Chris Patil - Comments

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Has anyone used Web 2.0 tools like FriendFeed, Twitter, etc. to initiate or implement collaborative science? I'm writing a series of pieces about new technology in scientific communication, and I'd love to talk to someone who's actually used these sorts of tools to do actual science. Let me know!

March 6 - Comment - Like - Share

george, Oliver Schuster, Mary Canady and 22 other people liked this

If you'd rather take it straight to email, you can email me at the address listed here: http://ouroboros.wordpress.com/about... - Chris Patil

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And by the way, this is for a journal, not my blog. - Chris Patil

example: http://tinyurl.com/63vurc - Pierre Lindenbaum

Thanks Pierre. I will definitely follow up with the people involved in that thread. Keep 'em coming, folks! - Chris Patil

I'm not sure this counts but the biogang (http://biogang.openwetware.org/) was sort of founded/created via Twitter/FriendFeed interactions. Lots of projects there. Also, the bioinformatics survey was also propelled by T/FF if I recall. - Ricardo Vidal

Jean-Claude Bradley started a spreadsheet where he wrote this kind of information : https://spreadsheets.google.com/ccc... - Pierre Lindenbaum

See also this post: http://friendfeed.com/e... - Pierre Lindenbaum

This is really amazing, you guys. Thank you. JC, the spreadsheet is incredible. - Chris Patil

There are so many examples on discussion boards like ScientistSolutions, Molecular Station, etc. (Disclaimer, I work for SSI). I could give a you a list of at least 50 specific threads on our site. Here's a recent favorite http://www.scientistsolutions.com/t8853-h... - Rusty Bishop

I just added to the spreadsheet re: the help I got with CSV munging shell scripts earlier. Would discovery of papers through social bookmarking be considered collaborative science? - Mr. Gunn

@Mr. Gunn - no, i don't think so. Collaboration suppose to be productive - if discussion about papers within the group brought all participants to consensus that could be collaboration via social bookmarking with discussions. But bookmarking sites don't provide discussions. Even they would, it will take for a long while for scientists to start discuss about papers online - simple online collaboration. My thoughts also here - http://hematopoiesis.info/2009... - Alexey

Chris - Carmen Drahl made a nice video showing how FriendFeed is used to collaborate with scientists (second vid on the right) http://pubs.acs.org/cen... - Jean-Claude Bradley

Pierre - thanks for posting the spreadsheet - it is nice to see these little projects get re-use - Jean-Claude Bradley

Concretely, the References Wanted room (http://friendfeed.com/rooms...) has really been useful in writing up articles so I can rapidly get my hands on hard-to-come by references in journals to which my institution does not subscribe. But I'm not sure this is a great thing to bring up in your article, except in a vague way; we're not quite clear which side of the law participating re-distributors are on (fair use, or not?) It's not quite the same as discovering papers as per Mr. Gunn. - Heather

Sci-Mate is a very recently opened collaboration to develop Web 2.0 tools for the benefit of researchers. http://www.sci-mate.org/ - Christopher Dyer

Check out: http://www.dental.pitt.edu/informa... - Heiko Spallek

I have recently started a project shared on a wiki + google code + zotero but it is still early days http://openwetware.org/wiki... - Pedro Beltrao

open notebook science should qualify, thinking about usefulchem as example of wiki and google spreadsheets like http://spreadsheets.google.com/ccc... - the list on wikipedia is helpful http://en.wikipedia.org/wiki... - Mike Chelen

I Added the GeneWiki paper in Jean-Claude's spreadsheet https://spreadsheets.google.com/ccc... - Pierre Lindenbaum

Chris - if you are asking for a more technical answer - UsefulChem and the ONSchallenge run mainly on a combination of wiki/blog/Google Spreadsheets - Jean-Claude Bradley

Pierre - thanks for the addition - Jean-Claude Bradley

Maybe this is where Google Wave will turn out to be useful once we all realise that we're not flying around Beginners Island naked like in Second Life ;-) - Sally Church

Sally - do you have a link to the island where everyone flies around naked? Sounds like fun :) - Jean-Claude Bradley

Of course I'm naked but my feline fur hides that pretty well - Jean-Claude Bradley

The Life Scientists: Chris Patil

I just realized there's no Wikipedia article for "Science 2.0". Seems like it's notable enough...

September 24 - Comment - Like - Share

novoseek, John Dupuis, Graham Steel and 4 other people liked this

I would start one today but my motivation is at an ebb, and I'll already be in lab until midnight. But still, I wanted to mention it. - Chris Patil

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The whole science2.0 web-science open-data open-science thing is a mess on Wikipedia to be honest. I certainly don't have the energy for a cleanup but maybe we could try and schedule something sometime and get the editors onside for it? - Cameron Neylon

Wikipedia is a hassle to get into. I wanted to add just a single link to ScanGrants to the Research Funding page and was thwarted at every turn. I finally gave up and concentrated on other avenues of public education: http://en.wikipedia.org/wiki... I’d be happy to help on a cleanup and would do so if asked by someone of Cameron’s stature as he could probably ensure that the whole thing was not an exercise in futility. But working on things only to see them obliterated is infuriating. - Hope Leman

Hope, the WP crowd is _definitely_ hypersensitive to any link with a .com domain name. I understand it since many commercial entities try to get visibility by posting a link to their website on WP, so WP has a specific policy on the subject (http://en.wikipedia.org/wiki...). Having said that, legitimate links just take a little persistence and substantiation to get in... - Andrew Su

Science 2.0... Hank Campbell's www.scientificblogginc.com - Fossil Huntress

Hope, after reading the talk page you linked to, hmm, you definitely did your due diligence. Did those links never get restored? did you never get a better explanation? - Andrew Su

Henry Gee's individualistic take on SideWiki on his End of the Pier Show blog is funny. Well, I thought so. Where is Graham when you need him to add the link? Ok, here it is: http://cromercrox.blogspot.com/2009... - Maxine

Crox, Cromer, Korma, Glasgow, Galapagos and chickens ?? One has no idea what you mean, Maxine :-) And BTW, has the Timo H wiki page been sorted out? Last time I looked, there was *still* some dought about his credability despite the responses left. Crazy. - Graham Steel

Andrew, is it worth considering a concerted effort here to do a clean up in this area? Might be good for everyone - get a few more people in as editors, and get past that initial scarey stage with the insiders that always seems to be end up being antagonistic with hopefully minimum fuss. - Cameron Neylon

Cameron, absolutely, if people here want to contribute the brain cycles, I'm happy to do what I can to make sure the effort sticks. As a general note on life sciences content, the "Molecular and Cellular Biology WikiProject" (http://en.wikipedia.org/wiki...) is a great place to go when you get knee-jerk reactions from the general editorship... - Andrew Su

Maybe a good start for science 2.0 article (and broader project of cleaning up "open science" "open data" etc. mess) would be to make a list of information sources somewhere? I was thinking where would be the best place to do that (google docs? wikipedia user page?) when it occurred to me that the best place to do that would be on the Science 2.0 article page. The only reason I didn't... more... - Steve Koch

The Life Scientists: Chris Patil

Now here's a great idea for a conference: Let's Have An Awesome Time Doing Science! http://awesomescience.wordpress.com/

September 24 - Comment - Like - Share

Berci Mesko, MD, Mary Canady, Steve Koch and 4 other people liked this

With conventional and "unconference"/barcamp-style components. At UC-San Francisco October 8-10. Free registration. - Chris Patil

If I was in SF, I'd totally be going to this. - Andrew Perry

Cameron Neylon

Call for JCOM papers on participative media - http://jcom.sissa.it/call

March 31 - Comment - Like - Share

Claudia Koltzenburg, joergkurtwegner, Antonella and 19 other people liked this

I know this has been posted a couple of times but does anyone think that it is worth trying to write a "Friendfeed for Science" paper for this (or somewhere else even)? - Cameron Neylon

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Absolutely. I'd say it's the first SM application that's truly been utilized by researchers. - Walter Jessen

Is Cameron the lead author? Someone needs to lead and we'll all follow and jump in and try to be generally helpful. - Bora Zivkovic

Sure, it's worth it. I repeat Bora's question: who's lead? - D0r0th34

I can write an abstract by the deadline and probably an outline. I can coordinate I guess and probably write an outline but would need a reasonable number of people committed to helping writing before going too far down the road. - Cameron Neylon

Is there an example of "citizen science" on FF? Not scientists collaborating, but non-scientists or amateur scientists pulling data about some aspect of nature together here? - Bora Zivkovic

Count me in .. I'll commit to writing. - Walter Jessen

What kind of writing help do you need, Cameron? I can maybe pitch in a few paragraphs. It seems to me that comparisons with e.g. academia.edu would be in order, f'rinstance. Can also offer to take other sections in, do basic grammar/sense check, integrate into a smoother paper. - D0r0th34

Dorothea that would definitely help. My experience of the crowd sourced grant proposal as that editing and sensemaking was a big part of the headache at the end. Just pulling all the pieces together and making sense of them. - Cameron Neylon

