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Arunn › Likes
PLoS Biology: Real Lives and White Lies in the Funding of Scientific Research - http://www.plosbiology.org/article...
Robert Spekkens, Cesar Sanchez, Geoff Wozniak and 31 other people liked this
"The peculiar demands of our granting system have favoured an upper class of skilled scientists who know how to raise money for a big group... They have mastered a glass bead game that rewards not only quality and honesty, but also salesmanship and networking." I agree with much in this article. Some years back I constructed a list of papers I especially admired, and was surprised to discover that with only a few exceptions they were produced from unfunded research. This was sobering, since it suggest that receiving research grants was (at least according to my judgement of scientific quality) anticorrelated with doing work of the highest quality. Grants seem to be good at sustaining an established area, but not very good at all at producing the conceptual innovations that start new subfields.
- Michael Nielsen
It's very clear that some scientists are just really good at getting money - good salesmen I guess, like you say. They are not always the best scientists yet seem to do well in the jobs market, as universities love scientists who bring in money.
- Sarah Kendrew
"She looked for a job in science publishing or in the granting agencies—both of which, ironically, offer better working conditions and much better security of employment than research."
- Duncan Hull
Depressing
- Rajarshi Guha
@Rajarshi Good to see the issues given a higher profile though...
- Duncan Hull
@Duncan, oh absolutely. The idea of long contracts (5 - 7 years) makes sense. But these approaches will really require systemic changes - even if I could get by with small amounts of money (say for 1 student), the university won't like the fact that I'm not bringing in gobs of money to pay for electricity
- Rajarshi Guha
I agree with Duncan that although the situation is depressing (and quite accurately represented in there), seeing it gain higher profile is refreshing.
- Daniel Mietchen
Pushing these issues more and more is vital if we want things to change - even if we don't agree on the solutions, awareness of the problems is a prerequisite for change.
- Björn Brembs
Interesting that similar sentiments have been expressed earlier in engineering. See my write-up Individual and Empire in Academics (on a research article) http://unrulednotebook.wordpress.com/2008...
- Arunn
To be nitpicky, I'm afraid that the following suggestion is as open to abuse and laziness as the current one: "Everyone should get slotted into a funding category and assessed every five years. If you're productive, you get five more years of resources. If productivity is down, you are moved down a category. If it is high, you can apply to move up. Starting PIs are in a different...
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- Heather
Hmm. can't write English today. The suggested improvement to the system is subject to abuse, as much so as the current system - dead wood will be carried along. No room will be made for younger people moving up the ranks. And I meant "effective".
- Heather
Lest we forget: http://www.nytimes.com/2008...: "Trained as a biochemist, Dr. Prasher, 57, was interested in the chemistry of how certain animals are able to glow. In the late 1980s, he applied to the National Institutes of Health for a five-year grant to track down the fluorescent protein gene...'I knew it could serve as a genetic marker and it would be really, really useful, which it has turned out to be.' That application was turned down..."
- Richard Klancer
Michael Nielsen wrote above: "Some years back I constructed a list of papers I especially admired, and was surprised to discover that with only a few exceptions they were produced from unfunded research. This was sobering, since it suggest that receiving research grants was (at least according to my judgement of scientific quality) anticorrelated with doing work of the highest quality....
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- Bora Zivkovic
I don't have a blog post about it. To make the judgement I used a large fraction of what I know as a scientist. I couldn't easily reduce that to a short list of criteria.
- Michael Nielsen
I'll fast if IIT faculty takes moksha: Kapil Sibal - dnaindia.com - http://www.dnaindia.com/india...
Arunn liked this
Sibal, the Lawyer: 6
- T.A. Abinandanan
Comparisons of citations in Web of Science, Scopus, and Google Scholar for articles published in general medical journals. - http://www.citeulike.org/user...
joergkurtwegner and Arunn liked this
Does anyone have access to this? http://ff.im/8qppH
- Duncan Hull
Advice on writing research articles - Statistical Modeling, Causal Inference, and Social Science - http://www.stat.columbia.edu/~cook...
Arunn liked this
Great advice on writing academic papers.
- T.A. Abinandanan
The Most Popular Myths in Science: Water drains backwards in the Southern Hemisphere due to the Earth's rotation - http://www.livescience.com/bestimg...
