Kevin Z - Likes - FriendFeed

Sarah Palin kicked out of hospital fundraiser in Canada. Palin has said that "Canada needs to dismantle its public health-care system and allow private enterprise to get involved and turn a profit" - http://www.reddit.com/r...

Sunday from Reddit - Comment - Like - Share

Steven Perez, Micah Wittman, Kevin Z and 6 other people liked this

It's amazing how some US citizens can be so blind to not see where market economy fails... free market requires buyers to be able to decide, "no, perhaps when you lower your price..." But it just does not work like that for health care... or housing... there does not exist something like a free market when basic needs are involved... - Egon Willighagen

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health care, housing: these are 'constrainted' markets... you just can't decide, no, let's not have a new kidney this year and wait until the market is better... no, let's use boxes this year until the house prizes have dropped a bit again... - Egon Willighagen

Egon, you have put your finger on the worst thing about the US (imo, as a recent immigrant). It's not so much that citizens are so blind as that the kleptocracy in power understands your point completely, and completely does not care. Government of the people, by the rich, for the rich... I just hope for the revolution to be a "velvet" one when it comes. - Bill Hooker

@Egon, I'm hardly an expert on policy issues, so I don't pretend to necessarily know best, but market failure doesn't necessarily mean a non-market solution is best; if anything it suggests that the focus should be in finding a way to establish a competitive market as to prevent a government from having too much influence over private citizens. Some ideas that I'd like to see evaluated... more... - Benjamin Tseng

Problem is that consumers lack the specialized skill to properly evaluate health care choices that means an expert ie The Gov must mediate the choices and provide regulations to preent the consumer from being unwitting victim same as they license doctors and lawters they must regulate teh healthcare indistry - WarLord

"given that the American system "works" broadly speaking" -- that stretches "broadly" to breaking point imo. Have you ever "been without health insurance" (honest term, "failed to pay the required protection money") in the US? - Bill Hooker

@Bill, I'm not going to pretend the American system is perfect (b/c it isn't), but almost all employed people in the US have healthcare that they are satisfied enough with such that they're not willing to take their chances on a public option; that doesn't mean I condone the failings of it with regards to access or equity, nor does it mean I wouldn't experience hardship if I lost my job... more... - Benjamin Tseng

@Benjamin, fair enough -- I can't pretend to be a policy or market expert either. I am also not exactly an impartial observer, being for the moment without health insurance in the US! (I spent my first 30 years in Australia, so my experience of a public option is that it has its problems too, but nothing like the massive systemic failures of the US system in its current form.) - Bill Hooker

@Bill, I'm sorry to hear that :(. Does your employer not provide coverage? I thought you were at a biotech firm? - Benjamin Tseng

"When there's a problem with your car engine, you fix the engine, you don't necessarily replace the whole car" Unless the engine was damaged because another part of the car is malfunctioning due to being poorly laid out. Many people can't switch coverage because of "pre-existing conditions" even though their current insurance is severely lacking in coverage and customer service. The... more... - Heather

Benjamin, I can point to a specific example (and I have always been covered and found the US system substandard). When you go to the ER, you could get billed the full amount for an emergency procedure, just because the doctor you saw wasn't contracted with your insurance company at that particular ER. Last I checked, when you go to the ER for an emergency procedure that's not what you... more... - Deepak Singh

@Benjamin -- we're working on it. I should have said "temporarily" or similar. Can't explain in detail -- public company disclosure blah blah blah. Suffice to say I'm not being exploited, and didn't want to give that impression! - Bill Hooker

Graham Steel

Open Science: Good for Research, Good for Researchers? - http://www.youtube.com/watch...

November 22 from YouTube favorites - Comment - Like - Share

Jan Schmirmund, Khalid Mirza, Cameron Neylon and 7 other people liked this

Hadn't seen this before. Featuring Bora Zivkovic, Jean-Claude Bradley and Barry Canton (OWW). - Graham Steel

nice find Graham! I had not seen the YouTube version - Jean-Claude Bradley

Jonathan Eisen

1 thing I love about teaching introbio at #UCDavis-topics inspire my kids-here's Analias take on box jellies http://twitpic.com/ptkri

November 16 from Twitter - Comment - Like - Share

Anna Croft, Kevin Z, Björn Brembs and Chris Lasher liked this

UCDavis courses are teh roxxors!! Invertebrate Zoology with Grosberg and Systematics with Art Shapiro FTW - Kevin Z

I want to take Gorsbergs and Shapiros classes - maybe they will let me audit - Jonathan Eisen

I love how art teaches systematics. Each student got a bucket of hardware and we classified it according to various methods, i.e. phenetics, cladistics, evolutionary phylogenetics. It was interesting how things changed depending on how you applied the rules. Of course any of Grosberg's classes are worth sitting in, he is so dedicated. I forced myself to work in his lab, left him with no... more... - Kevin Z from twhirl

John (a.k.a. dendroica)

Why bloggers should avoid The Associated Press & News Corp ... http://www.google.com/hostedn...

October 9 from Twitter - Comment - Like - Share

Tapio Kulmala, MVB (Grinch of FF), Helen Sventitsky and Kevin Z liked this

Zee.

The Wrong Way To Try & Pass A Class #Minx - http://www.zee.me/blog...

October 5 from Zee Slash Blog - Comment - Like - Share

David, Giancarlo Caparo, Lora Lufark and 36 other people liked this

btw, there are many more emails...it's not just that one above - Zee.

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ouch. - Yolanda

Yeah, I read all the way to the final humiliation. - Yolanda

Every professor's wildest dream...or nightmare. - Josh Haley

She kept giving him a way to not be an ass, he didn't pick up on it. - claudia

she kept giving him a way? - Andrizzle Gizzle

The TA handled it well. I wonder if he let the professor know what was going on - Shevonne

+1 Holden, the TA handled it admirably right till the end. - Bhowmik Shah

Are there pics of the student? Just to know how easy it was for the TA, lol :-) - Björn Brembs

Yeah, such a pic would've been nice.. - TrafficBug

Zee, I really like the bottombar on your site. Did you guys make that? It's state-of-the-art! - Richard pancakhaus Walker

I think he did the right thing, even AT the end. He gave her every opportunity to back off, and when she refused to he delivered the smackdown. Sorry, but harassment works BOTH ways and he had every right to protect himself. - Helen Sventitsky

... and adding a pic would *not* have improved this thread. I mean sure it is entertaining to gauge the temptation level but realistically the pic would get back to Caroline and further screw up her life. - Daniel J. Pritchett

.o0(wonders what experience Lindsey has with such things) ;-) - Jason Huebel

Am I the only one that thinks if she were super hot, then the email exchange would not have been as long? :) - Cristo

Perhaps. But it was obvious this guy knew what she was implying for the start. And it sounds like he wasn't going to have any of it. - Jason Huebel

Right, as in he knew what she looked like, and wasn't going to have any of it. Apparently she's as bad at assessing her likelihood of success using that technique as she is at her studies. - Cristo

I dunno. Even if she was hot, it is worth destroying your career for it? I certainly wouldn't. - Jason Huebel

*thinks about it* - Cristo

Okay, I guess you're right if you want to get all serious about it. :( - Cristo

Thanks Holden :) - Richard pancakhaus Walker

imabonehead to imabonehead's feed, Architectural & Interior Design

Inhabitat » Mesa Community College’s Physical Science Buiding Gets LEED Gold - http://www.inhabitat.com/2009...

October 5 from Bookmarklet - Comment - Like - Share

Kevin Z, A.T., Nia and chaz2b liked this

"Mesa Community College recently completed work on a stunning physical science building that exceeded LEED expectations when it was awarded LEED-NC Gold. Designed by the award-winning architecture firm, The Smith Group, the building is the first major LEED project to be completed within the Maricopa Country Community College District. The brand new 64,480-square-foot facility houses curriculum for the physics, astronomy, chemistry, geology and engineering departments including classrooms, laboratories, facility offices, an advising center and a 53 seat planetarium. Topping off the new space is an astronomy observation platform." - imabonehead from Bookmarklet

Joe

Ollie: Born sept 2nd 9:55 pm, 6 lbs 14 oz., 20.5 inches. Came a little early but we are stoked! - http://jyoseph.com/post...

September 2 from Tumblr - Comment - Like - Share

Kevin Z liked this

Bora Zivkovic

RT @p_binfield Impact Factor and its Role in Academic Promotion - Respiratory Editors make unified statement http://ajrcmb.atsjournals.org/cgi...

