Playing around with Paper.Li. Took feeds from the blogs and Twitter profiles of people in my lab. Seems to come out OK … http://widgets.paper.li/javascripts/sr.embeddable.js Paperli.PaperFrame.Show({ id: ‘6f0c6ad8-8b14-41e0-b46a-1a7592d3eadb’, width: 390, height: 480, background: ‘#ECECEC’, borderColor: ‘#DDDDDD’ })
Category: Misc.
Lake Arrowhead Microbial Genomes Meeting 2012 Speaker Gender Ratio #LAMG12
- Jeffrey H. Miller
- Jonathan Eisen
- Ashlee Earl
- Lisa Raleigh
- Jonathan Eisen
- Nina R. Salama
- Frederic Bushman
- Kristine Wylie
- Janet K. Jansson
- Forrest Rohwer
- Curtis Huttenhower
- Tanja Woyke
- Maomeng Tong
- Jeffrey Cox
- Susannah Tringe
- Julian Parkhill
- Rustem F. Ismagilov
- Gautam Dantas
- Pamela Yeh
- Mike Gilmore
- Lance B. Price
- James Meadow
- Jason E. Stajich
- Laura Sauder
- Tara Schwartz
- Susanna Remold
- Bernhard Palsson
- Anca Segall
- Trent Northern
- Rick Morgan
- Beth Shank
- Morgan Langille (added)
- Anthony Fodor (added)
- Peter Karp
- Tatiana Tatusova
- Timothy Harkins
- Katrine Whiteson
- Mallory Embree
- Varum Mazumdar
- Abigail McGuire
- Ee-Been Goh
- Shota Atsumi
- Howard Xu
So 37 39 speakers, 16 of which are women. So that comes to 43.2 41%.
Storify for Lake Arrowhead Microbial Genomes #LAMG12 Meeting
Meeting went well. Here is a storification of it:
http://storify.com/phylogenomics/lake-arrowhead-microbial-genomes-2012-lamg12.js?template=slideshow[View the story “Lake Arrowhead Microbial Genomes 2012 #LAMG12” on Storify]
Fun science art example: Jennifer Welsh on Zachary Copfer glowing microbe drawings
Microbiology art pops up again. This time in this story from Jennifer Welsh: Galaxies And Faces Drawn With Glowing Bacteria – Business Insider . For more see the artist Zachary Copfer’s website here: http://sciencetothepowerofart.com. Other stories about Copfer are popping up too – not sure if their is some publicity blitz going on or not but see below for examples:
- Bacteriograph: Photographs Printed with Bacterial Growth
- Zachary Copfer Blends Bacteria And Photography In Bacteriography …
- These Incredible/Gross Photos Were Printed With E. Coli Bacteria
- Here’s one I’ve grown earlier: Scientist-turned-artist uses bacteria to ..
- “Bacteriografia”: artista cria retratos de cientistas famosos utilizando …
A must read for those interested in "Spin" of science by press releases & in papers
A new paper in PLoS Medicine is of great interest to me: PLOS Medicine: Misrepresentation of Randomized Controlled Trials in Press Releases and News Coverage: A Cohort Study. Bad press releases drive me crazy. And it has been shown that press releases can frequently be a source of scientific misinformation in the press. Interestingly this paper concludes that spin in the papers themselves is correlated to spin in press releases … So in other words, the scientists are partly to blame … Not shocking but interesting …
Quick post: nice #openaccess review: Insights from Genomics into Bacterial Pathogen Populations
Just a quick post here. There is a new review/commentary that may be of interest: PLOS Pathogens: Insights from Genomics into Bacterial Pathogen Populations. By Daniel Wilson from the Wellcome Trust Centre at Oxford.
Full citation: Wilson DJ (2012) Insights from Genomics into Bacterial Pathogen Populations. PLoS Pathog 8(9): e1002874. doi:10.1371/journal.ppat.1002874
It is a nice and useful review …
Some quick comments on "Giant viruses coexisted w/ the cellular ancestors & represent a distinct supergroup"
Got asked on Twitter about this paper:
Hmm… @carlzimmer @phylogenomics? Weigh in?RT @diana_yates_: Study of giant viruses shakes up the tree of life:bit.ly/NqLX2u
— Ed Yong(@edyong209) September 13, 2012
//platform.twitter.com/widgets.js I answered briefly
@edyong209 @carlzimmer @diana_yates_ very unconvincing; no taxa in trees; no evidence FSF useful marker; Fig 3 strange; data not released ..