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Daniel Mietchen, RAPatton and Arunn liked this
"Not only is the Earth's rotation too weak to affect the direction of water flowing in a drain, tests you can easily perform in a few washrooms will show that water whirlpools both ways depending on the sink's structure, not the hemisphere."
- Pilsonia
from Bookmarklet
Deep Inside Bacteria, a Germ of Human Personality - WSJ.com - http://online.wsj.com/article...
metalerik, Arunn, Bluesun 2600 and LANjackal liked this
"Bacteria are the oldest living things on earth, and researchers have long felt that they must lead dull, unfussy lives. New discoveries are starting to show just how wrong that notion is. For a simple, single-cell creature, a bacterium is surprisingly social. It can communicate in two languages. It can tell self from nonself, friend from foe. It thrives in the company of others. It spies on neighbors, spreads misinformation and even commits fratricide."
- Joe Bonner
from Bookmarklet
Call for JCOM papers on participative media - http://jcom.sissa.it/call
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
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...
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- 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...
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- 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 -...
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- 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...
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- 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
@communicating Why is it extreme not to submit my papers to journals which do not accept LaTeX? Good journals accept LaTeX.
Radu Grigore, Robin Green, Arunn and Daniel Mietchen liked this
Science journalism: Breaking the convention? : Nature News - http://www.nature.com/news...
Chris Lasher, joergkurtwegner, Konrad Förstner and 19 other people liked this
I still think they should have interviewed other people than me, though. It is not like I was the main person behind what happened on FriendFeed at ISMB in Toronto.
- Lars Juhl Jensen
I guess you had the best sound-bites Lars :-)
- Neil Saunders
@Neil @Lars "bloggers don't need icebreaker events ;-)" heh
- Duncan Hull
Some of these comments confuse me slightly. The definition of "publishing" is the process of production and dissemination of literature or information (http://en.wikipedia.org/wiki...) why do some scientists confuse publishing only to be a peer-reviewed journal publication and assume other methods- giving talks, posters, slides, open notebooks are not "publication"?
- Frank
@Frank absolutely, publication is "to make content publicly known." public-ation
- Duncan Hull
That's a long story, Frank, but it boils down to the currently dominating definition of scientific "publication" stemming from the pre-web era when journals were more widely circulatable then the other kinds. And, for the last five decades or so, all major scientific journals have used pre-publication peer review to decide which content comes into the journal, since printing on paper was (and still is) expensive.
- Daniel Mietchen
Repost of my comment on the Nature web site: I also find it ironic that people go to conferences to present their work and at the same time want to keep their discoveries secret. On the other hand, if people abstain from presenting new results then why would anyone want to participate in conferences? In some fields, computer science comes to mind, the best work is published in...
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- Lars Juhl Jensen
RT @Ghattavi Many newspapers were blank today as there were nothing to say... and some people even bought them for support #iranelection
Arunn liked this
and those blank Iranian newspapers said more than US papers say when chock full of ink
- Bora Zivkovic
Scientia Pro Publica: Last Call for Submissions - http://scienceblogs.com/grrlsci...
Arunn liked this
Semantics Incorporated: The Definitive Definition of Web 3.0 - http://www.semanticsincorporated.com/2008...
Arunn liked this
Medical scam just got bigger: PG seats for Rs 2 cr - http://economictimes.indiatimes.com/Medical...
Arunn liked this
No wonder some see such "education" as "investments" that they MUST reap in years to come
- Arunn
English libel law adversely affects every publisher and website host that can be read in UK http://www.nature.com/nature... It must be changed.
Anne PAJON and Arunn liked this
new bog post: Everybody loses in the battle over our online identity: http://vanelsas.wordpress.com/2009...
Daniel Rowley, Darren Rollett, Mac Sharp and 15 other people liked this
Damn that was fast Robert! ;-)
- Alexander van Elsas
Good write-up :)
- Micah Wittman
@Micah thanks :-)
- Alexander van Elsas
Excellent post, Alex! Pity i haven't enough time to read Cris' post as well. As for me, I made the decision about a year ago, when i realised *what* friendfeed is. I delegate hosting of my digital identity to them =) To me, facebook is only starting to catch up
- Kirill Bolgarov
@Kirill thank you :-). The question I have though, is FF really the trusted party for your digital identity?
- Alexander van Elsas
@wecandobiz wrote: "I’ve been saying for some time that probably the best solution if we are all to have an online identity which becomes key in the Web 2.0 world and beyond is for a not-for-profit “authority” to issue and maintain our identities with all data stored in a central repository. Visiting social networking sites would have us “leasing” our identity to that site for the...
