The Tree of Life

Notes from my trip to #AAASMtg #EarthMicrobiomeProject #Storify

2012-02-22T23:02:00.001-08:00

I am hoping to write up some more notes from my trip to the AAAS meeting in Vancouver. But for now these pics and this Storification of tweets and related posts will have to do ...

Slideshow version of Storification

Second video of the week: Mackenzie Smith on Open Licenses

2012-02-22T16:43:00.001-08:00

Video of the week: Rosie Redfield on the Arsenic Life story #ILoveRosie

2012-02-22T16:40:00.002-08:00

Interesting piece by John Rennie at Smartplanet: What comes after antibiotics?

2012-02-22T07:39:00.000-08:00

Interesting piece by John Rennie at Smartplanet: What comes after antibiotics? | SmartPlanet. It discusses a variety of topics including antiomicrobial peptides, nanotechnology, Kary Mullis, Michael Zasloff, DARPA, Maryn McKenna, and more. Definitely worth checking out.

Notes for talk by Mackenzie Smith - candidate for #UCDavis University Librarian position

2012-02-21T18:11:00.000-08:00

Here are some notes I took using my iPAD for a talk by Mackenzie Smith about libraries: Note Feb 21, 2012.

She is a candidate for the UC Davis University Librarian position for which I am on the committee. This is the first time I have taken and posted notes from a talk using my iPAD - so please bear with me - it is an experiment of sorts. Note to do this I used an iPAD2, a Bamboo Stylus and the Notability App. I then exported to PDF and posted it (the Note above). For the images below I then had to export single pages to JPGs. If anyone knows an easy way to export a multipage PDF as a single JPG I would appreciate information ... Inspiration provided by Kosta.

Antibiotic use in animals (may) lead to superbugs in people #mBIO

2012-02-21T13:43:00.001-08:00

New paper in mBIO of potential interest from Lance Price et al.: Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock. For those not in the know, mBIO is a relatively new Open Access journal from the American Society for Microbiology. The paper discusses genomic studies of MRSA which has led the authors to conclude that antibiotic use in animals may contribute to the rise and spread of superbugs in people.

From here. Maximum-parsimony tree of the 89 CC398 isolates (including ST398SO385) based on 4,238 total SNPs, including 1,102 parsimony-informative SNPs with a CI of 0.9591. Clades and groups of importance are labeled in a hierarchical fashion to facilitate description in the text. The tree was rooted with clade I based on an iterative selection process that identified this group as the most ancestral (see Materials and Methods). COO, country of origin; AT, Austria; BE, Belgium; CA, Canada; CH, Switzerland; CN, China; DE, Germany; DK, Denmark; ES, Spain; FI, Finland; FR, France; GF, French Guiana; HU, Hungary; IT, Italy; NL, The Netherlands; PE, Peru; PL, Poland; PT, Portugal; SI, Slovenia; US, United States; P, pig; H, human; R, horse; T, turkey; B, bovine; MET, methicillin susceptibility; R, resistant; S, susceptible.

The figure above is the only figure in the main text of the paper. There are others in supplemental information which seems a bit strange to me - why put anything in supplemental information when the paper is only released online? Or at least have thumbnail images for all figures in the main text ...

Anyway, the paper and press release got picked up by many newsy places. See for example:

Pig-to-Human 'Superbug' May Be Due to Animal Antibiotics (US News)
MRSA Staph Strain Developed Drug Resistance in Your Burger (US News)
How Using Antibiotics In Animal Feed Creates Superbugs (NPR blog)
MRSA in Livestock May Spread to Humans (ABC news)
Staph Turns into Drug-Resistant Superbug on Farms (SciAm blog)

I note - the Press Release is MUCH better than the last one that was about a paper by Price that I wrote about here: The Tree of Life: #PLoSOne paper keywords revealing: (#Penis #Microbiome #Circumcision #HIV); press release misleading ... Lance was awesomally quick to respond to my complaints about that PR. The PR for this paper is not so bad --- a bit over the top in some of the quotes - but no need for comments I think.

