Gaurav Vaidya

TDWG 2011, day zero

Here's some fantastic stuff I discovered during the TDWG icebreaker yesterday:

• Mandala, a cross-platform, FileMaker® Pro database "designed to track specimen-based biodiversity data, loans, and detail complex nomenclatural histories with their associated literature". A book chapter describes the schema used, but if you prefer to just jump in and try it out, there is a live database of 130,229 specimens across 2,658 (possibly invalid) taxa citing 952 pieces of literature from the Therevidae (Insecta; Diptera).
  • (Bit of a coincidence there: I co-authored a chapter in the same book! How cool is that?)
• mx, a Ruby-based platform for "gathering and working with data", as per Matt Yoder's blog post explaining his approach to writing software for science, which is a great read if you write any kind of software for any area of science. And mx is available on Github, making it perfect to play around with.
• 3I Interactive Keys and Taxonomic Databases, a "set of software tools for creating on-line identification keys, taxonomic databases, and virtual taxonomic revisions". There are plenty of sample datasets here, too.
• Species File, "both a database and a website: The database provides the detailed information about all taxa contained within the scope of the "apex taxon" and the website provides the means to interact with and modify the information contained in the database", principally developed by David Eades. There are a lot of example 'species file' websites available.

And, off of science, Ray's Site, a blog about a blind cat, and how he navigates a world without his sight.

How awesome is Wikipedia?

Precisely this awesome:

So somebody (probably Wikipedia user midorigin) purchased Milo powder from two countries about two continents apart, photographed them on white paper, added scale lines, and uploaded their result, allowing Wikipedia to visually show the difference between Milo preferences in two very different geographical areas. Think about that one more time: an online, user-contributed, free-to-edit encyclopedia with a serious, well-illustrated discussion of Milo varieties around the world.

Truly, my friends, we are living in the future.

"The stories of the fabulous past"

Thanks to the Letters of Note blog, I just discovered this trove of letters addressed to the children of Troy, Michigan, collected by Marguerite Hart in the early 1970s, who asked dozens of "actors, authors, artists, musicians, playwrights, librarians, and politicians of the day" to pen down their thoughts on this day. I immediately read the letter written by famed actor Vincent Price. I was not disappointed. Here is my transcript of the letter he wrote, a beautiful paean to history, literature, language and libraries.

Dear Young Citizens of Troy,

Many centuries ago in Asia Minor in a city with the same name as yours, literature was born. One of the greatest poets who ever lived sat among his people and told the stories of the fabulous past. And they remembered them down through the years until the legends became fact, the fact not so much of history but of the word, of language.

Your new library is the home of language, yours and all others from the beginning. In it you will learn how others lived and thought and from it you will learn to live and think better for yourselves.

Vincent Price

The Journal of Universal Rejection's new blog

Since mid-February, the venerable Journal of Universal Rejection has taken us behind the scenes of their rigorous article review process - a review so exacting that no article has yet managed to pass through to publication.

By way of evidence, consider the short story Done, which - despite extensive changes made as required - was still rejected by reason of impatience. Consider the author's beautiful words explaining why a speaking monkey was not actually a speaking monkey:

The monkey is not in our world, but in a virtual reality, and thus not speaking at all. Indeed, the illusion of monkey-speak in this story is a postmodernist reflection on the collective cultural delineation of "speech" in contrast to the abstract notion of "silence" highlighted by appearing within artificial quotes in a story with no true dialog. It is a literary device representing man's struggle to be heard.

Well said.

Perseverance, tenacity and cogency

Assistant professor Matt Might is probably best known for his Illustrated Guide to a Ph.D.. I've just been reading his excellent article on the Three Qualities of Successful Ph.D. Students, and I'm finding it my favourite amongst his many articles on this subject. It's filled with fantastic nuggets, such as:

"A smart person would know better than to get a Ph.D."

"To survive this period, you have to be willing to fail from the moment you wake to the moment your head hits the pillow. You must be willing to fail for days on end, for months on end and maybe even for years on end. The skill you accrete during this trauma is the ability to imagine plausible solutions, and to estimate the likelihood that an approach will work."

"As you exit graduate school, an arc connecting your results should emerge, proving to faculties that your research has a profitable path forward."

"You will also need to actively, even aggressively, forge relationships with scholars in your field. Researchers in your field need to know who you are and what you're doing. They need to be interested in what you're doing too."