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- Alexander van Elsas
Alex: yeh, i mean i believe that they will never do anything with their social networking structure that could misinterpret my identity. as for security - i prefer to treat it like a myth. maybe because i live in a KGB country =)
- Kirill Bolgarov
Very insightful, thanks for this post, Alexander. It will be exciting if the paradigm can really change to be user-centric. I won't hold my breath but it's good to know the seeds are being planted.
- Laura Norvig
@Laura, thank you :-)
- Alexander van Elsas
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- Michael_techie
The Spooky World Of Quantum Biology - http://www.hplusmagazine.com/article...
Sally Church, Ruchira S. Datta, Iván Abrego and 3 other people liked this
"One hundred and fifty years ago, paleontologist Thomas Henry Huxley (an autodidact and philosopher who coined the term “agnostic” and was known as “Darwin’s Bulldog” for his passionate defense of natural selection) asserted that humankind would eventually take the processes of evolution into our own hands. Within a few decades of his proclamation, a cadre of equally brilliant scientists including Werner Heisenberg, David Bohm, and Max Planck began to unravel the mysterious properties of quantum mechanics. These two theories –- evolutionary and quantum dynamics -- can each be considered among the most important discoveries of all time. Taken together, they have changed almost everything about the way we understand reality. However, in spite of the popularity of interdisciplinary research and unifying theories over the last hundred years (despite, even, quantum physicist Erwin Schröedinger’s 1944 book, What Is Life?), it was only recently that the relationship between these two vastly...
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- Alejandro
from Bookmarklet
We are the universe waking itself up.
- Chrimmus Tad
Evolution: Education and Outreach, new issue (Open Access): http://www.springerlink.com/content...
Joelle Nebbe (iphigenie), Helen Sventitsky and Arunn liked this
@BoraZ "bring professional evolutionary scientific research community into closer & more productive touch with K-16 teaching" US spec. goal?
- Arunn
Don't know, but sounds like something US-centered but non-exclusive, i.e., made with US educational system in mind, but would be happy if used worldwide.
- Bora Zivkovic
Chemtweets and scientwists C&EN interview with @sciencebase (free to view) http://pubs.acs.org/cen...
Arunn liked this
Call to action - wikipedia editor questions the reliability of data from open science - please go to his talk page and add your support for the ONSchallenge: http://en.wikipedia.org/wiki...
Konrad Förstner, Arunn, Daniel Mietchen and 7 other people liked this
quote from editor: "Although I am sure that this school project was fun for the kids, Wikipedia needs to have data here from verifiable sources. Reference to a university site (Oral Roberts or Harvard) is not good enough. Otherwise your work risks being deleted. NIST, CRC etc, now they are authorities. I really encourage you to consult someone before launching on what looks like a well intentioned but naively planned project."
- Andrew Lang
Please help. Go to the talk page and make a comment. Thanks!
- Andrew Lang
There is probably a value in thinking carefully about the response here. I have heard some criticisms of the methodology being used and have suggested that people make those criticisms in the project notebooks but this hasn't happened as yet. Strictly the WP guidelines do require a traditionally published (non-web) verifiable source and one could make an argument that these results have...
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- Cameron Neylon
I think it has been peer reviewed - http://onschallenge.wikispaces.com/judges
- Andrew Lang
...but not in the traditional way...I agree with you but it's a subtle argument and it could get lost
- Cameron Neylon
I would also say that at the end of the day there is much more back up on our data than there is for a NIST or CRC value in many cases - at least you can tell what was measured. Just not sure whether that will be enough for the traditionalists. Just worth rehearsing the arguments I guess i what I am saying.
- Cameron Neylon
Can you link the actual page that's in dispute? Major flaw in WP talk imo, there are no auto links to the pages being discussed.
- Bill Hooker
@Bill Here's my edits - he's questioning them all: http://en.wikipedia.org/wiki...
- Andrew Lang
Lets keep in mind that none of the other properties even have references (see for example benzoic acid: http://en.wikipedia.org/wiki... )
- Jean-Claude Bradley
Just noticed in the urea talk page someone complaining in 2007 that all the solubility values were wrong and unreferenced :-)
- Cameron Neylon
Added my comment. It seems to me that, as a source to be quoted in WP, open notebooks are a new category (see http://en.wikipedia.org/wiki...). They are not "third-party published sources with a reputation for fact-checking and accuracy", but they are "produced by an established expert on the topic" in the sense that JC runs the project and we judges are all scientists. More to the point, WP has never been asked to consider this kind of source before.