August 22 from Twitter - Comment - Like - Share

Mickey Kosloff, Berci Mesko, MD, Shirley Wu and 5 other people liked this

You'd think this should not be behind a paywall. - Kubke

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My thoughts as well. If anyone can get this and knows my e-mail address (easy to find, on my blog for example), I did not ask you anything.... ;-) (thank you to the person who understood this cryptic message) - Bora Zivkovic

doesn't really say much "we propose that the impact factor calculated for individual journals should not be used as a basis for evaluating the significance of an individual scientist’s past performance or scientific potential." - Christina Pikas

It's the first step. I guess it would be quite revolutionary if they said "we will not use it any more at all - and that is mandatory". That would probably be too hard to agree to, let alone implement. - Bora Zivkovic

@Christina I was *very* surprised - when I brought this issue up at a meeting - to see how many of my colleagues considered impact factor as the only measure of success (scarey because these are also the people making the decisions on promotions and hiring). Not one of them considered that looking at article metrics was a valid alternative. So, if I put myself in their shoes, then this editorial says a lot. - Kubke

it's funny, though, because librarians are alternately faulted for heeding it too much in collection development decisions and heeding it too little. It's just one more data point, really, but we're judging the journal as a whole - it seems completely bizarre to judge a *person* using a *journal* metric. - Christina Pikas

It doesn't seem bizarre. It is bizarre. Not to mention absurd, uneducated and stupid. Any other fitting adjectives? - Björn Brembs from iPhone

Too many adjectives. The journal impact factor made sense (oh how old I am) when papers were not listed (let alone available) online (heck there was no bloody online back then!). Hence, your chances of getting cited significantly increased with the impact factor because a journal with high impact factor had a greater chance of being subscribed to by libraries and individual researchers.... more... - Kubke

I think perhaps the hard pill to swallow for my gen and above (i.e., those from the pre-internet era) is that this view is telling us that the standards upon which we built our careers are no longer valid. - Kubke

Hmm, didn't think about that aspect! Good point! Would add a complicating psychological perspective to how we can bring about change... - Björn Brembs

@Bjorn Just think that in the early 90's I could hardly find anyone at SocNsci meeting who knew what email was, and in 1994 I was looking for a postdoc using post letters because most people in my field did not use email. I would bet none of the PIs at work know what FF is. - Kubke

@kubke - oh I'm sure most scientists today still use their computers as to the level of of about 1990 (email and word) :-) What I hadn't thought about was the psychological aspect of people (probably subconsciously) feeling attached to a system which provided them with their career in the past. I was only looking at the present sad state of affairs and how it's loaded with historical... more... - Björn Brembs

@kubke just because the world has moved beyond a particular valuation standard doesn't mean it wasn't valuable when you used it! I don't see the downfall of IF as a statement on careers. - D0r0th34

@D, it's like Bjoern said -- maybe it's a scientist thing, but people in that tribe get very attached to "the way things have always been done". It's not rational and they get very angry if you point it out, because they like to claim they are eminently rational in all things, but it's real and it's a HUGE factor in any attempt to change their views or practices. Kubke's point is very valuable imo for anyone who wants to see scientific culture change. - Bill Hooker

Btw, Kubke, I too am old enough to remember the advent of email and those "request a reprint" postcards. I'm so old my first reference searches were in Index Medicus -- the *print* version. I remember being thrilled that I could get a list of articles that had cited a particular paper, and there they all (well, some) were, only two floors above me in the stacks! And here we both are on FF railing against the Impact Factor -- so you can teach at least some old dogs new tricks! :-) - Bill Hooker

@D0r0th3a I am not defending impact factor. There are lots of people who built their carreers on the "jounals" they published in (not the impact of the paper). The ranking of people within a department (which translates into space and other things) could change significantly. It will be good for some, but some will fall. As Bill says and Bjorn points out, understanding where the... more... - Kubke

I know you're not. :) And yes, it's definitely good to zero in on the folks who have, er, impact. - D0r0th34

chaz2b to chaz2b's feed, News Channel, Funny Funny

Woman sues zoo over splashing dolphins - http://news.yahoo.com/s...

August 21 from Bookmarklet - Comment - Like - Share

Caroline, Jason Huebel, Rich and 14 other people liked this

"A woman is suing a Chicago-area zoo for a 2008 fall near a dolphin exhibit, accusing zookeepers of encouraging the mammals to splash water and then failing to protect spectators from wet surfaces, local media reported on Thursday" - chaz2b from Bookmarklet

11 more comments

Idiots like this are holding us down, man. - Spidra Webster

+1 Spidra. - Tyson Key

Perhaps she bumped her head, and will be permanently stupid. Or...it was a pre-existing condition ( stupidity that is )... - Wallace

Jolie photo:-) - Gate53

Obviously the witch is allergic to water... - Peter Ghosh

is she still pissed that dorothy killed her sister with that house? - Jason Cox

Seriously, guys, the argument is that she slipped and fell because of the water. - Karl Knechtel

She slipped and feel due to the fact she was not careful and aware , how stupid do you have to be to not expect water on the ground around a big tank of water. - Lisa zahara Hopkins

This case is now live at the AllRise Court. Cast your vote and opinion - http://bit.ly/AllRise242 - AllRise

Bets on the outcome? My money is on the plaintiff, sadly. - Rene Wirtz

Honestly. - Ayşe E.

Why visit the place where there is water to be splashed? - ashish

Noah Gray to Noah's feed, The Life Scientists, Science 2.0

Science reviews the revolution in "strategic scientific reading." The target audience = those unaware articles are available online - http://www.sciencemag.org/cgi...

August 17 from Bookmarklet - Comment - Like - Share

Mickey Schafer, Kevin Z, suelibrarian and 7 other people liked this

This review seemed so ridiculously obvious and rudimentary to me, with the content only outdone by the sheer silliness and waste of space that is Figure 3. I *must* be missing something since gems like these just weren't cutting it for me: (a) "Nevertheless, reading-like engagement with scientific articles is not likely to disappear entirely: The natural language prose of scientific articles provides too much valuable nuance and context to be treated only as data ." (b) "The new functionality will sometimes be provided as part of the application interface (new features in PubMed, for instance) or as shared external tools that users can add to their Web browsers." - Noah Gray from Bookmarklet

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behind the pay wall, but I guess I am not missing much, am I? - Bora Zivkovic

"The system of digital publishing that emerged from 1993 to 2003 was impressive in some respects, but was still largely another case of new technology compromised by imitation of the old." - Björn Brembs

Scientists "use indexing and citations as indicators of relevance, abstracts and literature reviews as surrogates for full papers, and social networks of colleagues and graduate students as personal alerting services." Yet, they are not integrated in our current infrastructure. - Björn Brembs

Scientists "sweep through resources, changing search strings, chaining references backward and citations forward, dodging integrator and publisher sites to find open-access copies, continually working to reduce the number of clicks required for access." - Björn Brembs

"Today, an emerging infrastructure of education, research, conferences, organizations, and software tools is sustaining the development and adoption of scientific ontologies and providing opportunities for coordination to improve interoperability and share best practices. Particularly important for biology are the National Center for Biomedical Ontology, OBO, and the International... more... - Björn Brembs

Regarding iHOP: "Unlike similar explorations in the 1980s and 1990s, these are not computer science experiments or pilot projects requiring substantial investment and large upfront changes in infrastructure and practices to scale them up for general use. These are projects that are already producing practical and widely used tools." - Björn Brembs

My guess: for the people on here, nothing new; for 90% of bench scientists, this article is pure science fíction. - Björn Brembs

Just skimmed through it; agree with the assessments of Noah and Björn. Imagine, a world where we add tools to our browsers that help read literature! I can't wait ;-) - Neil Saunders

Oh brother... - Chris Miller

I agree it's easy to understand, but not everyone who hangs out here has the CIS knowledge many of you do -- from a reading perspective, the explanations of ontologies and related issues was easy to understand, which is a good thing -- from an education perspective, it leaves me wondering how we should be training undergrads to think about information. My sense is that much of the info... more... - Mickey Schafer

Hey, don't dis your allies. I wager the purpose of the article isn't to tell us what you and I already know but to *signify*. It's written by and for official information science experts in a way that basically endorses the assumptions of the "science 2.0" movement. So? Well, that technocratic seal of approval will be a necessary part of the process if the "science 2.0" meme is ever... more... - Richard Klancer

Brad Williamson to Brad's feed, Media News and Analysis, All Things Google, TheNextWeb Forum, The Reading Room

Internet Archive Announces Everybody-Against-Google Coalition - http://digitaldaily.allthingsd.com/2009082...

