Scary and funny: fake researcher Peter Uhnemann on OMICS group Editorial Board #JournalSPAM

OMG.  This is both hilarious and terrifying.

Many out there know there are journals out there that border on SPAM.  I have written about this often before (e.g., see For $&%# sake, Bentham Open Journals, leave me alone and Yet another SPAMMY Science publisher: Scientific and Academic Publishing and The Tree of Life: Really sick of Bentham Open Spam) as have many others (e.g., Open and Shut?: The Open Access Interviews: Matthew Honan and Academic spam and open access publishing - Per Ola Kristensson). UPDATE: forgot to include this link: Science SPAMMER of the month: OMICS publishing group

But this one takes the cake.  There is a journal called "Molecular Biology" from the OMICS Publishing Group (for more on this publisher see Open and Shut?: The Open Access Interviews: OMICS Publishing ...).  It seems new - as I cannot find any publications - but you never know - maybe they have been around a while and just have not gotten any submissions.

Boycotting Elsevier is not enough - time to make them invisible (UPDATED/RETRACTED)

Update: The original post here was written at midnight, with a cat on my lap.  I thought this post conveyed some tongue in cheek aspect of this idea to ignore work in Elsevier journals. (one could view it as a midnight middle finger to Elsevier over some of their policies).  But clearly, based on the responses I am seeing that did not come across.  I accept the error of my ways.  Drug Monkey is right - no work should be ignored - no matter where it is published.   I could explain in more detail what I was trying to convey - but in the end that is like explaining a bad joke.  Instead, I am therefore retracting my blog post.  That is one for Ivan Oransky I guess. Now back to your regularly scheduled programs.

There has been much written in the last few days about multiple calls to boycott journals published by Elsevier due to Elsevier's generally problematic publishing policies and support of SOPA/ RWA, etc.  People have called for people to not only boycott publishing in Elsevier journals but to also stop reviewing for them, editing for them, and also to try to get libraries to stop subscribing to them.  Some good reading in this area includes:

• Mathematicians boycott Elsevier publishing
• The Cost of Knowledge
• Elsevier - my part in its downfall
• Journal Publishing Reform
• Ban Elsevier
• Scientists organize Elsevier boycott
• Academic publishers have become the enemies of science

I think these are good steps.  But I also think they are not enough.  I am therefore calling for people to go one step further - to stop helping promote articles published in Elsevier journals.  Don't blog about papers in Elsevier journals.  Don't tweet about them.  Don't use Elsevier papers for journal clubs.  In essence, ignore them - consider them dead - make them invisible.  Not completely of course.  Any work should be considered a contribution to science or math or whatever your field is.  But there are LOTS and LOTS of things to do with your time.  And if you like to share - to communicate - to discuss - it is easy to find non Elsevier articles articles for those purposes (even better - pick open access articles ..)

This may be a minor thing in the fight for more openness in publishing, but it should help.  After all, for many scientists, the worst thing that can happen is to be ignored.

How are these @kejames re: #PLoSOne cc: @boraz @edyong209 @danielaphd

Having lots of fun with my @Olloclip macro lens for my iPhone

First "Guardians of microbial diversity" award to Rob Dunn #microbiology #GMDs

Nice piece by Rob Dunn: Eating off the floor: How clean living is bad for you | Guest Blog, Scientific American Blog Network

For this I am awarding him the first of what will be many "Guardians of Microbial Diversity" awards here (we can just call these the GMDs). Not only will he get an award - I am going to send him a GMD gift from the various GMD doodads I am putting together.

Congratulations Rob.  Now off to design some more diverse GMD doodads. 

Dear #AAAS, I am NOT embargoing my own talk & I plan to record it and post afterwards #embargowatch

Just got another email from AAAS regarding their big meeting in February in Vancouver where I am scheduled to talk:

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This request for materials is from the AAAS media relations team and is separate from any you may receive from your symposium organizer or the AAAS Annual Meeting office.
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Dear AAAS Annual Meeting Participant:


Thanks to all of you who uploaded materials to the AAAS Virtual Newsroom by Jan. 16. For those of you who have not submitted materials or want to submit additional materials, you may do so right up through the meeting. The materials will be available online to reporters, although we can no longer guarantee that we'll be able to copy new
submissions at our expense for placement in the on-site library of speaker materials. We will try to include materials received in the next several days in our copy order, however.

One old, one new - a few phylogeny papers worth checking out

Just a quick one here. A few days ago in my lab we were discussing some challenges with doing phylogenetic diversity (PD) measurements in very very large phylogenetic trees. PD is a measure of total branch length in a phylogenetic tree for a group of taxa ... and we use it for many purposes.

For many of our applications we have been using an algorithm described by Mike Steele "Phylogenetic diversity and the Greedy Algorithm". But alas, is is not keeping up with the massive tree sets we are dealing with. Fortunately Aaron Darling in my lab found a alternative paper with a perfect sounding title for us: Phylogenetic Diversity within Seconds from Minh, Klaere, and von Haeseler. This seems like it will do the trick. I note - Kudos to Systematic Biology for making some older papers freely available. Not sure of their general policies on this but good to see.