- Bill Hooker
Thanks Bill.
- Andrew Lang
@Cameron Good find! I can see the ppt slide now. Here's the quote from 2007 about the solubility in water - it seems to have never been resolved - "The article provides some specific information about the solubility of urea without giving a source. The values were out by at least a factor of 10 (probably g/L rather than g/100mL), which I have corrected by knocking off the last zero, but...
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- Andrew Lang
I added my 2 cents: http://en.wikipedia.org/w... . Still do not get why none of you guys - so much engaged in doing open science - seem to have ever shown up at Citizendium, a place where expertise is actually valued. It is currently very small compared to Wikipedia, but so is Open Science compared to the rest. See also http://en.wikiversity.org/wiki... .
- Daniel Mietchen
Thanks for adding a post to the discussion on wikipedia Daniel. I will check out Citizendium.
- Andrew Lang
I believe the reason most of us stick to Wikipedia is that we believe that it is (a) the appropriate general resource and (b) since it is the source most people, and Google, go to, information will be found there.
- Deepak Singh
Certainly nothing wrong with reading or editing Wikipedia entries. But the sort of problem discussed in this thread would be much rarer over there at Citizendium (they have others), and since it tends to affect scientists quite often, I am wondering why they do not give this alternative a try. Andrew Su has done that, and he was disappointed (a feeling I share for his case, since I...
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- Daniel Mietchen
Daniel - thanks for the comments and for the link to Wikiversity and Citizendium - we'll certainly check it out. A first look does not show any entries for common chemicals like methanol. Additional portals are always of interest though. The reason Wikipedia is useful is that it turns out to be a significant way people looking for specific non-aqueous solubility find our results.
- Jean-Claude Bradley
Anatomy of a Blog Post Well Received http://www.readwriteweb.com/archive... charting the rhythm of traffic & sources on a big blog post
Thomas Vander Wal, Nicholas James, Ian Wilker and 14 other people liked this
This may be one of the best analysis pieces explaining how blogging becomes viral and how to analyse/examine it. This is one to keep close and share repeatedly.
- Thomas Vander Wal
from FriendFeed MT Plugin
Thanks Thomas!
- Marshall Kirkpatrick
I love the links to your hard-working Greasemonkey scripts, Marshall. It's great to see which underrated tools other people are making use of.
- Daniel J. Pritchett
What was most amazing about this piece is to see how a professional blogger does to research information for a post. I feel good that I could follow almost all of the process. Thanks Marshall!
- Jorge Escobar
I imagine that Marshall is more engaged than the average blogger when it comes to the business end of blogging and site growth given his position as VP Content Development / Lead writer (http://www.readwriteweb.com/about_m...). Clearly Mr. K sets the standard for hard work at RWW.
- Daniel J. Pritchett
from IM
Can you share which analytics package gave RWW traffic metrics graphed here? http://is.gd/Obeq I use GoogleA and Sitemeter...
- Daniel J. Pritchett
Daniel, that was just a Movable Type traffic plug in exported as CSV and put into a spreadsheet. It took way too long! lol oops
- Marshall Kirkpatrick
RT @TrishaTorrey: Stem Cell Contact Lenses Cure Blindness in Less Than a Month: http://ad.vu/enh2 ☜ Watch the 2 minute news video!
Arunn liked this
Chemical Open Source For Free: How far it really matters - http://www.abhishek-tiwari.com/2009...
Egon Willighagen and Arunn liked this
Not a direct response to your post, but wanted to point out that the whole commercial software ecosystem is not that simple. For one, Univ tech transfer offices have a pretty strong hand in the models chosen. Second, the biology and chemistry communities have adopted very different approaches. Having worked at companies that have profited (although scientific software and profits are...
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- Deepak Singh
Indeed my opinion is quite simplistic, but I agree that whole open source oriented model is quite different for biology and chemistry. When it comes to biology industry has adopted best tools and techniques from open source community and integrated them with their product line. For example PipeLine Pilot and Inforsense have provided support for BioPERL, BioJAVA long back but they never...