August 21 from Bookmarklet - Comment - Like - Share

Mac Sharp, honeyhuyue, Werner Trotter and 10 other people liked this

"Restoring access to million of books that are today unavailable in any medium is worthy goal. So is enabling their authors and publishers to once again make a bit of money off them. Is there a better option for the publishing industry at this moment? Allow those works to lie fallow and unmonetized?" - Brad Williamson from Bookmarklet

10 more comments

Join us in the "Media News and Analysis" group as we examine the world's main source of information and entertainment, The Media ;-) http://friendfeed.com/media-n... - Brad Williamson

they lost me at "allow these works to lie unmonetized" - doesn't bother me at all - Joelle Nebbe (iphigenie)

http://www.googlepatrol.org/ - Igor The Troll יִצְחָק

I gotta disagree, Joelle. Until a new and guaranteed effective monetization model is developed for books, Google shouldn't be able to give away other people's literary content, all willy-nilly like. - Brad Williamson

Who's going to get the money if the copyright holders are unknown or unreachable? Better for the books to remain unmonetized than for the money to go to some third party. - John (a.k.a. dendroica)

I can see that point, John. I would assume, however, that some of that money would go to the family. And, if that's the case, I'd support that. - Brad Williamson

I could see that if the family or heirs are known and reachable. - John (a.k.a. dendroica)

So even though it might appear they are 'giving it away' knowing Google they'll find a way to shove ads there and make money. - Adi

it is nothing but google is building a large database of their own so they can cripple us - testbeta

Many tons of books are lying unread everywhere - I guess Google is asking for 'optin' from authors (publishers?) before making the book public, in exchange for a cut in ad revenues, with the costs of digitizing the books borne by Google. I guess we would need a third party here, you could read paper magazines, or you can read online or zinio-download it. If users wont pay for a digital magazine (or due to the problems of piracy), then advertising is the place to turn to for generating revenue. - TrafficBug

pay-for-reading is something i don't like i don't have problem with ads running on sites i browse as far as they remain in some limits, internet shouldn't be paid, i don't like the idea very much! - testbeta

Victor / Mendeley Team

Who is killing science on the Web? Publishers or Scientists? - http://www.mendeley.com/blog...

August 17 from Mendeley Blog - Comment - Like - Share

Dirk Derom, Cameron Neylon, Hope Leman and 14 other people liked this

I think we're all too aware of how the other major content distributors have decided to handle the transition to the new business models brought about by the web. Music and movie distributors were the first to show everyone how not to do it. Newspapers are doing better, but it's taken a long time, and there are still those (Mr. "shut-up-and-charge-already" Murdoch) who don't get it.... more... - Mr. Gunn

Great thoughts! Yesterday, I posted some thoughts on the Commonwealth Panel that appears to have motivated this blog post. (See it at http://hatchethead.posterous.com/panel-d... .) What I was struck by in the panel discussion was Dr. Friend's reference to 'the guild' that is protecting the status quo in science. (This is the 'even more guilty party of... more... - Jason Miller

"They decide what is and isn’t fit for publishing. They decide when and where you can self-archive manuscripts and supplementary data. They mesmerize and trap us with the lure of journal impact factors like a baby unable to wean itself. Whether we are conscious of it or not, much of the direction taken in labs isn’t based on pure science, but based on what the editors of a high impact journal will publish." - Björn Brembs

Shirley Wu

Overheard regarding papers published in PLoS ONE - "it was rejected somewhere else", "The bar is 'not crackpot'", "people publish in CNS because that's where the attention is, I don't know anyone who reads PLoS ONE", "The reputation of the journal is a good way to filter out noise". Is there truth to these claims? Discuss.

July 30 - Comment - Like - Share

Cesar Sanchez, 'Mummi' Thorisson, Mike Chelen and 19 other people liked this

Almost all papers, in all journals, have been rejected from somewhere else. Our bar is "is it science, is it conducted properly, is it reported properly, and do the conclusions follow the data etc" - the bar is not "is it sexy, or impactful, or a major advance". At the same time, we are not CNS - as we are not selective. CNS combined publish just 5,000 articles a year between them but... more... - Peter Binfield

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Peter, I certainly don't disagree with what you're saying and think PLoS ONE is valuable and innovative. But I was wondering if these negative judgments are pervasive (FF/twitter is a bit of an echo chamber and the real world can be a shock sometimes) and if so how to change them. There are those who argue that CNS has high precision even if they miss some good papers and so it's more... more... - Shirley Wu

The problem with echo chambers is that the Internet echoes forever; and forever is a long time. We just need to push out as much positive info as possible to try to combat any negative comments which may have been made rashly, or in error, but which get re-referenced for eternity. Our article-level metrics program will presumably show people whether any given paper in PLoS ONE is 'high'... more... - Peter Binfield

There's this thing known as FUD. Happens when someone sees their status eroding. The whole PLoS articles are not as good is just that, FUD - Deepak Singh

Indeed, it may be fear, uncertainty, doubt. It may also be lack of information and hard data. We are going to fix the latter. Certainly, people are voting with their feet - we have 37,000 published authors in under 3 years, and people are publishing with us in ever increasing numbers (http://poeticeconomics.blogspot.com/2009... ) - Peter Binfield

"it was rejected somewhere else" - perhaps. This is hard to tease out, but I have a feeling that most of the manuscripts that come to PLoS ONE have never been submitted elsewhere - Bora Zivkovic

"The bar is 'not crackpot' - good bar, IMHO. Why is any other bar necessary? Think. Really. - Bora Zivkovic

"people publish in CNS because that's where the attention is, I don't know anyone who reads PLoS ONE" - who still reads journals? Srsly? Don't people search online for papers they are interested in? Do physicists read biology papers when their copy of Nature arrives? No, they read Nature for "news and views". - Bora Zivkovic

"The reputation of the journal is a good way to filter out noise" - perhaps a century ago when every scientist could read every scientific paper and understand it, and every scientist was a 'Victorian scholar' who felt the need to keep up with ALL of science. Today, you read papers in your narrow field - you find them online. News from other sciences you can find in pop-sci magazines, on blogs, etc. - Bora Zivkovic

@Bora, I think there are still a fair number of people who don't search for papers necessarily, but browse TOCs, and so only browse the journals they're familiar with. During the discussion, someone asked, baffled, "but there are already so many papers [without PLoS ONE publishing so many more], how would people find ones of interest to them??" - Shirley Wu

A related discussion - based on a correspondence in Nature by a proponent of the views Shirley cites - is at http://ff.im/4GWlM . - Daniel Mietchen

@Shirley - although ToCs are certainly an important discovery tool, any publisher will tell you that the vast majority of their usage comes in from Google (who then read an article, and leave again to run another search) - Peter Binfield

@Peter, that would make sense, but I'm wondering if that necessarily translates into Google being the majority of people's preferred method for finding papers. At least the impression I got from folks in my lab was "so many papers, so little time" and so they're skeptical of anything that adds to the glut of papers without clearly adding value. They might agree on the principle that... more... - Shirley Wu

They also think, "if [a peer reviewer] didn't make a value judgment on whether this paper is significant, why should I waste time reading it?" - Shirley Wu

"I'm wondering if that necessarily translates into Google being the majority of people's preferred method for finding papers" - Good point. I guess you would want to measure time spent on page by people who come via the 2 (or more) routes to see how targeted their interest was - Peter Binfield

@Shirley - Then they are admitting that they would prefer one (or perhaps 2 or 3) other people to decide what is important for them, and so decide on their behalf what they should be reading. Doesnt sound like a very informed way to filter imho... - Peter Binfield

@Peter, more that a million people access papers through google 25% of the time will mean that publishers see google as a huge source of traffic, but doesn't mean that people think of google as their preferred method to find _NEW_ papers. - Shirley Wu

@Peter, well, it's using expert opinion. We all use it to some extent in areas we're not familiar with. If people aren't that internet savvy or aren't that organized, they depend on other people or name-brand journals to bring things to their attention. Also, commenting on papers hasn't really taken off yet - just a matter of time, probably - but it just means that the post-peer review process hasn't really proven its value yet. - Shirley Wu

"but it just means that the post-peer review process hasn't really proven its value yet." - indeed, and we DONT view our efforts as post-pub peer review. We view it as a new way to do post-pub evaluation / filtering / discovery. - Peter Binfield

Oh, the other thing that someone mentioned was "comments are valuable" - meaning "why would I give away my intellectual capital?" People are willing to share their comments with their labs or close colleagues, but not to the public or to the general scientific community. Is this just another mindset we combat with positivity and action? How to combat the vicious cycle of "no comments, so no value", "no value, so i won't comment"? - Shirley Wu

"Is this just another mindset we combat with positivity and action?" - I would say we combat it by showing them the power of being open about these things. For example, social bookmarking only works when everyone shares their bookmarks - in this example there is a clear benefit to both contribute and use. If people realised that by leaving comments they would be advancing science;... more... - Peter Binfield

@Daniel, ah yes, I remember that thread now. Unfortunately I think many scientists are similar in mindset to the letter writer. They don't know about or understand new ways of receiving content, which might seem strange to those of us here, but there are many more people out there than are in here. - Shirley Wu

Also, you could use the same argument about peer review: "My time and thoughts are valuable, why should I do peer review". Apparently academia feel that the quid pro quo works in that situation at least (and that is done anonymously!) - Peter Binfield

@Peter, true, though I think some of that is tied to the reputation of the journal again - being a reviewer for Nature > reviewer for PLoS ONE (in their eyes), editors know them, they can talk about it and gain status. They get tangible and subtle career boosts. Whereas commenting on papers online and publishing in PLoS ONE doesn't get someone tenure (yet). "It would be very brave and... more... - Shirley Wu

