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

Notes from 2007 for a blog post I should have written: How many microbial cells in humans?

Well sometimes you just screw up.  In 2007 I attended some planning meetings for the human microbiome project (see for example A human microbiome program? a post I wrote from one of the meetings in 2007).  And at those meetings I kept asking one question.  Where did this “fact” everyone kept citing that there were “10 times as many microbial cells in the human body as there were human cells” come from?  I could not find a citation.  So I started taking some notes for a blog post about this.  Here are those notes:

Wikipedia linkOnline textbook hereSears paper from Arizona site. She discusses only gut bacteria and cites a Gordon paper from 2001.
Seems to not be from this paper but really from here:
This in turn is not from there but apparently here

But, alas I got distracted.  And I did keep asking people – where did this “fact” come from.  And most people just brushed me off (and probably thought I was a bit of a crank …). And nobody had a good answer.  Well, I was both pleased and sad (because I should have done it) to see Is your body mostly microbes? Actually, we have no idea by Peter Andrey Smith in the Boston Globe who addresses this issue in much much more detail that I ever could have done.  Everyone who works on the human microbiome and who is interested in “facts” and how they can get misreported should read this.  As a side note, Smith reports in the article that this is even given as a fact in Ted talks.  Sadly mine was one of them.  This is despite the fact (yes, the fact) that I swore to myself that I would NOT say that in my talk since I have been such a crank about this issue at meetings.  OMG – such truisms are so pervasive that even someone who actively questioned the truism still used it.  Uggh.  Oh well.  I really should have finished that draft post.

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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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Don’t forget to positively highlight meetings w/ "good" gender ratio of presenters

As many know, I spend a decent amount of effort critiquing conferences that have poor speaker diversity (mostly focus on gender ratio).  Well I am also trying to start calling out in a positive way those meetings that do a good job with speaker diversity. And here is one: 2014 Xenopus Genetics meeting in Pacific Grove.  I was pointed to it in an email that was in response to a Tweet I posted (not sure if I have permission to say who this was from – will post if they say it is OK). (UPDATE 9/20 – it was Ian Quigley).

From what I compute – the ratio was 30:22 male: female.  I do not know what the ratio of the “pool” of speakers is but regardless, having 42% female speakers is a more even ratio than I have seen for most life sciences meetings.  So they deserve some props for this.

Female speakers highlighted in yellow.  Male in green.  

Keynote Lecture: Rebecca Heald

Special Lectures from John Gurdon and Marc Kirschner

Invited Speakers

Enrique Amaya, University of Manchester

Ruchi Bajpai, University of Southern California

Bill Bement, University of Wisconsin

Mike Blower, Harvard Medical School

Cliff Brangwynne, Princeton University

Josh Brickman, The Danish Stem Cell Center DanStem

Ken Cho, University of California, Irvine

Hollis Cline, The Scripps Research Institute

Frank Conlon, University of North Carolina

Lance Davidson, University of Pittsburgh

Eddy DeRobertis, University of California, Los Angeles

Amanda Dickinson, Virginia Commonwealth University

Carmen Domingo, San Francisco State University

Karel Dorey, University of Manchester

Jim Ferrell, Stanford University

Jenny Gallop, University of Cambridge

Jay Gatlin, University of Wyoming

Jean Gautier, Columbia University

Xi He, Harvard University

Ralf Hofmann, Karlsruhe Institute of Technology

Jubin Kashef, Karlsruhe Institute of Technology

Mustafa Khokha, Yale University

Mary Lou King, University of Miami

Laurent Kodjabachian, Developmental Biology Institute of Marseille (IBDM)

Branko Lantic, Cardiff University

Dan Levy, University of Wyoming

Soeren Lienkamp, University of Freiburg

Karen Liu, King’s College

Laura Ann Lowery, Boston College

Ann Miller, University of Michigan

Brian Mitchell, Northwestern University

Anne-Helene Monsoro-Burq, Institute Curie

Kim Mowry, Brown University

Shuyi Nie, University of Georgia

Christof Niehrs, German Cancer Research Center (DKFZ)

Nancy Papolopulu, University of Manchester

Sabine Petry, Princeton University

Susannah Rankin, Oklahoma Medical Research Foundation

Bruno Reversade, Institute of Medical Biology, A* Singapore

Dan Rokhsar, University of California, Berkeley

Hazel Sive, Massachusetts Institute of Technology

Elena Silva Casey, Georgetown University

Francesca Spagnoli, Max-Delbrück-Center for Molecular Medicine (MDC)

Elly Tanaka, Center for Regenerative Therapies Dresden

Gert Veenstra, Radboud University Nijmegen

Monica Vetter, University of Utah

Sara Woolner, University of Manchester

Phil Zegerman, University of Cambridge

Aaron Zorn, Cincinatti Children’s

——–
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 distasteful & disgraceful "Are there limits to evolution?" meeting at the University of Cambridge #YAMMM

Well, I saw this Tweet the other day

//platform.twitter.com/widgets.js And though there was a bit of a discussion on Twitter I felt I had to follow up with a blog post. When I saw the post I was at a conference (Lake Arrowhead Microbial Genomes) where I could get Twitter access but for some reason very little web access. So I could not dig around until now (I am home). 

