Video: A. Garrett Lisi on Using Wikis to Support Open Source Science

By Timothy M. O'Brien
September 25, 2008 | Comments: 1

A. Garrett Lisi is a Theoretical Physicist who has been developing a novel (and somewhat controversial) unified field theory known as the "An Exceptionally Simple Theory of Everything". You may have read about his work in the recent New Yorker Magazine Profile "Surfing the Universe" or the article in Outside Magazine titled "Has A Surfer/Snowboarder Who Lives In A Van Rewritten Physics? Maybe." Read these articles, and you'll walk away with the impression that Lisi is an interesting character challenging the institutional, academic inertia that has come to define the pursuit of Science.

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What brings Lisi to the pages of oreilly.com isn't the snowboarding or the "living a van" aspect of his personal story (although, admittedly, that is interesting). I'm also not writing to give you a summary of the E8 theory; I understand it only on a fuzzy, "surfacy" level, and there are glossy, biography-focused technology magazines which will satisfy your hunger for pop science factoids mixed with cool snowboarding pictures. It isn't the science I'm interested in, it is his embrace of technology and openness as a central feature of his own research. His personal story is relevant in that it sets up a context of revolution and initiative which reminds me of some of the motivations of open source contributors in the last decade. He's something akin to Linus Torvalds or Eric Raymond: one of many emerging voices for openness and transparency in the "open science" movement.

The Development of Open Source Science

The ascension of open source software happened because individuals took initiative to create extra-organizational communities necessary to build the sort of complex systems that a single institution could not create in isolation. To use the subtitle of Clay Shirky's book, Lisi is an example of "Organizing without Organization". He is a practicing Theoretical Physicist without an institution who broke on to the scene via arXiv without the benefit of a $23 billion accelerator or a team of weary grad students. If the Open Source Science movement gains the necessary support, one can expect more independent scientists able to secure funding without having to navigate the inefficient, political, and constricting infrastructure of the Academy.

There is much more to be written about the continued emergence of "open source" Science and how it is influenced by the well-established open source software movement which has only begun to affect the society as a whole. The analogy between Science and Software is not perfect; there are different camps within Science with a diversity of opinion regarding just about everything, and there are currently heated debates about changing/dismantling peer-review and breaking the choke-hold that copyright places on scientific data. There are surprising differences between software and Science, and it isn't as easy to make same sort blanket statements about "Freedom" which you hear in the discussion of open source software. There is also an inertia in Science that wasn't present during the emergence of open source software; scientific institutions are often hundreds of years old and it isn't as easy for scientists to take the same sort of risks that software developers are so used to taking.

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Where a software developer can drop everything to pursue several failed start ups, dusting him or herself off between each failure as if it never happened. The trajectory of a scientist's career can be ruined by just a single misstep. There is so much more competition for money and tenure in Science than is present in software development, and unlike open source software, the insulated nature of scientific communities does translate into cut-throat competition for grant money. Getting a community of competing scientists in a room and asking them to use "open, online Wiki notebooks" isn't practical given the current state of Science. In addition to issues of competition and limited resources, there are issues of copyright. While software developers might be very comfortable saying that software should be free, scientists often have to deal with copyright issues on scientific collections that would make Apple's iPhone NDA seem like a cakewalk.

While open source Science may be inspired by the success of open source software, the comparisons are not direct. Lisi and Neylon are not direct analogs to Torvalds and Raymond, but Lisi is an outsider using technology to challenge the establishment. That's interesting.

Lisi Discusses his Wiki

In this ten-minute video, Lisi discusses one of his primary research tools - a Wiki. This presentation was delivered in the context of a larger discussion of Open Source Science at SciFoo coordinated by Cameron Neylon a Chemical Biologist at Rutherford Appleton Laboratory in the UK interested in developing a similarly open "notebook" for scientific research.

You can browse the Wiki that Garrett Lisi discusses in this presentation by visiting: http://deferentialgeometry.org/. If you are interested in how Open Source Science is developing, you may also want to read Cameron Neylon's blog "Science in the Open".

Which Wiki does he Use?

Lisi uses Tiddlywiki a Wiki "engine" that makes heavy use of Javascript and stores the contents of an entire Wiki in a single HTML page. TiddlyWiki is best described by the author Jeremy Ruston on the TiddlyWiki project's TiddlyWiki:

TiddlyWiki is a complete wiki in a single HTML file. It contains the entire text of the wiki, and all the JavaScript, CSS and HTML goodness to be able to display it, and let you edit it or search it - without needing a server.

TiddlyWiki may seem an odd choice to an audience of web developers and technologists who, for the most part, are focused on systems to store content in either file systems or databases. Lisi makes it clear that he's most interested in portability and simplicity. From the perspective of someone not intimately familiar with the installation and setup procedures of a MySQL database or an Apache HTTPd server, the choice of a consolidated TiddlyWiki instance seems an obvious choice. There are fewer moving parts, and I would imagine that Theoretical Physics is best "performed" with the least number of technical distractions.

