A Differential Effect of Heavy Water on Temperature-Dependent and Temperature-Compensated Aspects of the Circadian System of Drosophila pseudoobscura — PNAS - http://www.pnas.org/content...
1973 study of D2O on circadian rhythms. A good quote from introduction: "Many subsequent studies, the most important of which are those of Suter and Rawson (2) and Enright (3), indicate this effect of D20 is widespread: it lengthens r in unicellulars (1), green plants (4), isopods (3), insects (Caldarola, in preparation), birds (5, 6), mice, and hamsters (2, 5, 7, 8). The effect is clearly widespread and since no exceptions have been found in 12 cases, it is likely to be truly general. As several authors have noted, it therefore merits closer study as a potential clue to the physical nature of the cellular oscillation responsible for circadian rhythmicity."
- Steve Koch
This paper has a fantastic introduction that succinctly reviews all the ways in which deuterium can affect enzymatic properties. I haven't looked at any of the papers it cites, but the way in which they outline it is very much in line with what I've been thinking now.
- Steve Koch
Oh yes, this one is a classic in the field.
- Bora Zivkovic
Gotta like every drosi paper on FF :-)
- Björn Brembs
Thanks for letting me know it's a classic, Bora! I'm not surprised, but on the other hand, it's only been cited 7 times this century...and 40 times over all...what's with that?
- Steve Koch
Nice one Bora. Man, there's gonna be free beer&wine at #scio10 - YAY. And looking for a bigger venue for 2011. Gosh, that's v. encouraging :)
- Graham Steel
Some will be free, some will be a very good deal, still negotiating with sponsors etc. too early in the game.
- Bora Zivkovic
Interesting point - could only track down Jon's tweet via Friendfeed. Possibly an argument for piping mine back in - or perhaps setting up a secondary account for archiving...
- Cameron Neylon
a secondary acct for archiving is a good idea.We tend to pull the RSS from tags on the day of any event and stick them in FF or google reader. Having an RSS feed of your own tweets into GR could work too. Tweetstream is definitely pretty transient these days.
- Jo Badge
I use FF as a searchable repository of my tweets, at least for now.
- Bora Zivkovic
The third para of that post was delightful. I also use FF exactly as Bora does, and to search for the tweets of some others. In fact I've toyed with setting up 'imaginary friends' of people / corporate tweets which don't have an FF account for this purpose but haven't got round to it yet. I really don't use FF enough!
- Jo Brodie
Love it: "...the natural unit of science research is the blog post".
- Bill Hooker
I think those who received the invitation from Google itself got 20 invites to give (there is a wave with them). People invited by a regular user that had invitations can't invite others.
- Bruno C. Vellutini
Just watched a good movie with wife, going to make a peanut butter and jelly sandwich and back to inbox zero! should be done by 10pm or sooner. What do you think?
- Wayne Sutton
dear people of email, please do not write any emails that has more than 2 paragraphs
- Wayne Sutton
3 paragraphs to me; 1 sentence back... and thats an action item. short and to the point.
- Wayne Sutton
You'd hate getting emails from my husband. He writes books.
- Anika
time for some Michael Jackson. Spotify has the This is it album online ...hoooooooo
- Wayne Sutton
wow - congratulations! I haven't been at Inbox Zero in something like 5 years. But I try to get down to Inbox 20 every night before bed. At Inbox 22 right now. Two to go.
- Bora Zivkovic
Inbox 16, but all of those require a lot of work - e.g., instructions for writing a paper and such...have to leave them for later....
- Bora Zivkovic
wow Bora, 5yrs? but I understand, I have a few action emails and some assigned to do later
- Wayne Sutton
or you could just set up a new acct! i have about that many and if I could figure out how to easily fwd emails that I want (only) to it, I would just dump the old one:)! good luck!
- Heather O'Sullivan Canney
Great going, keep us posted on how you did it or how you progressed...
- TrafficBug
how I did it? Simple: delete, archive, delete, reply, delete more
- Wayne Sutton
we still need a 'ban all idiot applications flooding the feed' button. i have more than 50 banned, but new ones pop up every day, and sometimes i can't see if something at least slightly interesting was posted.
- Endre Sebestyen
LOL. I just go to FB once a day, usually late at night, and click on all the "Ignore" buttons for all the invitations to silly apps.
- Bora Zivkovic
Hmmm, perhaps ask that question on the 'carpooling and room-sharing' page on the wiki. At least some locals may be interested. Perhaps you can visit Carrboro Creative Coworking space. Or do some other science-y stuff: http://scienceblogs.com/clock...
