anthropology.net

I just created an account over at
Anthropology.net (cue gratuitous linky banner thingo)

It’s a community site for Anthropology, with blogging, forums, and a wiki. So anything here that’s anthropological in the least will get posted there as well, ‘cos I’m all about blanket coverage.

ant-cam!

Went to Natural History Museum today. Disappointed like a seven year old when realised the new ANIMATRONIC DINOSAURS weren’t on show until the weekend. Was also annoyed by the dustiness and not-working lihgts in the gemstone collection. Consoled self with the zen of watching the leaf-cutter ants. Now you can too.

bayesian madness

A non-biologist friend of mine, on proofreading bits of the thesis-in-progress, got terribly excited about the program Mr Bayes.

"Mr Bayes!" she exclaimed. "That's the perfect name for a tabby cat!"

Her comments on the section where I actually described Bayesian methods in phylogenetics consisted mainly of and >.< faces. "The words seem to be in the right order for the English language?" was her concession.

Don't blame her, obviously. I periodically beat myself over the head with my notes about Bayesian & likelihood methods; this appears to be an effective means toward keeping the information in my head. Today I found a couple more implements of self-harm at Paul Agapow's site, the first his own primer, the second a link to Peter Foster's The Idiot's Guide to the Zen of Likelihood in a Nutshell in Seven Days for Dummies. Tee hee.

So browsing the talk titles for the Evolution 2006 meeting, I came to the conclusion that biologists, especially those who dabble in phylogenetics, tend to have a very specific sense of humour. By specific, I mean "take any opportunity to make a pun, an allusion, or maximise alliteration to the point of tongue-twisting" and dude, there's nothing wrong with that. You wrap your brain around priors and posteriors and your brain wants to crack a funny. It's just the way it is.

elsewhere on the internerd…

Presentation Zen has a great post on the rule of thirds in slide composition.

FrinkTank linked the site for Danny Boyle's new film Sunshine, which I will not embarrass myself by going OMGICANNOTWAITLKJSHDFALKJFSDA except how I totally just did.

Am following with interest the reponse to Nature's piece commenting on PLoS's "rocky" financial position, here. 

Long but thought-provoking piece on Savage Minds about the so-called "end of marriage", trying to take a more comparative perspective. 

printsetters clock + cultural bats

Wired has a nice little article on the molecular clock model being used by antiquarians to date prints/books etc. The original paper is here, describing how the properties of copperplate and woodblock degeneration (and the corresponding print quality features) can be used in a clock model to help date manuscrips. Nifty.

Also, via Afarensis (who has a cool picture), Current Biology reports that fring-lipped bats may be using social transmission mechanisms in order to learn a novel foraging behaviour (recognising frog calls as prey cues). Bats = always awesome.  

darwin was a pigeon fancier

… you all knew that.

Pigeon Blog makes me cry with laughter. This is no exception. 

molecule jewellery

Continuing my trend of providing free advertising to people who make science cool and accessible: Made With Molecules. ThinkGeek already did the t-shirt thing with their caffeine molecules, but the jewellery is very lovely, especially the earrings and simple necklaces (I loathe charm bracelets).  Putting on my once-was-jewellery-designer hat, I'm all for putting a premium on design work and charging people accordingly, but I think the prices are just out of reach for those (grad students/postdocs) who might want this sort of thing the most. I mean, I know precious metal prices have risen ridiculously in the last 2 years, but I wouldn't stretch to $85 for a simple silver necklace.

I know, what a killjoy, right? 

Quis custodiet ipsos custodes?

(Pretentious latin post title for the win!)

The tension in academia–especially science–between communication and discretion fascinates me. On the one hand, you want to be able to discuss your ideas with as many people as possible; on the other, those ideas are your intellectual currency and you don't want them stolen or misappropriated.

