Talk for UC Davis Pre-Health Meeting (#UCDPHSA): Opening up to Diversity

Sunday I gave a talk at the "12th National UC Davis Pre-Health Student Alliance Pre-Medical and Pre-Health Professions Conference".  I normally try to not give talks on weekends (to spend time with my family) but I made an exception here since this meeting has a strong commitment to issues relating to diversity in health and STEM fields.  This mission statement for the meeting reads:

The UC Davis Pre-Health Student Alliance’s objective is to introduce and support academic, admission, and preparatory opportunities for all students interested in health professions with a focus on those underrepresented in healthcare (with regard to gender, economic, social, educational, linguistic, cultural, racial, and ethnic background). We target universities, community colleges and high schools throughout the United States. The UC Davis Pre-Health Student Alliance aims to impact health education, increase diversity amongst the healthcare workforce, and inspire future leaders of healthcare through hosting the largest national pre-health professions conference.

It was that mission statement that got me to ditch my wife and kids Sunday AM (and also much of Saturday PM for a dinner and to work on my talk).  I went to a dinner Saturday for some of the speakers with the new Dean of the UC Davis School of Medicine Julie Freischlag.  The dinner had about 20 or so people and I met some quite interesting folks there working on various aspects of human and animal health.

And then Sunday AM I got up early, decided to use slides (was not sure) and finished off the slide set I had worked on the night before.  I decided that, in the spirit of the meeting, I would talk about two main things - diversity and access.  And I planned to tell three stories about my work in this area.  I wove in some personal stories since, at the dinner the night before Barbara Ross-Lee (who I sat next to) helped remind me of the importance of making talks personal.  So in the end I talked about myself, diabetes, diversity of microbes, antibiotics, diversity in STEM, and open science.  I came up with a title I was OK with: Opening up to Diversity.

My talk went well, I think.  I am pretty sure it was vbideotaped but not sure where that recording will end up. I did however post my slides to slideshare.  See below:

Opening up to Diversity talk by @phylogenomics at #UCDPHSA from Jonathan Eisen

And I also recorded the talk using Camtasia (basically, it allows recording of the screen, the video camera on my computer, and the audio).  I posted the recording (without the video feed which shows mostly my neck) to Youtube.  See below:

UPDATE 10/16 -

I have scanned in my notes that I made in planning this talk.  Figured, why not post them.

Update: 12/10/2014 - just discovered a video of the talk was posted to Youtube 

All Nobel Prizes in 2014 Will be Microbially Themed: The Microbes Guarantee It

So - last year I secretly created a microbiome based spying system that can transmit the thoughts and emails of people who they colonize.  I introduced this community into all the people on the various Nobel Prize committees in order to get information in advance about their plans for the Nobel Prizes. After getting such information, and discovering that the Nobel's this year were NOT focused on microbes, I then created a microbiome-behavioral manipulation system and re-infected the Nobel committees with this community.  This community forces their host to think about microbes all the time.  All microbes.  All the time.  And thus I am nearly 100% certain that all the Nobel's this year will be about microbes in some way.

Given that, here are my predictions for the All-Microbial Nobel Prizes.

Medicine:
The Human Microbiome and Methods for Studying Microbial Communities.  Should go to Norm Pace and some other people.  Possibly Jeff Gordon.  Possibly Jo Handelsman.  Possibly others.  Depends on how much the microbes in the committees emphasize themselves versus all microbes.

Physics:
Vera Rubin for her work on "Dark Matter" since we all know that the key dark matter in the universe is "microbial dark matter".

Chemistry:
Discovery and characterizing of the mechanisms of CRISPRs.  No clue who will get this but it likely could include Jennifer Doudna and Emmanuelle Charpentier and others.

Peace:
Bill and Melinda Gates and their foundation for their work on global health, especially on protecting from infectious diseases.

Literature: Ursula K. Le Guin in particular for her Wrinkle in Time series and its emphasis is on mitochondria.

Economics:
Well, since microcredit has already won an Economics prize, I am not sure how this will play out but certainly it will involve some type of microeconomics.  Definitely NOT macroecnomics. I think the most likely winner here is Esther Duflo because of her work on both microeconomic topics and microcredit.

Me: Will survey results be published openly. Them: yes. Me: OK - will do survey. #opensurveys

Got this email:

Dear Jonathan, 

Your peers at the University of California, Riverside, Stanford University, and the Coachella Valley Association of Governments are seeking participation in a survey designed to explore the relevancy and perceptions of basic natural history knowledge and skills among professionals and graduate students in environmental science-related fields.
Professionals and Faculty (including post-doctoral researchers) may access the survey through the following link:https://stanforduniversity.qualtrics.com/SE/?SID=SV_9XmYW9WipZ0JGm1 

If you cannot complete the entire survey all at once, you can return to the survey within 30 days to complete it at your convenience. 

This survey will be distributed at universities, organizations and agencies state-wide, and we would greatly appreciate your participation! All responses will be kept completely confidential. The information collected will be used to provide summary statistics and form the basis of a peer-reviewed publication. 

Please feel free to forward this survey link to peers within California that may be interested in participating. Thank you for your assistance! 

****************************************************************************** 

Should you have questions about this study please contact us: natural.history.survey@gmail.com

Michelle Murphy-Mariscal, M.S. (Center for Conservation Biology, UC Riverside)Cameron W. Barrows, Ph.D. (Center for Conservation Biology, UC Riverside)Rebecca Hernandez, Ph.D. (Stanford University, Carnegie Institution for Science)Kathleen Fleming, M.S. (Coachella Valley Association of Governments)

-----------------------------------------
I wrote back

Thanks for the invite.

Can you tell me more about what will happen to the results from the survey? I only participate in surveys if the data and publications from the survey will be released in an open access manner.