- Bora Zivkovic
Possibly, as I have family in the area. Haven't worked out my own schedule yet.
- D0r0th34
I was going to fly in on Thursday this time... I may try to switch to Wednesday though. I will let you know as we get closer to the date.
- Bill Hooker
<sniffs> yet again, I won't make it in person :-(
- Graham Steel
Yes - that's a good one. There were a couple of other critiques, notably one by danah boyd. And even Dunbar himself is smarter than this and said that his number does not apply to the online world. Search FF for tag: Dunbar - I've been collecting these, hoping one day to find time to write a blog post about it.
- Bora Zivkovic
Not a gambling person, but at a reasonable guess, I would guess that for circa Jan 2010, (unless hit by meteorite), FF will remain stable, as matters stand. As such, live-coverage via this FF room remains choice #1. As matters stand, I think that it might be not unreasonable to say that #wave might/could be a more interesting alternative, but I don't currently see this as being a viable option for #scio this year. Next year??
- Graham Steel
Oh the irony ;-) I composed my comment before Bora although I was boiling Tortellini during the process. I plead "I wuz cookin'"
- Graham Steel
I suppose a robot could be used to copy content to / fro friendfeed and wave?
- Steve Koch
If friendfeed's not around, someone better get cracking on a better client for Wave, because otherwise it's going to be unfollowable.
- Mr. Gunn
I now have access to Twitter lists, it doesn't look like there's an easy way to import the scientwist list...need someone with API skills...
- David Bradley
the issue with lists is you can only add people you follow, and lists are owned by individual users
- Richard Akerman
you can add people you don't follow to your lists
- Bora Zivkovic
I assume there is a large overlap between David's list and http://sciencepond.com/ list. Is there anyone on http://sciencepond.com/ that is NOT also on David's list? It is unfortunate, but the Twitter lists have to be built manually (for now, at least). It's a pain, but once done, lists are amazingly useful.
- Bora Zivkovic
From the comments, @brembs: "I found the best advice to be that you spend as much time in the lab as you *like*. If the lab pulls you out of bed in the morning and you have to find some activity (sports, music, friends) to drag you out of it in the evening, you’ll be fine. If some clock rules your lab hours, something is wrong." --hands-down the best advice to an intending grad student that I have ever seen.
- Bill Hooker
Funny how I liked that comment the best myself.
- Bora Zivkovic
Mind the caveat, though: today, there are fields which are ruled by the clock and their number is growing.
- Björn Brembs
Is any job a 9-5? None I've worked at
- Deepak Singh
I think this is correct to a degree. You have to be in the lab for as long as your experiment requires, I often had 14 hour experiments to do. Your experiments dictate your time, but then you plan your experiments and your day/week/month in line with this. If you have worked 50 hours in the first 3 days of the week and your experiment is finnished, then you stop working for the rest of the week
- Frank
Well, my inner clock works me more like 10-7 but I believe 9-5 is plenty if you WORK. Much better than hanging around day and night to be seen by the supervisor, but doing nothing. You have to be able to cope with the 24-7 folks' comments though...
- Oliver Schuster
The concept of "tacit knowledge" is very interesting.
- Mickey Schafer
Oh yes: http://en.wikipedia.org/wiki... I use it all the time when explaining to people why they should post comments on papers - to preserve the tacit knowledge to the next generation
- Bora Zivkovic
That's a nice point, Bora. I will use that to encourage students to participate more. Also explains why reading comments is important.
- Mickey Schafer
Absolutely, and wouldn't it appropriate for this user-generated video to be linked directly to the Manu. in question. Wait? Holy Spiderz... how did this happen :-) http://www.plosone.org/annotat...
- Graham Steel
Alerted the author who said:- "Thanks, a already saw the video. Not sure I understand. Who made it? Matjaz". NACProductions1 based in the UK I think, was my reply.
- Graham Steel
Seems like a reasonable call, Pete.
- Graham Steel
Excellent number of views though (considerably more than the paper itself has...)
- Peter Binfield
Actually, I take that back! I last looked at the paper yesterday, since which time it's views have increased by about 26,000!
- Peter Binfield
Wow - that's good :) I've emailed the person who uploaded the video and asked them to consider placing a link to the PLoS ONE Manu in the video information tab... ++UPDATE++ they now have. xlnt !!
- Graham Steel
Okay, so Florida is not such an exotic location, but our banana spiders (golden-orb) spin huge webs, and I've had to scramble to avoid walking into web that spanned 5-6 feet.