— Jonathan Eisen (@phylogenomics) September 13, 2012
//platform.twitter.com/widgets.js Don’t have time for a detailed blog post but here are some quick comments:
1. Giant viruses are fascinating and cool
2. I have done work connected to the topic of this paper and thus might not be considered fully objective. For example see
- Stalking the Fourth Domain in Metagenomic Data: Searching for …
- The challenge of microbial diversity: Out on a limb : Nature News
- Glimpses of the Fourth Domain? | The Loom | Discover Magazine
- The Tree of Life: The story behind the story of my new #PLoSOne …
UPDATE 9/19 – some prior stories about the “fourth domain” and ancient viruses – to counter notion in the press release for this paper that their findings “shake up the tree of life”. Even if their specific inferences about viral evolution are correct, such inferences / conclusions have been made before.
- The ancient Virus World and evolution of cells
- Viruses take center stage in cellular evolution
- Redefining viruses: lessons from Mimivirus
- Structural co-evolution of viruses and cells in the primordial world
- The 1.2-megabase genome sequence of Mimivirus
- The Science Breakthroughs That 2011 May Bring – FoxNews.com
- A new domain of life: Plenty more bugs in the sea | The…
- Did DNA Come From Viruses?
- Megavirus May Be Stripped-Down Version of Normal Cell |…
- The Birth of the Nucleus | Science/AAAS
NASA personnel ignore planetary protection guidelines and risk putting microbes on Mars
Many years ago I served on a NASA sponsored committee for a series of meetings about the handling of samples collected from Mars. One of the key points of discussion at those meetings was “planetary protection”. The involved protecting Earth from possibly strange life forms that in theory could exist on Mars. And it also involved protecting Mars from microbes and other life forms that could come from space ships/landers. I even posted all the materials from these meetings a few weeks ago: Notes and materials from MARS Sample Handling Workshops 2000 ….
It is thus with great distress that I read an LA Times article that reveals that some of the people involved in launching Curiosity decided to ignore some of the planetary protection guidelines and made some hands on modifications that may have contaminated some of the drill bits on Curiosity with microbes from people. See: If the Mars rover finds water, it could be H2 … uh oh! – latimes.com.
The LA Times reports that some NASA personnel opened a box of drill bits that had been sterilized and – in clean but not sterile conditions – installed one of these drill bits in a drill on Curiosity prior to launch. Apparently they were worried that a rough landing could prevent the bits from being installable in the drill which would make the drill not be of any use. And they appear to have now risked the sterility of the entire operation by doing this. Well crap. That just plain sucks. So much effort by “planetary protection officers” and others. That effort might all go down the drain because of this. I get that some times things seem urgent and that sure – if the drill was useless people would be pretty upset too. But this seems to me to be a serious error in judgement.
In a small way I helped develop the guidelines that were put in place to protect Mars from human induced contamination. And now that seems to have been a wasted effort as the guidelines were ignored. Not good.
Note – for those interested I have posted links below to the documents from my days at the NASA Mars Sample Handling Workshops. Most/all are public domain materials but not all are easy to find so I thought I would post them here. Note – I have done no clean up of scans – will do so at some point. Enjoy
- MSHP Workshop 1 handout
- MSHP Workshop 1 letter
- MSHP Workshop 1 Notes
- MSHP Workshop 1 report
- MSHP Workshop 1 report slides
- MSHP Workshop 1 self scan
- MSHP Workshop 2 agenda
- MSHP Workshop 2 agenda2
- MSHP Workshop 2 handout
- MSHP Workshop 2 letter
- MSHP Workshop 2 letter2
- MSHP Workshop 2 Notes
- MSHP Workshop 2.invite
- MSHP Workshop 3
- MSHP Workshop 4
- Report-Biological Containment of Mars
- Report-Comprehensive Protocol for Lunas Sampling Lab
- Report-Effect of sterilization
- Report-Mars Sample Return
- Report-Size limits very small microbes
- MSHARP
- MSHP Fax 2-28-2000
- MSHP Letter 3-9-2000
- MSHP RummelLetter 8-26-02
- Scientists fear Curiosity rover drill bits could contaminate Mars
- Hey, Curiosity scientists, didn’t you see ‘Alien’?