"Unfortunately, the only way to get better at writing is to do a lot of it. 10,000 hours is the magical number folks throw around to become an expert at something. You'll never even get close to 10,000 hours of writing by writing papers. [..] That's why I recommend that new students start a blog. Even if no one else reads it, start one. You don't even have to write about your research. Practicing the act of writing is all that matters."

Professor Might's other articles on the Ph.D. process are all brilliant as well — try A Thesis Proposal is a Contract, 10 Easy Ways to Fail a Ph.D., and the 5+5 Commandments to a Ph.D.

Some tips on screencasting on the Mac

We've made a screencast to promote Sequence Matrix, a genetic sequence concatenation tool I wrote at the Evolutionary Biology lab at the National University of Singapore. This was my first attempt at creating a screencast, so I learned a thing or two I'd like to remember the next time I make one of these.

This video was recorded and edited on a MacBook Pro using ScreenFlow, a piece of screencasting software I chose after surveying screencast products late last year. The audio files were recorded by Prof. Lohman using iMovie and uploaded to a file sharing service. This means that I got them as individual clips, which were much easier to work with instead of a single, large file which I'd have to cut up myself.

Here's what I'll be keeping in mind the next time I need to make a screencast:

• Use a separate account with minimal decoration: create a new user account on your Mac just for recording screencasts. In this user account, get rid of the status decoration on the status bar in the top-right corner of your Mac screen (you can drag them off by ⌘-clicking on them). Reduce your screen resolution: 1024x640 worked well for me. I think YouTube uses a 16:9 ratio on its videos, so this screen ratio (at 16:10) will be stretched slightly, but it won't be too bad. This also means you're using your entire screen, which really shows off the Mac's gorgeous user interface.
• Get rid of the time: beware of the clock in the status bar (upper left corner) and iCal (on your Dock), which will show the effect of your editing by jumping forward and backward in time. Even worse: record on multiple days, and both these apps will be changing days as well. Longtime Mac users might not realise that recent versions of iCal continue to show the correct date even when not running - the days of iCal Day has, it seems, come to pass.
• Pick a homing point to move your mouse pointer to in between clips. For this video, my homing point was about 2/3rd of the way down from the top of the screen and 2/3rd of the way from the left of the screen. I'd start recording a video clip with my mouse pointer there, and end the clip by moving the mouse pointer back there. That way, the mouse doesn't appear to jump around in between spliced cuts. Another added benefit - if you later decide to rearrange your clips, each video will continue to start and end with the mouse at the same place, so they'll all continue to fit neatly together.
• Use speedups to demonstrate something boring: I'm not so sure about this one, but it's something to think about. The first time we export a file in the video, I sped it up slightly (150% or so faster than usual) so as not to bore the viewers. The second time we export a file, I run it at between 300% to 500% normal speed. That way, the viewers can see what's happening (and realise that yes, it's pretty much exactly what they saw earlier), while also moving swiftly along to the interesting bits. I did this a lot towards the end of the video (during the Nexus and TNT exports), and I'd love to look at it again with fresh eyes in a while and see how it came out.

I'll move these tips into the Creating Screencasts WikiBook when I get the time, but for now please feel free to add your comments, suggestions and complaints on the YouTube video itself or on this blog post.

Why I love Henri Cartier-Bresson

Responding to Kim A. Thomas' request for my favourite photographer, I found some fantastic photographs by my favourite, the French photographer Henri Cartier-Bresson, so I thought I'd share them here. If I can find Creative-Commons versions of them, I'd put them up here, otherwise just click the links to go straight to the images. I'm afraid I don't know all their names, so I've just made my own up. Please feel free to correct me (or, even better, point me to higher-resolution images!) in the comments section.

• Woman and dog on a beach
• INDIA. Punjab. Kurukshetra. A refugee camp for 300.000 people. Refugees exercising in the camp to drive away lethargy and despair. Autumn 1947. (larger image)
• A boy with bottles of wine
• A couple kissing as their dog watches

The Mandatory Death Penalty and Vui Kong

... any man's death diminishes me, because I am involved in mankind, and therefore never send to know for whom the bell tolls; it tolls for thee.

