Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-06-04

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All times shown according to UTC.

Time Nick Message
00:54 kcranstn joined #opentreeoflife
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14:12 kcranstn jar286 - planning to do the namecheap business today during the site maintenance window
14:13 kcranstn would be helpful if you were around in case I have questions
14:13 jar286 ok, pretty sure i’ll be around
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18:04 jar286 https://github.com/pulls?user=OpenTreeOfLife
18:24 jimallman sorry jar286 , got distracted elsewhere. reviewing these now…
18:24 jar286 I think there are only two relevant ones, and they both fail travis
18:24 * jimallman nods
18:26 kcranstn what is the status of the stats page? what are we waiting on?
18:26 jimallman stats page is mostly in my court.
18:26 jimallman pmidford2 has generated lots of stats, and i need to shuffle and format them as we want.
18:27 jimallman also jar286(?) was going after historical stats from prior builds and taxonomy versions
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18:44 kcranstn I am in manuscript submission hell
18:45 jar286 oh no. what do  you need
18:45 kcranstn ears to vent into? shoulders to cry upon?
18:46 kcranstn the supplementary material is 1 text file + 8 figures + 2 tables and I need to cut two of them
18:46 jar286 pnas requirement?
18:46 kcranstn yup. max 10 supplementary files
18:47 jimallman colored inks + red/green 3D glasses?
18:47 jar286 damn.  move some to dryad?
18:47 jar286 does pnas coordinate iwth dryad?
18:47 jimallman 1 + 8 + 2 = 11… do you just need to cut one?
18:48 kcranstn right
18:48 josephwb cat sup* > sup_all
18:48 kcranstn I might cut figure 3 in the supplement
18:48 kcranstn no can do, josephwb
18:49 kcranstn pnas does not coordinate with dryad. I already tried putting a dryad link in for the supplementary tables, and they want them uploaded
18:50 jar286 damn
18:50 jar286 bundle some of them into an excel or doc file?
18:50 kcranstn one table per file, one figure per file
18:51 kcranstn only one supplementary text file allowed (as PDF)
18:51 jar286 ouch.
18:52 kcranstn thoughts on cutting supplementary figure 3? (I’ll pass this by cody and stephen as well)
18:52 kcranstn or 2?
18:52 kcranstn or 1?
18:52 kcranstn I think we need 4-8
18:52 jar286 ahh, didn’t know whether all these tables and figures went with the main article, or with the supplement.
18:53 josephwb joined #opentreeoflife
18:53 jar286 so put some of the supplement’s tables/figures inline, so that they end up in the pdf you’re going to make?
18:53 kcranstn all of the tables and figures referenced here are supplemental: https://docs.google.com/document/d/1qq9VZccfPMG9Xic0wmp5BXMur98KrjXOY3-ZVuKzz1U/edit#
18:53 kcranstn and you can’t put them inline
18:53 kcranstn pnas builds the pdf from text + figures
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18:53 jar286 oh.   you said so (supplementary *text* file)
18:55 jar286 I say blow away supp fig 1
18:55 jar286 if the supp. depends on any information in it, turn it into prose
18:56 josephwb fig. 8
18:56 jimallman i’m staring at Figs. 3 & 4, to see if either stands alone. so far i really want them both. :(
18:56 kcranstn I think we need fig8 one to help define terms in the conflict section
18:57 kcranstn I agree with jar286 about fig 1
18:57 jimallman agreed that fig 1 could be expressed in words, but this is so much easier to follow.
18:57 jar286 the supplement is about methods, not architecture
18:57 kcranstn yeah, that’s my thought too
18:57 jimallman fig 2 is useful/important background, but doesn’t directly contribute to understanding methods, does it?
18:58 jar286 fig 2 has actual real information in it, I’d like to keep if poss, but it could go if necessary
18:58 jimallman true that
18:58 jimallman (real information, i mean)
18:59 josephwb fig. 3 is covered by other figures (6+7)
18:59 kcranstn that was my first instinct - to remove fig 3
19:00 kcranstn also getting opinion from blackrim
19:01 kcranstn this is so fun, submitting papers
19:02 kcranstn stephen votes fig1 off the island
19:03 kcranstn *goes off to delete poor figure 1*
19:04 josephwb stop
19:04 josephwb stephen was mixed up
19:04 josephwb he doesn't like fig. 3
19:04 josephwb (he thought fig. 3 was fig. 1)
19:04 kcranstn got it
19:04 kcranstn ok, deleteing fig 3
19:05 jar286 the google doc doesn’t have a fig 3.