Bora - I'm not aware of "citizen science" per se but definitely examples of crowdsourcing (e.g. the comment categorization on PLoS ONE). Comparison with other networking sites would seem to fit with the call at some level - Cameron Neylon

Well, if you get enough buy-in to go for it, definitely count me in. - D0r0th34

Okey dokey - wiki set up at http://ff4s-paper.wikidot.com/ I've tried to set it up so that anyone can get in reasonably easily. If you get asked for a password for access then it is the name of our most prolific blogger all lower case twice no spaces - Cameron Neylon

Vivian Siegel and I have a manuscript in press that touches on the subject of FF in science; I started the research for it with a FF conversation http://bit.ly/1ZpfMJ Wanted to mention it so that it can be part of the discussion. Will post a link to this thread when we have a DOI URL. (If I forget and folks are interested, please remind me.) - Chris Patil

@Cam, xlnt but looks like I'm only the first through the gate other than you. Hint to others, *first name only* of our most prolific blogger x 2 ;-) - Graham Steel

@Chris - I just so happened to bump into Vivian over the weekend on Fb. Thanks for flagging up that other FF thread, which I don't think I'd seen before. - Graham Steel

Cmon Graham, he's only got one name :-) Like Madonna remember... - Cameron Neylon

Also pages are actually set to allow anonymous editing at the moment (I think) but obviously better if you do it under some name that can be credited. - Cameron Neylon

And now with a friendly cc0 at the bottom :-) - Cameron Neylon

Posted very quick paragraph for people to dissect as a starting point. - Matthew Todd

If you still need people, I'm up for it, too! - Björn Brembs

More the merrier... - Cameron Neylon

I already made some edits on the wiki... - Björn Brembs

Sounds like fun - I think the focus should just be on FF. Are we putting suggestions/questions in [.....] for Cameron to decide? Maybe we should tag them with our initials, like [..... -AL]. - Andrew Lang

I think we should be able to track who wrote what using the wiki functionality as long as people are logged in (see other comments for password) but tagging with initials is helpful. My thought was to let it run for a few days and then try to cut down to an abstract and save the rest of the text for the (hopefully) full paper. My experience of these things is that people don't like cutting other people's text out so we'll probably end up with lots of stuff that can then be re-used - Cameron Neylon

mmm ok wikidot isn't quite as functional in display as one might home but its ok. Certainly got a list of contributors but if you want to make a point about some specific writing or to propose a significantly re-written version then feel free to initial it. - Cameron Neylon

I probably cannot be an author, but I like your idea. I changed your first sentence to include "initiation" of collaboration...my first read-through it seemed to focus more on "carrying out" collaboration, which implied to me that the relationship existed prior to friendfeed. - Steve Koch

Part of the original call that's most relevant is perhaps: "How web tools are changing and widening this way of participating in the production of scientific knowledge. Do[es] this increase in participation consist in a real shift towards democratizing science or on the contrary is merely a rhetoric which do not affect the asymmetrical relationships between citizens and institutions?" FF is a case study in wideing participation. So, yes, we should discuss initiation as well as extension of collaborations. - Matthew Todd

Still only 183 words without the references. Perhaps need to select one or two examples. Also suggest we tone down how great FF is, and take an analytical approach - is it any good? - Matthew Todd

I agree with Matthew and suggest embedding the toned-down FF blurb into a solid description of the social media currently available (blogs, wikis, microblogging services, social networking sites are already mentioned in the abstract), pointing out for each the pros and cons in comparison to traditional means of communication (for wikis, I have started to compile such a comparison at... more... - Daniel Mietchen

This sounds like a good plan - compare and contrast and then try to pull out what the key features are. Will try to look at this tomorrow if I can find time. - Cameron Neylon

Ok, I'm bumping this up for another round. I think the abstract looks pretty good (less sure about the word "peripherality" but I get the idea at least). Two questions. 1) Is it time to start fleshing this out a bit more for the actual paper? 2) I am wondering about whether JCOM is the right place. No harm in putting the abstract in but what about somewhere like Nature Methods? Or both for that matter? But that involves writing two papers... - Cameron Neylon

Actually, we have two abstracts there now since the two paragraphs are basically paraphrases of each other. 1) probably yes. 2) The purpose of the article is to describe science 2.0 through FF glasses, ideally in an updatable way, to people who do not know either, i.e. to those who prefer paper-based journals. Neither of the two options allow for both, but that could be ok for this initial shot. Alternatives? A community page at PLoS Biology perhaps? - Daniel Mietchen

To see existing PB community pages, run this search: http://biology.plosjournals.org/perlser... (the resulting url is horrible which is why I'm not linking directly to the result) This option might require some kind of formal community, rather than the loose affiliation of the biogang. - Bill Hooker

I think the point of this paper is to lay down some markers in the conventional literature so I was thinking of it as as fairly conventional paper. I haven't checked the JCOM copyright arrangements but if it goes to somewhere with liberal pre-print approach then we can re-use and put up the pre-print version at least on a website for updating (OWW? Some other Wiki). I'd be inclined not to go to PLoS just because the impression could be that "of course PLoS would publish that but it's not a _real_ paper" - Cameron Neylon

Which is NOT my view I should add - just don't want to give people any excuses... - Cameron Neylon

the references i put there aren't really for the abstract submission - they're for later... i think we should have a new paragraph talking about what friend feed is and another maybe outlining some examples - Christina Pikas

A good wiki place for updated versions would be near http://openwetware.org/wiki... . As for people who do not see PLoS papers as _real_, I share Camerons concerns, so we should go that extra step in their direction to pick them up near their home base. But where are suitable _real_ journals that allow reuse in a wiki? JCOM use CC-BY-NC-ND ( http://creativecommons.org/license... ) which would prohibit it. - Daniel Mietchen

Another way to go might be to start out on-wiki directly (not at wikidot - at the "final" destination), get one version published on paper and continue updating. Nature Physics may be open to that, judging from things like http://www.nature.com/nphys... and http://www.nature.com/nphys... . - Daniel Mietchen

Any NPG journal is ok with a pre-print and that includes writing the paper completely openly and leaving the presubmission version on a Wiki. The only license allowed for a preprint on Nature Precedings is CC-BY so for that version, re-use is perfectly allowed. It is only the peer reviewed published version that has a six month embargo on re-use. - Cameron Neylon

I'm thinking more and more that a real practical "Web2 tools for the active and busy researcher" could be a worthwhile Nature Methods paper. We could get David Crotty to referee ;-) - Cameron Neylon

I had a closer look at Nature Methods now and think the topic would fit (closest match I found is at http://www.nature.com/nmeth... ). However, who of the "tactile" readers are actually subscribed to the print edition of this one? I found only two Nature Methods papers in my electronic database and have never actually seen it in print. - Daniel Mietchen

Interesting development. I would definitely agree that a submission to a NPG journal would be an excellent idea. I used to get Nature Methods in print, but no longer. It was very good last time I saw it. Something on Web 2.0 tools would be excellent. That leaves the JCOM paper. Still worth submitting an abstract, but we need to emphasise the 'democritisation' of research, rather than FF itself. - Matthew Todd

Someone want to start a Web 2.0 tools paper on a wiki, and we can flesh out something and ask Nat Methods if they would be interested? - Matthew Todd

15th May deadline approaches. The way the abstract currently looks includes mention of peripherality. JCOM itself is interested in participation in science of non-scientists, e.g. those at peripheral institutions (I guess) but surely more importantly those who do not have access to the hardware of science, so the public, librarians, curators, journalists. I think this is a slightly... more... - Matthew Todd

[And why is this whole thread not appearing at the top of my feed, despite my commenting on it afresh?] ugh - Matthew Todd

Bump - 5 days left. - Graham Steel

Two days left for this one now but I think we had agreed that Nature Methods would be a better location anyway. Still, without some sort of plan and deadlines, http://ff4s-paper.wikidot.com/ probably won't go too far but by means of http://friendfeed.com/ff-for-... we might actually get some concrete things to report about. - Daniel Mietchen

One day left, folks. - Graham Steel

One or two days? 15 May isn't it? I have received Nature Methods in the past, comes out monthly, got lots of good stuff in it. I agree with Mat that the focus of the current abstract is perhaps slightly off from the JCOM call but no harm in putting something in. I think we can talk about including people beyond research scientists and how that could lead to the general public. I was thinking of a NMeth paper as more of a "how to" than anything else. - Cameron Neylon

Looking at it it is actually well under 500 words even if we combine both versions. Can add some more but does anyone have a feel for what would be optimal? I've been caught out by funny cultural things about lengths of abstracts before... - Cameron Neylon

Chipped in a little more. Still around 400 words. Am still concerned about mentioning Friendfeed so much. Imagine in 10 years, and FF is no longer with us (I know, I know, but just imagine for a second), then this article will look terribly dated. We should mention FF, but try to also keep broadly mentioning aggregators as the central idea - the functionality is the key thing -... more... - Matthew Todd

I think the abstract is in good shape now, and with 459 words it's not too far off the mark. In case of a submission to JCOM, however, we should perhaps ask whether they agree for this article to remove the "ND" (possibly along with the "NC") from their default CC-BY-NC-ND license - otherwise there will be problems with updating the stuff the wiki way. - Daniel Mietchen

