Quotes from Reality is Broken

I'm currently supposed to be writing an article about scientific discovery games in biology, but I have writer's block.  So instead, I'm writing here.. which is much easier!  The article I am not currently writing will discuss recent successes like "Algorithm discovery by protein folding game players" by Firas Khatib and others.  In preparing to write this article (i.e. more not-writing), I assembled some inspiring quotes from the fantastic book "Reality is Broken" by Jane McGonigal.  I share them here below because, well they made me think a little bit and perhaps they will do the same for some else, and this allows me to push back my real work by another 5 minutes..

“It is games that give us something to do when there is nothing to do.  We thus call games “pastimes” and regard them as trifling fillers of the interstices of our lives.  But they are much more important than that.  They are clues to the future.  And their serious cultivation now is perhaps our only salvation” -  quote that opens McGonigal’s book - from Bernard Suits

“Games aren’t leading to the downfall of human civilization.  They’re leading to its reinvention” (p354)

“Game developers know better than anyone else how to inspire extreme effort and reward hard work.  They know how to facilitate cooperation and collaboration at previously unimaginable scales.  and they are continuously innovating new ways to stick with harder challenges, for longer, and in much bigger groups.” (p13)

“Game design isn’t just technological craft.  It’s a twenty-first-century way of thinking and leading.  And gameplay isn’t just a pastime.  Its a twenty-first-century way of working together to accomplish real change.” (p13).

“Anything else you think you know about games, forget it for now.  All the good that comes out of games-every single way that games can make us happier in our everyday lives and helps us change the world-stems from their ability to organize us around a voluntary obstacle” (p34)

“Compared with games, reality is unproductive.  Games give us clearer missions and more satisfying, hands-on work.” (p55)

“If you were able to focus the attention of the entire planet on a single goal, even just for one day, and even if it just involved dispatching aliens in a video game, it would be a truly awe-inspiring occasion.  It would give the whole earth goose bumps.” (p112)

Freebase authors semantic web book

I just noticed this post on the freebase dev blog - announcing the release of a new book about "programming the semantic web" written by freebasers Toby Segaran, Colin Evans, and Jamie Taylor. I haven't picked it up yet, but based on the description there and in the amazon reviews, it looks like a(nother) nice explanation of the concepts involved in the semantic web as well as a set of practical programming examples based on the W3C standards (OWL, RDF, SPARQL, etc.).

I found it surprising that freebase was not mentioned anywhere in the brief description given in the post or on Amazon.

Notes from Everything is Miscellaneous

I just finished David Weinberger’s book “Everything is Miscellaneous” and heartily recommend it. Appropriately enough, Amazon suggested it to me when I was looking for Clay Shirky’s book “Here Comes Everybody” which pretty much everyone in my online world has recommended and for Cass Sunstein’s book “Infotopia” which Michael Nielsen suggested to me in a response to a blog comment. Each of the three books is broadly about changes enabled by the Web, but they each focus on different aspects. To summarize full-length books on a variety of interesting topics in a couple words: Shirky focuses on the effects on human social groups, Sunstein on markets, and Weinberger on information itself. Of the three, I liked Weinberger’s the best – probably because it resonates most strongly with my own recent studies and interests. The topics cited in the book were uncannily related to my own personal reading/dreaming/experimenting list –Aristotle, Shirky, tagging, ontology, semantic Web, intertwingularity, blogging, Nature Publishing, Vanevar Bush, Dewey, it even mentions LSIDs of all things!

Weinberger writes in an imminently quotable style. Practically every paragraph contains a pithy sentence worthy of repetition. To illustrate, here are just a few that caught my attention (page numbers from paperback):

“...the solution to the overabundance of information is more information” p. 13

“...Making complex, meaningful phenomena explicit can leave us rudderless, force us to oversimplify, and result in statements that are incomplete and misleading.” p. 156

“The meaning of a particular thing is enabled by the web of implicit meanings we call the world” p. 170

“A Semantic Web that loosely stitches together imperfect, smushy, local efforts is not only more likely, it is to be preferred” p. 195

“Paper drives thought into our heads. The Web releases thoughts before they’re ready so we can work on them together.” p. 203

“That was Aristotle’s startling discovery: a thing, standing on its own, is what it is because of its connection to other things like it and other things not like it” p. 219

Obviously, I liked the book and tended to agree with most of its arguments (funny how liking and agreeing often go together). My only complaints about it related to its treatment of social tagging and of the semantic Web; these complaints likely arise from the book’s successful attempt to appeal to a very general audience and the coincidence that I might know a tiny bit more about these areas than the intended audience – hence I would like more detailed treatment of the consequences of more specific aspects of the technologies than is provided. For example, it annoys me when people talk about social tagging as if it is a permanent, stable technology, thus assuming that the ambiguity of tags (as simple Strings unlinked to concept definitions) is a fundamental aspect of all such systems rather than an optional weakness of the design of particular instantiations. It also annoys me when people talk about RDF as an “ontology language” – especially without at least making some attempt to explain its relationship to things that are most definitely ontology languages like OWL..

Overall a good quick read and a useful reference for anyone interested in the continuing evolution of the Web and, through it, our species.

decoded - first few chapters

Recently a friend lent me Craig Venter's autobiography "A Life Decoded". The first few chapters have been pretty interesting, particularly the part about his time in VietNam. Knowing quite a few people that have struggled to get into and out of medical school, its amazing to think of all the people that, like Venter, were conducting major life saving operations without the benefit of even an undergraduate education - talk about learning by doing... In relation to my last post, I found some solace in the fact that he apparently often feels very much the same way I do about the relationship between his visions and their ultimate reality:

"The sweetest moment of any project is not when it is finished but when the end is in sight [...] Today, ... I still find that the final version often falls short of the one glimpsed in my head during construction."
J.C Venter (2007) "A Life Decoded" page 14

That being said, the chapters describing his early scientific career are positively humbling - it seems that he went quite a ways before he really guessed wrong. One aspect of his career that he highlights is that, aside from his own drive and cleverness, he always had the benefit of being surrounded be truly world class mentors and collaborators - he lists one nobel prize winning colleague after another and he's barely out of grad school..

Another aspect of the book that is a bit jealousy inducing (as most of the book is likely to be for any scientifically motivated person) is the very clear, step by step progress of his brand of science (currently biochemistry). It reminds me of one of Duncan Hull's best remarks

"Nobody is going to win a Nobel prize for creating a standard schema, ontology or whatever".

This might be the essence of the bioinformatician's lament. Though we know intuitively that the work we are doing is important, many of us feel that it is just plain not as scientific an endeavor as establishing the reasons why a certain drug has a certain effect on a certain kind of cell. Despite knowing that our work is vital - the human genome project would certainly never have been possible without people like us working in the basement somewhere - the general absence of those hard and fast facts associated with real, tangible pieces of reality can be very trying sometimes. This is likely why you will see many of us get so excited about things like gardening and building fences in our backyards (even though such labor tends to damage are soft, uncallused hands).