Rendering Beautiful Math

jsMath "A Method of Including Mathematics in Web Pages" which was created and is maintained by Davide P. Cervone:

The jsMath package is based on the TeX mathematics layout engine as described in Appendix G of Donald Knuth's The TeXbook. Since jsMath uses the TeX fonts, it also has the font metric information from the associated .tfm files at its disposal, so it handles italic correction and kerning in essentially the same way as TeX. This makes the output of jsMath as nearly identical to that of TeX as I could manage.

BEGIN TRANSCRIPT

A. Garrett Lisi: I'm usually terrible at providing an example and that is how do we do what we're talking about which is do open source science in a way that works for theoretical investigation.

Basically what we talk about is putting a brain on line, theoretical science and how it's in our heads. You ask, "how do you guys put a brain on line?" One thing that works very well with that is the wiki. So, if you can manage to upload yourself to the web, you just have to do it with your fingers.

What you're actually looking at right here is my brain on line. It's a web page and the web page is http://deferentialgeometry.org/. If you go to that webpage, it's actually Wiki. These are my welcome slides, starting with what wiki is; and what is actually on there is my physics and research notes as I create them in theoretical physics.

These are the last two I've been working on. I've been working super connections and ? in physics, trying to increase my knowledge of these, fill out the slides in Wiki as I explore these areas and gather references in all of them.

But what happens when you do this is Wiki sort of mirrors a way for humans to think about these things. You learn the basics and then you build on them and you build on them again. And if you're trying to build out further, you build out what you already know until you build out your knowledge this way. And Wiki is a great way to do this and presenting to others so others can do it.

Say someone encounters my paper on line, they can follow a link back to Wiki; and Wiki displays information on paper that makes it much more accessible to someone who is trying to figure out what's going on. Over and over again I read a paper and there is some chart or variable find and I don't know what it is. I'll have to page through a paper only to realize that it isn't even in this page and that they have referred to some other reference... this goes on forever.

But, in a Wiki it is really cool. Even if I'm exploring some new area, say you're going to talk about investigating a superconnection and figuring out what that is. A part of the superconnection is a connection and I click here and it brings up that note there; and it talks about what a connection is. A connection is made up of a bunch of parts and they all operate on mathematical forms and it talks about that. You can bring up the page in one form and it talks about what that is. These things are all definitions going back-to-back. One form works on tangent-vectors and you bring that up and it describes what a tangent-vector is. So there is a short blurb on how a tangent-vector is defined.

This next operation is kind of different because you have to put a lot of thought on how these concepts are connected. It's very different than the usual way of operating a paper or book or you're thinking about the best way to segue from one section to another or how do I order them and all that.

But Wiki is not word. Wiki is, if anything, is hierarchial and does not break the frames of hierarchy. It is very useful as far as the learning curve.

Since I do my applied research in this open way, its been valuable to students who are trying to figure out math on line. Students have responded and sent me emails, saying thanks I did it this way, thanks for putting this up there. For me, personally, its good to have a centralized recording of my notes in one spot and its wonderful to work off of and build off of.

MN: (Question about peer review)

AGL: Yes, if anyone wants to spend time playing around on this website. I'm just trying to convince you you are looking at a web page. So this is your . . . there is a bounty. There are a few hundred pages here. Most of this is equations. If anybody (caveat: the first person who) finds three minus signs that are wrong, let me know and I'll give you a hundred bucks. That's the downside of the website.

Audience Member: (why is the site named "deferential" not "differential" geometry?)

AGL: I really love mathematics, and I love exploring how they are relevant to the physical work. Its the mathematical geometry that is deferential to reality.

Audience Member: The math is gorgeously formatted, what are you using to format your math on this Wiki?

AGL: This guy made this beautiful package for displaying math on the internet that is called jsMath. It has examples -- I'll just play around with one. Its really nice. The way it does it is it's all Javascript. You download a set of fonts and that makes it look really nice on the screen if you have the right fonts. If you don't have the fonts, the Javascript uploads tiny little image bits of the fonts and reconstructs them in all little bits.

This guy named Davide Cervone made this; it's wonderful. The wiki engine is also Javascript. Its all one webpage you're looking at. Its a few hundred notes, but its essentially choose your own adventure webpage in mathematics and physics. Its called the Tiddlywink.

Audience Member: It's interesting . . . you're building your own wiki for yourself. Its almost like you and the individual computer can set up your own whatever and then you're part of the community and you can start interacting within the community.

Audience Member: Its relatively straightforward for whatever they need. Stuff I do, others do . . . becomes much larger. You can do a pretty good job.

Audience Member: And it's collaborative.

AGL: Yeah, I want to talk about collaboration and I have other versions of this. There are collaborative Wikis that I use too. When I first made this, nobody was talking a few years ago. I made it the way I wanted it.

END TRANSCRIPT


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Another presentation about this wiki, given at the Perimeter Institute:
http://pirsa.org/08090057

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