Jonathan Eisen

And then got a very pleasing response:

Hi Jonathan, 

Yes, the results and data of the survey will definitely be published. Attached is a previous, survey-based study and we published the data set in Dryad (an online data repository that you are probably familiar with). The survey that my group and I are doing currently will follow the same format and strict adherence to open access. 

Thank you very much for your participation. 

Warmly,
Rebecca

And then I did the survey and sent this email:. 

Thanks so much for the response and I so pleased with your commitment to openness. I will now gladly participate and share w/ California colleagues.

Why I Tweet and Blog: Captured by Beryl Lieff Benderly

You know, many people ask me - why do I talk to science reporters so often.  They ask this and then claim that science reporters are just all kinds of evil because they always get quotes and facts and concepts wrong.  Well, that has really not been my experience.  Sure, I have my examples of problems.  But overall, I have been impressed and pleased more often than not.  And here is a great example. I was interviewed a while back by Beryl Lieff Benderly about my somewhat obsessive experimentation with social media for communicating science.  And then, of course, I forgot about it.  So I was exceptionally pleased when I saw the story come out today: To tweet or not to tweet? | Science Careers.  Beryl did a remarkably good job in capturing the essence of my thoughts about Tweeting, Blogging, social media, and science communication.

If you want to know what I think about how to not get overwhelmed with Twitter, how to not spend too much time on social media, and what I think abotu aboutb social media, you don't need to wait for me to try to write my thoughts on the topic down.  Read what Beryl wrote.

Crosspost from microBEnet: Some interesting new papers on functional analysius of metagenomics

Crossposting from microBEnet:

Some new papers that may be of interest to people:

• FOAM (Functional Ontology Assignments for Metagenomes): a Hidden Markov Model (HMM) database with environmental focus. 
• Statistical Methods for Functional Metagenomic Analysis Based on Next-Generation Sequencing Data PhD thesis from Pookhao, Naruekamol 
• Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data
• Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization 
• MP3: A Software Tool for the Prediction of Pathogenic Proteins in Genomic and Metagenomic Data   

Crosspost from microBEnet: Collection of papers on "The Science of Science Communication"

Crossposting this from microBEnet 

 Just got pointed to this by Sharon Strauss, the chair of the Evolution and Ecology department here at UC Davis: The Science of Science Communication II Sackler Colloquium.  This is a collection of papers from a colloquium held in Septment 2013.  Slides and videos of the talks are available online. The papers and links (copied from the PNAS site) are listed below.  There are many papers here of relevance to work done at microBEnet and are also likely of general interest to many:

• Science communication as political communication

  • Dietram A. Scheufele

  PNAS 2014 111 (Supplement 4) 13585-13592; published ahead of print September 15, 2014,doi:10.1073/pnas.1317516111
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  Gaining trust as well as respect in communicating to motivated audiences about science topics

  • Susan T. Fiske and
  • Cydney Dupree

  PNAS 2014 111 (Supplement 4) 13593-13597; published ahead of print September 15, 2014,doi:10.1073/pnas.1317505111
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  Leveraging scientific credibility about Arctic sea ice trends in a polarized political environment

  • Kathleen Hall Jamieson and
  • Bruce W. Hardy

  PNAS 2014 111 (Supplement 4) 13598-13605; published ahead of print September 15, 2014,doi:10.1073/pnas.1320868111
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  Creating a national citizen engagement process for energy policy

  • Nick Pidgeon, 
  • Christina Demski, 
  • Catherine Butler, 
  • Karen Parkhill, 
  • and Alexa Spence

  PNAS 2014 111 (Supplement 4) 13606-13613; published ahead of print September 15, 2014,doi:10.1073/pnas.1317512111
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  Using narratives and storytelling to communicate science with nonexpert audiences

  • Michael F. Dahlstrom

  PNAS 2014 111 (Supplement 4) 13614-13620; published ahead of print September 15, 2014,doi:10.1073/pnas.1320645111
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  The cultural side of science communication

  • Douglas L. Medin and
  • Megan Bang

  PNAS 2014 111 (Supplement 4) 13621-13626; published ahead of print September 15, 2014,doi:10.1073/pnas.1317510111
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  Prescriptive scientific narratives for communicating usable science

  • Julie S. Downs

  PNAS 2014 111 (Supplement 4) 13627-13633; published ahead of print September 15, 2014,doi:10.1073/pnas.1317502111
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  Communicating science-based recommendations with memorable and actionable guidelines

  • Rebecca K. Ratner and
  • Jason Riis

  PNAS 2014 111 (Supplement 4) 13634-13641; published ahead of print September 15, 2014,doi:10.1073/pnas.1320649111
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  The science of sharing and the sharing of science

  • Katherine L. Milkman and
  • Jonah Berger

  PNAS 2014 111 (Supplement 4) 13642-13649; published ahead of print September 15, 2014,doi:10.1073/pnas.1317511111
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  Integrating social networks and human social motives to achieve social influence at scale

  • Noshir S. Contractor and
  • Leslie A. DeChurch

  PNAS 2014 111 (Supplement 4) 13650-13657; published ahead of print September 15, 2014,doi:10.1073/pnas.1401211111
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  Team science for science communication

  • Gabrielle Wong-Parodi and
  • Benjamin H. Strauss

  PNAS 2014 111 (Supplement 4) 13658-13663; published ahead of print September 15, 2014,doi:10.1073/pnas.1320021111
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  Communicating scientific uncertainty

  • Baruch Fischhoff and
  • Alex L. Davis

  PNAS 2014 111 (Supplement 4) 13664-13671; published ahead of print September 15, 2014,doi:10.1073/pnas.1317504111
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