Monomorphic

Nomura's Jellyfish. Picture by Kenpei at the Osaka aquarium. GFDL license.

Nomura’s jellyfish, a species frequently encountered in Japan and China, is one of the largest in the world. The body can reach a diameter of 2 m. Since they create big problems for the fishing industry, Japan has now sought China’s help on the issue. It is thought that a recent proliferation of the species, huge swarms appearing every year since 2000, originates at the mouth of the Yangtze river.

Evolution can do fascinating things sometimes. Upon reading about this, a doubtlessly romantic and delusional notion entered my mind. What if the sea ecosystem, or a subset of it, say 10-100 species, perceive the human fishing industry as a threat that needs to be defended against, and in response create an evolutionary niche where a new kind of species can thrive, a species whose only purpose is to obstruct fishing? A romantic notion since it plays off the mythical idea that human beings are at war with nature, or that nature is good and man is evil, something I don’t really believe in. But an interesting one nonetheless. Is such a development possible?

Recently I watched a friend give a presentation on a research topic he’s been working on for years. I found the presentation to be fascinating, and the clearest explanation of his work that I have seen to date. But I felt compelled to criticise him on one point.

In order to lighten up the speech a bit, he had chosen to include characters from a popular science fiction movie on every other slide, using them to explain the results he had attained in theoretical computer science. The link between the characters and the results was nearly non-existent; the pictures were clearly only there to lighten the presentation up a bit. I had been irritated by people’s tendency to do these things for some time, so I decided to point it out. One extreme example of this tendency gone too far occurred recently in a presentation about the database CouchDB – readers can Google for the slides to see the full controversy, though they are somewhat NSFW. (I don’t want to make moral judgments in this context, but I think the academic/professional domain can be kept free of these controversies. Save those battles for where they belong!)

So there’s a tendency for people to sugarcoat their presentation topic sometimes. The arguments in favor of doing this are that it can lighten an intrinsically heavy subject a lot, and save people from nearly falling asleep from compounded boredom (such as a conference where 30+ presentations about results in theoretical computer science are given). Essentially it mixes in some sugar with the sour stuff, yielding what might be called a sweet and sour talk. The medicine becomes easier to swallow.

But isn’t there something essentially contradictory about mixing contemporary pop culture so freely with results that, in this case, were about essentially pure mathematical theory? For one thing it takes the essentially perennial and debases it, linking it up with images that are hopelessly stuck in a short timeframe. For another, it can be seen a vote of non-confidence in your own ideas. It can be seen as saying “I know this is boring and useless to you, so please bear with me, and look at these amusing pictures until it’s over.” I’m not a good presenter, but in order to become one, I think I need to have sufficient confidence in my ideas to present them unsweetened unless the circumstances are extreme. I need to make my audience see the value in my ideas. Also, it’s quite different if the sugar coating is of the kind that helps people get into your idea, or if it’s the kind that just distracts (this case).

My view is therefore that one should use one’s lumps of sugar with restraint. Maybe a situation where this is called for is when the audience necessarily contains some people who are on the level that you need to be talking to, and many other people who are not on that level, and cannot possibly be brought up to it. In this situation, the sugar might be used to keep the second group somewhat alive and alert. And this is in fact the kind of situation my friend wrote the presentation for originally. So, no scorn on him, just a word of warning to the general public!

The Guardian reports that a new government panel will henceforth judge what research is worthy of funding in the UK. Universities will have to make the case for their research projects in order to receive money. Reuters UK, perhaps keen to draw attention, blurt out that “‘Mickey Mouse’ degrees face [a] funding battle”.

Examples cited by Reuters UK include surf science, golf management and winemaking. I agree that these are probably vocational qualifications rather than fields meriting university study. But for blue skies projects in the natural sciences or the humanities, the payoff and effects on society are very hard to judge in advance. After all, we very often conduct the research precisely to evaluate these benefits.

The incentive situation with basic research is different today from what it was during the cold war era. When basic research was a national affair, not to be shared freely in the scientific community, it was probably possible to gain a national advantage by investing more in basic research. Today it’s all too easy to make the argument that other countries will reap the benefits, so why pay for the investment? Essentially a reverse prisoner’s dilemma: out of selfishness, you are tempted not to invest, but everybody benefits more if everybody invests. But surely this is too simple a view of the situation.

