There's a lot of misinformation about what "singulatarians" actually believe. Not everyone agrees with Ray Kurzweil's notions that he'll live long enough to upload his consciousness. The best resource I've found is Michael Annissmov's Accelerating Future blog: http://www.acceleratingfuture.... - Dan Kaplan
I'm all for it, only I say let Kurzweil go first when comes to the first downloading of brain contents. That way if something is missing, we'll know pretty quick ;-) - Dean Terry
Interesting, we were just talking about this last night: http://friendfeed.com/e/b3ce29... Doing a quick search, looks like singularity is on the brain of Friendfeed lately. Ooooooeeeeeoooo. - Mark Trapp
As long as more and more people spend all their time on FriendFeed, there won't be too much AI technology being developed. :) - Chris White
i think its at least a few years off, so you can relax, plenty of time for you to get used to it before it happens :P - bob
It's just amazing that I haven't seen any of the movies where this happens (Terminator, iRobot, etc.). What else are people working on from within the FriendFeed headquarters that can kill me? :) - Ana
I'm not convinced. still disconcerting as hell though. - Marco
ana, i think someone is working on doomsday devices over in the furniture graveyard :P - bob
I took Computer Ethics at SDSU (where Vinge taught) and one of our assignments was to compare Vinge's singularity essay to Ted Kaczynski's "Unabomber Manifesto." The similarities are rather striking. I'm not saying it's good or bad, but it is extremely fascinating the differing approach people take to similar topics. - Brooks Bishop
to counterbalance computers that are super smart, we need humans who are freakishly strong. - eviltom
I always thought the first sign of the singularity was twitter. sigh - Elad
Thanks for posting that link to Vinge's essay, Michael. You're right - a mind-boggling read on a fascinating subject that hadn't really crossed my radar until reading this terrific thread. Makes me appreciate FF all the more for putting it in front of me. Could its increasing popularity be another of the early signs indicating the onset of the Singularity? I think we should be told. - Bob Kingsley
movies are pretty bad at showing the future; they tend to show things that *look* cool - Amit Patel
@nick: Thanks for that wired link. Thanks to all for discussing this topic - very interesting. - nadim
Since there seems to be interest, most of the best reading on this is SciFi. Vinge's "Rainbow End" and Stross's "Accelerando" are probably the best "What happens when (if) the Singularity happens" books. (Interesting to note that Vinge is an ex CompSci professor and Stross is an ex-perl hacker). If you want to get scared by the singularity read "A Fire Upon the Deep", though. - Nick Lothian
@Nick: thanks for the link to the Bill Joy essay. Another fascinating, absorbing read. - Bob Kingsley
Ana, you should keep your eyes out for human sized bugs, among other things. - Clare Dibble
I'm a singularity skeptic - increasing compute power doesn't solve basic problems like global warming. - Piaw Na
Will the Singularity happen. Never say never, although I am a skeptic. I do think must Singularitarians completely underestimate the complexity of human biology and by orders of magnitude - Deepak
That's actually a pretty common response. Interesting side: I knew my wife was a keeper when she instantly took to the idea, not frightened or put off at all. - Mark "Rizzn" Hopkins
I choose subscriptions based on a core-perimeter model. The core are people whose interests I know overlap with my own. But I also try to have a strong perimeter - very high quality information sources across a wide variety of areas. So I read blogs by people like Robin Hanson (economist), Terry Tao (mathematician), Ethan Zuckerman (developing world), etc. Unfortunately, FriendFeed usage still seem to be mostly concentrated in a few areas. - Michael Nielsen
Michael, it will get more interesting over time. Waiting for the synthesizer geeks to show up :) - Deepak
Michael, that is one of the best comments I've seen on FF. - David Gutelius
This is true with most things in life. Your real friends, the sites you visit, etc. Why is this so shocking? Just saying... :P - James Mowery via twhirl
it's not shocking... It's justa useful quote that sums up the service... ;) - Chris Messina
I know, but, it could be applied to every social network: Facebook, Twitter, MySpace, and YouTube. Even forums and such. I'm sure the Bret guy is smart, but I mean... yeah. - James Mowery via twhirl
Yeah, I'm being really picky about what I read on FriendFeed. Trying to master the "hide" functionality like so many have suggested to filter out the not-so-useful stuff. :D - James Mowery via twhirl
DON"T GO TO YAARI.com!