I also need a list of all the people who feel they've contributed. Unfortunately the free settings only give us the last twenty edits and I have a feel there were more people who made some contributions at the beginning. I'm not so keen on upgrading to see whether I can recover those names...will draft up an email that says something about the ND bit - but as the license on the current piece is cc0 anyway they can't restrict our re-use anyway... - Cameron Neylon

And the word count is now 486.... Agree with Daniel re. dropping ND and possibly NC too. - Graham Steel

Just did another minor edit (anonymously by mistake)- 496 words! Again made FF an *example* of an aggregator, to try to make the article more general. - Matthew Todd

The deadline has been extended to June 1st - I just got an e-mail about it. http://jcom.sissa.it/call - Bora Zivkovic

i think it's pretty good right now. it's just an abstract and not the whole article so.. @Matthew - I like your edits making FF an example of a type of service. i'm fine with dropping the ND and NC and just keeping the by. how about we add a place for the authors on the page - with the names, e-mails and affiliation info we want to use (i use UMD for this not my place of work, btw) - Christina Pikas

Really like the new paragraph and additions to the first one. A call again. Anyone else in this conversation made contributions that they feel should be recognized by authorship at this stage (presumably can change later anyway if accepted)? I want to interpret that generously as well. Have put up a draft submission letter at http://ff4s-paper.wikidot.com/submiss... - Cameron Neylon

Ok so realized I can get a free upgrade for 30 days which lets me see all the revisions. So Dorothea, Graham Steel, Romney, and Walter made additions early on and aren't listed as authors currently. If you would like to be included (even if you just want to keep a hand in for potentially writing the paper) can you add your name/affiliation to the front page? - Cameron Neylon

Looks like you have plenty of help! Not sure another cook in the kitchen is needed. - D0r0th34

Am I just confused or has the deadline just shifted by two weeks in the last couple of hours? Now seems to be June 1. Still I'm pretty happy with abstract as stands and would be willing to put it in. - Cameron Neylon

+1 Cameron. Great submission letter (BTW). I say SHOOT and let's see what happens. - Graham Steel

If everyone is happy then I will submit it tomorrow. Speak now, or forever hold your pieces... - Cameron Neylon

i say shoot - but do we need a catchy title first? (agree with G.S. - like the submission letter) - Christina Pikas

Ah woops. Title. Mmmm. "Design Patterns for the Succesful Implementation of Web 2.0 Tools for Research: Does FriendFeed point the way for online tools that will enable and support widespread collaboration?" That's a bit unwieldy but it's a start... - Cameron Neylon

"A friend in feed is a co-author indeed" was/is the working title and I say keep it at that unless anyone comes up with a better one. - Graham Steel

+1 for Graham's -1 for Cameron's (bcs design patterns might be too hard to live up to in an article) - Christina Pikas

Do we need something a bit more explanatory though? Or is that the right style for this kind of journal? I agree design patterns is probably too much to get into this article. Guess that one will be further down the track. - Cameron Neylon

We're talking about collaboration, rather than co-authoring necessarily, so "A collaborator in need is a friend in feed" comes to mind (though now a bit of a mouthful!), then maybe followed by ": Democritisation of Research Through New Web 2.0 Tools." ?? Agree whole things looks good, and thanks for putting together the covering letter Cameron. You happy to submit, finally? Nice that deadline is extended, but don't think we need it unless we can't decide what to call it :) - Matthew Todd

I'll sit on it for the moment until we have had a bit more time to think about titles I think. Could benefit from a few cycles of discussion. I like Mat's but agree it is a bit more of a mouthful. My only concern with the Friend in Feed is a co-author indeed is that we probably won't write that much about authoring. Although that will be how the thing is put together so I'd be happy with it. - Cameron Neylon

Not having seen the latest discussion here, I have just put in "The social aggregator as a tool for user-led collaborative science" as a placeholder until we have agreed on a final phrasing. - Daniel Mietchen

How do people feel about double barreled titles. I find I do them by default but I know they irritate some. Thinking that "A friend in feed is a co-author indeed: The social aggregator as a tool for user-led collaborative science" might work? - Cameron Neylon

Fine with me. - Daniel Mietchen

And with me. - Graham Steel

Fine. Really hate double-barreled titles, but feels right here. - Matthew Todd

I would hate to impose my double-barreled tendencies on others ;-) - Cameron Neylon

it's been proven in a seminal article by L. Puppybreath that increased titular colonicity means increased citation: I agree :) - Christina Pikas

Ok peoples. Final draft version I propose to send off is available at http://dl.getdropbox.com/u... - Cameron Neylon

And submission letter at http://dl.getdropbox.com/u... - Cameron Neylon

Top man, Cameron =) - Graham Steel

Would I be right in thinking that if I could avoid submitting it by email then email will have played no part in the preparation process? - Cameron Neylon

Yes, absolutely. - Graham Steel

minor edit. on the draft version, 4. Patient Advocate, Scotland 5. University of Sydney, Australia should read:- 5. Patient Advocate, Scotland 6. University of Sydney, Australia - Graham Steel

fixed. Also minor edit to submission letter - Cameron Neylon

Will send at end of day today - Cameron Neylon

or tomorrow...but it's gone now... we see what happens - Cameron Neylon

Danka very much. - Graham Steel

just our affiliations alone are cool - what a diverse set! how exciting - Christina Pikas

Awesome, Cameron, thanks for sending it in, and for catalysing this whole (very interesting) process. - Matthew Todd

Well thankyou all for writing it! Now all we've got to do is turn it into a paper.. - Cameron Neylon

Can I add a paragraph about a commercial view on this? I will probably do it as free-citizen (private person), not as the employee of the company I am working for. - joergkurtwegner

This is cool: http://tinyurl.com/l98lwp - Bora Zivkovic

Just to keep the conversation together: Just received this back from the editor "I'm the editor of the JCOM's special issue about User-led, P2P Science. We hereby inform you that your abstract unfortunately has not been selected for publication. There was strong competition, several applicants for the limited places, and we wanted to strictly respect the topic of the call." - I guess... more... - Cameron Neylon

Yes, I think a Nature Methods paper would actually be the more interesting possibility in any case. Scope being Web 2.0 Tools for Scientific Collaboration? - Matthew Todd

Yes, that's what I was thinking, with some use cases and examples of "how to" effectively. probably still focussing on friendfeed - Cameron Neylon from twhirl

Yes, "Web 2.0 Tools for Scientific Collaboration" for Nature Methods sounds good to me too. - Daniel Mietchen

ok - best get on and write it then :-) Will try and get some sections put up over the next week - Cameron Neylon

Was wondering what has or has not happened since the last update in June. Any clues?? - Graham Steel

Ummm not a great deal I'm afraid. It is currently No 4 on my list of papers I really must do something about...Daniel has been regularly updating the bibliography section - Cameron Neylon

Thanks, Cameron. - Graham Steel

TWiT Conversations: Leo Laporte

Live now: Dr. Kiki's Science Hour with Kirsten Sanford and guest, Chris Patil, of the Buck Institute For Age Research. http://live.twit.tv. Discuss here...

July 30 - Comment - Like - Share

Dan Barber, Benjamin Taylor, Richard Pruen and 3 other people liked this

http://buckinstitute.org/ - Leo Laporte

51 more comments

thanks leo, chris patil is http://twitter.com/donotgo... and his blog is http://ouroboros.wordpress.com/ - Mike Chelen

here's a nice review on theories of aging: http://www.pubmedcentral.nih.gov/article... - Mike Chelen

thanks Mike! - Leo Laporte

Love this show because I don't understand any of this stuff, and by the end of the show. I know a decent amount. Keep it up! - Dakota O'Neill

agreed, so much exciting research to consider! thanks for having folks on that can help explain the topic and point us in the right direction to learn more. here's a good paper Patil mentioned recently that examines the mechanism of dietary restriction on lifespan (through HIF-1): http://www.plosgenetics.org/article... - Mike Chelen

Is de Grey going to get brought up? - Christopher A Carr

he said "consciouness is not a state function" however i'm unsure what that means exactly. even if the previous states must be considered, the following states can still be calculable. - Mike Chelen

He's a closet dualist, perhaps. - Christopher A Carr

That, or perhaps he finds the whole Chinese Room nonsense persuasive, supposing that meat has some semi-magical causal powers. - Christopher A Carr

chinese room? - Mike Chelen

John Searle's Chinese Room Argument: http://en.wikipedia.org/wiki... - Christopher A Carr

I would like to hear Patil's take on deGrey's "engineering problem" approach. - Christopher A Carr

you are in luck, they just started talking about deGrey :D - Mike Chelen

Yep; there we go. :-) - Christopher A Carr

there are only a few organisms known to be biologically immortal, such as the hydra - Mike Chelen

I wish Aubrey were in the studio. Not that he would necessarily be correct, but he would savage all of these complaints. It would be funny. - Christopher A Carr

yeah i don't see why engineering of complex machines is somehow different from complex biological systems. and research testing may not be successful at first but that doesn't necessarily make them reckless or harmful. - Mike Chelen