- Mickey Schafer
These are pretty well-known spiders here (the golden orbs; there is a brazilian banana spider that is actually horribly toxic) -- I leave their webs up all around the house because they eat grasshoppers like crazy -- have had them riding on my shoulders when clearing brush, and once on my calf...turns out they have very velvety-feeling undersides, and are the only spider that doesn't make me want to run screaming to someplace like Antarctica. "2 Princes"? One of my favorite tunes!
- Mickey Schafer
Spinning (sorry) back to PLoS EVERYONE from 2 days ago, it's worth tying in the post Worth a Thousand Threads http://everyone.plos.org/2009... into this one. Having re-read it, I see that there is a somewhat sombre note to this discovery and I must pass on my regards to Dr Matjaž Kunter in respect of the sad loss of their best friend Andrej Komac who died in an accident at the time of the discoveries. This I have now done.
- Graham Steel
which three? can you copy and paste here for everyone to see?
- Bora Zivkovic
Sure, Bora, but my selections have more to do with aesthetic reaction than information -- things that made me laugh or just go "yeah, that was nicely put."
- Mickey Schafer
#1: "I can encode a lovely simulation on my screen in which there is no theory of gravity, but if I attempt to drive my car off a cliff, empiricism is going to bite my backside on the way down."
- Mickey Schafer
#2 (this is for the info, too) "Data is not sweeping away the old reality. Data is simply placing a set of burdens on the methodologies and social habits we use to deal with and communicate our empiricism and our theory, on the robustness and complexity of our simulations, and on the way we expose, transmit, and integrate our knowledge."
- Mickey Schafer
#3 "Changing the public nature of the Internet threatens its very existence. This is not intuitive to those of us raised in a world of rivalrous economic goods and traditional economic theory. It makes no sense that Wikipedia exists, let alone that it kicks Encyclopedia Britannica to the curb."
- Mickey Schafer
#4: "As Galileo might have said, however, “And yet it moves.” [6] Wikipedia does exist, and the network—a consensual hallucination defined by a set of dry requests for comments—carries Skype video calls for free between me and my family in Brazil." (part of my appreciation for this derives from my trip to Rome, where I caught the Galileo exhibit at the Santa Maria del Angieli)
- Mickey Schafer
Love them all - all four. Thank you.
- Bora Zivkovic
#5: "Software built on the model of distributed, small contributions joined together through technical and legal standardization was another theoretical impossibility subjected to a true Kuhnian paradigm shift by the reality of the Internet. The ubiquitous ability to communicate, combined with the low cost of acquiring programming tools and the visionary application of public copyright licenses, had the strangest impact: it created software that worked, and scaled."
- Mickey Schafer
Guess I can't count 'cause there's one more: #6 "Eben Moglen provocatively wrote in 1999 that collaboration on the Internet is akin to electrical induction—an emergent property of the network unrelated to the incentives of any individual contributor." -- this one in particular helps provide a frame for understanding what happens "out here" -- I think this is what I try to get across to students.
- Mickey Schafer
Unfortunately there's nowhere to go. Nothing has FF's functionality, and the stuff being added to Twitter isn't going to close the gap significantly. Wave has some potential in time.
- Kevin Gamble
I still feel that Wave is orthogonal to FF in terms of its native functionality. You could build something in Wave but not sure that it would work neatly. The key success here in FF has been the way that communities have come together and that people can come in from the outside via search. We may simply have to build or adapt something for ourselves.
- Cameron Neylon
from twhirl
Again: I'm not saying that FriendFeed will go away. Just that its growth will stagnate for a period and then it'll either see growth because of new microcommunities like yours that find it useful or something else will come along that enables new communities and you all will go there. Either way, FriendFeed's "death" is due to the fact that they aren't working on it anymore.
- Robert Scoble
I agree with Micah. I've been here, but not using/posting much to my main feed.
- Tendonitis' Bitch
Bora: To Robert's point, seems to me a mature Wave might end up being better for that than FF.
- Christopher A Carr
I could be wrong but would see it mostly as mostly profit driven. PLoS ONE is showing the the most sustainable way to publish high quality open access is to have a base that publishes a lot more of more specific content that is not reviewed on perceived impact. If I was any other publisher (aside from PLoS and BMC) I would be concerned about this move to cover this broad base. How many...
