PLoS Computational Biology has embarked on a fascinating experiment in scientific publication to Wikipedia: Topic pages. That's a peer-reviewed article published in PLoS Computational Biology designed to be directly incorporated into Wikipedia. Unlike a conventional research paper, a topic paper is designed to comprehensively cover one specific topic. The first ever topic paper was about Circular permutation in proteins, a Wikipedia article which was significantly improved by the changes.
In one elegant step, this ties together Wikipedia and scientific credit: once your topic paper is published, you get the credit due to you, while Wikipedia is greatly improved by your contribution. It also ties together Wikipedia and journal publishing: one of the big problems in taxonomic informatics is tracking the bleeding edge as new species are discovered and named. By writing the articles in a wiki before submitting it for publication, the process of going from scientific paper to Wikipedia article can be simplified and sped up. Finally, by framing the goal of the paper as a "topic paper" rather than as a research question, the content is already in an encyclopedic tone and subject incompatible with a typical, hypothesis-based research paper.
Will we perhaps someday see taxonomic topic pages in which the cutting edge hypotheses about a clade's phylogenetic tree are presented, ready for inclusion into an encyclopedia? Or perhaps taxonomic review topic papers, with the most comprehensive knowledge assembled about a species or clade, summarized by experts, ready to be incorporated into the most widely used encyclopedia on the internet? I do hope so. Daniel Mietchen, the Wikimedian in Residence on Open Science, is already interested in taxonomic treatments, and I can't wait to see what he -- and the PLoS and OKFN teams -- come up with next.
This book is a pretty crazy beast. It would be a perfectly enjoyable science fiction/action novel, if it weren't based around Flavius Belisarius, one of the most fascinating generals of the sixth century and reconqueror of Italy. And it looks like he's going to be up fighting against the Guptas, of all people.
Right before sitting down to write, I've just read through a bit by a grumbling, unhappy semi-sentient jewel from the future (don't ask) which is very upset that Belisarius' famous victory at the Battle of Dara could have been so much simpler if only somebody had just bothered to invent the stirrup. I suppose it does have a point.
A few chapters later, the following charming piece of dialogue is said by Sittas:
"He [meaning Belisarius] probably swore an oath. He's always swearing oaths. Swore his first oath when he was four, to a piglet. Swore he'd never let anyone eat the creature. Kept his oath, too. They say the pig's still around, roaming the countryside, devouring everything in sight. The Bane of Thrace, the thing's called now. The peasants are crying out for a new Hercules to come and rid them of the monster". A belch. "That's what comes of swearing oaths. Never touch the things, myself." (chap 9, pg 160)
The book does love its historical references: Antonina is a major character (her fictional relationship with Belisarius is very different from the generally accepted historical narrative), we see Procopius being hired (and learn why he in particular was chosen), and of course Justinian and Theodora loom over everything. Where I am in the book (page 160), Narses and John of Cappadocia have just been name-dropped. And the authors make a passing reference to -- of all things -- Sailing to Byzantium. Presumably, just because they could.
So: science-fiction/historical/action/fun! An aside: there's a lovely scene early on in which Procopius is caught off guard by some praise from Belisarius. I loved the idea of seeing a famous writer of history flustered, especially since in our world we see those times through his eyes. It's like seeing Shakespeare caught cheating in grammar school, it's a lovely little touch.
(More spoilorific information on An Oblique Approach is available on TV Tropes)
Here's the strange thing about being born on the leap day. Most years (exactly three out of four) are just the same as anybody else's: you hit your birthday, think about the year behind you and the months ago, and take the day as a chance to be slightly weird for a bit. Apart from a bit of fiddling about when exactly to celebrate it (Feb 28? Mar 1? Whenever my friends are free, duh), it's just the same.
Not in the years of the Olympics, though. February 29th reminds me of February 29ths which have been -- 1996, 2000, 2004, 2008, 1992 -- and those yet to come -- 2064, 2016, 2032. So much has changed -- ``some are dead and some are living'' and all that -- but so much stays the same. It's strange to divvy up your life into sets of four years -- into Olympiads, if you will -- but every four years, that's what my life feels like.