Here comes the straw man... - Christopher A Carr

I think the "escape velocity" concept should be mentioned. - Christopher A Carr

they did a little earlier, saying that the rate of life extension could exceed the rate of aging - Mike Chelen

Ah, thanks. - Christopher A Carr

Q: wonder what the current rate of life extension is currently estimated to be? A: 2/10ths of a year per year - Mike Chelen

Organisms don't generally live long enough to manifest aging features that can be selected for... - Christopher A Carr

Plus, you would have to invoke group selection, which is problematic. - Christopher A Carr

aging is relative though right, surely there is selective pressure for humans to live past age 5. group selection is another interesting concept, for example grandmother helping offspring survive - Mike Chelen

Well, yeah, you have to get to sexual maturity. I'm saying pathologies associated with advanced aging can't really be selected for -- even invoking kin selection. Suppose a constrained lifespan helped your close relatives have more offspring; plausible -- problem is that an insufficient percentage of organisms in a pop. get to that point such that the particular things that kill you can be selected for. - Christopher A Carr

what percent of a population would be significant? if the increase in offspring were large, it seems like the selection pressure would be meaningful even if few individuals in a generation were able to take advantage of it - Mike Chelen

Good question. Let me think about this for a second. - Christopher A Carr

So, say you inherit a very strong propensity to develop some type of cancer n years after reaching sexual maturity; you have to live that long in order to die of the cancer thus freeing up resources for your younger kin. *If* your offspring inherit the same propensity, and all of them die of predation before getting old enough to develop the same condition, the subsequent generation does not benefit. - Christopher A Carr

And if this kin selection hypothesis is predicated on the idea that "early" death frees up resources for the next generation of your close relatives, it would seem to me that fluctuations in resource availability over generations would minimize the fitness of constrained lifespans. - Christopher A Carr

Oh, hey! Just remembered an interesting conversation on this very subject. deGrey and Yudkowsky - "Is aging an evolutionary adaptation?" at 6:29: http://bloggingheads.tv/diavlog... - Christopher A Carr

haveing weard trobel with the buffering on my windows to night never had it with the new freind feed browser b4 - daveccorey

Thanks for the comments, all (you do know I can hear you, right? :-) ). - Chris Patil

@Christopher Carr: I don't think that meat has magical powers, unless it's really good BBQ. I do think that some of the Kurzweil-type arguments about the feasibility of transferring human brains into digital representations are based on overly simplified models about how minds work, and on possibly inappropriate analogies motivated by our familiarity with digital computers. - Chris Patil

The idea that consciousness might not be abstractable and "uploadable" is my current favorite answer to the question "What if some dearly held conventional wisdom of the moment turns out to be wrong?" - Chris Patil

@Michael Chelen: On "consciousness as a state function." (Not crazy about how I phrased it.) What I was aiming at was this: How certain are we that a mind is something that could be encoded/represented/abstracted into another medium than the one that currently contains it? (in the way that music can be so encoded either on a CD or on a cassette). What if instead the medium is, somehow, the message? - Chris Patil

I'm not being dualist here; nor vitalist. I certainly believe that consciousness has a rigorous physical basis. I just sometimes feel that singularity proponents and others gloss over the challenges posed by abstracting consciousness, and assume far too much about how much of the physical system involved is redundant or inessential. - Chris Patil

Also, I think this causes problems when people start equating a neuron with a transistor, its state with a bit, and an axon or dendrite with a wire -- and then basing predictions about technology development based on approximations that are wrong by orders of magnitude even at the level of the most basic components of the system. - Chris Patil

I hope that clarifies matters somewhat. In any event, thanks for the comments. More from me on this and other subjects in an interview at Future Wiki, if you're interested: http://future.wikia.com/wiki... - Chris Patil

Thanks for commenting, Chris. Let me digest your position a bit, and I'll reply, insomuch as I'm able. And "magic" is probably as good a word as any for properly slow smoked meats. ;-) - Christopher A Carr

Chris: You seem to be conflating something called "consciousness" with "minds." I'm not sure what "consciousness" means exactly -- having, as I do, a Dan Dennett-type view of the "problem." Do you think that it's necessarily impossible that a software system (not running on meat) could reason across domains in a way functionally on par with humans (hopefully sans primate motivational... more... - Christopher A Carr

Christopher: wouldn't the kin selection hypothesis suggest that members of an extended group can increase the survivability of other individuals even if they are past reproductive stage? - Mike Chelen

Chris: abstraction depends on what resolution measurement is relevant to representing the mind. given that current estimates are wildly inaccurate, is there any evidence to suggest the level of biologically understanding is not finite? - Mike Chelen

Mike: To say that dying from some heritable, particular, age-induced reason, *can't* be selected for from kin selection dynamics, was incorrect of me. But I think I've addressed the issue of persistence. A genetically encoded likelihood of dying from X -- insomuch as X manifests only when living to an unlikely age -- won't be significant in terms of affecting the possible age of members a species. If you get a chance, you should have a look at that video I linked to. - Christopher A Carr

I hope Chris doesn't think that brains do quantum computing. ;-) - Christopher A Carr

I would like to thank Dr. "Kiki," Mr. Laporte, and Dr. Patil, for such an interesting program. More, please. I'm pretty sure that Leo could get deGrey via Skype, if not in the studio. In fact, he's a very approachable guy on Facebook. -- would make for another great show. - Christopher A Carr

@Christopher Carr, I hope you're not implying there's any sort of actual evidence that they don't. :-) Once again: The consciousness/mind stuff came up in the context of Kurzweil's approach to singularity issues. I think his projections about how soon the uploaded-mind-type singularity is based on oversimplified assumptions about how the brain works, and that's what I was aiming at. - Chris Patil

I don't think it's impossible we could abstract mind into software, but I don't think it's useful or interesting to be blithe about its essential inevitability. I don't think that AI is impossible, and I don't think that a silicon or other substrate couldn't harbor intelligence. I distinguish, however, between a mind and a specific mind, e.g. my mind, or your mind. - Chris Patil

What I said to Kiki had to do with my skepticism re: the ease with which one could transfer a specific human mind (which is what I meant by "consciousness") into another substrate. That would require making very precise measurements, possibly limited by quantum uncertainty (this is not equivalent to claiming brains perform quantum computations, in case that needs to be said), in very short amounts of time. To say it's a major challenge is a massive understatement. - Chris Patil

As a molecular biologist of aging, I've encountered many ideas that seemed reasonable run up against insurmountable problems when the time came to actually implement them -- i.e., projections and hypothesis aren't the same as demonstration or proof of principle. This heavily informs my skepticism. When someone proves that it's possible to transfer specific minds, I'll gladly do what all scientists do and say, "Hm. Thought you couldn't do that. Interesting. Good news." - Chris Patil

Ah, ok. I'm not sure Kurzweil would insist that a copied mind is the same mind, even if the meatless version has a sense of continuity and insists that it's the case. - Christopher A Carr

RE: quantum computing brains -- I was under the impression that there's a broad consensus among physicists and neurophysiologists that that the Penrose-Hameroff proposal is bunk. Aren't there in fact lots of reasons to think that big, hot brains are not -- in the relevant sense -- quantum devices? Are they doing anything more than supposing that a seemingly spooky phenomenon must have a spooky explanation? - Christopher A Carr

SciBarCamp: Bosco Ho

My vote for best dressed at #sbcpa is Jason Hoyt wearing the tight v-neck white t-shirt and a black tie.

July 10 - Comment - Like - Share

Jim Hardy, Cameron Neylon, Naomi Most and Chris Patil liked this

I dug Naomi Most's key necklace as well - Shirley Wu

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+1 to Naomi for her necklace and ninja shoes - Mackenzie Cowell

We should also do best T-shirts. Todd's "Science: It works, bitches!"; Duncan's "Alright my luvver". Others? - Chris Patil

Duncan's shirt was making me LOL - Mr. Gunn

w00t! yeah i dug Jason Hoyt's hipster geek look as well. - Naomi Most

I'm liking my new 23andMe and PLoS Hamster ball T shirts! Thanks guys! - Jim Hardy

In all fairness, Jason's shirt was collared, so technically "not" a T-shirt http://is.gd/1uNMQ - Jim Hardy

SciBarCamp: Cameron Neylon

Efficiency and incentives in research - How to bend the internet to scientists - Cameron Neylon, Jason Hoyt, Duncan Hull

July 9 - Comment - Like - Share

Michael Habib, Daniel Mietchen, Kubke and 10 other people liked this

http://livestream.com/cameron... - hopefully with sounds this time. OPr search fo @nthmost scibarcamp - she seems mjch better set up than I am - Cameron Neylon

63 more comments

What do we do as scientists, why do we do it, should we be allowed and funded to do it? - Kubke

Cameron starts with a few introductory slides he also showed at a recent NESTA workshop on "Science in Society": http://www.slideshare.net/Cameron... - Martin Fenner

Cameron: What do we do as researchers? - Chris Patil

Science in society? for society? with society? - Chris Patil

Science in society, vs. science *for* society, science *with* society - Kubke

We want to do great things, but what are the risks if we all try to change the world at the same time? - Chris Patil