Citation:

Price LB, et al. 2012. Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock. mBio 3(1):e00305-11. doi:10.1128/mBio.00305-11.

UPDATE 2/21 5:30 PM: an alternative (and much more pleasing) press release from ASM is here.

Slideshow w/ audio of my talk on "A Field Guide to the Microbes" from the AAAS Meeting #AAASMtg

2012-02-21T00:11:00.002-08:00

I recorded the audio of my talk on "Towards a field guide to the microbes" from the AAAS meeting on Saturday AM. Here is a slideshow of the talk with audio synched to the slides (I did this using Keynote on a Mac with the "record Slideshow" function).

My slides from the talk are available at Slideshare.

Jack Gilbert @gilbertjacka clarifies comments at #AAASMtg re: opening windows, cleanliness & microbes

2012-02-20T16:16:00.001-08:00

Just got this to post from my college Jack Gilbert in regard to some comments he made to the press at the AAAS Meeting a few days ago. He sent this in part in response to some news stories that came out of the press conference we had at the meeting (e.g., see Florence Nightingale approach 'could help fight infection in ..., Open hospital windows to stem spread of infections, says ... and others). And I encouraged him to consider whether or not he needed to clarify some of his comments - and here is his response.

A confession, lesson and retraction
By Jack A. Gilbert

At the AAAS 2012 annual meeting on Friday, I was involved in a press conference to announce the initial results and ideology for the Earth Microbiome Project (http://www.earthmicrobiome.org). Following the press conference we went to another room, where we were openly discussing these concepts with the reporters. Several reporters asked me to comment on the potential impact of this research in the medical sphere. At which point I started to discuss some excellent research by Jessica Green (http://biology.uoregon.edu/people/green) regarding her recent evidence that improved ventilation in hospital wards reduced the airborne abundance of organisms that were related to pathogens. I showed these reporters the paper
(http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej2011211a.html) and asked them to discuss this with Jessica Green.

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w/o a doubt the best aspect of #AAASmtg - giving my kids science schwag #GoScience

2012-02-19T19:41:00.001-08:00

Here we go again: discouraging PR #SPAM by posting them pre-embargo: Here's one about smokeless tobacco #AAASMtg

2012-02-18T06:32:00.000-08:00

Just received this in my email. As I have said before (The Tree of Life: How to stop press release spam? Post embargoed press releases) I am sick of getting unsolicited press releases that are embargoed and do not have any relevance to my work. They are SPAM. And to discourage this practice I am posting them to my blog when I receive them in order to break their embargo which I did not agree to. Please - all of you out there sending out unsolicited PR SPAM - stop it. Stop it. Stop it.

EMBARGOED TO 6 P.M. EST, SATURDAY, FEB. 18, 2012
(3 P.M. PST, SATURDAY, FEB. 18, 2012)
Contact: Jill Scoggins, 502-475-2428, jill.scoggins@louisville.edu

UofL RESEARCH SHOWS SUBSTITUTING WITH SMOKELESS TOBACCO SAVES LIVES
Presentation at AAAS shows scientific foundation for tobacco harm reduction efforts

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Results of #UCDavis Faculty Resolutions released re: Katehi, Pepper Spray, #OccupyUCDavis

2012-02-17T20:43:00.000-08:00

Just received the three emails below regarding results of three UC Davis Faculty Senate Resolutions regarding the pepper spray incident from November and thought they might be of some interest. See this post for a little background.

REPORT OF THE DAVIS DIVISION OF THE ACADEMIC SENATE COMMITTEE ON ELECTIONS, RULES AND JURISDICTION

On December 20, 2011, a petition bearing the signatures of at least 50 members of the Davis Division of the Academic Senate of the University of California was submitted asking that the following Motion Concerning Police Actions be voted on by the membership of the Davis Division (tenure/tenure-track faculty of the UC Davis Campus):

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Calling on AAAS to Deposit all Archives of Science in Pubmed Central

2012-02-16T15:30:00.000-08:00

Much has been written recently about a call to boycott Elsevier due to their outrageous policies regarding academic publishing. I support the boycott but I also agree with many others who have said it perhaps unnecessarily singles out one publisher over others who also have publishing policies that could, well, use a bit of work. And one such publisher is AAAS - the American Association for the Advancement of Science.