I had a touch of the depressions earlier in the evening (after yet another amazing D&D game), which is slightly odd, since this is definitely one of my best February 29ths in a while. And yet, and yet. To quote White Teeth, there is a sense of having picked up the wrong jacket from the cloakroom of life. Which is strangely self-contradictory: on almost every measure, my life today is many times better than it has been in years, even in Olympiads. Perhaps that has something to do with it? The feeling that life is almost, but not quite, perfect? The frustration of being at the right place at the right time with the right people but with just slightly the wrong clothes?
Anyway. I'm lucky enough to have been born an optimist (28 years ago today, as it happens), which means that I live in the belief that tomorrow -- tomorrow! -- it's all going to be a little bit better than today. So. So.
People who know me know that, even as I acknowledge Lolita as the finest novel I've ever read, my heart belongs to my favouritest novel in all the world, the little known The Year of the Death of Ricardo Reis, a novel published in 1984 by genius Portuguese novelist José Saramago, who died last June at the age of 87. Saramago wrote Year of the Death when he was 62, and death is very much at the heart of the novel. But that's not why I like it.
On the surface, Year is an almost unbelievably dull book. Spoilers begin: Reis, a nobody Doctor who has lived in Brazil for years, has migrated back to Lisbon after learning of the death of his friend Fernando Pessoa. He spends a listless year falling in love with the young, unobtainable Marcenda, who in her shy way responds to his affection; while sleeping with Lydia, the chambermaid at his hotel, an affair he hides from the world. The ghost of Fernando Pessoa meets him occasionally, bringing wisdom, humor and friendship from a afterlife shrouded in darkness. Twisty plotlines following the state's suspicion of his sudden return to Portugal, the power dynamics at the hotel at which he stays, and his delicate balancing of his two, different loves. And then, on the second last page of the novel, as its title promises, Pessoa's ghost arrives to usher Reis into the afterlife.
So, why the love? I always knew that it was because I felt a link with Reis, buffeted by the forces of love, desire, boredom, fear and society, and unable to do more than to batten down his hatches, to take joy in a cold, friendless life when and where he could. Reis is a man who slips so quietly and unceremoniously out of his own life that nobody except the grieving Lydia and her unborn child -- Reis' only legacy -- notice his passing.
Tonight, I compare my behavior in areas like science and Wikipedia -- where I believe I would push to have my way, in some shape and form, if I was convinced that truth was on my side -- with how I act and react to human relationships. The twisty thing about simultaneously feeling worthless and unique is that you never, ever want to stand up for yourself. It's the path in the middle: the worthless part of my psyche insists that imposing myself on another human being is a crime, right up there with talking loudly on a phone on a bus, while the egotist in me insists that, welp, hey, if they don't want to interact with me, it's their own loss.
No, it isn't. And this is important.
Another teeny, tiny little point: there is one, single bit in the entire book where Reis goes out and does something. Knowing that Marcenda is heading to Lourdes in a final attempt to heal her paralyzed arm, Reis heads there himself to plead his case, to risk all in the name of love blah blah and so on and so forth. But, this final foray into standing up for his own affection, to condemn with his actions the line fate has drawn for him, is an utter failure. The lesson learned is not to fight.
Post scriptum (Dec 19, 2011): Bob Corbett reminds me of these glorious lines from the novel:... human unrest is futile, the gods are wise and indifferent, and above them is fate, the supreme order to which even gods are subject. And what of men, what is their function. To challenge order, to change fate. For the better. For better or for worse, it makes no difference, the point is to keep fate from being fate.So.
While I have been letting this blog fall asleep in the run-up to the ever-so-busy final weeks of school, I have been busily blogging, writing and scheming elsewhere! Here are some updates:
Co-wrote What’s new, October edition on the Map of Life blog.
Kicked off a WikiMedia Commons project for the Biodiversity Heritage Library. So far, we've tagged 16 files from BHL, fixing their copyright status and linking back to the BHL website in the process. Jean-Frédéric created this gorgeous template to use as a source template on BHL images. The plan (my plan) is to keep tagging images into the New Year, and see where we are after that.
Co-wrote Field Note Challenge Part 2: Veni, Vidi, Wiki on the So You Think You Can Digitize blog.
Excited by all the taxonomically interesting information already in WikiSource, I created a portal to try to coordinate efforts to annotate, organize and connect these resources with counterparts on WikiSpecies, Wikipedia and (especially) the WikiMedia Commons.
