Wrap up of talk by Rich Lenski at UC Davis

Feed: The Tree of Life

Rich Lenski gave a talk today at UC Davis - part of a two talk series. This was a presentation more for the public and tomorrow he gives one more for the science crowd. Today's talk was a really nice overview of Lenski's work on long term evolution experiments in E. coli. I made a Storify of the tweets about the talk: [View the story "Talk by Rich Lenski @relenski at #UCDavis on LTEE - long term evolution experiment " on Storify]
This is from the "Tree of Life Blog"
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis.

Does context alter the dilution effect?

Feed: The EEB and flow

Understanding disease and parasites from a community context is an increasingly popular approach and one that has benefited both disease and ecological research. In communities, disease outbreaks can reduce host populations, which will in turn alter species' interactions and change community composition, for example.

Journal Club at #UCDavis on Co-evolution of Microbiomes and Hosts - ideas wanted

Feed: The Tree of Life

I am going to be running a journal club this quarter at UC Davis for the Population Biology Graduate Group.  The topic is Co-evoution of Microbiomes and Hosts.Meeting time is 12:10-1:00 PM if you want to participate let me know.A link to the Draft Outline is here. And I am trying to embed it in this post ...     If anyone has other ideas for interesting papers on co-evolution of microbiomes and hosts, please let me know and I will add them to the list. Stay tuned as each week I will post about the discussion topics and notes from the discussions.

Visualising big phylogenies (yet again)

Feed: iPhylo

Inspired in part by the release of the draft tree of life (doi:10.1073/pnas.1423041112 by the Open Tree of Life, I've been revisiting (yet again) ways to visualise very big phylogenies (see Very large phylogeny viewer for my last attempt). My latest experiment uses Google Maps to render a large tree.

Post at Oikos + why do papers take so long?

Feed: The EEB and flow

This is mostly a shameless cross-post to a blog post I wrote for the Oikos blog. It's about an upcoming paper in Oikos that asks whether beta-diversity null deviation measures, which originated in papers like Chase 2010 and Chase et al. 2011, can be interpreted and applied as a measure of community assembly. These measures were originally used as null models for beta-diversity (i.e. to control for the effects of alpha diversity, etc), but increasingly in the literature they are used to indicate niche vs. neutral assembly processes.

Towards an interactive web-based phylogeny editor (à la MacClade)

Feed: iPhylo

Currently in classes where I teach the basics of tree building, we still fire up ancient iMacs, load up MacClade, and let the students have a play. Typically we give them the same data set and have a class competition to see which group can get the shortest tree by manually rearranging the branches. It’s fun, but the computers are old, and what’s nostalgic for me seems alien to the iPhone generation. One thing I’ve always wanted to have is a simple MacClade-like tree editor for the Web, where the aim is not so much character analysis as teaching the basics of tree building.

On having multiple DOI registration agencies for the same journal

Feed: iPhylo

On Friday I discovered that BHL has started issuing CrossRef DOIs for articles, starting with the journal Revue Suisse de Zoologie. The metadata for these articles comes from BioStor. After a WTF and WWIC moment, I tweeted about this, and something of a Twitter storm (and email storm) ensued: .@BioDivLibrary WTF?! When did #bhlib start minting DOIs for articles ("parts") e.g. +1, but a little heads up maybe— Roderic Page (@rdmpage) September 11, 2015 To be clear, I'm very happy that BHL is finally assigning article-level DOIs, and that it is doing this via CrossRef.

Throwing "like a girl"

Feed: Evolutionary Novelties

A recent exchange arose when a scientist used the phrase "throws like a girl" on twitter. I had a conversation about this very recently, and so I was inspired to record that interaction here. The upshot is that I was surprised to find out that there is a lot of scientific literature about the differences in throwing ability between males and females. This got me thinking about the question of when political correctness could go too far.I play and coach a lot of baseball and I have an interest in the origins of baseball.

Roundup of microBEnet posts of (possible) interest

Feed: The Tree of Life

I spend a decent amount of my blogging time these days writing posts for microBEnet (the microbiology of the built environment network) which is part of a project funded in my lab by the Sloan Foundation.Some recent posts that may be of interest are listed below:2015-09-11Another blast from the past: Simple fools guide to PCR v12015-09-10Gates Foundation seeking proposals on Characterizing and Tracking Antimicrobial Resistance2015-09-09“A diversity of gifts”: article about the MBL Microbial Diversity courseThe White House Webcast on Citizen Science and Crowdsourcing 9/302015-09-08Another impor

Possible project: natural language queries, or answering "how many species are there?"

Feed: iPhylo

GoogleGoogle knows how many species there are. More significantly, it knows what I mean when I type in "how many species are there". Wouldn't it be nice to be able to do this with biodiversity databases? For example, how many species of insect are found in Fiji? How would you answer this question? I guess you'd Google it, looking for a paper.

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