Eisen Lab Blog

Dear Potential Post Doc or PhD Student – top10 ways to get a position in my lab

Dear Candidate (for any type of position in my lab)

I thought I would write a letter to you to help guide you in how to apply for a position in my lab.  Here are some suggestions for things that really help out – based on real emails I note …

  1. Describe your interests by copying text from my web site.  This shows that you are not only able to read, but also able to either copy directly or retype what you have read.  It is very appealing.
  2. Get my name or institution wrong in some way.  This shows that you are likely being industrious in applying for lots of jobs.
  3. Include attachments that do not open on Macs. Screw Steve Jobs and all of his fans.
  4. Send the same email multiple times – once to Prof. Eisen at UC Davis, once to Dr. Eisen at JGI, and once to Prof. Eisen from the “Genome Center at UC Davis.”  Repetition is an important literary technique. 
  5. Refer to the “reputation” of my group without saying anything specific about what interests you.  I love things based on reputation alone.
  6. Describe your background as very relevant to our work and then say that you too have focused extensively on microarray based studies of gene expression (I love stealing candidates whose original goal was to work in my brother’s lab).
  7. Have no publications but a list of more than 10 as “in preparation”.
  8. Include viruses in attachments – as I am interested in evolution of microbes this is appealing.
  9. Express an interest in biological weapons and biological defense and be from a terrorism sponsoring country.
  10. Have the original email message be more than four pages long with dozens of questions for me about my institution and my open positions.
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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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Some links worth checking out regarding suppressing publishing and bioterrorism

Just a quick one here with some links worth checking out regarding the recent discussion of suppressing some parts of a paper on engineering flu viruses
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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.

——–

Reminder – Monthly Omics Office Hours at #UCDavis Genome Center – Schedule

For those at UC Davis interested in learning a bit about various omics issues – this may be of interest:

Email from the responsible parties:
The UC Davis Genome Center holds an Omics Office Hour from 9:00-10:00am each month in Room 3209 of the Medical Education building in Sacramento. These drop-in sessions are open to anyone in the SOM community with questions regarding Genomics, Epigenomics and Gene Expression, Proteomics, Metabolomics, Network Biology and Bioinformatics.

The mission of the Genome Center is to facilitate your “omics” research at UC Davis. Genome Center staff and faculty will be on hand for consultation in a friendly, informal setting. If you have ideas that you would like to explore, we would be happy to discuss it as well as the possibility of pilot grants.

The next session will be Friday, January 6, 9:00 am in Room 3209 of Med Edu Bldg.

NOTE: THE DECEMBER 23, 2011 MEETING HAS BEEN CANCELED!!!!!

For more details, please link to:
http://www.genomecenter.ucdavis.edu/outreach-and-giving/omics-office-hour-2012

The schedule is also available as a Google Calendar called “‘Omics Office Hours”. For anyone who wants to subscribe to the calendar, here are instructions:

For Google Calendars:
1- go to Google Calendar
2 – under “Other calendars” click Add/Add by URL
3 – past the iCal link shown below into the box (https://www.google.com/calendar/ical/o6rt68uree1205hictul75m614%40group.calendar.google.com/public/basic.ics)
4 – click Add Calendar
5 – DONE

For iCal:
1- just click on the link below (might require some advanced Mac skills)
– or –
1- open iCAL
2- in the menu select Calendar/Subscribe
3 – past the iCal link shown below into the box (https://www.google.com/calendar/ical/o6rt68uree1205hictul75m614%40group.calendar.google.com/public/basic.ics)
4 – click Subscribe
5 – DONE


——–
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.

——–

Email regarding UC Davis Academic Senate Special Committee re: Pepper Spray

Posting for anyone interested (email from Linda Bisson – Chair of UC Davis Academic Senate)


Dear Colleagues:

There was an issue with the set up of the email address for the Special Committee that has now been corrected by IT. If you sent an email to the committee prior to Wednesday December 21st,  we request that you send it again. Sorry for the inconvenience.

Linda


 *original message*
Dear Colleagues,

During an emergency teleconference meeting, on November 20, 2011, the Davis Division Executive Council approved formation of a Special Committee to review the incident in which protestors were pepper sprayed on November 18, 2011. The Executive Council Special Committee on the November 18th Incident has been appointed.   The charge and membership are available on the Academic Senate website: http://academicsenate.ucdavis.edu/committees/exec-council-nov-18.cfm.  If you wish to provide the Special Committee information, please forward an e-mail message to: specialcommittee@ucdavis.edu.  I anticipate receipt of the report from this committee in February 2012.  