Fun times! I brazenly anticipate even. more. fun as I get a week to push ahead on the Map of Life after Tuesday, followed by a week of fun with sister and cousins in East Brunswick, NJ, followed by another week to code, ruminate and discuss, followed by another two weeks (back in Boulder, now) to work on things before the next semester smashed into my life like a grammarian smashing into someone misusing a simile.
My post on TDWG 2011, day two, part two, starts at 2pm with the symposium on "Global biodiversity informatics initiatives update". This symposium was hugely useful to me as a biodiversity noob, giving me a broad overview of the major #biodinfo initiatives, which problems they are tackling, and where they are headed. I don't need to repeat that these are all based on my very wonky notes; all errors here are mine, and -- when you spot them -- please let me know in the comments section. The talks in this symposium were:
Eamonn O'Tuama talking about the Global Biodiversity Information Facility (GBIF) and its recent improvements, including:
Switching to using DarwinCore Archives as an input format: spreadsheets are easier for people to work with than XML! It now takes a month for new data to go from upload to being published; GBIF's goal is to get that down to a week.
GBIF has also revamped their taxonomic validation, adding other authority checklists their current taxonomic authority, the Catalogue of Life. In fact, they're now assembling a database of taxonomic checklists! I wonder if they'll show the changes in checklists over time.
A brand new GBIF Online Resource Center has been set up to make it easier for people to find out about and upload data to GBIF.
William Ulate talked about the Biodiversity Heritage Library, with a presentation explaining how the BHL network looks today, with nodes spread out across the planet. Books, journals and periodicals are uploaded through BHL nodes, and are then distributed to the others (and to the Internet Archive). Prime among these were BHL Europe and BHL-Australia (a part of the Atlas of Living Australia); he particularly noted BHL-Au's fantastic user interface, which will form the basis of UI improvements to the US website. He also mentioned BHL's Egyptian collaborator, Bibliotheca Alexandrina (a project older than BHL itself!).
William also pointed out that anybody could suggest books or journals for BHL to scan, and they would try their best to do it as fast as possible. Also, BHL's source code -- including the code that powers their website, APIs, and Citebank -- is publicly available.
BHL is also developing CiteBank, a database of biodiversity citations. Put that together with Rod Page's iTaxon idea, and you can see some really amazing -- and amazingly useful! -- interlinks between taxonomic names and literature happening.
Cyndy Parr presented on updates from the Encyclopedia of Life (EOL) project. She pointed out that EOL is all about aggregating and curating data; it's never going to be as smooth as Wikipedia, where all the data is in one place. However, it can have better import processes: all new names on ZooKeys/PhytoKeys are immediately added to EOL; it can also get feedback and corrections back to the original publishers much more efficiently than Wikipedia can.
Cyndy also showed off EOL collections of taxa, across any kingdom of life and collected by any criteria, from birds at the Smithsonian's National Zoo to the colour blue. Collections can have EOL communities form around them.
EOL also plans on moving to DarwinCore Archives flat-files, as an easier way of moving data in and out of their system. They have released a the largest possible phylogenetically-organized tree, representing the state of our phylogenetic knowledge.
Donald Hobern spoke about developments at the Atlas of Living Australia (ALAu) focusing -- much to my excitement -- on taxonomic issues.
He began by talking about descriptive taxonomy. He mentioned IdentifyLife, a database of identification keys, including -- get this -- a plan to build a single, gigantic Key to All Life. The idea is to support citizen science "in the broadest sense". ALAu is working on a project to port the DEscriptive Language for TAxonomy (DELTA) software suite into Java. Finally, he mentioned the Taxonomy Research and Information Network (TRIN), which hosts a pretty well-organized wiki.
Donald pointed out that ALAu's taxonomy arm had two primary communities to serve: the one interested primarily in geographical data, and the one interested primarily in taxonomic/collection data. I think he demonstrated this division by comparing the Australian National Herbarium datasets with Australia's Virtual Herbarium, but to be honest, my notes are somewhat in disarray at this point. This is because Donald is an excellent presenter, and so I wasn't focusing on my notes so much. Sorry about that!