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- Abhishek Tiwari
Abhishek, can you back up the statement that commercial offerings are significantly better or even superior than open source cheminformatics tools? I think I missed that publication...
- Egon Willighagen
Seriously, surely they are better in support, that is what you pay them for, but I have not seen any writing showing that there algorithms are better at making drugs, predicting properties, ...
- Egon Willighagen
My statement can not be supported by any publication, however there are some advantages by using commercial offerings. Don't take me wrong but even for simple algorithms like ALogP there is a difference but in my opinion how they can handle large scale data sets is key issue, i.e data cartridges. Although Open source efforts have great collective potential but quite scattered. Take CDK,...
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- Abhishek Tiwari
That's a support issue. *Not* a problem with the libraries. This sounds like a request for a consultant to glue stuff together for you. The fact that you feel such glue is missing (btw, this is exactly what Bioclipse is solving) does not make tools like OpenBabel or the CDK inferior. Also, ALogP being better by other tools... you cannot back that up either? If we had enough OpenData that would have been easy to quantify...
- Egon Willighagen
Anyway... don't worry about how easy you can use your black box, worry about how well you can validate the box you use. Open Source cheminformatics offers you transparent boxes. That's what is important, not the price tag.
- Egon Willighagen
I have to disagree - CDK + OB + Postgres etc can lead to powerful cheminformatics applications. AS Egon pointed out it's mainly a matter of glue. While Bioclipse is certainly one sort of glue, there's scope for other forms as well. But at the same time I will say that OSS cheminformatics does have holes - depending on the specific toolkit, onemight need to employ another toolkit to fill in those holes. This aspect makes broader usage of OSS toolkits problematics.
- Rajarshi Guha
Which brings in the Interoperability promoted by the Blue Obelisk. Blue Obelisk members generally try/tried to keep the various tools non-overlapping, though increasingly duplication of code happens, just because a different programming language or different license is more convenient. So, e.g. Jmol has the same UFF code as OpenBabel; but, it is common to use different open source cheminformatics tools indeed.
- Egon Willighagen
Abhishek, as you seem to be a demanding end user (meant in the most positive way possible), maybe you can blog about the whole you see, and then the Blue Obelisk (and the rest of the open source cheminformatics) community can respond, fill the gaps, or pointing to existing tools? Yes, this support comes for free... no entrance fees or yearly contracts required.
- Egon Willighagen
Abhishek, that was kind of my point. In chemistry, you can make money from the underlying tools, e.g. Glide, but in biology, esp informatics, you have to go up the stack, focus on pipelining and data management (noting that pipeline pilot's origins are completely in cheminformatics).
- Deepak Singh
Egon, I am already in process to compile a comparison table of all chemoinformatics toolkits, and will blog that soon. Also regarding support from community, I must say even commercial products have developed very strong community around their products. Product is commercial or open, I don't expect any support from producer but from user group. And that what really matters.
- Abhishek Tiwari
Cheminformatics does face challenges though, and I am not sure why. The same organization will primarily use an open source bioinformatics stack, but a proprietary cheminformatics stack with crazy licensing with only a few OSS tools in regular play, but that's what Egon etc are trying to change.
- Deepak Singh
And the reason for this, IMO, is that when companies aw the need for bioinformatics tools ,they were able to find a comprehensive OSS stack. OSS chemifnormatics has had a much later start and hence has to prove itself to a higher degree. Another aspect I think plays a role - there are *many* more people able/willing to write bioinformatics code than cheminformatics code. (But of course this is a vicious cycle)
- Rajarshi Guha
Egon , wrt interoperability - that's nice. But the fact is that if I'm using a low level toolkit I expect it to provide all the core components without having to integrate another toolkit. Yes, ideally, all OSS toolkits would have the same/similar interfaces, API's etc. But that's an unrealistic expectation IMO. Right now, if somebody uses the CDK and needs stereochem support, they are out of luck and will likely shift to OB. But if they're a Java shop, they'd likely rather switch to JChem.
- Rajarshi Guha
Rajarshi, don't disagree. Bioinformatics codes are a lot more generalized from the computer science point of view and the number of people came from there. But even culturally chemistry-oriented codes (I put MD in the same category) have often not been free for academics either. They've had source available, especially to academics, but it's not an open source model. Quantum chemistry...