This meeting is a complete disgrace and an embarassment for the field of evolutionary biology, for the University of Cambridge which is hosting the meeting, and for the Templeton Foundation which is sponsoring it.

Why do I say this? Well, pretty simple actually. The meeting site lists the Invited Keynote speakers for the meeting.  Notice anything?  How about I help you by bringing all the pictures together.

Notice anything now?  How about I help you some more by masking out the men and not the women.

Impressive no?  25 speakers – 23 of them male.  I guess that means there are no qualified female speakers who coudl discuss something about evolution right?  It would be worth reading “Fewer invited talks bu women in evolutionary biology symposia” to get some context.  What an incredible, disgusting, distasteful and disgraceful meeting.  
I recommend to everyone who was considering going to this meeting – skip it.  Also consider writing to the University of Cambirdge and the Templeton Foundation to express your thoughts about the meeting.  This certainly is a fine example of Yet Another Mostly Male Meeting (YAMMM).  Well, maybe I should word that differently – this is a disgusting example of a YAMMM.  

For more on this and related issues

  • Posts on Women in STEM


    • Also see

    //platform.twitter.com/widgets.js

    ——–
    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.

    ——–

    Everything You Wanted to Know about the Lake Arrowhead Microbial Genomes meeting #LAMG14

    The Lake Arrowhead Microbial Genomes meeting, which happens every other year, is starting tonight.  I love this meeting.  No bias here since I am now a co-organizer.  But I really love this meeting.  I am posting here some background information about the meeting for those interested.  We will be live tweeting the meeting using the hashtag #LAMG14.  This years program is here.

    Posts of mine about previous meetings

    Blog posts by others

    Programs and notes from past meetings

    Meeting Web Sites

    I have uploaded slides from my previous presentations at the meeting

      ——–
      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.

      ——–

      Fun read of the day: On whimsy, jokes, and beauty: can scientific writing be enjoyed?

      This is such a fun paper: On whimsy, jokes, and beauty: can scientific writing be enjoyed? by Stephen Heard in Ideas in Ecology and Evolution 7: 64–72, 2014  I found out about it in an email from Heard, who sent it to me because he had earlier commented on a blog post I had written: The best writing in science papers part 1: Vladimir Nabokov in Notes on Neotropical Plebejinae (Lycaenidae, Lepidoptera).

      Anyway – enough about me – what about this paper?  It has so many nuggets of interest I am not sure which to highlight so I will just go through some of it.  Oh – and it is published with a Creative Commons Attribution license (yay).

      Abstract: While scientists are often exhorted to write better, it isn’t entirely obvious what “better” means. It’s uncontroversial that good scientific writing is clear, with the reader’s understanding as effortless as possible. Unsettled, and largely undiscussed, is the question of whether our goal of clarity precludes us from making our writing enjoyable by incorporating touches of whimsy, humanity, humour, and beauty. I offer examples of scientific writing that offers pleasure, drawing from ecology and evolution and from other natural sciences, and I argue that enjoyable writing can help recruit readers to a paper and retain them as they read. I document resistance to this idea in the scientific community, and consider the objections (well grounded and not) that may lie behind this resistance. I close by recommending that we include touches of whimsy and beauty in our own writing, and also that we work to encourage such touches in the writing of others.

      OK – the title would have drawn me in anyway but the abstract definitely had me.

      If scientific writers aren’t sure how to write better, it isn’t for lack of advice. Dozens of guidebooks discuss form, style, and goals in scientific writing (e.g., Montgomery 2003, Davis 2005, Day and Gastel 2006, Katz 2006, Matthews and Matthews 2007, Rogers 2007, Harmon and Gross 2010, Hofmann 2010, Pechenik 2010, Greene 2013, Heard unpubl.).

      OK – I am going to have to look at some of these.

      Heard documents a bit of a spat between Sprat and Boyle from the 1660s regarding scientific writing.  I especially like the Boyle quote:

      To affect needless rhetorical ornaments in setting down an experiment…were little less improper than…to paint the eyeglasses of a telescope…in which even the most delightful colours cannot so much please the eye as they would hinder the sight…And yet I approve not that dull and insipid way of writing, which is practiced by many…for though a philosopher need not be solicitous that his style should delight his reader with his floridness, yet I think he may very well be allowed to take a care that it disgust not his reader by its flatness…Though it were foolish to colour…the glasses of telescopes, yet to gild…the tubes of them may render them most acceptable to the users (Boyle 1661:11-12, spelling and punctuation modern- ized).

      Heard then goes through some different aspects of good scientific writing

      • Sightings (1): Playfulness in the scientific literature
      • Sightings (2): Beauty

      Also – he then doscusses pushback against the “notion that whimsy, jokes, and beauty can have a place in our scientific literature.” which I have also seen in many contexts.

