Microbiomes of the Built Environment NAS Meeting Webcast 4/11 10:30-5 EST
This study is intended to provide an independent, objective examination of the current state of science regarding built environment microbiomes and their impacts on human health, and then attempt to bridge gaps in moving this research to an application stage, in which building materials and architecture will be designed with microbiomes in mind. The study is being conducted by a committee of experts and the consensus report is expected to be released in 2017.The study’s first public meeting will be held on April 11, 2016 in Washington, DC. You may view the webcast of the public sessions, to be held from 10:30am – ...
Source: The Tree of Life - April 10, 2016 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs
Storify of talk by Robert Edgar at #UCDavis
[View the story "Robert Edgar at #UCDavis: not metagenomics, not humble, not open" on Storify]
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This is from the "Tree of Life Blog"
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.
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Source: The Tree of Life - March 31, 2016 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs
How to analyze next-gen DNA uptake data
We want to understand why competent Haemophilus influenzae cells take up some parts of H. influenzae chromosomes more efficiently than others. To this end, before Christmas the grad student reisolated preparations of DNA fragments of chromosomal DNA from strain 26-028NP (hence 'NP') that had been taken up by competent cells of the standard lab strain Rd. He sent these DNA samples to the former post-doc for sequencing (with the original 'input DNAs as controls). The post-doc has now sent us the sequencing data, and the grad student is going to analyze this, with two main goals:Determine how a DNA fragment's prob...
Source: RRResearch - March 30, 2016 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
If you want to go to a #manel or a #YAMMM check out Cold Spring Harbor Asia meetings - where men get to speak about stuff
I just got an email about this meeting: CSH Asia 2016 Conference on Microbial Communities in the Environment: Emerging Technologies and New Frontiers:So the first thing I did was to look at the gender ratio of speakers. I dug into each person listed here as much as a I could and attempted to infer what their gender is. I realize this is fraught with problems and have written about this previously. So as much as possible I looked for what pronouns were used to describe these people before infer their possible gender. I was unable to get any clear gendered pronouns for one person but the others I think...
Source: The Tree of Life - March 29, 2016 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs
Some notes on requesting for 700s for UC Admins ...
How to find form 700s for UC officials?This turns out to be simple yet slow and offline. Here is what I found from the UC Davis Counsel site.Accessing UC Davis RecordsIdentifying Records: To help us provide records promptly, please provide specific information about the records you seek including the record name, subject matter, author's name, date, office, or department that created the record.Time Deadlines: UC Davis has 10 days to determine if it will disclose the requested records. A limited 14-day extension may apply. If records cannot be provided within these deadlines, we will provide an esti...
Source: The Tree of Life - March 27, 2016 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs
Blast from the not so distant past - special issue of JMBE on Scientific Ethics
Discussions in Your Science Class Author: Kelly C. SmithCitation: Smith K. 2014. Ethics is not rocket science: how to have ethical discussions in your science class. J. Microbiol. Biol. Educ. 15(2):202-207 doi:10.1128/jmbe.v15i2.784DOI 10.1128/jmbe.v15i2.784[+] MORE Cautionary Tales: Ethics and Case Studies in Science Author: Clyde Freeman HerreidCitation: Herreid C. 2014. Cautionary tales: ethics and case studies in science. J. Microbiol. Biol. Educ. 15(2):208-212 doi:10.1128/jmbe.v15i2.761DOI 10.1128/jmbe.v15i2.761[+] MORE Infusing Bioethics into Biology and Microbiology ...
Source: The Tree of Life - March 25, 2016 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs
Occam’s Razor v. Noam Chomsky
Here’s a puzzle for you: Study the four sentences below and provide a rule that explains (a) why the first 3 are correct while the last one (marked with an *) is incorrect, and (b) why sometimes the reflexive pronoun (ending in –self/-selves) appears before its referent (underlined) and sometimes after:
Pete shot himself in the foot.
Speaking for himself at last, John proposed to Priscilla.
The picture of himself on the post office wall disturbed John quite a bit.
*Joan told me herself hates chocolate.
Shouldn’t that first sentence be as easy to explain as Pete shot Joe in the foot?
Maybe so, but generative...