Peter - given the problems that journals have finding suitable reviewers, I would hesitate a bit calling that a working system. - Daniel Mietchen

@Daniel :) - Peter Binfield

Another link that may be useful reposting here: Pubfeed at http://pubfeed.cs.toronto.edu/ basically allows you to treat the whole web of scholarly articles like a TOC alert (just a bit more customizable) and pipe that into your preferred feed reader. - Daniel Mietchen

@Shirley - please dont forget that there are 25,000 journals in the world and millions of papers published per year. CNS is just 3 titles, and if you lump together all similar titles (highly exclusive, professional editors, well known brands, conferring 'bragging rights' on anyone who works with them) then you are still talking about just a handful of the titles, with a small percentage of the content. We need a system that works for everyone, not just a small sub-set - Peter Binfield

@Peter, oh, I'm well aware, just parlaying bits of an impromptu debate I had earlier today with people who don't see the value of venues like PLoS ONE. These are all arguments they make, and while I don't agree with them, it is tough to convince people - Shirley Wu

You could try asking them exactly how many downloads their last paper in a 'high impact' journal got... - Peter Binfield

Fair enough, but you know, I really don't think they think about that. They think "what will be in my CV?" and they think any journal that is somewhat competitive [includes other PLoS journals, BMC journals, etc] looks better than one that accepts anything that's methodologically sound. Again, not my view, but perhaps one that is held by many. Do people list # of downloads on their CV for publications? - Shirley Wu

They dont, because they dont have the data. However, people do list if their paper was rated by F1000; or if BMC designated it a 'highly accessed' article. So I think they will start to say "this paper was downloaded 5000 times in the first 3 months which put it in the top x% of all PLoS ONE articles, the top y% of all PLoS articles, and the top z% of ALL articles" (when the rest of the world starts quoting this data) - Peter Binfield

Ironic isn't it; it's not a battle with the publishers, but with other scientists! I overheard a conversation yesterday concerning choice of bioinformatics journals. It centered entirely around impact factors and at one stage someone said "I think BMC Bioinformatics is online *only*" - as though that were a bad thing. - Neil Saunders

And it's clear that anyone who mentions "filtering noise" simply is not using the web effectively. Presumably their web use is limited to search, after which they print PDFs and go away. Concepts that seem simple to us - RSS, feed readers - are unknown to them. - Neil Saunders

I think of it as trying to set up a social experiment. If I'm right and a more cooperative model can produce better science than the current hypercompetitive structure, then over the next decade or so, facility with new methods and metrics that center on Open practices will provide a competitive edge for some researchers, and unwillingness to change will put others at a disadvantage. We... more... - Bill Hooker

Good thoughts Bill. It's not enough to say "this way is better" just because we believe it to be. We have to demonstrate that it's better - or find out that it isn't. - Neil Saunders

And isn't that the scientific way? - Deepak Singh from IM

"I think there are still a fair number of people who don't search for papers necessarily, but browse TOCs" Could it be that those are the people publishing in CNS and miss the most important papers for their work? http://bjoern.brembs.net/comment... It's only one example, as anecdotal as it gets, but it shows two things: 1. CNS 'quality' is merely correlational and highly noisy.... more... - Björn Brembs

My environment is rather positive about PLoS ONE. We all know about the difference between relevance and quality. While many PLoS ONE papers might not be of widespread interest, the review process is of comparable quality or better to smaller conferences and e.g. high volume BMC journals. Other journals have severe issues with reviewer quality these days, and it seems to become worse. - Roland Krause

I'm still wondering about the degree of scalability of post-publication (significance) peer review systems. Is it really realistic to think that once (all) journals go OA and implement such a system that the entire scientific community will benefit? Assuming that it's "fair" for all journals to get equal amount of attention from "scholarly feedback communities", how can we encourage... more... - Wobbler

I agree with Bill Hooker's statement just above. Those who echo Shirley's original quote will be at a disadvantage, which means better odds for the Shirley's of the research world. - Jason Hoyt

I often say something along the lines of what Bill said. The environment is changing. To succeed in the new environment, one has to change not just one's publishing habits, but also rethink how to do research and how to write it. Thus, people who think about it early on will be able to gain advantage over people who are still stuck in the old ways of doing things. As the new environment... more... - Bora Zivkovic

Ricardo Vidal

Gigantic Spider Gobbles Bird in Front of Camera - http://www.environmentalgraffiti.com/feature...

July 21 from Bookmarklet - Comment - Like - Share

tim, Ian Holmes, Mickey Kosloff and 7 other people liked this

Dear. Ghod. - Bill Hooker

4 more comments

Gaaaaaaaaaaah right before bed time, too... - Shirley Wu

It must be a very very very very small bird... burk... - Pierre Lindenbaum

About 10-12 cm, http://www.birdsinbackyards.net/bird.... Few errors in that blog post: it's a chestnut-breasted (not breeded) mannikin (not mannakin) and the Flickr photos are geotagged in Perth, WA, though the article states QLD. - Neil Saunders

Thanks for the corrections Neil. Anyhow, I found it quite impressive (if not freakish!). - Ricardo Vidal

this is one of those occasions when the verb "Like" is entirely inappropriate - Ian Holmes

Steven Perez to Steven's feed, US Politics

Think Progress » Jimmy Carter: ‘The words of God do not justify cruelty to women.’ - http://thinkprogress.org/2009...

July 21 from Bookmarklet - Comment - Like - Share

J. Abdul-Qahhar, Tracy Benham, Jamelle and 36 other people liked this

"The truth is that male religious leaders have had - and still have - an option to interpret holy teachings either to exalt or subjugate women. They have, for their own selfish ends, overwhelmingly chosen the latter. Their continuing choice provides the foundation or justification for much of the pervasive persecution and abuse of women throughout the world. This is in clear violation not just of the Universal Declaration of Human Rights but also the teachings of Jesus Christ, the Apostle Paul, Moses and the prophets, Muhammad, and founders of other great religions - all of whom have called for proper and equitable treatment of all the children of God. It is time we had the courage to challenge these views." - Steven Perez from Bookmarklet

28 more comments

He's still my favorite ex-President. - josh neff, geek at large

ditto joshua - tiffany

That is AWESOME. - Ladybug Heather

Ditto tiffany and joshua. - Betsy (bentley) Vera

Ditto tiffany, joshua and betsy. He may not have been the best president, but I love what he does now. - Lis Miller

He was the best President of the last forty years. - Eric P

Eric - I'm of the opinion that Clinton was. - Lis Miller

I appreciate the sentiment, but I don't agree that the subjugation of women requires some incorrect interpretation of these texts. From stoning women to death who didn't cry out loudly enough while being raped, to women being instructed to keep their mouths shut in church, it's the religious texts themselves that provide the "justification." - Christopher A Carr from Android

I would disagree. As heinous as the punishments of the Mosaic Law sounds to modern Western ears, the majority of the Law's canon was superseded by the Christ's sacrifice, and the first century governing body of elders made that quite clear in Acts. So any justification for violence towards women or capital punishment would be heavily dependent on the interpretation of the reader. - Steven Perez from IM

"male religious leaders have had - and still have " - screw that.. drop the "relgious" of it!! In short Men of power generally abuse women... check of good old clinton ! - Peter Dawson

That argument is not germane to the discussion, Peter. - Steven Perez

oh what about Jimmy Swagat(?) He is a Christian leader too ?? so lets not just point to the Mosaic law or the Christian law. The issue is that 'leaders' tend to bend the interpretation to suit their own convictions, and at times have a very good way of pursudeing the others that its just A-OK . Who is to blame ?the peopel that belive them or the Leaders who make the belief ? - Peter Dawson

I think you misunderstand, Peter. No one here is saying that men in positions of power do not misuse their power. What we are discussing is whether the blame for such actions lie with the texts they call on or whether the misinterpretation of the texts is responsible. - Steven Perez

And for the record: not a big fan of Bill Clinton, but she showed him her thong. He simply took advantage of the situation and then tried to lie his way out of it. Again, nothing to do with the above, but there it is. - Steven Perez

Steven: "For assuredly, I say to you, till heaven and earth pass away, one jot or tittle will by no means pass from the law..." At any rate, Carter wasn't just talking about Christianity. And the NT makes it pretty clear (especially via Paul) what is a woman's station, relative to men. - Christopher A Carr from Android

Christopher: You left out the first part of that scripture in Matthew 5: "“Do not think I came to destroy the Law or the Prophets. I came, not to destroy, but to fulfill; for truly I say to YOU that sooner would heaven and earth pass away than for one smallest letter or one particle of a letter to pass away from the Law by any means and not all things take place." This is not say that... more... - Steven Perez