Q-Bio conference in Hawaii, bring your surfboard & your Y chromosome b/c they don’t take a XX
Wow. Just wow. And not in a good way. Just got an email invitation to a meeting. The meeting is
“THE FIRST ANNUAL WINTER Q-BIO MEETING: Quantitative Biology on the Hawaiian Islands. February 18-21, 2013.”
“brings together scientists and engineers who are interested in all areas of q-bio.”
“Each year, the meeting will rotate on the Hawaiian Islands with a different thematic focus within q-bio.”
“The focus for the meeting this year will be Synthetic Biology, with about half of the invited speakers chosen as renowned experts in this area.”
2013 CONFIRMED SPEAKERS:
- Jim Collins, Boston University
- Johan Elf, Uppsala University
- Michael Elowitz, California Institute of Technology
- Timothy Elston, UNC Chapel Hill School of Medicine
- James E. Ferrell, Stanford University
- Martin Fussenegger, ETH Zurich
- Leon Glass, McGill University
- Terry Hwa, University of California, San Diego
- Roy Kishony, Harvard Medical School
- Galit Lahav, Harvard University
- Andre Levchenko, Johns Hopkins University
- Wendell Lim, University of California, San Francisco
- Andy Oates, The Max Planck Institute, Dresden
- Bernhard Palsson, University of California, San Diego
- Gurol Suel, UT Southwestern Medical Center
- Chao Tang, Peking University
- John Tyson, Virginia Tech
- Craig Venter, The J. Craig Venter Institute
- Chris Voigt, Massachusetts Institute of Technology
- Ned S. Wingreen, Princeton University
CONFERENCE ORGANIZERS:
- Bill Ditto, University of Hawaii
- Jeff Hasty, UC San Diego
- Bill Hlavacek, University of New Mexico
- Alex Hoffmann, UC San Diego
- Brian Munsky, New Mexico Consortium
- Lev Tsimring, UC San Diego
For other posts on this topic see
- Posts tagged women in science
- The Tree of Life: Diversity (of speakers, participants) at meetings: do …
- The Tree of Life: A conference where the speakers are all women?
- A conference where the speakers are all women? (with tweets – Storify
- “Genomics: the Power and the Promise” meeting – could be called “Men Studying Genomics” instead
- The Tree of Life: Overselling genomics (and men) award #3 …
UPDATE – I have now submitted an abstract to the meeting. The abstract I submitted is available here and posted below
n = NP = number of participants
k = f = the number that are female
p = percentage of f in population being sampled
UPDATE 2: Here is the full email I received, just for the record
ABSTRACT SUBMISSION DEADLINE 09/15/12http://w-qbio.org/abstracts.html
THE FIRST ANNUAL WINTER Q-BIO MEETING
Quantitative Biology on the Hawaiian Islands
February 18-21, 2013http://w-qbio.org/
The Winter q-bio meeting brings together scientists and engineers who are interested in all areas of q-bio. Each year, the meeting will rotate on the Hawaiian Islands with a different thematic focus within q-bio. The focus for the meeting this year will be Synthetic Biology, with about half of the invited speakers chosen as renowned experts in this area.