Anyway - back to the grind ...

A science birthday party for a five year old

Some pics from my son's fifth birthday party - chemistry & geology focused (we may sample microbes later ...).  For the geology part we cracked open geodes.  For the chemistry part, we played with citric acid, baking soda, some dyes, and other things ...

Experimenting with Blogger's "Dynamic Views" format and a way to use with without changing my front page

A while ago Blogger announced "Dynamic Views" for Blogger blogs (Dynamic Views: seven new ways to share your blog with the world). Some of these seem pretty near but I kind of like the non dynamic format for my blog and I am reluctant to jump into the new dynamic world.

Then I discovered a trick.  Dynamic views are there and you do not have to switch over the front page for people to still play with with views.

To get to the dynamic views for this blog go to one of these links:

• http://phylogenomics.blogspot.com/view/classic
• http://phylogenomics.blogspot.com/view/magazine
• http://phylogenomics.blogspot.com/view/flipcard
• http://phylogenomics.blogspot.com/view/mosaic
• http://phylogenomics.blogspot.com/view/sidebar
• http://phylogenomics.blogspot.com/view/snapshot
• http://phylogenomics.blogspot.com/view/timeslide

Seems like this may work for most blogger blogs too.  Not sure whether this is on purpose by Blogger and/or whether they have written about it or not but I like that it is there to play with.  If people have any opinions about the Dynamic Views let me know.  I note - one you go to the dynamic views you can switch between the different views using the drop down menu on the left.

Notes on #UCDavis Citizen Microbiology Meeting #UCDCitSci

We had a meeting at UC Davis on "Citizen Microbiology" from 1/23-1/24. It was a small meeting funded via my microBEnet project which itself is supported by a grant from the Alfred P. Sloan Fundation. The meeting was held at UC Davis - participants stayed at the new Hyatt on campus. We met in the new Conference Center. Participants at the meeting were me, David Coil (post doc in my lab), Paula Olsiewski (from the Sloan Foundation), Holly Bik (post doc in my lab), Darlene Cavalier (founder of ScienceForCitizens.Net), Dan Smith from Argonne National Lab, Denneal Jamison from UC Davis, Holly Menninger from NC State, Noah Feirer from CU Boulder, Josh Neufeld from Waterloo, Jason Bobe from The Personal Genome Project, Tom Bruns form UC Berkeley, Madhu Katti from Fresno State, Chris House from Penn. State, and Patrik D'haeseleer (from Lawrence Livermore National Lab).
Below is a "Storification" I made of the tweets and links from the meeting.

A conference where the speakers are all women?

So - I was working on organizing a conference - a part of a series - and I was frustrated that prior conferences in the series had only or mostly male speakers. So I suggested for the new conference in the series we have only female speakers. Still working on pulling that off but probably won't quite happen. So then I posted to twitter and Google+ the idea - and asked a question about it. I made a "storification" of this which you can see below the fold:

Crossposting from microBEnet: architecture and microbes

Crossposting this from microBEnet: “Architectural design influences the diversity and structure of the built environment microbiome” – paper by the BioBE Center group | Microbiology of the Built Environment Network (post by David Coil).

We’ve posted in the past (here, here, here, and here) about some of the interesting work taking place at the BioBE Center regarding microbial community structure in health-care facilities. Today a paper on this topic came out in the ISME Journal.

This paper is certainly worth a read for anyone interested in the microbiology of the built environment. In particular they show that microbial community structure depends largely on the type of ventilation present in a room. Furthermore, they show that the microbial community present in a mechanically vented room has lower diversity than rooms with open windows or the outside air… and that lower diversity is comprised largely of human-associated microbes.

Here’s the abstract:

Buildings are complex ecosystems that house trillions of microorganisms interacting with each other, with humans and with their environment. Understanding the ecological and evolutionary processes that determine the diversity and composition of the built environment microbiome—the community of microorganisms that live indoors—is important for understanding the relationship between building design, biodiversity and human health. In this study, we used high-throughput sequencing of the bacterial 16S rRNA gene to quantify relationships between building attributes and airborne bacterial communities at a health-care facility. We quantified airborne bacterial community structure and environmental conditions in patient rooms exposed to mechanical or window ventilation and in outdoor air. The phylogenetic diversity of airborne bacterial communities was lower indoors than outdoors, and mechanically ventilated rooms contained less diverse microbial communities than did window-ventilated rooms. Bacterial communities in indoor environments contained many taxa that are absent or rare outdoors, including taxa closely related to potential human pathogens. Building attributes, specifically the source of ventilation air, airflow rates, relative humidity and temperature, were correlated with the diversity and composition of indoor bacterial communities. The relative abundance of bacteria closely related to human pathogens was higher indoors than outdoors, and higher in rooms with lower airflow rates and lower relative humidity. The observed relationship between building design and airborne bacterial diversity suggests that we can manage indoor environments, altering through building design and operation the community of microbial species that potentially colonize the human microbiome during our time indoors.