And given the fact that the vast majority of societies at the time of the Bible's writing were patriarchal societies, it should not be surprising that a 2000-year-old book would have such patriarchal ideas. What is quite revolutionary about the Bible, though, was that God expected men to be every bit as subjective to His wishes. The entire hierarchal structure for first the Jews and... more... - Steven Perez

Treating a women as less than a man is down right un-american. That's how I see it! - Charlie Barone

Fine. In 2009, that makes sense. - Steven Perez from IM

Steven: If it's your contention that these documents are at least to some degree inspired by an omniscient being, then it *is* surprising that the texts would be written in a manner as to require such convoluted apologies by adherents living in less "patriarchal," future times. - Christopher A Carr from Android

"Let the women keep silent in the churches; for they are not permitted to speak, but let them subject themselves, just as the Law also says. And if they desire to learn anything, let them ask their own husbands at home; for it is improper for a woman to speak in church." (NASB, 1 Cor. 14:34-35) ... I suppose "...it is improper for a woman to speak in church" really means something else? Perhaps Paul was just a product of a patriarchal culture -- but isn't that the point? - Christopher A Carr

In Cor 11:5 - Women are allowed to allowed to Pray and Prophesy in Church. So "Speak" in Ch 14 may be describing the demanding for an explanation to the speaking of tongues.e.g. "please keep silent, and ask your husbands when you get home, what the speaking in tongues meant." This was only directed to 1 church. Corinth was a rather interesting city too.... - Mike Nencetti

Mike: Speaking in tongues? Is that what's that's about? The explanations always get more circuitous. Best just to jettison all this Bronze Age-derived horseshit. - Christopher A Carr from Android

An interesting hypothesis, Christopher. I often say the same about Stoic and Epicurean philosophy. - Steven Perez

liking for the comments. - Alex Scrivener

The day that all organized religions die, is the day that the mankind will be free. - Robert Couture

@Christopher, I believe that the bible is a living text, and that interpretations of scripture change and evolve over time, as humans change and evolve over time. You can prooftext to support enslaving others, to support subjugating women, to support many kinds of intolerance and even genocide. What I do *not* believe is that a given passage can have one and only one meaning, from when it was first written and until the end of time. - Ladybug Heather

All words come from people. God only purrs. - Mark Czerniec

@lis: Clinton repealed Glass Steagal, telecom deregulation, gave us DADT and DOMA, and botched healthcare reform so badly we had to wait 16 years to try again. The economy of the late 90's was largely attributable to the dotcom bubble. While he was great on issues of foreign policy and national security, that other stuff weighs heavily against him. Carter, on the other hand, is the only... more... - Eric P

Joe

Remember the buy-a-truck-get-an-AK-47 guy from Missouri? Check out this CNN interview: http://www.youtube.com/watch... #NRA #God #Guns

Remember the buy-a-truck-get-an-AK-47 guy from Missouri? Check out this CNN interview: http://bit.ly/PK2G9 #NRA #God #Guns

July 21 from Twitter - Comment - Like - Share

Kevin Z liked this

Now thats "real" america there ;) - Kevin Z from twhirl

Bill Hooker to Bill's feed, The Life Scientists

Info request: does anyone know anything about Calypte Biomedical? (http://www.calypte.com/) I'm interviewing this weekend for an R&D position.

July 10 - Comment - Like - Share

Khader Shameer, Mike Chelen, D0r0th34 and 12 other people liked this

Good luck! We all know you're a great, tenacious scientist, so I'm sure you'll do well. - Mr. Gunn

43 more comments

You can find 4 people working here via LinkedIn. May be, you can try to find what are their interests, etc... - Pierre Lindenbaum

Thanks guys. @Pierre, I have been reading the company SEC 10-K, and I don't think those people are actually still with the company, except maybe Dr Lewis. - Bill Hooker

Good luck mate! - Björn Brembs

Knock 'em dead, BIll. - D0r0th34

Good luck and please let us know how it goes. - Maureen

I think I'm too late, but good luck / hope it went well! - Steve Koch

Interview 1 (company director) went well on Saturday, interview 2 (director of quality) went well today. Apparently I'll hear back in a couple of days... - Bill Hooker

just seeing this now (sorry!) - Calypte Biomedical Corp (Duns:18-629-1910 ) - nothing in ABI/Inform after the 90s (urine test for HIV, Gulf War syndrome?), from other db: Magic Johnson was on the board, introduced a new oral specimen collection device in 2008, distribution deals for urine hiv test in Asia, middle east, Africa... - Christina Pikas

have the S&P report in front of me - only 18 employees! stock was delisted (ew- that doesn't seem good), ticker symbol CMBCE (but trading otc), - hoover's says 2 employees and spun off some stuff in 2005 - working on HIV in saliva - most of this stuff you can get from the website though. There are a bunch of articles in Lexis-Nexis. -- so good luck with your interviews! - Christina Pikas

Thanks Christina! From what I can tell they have two very good products and a huge potential market, so if they offer me the job I'm going to take it. Worst case scenario is a brief but informative ride on the struggling startup rollercoaster, best case scenario is getting in early with a growing company that does good things. - Bill Hooker

my only comment would really be about stability - but that might be a plus - get some experience in a more bottom-line environment to see what it feels like and if the rollercoaster goes down instead of up, you won't really be any worse off than if you hadn't tried and learned. IMHO. - Christina Pikas

I used to know most of the people there in 2000 when they were still in Maryland. I think they closed that facility in 2002-3. Looks like they're still viable. I was talking to them about a dipstick assay, but that may be the urine test. - Jim Hardy

@Jim, yes, the Maryland facility is closed. They're down to a skeleton operation here in Pdx and "rebooting", focusing on the saliva HIV test and a really neat (IMO) ELISA assay that can distinguish between infections less than, or more than, 6 months old. - Bill Hooker

@Christina, that's a good point and was openly discussed in both interviews. My pov is as you describe: I'm likely to get to do more things and be privy to more decision making in a small firm working hard to find its feet, and no matter what I'll be better off for the experience. - Bill Hooker

Bill, are you going to do bioinformatics there (if you get the job)? - Mikael Huss

Ahem. Meet the new Senior Scientist at Calypte Biomedical Corp. :-) I start Wednesday; horrible commute, nice people, whole new world for me (first job in industry). I'm nervous and excited and just relieved to have a damn job! - Bill Hooker

Congratulations!!! I hope you are going to celebrate appropriately - Deepak Singh

Hey, congratulations, Bill! - Chris Lasher

@Mikael, no, I'll actually mostly be doing QA/QC and troubleshooting for several months. I've been warned it might get boring but industry is so new to me that I suspect I will have quite a steep learning curve anyway. After that, molecular diagnostics R&D (which of course I can't talk about in specific terms -- that will take some getting used to, but it's not so different from a competitive academic lab). - Bill Hooker

Celebration = buying pizza tonight (haven't been able to afford takeout!) and buying several presentable new shirts later this week. :-) - Bill Hooker

Great job Bill! Raising a Yuengling in your honor! - Kevin Z from twhirl

Congratulations! I expect a drop-off in online activity :-) - Neil Saunders

Awesome Bill! Congratulations! This is really great news! - Björn Brembs

I'm so happy for you! - Maureen from iPhone

"I expect a drop-off in online activity" -- you're right, it's not all good. :-) I'll also have to sleep only at night, change out of my pyjamas every morning and bathe once a day whether I need it or not. Bah. Oh, and shaving. And ironing. And clean clothes every day, which means washing. You know, the more I think about this... - Bill Hooker

Congrats, Bill! Let me know if you want to commiserate about making the academia-industry transition. Remember, it's not like academia. Be smart, but make the others feel like they're smarter. - Mr. Gunn

Great news Bill. Congratulations! - Pawel Szczesny

Hey .. congratulations Bill. Looks like it will be an interesting change, even if we do see a little less of you around here. - Andrew Perry

Congratulations ! :-) In my experience, academia is worse when it comes to holding back on online activities - be seeing you in this space - a lot, I'm sure. - Nils Reinton

Congratulations! Glad the persistence paid off, even it does mean doing more laundry... - Cameron Neylon

Congrats, Bill! - Daniel Mietchen

Congratulations! - Steve Koch

I'm so happy for you! Well done! - D0r0th34

Fucking brilliant news mate :) - Graham Steel

That's fabulous! Congrats! - what is the commute like? Starting Wednesday - like tomorrow? That's great. (unlike gov't jobs that take 2 years to get started - even the job I have now it was like a month from the time I heard I got it and 2months from the interview when I started work) - Christina Pikas

Congratulations Bill! Although you will not be able to talk about specifics, you might get a ton of general advice here. And not just tie recommendations. - Martin Fenner

Bill - that's fantastic! - Jean-Claude Bradley

A belated congratulations, Bill! - Michael R. Bernstein

Well, stock's trading at $0.009/share. Doesn't appear to be much more room for bottoming out. I'll keep an eye out for a spike in activity based on your hiring. - Jim Hardy

Congratulations, Bill! - Shirley Wu

Thanks, all. At the risk of sounding sappy, this little community has been a big help in staying sane and reasonably positive these last few months. So thanks not just for the well wishes now, but for months of help and advice and company. - Bill Hooker

@MrGunn, @Martin -- I am sure I will be picking your brains, and the FF hive mind also, about the industry/academia divide. You'll all be sick of my n00b questions soon enough! - Bill Hooker

@Christina -- commute is 90 minutes outside of rush hour, but there's only one change (short walk -- train -- bus -- short walk) so I should at least be able to get some reading done. Also, the spousal unit isn't working so she can chauffeur me occasionally. :-) - Bill Hooker

@Jim -- yes, it's no secret that the company has pretty much stalled. The director (my new boss) uses the analogy of a computer rebooting. It's an adventure! :-) - Bill Hooker

The Life Scientists: Jack H. Pincus

What do you think of web-based research collaboration tools such as: 2Collab; MyNetResearch; Laboratree; MyExperiment; LabMeeting; and BIOCORE? Are they useful tools for internal and distance collaborations? What features would nake them more attractive?

