The Tree of Life

A science birthday party for a five year old

2012-01-28T17:15:00.000-08:00

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

2012-01-28T00:28:00.000-08:00

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:

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

2012-01-27T10:48:00.000-08:00

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. ...... READ MORE .......

A conference where the speakers are all women?

2012-01-27T10:45:00.000-08:00

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:

...... READ MORE .......

Crossposting from microBEnet: architecture and microbes

2012-01-26T10:56:00.000-08:00

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

2012-01-25T20:42:00.000-08:00

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

The text reads:

Support good science writing - pay for it

2012-01-25T18:33:00.000-08:00

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

2012-01-25T18:19:00.000-08:00

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

2012-01-24T07:41:00.000-08:00

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 emails like this in the hope that in Google search results people at east 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.

...... READ MORE .......

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

2012-01-23T00:26:00.000-08:00

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

2012-01-22T19:53:00.001-08:00

See the full gallery on Posterous

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

2012-01-22T11:47:00.001-08:00

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

2012-01-20T08:00:00.000-08:00

Yet another post in my "draft blog post cleanup" series. Here is #22. Written 5-5-2007 ...
----------------------------------
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)
...... READ MORE .......

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

2012-01-19T08:00:00.000-08:00

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

2012-01-19T06:49:00.001-08:00

Is stupidity important in scientific research?

2012-01-19T04:30:00.000-08:00

Just got sent this article which came out in 2008 but I do not remember seeing previously: The importance of stupidity in scientific research. The title seems a bit trite and in some ways the article is. But it has a resonance with many people and I thought I would at least post the link here. Some comments about it I found on the web include:

I can see why it resonates with people even though I am not sure I personally agree with the sentiments. It is definitely worth a read.

Hat top to Melanie Melendrez for pointing it out.

Draft post cleanup #20: Retaking the biology GRE

2012-01-19T04:00:00.000-08:00

Yet another post in my "draft blog post cleanup" series. Here is #20:

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)

2012-01-19T03:01:00.000-08:00

Just got an email from YAP (yet another publisher) recruiting articles for new journals. These ones seem just about as SPAMMY as some of the other recent ones to come out. Uggh. Double uggh. Email is posted below:

...... READ MORE .......

UC going smoke free sometime soon apparently

2012-01-17T19:10:00.001-08:00

Just got this email:

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.
Sincerely,
John Meyer

Vice Chancellor, Administrative and Resource Management

Draft post cleanup #19: Spam and biased spam at that

2012-01-17T08:00:00.000-08:00

Yet another post in my "draft blog post cleanup" series. Here is #19 from September 2011:

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.

(http://www.onlinephdprograms.com/15-fictional-professors-we-wish-were-real/)

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,
Liz Nutt

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:

Eleanor Arroway - Jodie Foster's character in Contact
Susan Calvin - character in Isaac Asimov's I Robot series

....

But then I stopped because I was disappointed I could not find more functional female professors to add to my list. I do think the list posted by the OnlinePhD site could certainly have had more women on it ... but I never posted the post because I had a hard time coming up with a lot of examples ... but now that I am trying to revive draft posts ... well ... I will put this out there even if it is an incomplete thought

Draft post cleanup #18: Epernicus

2012-01-16T08:00:00.000-08:00

Yet another post in my "draft blog post cleanup" series. Here is #18, from July 2008.

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.

Draft post cleanup #17: Obama overqualified for application to be president

2012-01-15T08:00:00.000-08:00

Yet another post in my "draft blog post cleanup" series. Here is #17 from October 30, 2008. I note - I never posted it because I tend to avoid politics here on the blog --- but three+ years later I think it is OK ...

Dear Mr. Obama

Thank you for your application for the position of

President of the United States

Unfortunately we are unable to consider you for this position because you have been deemed overqualified.

Draft post cleanup #16: Science and Title IX

2012-01-14T08:00:00.000-08:00

Yet another post in my "draft blog post cleanup" series. Here is #16 from July 2008.

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

2012-01-14T06:40:00.000-08:00

Uggh - just got this email. Seems there is yet another SPAMMY Science Publisher trying to get established. Here's is a suggestion for all. Avoid these kinds of publishers. They probably do more harm than good ... Plus if you can label their emails as SPAM to help out others. And I think posting comments like this will help since when people do google searches they may see the critiques as well as the journal sites.

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.

Draft post cleanup #15: Now this is how to write a scientific paper

2012-01-13T08:30:00.000-08:00

Yet another post in my "draft blog post cleanup" series. Here is #15, from May 2010.

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).