Sincerely,
Linda F. Bisson, Chair
Davis Division of the Academic Senate

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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.

——–

A few tweets about open science for the non twitterati

Just posting a few tweets of mine regarding open science – for those who do not follow me on twitter. Each of the four stories linked to below are worth a look.
phylogenomics
“A blogger’s quest to replicate ‘arsenic life’ led to a remarkable experiment in open science.” #ILOVEROSIE http://t.co/s1qBKpvW
12/22/11 6:37 AM
phylogenomics
Open and Shut?: The Open Access Interviews: OMICS Publishing Group’s Srinu Babu Gedela http://t.co/AZyCqx4C #Wow
12/20/11 8:05 A

phylogenomics
Must read of the week: Goodbye F1000, Hello Faculty of a Million from @caseybergman http://t.co/wwwO3061
12/19/11 9:02 AM
phylogenomics
What does Creative Commons mean for science? (Wired UK) http://t.co/77wmWzv2
12/16/11 4:39 AM
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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.

——–

The must have job of 2012: Faculty position in Evolution of Organismal Diversity at #UCDavis

The must have job of 2012 – a faculty position in my Department at UC Davis.  It is a GREAT department both scientifically (UC Davis is consistently ranked as having one of the best Evolution/Ecology programs in the country) and personally (the faculty, staff and students are great to be around).  See below for more information.  I am happy to give people any details of the Department, School, campus, etc if you are interested.

EVOLUTION OF ORGANISMAL DIVERSITY, UNIVERSITY OF CALIFORNIA, DAVIS 


The College of Biological Sciences, University of California, Davis invites applications and nominations for a tenure-track position in the Department of Evolution and Ecology at the ASSISTANT Professor level, with the possibility of ASSOCIATE appointment with tenure. Candidates must have a Ph.D. (or equivalent) in the biological sciences or related fields. 


They should have a strong record of integrative approaches to the evolution of organismal diversity. We seek candidates with expertise in the organismal biology/natural history of a multicellular group, and whose research uses genomic data in an explicitly phylogenetic context to address questions in macroevolution, ecology, behavior and/or development. The successful candidate will be expected to teach in the department’s undergraduate program and in the Population Biology Graduate Group and should be committed to departmental service. 


Applicants should submit materials online at this site which contains additional information about the position. Materials required include: curriculum vitae, description of current and projected research, summary of teaching interests and experience, and up to five publications. Applicants should also provide the information requested for three referees. Once entered, referees will be prompted by email with upload instructions for their letters. 


Closing Date: Open until filled, but all application materials, including letters of recommendation, must be received by February 6, 2012, to assure full consideration. 


Administrative contact: Carla Munoz (camunoz@ucdavis.edu). 


Faculty contacts: Peter Wainwright, Michael Turelli, and Rick Grosberg. 


The University of California is an Equal Opportunity/Affirmative Action Employer with a strong institutional commitment to the development of a climate that supports equality of opportunity and respect for differences.

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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.

——–

PROMED-MAIL – Nice resource to keep up with stories on outbreaks of infectious disease

For those interested in outbreaks of infectious diseases (which I assume is actually everyone in the world) – there is a nice resource out there called PROMED-MAIL.  It comes from the International Society for Infectious Diseases and it catalogs some recent stories from around the world on outbreaks.  It is worth checking out.  And if you like it, they are trying to raise some funds to keep it going with an Internet-A-Thon so consider donating …

Some recent stories I found there:

And more … fun for the whole family
——–
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.

——–

Meeting of interest: 16th Evolutionary Biology Meeting at Marseilles

Just got an email about a meeting of potential interest and thought I would share:

It is my pleasure to announce that registration and abstract submission for the 16th Evolutionary Biology Meeting at Marseilles, September 18-21, 2012, is open. Please visit the web site of the meeting http://sites.univ-provence.fr/evol-cgr where you will find all relevant information. 