-- John Donne, Devotions upon Emergent Occasions (1623), XVII

I'm opposed to the death penalty. My reasons aren't for moral reasons, but economic and jurisprudential. Still, I think it's the right of every state - and particularly every democratic state - to decide how to treat its own people, and based on the few people I've talked to about this, the death penalty against drug traffickers does appear to be popular in Singapore.

The target of several campaigns are the against the Second Schedule of Cap. 185, the Misuse of Drugs Act, which prescribes a mandatory death penalty to certain drug-related offenses. Under this act, judges have no discretion in issuing the death penalty (M. Ravi, 2007): once the prosecution proves that an individual was carrying the minimum prescribed quantity of a particular drug (which is what the Second Schedule lists), the judge has to hand down the death sentence. Unless a Presidential Pardon is granted, the individual will end their life by being hanged at Changi prison, a particularly violent means of execution.

When we say mandatory death sentence means basically judges don’t have discretion. Just close your eyes, and that’s it, and execute. Don’t have to look at the person’s background and all that. You know in a sentencing regime, there’s a plea in mitigation, to mitigate your circumstances, it’s part of the sentencing process, so, it was not only that the death penalty was already harsh, but to impose that, it’s just cruel and unusual punishment.

-- M. Ravi, as reported by Asia Calling

Tomorrow, a twenty-two year old Malaysian kid who brought 47 grams of heroin into this country will be in court to hear out his appeal. Unless this is to his benefit, he can expect to be executed by the Singaporean state. As a certain religious leader once said, He that is without sin among you, let him first cast a stone at her. Do read Vui Kong's journey, a description of his life so far.

Last year, the mandatory death penalty was found to be constitutional in Singapore. Thus, the only way for judges to be given the power of discretion in such matters - and the success I hope the We Believe In Second Chances project achieves - will be to convince parliament to change this law. If you are a Singaporean citizen, I hope you will consider this question.

---

This post was written as part of the Blogging for Life initiative of the We Believe In Second Chances campaign.

References

• M. Ravi. 2007. Briefing paper: Death Penalty in Singapore. Published by the policy department of the Directorate-General for External Policies of the Union Directorate B. Reference: EXPO/B/DROI/2007/07, PE 348.620

Saving the tiger, cost: 82 million dollars a year

With the recent summit meeting on the conservation of the tiger, the largest cat in Asia is suddenly back in the news. The numbers, as always, are dismal: according to the BBC, there are now 60% as many tigers in the wild as there were in the year 2000. Of the 3,500 tigers remaining in the wild, only around 1,000 are breeding females. An agreement to double tiger numbers over the next twelve years was reached, which - seeing the seemingly unending downward slipping of tiger numbers, to say nothing of the population, climatic and other stresses the great cat will see in the coming decade - sounds just a little optimistic to me.

Despite the gloom, seemingly indefatigable conservationists continue fighting to keep the tiger in the jungles and forests of Asia. A really interesting paper in PLoS Biology proposes focusing conservation efforts on forty-two "source sites". These sites cover a tiny area, just 88,000 square kilometres or 6% of the current distribution of the tiger, but contain 60 to 70% of the remaining wild tigers in the world. They are estimated to contain 2,126 tigers at present, but might be capable of supporting as many as 4,000 tigers in all.

All the source sites are already legally protected and can support at least 25 breeding females each. They are contained inside larger landscapes which can support at least 50 breeding females each. The authors estimate a total of 82 million US dollars a year to maintain this arrangement - a large sum, but a small price to pay to ensure the continuation of an important apex predator.

While efforts to limit trade in tiger parts and larger-scale conservation efforts to protect larger tiger habitats are essential, the authors argue that the most urgent need right now is to ensure that breeding tiger populations survive long enough that, as and when tiger habitats rebound, viable tiger populations are still around to recolonize those habitats.

Other options are being suggested. The Economist's blog Babbage points out that tigers are immensely valuable (The Guardian reports their value as US$ 50,000 for a whole animal). At that price, Babbage argues, it will always be in somebody's interest to try to sneak a tiger out of a protected area; the best solution would be to meet that demand by farming tigers for their body parts, letting prices drop and keeping the wild tiger out of the poacher's sights.

This is not a popular idea: as Babbage points out, tigers are "cute" animals, and many people immediately sympathize with them being kept in tiny cages and prematurely separated from their mothers. There is also a fear that creating a legal market in tiger parts will encourage further poaching.