The money that goes towards science (including the naturally expected failure of it) could go into hospitals, secondary teacher salaries, etc. - Kubke

Do we want to put more money into scientific research? Or should we rather spend that money to build hospitals or pay teachers? - Martin Fenner

...and government expects a return on the investment. - Martin Fenner

Trying to watch the stream but sound is rather low and image pointing towards the ceiling. - Ricardo Vidal

How do you maximise efficiency in generating impact for your research? - Martin Fenner

Thanks!!! :) - Ricardo Vidal

Hi Ricardo. - Martin Fenner

Now over to Jason and Duncan... - Martin Fenner

We aim to please. - Chris Patil

Hi guys. Now this is power. Interfering with a presentation from across the Atlantic via FriendFeed. Carry on, Cameron. LOL - Ricardo Vidal

Jason Hoyt: Bending the Internet to Scientists or maximizing efficiency. - Martin Fenner

Most social networks for scientists are a failure. - Martin Fenner

The problem: research is inherently social, but the tools we are using are not. - Martin Fenner

If you build it, they will not come... build projects for communities that already exist (Sean Mooney from yesterday) - Kirsten Sanford

Many social tools need a critical mass, maybe that is not the right way to go. - Martin Fenner

Tools should work with a userbase of 1. - Martin Fenner

The internet needs to bend over for scientists. - Bosco Ho from iPhone

Seems like a good place to plug an article I wrote recently about the barriers that prevent scientists from adopting social tools: http://dx.doi.org/10... - Chris Patil

Jason talks about last.fm. - Martin Fenner

interesting that the musician scientist is making comparisons between music and science... - Kirsten Sanford

Could papers as social objects work? - Martin Fenner

Jason needs to move from between cameron and the screen - Mr. Gunn

I hear a familiar point being made here - networking is an emergent property of good tools. - Mr. Gunn

Peter Binfield asks about the analogy between last.fm and Mendeley. - Martin Fenner

The Mendeley approach to articles could also apply to other "habits" of scientists. - Martin Fenner

There might be a million people with Micheal Jackson on last.fm, but how many scientist for an article in medeley? - Bosco Ho from iPhone

Bosco - can't hear audio(just questions, speaker OK), but did you mean articles/scientist? - Mr. Gunn

Now over to Duncan... - Martin Fenner

Shared annotated documents collection - will people use this feature? - Bosco Ho from iPhone

Duncan Hull: Digital Identity on the Web - Martin Fenner

annotation of documents will increase interaction and usability of information contained within papers. I totally see people using that feature... - Kirsten Sanford

I love the idea of having an embed code for a collection. I can share bib-lets. - Mr. Gunn

Duncan Hull - who am I, digitally speakin? - Bosco Ho from iPhone

All the social tools for sharing data on the web rely on some kind of digital identity. - Martin Fenner

Traditional way to gain identity as scientists: publish a journal article. - Martin Fenner

Julian Gough is digitally schizophrenic. - Bosco Ho from iPhone

scientist identity has changed. Much more complicated than traditional list of publications. Now includes, social alignments (research groups), work (research projects), friends (social web)... - Kirsten Sanford

Many papers by "forgotten password", "already registered", etc. in Google Scholar. - Martin Fenner

A popular user on google scholar: Mr F. Password. - Bosco Ho from iPhone

machines are too stupid to tell the difference between real authors and random words... is this something that could be solved by better AI? artificial learning algorithms> - Kirsten Sanford

Author disambugation in article is hard comp sci problem. - Bosco Ho from iPhone

this paper talks about "page rank for people" not nec. a new idea, but could be important for research reputation / attribution - Kirsten Sanford

oops... link: http://threeminds.organic.com/2009... - Kirsten Sanford

MyExperiment allows OpenID, but only 16% of users use it. - Martin Fenner

OpenID is prohibitively complicated to start using... anti-intuitive... barrier to entry. - Kirsten Sanford

Openid seems to be pretty hard to use for most scientists. - Bosco Ho from iPhone

OpenID is probably not secure enough for some scientific applications. - Martin Fenner

Some universities are requiring ResearcherID for admin. - Bosco Ho from iPhone

Researcher identifiers would make life for journal publishers such as PLoS easier. - Martin Fenner

Will there be a tipping point from NIH or NSF or PLoS in the use of a unique identifier? - Bosco Ho from iPhone

What will change if we had the perfect researcher identifier? - Martin Fenner

Unique researcher ID would level the publication playing field between men and women. Women often struggle with name changes and loss of recognizability due to name changes at marriage. - Kirsten Sanford

Long discussion about potential benefits of researcher identifiers. - Martin Fenner

I do wonder about the pitfall of the identifier in non-democratic states... could make scientists easier government targets? - Kirsten Sanford

Thank you all for the comments. This plus Cameron's video stream was as is if I were there. - Ricardo Vidal

Awesome awesome awesome! - Bill Hooker

Thanks to everyone who participated virtually and actually, we had some great questions and feedback - Duncan Hull

16% is actually pretty good for such a new technology. there are also some user interface designs which would help such as http://drupal.org/project... - Mike Chelen

SciBarCamp: Chris Patil

Aaron Rowe & Rick Henrikson: The future of medical technology

July 9 - Comment - Like - Share

Jim Hardy, Bosco Ho and Mackenzie Cowell liked this

"ASSURED" Solution: Affordable, Sensitive, Specific, User-friendly, Rapid, Equipment-free, Delivered to those who need it. Important for the third world. - Chris Patil

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"Africa is like space" : limited resources, harsh environment. The main difference is financial. - Chris Patil

Biosensor kiosks: Swab yourself, drop off the goo in a kiosk (like an ATM), get a prescription automatically sent to you. - Chris Patil

Aaron sees small siRNAs designed against specific diseases as an important future strategy for the "long tail" of diseases (i.e., rare illnesses) - personalized medicine made easier - Chris Patil

DX-box: a home device that would schedule and collect biological samples for diagnostic purposes, based on the user's risk factors. (Under development at Microsoft) - Chris Patil

Rapamycin: effects on aging, immunology - Chris Patil

Chris Lipinski: "god of medicinal chemistry" - ways to repurpose drugs: start with drugs that are already known to be bioavailable and safe, and then test them with clever assays for their effects in other contexts - Chris Patil

Jim Hardy from HemaCell: Rapid PCR machine that works on a small thermal loop. Battery-operated, loaded/sealed loop. Good amplification and selectivity. Problem: How to detect the product? Aaron: use a compact electrochemical DNA detector. - Chris Patil

repurposing drugs example announced yesterday re: immune-suppressor rapamycin used for life extension http://bit.ly/o5usp - LaBlogga

Many drugs that are viable, even efficacious, don't make it into the clinic - these are a potential gold mine for repurposing efforts - Chris Patil

The bioengineering field has become "MacGyver-esque": cool new diagnostics using sometimes mundane starting materials: eggbeaters, CD players, paper microfluidics - Chris Patil

Fast sequencing is useful for infectious disease diagnostics - Chris Patil

There are only two major classes of flu drugs, but already strains immune to both. There are "entry inhibitors" undergoing trials - Chris Patil

Zinc finger nucleases: Engineer an enzyme to find a site in the genome and then clip it out. Currently claimed by Sangamo, but there is an academic consortium that is challenging them -- and making their information public! - Chris Patil

If you want to be a good science reporter, be out of phase with the press release cycle <- Aaron Rowe - Chris Patil

Affordable metagenomic sequencing (~$5 / sample): http://bioweathermap.org - Mackenzie Cowell from iPhone

SciBarCamp: Martin Fenner

Peter Binfield: Article level metric from the PLoS perspective

July 9 - Comment - Like - Share

Michael Habib, Julien Sicot, marlene and 4 other people liked this

What is the problem: how do you access the worth of impact of journal articles? - Martin Fenner

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What is the granularity to measure impact: journal, research institution, individual researcher? - Martin Fenner

important decisions made on the basis of "impact" which covers many things, interest, usability etc - Duncan Hull

So much to read need metrics to winnow things to read a lifetime. - Bosco Ho from iPhone

We talk about "metrics", but many signs of impact are hard to measure - Duncan Hull

Usage-based measures are still pretty rare - Martin Fenner

Current metrics include impact factor, citation based measures (h-index) - Duncan Hull

Most measures are journal level - Duncan Hull

Dowload stats - Duncan Hull

There is no substitute for reading the literature yourself and forming your own opinion - Duncan Hull

Most people filter based on the impact factor of the journal. - Martin Fenner

All metrics are terrible, some metrics are more terrible than others - Duncan Hull

Potential metrics: citations, usage, discussions, social bookmarks, etc. - Martin Fenner

Martin made a great point: Why should we even want to assign a number to the quality of a paper? - Chris Patil

Web 2.0 is the solution. - Bosco Ho from iPhone

People are starting to use these, but not very much, so PLoS ONE wants to start the ball rolling. - Chris Patil