April 28 - Comment - Like - Share

Andrés David Aparicio, Véronique Rabuteau, Richard Klancer and 23 other people liked this

Hi Jack! I wrote a longish post about this some time back. Blog post here:http://synthesis.williamgunn.org/2009... I now use Mendeley (http://bit.ly/181tmi) to collect and share papers. An RSS feed for new entries and a recommendation engine would make it a lot better for my purposes. - Mr. Gunn

37 more comments

Thanks for your comment. The tools that I listed are not social tools although they have some of the same features. They are designed to facilitate collaborative research projects. They allow colaboration on grants and manuscripts, messaging, and organizing into groups and projects. Some incolude workflows, project management, and data analysis tools. The closest non-science analogy is... more... - Jack H. Pincus

IMO collaborative workspaces are very important. That said, I am not sure we've managed to create one that really works specifically on the scientific side any better than MindTouch or Sharepoint (which I loathe having had to use it) - Deepak Singh

Deepak, what would make science collaborative workspaces more useful than MindTouch or Sharepoint? - Jack H. Pincus

Ideally I like the idea of using existing platforms and building on top of those with plugins and services. A science native one would have to be very specific to some particular workflows and optimized for that. Not sure how you'd make any money on that though - Deepak Singh

I guess that depends on whether a science-native collaboration platform is intended for public or private collaboration. You could make public collaboration free, and charge premium accounts for the ability to host private workspaces on the public service, or you could sell service and support for privately-deployed instances. There could be some interesting wrinkles depending on whether the platform supports public-public, public-private, or private-private federation between instances. - Michael R. Bernstein

Michael, Mendeley has discussed doing exactly that. I think the form the private instances would take is that of a local install of the web component, so there would be no private-public issues there, as nothing would leave the local network. - Mr. Gunn

The thing is, isolated behind-the-firewall deployments are not very interesting or useful (though they can certainly be very lucrative for vendors) except in the largest organizations. Think of it in this light: How useful (and used) would a corporate email system that only allowed messages between addresses within the corporate domain? Email succeeded because it was a *federated*... more... - Michael R. Bernstein

As far as I know, Ray Ozzie's Groove Networks was close to cracking that nut, but then got swallowed by Microsoft in 2005, never to be heard from again. - Michael R. Bernstein

I see what you're getting at now. A sort of abstraction layer over multiple instances would indeed be cool. The people I've talked to who have expressed interest in this have been thinking much smaller (or more paranoid) than this - just a way to share things with other members of their particular research group. Everyone else seems comfortable with using it as a desktop client... more... - Mr. Gunn

The acid test is this: can I collaborate using this software as easily/effectively as if my collaborator was sitting next to me with a paper and pencil (and maybe laptop). Essentially the answer at the moment is..? I have never used the software you're talking about above. My experience is limited at the moment to blogs and wikis, which are both completely inadequate. Which would you rather use - the wiki method, or the" paper-pencil-coffee" method? - Matthew Todd

It depends on what we're doing. If it's hashing out ideas and prototypes, paper&pencil works great. If it's asynchronous collecting of references or working out a protocol, then a tool that captures this and allows each person to easily see what the other person is doing is probably best. Mendeley http://bit.ly/181tmi does a pretty good job of collecting references and sharing them. The... more... - Mr. Gunn

I'm currently in the process of applying for a grant who will sponsor the development of a collaboration system for scientists: http://docs.google.com/Doc... Leave your input on that document and we might still be able to incorporate it into the grant application. - Björn Brembs

@Björn does not have access to this document? - Abhishek Tiwari

I've requested access, Björn. - Mr. Gunn

Also requested access (no worries if not appropriate). - Neil Saunders

Mat what specifically do you find inadequate about blogs and wikis for open collaboration? - Jean-Claude Bradley

JC - well, data entry is slow (anyone who blogs complains about how long it takes to do one entry), partly because to cross-link data/pages requires very careful curation, which scales monstrously with the volume of data. To collate pages and draw conclusions needs to be quick. Pages from a project need to be linked in a 3D web of relevance, i.e. rather than just links to similar pages,... more... - Matthew Todd

Very interesting random thoughts. We've talked a lot about how you can imagine using a massive touch screen with different elements laid out on it, dragging, dropping, connecting up. Unfortunately Microsoft don't seem to be read to just give us a "Surface" as yet. Can't think why not ;-) - Cameron Neylon

Exactly, a surface or shape where posts/data/elements may be perceived and connected as simply as tracing a line between them. If I want to highlight a key concept on a whiteboard, I circle it several times. If I want to emphasise something to a colleague, I shout/repeat myself. Doing such things using a linear progression of wiki pages at the moment: very difficult to do it effectively in any decent timeframe, or in a way that rapidly engages passing readers. - Matthew Todd

I'm sure Daniel will grant all of you access. - Björn Brembs

Mat - you are right that you can't draw directly on the wiki using your tabletPC and if you are used to that on paper that is probably annoying. Maybe I'm just used to text but I find that I am able to express my points most of the time by leaving a bolded comment in the relevant place on the wiki page that serves as our lab notebook. For the type of work that we do it seems to work quite well. - Jean-Claude Bradley

Access granted for all requests so far. - Daniel Mietchen

Mr. Gunn, I just watched the Groove 2007 demo (somehow I missed that an MS-branded version had eventually been released). Looks reasonably similar to what Groove Networks had, except that certain features seem to have been shorn away as a sort of 'Sharepoint Tax', and of course it is very Office-centric now. - Michael R. Bernstein

As for the need for an 'abstraction layer', that depends on what you mean. Do you consider a syndication feed aggregator (whether server-based like Google Reader, or desktop-based like FeedDemon) an 'abstraction layer' over the blogs you read? For that matter, do you consider FriendFeed itself to be an abstraction layer? - Michael R. Bernstein

Incidentally, the small/paranoid approach is *totally* valid, the only question is how well these solutions support nested, intersecting, and disjoint groups. IOW, how does one use it when one is a member of more than one research group (perhaps with different roles in each)? - Michael R. Bernstein

I started this discussion on April 28 and last looked at it when there were four comments (about five days ago). I checked the thread again this morning to find an active discussion. I guess the secret is to not watch the pot before it boils :-). Collaboration can range from a project beteen two labs "down the hall" from each other to large aboratory, multiorganizational collaborations. The Human Genome Project and SNP Consrtium are examples of the latter. (continued) - Jack H. Pincus

Collaboration between companies or companies and universities is also becoming more prevalent, especially in the biotech and pharma industries. Lilly refers to its new business model as FIPNET (fully integrated pharmaceutical network). It may be possible to do small collaborations with existing tools. But larger collaborations may require a new type of virtual research environment. - Jack H. Pincus

Michael, yes, I would, in the general sense of the word. Just wanted to make sure I understood what you meant when you were talking about federation. - Mr. Gunn

It looks like there's two kinds of collaboration we're talking about here. Small group collaboration where all members are only part of that group is where online sharing of references and annotations works well enough. Larger, distributed collaboration requires the open, federated approach. - Mr. Gunn

Yes, smaller collaborations may be in one location. Document management may also be important for small collaborations. - Jack H. Pincus

I have requested access, too and thank you, Jack, for asking the question that generated this very edifying discussion. - Hope Leman

Mr. Gunn, distributed collaboration requires an open federated approach even when it is *small*, otherwise the overhead of setting up a collaboration space of some sort overwhelms the benefit. Note that distributed collaboration in-the-small therefore always ends up happening via email, an existing ubiquitous federated system that does not require that same coordination overhead. - Michael R. Bernstein

There are three dimensions here: Size of the group, distribution of participants among organizations, and - for lack of a better term - spontaneity. The three aren't entirely unrelated, for example the odds that all participants will belong to the same organization goes down as the number of participants increases, but they can be thought of as orthogonal for most purposes. - Michael R. Bernstein