Depressing? Certainly, and that's why I usually avoid conservation issues. However, this paper piqued my interest for two reasons: firstly, I'm reading a fascinating book called Where the Wild Things Were which argues that predators exert tremendous influence over the landscapes that they have evolved in. If that is true, as India's only major apex predator, the loss of tigers could have a huge effect on India's wilderness areas.

Secondly, the discovery that 60-70% of all wild tiger are found in just 6% of their current distribution mirrors another very interesting observation - that as many as 44% of the world's vascular plant species and 35% of all species in four vertebrate groups are confined to just 1.4% of the planet's land surface area (Myers et al, 2000). True, we're comparing apples and oranges here - specimen counts aren't the same thing as species counts at all - but it's interesting to see this pattern reappear here.

One last thing: as always with living organisms, and particularly with the study of wilderness areas, there are always happy surprises waiting to be discovered. Maybe the tiger will surprise us after all?

References

• Myers, N., Mittermeier, R. A., Mittermeier, C. G., da Fonseca, G. A. B., and Kent, J. 2000. Biodiversity hotspots for conservation priorities. Nature 403:853-858. Available online as doi:10.1038/35002501 or freely available from Nature Scitable.
• Walston, J., Robinson, J. G., Bennett, E. L., Breitenmoser, U., da Fonseca, G. A. B., Goodrich, J., Gumal, M., Hunter, L., Johnson, A., Karanth, K. U., Leader-Williams, N., MacKinnon, K., Miquelle, D., Pattanavibool, A., Poole, C., Rabinowitz, A., Smith, J. L. D., Stokes, E. J., Stuart, S. N., Vongkhamheng, C., and Wibisono, H. 2010. Bringing the tiger back from the brink—the six percent solution. PLoS Biology 8:e1000485+. Available online as doi:10.1371/journal.pbio.1000485.

Aspyr asks: To SteamPlay or not to SteamPlay

There's been a lot of nervousness about whether the upcoming release of Civilization V for MacOS X will be marked SteamPlay (i.e. free for those who already own Civ5/Win on Steam). Of course, while that's arguably the Right Thing to do, it means Aspyr will be giving out free copies, since they won't get paid for Civ5/Win releases. So, in an unusual move for a relatively large game distributor, they've gone to their community to see what they have to say about this issue, being open and honest about how important this lost revenue is for them. How awesome is that?

Unfortunately, I can't post to their website (something about a proxy; not so surprising when you consider the Singapore isn't on their list of supported countries for GameAgent.com, their online game store). So I'm leaving my comment here:

First off, let me just say that I really appreciate how open and honest you are being with us about this. It's too easy for us to forget the Civ5/Win and Civ5/Mac are practically two separate games, put out by two awesome companies, who have their own interests to look out for.

My primary gaming machine is a Mac, and I haven't have a Windows computer for myself in years. Therefore, SteamPlay doesn't mean much to me: while it's of course possible that I will own a Windows machine at some point in the future, and it'd be nice to have SteamPlay so I don't need to re-purchase the Windows versions of my favourite games, but it isn't at the moment a very big deal for me.

However, I do really hope that Civ5Mac will be released *on* Steam, and not just on GameAgent. As a Singaporean resident, I can't purchase games from GameAgent (at any rate, Singapore is not listed as a supported country in your FAQs). I *could* spend next weekend running around from Mac shop to Mac shop, hoping to find a box set of Civ5Mac, but it'd be an effort (and certainly isn't something I'd do for most other Aspyr games: that much effort is only really worth it for known-great games like Civ5 :). On the other hand, despite wanting to wait until a Steam sale, I really can't imagine *not* pre-ordering Civ5Mac if it becomes available on Steam before launch - it's easy, convenient, and I get to play the game on day one. Steam is also becoming a fantastic global marketplace for Mac games - I know I check if a game is available on it before looking for it anywhere else - so it can only be in your interest to get involved, so your fantastic games have access to the largest number of possible customers.

That's just my perspective. In any case, I'm really looking forward to November 23, and all the best for a fantastic launch!

By the by, I don't know how SteamPlay works, but this sounds like it's confirmed that Civ5 will be available for sale on Steam, and that Aspyr are just trying to work out whether to mark it as a SteamPlay version of Civ5/Win or as its own game. If so, I'm really going to be pleased, and will definitely consider (read: not sure how I'll resist) pre-ordering -- there's nothing quite like being able to support a good game developer.