals in a variety of disciplines.

I’ve decided some form of open-access is essential for interdisciplinary work. The paper stands or falls on whether or not the binomial distribution is the right tool for the task. That means for academic honesty I have to submit it to a journal where the I can be reasonably sure it will be scrutinised by people familiar with basic statistics. Scientists might laugh at that as the mathematics in the paper is very simple. I think any classicist could follow it, but some could quite reasonably be wary of it. Is it statistical sleight-of-hand? They can read any comments left by statisticians or astronomers and judge how confident they should be in the findings. Likewise people unfamiliar with the Greek material can read the classicists’ and archaeologists’ comments and see if the human aspect of the research is sound.

It’s also important for me because I might learn something, and indeed I did. This is a better paper post-review than it was when I submitted it. I’ve re-thought how I process some of the data and that will have a positive on the next project I do.

After going through the process I’m impressed with PLoS. I think I hit every bump in the submission process, most of it due to the ordering of the paper being different to how I would normally write it. Still, the everyone was very helpful along the way. If you’re a recent PhD or grad student with a need to put out some publications, I’d recommend publishing with PLoS One. Of course I’m writing this before I’ve seen how the paper has been received, so you can check on my article metrics yourself to see if it’s being read or else sunk into obscurity.

Creating Collective Identities through Astronomy, a thesis about time and space. Passed by Prof. Giulio Magli (Dipartimento di Matematica, Politecnico di Milano) and Prof. Graham Shipley (School of Archaeology and Ancient History, University of Leicester). Coming soon to an open access research archive near you. If you live near Leicester.

Update: Lagomorph, the family of animals that includes pikas, hares and pesky wabbits.

How should an exhibit be lit?

This is a development of an idea I had last year after reading a post by Christina on a visit to the National Museum in Copenhagen. In short most museums I go to seem to have much darker galleries for prehistoric material that classical material. That has to have a psychological effect, but does it also have a physiological effect? Is the difference in light enough that there’s a difference feeling to observing prehistoric material to classical material because of the room and not the content? You could also ask similar questions of European and Rest of the World exhibits. Are African exhibits in more dimly lit rooms, and if so what does this say about ‘world museums’.

It should be an easy enough question to answer; simply visit a range of museums in exotic locations with a light-meter and then number-crunch to find the answer. That’s not very efficient though. It means arranging permissions, travelling to the museums, and logging the data. It could take three or four days in terms of travel to some places to log 50 numbers. When it comes to number crunching more is better so is there a way round this? I suppose I could hire people to wander round museums for me with lightmeters, but that would be expensive and my bank is already experimenting with new shades of red to print my balance. It’d be handy if I could just find the data I want lying around the net somewhere. Regular readers will know I’ve been thinking about Flickr’s API a lot, and they won’t be surprised to hear that’s where I might have found the answer. A lot of people have been taking photos in museums and I think they could help.

It might sound bleeding obvious that all of Flickr’s photos were taken with a camera, but in the case of digital cameras Flickr can also store a lot more data. Attached to a lot of the photos is EXIF data. If you visit a photo like this one, you’ll see there’s a more properties link on the right side of the page. That takes you to a page like this one. It tells you the ISO setting, aperture and shutter speed for a photo. ((Usually — HDR photos won’t because the have multiple exposures)) If the camera is automatic then it will pick what it thinks are the best settings. The camera is set to manual, then the photographer is still probably going to choose what it thinks are the best settings. Therefore this gives a way to calculate relative changes in light.

For example ISO settings come from the days when people used film for photos. ISO 200 would react to light one ‘stop’ faster than ISO 100. ISO 400 was one stop faster than ISO 200 and two than ISO 100. So the ISO setting will let us calculate how many stops down the film speed is. The aperture is an odd scale because it relates to the size of the aperture of the lens relative to the focal length. But it can be calculated, f/22 is a stop up from  f/16 and f/11 is another stop down and so on. The same can be said for shutter speed You can go from 1/800 to 1/400 to 1/200 and so on.

Therefore, if you fix a datum you can measure how many stops up or down from that datum a photo is from the EXIF data. This is related to the light in the image and the camera lens looking into a gallery or display is a proxy for the human eye. It’s not perfect, you’d want a lot of photos but one thing Flickr has is a LOT of photos. It also has the API, which makes it very easy to transfer the relevant meta-data into a database for interrogation.

One reason I’m interested in doing this project is that I have no idea what the result would be. It could be emphatic, ambiguous or show that I have a very selective memory when it comes to lighting. It might sound obvious that you’d want to research something you don’t know the answer to, but to gain funding you have to show a likelihood of a positive outcome — or that the methodology is at least sound. I don’t know if this is the case, so the project won’t attract funding, but the API makes it cheap. Certainly cheaper than flying on budget airlines round Europe.

In terms of publication it seems like a good fit for Internet Archaeology. Internet Archaeology is moving in steps towards open access. Given the… umm… eccentric attitude the AHRC takes to digital media, and the current economic climate that’s a difficult move they’re making. The fact they are moving to Open Access makes it one of the most attractive venues to publish in academic archaeology. In this instance a database which can link back to the source files at Flickr would fit neatly into their hyperlink-friendly model. A bit of ingenuity with the SQL queries and database fields and it should be possible to make it a useful application for further research.

The biggest problem I see at the moment is whether or not estimating relative light levels from the ISO, aperture and shutter speed will be enough to distinguish between genuine differences in lighting. There are other non-trivial questions. If photos are of the exhibits rather than the galleries, then will the artificial light negate any measurable differences? It would certainly lose darkness in the peripheral vision. How do I gather the data? Can I pull it straight from the EXIF files from any photo on the site, but would this be reasonable if the photo itself is set to copyright? Would setting up a Flickr group for the project and trying to herd in volunteers, or sticking to CC licenced photos be better?

I think I could probably set up a small-scale test of this over the autumn and then take it from there, Still, it would be helpful if someone could spot all the flaws in this plan for me, rather than leaving me to stumble into them, so feel free to leave your comments below.

This very briefly introduces the statistical method I used to analyse the Greek temples of Sicily for astronomical alignments. It’ll be the basis for a paper On the Orientations of Greek Temples in Sicily. The whole thesis will be made available later via Open Access some way or another. I would say via the British Library’s EThOS system, but I’ve had no luck with that.

This is (what I hope is) the final version of the Delphi presentation. It briefly covers the ground that formed the basis for Knowing when to consult the oracle at Delphi. There’s more unpublished material, but rather than trying to produce Delphi II, I’m going to make it part of the forthcoming Calendrical Calibration paper.