I received a spam invite from someone I know and went to the site. I added my email and created password. it just so happened that the password I created for the site was the same as for my email. Yarri then spammed everyone in my gmail address book (the email i used). Even after i asked in NOT to invite the ten or so people it selected for me to invite. - Christian Anderson
seems a lot of motherhood and apple pie there. I would guess either they are a bunch of geniuses who have really solved these problems or its just going to add to the noise - Cameron Neylon
The name is a bit of a nonsequitur, and their differentiating factors are all future plans. The "identity import" sounds the most real and likely to happen, which would be great, but we're still left wondering why we should bother, aren't we? - Mr. Gunn
I program in python (and use NumPy, matplotlib, biopython etc.) and I think it is great. And if you use a modern GNU/Linux distribution with a large package database - like Ubuntu/Debian or Gentoo you don't even need this kitchen sink package. Then the scientific python packages are just one command away. Eg. "apt-get install python-numpy python-biopython python-matplotlib" - Anders Norgaard
I am pretty convinced by now (based on other anecdotal evidence) that Perl's days as being the main bioinformatics language are numbered. - Deepak
@Deepak Really? I'm a Python evangelist and biased, but even so, I do not see Perl prevalence decreasing in bioinformatics. For example, the traffic to the Bioperl mailing list is twice that of the Biopython mailing list. And I wonder if Jason Stajich or someone with OBF can provide an estimated download count. Perl has simply snowballed as the de facto language of bioinformatics and despite my abhorrence for it, some really useful, powerful libraries have been written in it that I wish were in Python. - Chris Lasher
@Chris But what is the rate of new development? - Kevin D. White
@Kevin I don't know. That's a very good question. What metrics could we use to assess this? I can't come up with an apples-to-apples comparison at the moment. - Chris Lasher
Perl in general seems to generate less buzz these days (e.g. see http://www.google.com/trends?q...). But if "amount of buzz generated" is a predictor of future performance, the smart money would be on Ruby... Would be interesting to do a survey of what languages are used at major bioinformatics centers (and elsewhere)? - Eric Jain
@Chris, there is still Perl code around, but a good chunk of it seems like legacy code. A lot of the companies and dev groups that I have been around are using less and less Perl (more Python, some Ruby) - Deepak
Download counts are notoriously hard to measure since one can get code from SVN or as a package from CPAN or from obf site. Website gets about 1M hits a month FWIW. I don't think Biopython should be used as a measure for python in bioinformatics though - it seems like lots of ppl are rolling their own in python and maybe that's the problem? - Jason Stajich
@Jason re: rolling their own. Absolutely correct. This is a major issue that was discussed without resolution a year ago at SciPy 2007. It led to the creation of the Biology in Python list and group. http://bio.scipy.org/ There's been chatter, but it still doesn't feel like a unification of Python efforts in bioinformatics. - Chris Lasher
I don't know about all this Ruby and Python nonsense... but *real* scientific software is still written in Fortran. ;-) - Adam Kraut
It might and GenesWiki is a cool concept. However, I am not sure Wikipedia is the right place for such a resource. You can use the MediaWiki engine to build a dedicated resource, but IMO a gene is not the kind of info I would really look for on Wikipedia (too dynamic). Of course in the grand scheme of things, if it's well curated and indexable (perhaps the biggest advantage of Wikipedia), then should NOT really matter - Deepak
MediaWiki doesn't seem ideal for this kind of data (too many reasons to list here). But it's simple and reliable and perhaps better than nothing. On the other hand I'm not sure the automatic seeding is a good idea (in fact I'm surprised there is no policy against this). They're doing a one-off copy of information from maintained sources into stub articles that might get outdated soon. WikiProteins has similar issues, but at least the stubs are updated automatically until they are edited for the first time. - Eric Jain
@Deepak, agreed that gene annotation is dynamic, but what alternatives do you see that would handle dynamic content better than Wikipedia? (Non-rhetorical question -- really, are there other things that biology should be using?) Certainly non-wiki gene portals and journal review articles are even less responsive to new findings... - Andrew Su
@Eric, the way we've structured the stubs will allow for periodic updating of content. The bot-generated content is separated from human edits using mediawiki templates, and the automated updating can be individually controlled for each gene page. Agreed that MediaWiki isn't *ideal*, but are there better alternatives that we should be considering? I'd be interested in having that discussion, here or offline... - Andrew Su
@Andrew Wikification of substantial amounts of functional data is a watershed event, and I say this as one of the maintainers of a large MOD that wasn't mentioned in the MS. I do take exception with the statement that MODs rely on large contributions from a small number of contributors. But our ability to incorporate new data is much slower than a wiki. - Todd Harris
Whoops. Instinctive carriage return. I think wikis are part of the solution to faster and easier data submission. We are also exploring social features, faceted classification, threaded discussion, and easily customizable views of swaths of data, not just single genes. These things aren't as easily accomplished in a wiki framework. - Todd Harris
@Andrew: The ideal wiki for such data would have better support for structured data (see e.g. Freebase). This is important for people who need to work with sets of genes rather than just individual genes. The other major issue is better support for tracking and indicating data provenance and attributing changes (without making the wiki tedious to use). Don't know if there is any existing software that fulfills these requirements, doubt it. - Eric Jain
@Todd, Profuse apologies for neglecting WormBase and perpetuating the "higher-organisms first" bias. Of course, I have incredible respect for your team and the many MODs I didn't mention... And, of course, I'm very interested to see the Web 2.0-ish stuff that exiting MODs are coming up with. As an aside, it seems like many other efforts try to find a balance between structured and unstructured data, whereas our Gene Wiki was an effort to explore the extreme end of completely unstructured data. - Andrew Su
@Eric, yes, we certainly are aware of Freebase and I think it would be cool to see something similar there. As alluded to in my reply to Todd though, I think though that there is a tradeoff between requiring contributions to be structured and increasing the barrier to participation. The Gene Wiki is clearly meant to have as low a barrier as possible. But I'm sure there will be good synergy between tools all along that spectrum... - Andrew Su
Great people shouldn't have a resume.