Source: Babel's Dawn - March 22, 2016 Category: Speech Therapy Authors: Blair Source Type: blogs
Occam ’s Razor v. Noam Chomsky
< div xmlns="http://www.w3.org/1999/xhtml" > < p > < a class="asset-img-link" href="http://www.babelsdawn.com/.a/6a00d83452aeca69e201b7c8287f95970b-pi" style="display: inline;" > < img alt="William of Ockham" border="0" class="asset asset-image at-xid-6a00d83452aeca69e201b7c8287f95970b image-full img-responsive" src="http://www.babelsdawn.com/.a/6a00d83452aeca69e201b7c8287f95970b-800wi" title="William of Ockham" > < /img > < /a > < /p > < p > Here ’s a puzzle for you: Study the four sentences below and provide a rule that explains (a) why the first 3 are correct while the last one (marked with an *) is incorrect, and (b...
Source: Babel's Dawn - March 22, 2016 Category: Speech Therapy Authors: Blair Source Type: blogs
The #UCDavis Chancellor's Board Positions and the Need for a More Public, Open and Early Disclosure System
So, I assume by now many people out there have heard about the controversy going on at UC Davis over the board positions taken by the UC Davis Chancellor Linda Katehi. If you have not - here is a brief summary.In late February, Chancellor Katehi accepted a board position at the for profit educational company Devry but then steeped down after complaints. See for example this story by Diana Lambert in the SacBee for details. Note - she has admitted that her accepting of this position prior to getting approval from the UC President was a violation of UC policy.Chancellor Katehi received $420,000 in compensat...
Source: The Tree of Life - March 17, 2016 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs
Have Linguists Been Barking Up the Wrong Tree?
Inquiring into language’s origins can seem like a quixotic adventure, but it does bump you into the heart of the classical humanist question of what makes a human human. Two issues in particular stand out:
How much of language is cultural and how much inborn? This is a variant on the widespread dispute about nature or nurture, but it provides a specific focus. It does not seem unreasonable to think the question might have an answer.
Why is language so different from other animal communications? Animal signals are nothing like sentences, either in semantics, syntax, or vocabulary. Other animals do not discuss topics t...
Source: Babel's Dawn - March 16, 2016 Category: Speech Therapy Authors: Blair Source Type: blogs
Janelle Ayres talk at #UCDavis on host-microbe-microbiome interactions
[View the story "Janelle Ayres talk at #UCDavis on host-microbe-microbiome interactions " on Storify]
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This is from the "Tree of Life Blog"
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.
-------- (Source: The Tree of Life)
Source: The Tree of Life - March 13, 2016 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs
Time for #DegreeMadness - where we rank people's statements by what degrees they have not by science
[View the story "Time for #DegreeMadness - where we rank people's statements by what degrees they have not by science" 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. For short updates, follow me on Twitter.
-------- (Source: The Tree of Life)
Source: The Tree of Life - March 8, 2016 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs
Ready for sequencing?
I think I finally have the appropriate PCR fragments from my A. pleuropneumoniae mutants, to be sent for sequencing:I have 3 knockout mutants, removing the toxin, antitoxin and toxin+antitoxin segments (∆T, ∆A, and ∆TA respectively). I designed new 'S-up' and 'S-dn' primers to use with the original 'F' and 'R' primers amplify the segments on either side of the Spectinomycin-resistance cassette that's inserted at the sites of deletion. I need to check the sequences of these to be sure that the appropriate segments have been removed, and that the remaining gene is intact.I've successfully used these primers...
Source: RRResearch - March 6, 2016 Category: Molecular Biology Authors: Rosie Redfield Source Type: blogs
Conferences on Weekends? Good or Bad Idea? Summary of responses to query ..
Lots of fascinating and very useful response to a question I asked yesterday about conferences on weekends. When I wrote the post I had a personal point of view - that conferences on weekends were bad. But I knew I had heard many others argue that it was better for some people to have them on weekends and I thought it might be good to hear what people thought. So I made a Storify of the responses so far. [View the story "Conferences on Weekends? Good or Bad Idea?" on Storify]I also got some good responses on Facebook.Some of the themes so far are discussed below:Many factors come into play includingJob typeFina...
Source: The Tree of Life - March 5, 2016 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs
Case Study - what to do when there are disagreements about whether a paper has problems
In light of the ongoing PLOSOne #Creationgate controversy (e.g. see this write up here), I thought I would share a story I have been working on about a case where there are disagreements about whether a paper has problems or not.So I got this email the other day. It was from an author of a paper who I know who was upset about a paper that was published a while back for which I was the editor. This person wrote to me and the authors of the new paper somewhat angrily critiquing them for some aspects of their paper that related to this person's work. The authors responded to the critique and, well, did not agree with the p...
Source: The Tree of Life - March 4, 2016 Category: Microbiology Authors: Jonathan Eisen Source Type: blogs