Today, the annual meeting of AAAS begins today in Vancouver. I was supposed to be there by now, but thanks to some technical problems at Alaska Airlines, I am back in Davis for the day. AAAS has some policies regarding openness that I believe are unnecessary and not in the general interest of scientific progress. One is the strange "talk embargoes" I have written about recently. Another, which is much more problematic, is the fact that Science Magazine (published by AAAS) does not deposit archival content in Pubmed Central. Now, mind you, I think all scientific publishing funded by taxpayer money should be openly and freely available immediately. But that is not going to happen immediately.

One helpful tool in making scientific literature freely available is Pubmed Central. Most scientific societies I know of deposit published material in Pubmed Central after some initial delay of 3-6-12 months. But for reasons that are not entirely clear (to me at least, or to a Google search), AAAS clings to their archival material making it only available through their own web site. Sure - they do allow authors to deposit their version of their manuscripts in Pubmed Central after a delay. But most alas do not do this. And I note - this option is only open to NIH and Wellcome Trust funded work. So much material cannot be deposited anyway.

AAAS's policy seems unnecessarily closed accessy and limits the impact and spread of the knowledge contained within papers in Science. I note - this policy is yet another reason to not publish in Science and to instead choose either fully open access journals or ones that at least release their stranglehold on the papers after a short delay.

Today I call on AAAS to make archival literature from Science Magazine available in Pubmed Central. And I call on others out there, such as those at the AAAS meeting, to pressure AAAS to do this. Write blog posts. Call and email AAAS members and leadership. Email AAAS. And so on.

Ideally everyone would just publish in fully open access journals and the journals would deposit material in archives. But until that happens, we need to make every effort to increase the amount of literature getting into Pubmed Central and other archives. So - pressure AAAS. And while everyone is at it, please deposit whatever you can in preprint servers, in various repositories and in Pubmed Central. Every little bit helps.

Calling all phylogeneticists: Encyclopedia of Life Phylogenetic Tree Challenge

2012-02-16T13:46:00.000-08:00

Just got an email from Todd Vision about this. Definitely seems worth checking out: EOL Phylogenetic Tree Challenge - Encyclopedia of Life

The challenge is summarized on their web site and I quote it here

"A prize is offered to the individual or team that can provide a very large, phylogenetically-organized set(s) of scientific names suitable for ingestion into the Encyclopedia of Life as an alternate browsing hierarchy.

Names must be provided in Darwin Core Archive1 format.

Extinct organisms may be treated but are not required.

Ranks are not required for names but may be included.

Internal nodes need not all have formal Linnaean names but require a label which can be arbitrary. Leaf nodes also need not have formal names but ideally most will overlap with current EOL species pages.

For the purpose of this contest, metrics and source of node support, branch lengths, vernaculars, and synonyms are not required. These may be included; not all are currently displayable on EOL.

Trees must be rooted. Multiple, overlapping hierarchies may be submitted as a set (e.g. to handle reticulation)

Among other factors, the total number of uniquely named nodes, node/leaf ratios and tree height may be used to compare entries so contestants should consider how they wish to trade off strict consensus versus other methods of reflecting the state of phylogenetic knowledge.

Problems to solve include 1) how to assign labels to unnamed nodes, 2) how to fill in gaps so that the set of taxa included is as comprehensive as possible, even if trees are not fully resolved or all taxa have not been analyzed, 3) how to handle competing hypotheses, 4) how to update the hierarchy at least annually.

The winning submission must be available to EOL and others under an acceptable CC license if it is under copyright. The tree need not be previously published in peer-reviewed form.

Questions about the challenge may be asked in the Phylogenetic Tree Challenge community on EOL."

Leaked insider docs from Heartland Institute goal: "dissuading teachers from teaching science" (ps hey Scholarly Kitchen do you support this?)