SPONSORED BY:UC San Diego’s Division of Biological Sciences and BioCircuits Institute
San Diego Center for Systems Biology
University of Hawaii
Office of Naval Research
2013 CONFIRMED SPEAKERS:
Jim Collins, Boston University
Johan Elf, Uppsala University
Michael Elowitz, California Institute of Technology
Timothy Elston, UNC Chapel Hill School of Medicine
James E. Ferrell, Stanford University
Martin Fussenegger, ETH Zurich
Leon Glass, McGill University
Terry Hwa, University of California, San Diego
Roy Kishony, Harvard Medical School
Galit Lahav, Harvard University
Andre Levchenko, Johns Hopkins University
Wendell Lim, University of California, San Francisco
Andy Oates, The Max Planck Institute, Dresden
Bernhard Palsson, University of California, San Diego
Gurol Suel, UT Southwestern Medical Center
Chao Tang, Peking University
John Tyson, Virginia Tech
Craig Venter, The J. Craig Venter Institute
Chris Voigt, Massachusetts Institute of Technology
Ned S. Wingreen, Princeton University
CONFERENCE ORGANIZERS:
Bill Ditto, University of Hawaii
Jeff Hasty, UC San Diego
Bill Hlavacek, University of New Mexico
Alex Hoffmann, UC San Diego
Brian Munsky, New Mexico Consortium
Lev Tsimring, UC San Diego
***REGISTRATION NOW OPEN***
Registration fee covers conference venue, opening reception, banquet, coffee & snacks.
EARLY BIRD ($450.00) REGISTRATION DEADLINE: December 1, 2012
REGULAR REGISTRATION ($550) DEADLINE: February 5, 2013
REGISTER NOW: http://w-qbio.org/abstracts.html
HOTEL: A block of rooms have been reserved for registered conference participants available for a negotiated rate of $199 per night at the Hilton Hawaiian Village in Waikiki. The rooms are available on first come first serve basis and will be available soon, so book early!
CONTRIBUTED TALKS: If you wish to present your work at the conference, either as an oral talk or a poster, you must submit an abstract through the conference website by the September 15th deadline. Abstract guidelines and submission information at:http://w-qbio.org/guidelines.pdf
ABSTRACT DEADLINE: September 15, 2012
Accepted abstracts will be announced October 31, 2012.
We encourage you to forward this message to any colleagues that may be interested in taking part in this exciting event.
Questions should be emailed to: coordinator@w-qbio.org
UPDATE 3: (9/18/2012)
Some comments/responses about my post or related posts
UPDATE 4: (9/18/12)
Plus some links that may be of relevance
- MOVING TOWARD FACULTY GENDER EQUITY AT UC
- Sex and Science: How Professor Gender Perpetuates the – Economics
- Engineering gender parity – – The Washington Post
- Why do so few women speak at science meetings? : Article : Nature
- Patching a leaky pipeline.
- Review Gender inequity: challenging business as usual.
- Swinging pendulums.
- Science gender gap probed.
UPDATE 5: 9/19/12
Some more links of relevance
UPDATE 6: 9/23/12
Some more links on the recent PNAS paper on gender bias and evaluating scientists
- Scientists, Your Gender Bias Is Showing | Cosmic Variance …
- New study shows gender bias in science against female students …
- Smoking Gun on Sexism?
- Science Confirms The Obvious: Science Faculty Think Female …
UPDATE 7: 9/23/12
UPDATE 9: Other posts on gender bias of interest
UPDATE 10: 11/21/13
http://w-qbio.org/abstracts/
UPDATE: In response to participant interest, the submission deadline has been extended to December 2, 2013. This year 15 contributed talks will be selected from the submitted abstracts to be presented with the invited talks during the plenary sessions. Contributed talks will also be selected for parallel breakout sessions which commence in the late afternoon.
THE SECOND ANNUAL WINTER Q-BIO MEETING
Quantitative Biology on the Hawaiian Islands
February 17-20, 2014
http://w-qbio.org/
The Winter q-bio meeting brings together scientists and engineers who are interested in all areas of q-bio. The venue for 2014 is the Hilton Waikoloa Village, which is located on the Kohala Coast of Hawaii’s Big Island. The resort lets you experience breathtaking tropical gardens, abundant wildlife, award-winning dining, world-class shopping, art and culture, and an array of activities. The Island of Hawaii is the youngest and biggest in the Hawaiian chain, providing a vast canvas of environments to discover–home of one of the world’s most active volcanoes (Kilauea), the most massive mountain in the world (Maunaloa), and the largest park in the state (Hawaii Volcanoes National Park).