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- Pedro Beltrao
I'm a bit confused as to why communications or letters journals are coming out now. I blogged this last time I had reliable Internet at home. & +1 for Pedro's take
- Christina Pikas
from iPhone
Pedro, I think that is kind of the point I was trying to make. If N Comms goes for volume they will be accused of diluting quality - and devalue the brand. But if they don't then what is the point? Sure its about profit. But so is PLoS ONE, nothing wrong with that - particularly if it supports good service provisions. But I agree I still think we have too many journals and making more isn't going to help - it just seems all that we are capable of doing at the moment. It will break, sometime soon.
- Cameron Neylon
Other thing that I forgot to raise from the Scientist article. Page Limit?!?!?! In an online only journal?
- Cameron Neylon
well, there are length-sensitive issues that have nothing to do with typesetting. Copyediting, for instance.
- D0r0th34
I was thinking about the page limit thing for digital papers wrt peer reviewing the other day (actually, I seemingly always think about most things from the peer review perspective), but wouldn't a "no page limit" journal be a b*tch to peer review for? Nowadays, the limit is like 10-20 pages per article, right? What if the "no page limit" thing increases that "acceptable standard" to 30-40 pages? That's like twice the content to peer review? Ouch...
- Wobbler
Page limits vary a lot from journal to journal. I've occasionally seen extremely dense 100,000 word articles in mathematics. Peer review at the standards expected by mathematicians may take several months of full time work or even more for such a paper.
- Michael Nielsen
Wow, really? Amazing. So how does that work exactly? I assume they can somewhat figure out beforehand whether it's worth publishing or not and peer review is there mostly to make sure everything is written down right before they publish it? But with the whole idea of "no page limits", I'm assuming we're also expecting scholars to spend more time peer reviewing longer articles? Or "no page limits" in the sense of "everything else is supplemental, like (raw) datasets for example"?
- Wobbler
I figured it would be either trying to contain the time or costs of copyediting and refereeing but again it seems to me to miss the point of the opportunities offered by online only. Anyway doing a Q&A with them to hopefully appear next week so we get some answers - also apparently more information coming with the call for papers next week as well.
- Cameron Neylon
I guess one approach of longer articles is for the authors to include a 1 page "summary" of the article and which parts describe what so editors/peer reviewers have an easier time screening for what they think is suitable for their journals or not? I think I read about such an idea before. When articles do get lengthier, I think this idea becomes more feasible.
- Wobbler
Well my answer would be to admit that in depth peer review of every paper in a timely fashion is simply not feasible and is in any case unaffordable. If we could admit that and move on then we might make some progress.
- Cameron Neylon
fully agreed - so where go next? open post publishing peer review - then why do the (traditional) 'publishing' in between at all? how much 'branding' do readers really need to figure out what they want to read?
- Claudia Koltzenburg
I think, on average, lengthier articles create issues with peer review. And to make the problem worse, those articles are also going to be more prone to mistakes (because there's more content in the article). That's two things you absolutely do not want even as separate issues. And with the page limit change they will come in pairs, because they're somewhat mutually inclusive. Then...
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- Wobbler
@Claudia - I think the evidence shows that readers are less and less interested in branding. It is authors that care about it. @wobbler there is clearly a place for comprehensive reviews, but I agree that really length papers probably are mostly data rather than paper and should be treated differently. It would be interesting to know whether there was a correlation between the length of papers and the time referees spend on them. Very difficult to measure accurately though.
- Cameron Neylon
@Cameron, yes, agreed, I guess it would be interesting to compare the author/reader overlap in scholarly output/process/input workflows with any other slice of life where two or more such overlapping interest stakeholders are involved in a jousting game - and then see if this gets us new aspects to look at - or indeed to add in Björn's recent one: http://ff.im/9rySu
- Claudia Koltzenburg
@Cameron: currently, that seems to be the only type of a lengthier article that would not decrease but increase peer review effectivity and efficiency. All the others are bound to make the (current) certification processes a lot tougher. Oh well, guess something to think about when it happens on a large scale. Maybe, as you've said, we'll have found a good solution for that.
- Wobbler
Well, palaeontologists LOVE no page/figure limit because they can finally describe their fossils in detail that is useful to other researchers: http://svpow.wordpress.com/2009... . Also, don't forget that longer papers tend to gain more citations (either because there's more data, or because they are more memorable, or because they are more like reviews).
- Bora Zivkovic
just added to the OAD list of research questions the jousting game idea voiced 3 comments further up in this thread, check out the list and add your own: http://oad.simmons.edu/oadwiki...
- Claudia Koltzenburg
it's been on-and-off and hiccuppey for me, but mostly working today....I see lots of people have problems. May work better on apps than on the twitter.com site.