PLoS provides article-level metrics for all their articles, e.g. citations, usage, blog posts, etc. - Martin Fenner

there's some good arguments against assigning numbers to students in school, also. I think stats are a good thing, as long as they aren't the only thing. Remember, Mendeley http://www.mendeley.com/stats also is collecting usage stats, in which PLoS figures quite well. - Mr. Gunn

article level metrics fall into six areas 1. citation metrics 2. usage metrics 3. expert rankings (F1000) 4. Conversations (blogs, media coverage, comments) 5. social bookmarking (citeulike etc) 6. Other cools stuff (geotagging of authors etc) - Duncan Hull

Number of blog posts about an article isn't necessarily a measure of quality - a flawed paper might attract more commentary and blogging than a flawless one. - Chris Patil

Article-level metrics as post-publication peer review. - Martin Fenner

pre-publications and post-publication metrics - Duncan Hull

Need open APIs to access the data (not proprietary) - Duncan Hull

@patil a flawed paper could potentially be more interesting. - Bosco Ho from iPhone

ResearchBlogging.org are building an Open API at the request of PLoS one - Duncan Hull

usage numbers going to be available soon at plos - Pedro Beltrao

Example http://www.plosone.org/article... - Duncan Hull

Use open API data of other web sites to aggregrate stats. - Bosco Ho from iPhone

click on "related content" http://www.plosone.org/article... - Duncan Hull

citeulike more heavily used than connotea according to plos one - Duncan Hull

Citeulike >> connotea - Bosco Ho from iPhone

very few comment or add ratings - Duncan Hull

Let people comment in whatever space they feel comfortable (friendfeed, blogs, disqus, citeulike, whatever etc) and then aggregate that content. e.g. www.postgenomic.com requires use of rel="rev" tag in html - Duncan Hull

Future work, integration with mendeley, zotero, papers, researchblogging.org add usage data (coming in August) - Duncan Hull

Plosone is big enough to twist the arms of big sites to provide an open API. The possibilities are endless. - Bosco Ho from iPhone

friendfeed and twitter discussions difficult to aggregate, rarely mention DOI or authors or title of paper :-) - Duncan Hull

Don't expect conversations on http://www.plosone.org anymore, this is crucial - Duncan Hull

BUZZWoRD alert: crowdsourcing. - Bosco Ho from iPhone

question from Alex Tolley https://twitter.com/atolley How are you going to do it? - Duncan Hull

CrossRef is working on the heuristics of a citation, e.g. good or bad paper. - Martin Fenner

Usage statistics will show trends over time. - Martin Fenner

Otherwise only bmc provides download stats for authors limited data for public. - Bosco Ho from iPhone

Usage statistics is extremely time-consuming, largest EC2 instance is working for 9 days already on PLoS One usage data. - Martin Fenner

What is a "big number" of downloads? Difficult to know because much of this data is currently hidden - Duncan Hull

Tufte fanatic is critiquing the aesthetics of a beta release graph. - Bosco Ho from iPhone

Still critiquing. - Bosco Ho from iPhone

Currently no open API for PLoS One usage statistics. - Martin Fenner

This man really cares about aesthetics - his apartment must look fabulous. - Bosco Ho from iPhone

Future developments at PLoS: provide open data sets, hope other publishers will follow, hope standards will evolve - Martin Fenner

Article statistics on plos one throws down the gauntlet against elsevier and friends - Bosco Ho from iPhone

SciBarCamp: Cameron Neylon

Chris Patil - Open Source Textbooks #sbcPA

July 9 - Comment - Like - Share

marlene, Michael Nielsen, Martin Fenner and 3 other people liked this

John Cumbers - what is the size of the market, do people make money out of textbooks. Example of Cell - Alberts etc. - Cameron Neylon

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Some people make a lot of money out of textbooks but not very many. Very long tail. - Cameron Neylon

Big text books take a lot of work - how does the textbook look in a web based world. What is a textbook for if the university doesn't exist any more. - Cameron Neylon

chris is pretty god like ... but not christ, i dont think. :) - Kaitlin Thaney

thanks for that - typing not good at this time in the morning - insufficient coffee... - Cameron Neylon

Chris - the lack of return on text book authoring is an opportunity for new types of approach. - Cameron Neylon

There is no shortage of text books, there is a glut - Cameron Neylon

Alicia, "I would pay $20 if I knew it went straight to the author" - Cameron Neylon

discussing the concept of "beta" versions of books. The Pragmatic Programming series. - Cameron Neylon

Alicia - benefits for people who need accessible versions - Cameron Neylon

John - PDF sucks, need something much better than PDF for flexibility. - Cameron Neylon

Martin - but want access to multiple formats - Cameron Neylon

Bosco - print on demand is getting cheap and very high quality - Cameron Neylon

Sean - open access text books is not a technical problem but a social problem - how do you fund the content - Cameron Neylon

Project at stanford to support making course material creative commons - Cameron Neylon

Problems - how do you create new content (resource). If use legacy content then there are problems with copyright infringing content - Cameron Neylon

Me - what about using Wikipedia? - Cameron Neylon

Chris - Wikipedia a reference, not a teaching tool. These things are different. Need to provide a route through the content for the average student. - Cameron Neylon

Needs to be seen from the perspective of the teacher. - Cameron Neylon

Good question - what do teachers use a textbook for? How do you leverage the needs of the teacher to support the creation of better objects that could replace textbooks. - Cameron Neylon

Bosco - major contribution of publishers is the editor - collabortive authoring is a challenge for long documents - Cameron Neylon

debate over the value of a well integrated long work - clearly works well when you actually work through the whole book - does anyone ever really do that? - Cameron Neylon

John - would like guidance through the process of using a "text" - where you've been and where you're going - quizes, checkups etc.. - Cameron Neylon

comment from boston: what to do about the various flavors of CC licenses on OCW content? most have BY-NC, some materials with SA - a design decision made without the forethought of interoperability, reuse (in the context of virtual textbooks) and remix. how/ what to do? - Kaitlin Thaney

How much does it cost to fly in eight people for four weeks to get a draft together. Suggesting around $50k, so 500 people at $100 each. Bosco points out many people who are setting up courses for the first time could have an interest in putting the work in. - Cameron Neylon

Kaitlin - I'll try and feed that in. I think people here are relatively unaware that these already exist. Do you know what the best current examples are? - Cameron Neylon

Question: Is this something Google.org might fund? (that's a reminder to myself) - Cameron Neylon

Chris - in the world where we have $50k to support one of these could put out a call for proposals - Cameron Neylon

would have to check OCW policies, but i know that they're not all consistent across the board for various universities across the world, and most definitely not CC-BY ... lemme look :) thanks cameron. just something to noodle on. - Kaitlin Thaney

Need to identify a good area where a current text doesn't exist - Cameron Neylon

Martin - is the two week retreat model a good one or a wider online collaboration - Cameron Neylon

Me: need the "retreat" or a focussed effort to get the seed content in palce - Cameron Neylon

Martin is a retreat per se great or does it need to be cheaper? What is the right number of people. - Cameron Neylon

Chris - what field is small enough and needs a textbook- me thinking Small Angle Scattering but not sure this is of interest to this group really - Cameron Neylon

K, so to be part of the OCW consortium, the content needs to be subject to a CC license, it seems, or at least is strongly recommended. MIT is CC-BY-NC-SA. but other institutes, such as Michigan State doesn't cite a CC license and provides some content only read-only. So short answer ... it varies. Ugh. - Kaitlin Thaney

Sean discussing status of Stanford efforts on open curriculum content - currently in a holding pattern - Cameron Neylon

Asking the question - why is there no secondary market for teaching materials given the popularrity of blackboad and moodle - Cameron Neylon

Fabbiano talking about NZ universities purchasing Springer textbooks "like journals" on a chapter by chapter basis - Cameron Neylon

The books are purchased as electronic versions by libraries, as far as I know as whole, not chapter per chapter, but can download only chapter of interest - Kubke

Hey I'm in this meeting. - Bosco Ho from iPhone

science has a strong culture of attribution, but can be tough to do on the web - Duncan Hull

I was too busy following the discussion, forgot to comment here. - Martin Fenner

Thanks for the input from afar, KT, esp, your first comment - rumors of my divinity are greatly exaggerated. :-) - Chris Patil

Sorry, coming in late. Before O'Reilly programming, etc books weren't exactly what we've become used to. I wonder, even in a non open-textbook world, what would happen if a publisher that enabled people perhaps not that well known to just write stuff. - Deepak Singh

Complete Yale course on iTunes University: http://www.tuaw.com/2009... - Martin Fenner

Just came across wikibook (http://en.wikibooks.org/wiki...) through this article (http://mashable.com/2009...) (via @edNZ). I also read (where?) a suggetsion to have students 'edit' wikipedia pages instead of handing in papers in their courses. Maybe a collaborative effort having the students contribute to wikibook content as part of their course requirements might be a good place to start? - Kubke

OH well, I came across this page in wikibook: http://en.wikibooks.org/wiki... I guess any project will have to have better editorial control? - Kubke

SciBarCamp: Andrew Lang

Where are people staying? In the same hotel as the scifoo people?