SPONSORED BY:
UC San Diego BioCircuits Institute and the San Diego Center for Systems Biology
The University of Hawaii at Manoa
UC San Diego Divisions of Biological Sciences and Engineering
The Office of Naval Research
2014 CONFIRMED SPEAKERS:
Naama Barkai, The Weizmann Institute of Science
Sangeeta Bhatia Massachusetts Institute of Technology
Hana El-Samad, University of California, San Francisco
Zev Gartner, University of California, San Francisco
Taekjip Ha, University of Illinois
Shigeru Kondo, Osaka University
Arthur Lander, University of California, Irvine
Andrew Murray, Harvard University
Steve Quake, Stanford University
Petra Schwille, Max Planck Institute
Christina Smolke, Stanford University
Aleksandra Walczak, Laboratoire de Physique Théorique
CONFERENCE ORGANIZERS:
Kevin Bennett, University of Hawaii at Manoa
William Ditto, University of Hawaii at Manoa
Hana El-Samad, University of California, San Francisco
Jeff Hasty, University of California, San Diego
Alexander Hoffmann, University of California, San Diego
Galit Lahav, Harvard University
Eva-Maria Schoetz-Collins, University of California, San Diego
Chao Tang, Peking University
Lev Tsimring, University of California, San Diego
***REGISTRATION NOW OPEN***
Registration fee covers conference venue, registration reception, banquet, coffee & snacks.
EARLY BIRD REGISTRATION ($500/$425 Student) DEADLINE: December 20, 2013
REGULAR REGISTRATION ($600/$525 Student) DEADLINE: January 31, 2014
LATE REGISTRATION ($675/$600 Student) After January 31, 2014
REGISTER NOW: http://w-qbio.org/
HOTEL: A block of rooms has been reserved for registered conference participants at a negotiated rate of $199 per night at the Hilton Waikoloa Village. The rooms will be available soon on a first-come, first-served basis, so book early!
CONTRIBUTED TALKS: If you wish to present your work at the conference, either as an oral talk or a poster, you must submit an abstract through the conference website by the November 5th deadline. Abstract guidelines and submission information at: http://w-qbio.org/abstracts/
ABSTRACT DEADLINE: EXTENDED UNTIL MONDAY, December 2, 2013 (Extended due to large volume of interest!)
Accepted abstracts will be announced by December 6, 2012. You may submit your abstract now and if accepted, still register by the early bird registration deadline of December 20, 2013.
Abstract guidelines and submission information at: http://w-qbio.org/abstracts/
We encourage you to forward this message to any colleagues that may be interested in taking part in this exciting event.
Questions should be emailed to: coordinator@w-qbio.org
Hmm .. apparently I am not supposed to be posting about #UCDavis in "social media" (SEE UPDATE AT BOTTOM)
At the suggestion of a colleague I have been browsing through the UC Davis Policy and Procedure Manual – Chapter 310, Communications and Technology Section 40, University Communications: Publications, Graphic Standards, Marketing, and Media Relations.
Much of it is straightforward but much of it seems to basically be discouraging any direct social media posts or interaction with the press. See for example:
The News Service unit in University Communications is the exclusive source for developing and disseminating news about UC Davis to the general public via newspapers, radio, television, magazines, and the World Wide Web, including social media and related channels. The News Service unit determines the newsworthiness of significant developments and activities in academic research; administrative programs; accomplishments of faculty, staff, or students; events; and other campus matters. It conducts or coordinates direct contact with news media representatives, and assures that media relations are timely, accurate, comprehensive, and of broad public interest.
and
Generally, the news media will contact the News Service to find a source for a story. If a reporter contacts a source directly, that faculty member, staff member, or student shall notify the News Service
I’m replying directly and publicly as an expression of transparency, and professional respect for you.
You indeed misinterpret the policy. It was, and is, intended to optimize coordination with the media – not, as is inferred by your post, to inhibit anyone. Coordination, by the way, is as beneficial to the media as anyone. They appreciate knowing their go-to points of contact. That said, reporters contact faculty, staff and students without interference or inhibition. All the time.
It may be that this policy fails to clarify or contemporize the distinction between “reporters” and social media content creators, including bloggers. If so, we will take a look at it; I’d welcome your input.
But let me be clear: as you well know, many university constituents actively blog, tweet, post, opine. (I’m among them.) In this age, it is an important ingredient in telling our story. The policy is not intended to discourage that