Where will countries that cut down on basic research be in the league tables of the future?

Following a comment on my previous foray into bibliography management systems, I had a look at the product known as Mendeley.

In order to evaluate Mendeley, let’s ask ourselves what we want from a bibliography management system in the modern research environment. At a bare minimum, we want an easy way to catalogue and search PDF documents, and of course compile the all-important reference list at the end of the laborious writing process. Mendeley does this, as well as bring a social networking aspect into the picture. It tries to recommend papers that are relevant to your work, as well as give you an easy way of sharing interesting papers with colleagues.

In contrast to Aigaion, which I wrote about previously, Mendeley is not a web based system but a desktop application. This definitely has benefits as the interface is quite slick. I can set the application to watch my “papers folder”, and any PDFs I save to that folder, or its subfolders, will automatically be scanned and entered into Mendeley. Metadata, such as author, title and references, is automatically extracted from the document in most cases, though I found I had to manually revise it sometimes. There’s a built in command that searches for the metadata by paper title on Google Scholar, which comes in very handy in such cases.

Mendeley is built around an internal PDF viewer where the user can highlight text, add little stickies with notes, and so on. This works quite smoothly, but on the Mac platform, it’s definitely not as polished as the Mac’s built in Preview PDF viewer. Mendeley is using its own PDF rendering layer, and it shows in the slower loading times when you scroll the documents. Some additional work could be done here. This is my only major complaint so far, though.

Much like the Evernote application, Mendeley has the option of storing all the papers on a central server, so that I can easily access them (and any annotations I might have made) from a different computer by signing in with my user name and password and then syncing the files. This means I don’t have to give up the benefits I get from a centralized server. It might be nice, however, to have the option of running my own Mendeley server, so I’m not dependent on the Mendeley company’s server somewhere – but then I would forgo the social networking benefits of course.

This application has similarities to how last.fm is used for music, in that people build a profile based on what they consume. Indeed, Mendeley is describing itself as a last.fm for research (video presentation). Let’s compare research and music as forms of media.

• Most music listeners probably don’t make their own music – most people who read research papers probably write their own papers.
• Songs sample other songs (the remix culture), but it’s relatively recent – researchers have always done this in order to establish basic credibility.
• The atomic unit of music is the song. The atomic unit of research is the research paper (the PDF in today’s internet based world, at least in my discipline) – but could this change in the future? Do we have to constrain ourselves to the article format?

In summary, Mendeley is probably the most useful, workflow friendly bibliography system I’ve tried so far. If you’re in research, I’d recommend you give it a try. If I get time, I plan to also investigate a more Mac-centric tool called Sente in the future.

The Savage Minds blog recommends that you don’t use Mendeley as your main tool yet due to its relative immaturity, but I have seen no showstopper bugs so far.

The web browser, it is safe to say, has gone from humble origins to being the single most widely used piece of desktop software (based on my own usage, but I don’t think I’m untypical). This development continues today. The battles being fought and the tactical decisions being made here reach a very large audience and have a big impact.

When exactly did the web browser make the transition from being a hypertext viewer to an application platform? This transition seems in retrospect to have been a very fluid affair. Forms with buttons, combo boxes and lists were supported very early. Javascript came in not too long after. When the XmlHttpRequest was introduced it wasn’t long until AJAX took off, paving the way for today’s “rich” web browser applications.

A couple of years ago I had a personal project ongoing for some time. I had decided that web browsers weren’t designed for the kind of tasks they were being made to do (displaying applications), and I wanted to make a new kind of application platform for delivering applications over the web. Today I’m convinced that this would never have succeeded. Even if I had gotten the technology right (which I don’t think I was ever close to), I would have had no way of achieving mass adoption. Incremental developments of the web browser have, however, placed a new kind of application platform in the hands of the masses. Today the cutting edge seems to be browsers like Google’s Chrome, aggressively optimised for application delivery. But some new vegetables have been added to the browser soup.