The symposium ended with Dave Roberts talking about ViBRANT. He spoke mainly about the exciting new changes coming in Scratchpads 2.0, which -- based on Drupal 7 -- will have a prettier user interface, snappier access times, and much better scalability. There are ambitious plans to plug in Scratchpads to biodiversity publishers (such as PenSoft) as well as biodiversity producers and consumers (such as the Encyclopedia of Life and LifeDesks). Even more interestingly, they're setting up a job-processing backend for Scratchpads on the Oxford Batch Operations Engine (OBOE).
A sandbox Scratchpad is available, if you want to play around with the technology in its current state. Their source code is available, including Scratchpads 2.0. And, being on Git, all that code is easy to play with.
After a short trip to meet Walter Jetz at Yale, I'm back in Boulder, have seen Paul Simon in Broomfield, CO and Wikipedia Loves Libraries! at Norlin last week, and am making a start at putting together my research ideas. Fun times ahoy!
But first, I'm still working through my notes from TDWG 2011. Here's a first installment of my treasure trove from day two; obviously, many awesome presentations and parallel talks were missed, probably because I was too busy enjoying them to take down notes. All errors are mine, and when you spot them, please do let me know in the comments!
Part two will be out as soon as I can get around to it. Also: getting more and more excited for Life and Literature, just a week away tomorrow. It'll be great to see familiar faces from TDWG so soon after TDWG 2011 New Orleans!
I just discovered the #SciFund challenge, a Kickstarter-like project to raise money for scientific projects by promising deliverables created as part of the project. I think it's a great way of getting non-scientists involved in science, to say nothing of getting funded and of creating a concrete science-to-public deliverable system. So: excited!
Here's some of the projects I took a fancy to. Unfortunately for me, as a grad student lacking money, RocketHub (the hosting website) has no mechanism for "subscribing" to a project without paying that I can find. So this might be the only way for me to keep an eye on them (and maybe make a contribution with my next paycheck).
The most fascinating part of this enterprise for me is the connection between the science projects and the contributors: the deliverables. Rewards for donating ranged from credit (on websites or in publications), to a copy of the research results, to exclusive access to project blog and Twitter feeds (which make no sense to me: wouldn't you want those feeds to be as public as possible, to encourage more people to join in and contribute?). More interesting deliverables were also on offer, from elephant dung paper and calendars with photos of the research subject, to photos taken during the study, clay sculptures of dolphin fins, lyrics to a Tanzanian children's song, and comics personally drawn for you by Zach Weinersmith of Saturday Morning Breakfast Cereal fame. Allegedly, a comic of "Carl Sagan riding a unicorn" is not out of the question.
One thing I did find odd was the lack of links in the project descriptions. Only a few projects linked to websites, blogs, Facebook pages or Twitter feeds (one project going so far as making the Twitter and blog feeds "contributor only"), although just about all of them had really excellent websites hidden away in the "About Me" section. I love Twitter for letting me follow a project without getting too involved, so more Twitter feeds would have been great to see.
Thinking in the longer term, I wonder how well this would work without the #SciFund banner, though. Unlike music or movie crowdfunding, where artists can put up samples beforehand, it might be harder to prove your scientific worth to a broader audience. For instance, how would I differentiate between a serious project to study bee evolution and some nutjob trying to prove that evolution didn't happen? I could look at the project description, sure, but it's not hard to reference many scientific studies to give yourself an air of authenticity. Perhaps the #SciFund banner will eventually be replaced with institutional banners: if the research is being carried out by the Smithsonian, the University of Colorado or is partially sponsored by National Geographic, you can be pretty sure it's been vetted.
Yesterday (Monday) was the first full day at TDWG 2011. This post is an extraordinarily incomplete summary of some of the things I learned that day; a lot happened on that day, and I really don't have time to write about it all here (although I might post my thoughts in future posts). I'm writing down some URLs for my own interest. If I missed something you found interesting, it's likely that I was just too fascinated by the presentation to take notes (see my single sentence describing Michael Donoghue's keynote speech for a perfect example). All errors are mine, and when you spot them, please do let me know in the comments!
I'm dreading writing tomorrow's blog post, since today (Tuesday) was an incredibly valuable day for finding out about projects, websites, ambitions and niches. Luckily, I don't have to worry about that for a day at least, maybe more.