Evolution and iEvobio conference notes


  • Jeremy Brown
  • Graham Slater
  • (Education Data Symposium)
  • Cecile Ane
  • Joe Felsenstein
  • Lars Schmitz
  • Carl Boettiger
  • Liam Revell
  • Brian O’Meara (Leithan McGonigle)


  • Marie-Josee Fortin
  • Emma Goldberg 10:45 rm 209
  • Networks Symposium
  • Jeremy Fox 1.30p Rm 201 (Adaptation B)
  • Schluter 2:15p Canada 2-3
  • Rosie Redfield public lecture


  • 9:00 Michael Landis, 203
  • 9:30 Dick Gumolkiowicz 214
  • 10:30 Dean Adams
  • 11 (Cavender-Bares, 214) (Bolnick, 213)
  • 11:30 Mark McPeek 214


  • Luke Harmon 9am rm 214
  • Luke Mahler 9am rm 210
  • Rafael Maia 9:15a rm 210
  • Sam Price 11:15a rm 210
  • Liam Revell 11:30 Canada 2-3
  • Dan Rabosky 2:30pm Canada 2-3
  • Tanja Stadler 3pm Canada 2-3
  • Chris Martin 3pm rm 213

Also: ievobio Day 1.


Sunday - Tuesday twitter notes

Grabbing my twitter-notes with R

Extracted with a few twitter commands

me <- userTimeline("cboettig", n=300)
me <- twListToDF(me)
evol2012 <- grep("#evol2012", me$text)
ievobio <- grep("#ievobio", me$text)
writeLines(con="evol2012.txt", me$text[evol2012])
writeLines(con="ievobio.txt", me$text[ievobio])

Should add some gsub commands to provide html markup. For the moment used vim:

:%s/@\([A-Za-z0-9_]\+\)/<a href="https:\/\/twitter.com\/\1">\1<\/a>/g

Tweet log

Wishing I had checked flight timezone earlier and not had to make hasty exit from #ievobio #whoops but #justmadeplane

You’re right of course! #oversimplified 5min RT @snacktavish “Why R? - 99% of people are already there.”- @cboettig. I disagree! #iEvoBio

J Sachs gives us ontology and semantics 101, & quoting the referees critique followed by many acronyms… owl ?= rdf #ievobio

.@BetaScience brings us back to phylogenetic tools, but plugs his #openscience by mentioning biotorrents https://t.co/NiRtPuIr #ievobio

RT @kcranstn: .@tjvision giving a shout-out to totalimpact https://t.co/RhGLCIry at #ievobio with @jasonpriem and @researchremix

Help @researchremix + @tjvision hypothesize why sharing public data results in increased citation rates: https://t.co/Ka5nTleU #ievobio

@neurocy definitely. I can’t stay for the +1 day, but maybe get those guys involved too

.@tjvision presents on “Data reuse and scholarly reward” study with @researchremix, discussing #PLoS paper https://t.co/iSyCRlkw #ievobio

@pete_cowman @LSU_FISH rm 214

and my lightening talk coming up! RT @rOpenSci: Hey #ievobio, @_inundata explained @rOpenSci at #rstats user group https://t.co/MgGYIYGS

@neurocy interesting idea! Could be very helpful both as a resource & a model of how to make these things mainstream science in diff fields?

sounds like many similar ideas are in hypothes.is RT @omearabrian: reputation seems to work well on #stackoverflow, imho #ievobio

@neurocy yup. but methods developers just took the 3 young investigator awards at main conference too… a promising sign?

@neurocy at least part of it is I think; on the informatics/developer side. Can only hope the rest of our community will follow.

RT @neurocy: @cboettig is the #ievobio community really as forward-thinking as you make it sound? you may as well be at a science 2.0 conf!

50-90%, some refs here: https://t.co/t8GA0Q5y RT @hlapp @omearabrian: peer review not limiting vol of papers – gets out eventually #ievobio

Whaley cites @mbeisen https://t.co/g7tnuxgu “Peer review is f**ed – let’s fix it" #ievobio

“That is why arXiv readers are eager to nav the raw

material, and value the accel avail over the filtering by the journal” Ginsberg #ievobio

Dan is founder of https://t.co/Py8JSR03 and an established web entrepreneur #ievobio

MT @kcranstn: download Whaley’s presentation, “Re-imagining peer review” at #ievobio https://t.co/orQBtzyz

@matstopel Hi! Yup: @RoseRedfield mentioned her open notebook and encouraged others, & Liam Revell mentioned his #ONS dev blog.

@hylopsar @phylorich sounds like “sometimes?” Don’t think is doing quasse+auteur with dens dep model + exp scaling on tree?

Stadler adapting her speciation-extinction models 2 SIR dynamics. Cool! but I missed what’s new here to the epi lit & can’t find the JTB pub

Stadler: “cannot explain high imbalance” #evol2012 wouldn’t an explanation require a non-Markovian branching model? / @jembrown

Tanja (Gernhard) Stadler gives Maynard Smith award talk also describing phylo methods in #rstats: TreePar. #evol2012 https://t.co/odxYnD0j

.@hylopsar @richfitz know if Rabosky’s BAMM is est. trait + speciation together (diversitree style?)

RT @hylopsar Rabosky: BAMM: RJMCMC to identify shifts in diversification models in trees (incl time/density dpdt, incomp samp) #evol2012

Yay for self-updating! RT @matstopel RT @rob_beiko: #ievobio Antonelli: goal is self-updating thingo that supports many downstream analyses

.@omearabrian has also cloned himself to speed up writing of datelife #ievobio (writes code from two computers nearly simultaneously)

who says #rstats can’t be a webserver? RT @rob_beiko: #ievobio O’Meara just got possessed by the R daemon, I think.