- Bora Zivkovic
Since I'm one of the lucky few, I guess I ought to make some lists.
- John (a.k.a. dendroica)
am particularly looking forward to this one: "The commenting conundrum: about where and why scientists do or don’t comment on scientific articles"
- Claudia Koltzenburg
especially looking forward to The commenting conundrum AND the article-level metrics... ;-)
- Bora Zivkovic
http://www.wikimatrix.org/ shows quite a few in comparison. I like wikis best that show changes in detail. And I want menues to be availabe in many languages.
- Claudia Koltzenburg
We use DokuWiki here at work, because it has a very low barrier to entry.
- Simon Cockell
It really all depends on how big the wiki is going to be an how many users. If it is just a few people and a few 10's of pages then a simple one-file flat-file wiki is the way to go. A few more pages and users ~100 then go for a more complicated flat-file like dokuwiki. If you have 1000s of users and pages then use a database-backed wiki like mediawiki. Also depends on your server environment, e.g. on shared hosting a wiki written in PHP may be easier.
- Matt Leifer
I guess about ~50 pages, with a couple of hundred potential users though, as it usually goes, only a handful would really do the editing.
- Bora Zivkovic
I'd be tempted to go with dokuwiki for that due to the ease of setting it up.
- Matt Leifer
make sure that with dokuwiki the extension and maybe also a few more libraries are installed that allow for a detailed visibility of changes - helps users keep their trust in the transparency of the process :-)
- Claudia Koltzenburg
+1 for MindTouch, which is based on MediaWiki, it just comes with 'easier' (non-tekki) editing and widgets.
- joergkurtwegner
I found this a while ago, but no one, to my knowledge, seems to have blogged about it:Real Lives and White Lies in the Funding of Scientific ResearchThe granting system turns young scientists into bureaucrats and then betrays themLawrence PA (2009) PLoS Biology 7(9): e1000197 (open access)Go read the article. It's scary. And seems accurate enough even to an undergrad with limited experience. (Shit, I've been jaded already before even going to grad school...)Within the article is this quote:“Scientists might have had a Hippocratic oath of their own. They might have promised their gifts to mankind. But instead, I have fathered a race of inventive dwarfs who can be hired for anything.”—Bertolt Brecht “The Life of Galileo,” version by David HareTo be fair, doctors aren't exactly saints these days either, being tied up by the madness of insurance policies and a culture that deems it acceptable to SUE(!) a doctor for trying to help a patient. But at least doctors can have their own...
I found this a while ago, but no one, to my knowledge, seems to have blogged about it:Real Lives and White Lies in the Funding of Scientific ResearchThe granting system turns young scientists into bureaucrats and then betrays themLawrence PA (2009) PLoS Biology 7(9): e1000197 (open access)Go read the article. It's scary. And seems accurate enough even to an undergrad with limited...
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Thanks. It's combining avian ecology and physiology, taking my old lab work and testing ideas out in the field for the first time. Accepted by Condor (yes, I wanted PLoS ONE, but I am just the 3rd author here....). Trying to persuade the editor that citing a blog post is OK these days was a challenge... ;-)
- Bora Zivkovic
hm, I wonder: what kind of difference does such 'paper accepted'-type of 'publishing' mean to you - (if - why/ how) does it make any difference re blogging (for you)? see also "publish fair trade" http://ff.im/8cGP3
- Claudia Koltzenburg
It's fun. It is nice publishing one's ideas and data when one is NOT in the rat-race for promotions, tenure, etc. I don't have to care what, when, where, how or even if. If it happens, fine, if it doesn't fine, too.. A very pleasant nonchalance about the whole process - nice to be able to afford it.
- Bora Zivkovic
"not in the rat-race for promotions" Ah, the pleasures of liberty. Congrats and best wishes for more acceptances like this.
- Polly Potter
@Claudia -- my position as a lecturer doesn't require research either, though in my unit, we earn "merit" pay for activities outside our job descriptions (those that contribute to the university, unit, community, etc). One of the unanticipated rewards of learning about the science/web2.0 community has been space for doing research again --and being willing to make time for it --...
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- Mickey Schafer
"nonchalance about the whole process" - would this liberty contribute to whatever me might figure out we can call "fair trade" publishing? http://ff.im/8cGP3
- Claudia Koltzenburg
Only you think that ....we all believe in your sci work!
- Ana Ivkovic
Nice! Be sure to blog about your own paper :-)
- Björn Brembs