2012-02-14T19:34:00.000-08:00

Yesterday I worried about the deceptive climate change related writings and work of one of the authors at the Scholarly Kitchen blog: Something rotten in the Scholarly Kitchen?

Basically, I wrote about how one of the authors at the Scholarly Kitchen - David Wojick - has been involved in some groups that have taken a decidedly deceptive anti-science stance on the issue of climate change.

I did not translate all of my worries into words because they were not completely formed. One of the reasons for my concern was the feeling that Wojick might be using his position in a apparently scholarly group to boost his authority in some way. Note - he has no apparent record of working on climate science yet he has written about it extensively with attempted authority.

Well, my unformed thoughts have hit me smack in the face today. Alexy Merz pointed me to this article published today:INTERNAL DOCUMENTS: The Secret, Corporate-Funded Plan To Teach Children That Climate Change Is A Hoax | ThinkProgress

The article quotes internal documents from the "Heartland Institute" discussing the development by one David Wojick of a "global warming curriculum for elementary schoolchildren that presents climate science as 'a major scientific controversy.' "

And more disturbing, the internal papers imply that they believe Wojick's curricula have great potential for spreading because of his connections to organizations involved in "producing, certifying, and promoting scientific curricula." So, in a way I think it is not a stretch to interpret his involvement in the Scholarly Kitchen as a way to boost his "authority" in academic circles even in the absence of any expertise in climate science.

And then as the evening progressed I found out more detail from the internal documents of the Heartland Institute that are even more disturbing:

Mind you, I generally try to avoid mixing writing about science and politics - and I am pretty open to diverse political points of view. But this is different. The Heartland Institute and Wojick and others are using the same strategy used by Intelligent Design advocates. They want to "teach the controversy" and they want to make equivalent the thoughts of a few people with actual research by 1000s of scientists. I am all for freedom of speech and think anyone should be able to express their beliefs and opinions in a free and open manner.

The ultimate to me is in this leaked document:

Development of our "Global Warming Curriculum for K-12 Classrooms" project. Principals and teachers are heavily biased toward the alarmist perspective. To counter this we are considering launching an effort to develop alternative materials for K-12 classrooms. We are pursuing a proposal from Dr. David Wojick to produce a global warming curriculum for K-12 schools. Dr. Wojick is a consultant with the Office of Scientific and Technical Information at the U.S. Department of Energy in the area of information and communication science. His effort will focus on providing curriculum that shows that the topic of climate change is controversial and uncertain- two key points that are effective at dissuading teachers from teaching science. We tentatively plan to pay Dr. Wojick $100,000 for 20 modules in 2012, with funding pledged by the Anonymous Donor.

Let me repeat one part:

His effort will focus on providing curriculum that shows that the topic of climate change is controversial and uncertain - two key points that are effective at dissuading teachers from teaching science.

Wow. Not anything else to say here. I wonder if any of the other writers at the Scholarly Kitchen will comment about this.

UPDATE: Some additional news stories and posts of relevance

UPDATE 2: more posts

UPDATE 3: discussion with some Scholarly Kitchen bloggers about the issue

UPDATE 4: More stories

UPDATE 5: 2-15 Kent Anderson, head of The Scholarly Kitchen blog responds and says actions of Wojick are irrelevant to his blog.

@phylogenomics @drs1969 it's an irrelevant topic to this blog. It's not a science blog, it's a publishing blog.

Incredible. So - apparently being paid to deceive about the science behind studies of climate change is not relevant to a blog about publishing which has a big emphasis on peer review and science.

