Monday, January 30, 2012
Scary and funny: fake researcher Peter Uhnemann on OMICS group Editorial Board #JournalSPAM
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)
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
Sunday, January 29, 2012
First "Guardians of microbial diversity" award to Rob Dunn #microbiology #GMDs
Dear #AAAS, I am NOT embargoing my own talk & I plan to record it and post afterwards #embargowatch
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.
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
Saturday, January 28, 2012
A science birthday party for a five year old
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:
Friday, January 27, 2012
Notes on #UCDavis Citizen Microbiology Meeting #UCDCitSci
Below is a "Storification" I made of the tweets and links from the meeting.
A conference where the speakers are all women?
Thursday, January 26, 2012
Crossposting from microBEnet: architecture and microbes
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.
Wednesday, January 25, 2012
Letter from Justice Cruz Reynoso to President Yudof regarding pepper spray investigation at #UCDavis
Support good science writing - pay for it
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 -
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
Tuesday, January 24, 2012
UCDavis IT and GMail think this "Open Journal of Genetics" journal announcement is SPAM, I do too #EndScienceSpam
Monday, January 23, 2012
Scientists have .... (impressions from #scio12)
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 ...
Sunday, January 22, 2012
The Books of Science Online 2012 #scio12 #bookporn #sciencerocks cc: @avflox
UPDATE 2: August 2013. Posterous is dead so deleted the links to the book pictures from Posterous below. Changed it to Picasa.
Friday, January 20, 2012
Draft post cleanup #22: Fun emails for another Jonathan Eisen
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)
Thursday, January 19, 2012
Draft post cleanup #21: Tracking progress on the vertebrate tree of life
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
Is stupidity important in scientific research?
- The Importance of Stupidity - Improbable Research » Blog Archive
- On the importance of stupidity in scientific re... - For the Graduate ...
- "The importance of stupidity in scientific research" from J Cell ...
- The Importance of Stupidity in Grad School CaPS
- The Dynamic Earth: The Importance of Stupidity in Research
- The importance of feeling stupid
Draft post cleanup #20: Retaking the biology GRE
In 2008, I had this idea that it would be interesting for biology faculty to retake the Biology GRE and see how they do. I never got around to trying to register to take it and thus never wrote about it ... Any Profs. out there who have gone back and taking the GREs?
YASSP (Yet another SPAMMY science publisher)
Tuesday, January 17, 2012
UC going smoke free sometime soon apparently
UC Davis community members,
I am writing to share with you the attached letter
from President Mark G. Yudofto chancellors regarding the University's recent decision to make all campuses tobacco-free by 2014. The new policy direction will prohibit the smoking and chewing of tobacco, as well as the sale of tobacco products, and aligns with practices already in place at UC medical centers and many other universities.
As the President's letter indicates, each campus will soon be developing plans for implementing this decision, and we will have more information about what this new policy process will entail for our community as the UC Davis plan takes shape. We will, of course, consult with a broad range of our campus community as we develop mechanisms to implement this new policy direction.
Vice Chancellor, Administrative and Resource Management
Draft post cleanup #19: Spam and biased spam at that
I am sure many others out there who blog have gotten this kind of message:
We at Onlinephdprograms.com recently came across your blog and were excited to share with you an article “15 Fictional Professors We Wish Were Real” was recently published on our blog and we hoped that you would be interested in featuring or mentioning it in one of your posts.I assume that these posts that are written for this, and various other sites, are all about driving up Google Search ranking somehow. So I normally avoid writing about them. But I thought I would in this case because, well, their post annoyed me because of the 15 functional professors they wrote about, only one is female. Really, that is the best they could do? In three minutes of web surfing (e.g., browsing this site and this one) I have come up with a list of fictional female professors who certainly could have been included in their list. And many are much more interesting than some they wrote about. Here are some examples:
Either way, I hope you continue putting out great content through your blog. It has been a sincere pleasure to read.
Thanks for your time,
- Eleanor Arroway - Jodie Foster's character in Contact
- Susan Calvin - character in Isaac Asimov's I Robot series
Monday, January 16, 2012
Draft post cleanup #18: Epernicus
Well, was going to write about Epernicus in 2008 as an interesting tool for networking scientists. I still have an account there which I just updated a bit. But I am not sure if Epernicus is being used much anymore. I have focused a lot on a similar system: Mendeley though they have differences.
Sunday, January 15, 2012
Draft post cleanup #17: Obama overqualified for application to be president
Dear Mr. Obama
Saturday, January 14, 2012
Draft post cleanup #16: Science and Title IX
I had seen an article that surprised me: Findings - John Tierney - Science Has Become the New Frontier for Title Nine - NYTimes.com
In the article Tierney discussed how the Title IX statute which forbids discrimination based on gender in education and has been applied extensively to athletic endeavors was beginning to be applied to science. Not sure what has become of this over the last 3+ years --- if anyone knows more please post ...
Yet another SPAMMY Science publisher: Scientific and Academic Publishing
Dear Jonathan A Eisen,
This is Scientific & Academic Publishing, USA. Nice to get your information from the journal PLOS Biology and also happy to pass on our regards to you from the editorial department of SAP.