The following subjects will be discussed:

  • – Evolutionary biology concepts and modelisations for biological annotation;
  • – Biodiversity and Systematics;
  • – Comparative genomics and post-genomics (at all taxonomic levels);
  • – Functional phylogeny;
  • – Environment and biological evolution;
  • – Origin of Life and exobiology;
  • – Non-adaptative versus adaptative evolution;
  • – The « minor » phyla: their usefulness in evolutionary biology knowledge;
  • – Convergent evolution

Looking forward to your participation.

——–
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.

——–

This land is your land – inspired by Woody

p101.mov Watch 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.

——–

Transfaunation and Fecal Transplants: What Goes Around Comes Around, Literally and Figuratively

In 2006 when I had just moved to UC Davis from TIGR, I was on a Southwest flight from Sacramento to (I think) Arizona. The person sitting next to me and I did the normal chit chat – what do you do? where are you going? etc. And the conversation became fascinating. The person sitting next to me was Mike Lagrone – a farrier (I forget people’s names frequently ten minutes after meeting them – but his name I remember even today, so he clearly made an impression). He travelled around the West helping take care of people’s horses. (I note – I think more information about him is here Mike Lagrone | EquiMed – Horse Health Matters).
Anyway – we ended up talking about microbes and animals and I told him about a project my lab was working on on tracking the microbes after ileal transplantation in people (see our paper on this here – the result of a collaboration between Amber Hartman in my lab and the lab of Michael Zasloff’s at Georgetown). We then discussed probiotics and he then told me an amazing story about how the old school farriers used a special method to treat horses if they were sick with some sort of gastrointestinal distress (e.g., colic). They would make the sick horse “poo tea” by taking feces from healthy horses and making it into a tea of sorts and then they served this to the sick horses. Anyway – the flight ended and he told me I should talk to some of the old school people in the Vet School at UC Davis and they might know more about it.
And then a few months later I had an interesting conversation with someone from the UC Davis Vet School – Jonathan Anderson – about horses. And as part of the conversation I told him of the discussion with Mike Lagrone and Jonathan told me there was a method called “transfaunation” which was analogous to the poo tea treatment – and was used for cows and horses and possibly other animals. Jonathan suggested I talk to Dr. Nicola Pusterla at UC Davis about this … but alas I never did.
And so – the seed of “transfaunation” and “poo tea” faded. And some things that should not have been forgotten were lost. History became legend. Legend became myth. And for four and a half years, the idea passed out of all knowledge.

But like the ring of power, transfaunation and poo tea could not be suppressed forever.  And magically, people began to talk about it over the last four years.  The human microbiome became hot.  Fecal transplants became a topic of conversation (with a little help from Carl Zimmer).  Even Colbert covered the topic.  And the final straw for me to get me to write about Mike Lagrone was when a few days ago my mom showed me an article in Scientific American by Maryn McKenna entitled “Swapping Germs: Should Fecal Transplants Become Routine for Debilitating Diarrhea?”  I knew then that the time had arrived for me to write about Mike Lagrone.  So I have.

I note, one reason I wanted to write up the story of meeting Mike Lagrone was because I personally had not noticed much in the coverage of human fecal transplants discussing the animal side of things.  This seemed a bit odd as transfaunation and poo tea and such are clearly closely connected in concept to fecal transplants in people.  A little digging (well, actually, a few Google searches) showed that many in fact have made the connection.  See for example these stories/articles:

To help those who might be interested in the animal side of “fecal transplants” I have made a mini-Mendeley collection of papers on the topic:

http://www.mendeley.com/groups/1716865/_/widget/29/10/

It is interesting to me how what goes around comes around (literally and figuratively).  This is probably a very ancient methodology – trying to move microbes from healthy individuals to sick ones to help treat them for various GI ailments.  And lets not even start talking about coprophagia which almost certainly has some “microbial colonization” component.  Thus, I conclude that, though fecal transplants in people may seem gross, it certainly makes a lot of sense that it could provide some benefits.  Not saying we know how to do it best or that it can cure everything – but it certainly seems worth pursuing in more detail.

Stay tuned – it seems very likely we will here much more about this in people over the next few years.  For some of the latest on the human side of things see
Fecal Transplants: They Work, the Regulations Don’t – also by Maryn McKenna.

Seems that medicine is catching up to what animals (and their caretakers) have known for some time …

UPDATE 1/16/2003 – Embedding my Ted talk on a related topic here

http://embed.ted.com/talks/jonathan_eisen_meet_your_microbes.html

More on fecal transplants and bacteriotherapy from my blog can be found below:

——–
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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