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- Deepak Singh
Signup to the Sense About Science statement to keep England's ludicrous libel laws out of scientific debate http://www.senseaboutscience.org.uk/index... (HT S Curry)
Arunn and Duncan Hull liked this
RT @girlscientist: See, not just me and @noahwilliamgray grappling with the morality of twittering from CSHL: http://blogs.sciencemag.org/science...
Jason Tsai, Wladimir Labeikovsky, Alexey and 10 other people liked this
Better late than never. All meeting organisers need to wake up to social networking, decide on their policy and make it explicit, before the meeting. There's also a difference between broadcasting the details of a presentation and a tweet such as "person X is about to talk on topic Y".
- Neil Saunders
Not sure what the best policy is - it seems like requiring bloggers and twitterers to register beforehand and get presenter approval is going to result in far fewer people covering the conference - but I suppose that might not be considered a bad thing by some, if that coverage means blog and twitter posts.
- Shirley Wu
Wow! That just boggles the mind. I never thought the line between scientist and journalist was that thin.
- Peter Murray
“They weren’t held to the same standards as the media” - that's just a failure to recognise that on the web, we are all "the media".
- Neil Saunders
Seems fair enough. It's just common courtesy to get approval before discussing/disseminating someone else's unpublished results. Although, I think it's kind of dumb. If you paid the entrance fee, you get to hear the talk, the results are no longer secret, and the biggest competitors are probably in attendance anyway, so really, what's the big deal.
- Brian Krueger - LabSpaces
I think people come to conferences exactly to have this kind of interaction they're trying to squelch. It's going to be hard to draw the line here, too. I think the only people who should have to ask for permission are the people who have a reason to sensationalize or spin the material, which are mostly journalists and not bloggers. Even in the case where a blogger does hype or...
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- Mr. Gunn
They should take a page from tech conferences. There are accredited journalists, many of whom blog and twitter. They can even have a dedicated bloggers section for full time bloggers, but you can blog and tweet about talks unless the speaker says otherwise
- Deepak Singh
Similar thread here: http://ff.im/3xNjm
- Brian Krueger - LabSpaces
Will Higher Education Be the Next Bubble to Burst?: http://chronicle.com/free...
Iddo Friedberg, Jo Young, David Young and 14 other people liked this
Interesting quote: "According to the National Center for Public Policy and Higher Education, over the past 25 years, average college tuition and fees have risen by 440 percent — more than four times the rate of inflation"
- Hilary
Wow! Looks like Elsevier...
- Björn Brembs
You can get the same education from a community college that you could get at Harvard; what the cc won't give you is the ruling class' stamp of approval. It's that certification function ("this is a wealthy, therefore a worthwhile, person") that drives higher education in the US. The financial bubble may be deliberately maintained for a long time, but in the meantime I hope the web will burst the class bubble.
- Bill Hooker
it pains me to see all those young adults with debt because Higher Education is a market in this country...
- General Kafka
from twhirl
Harvard (and others) also gives you connections (=stamp) - but isn't it true that selection is based mostly on academic capabilities?
- General Kafka
from twhirl
I agree there is value to the "stamp" from elite schools. But in my opinion, the most valuable parts of a university degree in the US are obtained from the interactions with peers and others on campus. Learning how to network, chart a career path, extra-curricular activities, etc. -- many of these things cannot be replaced by a simple online degree. And I think they can be obtained at...
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- Steve Koch
If they are thinking that acquisition of knowledge is the main point of higher education, they are doing pretty well - many think the point is getting a diploma ergo job ergo money. They do, mainly, figure things out by the time they graduate (observe traditional exodus of students out of business majors they start with into other majors they got attracted to by taking the required non-business classes).
- Bora Zivkovic
@Steve: compare the job prospects of a UNM graduate with those of a Harvard graduate. If they are different (and I'm pretty sure they are), there's a disparity in access (to the stamp of approval), since Harvard costs whatever ridiculous amount it costs and UNM is ~free. My whole point is that education doesn't matter a damn, what counts is the stamp.
- Bill Hooker
When I say that I hope the web will burst the class bubble, I mean that I hope wider access to online resources will lead to more and more emphasis on competence and less on the stamp. I'm not gonna hold my breath though.
- Bill Hooker
Lets not kid ourselves, Harvard should not be compared to any CC.
- Vedran Agovic
Fact is today we students have a lot more options to attain their degree. They can go ground, online, flex etc. It all depends on the student. No matter the economy, people go to school. They will continue to go to school especially with many more options available. Students may not go to their first choice due to rising costs but there is plan B, C, D that will offer similar degree programs for the price.