Friday, January 13, 2012
Draft post cleanup #15: Now this is how to write a scientific paper
I had written:
Just found an old fax I received from my brother of a paper published in 1974 in Scientia Sinica. "Studies of the insulin crystal structure: the molecule at 1.8Å resolution." Sounds pretty straightforward right? But then you read the paper: Here is the abstract (could not find a PDF so scanned in the fax I got).
Request for input - are there any rules regarding posting text of one's own NSF (or other) grant proposals?
I have posted some of the twitter conversation below. But to get directly to the point the question I have for everyone here is - are there any rules at the National Science Foundation that would prevent one from sharing with others a grant proposal that one has submitted? Are there any rules against this at any agency? I think there are none but apparently some are telling Karen otherwise.
Any information on this would be useful. Some of the twitter conversation is below:
Thursday, January 12, 2012
Storification of Tweets from talk by Jane Lubchenco at #UCDavis
Letter from Chancellor Katehi to #UCDavis Community
Posting this email I received for those interested. Not sure what will happen this quarter in terms of Occupy UC Davis actions and related issues ... but will post as things develop.
Dear UC Davis Community,
Happy New Year! I am writing to welcome everyone back to campus and to share my thoughts about the coming year at UC Davis.
Google scholar missing paper issue clarified, though not corrected, but glad Google responded
The following important and highly cited reference is somehow missing from Google Scholar although it was there a few months ago - it would be useful to have it back:
Draft post cleanup #14: Video of Talk of mine from 2005
Embedded here is a video of a talk I gave in 2005 at the NIH entitled "More Questions Than Answers Insights into DNA Repair Processes from Genome Sequencing Projects"
Wednesday, January 11, 2012
OK - testing "threaded commenting" on my blog
Diplomacy fails? Military options off the table? Let's assassinate the scientists
Wrap up of tweets from Joe Derisi talk
Joe DeRisi getting ready for his talk at the #ucdavis Genome Center this am http://t.co/OwZbM2nn
1/9/12 9:57 AM
Joe Derisi's first slide : "Bees, viruses, and plastids: a seminar in two parts" - I think he needs to work on his math http://t.co/0nPjChlc
1/9/12 10:05 AM
Another seminar at #UCDavis 1/11 - Evan Eichler - #TooManyChoices
UC Davis M.I.N.D. Institute's 2011-2012 Distinguished Lecturer Series
SPEAKER: Evan E. Eichler, Ph.D.
TOPIC: Copy Number Variation, Exome Sequencing and Autism
DATE: Wednesday, January 11, 2012
TIME: 4:30 pm - 6:00 pm
LOCATION: M.I.N.D. Institute Auditorium (2825 50th Street, Sacramento)
Two seminars from Jane Lubchenco at #UCDavis - fun, fun and fun
Draft post cleanup #13: Twisted tree of life award: MSNBC, Aliens and Photosynthesis
I wanted to give this article a "Twisted Tree of Life Award":
How to find aliens: Follow the photosynthesis - Technology & science - Space - Space.com - msnbc.com
It is pretty painful to me. Basically the people they are quoting argue that since "complex" life on Earth requires oxygen and since oxygen only comes from photosynthesis, therefore we should look for planets where photosynthesis is possible as the place where life is most likely to be interesting. Uggh. So many things in the article I did not like ... but just not enough time I guess to bitch about it then. I will leave it to readers to decide for themselves I guess ...
Tuesday, January 10, 2012
To be discussed in journal club here today: eukaryotic metatranscriptomics
Note - am copying the whole text here to mark it up a bit since it it awkward to try and mark it up at the PLoS One site
Draft post cleanup #12: RecA is cool (and interesting)
I have been interested in RecA and related proteins for many many years. In particular I have been interested in structural and functional evolution of RecA and its relatives. This all started when for my second scientific paper I helped a post doc in the lab where I was doing my PhD do some structure-function-evolution studies (with a little help from Chris Lee, then in Mike Levitt's lab, and my brother, then in Don Wiley's lab).
AAAS meeting - is this one for embargo watch?
Apparently, my talk is "embargoed" - though I am not sure I understand how that works for a talk (see the part I highlighted in yellow which, well, I almost certainly will not be following). I do not understand actually what a talk embargo means - am I supposed to not share with people what I am working on so that every piece of data I present at the meeting will never have ben seen by anyone? Or am I just not supposed to show my talk to anyone? What exactly is a talk embargo? And what will they do when I do not follow it? Maybe Ivan Oransky knows.
How to stop press release spam? Post embargoed PRs. Here's one about Mayans using tobacco.
Press release below:
Monday, January 09, 2012
Cracking the microbial code: Pam Ronald @pcronald and her story behind recent papers
Please contact her if you have questions. I am leaving the text of the post below based on the notion that one should not completely delete anything from the record but rather post corrections and retractions. More detail will be coming from Pam soon. Kudos to Pam for trying to make sure the scientific record is accurate and for contacting me about this.
Most recent post
Panoramas from the past ...
In 1997, my then girlfriend (now wife) and I went camping in Death Valley. It was our fourth trip there to camp in grad. school. I brought m...
Just got this press release by email. I am sick of receiving dozens of unsolicited press releases, especially those in topics not related ...
New article out from the Eisen Lab: Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarumSee Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum Paper based on PhD thesis work of Katie Dahlha...
I have a new friend in Google Scholar Updates I have written about the Updates system before and if you want more information please see...