May 21 - Comment - Like - Share

Where is the SciFoo hotel? I have not booked anywhere yet. - Jamie McQuay

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http://www.jdvhotels.com/hotels... - Andrew Lang

I think that i'm going to stay in SF, I have meetings there before and after sbcPA. - Jamie McQuay

Admins: Might not be a bad idea to ask the IFTF people whether they have a standard hotel where they put up their guests. Maybe they can even get discounts if it's a place they have relationships with...? - Chris Patil

Chris +1 - Andrew Lang

email sent to IFTF... - Jamie McQuay

Yes. Last year, SciFoo people stayed in Sunnyvale which was either a 40 min bus ride or 20 min taxi to Palo Alto. IFTF is right off the PA CalTran station, but the SciFoo Hotels were 3-4 mi walk to the nearest CalTran station. I'm looking for something in Palo Alto, proper. - Jim Hardy

IFTF does not have any corporated rates. Here are their hotel suggestions: Right around the corner (walking distance of less than 5 minutes there are two hotels that are next to one another): · Sheraton – http://www.starwoodhotels.com/sherato... · Westin - http://www.starwoodhotels.com/westin... Six... more... - Jamie McQuay

I will get these hotel suggestions onto the scibarcamp website this week. - Jamie McQuay

There's a B&B called the Cowper Inn www.cowperinn.com only 5-6 blocks from IFTF and *only* $150/night. Think I'll shack up there. - Jim Hardy

I'm at Days Inn Palo Alto which is a mile or so down the Camino Real I think - assuming it's not so hard to get there by bus and not so far as it was back down to Sunnydale like last year :-) - Cameron Neylon

I just booked in San Francisco for 107 a night at the kimpton. The Cal Train to Palo Alto is a fairly quick trip. - Jamie McQuay

Chris Patil

Senescence as an adaptation to limit the spread of disease. - http://www.hubmed.org/display...

June 2 from Connotea: chrispatil's... - Comment - Like - Share

Posted by chrispatil to "evolutionary theories of aging" pathogens parasites aging Disease evolution on Tue Jun 02 2009 - Chris Patil

The Life Scientists: Chris Patil

Does anyone know how to convert PowerPoint slides into 600 dpi TIFFs? A journal editor wants them that way, but the only thing I've got is a .ppt file. ... any help would be appreciated. More details in a comment below.

May 29 - Comment - Like - Share

I need to export some PowerPoint slides as 600 dpi TIFF files. (I'm using Office 2008 for Mac). The options don't seem to work: I "Save as" or "Save as Pictures"; select TIFF format; then click "Options" and then under "Advanced resolution settings" I select 600 dpi. Unfortunately, the resulting files are always 72 dpi TIFFs. Does anyone know how to solve this problem? - Chris Patil

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Right now I'm trying to go through PDF and then use Photoshop to change the resolution, but any other advice would be great. - Chris Patil

Short of going back to the original files, no. It's never a good idea to come out from PPT. It's the end of the road. - Richard P Grant

Based on my exp w/PPT in Windows, I'm not holding out a lot of hope for a solution other than your current workaround, but if a solution exists, it's likely discussed in here: http://groups.google.com/group... or here http://groups.google.com/group... and will have been answered by either Jim Gordon or Steve Rindsberg - Tony Ramos

Hey Chris, you may enjoy given link to convert pps to tiff via http://www.verypdf.com/artprin... - YunusYAMANER(CITRIL)

Yeah. It was my collaborator who made the PPT files. - Chris Patil

Problem solved. Convert slides to PDF and then open in Photoshop, which allows you to set the resolution. Thanks to everyone for their help! - Chris Patil

Ops, sorry you mentioned that you have .ppt files. May be you can save them as pss to use this program...of course if it's possible... - YunusYAMANER(CITRIL)

install this (http://sourceforge.net/project...) it is set up as a printer that lets you print any document to PDF and image files (tif included). you can set the resolutions and other properties. then from any program you just print to file using this "printer" and select the file type (PDF/TIF/etc) - Pedro Beltrao

Quickie : go full screen mode of your ppt - take a full screen shot, paste it in a Photoshop file with 600dpi resolution. :) !!! - Khader Shameer

Well, my first thought was rather focused on stupid demands from certain editors, not on the technical problem. Why don't we ask them to publish with no peer-review in exchange? :) - Marcin

The Life Scientists: Attila Csordas

email from Mary Ann Liebert C.:'Many of our authors have inquired about making their articles free online permanently, immediately upon publication. Rejuvenation Research offers its authors "Liebert Open Option" to enable them to do so. The cost of Liebert Open Option is $3,000 for each article.'

May 28 - Comment - Like - Share

Graham Steel, Paul Bacchus, Jim Hardy and Mr. Gunn liked this

what? Authors should pay $3,000 if they want Open Access for making their stuff publicly available for others? Not sure I understand. Do you? - Attila Csordas

18 more comments

That sounds awfully expensive - Andrew Clegg

Obviously there's a price to pay to be OA. Someone has to pay for Free Access, too - Jim Hardy

more expensive than BMC, but understandable. - Paulo Nuin

I would really love to see a dollar-by-dollar breakdown of that $3000. - Colin Ashe

Is that in addition to page charges? Then no, or at least not until I'd exhausted the open-access options. - Chris Patil

I think since the authors are providing the content, and we are talking about academic articles here, you are getting into a weird area of Pay to Play/Publish that is a very slippery slope. The question is to have open access- should there be perhaps a yearly fee? Should regular subscriptions by libraries allow open access to web based content? What about medline? - Whitney Hoffman

so we put the burden on libraries? - Paulo Nuin

Springer's Open Access fee also used to be $3000 (I don't know what it has been recently). Oxford journals such as NAR charge reduced OA fees to publishers at institutions with a subscription, so the cost is basically shared between the institution/library and the author. The Berkeley Research Impact Initiative http://www.lib.berkeley.edu/brii... subsidizes fees like this for those who... more... - Ruchira S. Datta

From the transfer of copyright form [http://www.liebertpub.com/media...] from Mary Ann Liebert, Inc., about the NIH Public Access Policy: "In order to assist our authors who have NIH funding to comply with this policy, Mary Ann Liebert, Inc. publishers will deposit the final accepted paper (after copy -editing and proofreading) to PubMed Central (PMC) on... more... - Jim Till

The restriction on self-archiving and long embargo is likely to make some people think, hmm, I'll just send it to PLoS and not deal with that. - Mr. Gunn

Actually, Rejuvenation Research has no page charges http://www.liebertpub.com/product... So the $3000 is in line with the $2850 charged by PLoS Biology but significantly higher than PLoS ONE. Thus fees are RR>PB>PO whereas impact factor goes PB>RR>PO. - Chris Patil

Not much of a difference from other OA publications, as pointed out. Funding agencies are supporting line items for OA publications. I ask for $5000/yr routinely for publications in my grant applications. - Iddo Friedberg

Chris, IF won't remain that way forever, and I think it's a poor decision-making factor as well. - Mr. Gunn

For a recent post about Article-Level Metrics at PLoS, see: http://tinyurl.com/qwvfxc - Jim Till

Maybe instead of putting the burden on libraries it would take the burden off of libraries. Presumably, authors who want this will build it into their budget and it will be covered by grants, funding, etc and libraries will not have to buy a subscription to the journal. - Angela Hamilton

I also would suggest not confounding the OA/author pays model of publishing with the deposition. Nature Publishing Group for example mostly consists of subscription journals but these journals (including Nature itself) provide the automatic deposition to PMC (as described above by Jim Till) as a free service to authors. - Maxine

@Mr. Gunn - I don't make my decisions based on impact factor, and I agree that it's a poor basis for distinguishing between journals. I do think that that relative relationship of impact factors between those three journals is likely to remain the same for a while, however. - Chris Patil

A fish-supper, anyone ?? - plus I have a fine pot of Earl Grey on (the) simmer...... - Graham Steel

"the OA/author pays model" -- just to clarify, OA and "author side fees" (a more accurate term) are two different things. The majority of OA journals don't charge any author side fees (though the best known ones, PLoS and BMC, do), whereas many toll-access journals charge page and color fees in addition to their subscriptions. For details see Peter's comments here: http://www.earlham.edu/~peters... - Bill Hooker

Chris Patil

Stepwise up-regulation of MicroRNA expression levels from replicating to reversible and irreversible growth arrest states in WI-38 human fibroblasts. - http://www.hubmed.org/display...

May 29 from Connotea: chrispatil's... - Comment - Like - Share

"Our comprehensive evaluation of miRNA target correlations with known biomarkers for replicative senescence suggests that miRNAs may repress pathways controlling not only cell cycle traverse and proliferation, but also insulin-like signaling, DNA repair and apoptosis, all of which are cellular functions deficient in senescent human fibroblasts." Posted by chrispatil to senescence miRNA on Fri May 29 2009 - Chris Patil

Chris Patil

Rapamycin decelerates cellular senescence. - http://www.ncbi.nlm.nih.gov/sites...

May 28 from Connotea: chrispatil's... - Comment - Like - Share

""In human and rodent cell lines, rapamycin (an inhibitor of mTOR) dramatically decelerated loss of proliferative potential caused by ectopic p21, p16 and sodium butyrate-induced p21."" Posted by chrispatil to rapamycin tor senescence on Thu May 28 2009 - Chris Patil

Chris Patil

At concentrations that inhibit mTOR, resveratrol suppresses cellular senescence. - http://www.ncbi.nlm.nih.gov/sites...