UPDATE 6: 2-15 8 PM More stories

Leak Offers Glimpse of Campaign Against Climate Science NY Times
Climate science attack machine took donations from major corporations The Guardian
Climate change sceptic body's donor list leaked Financial Times
The Heartland Files and the Climate Fight Andrew Revkin
Heartland And DeSmogBlog Square Off Over Incendiary Documents Forbes
The Heartland Institute Responds to Stolen and Fake Documents Forbes
Openness: A Heartland-warming tale BBC
Heartland burned by 'DenialGate' memos - Politico
Leaked docs: Heartland Institute think tank pays climate contrarians very well Ars Technica

UPDATE 7 with even more links:

UPDATE 8:

UPDATE 9: Peter Gleick revealed as source of the documents

Some of the more interesting papers in Pubmed Central that reference Valentine's Day

2012-02-14T07:30:00.000-08:00

Earlier this AM I posted to twitter a brief comment about articles in Pubmed Central that reference Valentine's Day.

Yes, there are 120 papers that come up in Pubmed Central w/ a search for "Valentine's Day"shar.es/fSi8b
— Jonathan Eisen (@phylogenomics) February 14, 2012

Kay Thaney's response caught my eye b/c she called attention to some of the more interesting papers from my link:

@phylogenomics @David_Dobbs uplifting. among results, "sweet nothings?", "parasuicide","diabetes bingo" + "HIV epidemics". #loveisintheair
— Kaitlin Thaney (@kaythaney) February 14, 2012

So I thought I would post a few of the links here:

Enjoy ...

Paper out from the "Evolution in the Deep Biosphere" workshop I went to #OpenAccess

2012-02-14T06:50:00.000-08:00

Just picked up this paper in one of my automated Google searches for, well, my own name: Prospects for the Study of Evolution in the Deep Biosphere.

The paper is the result of a workshop I went to at the USC Wrigley Marine Station on Catalina Island. See my notes on the trip here: A "work" trip to Catalina Island: USC, Wrigley, C-DEBI, dark energy biosphere, Virgin Oceanic, Deep Five, & more. I note - the group of people at the meeting worked on their paper after the meeting and invited me to be a co-author on it. However, I was busy and I felt like I could not contribute to it in a way that would qualify for authorship. So I sent them comments here and there and had also given them some ideas while at the meeting. And now I am happy to report their paper is out.

I note - the paper is in "Frontiers in Extreme Microbiology" one of the new Open Access journals in the Frontiers series. Not sure yet what to think of all these Frontiers journals. But they do have a suite of journals in "Microbiology" so I will keep an eye on them ...

Something rotten in the Scholarly Kitchen? (Climate Change Denialism is Everywhere)

2012-02-14T00:51:00.000-08:00

I never ~~not~~ previously paid much attention to the "Scholarly Kitchen" site before. Every once in a while I have noticed their posts and usually have found them off in some way. But then my brother Michael decided to respond to a recent posting from someone named Kent Anderson there.

I wrote about this briefly here: Trolls and flames discuss #NotSoFunny satire at the Scholarly Kitchen.

And the twitter had quite a bit too. So, of course, I made a "Storification" of this:

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Cool paper from DerisiLab on viruses in unknown tropical febrile illnesses #metagenomics #viroarray

2012-02-13T18:00:00.000-08:00

Quick post:

Figure 3. Circovirus-like
NI sequence coverage and phylogeny.

Cool new paper from Joe Derisi's lab: PLoS Neglected Tropical Diseases: Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing

Full citation: Yozwiak NL, Skewes-Cox P, Stenglein MD, Balmaseda A, Harris E, et al. (2012) Virus Identification in Unknown Tropical Febrile Illness Cases Using Deep Sequencing. PLoS Negl Trop Dis 6(2): e1485. doi:10.1371/journal.pntd.0001485

They used a combination of a viral microarray and metagenomic sequencing to characterize viruses in various samples from patients with febrile illness. And they found some semi-novel viruses in the sample. Definitely worth a look.

Note - here are some other posts of mine about Derisi:

See some follow up discussion on Google+ here.

Trolls and flames discuss #NotSoFunny satire at the Scholarly Kitchen

2012-02-13T01:15:00.000-08:00

Bit of a tiff going on over at the Scholarly Kitchen over a "satire" someone named Ken Anderson wrote related to the Research Works Act. The piece was about the "Restaurant Works Act" -- Someone pointed me to the post and I found the satire to be, well, unfunny so I chose to ignore it. My brother alas could not ignore it, nor could some others and there is some discussion going on there now.