Datelife is running an #rstats server FastRWeb https://t.co/McBYogHl and https://t.co/6KDYtK8R on backend for computations #ievobio

Link to API documentation? RT @rob_beiko: #ievobio O’Meara: uses restful API, allows embargoed data with appropriate flag set / @rOpenSci

.@omearabrian Why not use https://t.co/lKICFiOm ? Not open software, not open data, forbids data mining. #ievobio. Use https://t.co/QSE9QO15

.#ievobio: @omearabrian: why do this? Because one of the most popular ways is just to make it up.

.#ievobio @omerabrian presents DateLife for the Challenge Entry on huge phylogenies. Check it out on https://t.co/IxJbAJoa

Liam’s dev blog is a kind of open lab notebook; a reference source for himself and the community #evol2012 #openscience https://t.co/iKaRJjhn

.#evol2012 #littleknownfact Liam has an active herp research program. (if he’s not replying on #r-sig-phylo in 20sec, he’s catching lizards)

Liam Revell gives the @ASNAmNat Young Investigator award, talking about “New phylo comparative methods” #evol2012

Price uses sgima^2/alpha ratio to estimate disparity, `cause alpha is better measure of phylo signal than lambda #evol2012 #verytrue

Sam Price https://t.co/L0PNq599 asks: do vertebrate eyes evolve slower than teeth? Phylo methods to compare rates across traits #evol2012

@phylorich @michaelbarton agreed – I think ecologists prefer the messy syntax of #rstats to the sterile whitespace of python! #ievobio

RT @michaelbarton: #bioinfsurvey python is the fastest growing in life sciences, while R is current most used. https://t.co/n3qo7Ufe #ievobio

@michaelbarton @hylopsar is being modest. folks I hear are raving about a nice presentation of so many cutting edge methods ;-)

Ree chooses #python, despite 99% of phylogenetics being in #rstats. Notes natural sciences/industry python is widespread #ievobio

Ree says current (& future) is in scripting. extensible. modular. API == #rstats. but needs more interactive & dynamic graphics. #ievobio

Ree describes evolution of phylo software: console (no GUI, no interaction) -> desktop app (GUI, interactive) -> scripting #rstats #ievobio

RT @hlapp: . @kcranstn: Remote participation using G+ hangouts worked quite well. #ievobio

A well-named team for working on front-end UI! RT @rob_beiko: #ievobio Cranston: five subgroups including my favorite, “shiny”

This time with targeted goals, worked well! RT @BrownJosephW: Phylotastic == lock a bunch of geeks in a room for 5 days. #evol2012 #ievobio

.#ievobio @kcranstn visit phylotastic on github: https://t.co/W7tHJTNw or check out the demos: https://t.co/FoZUWEyB #evol2012

@pleunipennings The OneZoom huge tree visualization? not up yet, will be at https://t.co/FB2XfO8T

.@hylopsar also uses musse approach to show these sexual color changes impact diversification rates #evol2012

Mahler used a mecca (stepwise AIC) approach to multi OU (ouch) model. #evol2012

.@hylopsar looks at evolution of irridescent colors in african starlings (using OUwie & pmc!)

Luke presents a mecca (stepwise AIC) approach to multi OU (ouch) model. #evol2012

Luke Mahler puts the replicated evolution story of the Anoles to the test: phylo analysis including weird taxa #evol2012

.@phylorich he omitted the error bars… still makes you wonder how far purely phylo approach to diversification can go… #evol2012

In a bonus slide in the Q&A, Mark shows each speciation event matched to a glaciation event #evol2012

McPeek’s synthesis of detailed community ecology, habitat, behavior, phylogenetics & evolution is mindblowing. #evol2012

Mark McPeek Macroevolutionary ecology: a tale of woe and intrigue in Damselflies of N America. Lake systems make replicate #evol2012 expts

The tree of millions of tips is, at it’s original scale, larger than the known universe. Feels like a flyby in Google earth. #evol2011

Rosindell: The Google Maps of the “Tree of Life” presented for the first time at #evol2012 zooming in with rich metadata

Dick Gomulkiewicz: a pop gen look at evolution’s impact on community assembly (well, invasion when rare) #evol2011

Cavender-Bares: Oaks are a “worst case scenario for the biological species concept” Coyne & Orr #evol2012

I don’t get it Dean. How do we pick units to compare evolution in widely different traits? #evol2012 constrained Cholesky doesn’t address?

Dean Adams packing the house at #evol2012; explores thorny question of comparing rates of evolution between different traits

See the nice model of Gomulkiewicz & colleagues here https://t.co/boPzbVBV #evol2012

Dick Gomulkiewicz brings a pop gen view to evolution on invasion “Evolution doesn’t always matter – that’s what the theory says” #evol2012

@jembrown How’d I miss this! Does Landis have software or pub on this work out yet?

@CMastication an Anolis grahami I’m told! Perhaps you are in Jamaica (where grahami is native) or Bermuda (where it is introduced)?

Who says you can’t publish #openaccess null results or replications of previous studies in @sciencemagazine? https://t.co/Z5f4j5oL #evol2012

Here comes @RosieRedfield #openscience punchline, calling the bluff of Science and sharing her work before July 26 embargo #evol2012

.@john_s_wilkins @ironlisa @Boraz exactly! as @RosieRedfield says, they reversed their thoughts on social media over this #evol2012 #irony

.#arseniclife authors used social media to promote– & still do: check out lead author Felisa’s views on this story too: @ironlisa #evol2012

RT @David_Dobbs: the #arseniclife saga continues to highlight and recast both problems & ops in scientific publishing and media. #evol2012