May 28 from Connotea: chrispatil's... - Comment - Like - Share

""Here we demonstrated that, at cytostatic, near-toxic concentrations, resveratrol inhibited S6 phosphorylation and prevented the senescence morphology in human cells."" Posted by chrispatil to Resveratrol tor senescence on Thu May 28 2009 - Chris Patil

The Life Scientists: Chris Patil

Why do origin-of-life and evolution folks sometimes assert that eukaryotic cellular organization was a necessary precursor to multicellularity? A book I'm reading ("Vital Dust" by C. de Duve, http://www.amazon.com/gp... ) got me thinking about this.

May 27 - Comment - Like - Share

I get that prokaryotes *didn't* evolve multicellularity; I'm looking specifically for arguments about why they *couldn't*, if such arguments exist. - Chris Patil

Many prokaryotes did evolve "naive" forms of multicellularity -- e.g. quorum sensing - Benjamin Tseng

Perhaps the answer to your question (and this is pure conjecture, but it should be testable/evaluatable) is related to the amount of genetic material and transcriptional control necessary to sustain complex/full multicellularity -- it may have required a nucleus? - Benjamin Tseng

Chris Patil

Translational reprogramming following UVB irradiation is mediated by DNA-PKcs and allows selective recruitment to the polysomes of mRNAs encoding DNA repair enzymes - http://genesdev.cshlp.org/content...

May 18 from Connotea: chrispatil's... - Comment - Like - Share

""Experiments with DNA-PKcs-deficient cell lines and a specific DNA-PKcs inhibitor demonstrate that both the general repression of mRNA translation and the preferential translation of specific mRNAs depend on DNA-PKcs activity, and therefore our data establish a link between a key DNA damage signaling component and protein synthesis."" Posted by chrispatil to polysomes "DNA damage response" uv DNA-PK translation "DNA repair" mRNA on Mon May 18 2009 - Chris Patil

Chris Patil

Polycomb Mediated Epigenetic Silencing and Replication Timing at the INK4a/ARF Locus during Senescence. - http://www.hubmed.org/display...

May 18 from Connotea: chrispatil's... - Comment - Like - Share

"Together, these results provide a unified model that integrates replication, transcription and epigenetics at the INK4/ARF locus." Posted by chrispatil to p16 INK4a silencing epigenetics polycomb senescence on Mon May 18 2009 - Chris Patil

A Roy

A Human Protein Interaction Network Shows Conservation of Aging Processes between Human and Invertebrate Species - http://www.pubmedcentral.nih.gov/article...

May 14 from Bookmarklet - Comment - Like - Share

Chris Patil liked this

"We have mapped a protein interaction network of human homologs of proteins that modify longevity in invertebrate species. This network is derived from a proteome-scale human protein interaction Core Network generated through unbiased high-throughput yeast two-hybrid searches. The longevity network is composed of 175 human homologs of proteins known to confer increased longevity through loss of function in yeast, nematode, or fly, and 2,163 additional human proteins that interact with these homologs. Overall, the network consists of 3,271 binary interactions among 2,338 unique proteins. A comparison of the average node degree of the human longevity homologs with random sets of proteins in the Core Network indicates that human homologs of longevity proteins are highly connected hubs with a mean node degree of 18.8 partners. Shortest path length analysis shows that proteins in this network are significantly more connected than would be expected by chance. To examine the relationship of... more... - A Roy from Bookmarklet

A bit of analysis at Ouroboros: http://ouroboros.wordpress.com/2009... - Chris Patil

@ Chris Patil, I should have read your analysis first, nice work. - A Roy

Chris Patil

Aging: Central role for autophagy and the lysosomal degradative system. - http://www.hubmed.org/display...

May 12 from Connotea: chrispatil's... - Comment - Like - Share

"In this review, we discuss the cellular and molecular mechanisms involved in autophagy and the role of autophagosome/lysosome network in the aging process." Posted by chrispatil to senescence Autophagy aging on Tue May 12 2009 - Chris Patil

The Life Scientists: Chris Patil

Just found this page about the use of the "glider" logo as a "universal hacker emblem". http://www.catb.org/hacker-... It's dated August 4 2008. The particular glider image used on that page is similar to the one in the Life Scientists room logo -- is our logo derived from this idea, or is this an example of convergent logo design?

May 12 - Comment - Like - Share

Ah, I see now that the author of that page says he suggested the logo back in 2003. - Chris Patil

2 more comments

See http://friendfeed.com/the-lif... and my own attempt to design the biohacker logo http://freelancingscience.com/2008... The Glider emblem is quite old :) - Pawel Szczesny

Here was the first attempt: http://friendfeed.com/the-lif... Chris did a very good job. :) - Pawel Szczesny

Thanks. - Chris Patil

SciBarCamp: Chris Patil

Re #sbcPA, Has any sort of coherent effort been made to reach out to people who are attending Scifoo but might otherwise not be on our radar? Even something as simple as adding the #scifoo tag to a couple of tweets, in order to get SciBarCam into that conversation. Just wondering whether anyone had thought about this / taken action to that effect?

May 5 - Comment - Like - Share

Jim Hardy liked this

only group mail I have from BioBarCamp was sent to biobarcamp@googlegroups.com - Jamie McQuay

3 more comments

you could try contacting the people here: http://upcoming.yahoo.com/event... - Andrew Lang

I sent an email to Timo Hannay (scifoo organizer) to pass on SciBarCamp info to scifoo people - Jamie McQuay

That sounds great. Timo's a great guy, so hopefully he'll be effective in communicating that info to people -- and coming from him, it's "news from the organizer," not "spam" :-) - Chris Patil

Maybe Shirley has the ability to post this on the SciFoo wiki? Didn't we do that last year? - Jim Hardy

Chris Patil

Yeast Silent Mating Type Loci Form Heterochromatic Clusters through Silencer Protein-Dependent Long-Range Interactions - http://dx.doi.org/10...

May 10 from Connotea: chrispatil's... - Comment - Like - Share

""Our results indicate that formation of heterochromatic clusters depends on correctly assembled heterochromatin at the silent loci and, in addition, identify an Asf1p-, Esc2p-, and Sir1p-dependent step in heterochromatin formation that is not essential for gene silencing but is required for long-range interactions."" Posted by chrispatil and 1 other to Sirtuins silencing heterochromatin chromatin yeast on Sun May 10 2009 - Chris Patil

Chris Patil

Stimulation of Autophagy by Antilipolytic Drugs May Rescue Rodents from Age-Associated Hypercholesterolemia - http://www.liebertonline.com/doi...

May 9 from Connotea: chrispatil's... - Comment - Like - Share

"Results show that the stimulation of macroautophagy reduces the total LDL and high-density lipoprotein (HDL) cholesterol plasma level to juvenile values, and triglycerides levels even lower." Posted by chrispatil to trigycerides antilipolytic Autophagy liver cholesterol aging on Sat May 09 2009 - Chris Patil

Chris Patil

A comparative analysis of the cell biology of senescence and aging - http://www.springerlink.com/content...

May 8 from Connotea: chrispatil's... - Comment - Like - Share

"Comparison of age-related changes and their underlying mechanisms in in vitro senescent cells and aged postmitotic cells would reveal the relevance of replicative senescence to the physiological processes occurring in postmitotic cells as individuals age." Posted by chrispatil to senescence aging on Sat May 09 2009 - Chris Patil

Chris Patil

Pathway analysis of senescence-associated miRNA targets reveals common processes to different senescence induction mechanisms - http://www.sciencedirect.com/science...

May 8 from Connotea: chrispatil's... - Comment - Like - Share

"In this study we investigated 12 miRNAs previously identified as senescence regulators. Using pathway analysis of their target genes we tested the relevance of miRNA regulation in the induction of senescence. Our analysis highlighted the potential of these senescence-associated miRNAs (SA-miRNAs) to regulate the cell cycle, cytoskeletal remodelling and proliferation signalling logically required to create a senescent cell." Posted by chrispatil to senescence miRNA on Sat May 09 2009 - Chris Patil

Chris Patil

Labeled microRNA pull-down assay system: an experimental approach for high-throughput identification of microRNA-target mRNAs - http://nar.oxfordjournals.org/cgi...

May 8 from Connotea: chrispatil's... - Comment - Like - Share

"We concluded that LAMP is an experimental approach for high-throughput identification of the target gene of known miRNAs from both C. elegans and zebrafish, yielding fewer false positive results than those produced by using only the bioinformatics approach." Posted by chrispatil to miRNA on Fri May 08 2009 - Chris Patil

Chris Patil

GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists - http://nar.oxfordjournals.org/cgi...

May 8 from Connotea: chrispatil's... - Comment - Like - Share

"GeneSet2miRNA is the first web-based tool which is able to identify whether or not a gene list has a signature of miRNA-regulatory activity." Posted by chrispatil to "computational tool" miRNA on Fri May 08 2009 - Chris Patil

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