Similarly, spontaneity decreases with the size of the group (at least at the outset, small groups can grow into larger ones organically). It is unlikely that a large working group will spring into being on it's own without some large-scale negotiations and planning behind it, including setting up a collaboration space. - Michael R. Bernstein

And yet, large-scale spontaneous collaboration *does* happen, when the infrastructure exists to support it. Case in point: Some Wikipedia articles which come together eliciting the contributions of thousands of participants in a very short period of time. - Michael R. Bernstein

Michael, good points on spontaneous collaborations. There are also organized collaborations funded collaborations such as the NIH Clincial Translational Sciences program or established multiorganizational research projects, intercorporate collaborations, or collaborations between corporations and universities. Are there different issues/parameters for these? - Jack H. Pincus

Perhaps we should distinguish between spontaneous collaboration (which can happen within an already organized system/organization, as it does within Wikipedia) and spontaneous organization, ie. ad-hoc group forming, for purposes of collaboration. There are slightly different thresholds to cross in either case. Note that the main advantage of a federated approach is *radically* lowering... more... - Michael R. Bernstein

An example of an effective platform was used in this topic: Google Docs. It allows multiple collaborators to edit a document through a graphical user interface. Concepts through text, and support for presentations and spreadsheets is improving. Access can be controlled, or published to allow collaboration, with compatible machine readable file formats to provide federation. - Mike Chelen

Jonathan Eisen

The Imaginary Journal of Poetic Economics: The dramatic growth of PLoS One: soon-to-be world's largest journal - http://www.facebook.com/ext...

July 7 from Bookmarklet - Comment - Like - Share

Björn Brembs and Kevin Z liked this

John (a.k.a. dendroica) to John's feed, US Politics

The Minnesota Senate Race Is Over -- Coleman Has Conceded Defeat To Franken | TPMDC - http://tpmdc.talkingpointsmemo.com/2009...

June 30 from Bookmarklet - Comment - Like - Share

Joe Silence is not Santa, martha, Beth K and 19 other people liked this

"In a press conference just now, former Sen. Norm Coleman (R-MN) has conceded defeat to the Democratic comedian Franken in the 2008 Senate race -- nearly eight months after Election Day, and six months after the seat went vacant when Coleman's single term had expired. Coleman said that further litigation would damage the state, and congratulated Sen.-elect Franken on his victory. He said his future plans in politics "are a subject for another day."" - John (a.k.a. dendroica) from Bookmarklet

12 more comments

"But now it's over. Really and truly over. Sen.-Elect Franken is expected to be sworn in early next week, taking the seat once held by the late Sen. Paul Wellstone -- a staunch progressive and close personal friend of Al's, whose death in 2002 plane crash clearly had a profound effect on the comedian, and spurred him to get seriously involved in politics, and to travel down the road that led us here." - John (a.k.a. dendroica)

It's about fracking time, too. Now Norm Coleman can focus on those pesky Federal charges and inventorying all the clothes and gifts he received last year. - Bill Sodeman

Had to check for the link to The Onion. :) - Edward Zwart

""We are a nation of laws and not men and women." wtf, is that a thing? - Edward Zwart

Edward: yes. http://oll.libertyfund.org/... - except I guess the original quote was "empire of laws, and not of men." The phrase means the rules are the same no matter who's affected. - Andrew C

That's basically my understanding of that phrase. The rules are supposed to apply to everyone and not changed to suit the whims of the powerful. It doesn't always work that way in practice, but it is the ideal. Of course, the nation (or empire) does comprise men and women. - John (a.k.a. dendroica)

about time - Ethan

NPR article says that Franken will be sworn in next week and will be placed on the Judiciary Committee in time for hearings on Sotomayor - Ethan

That's good news. The Dems could use the extra vote for various confirmations hearings, but especially Sotomayor's. - John (a.k.a. dendroica)

+1 Scott - Bill Sodeman

Now we can talk about more important issues - like when we're shipping Bill O'Reilly's cankered butt off to Ireland: http://friendfeed.com/us-poli.... - Steven Perez

@Andew C thx, didn't sound right but makes sense now.. I thought he was just winging it. :) - Edward Zwart

Via Krugman's blog, a quote from O'Reilly: “Look at Al Franken — one day he’s going to get a knock on his door and life as he’s known it will change forever.” I guess it has. http://krugman.blogs.nytimes.com/2009... - John (a.k.a. dendroica)

Live4Emma (L4S) to Live4Emma's feed, ad gallery, Ads of the World

“There is no substitute for the zoo” Calgary Zoo Ads - http://www.canadiandesignresource.ca/officia...

June 30 from Bookmarklet - Comment - Like - Share

Nikos Anagnostou, Emma, Ken Morley and 30 other people liked this

Those are great. - pea

3 more comments

I know, right? :-)) - Live4Emma (L4S) from iPhone

*snort* omg! what pea said. these are fantastic. - tiffany

Hahaha! - Anne Bouey

I want an Airedale terrier... - Christopher A Carr

Bora Zivkovic

RT @edyong209 PLOS ONE paper: Impact Factor @ the "periphery" of measuring scientific impact rather than its core http://www.plosone.org/article...

June 26 from Twitter - Comment - Like - Share

Kevin Z, Pawel Szczesny, Richard Akerman and 5 other people liked this

Impact factor and citations not good measures? Wow. Re: http://www.plosone.org/article... - Daniel Lemire

17 more comments

I love papers that put hard numbers on the obvious ;-) - Bora Zivkovic

"Our results indicate that the JIF and SJR express a rather particular aspect of scientific impact that may not be at the core of the notion of scientific “impact”." and "Contrary to expectations, the IF as well as the SJR most strongly express scientific Popularity." - Daniel Mietchen

"Published: June 29, 2009" - I love this future past tense... - Daniel Mietchen

In case there are technical problems, all our papers are uploaded the night of the previous weekday. Thus we are sure that the article is actually online on its publication date. - Bora Zivkovic

This is just yet another paper showing that worship of IF is silly. I have linked to a bunch of others at the bottom of this post http://tinyurl.com/qmgq3p but there are some newer ones that are not there, but others on FF will know. - Bora Zivkovic

or, as put here http://scienceblogs.com/clock... "I think that as more and more people abandon the foolishness of IF, there will be more and more submissions to PLoS ONE (which is what we actually see). Those who abide by the IF gods the longest will find themselves in the worst position in the end, as the forward-looking folks will already position themselves in the new world and new hierarchies that come with it." - Bora Zivkovic

On the technicalities - when do you actually upload the metadata to DOI? PLoS journals are prominent amongst those whose metadata cannot be fetched on the day of publication. - Daniel Mietchen

I don't know, but can ask the IT/Web folks on Monday. I bet some of that information can be found on the PLoS site or the PLoS Blog in the Technology category. - Bora Zivkovic

Is anybody maintaining a bibliography of stuff about metrics? - D0r0th34

Gasp! D0r0th34! I thought you were! - Bora Zivkovic

Gah. No. Honestly, my interest in the area is insufficient, as are my maths/statistics skills. - D0r0th34

I bet Bjoern and Bill and a few others have collected a bunch of those references over the years. They just need to be dusted off, placed in one spot online and promoted for everyone to see. - Bora Zivkovic

My Simpy tag is "impactfactor"; I've switched to Diigo but import is still problematic so most of my collection is best accessed here (http://www.simpy.com/user...). Items tagged since the switch are here (http://www.diigo.com/user...) under the improved tag. It's a very patchy collection though (only 25 items in all) because I... more... - Bill Hooker

Mine is also fairly patchy, I must admit to my shame. For instance, I wouldn't even now in which of my lists to look: I have the strong impression I have already seen a paper like this one somewhere. Different data, different figures, similar methods and similar results. But where? - Björn Brembs

My Papers library has several dozens of papers tagged with "scientometrics" but I also never became systematic about that topic. So what about collecting the information at http://en.citizendium.org/wiki... ? - Daniel Mietchen

Bora, did you ask the Tech guys? I tested fetching (via Papers) again yesterday (i.e. on the day of official publication), and it did not work. Now, a day later, it works. That's usual for PLoS ONE in my experience. - Daniel Mietchen

I tagged some stuff with impact factor on Connotea last year, but haven't done anything more. - Bob O'Hara

Incidentally, the paper says nothing about how any of the metrics measure impact. It only says something about how they co-vary. Oh, and read Mike Fowler's post on citation metrics: http://network.nature.com/people... - Bob O'Hara

Bill Hooker

OA vs TA costs: I think I have finally got this straight. - http://www.sennoma.net/main...