19:05 jar286 be sure you agree on which fig of which you speak
19:05 kcranstn sure it does
19:05 kcranstn Figure 3. Diagram of synthesis of taxonomy and phylogeny. A. Taxonomy of 12 hypothetical species and a source tree combine in a synthesis with m and n monophyletic. B. Taxonomy of the same 12 species and a source tree combine in synthesis without m and n monophyletic.
19:05 jar286 oh, i see shares a page with 4
19:05 jar286 missed that
19:06 kcranstn thanks for the help, all!
19:12 josephwb i don't agree with that pnas authorship email, but will send it anyway to get this thing done. since we have to do this hoop-jumping anyway, should have considered a full re-ordering.
19:12 josephwb glad peter is included now, thgouh.
19:12 kcranstn thanks, josephwb
19:19 josephwb i have an R script which randomizes the middle 20 authors. many replicates seem closer to the "truth"
19:19 josephwb Hibbett is out of place, too (alphabetically)
19:19 jar286 oh no!
19:19 kcranstn in which doc?
19:19 josephwb the email you sent
19:20 josephwb never mind
19:20 josephwb tired eyes
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19:32 josephwb are the submission files put somewhere?
19:33 kcranstn I *just* pushed the button
19:33 kcranstn will put in google drive
19:34 josephwb ok
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20:34 josephwb i don't understand that no one cares about authorship order. sure, middle authorship doesn't mean very much (i.e. in terms of getting a job), but it is the principle of the thing.
20:35 jar286 personally I don’t think it’s a principle worth fighting for
20:35 jar286 I’ve always used alphabetical order, period, whenever I’ve been able to influence the order
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20:35 josephwb i see that in math journals, but in bio it is in order of contribution
20:36 jar286 bio is full of people who want nobel prizes
20:36 josephwb no, jobs
20:36 josephwb recognition of relative contribution
20:37 jar286 if you want a job, you should probably be first (or last) author, can’t imagine it matters much after that
20:37 josephwb that is true
20:38 josephwb but our field understands that author no. 3 contributed more than author no. 79
20:39 jar286 give job to Alice or Bob? well, Alice was a 3rd author, and Bob was a 4th, so Alice
20:39 jar286 if papers and order are so important I think people should publish more of them, with fewer authors
20:40 josephwb i'm not talking about jobs, but about honest reporting of contributions
20:40 josephwb yes, everyone should publish more papers
20:41 josephwb i just think it is funny that we are so "open" about every aspect of the project except this one
20:41 josephwb even if it doesn't matter in the grand scehem
20:42 jar286 what was not open?  openness and democracy aren’t the same
20:42 jar286 a decision had to be made, was the reasoning not aired? I don’t know
20:42 josephwb nope
20:42 josephwb never brought up among us mortals
20:43 jar286 oh well, you’ll have to bring it up with kc.  she should have responded if you had said something or asked
20:43 josephwb i did. she didn't.
20:45 jar286 what can I say.  I’m not in charge here. if you needed (or need) an advocate with rank that would have been stephen
20:46 josephwb openness would have a superscript for all middle authors with the footnote "these authors are listed in alphabetical order irrespective of relative contribution"
20:47 josephwb it is just unheard of in our field
20:47 jar286 grumble.  if they’re in alph order, and they are, then it’s obvious the order is not relative contribution. would be too much of a coincidence
20:47 josephwb hah
20:51 josephwb here is an example with more coauthors: http://www.biomedcentral.com/1471-2105/14/158/
20:52 josephwb i think i would rather be near the end of the list (reflecting my lack of contribution) than listed in alphabetical order; it takes away from people who did far more than i did.
20:53 josephwb anyway, nothing you can do, and you don't seem sold on it anyway. i am just venting.
20:54 jar286 maybe you need to go do some science, or else read some of those why-I-left-academia blog posts
20:55 jar286 I will agree that the system is very frustrating, and that having to pay attention to author order is demeaning
20:58 josephwb i think the system is fine and fair
20:59 jar286 slaving as a grad student for some prof, then endless postdocs, then an adjunct on food stamps?..
20:59 josephwb oh, that
21:00 jar286 if it weren’t so cutthroat, we wouldn’t have to worry about author order
21:06 josephwb i don't know. even if we were all comfortable enough to do science for the sake of science, i'd want it to be explicit who carried out the lions share. 1st and last mean something, but there are often more than 2 drivers.
21:06 jar286 the paragraph in the paper explaining who did what is much better than depending on author order communicating anything.
21:07 josephwb right
21:07 josephwb i would expect there to be a monotonic correlation
21:07 jar286 by paying attention to author order, you only reinforce those who pay attention to author order
21:22 josephwb every institution i've ever been a part of has had explicit guidelines on the topic of authorship. e.g. http://www.lsa.umich.edu/UMICH/eeb/Home/Internal%20EEB/fac_student_authorship_guidelines-9-15-08.pdf
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