Here's why: A resume is an excuse to reject you. Once you send me your resume, I can say, "oh, they're missing this or they're missing that," and boom, you're out. - Berci Mesko
This is true in many ways, but I don't think you'll get very far with a government HR hiring process saying "just read my blog". Once you have an entrenched hiring process with specific requirements, it's pretty slow to change. - Richard Akerman
Or for that matter a corporate HR process. - Deepak
Sometimes Mr. Godin's brilliant, other times he is just restating the obvious from a slightly different viewpoint. Yes, a resume is a compact summary of what you do have and what you don't. HR wants to know these things so they can triage the applications that are missing important stuff and pass only the best on for further follow-up, interviews, etc. Being able to say, "oh, you're missing this or that" is precisely the point. - Mr. Gunn
"Bowie is marvelous as Tesla, who appears as a quiet, calm genius, one all-too painfully aware of the dangers of obsession.
For that matter, most of the cast is truly top notch. Particularly, Bale and Caine, reteaming with their Batman Begins director, Christopher Nolan. Jackman also delivers great performances as both Angier and his drunken doppelganger.
Surprisingly, the weakest link in this magic trick is Scarlett Johansson as Olivia, the lovely assistant who serves both Borden and Angier on stage and at home. Normally a solid performer who’s comfortable in foreign territory (as in Girl with a Pearl Earring and Scoop), she seems a little out of place amidst the fine-tuned talent of her cast mates; her faux British accent frequently does its own disappearing act. That’s not to say she’s terrible, but she has done better." - Attila Csordas via Bookmarklet
I liked the movie. I actually like the Illusionist better for some reason. Scarlett's accent is pretty bad isn't it :) - Deepak
I find sites with "remember me" boxes very confusing - it's never clear exactly what they remember. Usually to do with cookie storage, I think. - Neil Saunders
It's pretty much permission for the site to store a cookie, although I agree, the NN cookie doesn't seem to work - Deepak
It was working for me for a while. Now it doesn't always remember me. Guess it's because I've been neglecting it so much... :( I'm sorry NN!! Please remember me again... I promise I'll come around more often. - Ricardo Vidal
Remember to also check the "remember to remember me" checkbox... - Eric Jain
It remembered me today, but usually I just use Firefox's remembering powers so my info is at least filled out and I only have to click a button. - Eva
It remembers me for longer than claimID does - who was it who recommended me claim ID for an openID? - Maxine
I also rely on Firefox so it is easier to login, otherwise I would have to type everytime I access it. - PauloNuin
I'm using the Sxipper Firefox extension to remember my login information. It has some nice features for automatic form filling. - Yuval Langer
Maxine, not too late to switch to myopenid.com. They do a great job - Deepak
"HealthMap goes beyond the standard mashup and is more like a small-scale implementation of the long-awaited semantic web. The site, which the researchers describe in the latest issue of open access PLoS Medicine, creates machine-readable public health information from the text indexed by Google News, World Health Organization updates and online listserv discussions." - Attila Csordas via Bookmarklet
UniProt is one of the first life sciences databases to distribute all of their data in RDF format (both via FTP and the Web, ~1B triples) -- that ought to count for something :-) - Eric Jain
For my money, OBO is trying to do semantic web in a big ambitious way, some success already but still a long way to go http://www.obofoundry.org/ - Duncan Hull
WormBase - one of the first model organism databases - is in the middle of a ground up rearchitecture that embraces (some) semantic web principles. All vapor ware at this point but I hope to have a public test site available soon. - Todd Harris
Also, if I remember correctly, EColiHub is also planning an RDF backend (I could be wrong) - Deepak
Agree that OBO are trying to do good stuff with OWL, etc. I think SBML is impressive too. So semantic web == RDF ? If it were that easy, every web service would emit it :) - Neil Saunders
IMO RDF is a sufficient condition for an application to be considered SemWeb. In the end it's a representation of a graph, which is what the SemWeb is all about. Ideally RDF with a SPARQL end point. That's pretty much what the Talis platform offers. OWL is a part of the SemWeb stack, but you don't always have to define a vocabulary. - Deepak