I will skip commenting on the discussion itself - go read it. But a few things there annoyed me. One of these is that Anderson has resorted to criticizing the punctuation of some of his critics there. That is pretty lame. See start of thread below

Alex Merz wrote

The inappropriateness of the analogy was clear by the end of paragraph 2. For the rest: TL;DR

To which Anderson responded

For those of us not as hip as Alex, TL DR means “too long, didn’t read.” I won’t comment on the inappropriateness of the semicolon in his Urban Dictionaryesque construction. The post is about 850 words, by the way

Storification of Fake Science Publishing @fakeelsevier @fakeplos @realelsevier @fakeeisen @closedaccessj

2012-02-12T16:05:00.000-08:00

So - I have been enjoying all the Fake Scientific Publishing Posts on Twitter from @fakeelsevier @fakeplos @realelsevier @fakeeisen @closedaccessj and others. Now I understand why some people think I am behind some of these (e.g., here are some of my Fake Science News posts). But alas though I WISH I was behind some of these accounts, I am not. Anyway - I created a storification of the beginning of some of these postings if you want to see some of the origins of the fakery.
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Hmm ... City of Davis definition of microorganism needs work

2012-02-12T14:23:00.000-08:00

From City of Davis Guide to Composting

MICROORGANISM microscopic plants and animals.They exist in soil for the purpose of breaking down organic matter into basic mineral elements.They include bacteria, fungi, actinomycetes, algae, protozoa, yeast, germs, ground pearls, and nematodes.

Gonna have to get them to work on this ...

One of the coolest things I discovered at Science Online 2012: Science Scout Stickers #scio12

2012-02-12T11:10:00.000-08:00

Love this concept: Science Scout Stickers | Hydra Creations | Hydra Creations

They were giving some out at Science Online 2012 and I really like them. They had texture and look very cool on my laptop (computer that is). Pondering getting some more. Wondering how I convince them to make some other kinds ...

Here are scans of the handout from Science Online 2012

@phylogenomics you should add in the Official Sci Scout page too: scq.ubc.ca/sciencescouts/ Explains the backstory
— Karyn Traphagen (@kTraphagen) February 12, 2012

Microbial metaomics discussion group this week: metatranscriptomics and biogeography

2012-02-12T08:18:00.000-08:00

A visiting student at my lab Lea Benedicte Skov Hansen will be leading our "metaomics" discussion group this week. We will be discussing a combination of metatranscriptomics and biogeography and the papers of the week are:

Metatranscriptomics paper:

Microbial community gene expression in ocean surface waters. Frias-Lopez J, Shi Y, Tyson GW, Coleman ML, Schuster SC, Chisholm SW, Delong EF. Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3805-10. Epub 2008 Mar 3.

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Hard to tell if this is a SPAM conference or not "4th Intntl. Science in Society Conference"

2012-02-12T07:52:00.000-08:00

Hard to tell if this is email I just got is about a SPAM Conference or not.

Dear Colleague,

On behalf of the Conference Organizing Committee, I would like to inform you of the:

FOURTH INTERNATIONAL CONFERENCE ON SCIENCE IN SOCIETY
University of California, Berkeley, USA
17 - 19 November 2012
http://science-society.com/conference-2012/

This conference addresses the social impacts, values, pedagogies, politics and economics of science. It is an inclusive forum that welcomes a breadth of perspectives on science from practitioners, teachers and researchers representing a wide range of academic disciplines.

New #openaccess paper in G3 from my lab w/ many others on 'Programmed DNA elimination in Tetrahymena' #CiliatesRule

2012-02-11T08:21:00.000-08:00

A new paper in which the lab was involved has been published recently (just found it though it is not in Pubmed yet): Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila. It was a collaboration between Kathy Collins, multiple Tetrahymena researchers, the Eisen lab, and the UC Davis Genome Center Bioinformatics core (Joseph Fass and Dawei Lin). The paper is in G3, an open access journal from the Genetics Society.

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