A room for all the life science types on FriendFeed (and everyone we've co-opted). Topics tend to focus on bioinformatics and computational biology, but discussion from any area in biological sciences is welcome.
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Assembled Tree of Life :: David Hillis, Derrick Zwickl and Robin Gutell analyzed small sub-unit rRNA sequences sampled from about 3,000 species - http://www.zo.utexas.edu/faculty...
See the beautiful tattoo visualization via Monica Quast, who is a Ph.D. student at the University of Campinas, Brazil, working on bivalve phylogeography. The organisms depicted are (going clockwise): a cyanobacterium, a foraminiferan, 3 diatoms, an oak leaf and acorn, a Spirogyra cell, a red cage fungus, a stauromedusa, a nautilus, a tardigrade, an ophiuroid, and a badger. \\ At first biologists could draw only small trees, typically with a dozen branches at most. They were held back by the fact that a group of species may possibly be related in many different ways. If a biologist adds more species to a group, the possibilities explode. For 80 species, there are more trees than there are atoms in the known universe. Simply comparing every single tree would be impossible. Fortunately, mathematicians developed statistical methods for searching quickly through potential trees to find the ones that do the best job of explaining all the evidence.
- Adriano
The subject matter came up on Twitter a couple of days ago. I plan to raise it with David Lipman early next year, so thought it would be useful to have some data to show him. As such, I would be most grateful for responses on the poll itself.
- Graham Steel
I will send this to a buncha discussion lists. When does the poll end?
- Yo. Shark Dog.
from iPod
Ace, Joe..Thankee .I'll keep it open.
- Graham Steel
I'll try to send it tonight or tomorrow, but who knows how many peeps will read their email tomorrow.
- Yo. Shark Dog.
from iPod
I was thinking, it would be cool if PubMed and PMC had uservoice suggestion boxes/voting. Would be cool to hear what features people want (like perhaps this one?), and which bugs are most bugging people. Right now PubMed and PMC are missing a strong feedback loop imho.
- Heather Piwowar
<quiet voice> I wouldn't mind if pubmed were just a bit easier to search </quiet voice>
- $tephanie•Cog$ciLibrarian
^^^ by which I mean, sophisticated, library-type searching & assessing results - like looking at MeSH terms (where do I find them again?!) and the "more like this" hasn't typically been too useful imho. Sorting results by some kind of relevance, embedding the OpenURL resolver button for thems that has 'em. "Related articles" that are, actually, related.
- $tephanie•Cog$ciLibrarian
I hear ya Stephanie•CogSciLibrarian
- Graham Steel
RT @wilbanks For a license that traditional publishers say isn't appropriate, CC-BY sure is taking off in scholarly publishing http://oaspa.org/growth-...
RT @mbeisen @pf_mg I am pushing PLoS towards a system that is arXiv with structured pubs (ala PMC) + structured reviews alongside and after publication https://twitter.com/mbeisen...
A recent article in the Guardian proposed anonymous post-publication peer-review. But this idea was firstly introduced at FriendFeed in 2009. Here is the link to this discussion: http://friendfeed.com/science.... And here is the paper: http://arxiv.org/abs/1301.2522
Via Peter Suber on G+ +Jeffrey Beall is the target of a dishonest smear campaign. This is his reward for investigating scam OA journals that give OA a bad name. https://plus.google.com/u...
Beall does some smearing of his own. Which doesn't justify the attacks, of course, but *does* mean we need a collective Beall Solution. Ideally such a solution would take Beall out of the journal-judging business while presenting a target much harder to impersonate/troll. I'd say OASPA, except OASPA shows a distinct unwillingness to get its thumb out of its arse.
- RepoRat
I agree that OASPA need to better engage with this. Some of Beall's criteria are faulty, and overall he gives the appearance of a bias against APCs as a business model. "Depends on author fees as the sole and only means of operation with no alternative, long-term business plan for sustaining the journal through augmented income sources" is silly; PLOS, BMC and Hindawi have shown that...
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- Matt Hodgkinson
Thanks Matt. TBH, I haven't had the time to fully read up on all posts/discussions about predatory OA Journals of late. I do however think this recent post by Mike Taylor and especially the comments section was of interest. http://svpow.com/2012...
- Graham Steel
Wonder if we could have a publisher rating service like Yelp. But, I could see scholars really /really/ gaming that system.
- Yo. Shark Dog.
I think some kind of authority is needed. The authority vacuum is what let Beall emerge. N.b. not all forms of authority come from duly-constituted organizations, of course.
- RepoRat
Here's a start: http://www.is4oa.org/News.html "...And we will indeed address the issue of publishers not living up to reasonable standards both in terms of content and of business behavior." Hoping we can make real progress with a re-invigorated DOAJ
- Cameron Neylon
Yes. Using the DOAJ would be a great place to start.
- Yo. Shark Dog.
"The examples of scientific investigation. It is interesting, therefore, to bring it out now and speak of it explicitly. It’s a kind of scientific integrity, a principle of scientific thought that corresponds to a kind of utter honesty—a kind of leaning over backwards. For example, if you’re doing an experiment, you should report everything that you think might make it invalid—not only what you think is right about it: other causes that could possibly explain your results; and things you thought of that you’ve eliminated by some other experiment, and how they worked—to make sure the other fellow can tell they have been eliminated. Details that could throw doubt on your interpretation must be given, if you know them. You must do the best you can—if you know anything at all wrong, or possibly wrong—to explain it. If you make a theory, for example, and advertise it, or put it out, then you must also put down all the facts that disagree with it, as well as those that agree with it. There...
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- Amira
from Bookmarklet
"We’ve learned from experience that the truth will come out. Other experimenters will repeat your experiment and find out whether you were wrong or right. Nature’s phenomena will agree or they’ll disagree with your theory. And, although you may gain some temporary fame and excitement, you will not gain a good reputation as a scientist if you haven’t tried to be very careful in this kind...
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- Amira
"I would like to add something that's not essential to the science, but something I kind of believe, which is that you should not fool the layman when you're talking as a scientist" http://calteches.library.caltech.edu/51...
- golyandro
Very interesting information on blood feeding Dracula bats! The Blood Feeding Vampire Bats – The Sanguivorous Mammals!! At http://adidarwinian.com/the-blo...
"Virtual conferences becoming a reality" Welch et al 2010 - Nature Chemistry came up in convo. last night with Stuart Cantrill, Chief Editor at Nature Chemistry. Here it is....