Letter from Justice Cruz Reynoso to President Yudof regarding pepper spray investigation at #UCDavis

Just got this in email and thought it would be good to share

The text reads:

Support good science writing - pay for it

A quick one here since I think there is not much complication to this issue.  As many know - I am a big big advocate of "open access" to the scientific literature.  I think if the taxpayers / government pay for research (and pays for salaries/indirect costs/etc that go into publishing) then the results of that research (data, papers, software) should be available freely and openly.  I think it is also better if ANY scientific writing could be freely and openly available (e.g., research paid by private funds).

However, this does not mean that one should not pay for writing about science.  I think we as a society need to support good science writing and reporting.  I subscribe to the New York Times - party partly for access to the science writing (not all of which I like but some of which is phenomenal).  I subscribe to Wired.  I donate (occasionally) to blogs.  I subscribe to Scientific American.  I buy good science books (sometimes many copies and then give them out - like I did with Rebecca Skloot's HeLa book which).

So I call on people out there - whether you support Open Access to government funded work or not - pay for some good science writing.  Buy a book.  Subscribe to a magazine.  Donate to a blog.  Do something to support those who enrich our lives.  Science writers need to earn a living after all ...

Real science vs. fake science in advertising

Just a quick one here - already tweeted about this but I know some people out there do not use the twitter. There is a great article in BlogHer from Emily Willingham on Science vs. "Fake" Science in Ads: How Do We Tell Real Science from Fake Science in Ads? | BlogHer

It goes through many ways to do a sniff test on scientific claims that seem off. I have blogged many times here about how fake science in ads and the media drives me crazy (e.g., see my overselling the micro biome awards)) and have thought about some of the items on Emily's list here but not all of them. And it is very helpful to see them all together. This is one article worth sending around.

UCDavis IT and GMail think this "Open Journal of Genetics" journal announcement is SPAM, I do too #EndScienceSpam

Just got this email which both Gmail and UC Davis systems think is SPAM (see below). It is from yet another new journal and the journal certainly seems a bit, well, off to me. I am posting such emails from journals like this in the hope that in Google search results people at least see some comments on the web at least asking questions about the quality of these journals. I do not know any details about this journal but I note I could not find any actual description of their licensing/copyright policies and all the papers list the copyright as belonging to the journal.  This seems to me to be unlikely to fit the standard definition of "open access" though it is very hard to tell from their website. 

Scientists have .... (impressions from #scio12)

Made using Wordle.Net

When I was enduring a painfully extended journey home from Science Online 2012 I kept thinking about the essence of the meeting.

And for reasons I am not entirely clear on, the essence kept coming up as single words.  So I tried to write them down but it was a bit too vague ... so then I thought - what about giving those words some friends ...

Microbial & Evolution art by @artologica has whole new meaning now that I met her at @scio12

See the full gallery on Posterous

The Books of Science Online 2012 #scio12 #bookporn #sciencerocks cc: @avflox

Flash

Flash

Well, I am a book geek.  While others took pictures of all the tatoos, people, and more -- the #1 thing I took pictures of were the books on display ... (UPDATE - made a mini Amazon Store with all the books here).

See the full gallery on Posterous

Draft post cleanup #22: Fun emails for another Jonathan Eisen

Yet another post in my "draft blog post cleanup" series.  Here is #22.  Written 5-5-2007 ...
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I have decided to start posting some of the more fun real emails I have gotten relating to some of my scientific work or supposedly related to it.

The best I get are usually not related to my work but instead are related to another Jonathan Eisen out there. There is this other person with my name who has written some off-kilter books about conspiracy theories. And every once in a while I get an email means for him. For example, here is one (with some personal information about the sender removed)

Draft post cleanup #21: Tracking progress on the vertebrate tree of life

Yet another post in my "draft blog post cleanup" series. Here is #21; from March 2010:

A very interesting paper came out recently from colleagues of mine at UC Davis:  Rapid progress on the vertebrate tree of life.  I did not know they were working on this but perhaps should have.  It has some fun/interesting analysis of the accumulation of phylogenetic knowledge over time.  For example see Figure 1

Cumulative phylogenetic information amassed for the last 16 years. The accumulation of sequences for vertebrates in GenBank (a), papers using the term 'phylogeny' or 'phylogenetics' in the Web of Science database (b) and phylogenetic resolution (measured as the proportion of nodes with at least 50% bootstrap support) in the vertebrate tree of life resulting from these research efforts (c). In all cases, the data are cumulative from the start of each analysis. Phylogenetic resolution is calculated as in Table 1. Trend lines are exponential in (a), and second order polynomial in (b) and (c).

Nice walk to #scio12 - now on o the virtual world