Semantic web (as defined by the W3C) != speaking toasters. It's "just" data (RDF/OWL) that is accessible on the Web. Bonus: Provide a SPARQL endpoint so people can query the data rather than just retrieve it by URI. Challenges: Data modeling, scalability (if you have a lot of data), and creating generic-yet-usable end user tools that work directly with the RDF graph data model (I have yet to see any of these)... - Eric Jain
"generic-yet-usable" you hit the nail on the head :) - Deepak
RDF, OWL, OBO, SPARQL endpoints WHATEVER, doesn't really matter. One of the most important things is agreeing on, defining and sharing vocabularies. Easy to say, much harder to actually do. Despite all the semantic web hot air daydreaming, there aren't actually that many people actually doing it. - Duncan Hull
Some of the Semantic Web standards and tools may be useful for defining and sharing vocabularies, but where they really shine (and stop being overkill) is when you realize that you won't ever agree on one true shared vocabulary, but still need to be able to map/relate concepts from different vocabularies. That, and the generic, graph-based data model is kind of neat :-) - Eric Jain
Thanks folks for giving a little homework for the poor experimental scientist. :) - Attila Csordas
Just received a mail from metaweb/freebase: they want to send me a T-shirt :-) . At this time I want to finish to add infoboxes in scientific biographies in wikipedia. Freebase will come later. - Pierre
I don't think it is possible to force start collaborations but I suspect that we have plenty of common ground to work with. Maybe we could take one or two hours to explore possible collaborative projects. This could take any form from brainstorming over a glass of beer, writing up some possible projects or really hacking away at something. Possibly some of the current projects listed in the Biogang wik (http://openwetware.org/wiki/Bi...) - Pedro Beltrao
I can try to provide the space. I will see if there is any meeting room available at MaRS as soon as I get back there next week. Would be good to know the number of people. - PauloNuin
Ah now this is what we're talking about ... good luck folks - Deepak
Just resharing to my feed, for those not following Life Scientists - Neil Saunders
You mean there are those who don't!!!???!!!##**&& :-) - Deepak
I shall not be there.. Deepak: would have been nice to meet you in person. Just subscribed to the room, virtually I'll be present... - Egon Willighagen
So, let's kick things off. Who is (a) attending ISMB 2008, (b) attending a special pre-conference but not the main event or (c) not attending, but will be in the area? - Neil Saunders
I'll attend the main conference only. - Roland Krause
(c) - I live in Waterloo, just outside Toronto. If some open-sciency people want to meet up, I'd be keen to meet. The Duke of York is a pretty good pub near the University of Toronto (http://york.thedukepubs.ca/). The Linux Caffe (http://linuxcaffe.ca/) is a slightly longer walk, but also good. - Michael Nielsen
I live in TO but I am not attending ISMB. - PauloNuin
I won't be there, but let's see what the back channel is like - Deepak
I'll be at ISMB only and will be in town July 16-24 - Neil Saunders
I'll be there for the conference and presenting a poster - Daniel Jurczak
would be interesting to know where everyone is staying so we can plan something (pub, restaurant, etc). The conference venue is really close to the entertainment district, but we can always arrange something close to UofT. - PauloNuin
I will be there for the main conference. - Pedro Beltrao
I will be at the 3Dsig satellite meeting on the 18th-19th but not the main event. - Adam Kraut
LinuxCaffe? How deliciously geeky and cool. Must go there. - Neil Saunders
I'll be there, between July 17-23 (main conf. + student symposium). - Michael Kuhn
Neil - it's got free wireless, and stacks and stacks of geeky books piled all around, free for the reading. Plus, it's got a nice atmosphere. - Michael Nielsen
In my opinion, Google is only the first level of worthiness. The second level comes from an individual's ability to think (or is Google making us dumb :) ), and our circle of trust. - Deepak
CS is on it's way to become the first point of entrance for molecular data... - Egon Willighagen
DUD is a subset of ZINC. Doesn't CS already have ZINC? - Noel O'Boyle
I think the difference is that the DUD identifiers are in CS now, instead of ZINC identifiers... Antony, is this correct? The advantage of this would be that one could easily isolated the decoys... - Egon Willighagen