Google’s GWT web toolkit has been available for some time. This framework makes it easier to develop AJAX applications. Some hardcore AJAX developers may consider it immature, but these frameworks are going to be increasingly popular since they bridge the differences between browsers very smoothly, I think. What’s interesting is that the same company is developing GWT and Chrome though. The two sides of the browser-application equation have a common creator. This helps both: GWT can become more popular if Chrome is a popular browser, and Chrome can become more popular if GWT is a popular framework. Google can make and has made GWT apps run very fast with the Chrome browser (I tested this personally with some things I’ve been hacking on). The sky is the limit here; they can easily add special native features in the browser that GWT alone can hook into.

Microsoft have something a little bit similar with their Silverlight, which while not playing quite the same role, has a co-beneficial relationship with Internet Explorer.

Everyone’s favorite browser, Firefox, recently passed 1 billion downloads. Firefox doesn’t really have a web development kit of their own as I understand it. It just tries to implement the standards well. Which is fair and good, but it demotes FF from the league of agenda setters to people who play catch up, in some sense. Though, it must be said, the rich variety of plugins available for FF might go a long way to remedy this.

All this, and I haven’t even touched on Google’s recent foray into the OS market with “Chrome OS”…

A question for readers who happen to manage bibliographies: what, if any, bibliography management systems do you use?

I started using Aigaion for mine. Then I found out that there’s an open system called bibsonomy, which is potentially much better since it lets you tag and share bibliographies socially, and it seems to already know about all the major computer science papers.

Again (see: The problem with standards), I’m frustrated by the fact that I can’t move my data around between applications as I like without lots of manual effort. A worthy research problem would be making data truly application independent once and for all.

I use the tool Evernote on my iPhone and my desktop computers. It’s pretty nice. You can upload “notes” such as PDFs or images from your desk or from the phone, and the software makes them all searchable and syncs all data between all the different places where you use it. It OCRs photos, so if you take a photo of text, that text will be searchable. It can also show on a map where notes added from the phone were taken.

But this seems to be the icing on the cake: Pixily can scan your paper documents for you, supposedly even handwritten notes. (If they can do my handwriting, and I’m not sure they can, then they can surely decipher absolutely anything, even lost alphabets.) Apparently you send them all your stuff in boxes or envelopes, and they will OCR it into your Evernote account so it all becomes searchable. I would definitely do this if it were cheap, but I suspect shipping to and from Japan is too expensive for me to do this in bulk.

We’ve now had just over a decade of truly mainstream access to and use of the internet. I think I personally took my first stumbling steps on the web around 1995-1996. At the time, it was a limited phenomenon, rife with poor design. It was hard to see what was eventually going to come out of that. And even today, it’s hard to see what today’s internet will eventually evolve into.

If it wasn’t clear before, the events of the past week have made it clear that the internet is a valuable tool for democracy. When everybody can broadcast to everybody else, as opposed to just a select few broadcasting, it’s difficult to control the information flow. Repressing select bits of information becomes hard – the repression just results in the information getting more attention. In the aftermath of Iran’s elections, it seems one of the most important communication channels for protesters was Twitter.  The situation is being likened to Tiananmen square. Together with everybody else, I could follow #IranElection as the events unfolded. It went to the point where the US State Department asked Twitter to delay upgrades in order to keep the service operative, supposedly because of Twitter’s importance in Iran.

I don’t know enough about the candidates to take sides in Iran, but I think one of our fundamental principles should be that nobody should seek to rule by repressing communication. Today, the Internet is a free communications device that anyone can use. How long will it stay this way? When legislators seek to clamp down on the Internet’s uncontrolled nature and regulate it for one reason or another, we should protest. Unrestricted mass communication for everyone is too important an invention to give up.

For those who read Swedish, Rasmus Fleischer has written a brilliant post on the events from a philosophical-historical perspective.

I enjoy experimenting with new software  just to see what people come up with. There’s just so much unknown software to discover. I suspect most people find something they like and then stick with it until it doesn’t work anymore, but there’s something to be said for proactively replacing your software and searching for better things. Here are some things I’ve taken a liking to recently.

