Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

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 …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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. 




Please circulate this CFP among your colleagues and students. 

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CALL FOR PAPER:
Open Journal of Genetics
ISSN Online: 2162-4461
www.scirp.org/journal/ojgen 

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Dear Jonathan A Eisen

Open Journal of Genetics (OJGEN) is an international journal (Open Access) dedicated to the latest advancement of Genetics. The goal of this journal is to provide a platform for scientists and academicians all over the world to promote, share, and discuss various new issues and developments in different areas of Genetics. 

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Topics:
www.scirp.org/Journal/AimScope.aspx?JournalID=613 
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+ Behavioural genetics
+ Classical genetics
+ Developmental genetics
+ Conservation genetics
+ Ecological genetics
+ Evolutionary genetics
+ Genetic engineering
+ Genetics of intelligence
+ Genomics
+ Human genetics
+ Medical genetics
+ Microbial genetics
+ Molecular genetics
+ Population genetics
+ Psychiatric genetics
+ Quantitative genetics

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Editorial Board:
www.scirp.org/Journal/EditorialBoard.aspx?JournalID=613 
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Editor in Chief
Prof. Benoît Chénais, Université du Maine, France
Editorial Board
Prof. Jinsong Bao, Zhejiang University, China
DR.   Gonzalo Blanco, University of York, UK
Prof. Yurov Yuri Boris, Russian Academy of Medical Sciences, Russia
Prof. Hassen Chaabani, University of Monastir, Tunisia
DR.   Craig E. Coleman, Brigham Young University, USA
DR.   Ming-Shun Chen, Kansas State University, USA
DR.   Philip D. Cotter, American College of Medical Genetics, USA
DR.   Clark Ford, Iowa State University, USA
DR.   Andreas Futschik, University of Vienna, Austria
DR.   Cenci Giovanni, University of L’Aquila, Italy
DR.   Tomonobu Hasegawa, Keio University School of Medicine, Japan
DR.   Karen Elise Heath, Hospital Universitario La Paz, Spain
Prof. Gregg E. Homanics, University of Pittsburgh, USA
DR.   Nilüfer Karadeniz, Ankara Training and Research Hospital, Germany
Prof. Presa Martínez, Universidad de Vigo, Spain
DR.   James Michael Mason, National Institute of Environmental Health Sciences, USA
Prof. Pratibha Nallari, Osmania University, India
DR.   Georges Nemer, American University of Beirut, Lebanon
Prof. Ettore Olmo, Università Politecnica delle Marche, Italy
DR.   Drewell A. Robert, Harvey Mudd College, Canada
DR.   Surasak Sangkhathat, Prince of Songkla University, Thailand
Prof. Bernd Schierwater, Yale University, USA
Prof. Genlou Sun, Saint Mary’s University, Canada
DR.   Reshma Taneja, National University of Singapore, Singapore 

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Authors’ Guidelines:
www.scirp.org/Journal/ForAuthors.aspx?JournalID=613 
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+ All manuscripts must be prepared in English.
+ Review paper is warmly welcome.
+ Submit your paper via online submission system papersubmission.
www.papersubmission.scirp.org/admin/initLoginAction.action?journalID=107 
+ To expedite the review process, please format your reference as the guideline,
+ Please visit journal homepage for more information.


Best Regards, 

Joyce Y.
Editorial Office of OJGEN
Scientific Research Publishing, USA 
Email:ojgen@scirp.org

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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 …

So I decided to try to come up with 100 words to complete the phrase “Scientists have …” I made a list and then gave each word a “weight” and used Wordle.Net to make a word cloud with them.

This word cloud, in the context of “Scientists have …” captures a lot of meeting for me.

Would be great to see other people come up with their 100 words for this …

My full list with scores is below:

art 15
awkwardness 5
badges 10
biases 10
bills 5
blogs 5
blues 5
bodies 5
books 20
bugs 5
cameras 5
cards 20
cash 5
cheerleaders 20
chocolate 10
circles 10
cliques 5
coffee 5
color 5
companions 10
computers 10
creeps 5
culture 10
data 20
debates 15
degrees 10
diversity 20
drinks 5
enemies 5
favorites 5
fears 20
feelings 10
fights 5
flavors 10
friends 20
fun 20
futures 5
glasses 5
goddesses 5
gossip 5
hangovers 20
hates 5
heroes 20
historians 5
homes 5
humor 20
ideas 10
institutions 10
issues 5
jargon 5
jobs 5
journalists 20
journals 20
languages 5
leaders 15
lemurs 15
love 10
lovers 20
microbes 5
money 5
museums 5
music 20
networks 5
nicknames 5
obsessions 20
papers 10
pasts 5
patience 20
pets 5
phones 20
pictures 5
piercings 10
pleasure 20
politics 10
porn 5
power 20
press 10
principles 5
prizes 5
problems 10
pseudonyms 20
respect 15
rights 5
scandals 5
science 20
sex 20
skin 15
stories 20
students 10
style 20
surprises 5
t-shirts 10
tattoos 20
teachers 20
tears 5
tolerance 5
toys 20
trolls 20
videos 5
weaknesses 10

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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

P164 P165

See the full gallery on Posterous

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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

P164 P165

See the full gallery on Posterous
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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

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).

UPDATE 2: August 2013.  Posterous is dead so deleted the links to the book pictures from Posterous below.  Changed it to Picasa.

https://static.googleusercontent.com/external_content/picasaweb.googleusercontent.com/slideshow.swf

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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)

Dear Jonathan:
My name is xxxxxxxxxxxxxxxxxx. I am writing you from Ontario, Canada. The purpose of this e-mail is to gather information from you for the book I am writing for the World! The book is entitled “XXXXX.” The book’s purpose is to expose to the world, World Peace and how to achieve it – free energy and how to harness it, along with many government coverups, e.g. Who really killed J.F.Kennedy (the driver!)? and who is really behind the attacks of 911?, along with cures for AIDS, cancer, and a long list of other diseases that you have written about in your book that I intend to expose to the world!

I would appreciate a response via any means necessary…..a phone call (xxx) xxx-xxxx, e-mail, with a contact number I can get in touch with you personally!

The world must be made aware of what’s really going on and, along with your help and others, WE CAN SAVE THE WORLD!!!!!

I am one who is aware that anything I type and send to you will be read by not only yourself – but by others (the Government)! These people will go to any great lengths to prevent us from speaking or having contact, because, we, in fact, know what’s really going on, and we know who is responsible for suppressing all the information that the world must know. I will leave the rest of the conversation for, hopefully, a face-to-face sit-down, or any future conversations that we MUST have.

Your new best friend,
xxxx.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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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).

The rest of the paper is worth a look.

And alas I stopped there … I think I wanted to get Brad Shaffer and Bob Thomson’s comments on the paper but never got around to it.  Two years later the paper still is worth a look …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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