June 21 from Open Reading Frame - Comment - Like - Share

Anders Norgaard, suelibrarian, Kevin Z and 2 other people liked this

Average TA publisher revenue per article $2500 - $3500. Unless I did something stupid. Edit: I did something stupid. See my comment #4 below. - Bill Hooker

7 more comments

Not stupid exactly... but there are revenue streams I'm not sure you've accounted for, such as royalties on e-reserves and per-article payments. The latter is probably minimal, but the former might add up to something. - D0r0th34

Thanks D. I've embedded this thread in the post as an update! - Bill Hooker

Gah. Note to self: post in haste, repent at leisure. Peter Suber pointed out that the NIH calculation results in an underestimate, and I realized I'd used the wrong average from the damn spreadsheet. I've quietly edited the post and am only owning up here. :-) Final numbers a little less dramatic, $2100 to $2900. - Bill Hooker

If Peter is factchecking you, that means he thinks you're on to something, you realize. - D0r0th34

What I find interesting is the implication that the average TA publisher would have to charge *more than* $2100-2900 in order to switch to upfront-fee OA and maintain revenue. (I remain convinced that 90% is a decent estimate of the proportion of serials budget that goes to scholarly works, and we know the numbers are *under*estimates, and as D points out there are revenue streams specific to TA -- so in fact I'd say "at least $3000"). - Bill Hooker

That's interesting because the OA publishers/journals currently showing a profit (BMC, Hindawi, PLoS ONE) don't charge nearly that. Quite apart from the gouging that some TA publishers have been doing for decades, I wonder whether the new OA outfits are leaner and more efficient? An often-overlooked advantage of the OA model is that when there are fees, they are upfront and one-time. TA... more... - Bill Hooker

That's what worries me somewhat about the movement toward making gold OA an institutional fiscal responsibility. We haven't made much progress toward sustainability if we just dump an opaque TA system for an opaque OA one. - D0r0th34

Another (imo important and overlooked) point from Carl Bergstrom, by email: "It is certainly true that making the cost visible increases the competitiveness of the market. But there's more than that: when sold as toll access, Journal of Theoretical Biology and Mathematical Biosciences (for example) are economic complements. A library has to have one copy of each, even if the prices are... more... - Bill Hooker

Mona Nomura

Riyad sand storm - massive sandstorm hits Saudi Arabia : International News Bureau - http://www.intnewsbureau.com/riyad-s...

June 20 from Bookmarklet - Comment - Like - Share

Waldemar Schott, Mahdi Ebrahimi, Shey, Jamaican of FF and 110 other people liked this

Crazy. Video and more pictures here: http://thechive.com/2009... - Mona Nomura

19 more comments

Golly! - Kate Foy

unbelievable. OMG!! - karthick

no, please. - ::Kristen::

That looks unreal. - Tsega Dinka

ut oh, they inherited the curse and awakened the mummy, someone call Brendan Fraser! - Adam Turetzky

seen that in Texas a few times in my life, actually. not on the same scale, however, as it was usually "just" dust. - Joe Silence is not Santa

Crazy. - John (a.k.a. dendroica)

Eerie. - Chris Lasher

I've got friends in Riyadh. Sandstorms are crazy there. Amazing how it's captured on photos. - Dee S.

Frightening! - Thierry R. Andriamirado

I've seen this in Phoenix too. Maybe not quite as big, but it sure felt like it when you're watching it come at you. A giant wall of dirt. - Fa La La La Lindsay

that is an incredible sight. Wow! - Anna Lynn M.

Grew up in Muscat, Oman. Have been in these massive sand storms a few times when my dad used to take me on his plant inspections in the dessert. [Edit] They are not as frightening as they look. - Kamath (नमः)

Kamath - it sure _looks_ horrifying, from the picture. Wow. - Rick Cogley

Looks painful! - Alison Robb Astair

I've been in Saudi sandstorms, but this is something else entirely... wow. - Michael W. May

crazy.. - yagami

We had a mini sandstorm while in Baghdad. It just looks strange. Not scary, just weird. - Michelle Martinez

Yikes. I might just never complain about an Israeli sharav again. - Miriam

creepy - Susan Beebe

Bindu Reddy

Mulligatawny Soup Recipe - http://likaholix.com/bindu...

June 20 from Likaholix - Comment - Like - Share

Morton Fox, Noah David Simon, Iván Abrego and 14 other people liked this

I have only had this soup at restaurants. Have really liked it a lot every time I have had it. I am pretty excited that I am going to be cooking it today... Wish me luck :) - Bindu Reddy from Likaholix

9 more comments

g'luck :) - Michael W. May

Thanks, I need it... :) I am really new to cooking but I have been enjoying learning to make food so much. - Bindu Reddy

*smile* Cooking is love... love always makes it taste better too. This sounds good... I may need to do something similar myself today. - Michael W. May

The process was pretty involved but it actually turned out OK... - Bindu Reddy

I did much replacing of items, but am eating a chicken soup spiced nearly the same right now. Pics should come through soon :) Thanks for this, it's good, even my bastardized version. - Michael W. May

Is this the Soup Nazi's recipe?? - Kev

I'd like to try it too, although also with much replacing of items like Michael. Very interesting - Soup

Wow this looks great. - anna sauce

Michael, your version sounds very neat... - Bindu Reddy

mmmmmmmmmmmmmm - Noah David Simon

RJS

RT @AndyBumatai: Lots of talk about the UV index being high. What I need is a BS index and some rated lotion to screen it out.

June 21 from Twitter - Comment - Like - Share

Kevin Z liked this

Daniel Mietchen to Daniel's feed, Science 2.0, The Life Scientists, Young scientists

Are there too many PhDs? | Mendeley Blog - http://www.mendeley.com/blog...

June 16 from Bookmarklet - Comment - Like - Share

Karen James, Alexey, Lane Rapp and 18 other people liked this

"While more money in science is a great thing and should be increased, the data suggests that money alone is not the answer to improving the engineer/scientist quality of life. Specific policy to increase salaries would do this, but the reality of that occurring is thin at best." - Daniel Mietchen from Bookmarklet

4 more comments

A good time to bring this up again: http://friendfeed.com/ruchira... "How and Why Government, Universities, and Industry Create Domestic Labor Shortages of Scientists and High-Tech Workers" - Ruchira S. Datta

Its interesting. THere is this disconnect between career and quality of life. At a dirt poor shit pay of ~36K/yr I have a great quality of life. I live in a beautiful area, have a fun and rewarding job in basic research (i'm a lab technician). I work with people that view me as a colleague instead of a Masters level indentured servant. I wish I could make more pay, but the reality is... more... - Kevin Z from twhirl

Interesting comments, Kevin. I think I'd be a lot better off if I'd stayed a tech and devoted the time my PhD used up to finding a research niche that really, really floated my boat. (Still haven't done that -- I find everything fascinating, for about five minutes.) Oh, and about that pay -- except for two years on an NIH fellowship, that's about as much as I've ever been paid as a... more... - Bill Hooker

Kevin and Bill, thanks for the comments. I'm currently in a situation where I'm finishing my Masters and have a pretty good opportunity to move in either direction, academia (PhD) or "real world". It's not an easy decision to make and there are various factors that have to be weighed in. You'd think that getting a PhD would guaranty you a good position down the road, but it can actually... more... - Ricardo Vidal

My bro is a social scientist studying science policy and international funding trends. He says Msters degrees will become in high demand with the next few years. He used to work for NAS and now is making real good money with a private consulting company. He pointed me to this NAS report: http://www.nap.edu/catalog.... It is titled "Maste's Education for a Competitive World". The summary itself is worth reading. - Kevin Z from twhirl

Paulo Nuin

PhyloBayes 3. A Bayesian software package for phylogenetic reconstruction and molecular dating. - http://www.ncbi.nlm.nih.gov/entrez...

June 19 from Google Reader - Comment - Like - Share

Kevin Z liked this

Ladybug Heather

Giant sperm stretch back millions of years - life - 18 June 2009 - New Scientist - http://www.newscientist.com/article...

June 18 from Bookmarklet - Comment - Like - Share

browneyes, Kevin Z, Lars Clausen and 5 other people liked this

"There's sperm and then there's super sperm – gigantic reproductive cells many times longer than the minute crustaceans that produce them. Now, scientists have discovered that ostracods, or seed shrimp, have been cranking out these giant sperm for at least 100 million years." ... - Ladybug Heather from Bookmarklet

3 more comments

With a headline like that, it just BEGGED to be ffed! :-) - Ladybug Heather

Too many potential jokes... - John (a.k.a. dendroica)

@Dave, I think you mean: Cum on, John, you can do it! (heh heh heh -- I said "do it"!) - Ladybug Heather

*giggling at Dave* That's one of the best parts about being an Episcopalian; we don't have to be hung up about sex, alcohol, and dancing. Of course, we *can* get hung up about wearing the wrong kinds of vestments, poorly-rendered music, or whether wax or oil or liquid wax candles are best. :-) - Ladybug Heather

RJS

RT @greenkelly: Blue whale sighted off the coast on New York! http://ecologycenter.org/terrain... http://www.birds.cornell.edu/brp... #ocean #wildlife

June 18 from Twitter - Comment - Like - Share

Neil Saunders and Kevin Z liked this

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