New iPhone OS: Apple released version 3.0 a few days ago. It’s been all positive so far. I get spotlight search for the phone, the keyboard feels more responsive, it finally has copy and paste, Youtube appears to have higher quality, and a slew of other features. (Also MMS which I don’t really need in Japan).

GWT: I started playing with the Google Web Toolkit just for fun. For those who don’t know, it’s an API for developing AJAX based web applications using pure Java, which is then compiled to client side Javascript and a Java servlet. It turns out I can be extremely productive with it – I found that it lets me develop fairly advanced web applications using my existing skills. There’s a very high reward/effort ratio that makes me excited. It feels like I don’t need to learn Ruby on Rails properly when I have GWT given that I’m very comfortable developing in Java.. but we’ll see.

Fluid.app: A web browser enhancement for the Mac that allows you to create separate “applications” from web sites you visit often. This means they will show up in the task bar and application switcher, have their own icon, and occupy less screen space. It sounds simple, but it’s a revelation. (And if you’re like me, you tend to have 15+ tabs open in your web browsers constantly, which is a poor way of managing windows).

Chandler: Like many others, I found out about this little calendar and note manager by reading Scott Rosenberg’s Dreaming in Code , which chronicled the misfortunes of an open source startup project. It went 1.0 last year after many years of development. The impression you get from the book is that the developers had a lot of bad luck despite setting out with the right ambitions. This is now an old debate, but the tool is actually usable today – I’ve been using it every day to manage myself for 3 months. Aside from slight bugs, it feels very smart sometimes, thanks to its unique user interface and features.

Micropayments are an old idea.

Examples of services using something that might be called micropayments today are Apple’s App Store (for the iPhone), Sony’s Playstation Network, various MMORPGs, etc. However the typical payment sizes are still quite large:  the smallest possible payment on the App Store is 100 yen (1 dollar). With even smaller payments, say around the value of 0.001 dollars or less, a new range of possibilities is opened up. For those who worry about payment costs, it will probably soon be economically feasible to make payments in the order of 1 millionth of a dollar, given that network costs, processing costs, and storage costs go down all the time – the economics of electronic payment are really changing. Fraud is probably a much bigger hurdle to overcome.

My case for micropayments is about derivative works. I’m not sure what copyright laws will look like in the future, but it is likely that payments and some kind of monetary system will remain in the picture. With the rise of the internet and various kinds of legal and quasilegal file sharing (the American term “fair use” might apply here), a certain kind of derivative work has proliferated. Songs being remixed, music videos being created by fans on Youtube (usually consisting of the song in its original form and fan-made footage), memes floating around. The available technology eases the process of creating derivative works massively.

The existing legal framework was clearly not designed for this. As an amateur musician, I sometimes make music. Once, several years ago, I wanted to sample a tape recording made by Andy Warhol and use it as part of one of my works. After having e-mailed the Andy Warhol Museum, I was told that a written agreement would have to be set up with the Andy Warhol estate. (I have never made a penny from my recordings; they are made strictly for my own amusement, so there was no benefit for me in going through with a cumbersome process). Different countries have different sampling laws, for instance in Sweden sampling something like 10 seconds for use in your own music is allowed without prior agreement. However, the point here is that with a sufficiently advanced major micropayment system, this process could be made much smoother.

Consider completely original works, their derivative works, derivatives of the derivatives, and so on for a certain number of steps. In mathematical terms, this forms a graph (or rather a tree/DAG), branching out and connecting all the included and indirectly included items. With micropayments, it might be possible to pay the creators of each included work automatically by sending money down these connections, slightly reducing the payment amount on each depth level. (The hard thing here is determining the amount to pay and the reduction amount on each step – this would depend on how much the included work has been changed and how prominent it is, among other things). All of this should be fully automatic.

With such a system in place, anyone could sample anything at any time without worrying about legal agreements. Creators might receive a very large number of possibly very small payments. It’s unclear if the final payment distribution would be different from today, but I’m convinced that more derived works would be created.

However, it’s an open question whether these payments always have to be monetary. Can we envision other compensation systems for the digital world (which do not convert to cash)?