- Vedran Agovic
This article does pose a solid question that we must ask, it is that important and much depends on the higher education institutions.
- Vedran Agovic
Some of the dif between public vs private is the class size. For my undergrad, I would've had a hard time learning in class sizes of 100+. So I chose small liberal arts private. (good financial aid also helped.) For my masters, class size and teacher interaction wasn't as much a problem, but local geog helped me pick a public U. I do see the cost of private educ getting out of control. (I work at a medium private non religious U.). Something is going to break. Not sure what colleges or Univs. or when.
- Joe
Also, many grad students or adjuncts may teach at public or CC places, particularly the intro courses. Now, I have had some great adjunct teachers, but there is more variability.
- Joe
Things may certainly be changing with doing science using Web2.0 tools - one benefit is that the person's contributions can be accepted without knowing their credentials. I take great pleasure in the thought that some of our contributors on our ONS projects could be precocious 14 year olds. These people get known by their work and thoughts alone and will quite possibly find their future...
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- Jean-Claude Bradley
Great point, Jean-Claude. That's where I was trying to go by saying "simple online degrees" miss the point. As far as I know a basic online degree does nothing to build your network or networking skills. @Bora, yeah I agree, it's a huge step and a good one to get to the point of thinking that there's more to school than just the degree (e.g. useful knowledge). @Bill, I guess we're miles...
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- Steve Koch
I'm not sure the Harvard vs UNM argument extends very well to most PhD graduate programs though. With higher degrees, it seems to depend more on your thesis advisor, his/her recommendation, and your publication history. That's just been my experience. The last 4 graduate students here got post docs at Harvard, UCSF, Stanford, and the 4th went straight to an industry job. Of course,...
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- Brian Krueger - LabSpaces
@Steve -- "I don't really care how ridiculously expensive or elitist Harvard becomes" -- that's fine so long as you also don't really care how the country is run. Ivy League = roughly 1/3 of US Senators, 1/3 of Forbes richest list, 20-50% of degrees held by Presidential cabinets since Nixon. Pretty heavy over-representation, given that it's just 8 schools. (Note source = quick Google around, not exactly rock solid, but it accords with my prejudices...)
- Bill Hooker
@Bill, any problem I have with that is dwarfed by the problem I have with almost 100% of them being politicians.
- Steve Koch
@Steve: OK, now there's something we agree on.
- Bill Hooker
:)
- Steve Koch
How science works. - http://network.nature.com/people...
Arunn, Bora Zivkovic, Michael Nielsen and 12 other people liked this
I agree, explorations and discovery are underrated, but it is much harder to write grant proposals that way, its almost a self-reinforcing system!
- Dave Lunt
Like that second figure very much.
- Neil Saunders
Too simple (oh yes)
- Duncan Hull
Nice, that website (Understanding science: http://undsci.berkeley.edu/article...) is most excellent!
- Shirley Wu
Great diagram. I really enjoyed Paul Feyerabend's book "Against Method", about the idea that standard explanations of the "scientific method" are way too simplistic. Read it 20 years ago, though, so take that recommendation with a grain of salt...
- Michael Nielsen
I second the recommendation.
- Ruchira S. Datta
This is very true and yet not acknowledged by most funding agencies - you are generally required to write proposals within a traditional hypothesis driven paradigm.
- Jean-Claude Bradley
"tired of reassure...my graduate students...despite what other faculty imply...they are doing good science" <-- true even for curiosity driven research
- Arunn
@Jean-Claude Bradley; I always thought that too but I was surprised, and reassured, that NERC (UK funding agency) begin each panel meeting reminding us that grant proposals do NOT have to be hypothesis driven. Neither of the two highest ranked proposals at the last meeting were hypothesis-testing, but they were both truly outstanding science. Not sure how other agencies react, anyone got first-hand knowledge?
- Dave Lunt
Dave that's good feedback. To be fair what I said was a bit of an oversimplification - synthetic sciences (like organic) are not necessarily hypothesis driven but proposals are expected to have "rational planning" with contingencies mapped out. That isn't necessarily a bad thing but it isn't the whole story.
- Jean-Claude Bradley
Triangular buttons key to touchscreen typing success - inventor • Register Hardware - http://www.reghardware.co.uk/2009...
Kishore Balakrishnan, Ron Bailey and Arunn liked this
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