The publishing process also intrigues me. It appears to be undergoing a sort of quiet revolution at present, with open access journals becoming more common, and with the review process itself being opened up by journals like Biology Direct. Nature has a commentary on that journal's review/editorial process and how it is faring here.

I'm all for this. I know the arguments about what the anonymous process allows/preserves, but I think that on balance science would be greater served by open peer review. Perhaps it's a naivete to assume that the majority of reviewers play the game correctly–review a paper irrespective of their personal feelings on the authors and their particular theoretical biases. Sure, there are always going to be vindictive wankers. But it's actually very easy to tell a vindictive wanker from someone making justified criticisms. Open peer review means that the wider science community can review the reviewers.

It's also a means to what I see as a desirable end: chopping up undeserved status hierarchies and allowing smaller voices to be heard without fear of career-hurting reprimand. People already mostly find out–through the grapevine or guesswork–who reviewed their paper. And so any wankery that goes on does so anyway, but with the protection of psuedo-anonymity for those playing pay-back games, and without recourse for anyone who has had a grant rejected or employment opportunity stifled. OPR leaves a public trail of cause and effect.

Of course, this means that one has to overcome one's need for approval, be it social or professional, in order to write that justifiably-critical review of someone with more status/funding/publications/associates than you. But science needs brave Gryffindors.

order online: bits of deadly virii

The Guardian reports they ordered a chunk of the smallpox virus DNA sequence online from a molecular biology supply company. It's not as dire as it might sound: you gotta have graduate-level expertise and more than a kitchen sink to recombine DNA sequences. What was interesting was that there is no across-the-board screening of all material sent out. The company that provided the DNA don't screen sequence below 100 bp against a database of potentially harmful organisms, and there's no standard regulations about the screening process. The Guardian ordered their sequence with a couple stop codons added to comply with safety and legal regulations, but it will be interesting to see if there are any developments from this, and also, how the rest of the media picks up on it.

ETA 15/7: Nature discusses the article and frowns upon the Guardian, highlighting that ordering bits of DNA is routine for the research community even though it might shock the general public, and pretty much disapproves of such a "stunt". I still think the attention it draws to the inconsistencies in the regulatory process is the interesting point. And also? Of course Gn. Public might be suprised by what you can buy over the internet–there's no need to flash your boffin-club badge about it and act all jaded, Nature Editors.

more chaucerian phylogenetics

Eagleton, C. & Spencer, M. 2006.

Copying and conflation in Geoffrey Chaucer’s Treatise on the astrolabe : a stemmatic analysis using phylogenetic software. Studies In History and Philosophy of Science Part A [link]

Chaucer’s works seem to be the focus of what one might call literary phylogenetics. This new paper uses network methods to try and unravel the lineages and relationships amongst multiple copies of his “Treatise on the Astrolabe”, a work that was copied at least 30-odd times, some in fragmentary pieces. Using NeighbourNet, the  authors construct diagrams of interelatedness, showing areas of “hybridisation” between manuscripts. They find that the scribes were diligent about creating a complete copy, and would consult other versions to fill in the gaps or verify uncertainties contained in a single exemplar. 

Other cool things in my inbox today included the ToC for PLoS Biology, which contains an article about Siphs, a community expertise-sharing forum for the life sciences. The article discusses the benefits of online databases for journal articles (less arduous time in the library) but the highlights that things like PubMed and WoS don’t actually tell you what is important, or answer your question. We have an information overload without access to expertise, and the Siphs project looks to be set up to counter that. Of course it will only succeed if individuals participate, but announcing it in PLoS is a good idea.

This information age is an exciting time in that knowledge is at our fingertips. But if we fail to innovate upon our means of accessing information, the Internet’s promise of providing us what we want will be lost as knowledge is drowned in a sea of facts. These new tools are founded upon the belief that we’re better off working together, but they work only if you think so too.

The article also linked to Connotea, which I’ve known about for a while but haven’t set up. Given how much I love the social bookmarking available at del.icio.us, I really have no excuse.