      He ends with suggestions and I quote the whole section with some highlights:

      If you write papers that are crystal clear and thus effortless to read, you’ll have achieved the primary goal of scientific writing and your work will be among the best of our literature. But if you want to reach for even more, if you agree with me that we can also offer our readers some pleasure in reading, what can you do? To begin, you can try to write with small touches of whimsy, humanity, humour, and beauty—without, of course, compromising clarity; and even knowing that sometimes, reviewers will make you take them out. I am not suggesting writing in which art shares the stage equally with content (as can be true in the lay literature). Rather, the goal that’s within our reach is clear, functional writing punctuated with occasional nuggets of playfulness or glints of beauty—to extend Boyle’s metaphor, not a telescope of solid gold but one lightly gilded. 

      You can also work to encourage pleasure in what your colleagues write, in two complementary ways. First, when you review manuscripts, you can suppress the reflex telling you to question any touches of whimsy, humour, or beauty that you find; you can even (gently) suggest some be put in. Second, you can announce your admiration of writing that has given you pleasure. Announce your admiration to the writers who crafted the passage, to editors who might be considering its fate, and to students or colleagues who might read it. If we choose to, we can change our culture to deliver, and value, pleasure along with function in our writing.

      This is a must read paper.  And I really wish more people would endorse the idea that scientific writing can include more than just science.  Of course, there are many who already endorse this notion but for those who do not – give it a try.

      ——–
      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.

      ——–

      Cornell University-MBG job posting

      Posting this:

      Dear Dr. Eisen,

      We are writing to enlist your assistance in identifying talented candidates for a tenure-track Assistant or Associate Professor position in the Department of Molecular Biology and Genetics at Cornell University in Ithaca, NY. We are seeking to fill this position with a creative individual in the area of Computational Genomics.

      Our hope is that this individual will interact synergistically with existing department strengths as well as those in other departments at Cornell including Biological Statistics and Computational Biology (BSCB). We envision that the ideal candidate will develop innovative computational genomics methods to solve novel problems in genome biology. An advertisement, which is attached, will appear in the September 19, 2014 issue of Science and more information is available at http://mbg.cornell.edu/jobs

      This is a very exciting time at Cornell as the University has specifically targeted computational biology for expansion, and is making a concerted investment in interdisciplinary studies that bridge existing strengths in the University.

      The Department of Molecular Biology and Genetics (www.mbg.cornell.edu ) includes a highly interactive faculty with research programs in genetics, molecular biology, comparative and population genomics, cell biology, developmental biology, biochemistry and structural biology. Excellent students are attracted to graduate programs in Biochemistry, Molecular and Cell Biology (BMCB), Genetics, Genomics and Development (GG&D), Computational Biology (CB), and Biophysics.

      Please bring this great opportunity to the attention of outstanding junior scientists in your department. It would help us enormously if you could post the attached advertisement. If you have any questions, please do not hesitate to contact me at barbash.

      Sincerely yours,

      Daniel Barbash, Ph.D.

      Associate Professor

      Chair, Computational Genomics Search Committee

      Computational Genomics Ad September 2014.pdf

      Kudos to Tedmed for the gender ratio of speakers for this year’s event

      Well done Tedmed.

      Here are the speaker pages below.  Notice anything?

      The gender ratio of speakers is actually well balanced.  Well done Tedmed.  Well 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.

      ——–

      International Symposium on Subsurface Microbiology – where men tell us about deep things

      Just saw this Tweet:

      //platform.twitter.com/widgets.js This refers to this meeting: Call for Abstracts for 2014 Ninth International Symposium on Subsurface Microbiology, Pacific Grove California

      The plenary speakers for this meeting are all men

      • Peter Girguis
      • Terry Hazen
      • Rainer Meckenstock
      • Lars Nielsen
      • Aaron Packman
      • Karsten Pedersen
      • Timothy Scheibe
      • Jack Schijven

      The last meeting was in 2011 and it was not much better – with one female keynote speaker.

      • Andreas Kappler
      • Karsten Pedersen
      • Christian Griebler
      • Ian Head
      • Frank Löffler
      • Babara Sherwood-Lollar
      • Bo Barker Jørgensen
      • Ken Takai
      • Kai-Uwe Hinrichs
      • Tori Hoehler

      Apparently, only men can talk about deep things.  Fun times.

      ——–
      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.

      ——–

      Grant opportunities from the Bill & Melinda Gates Foundation

      Received this email:

      Dear Colleagues,

      The Bill & Melinda Gates Foundation is now inviting applications to Grand Challenges Explorations, which has awarded over 1070 grants in over 58 countries to date.

      Grand Challenges Explorations seeks innovative global health and development solutions. Applicants can be at any experience level; in any discipline; and from any organization, including universities, government laboratories, research institutions, non-profit organizations as well as for-profit companies.

      Two-page proposals are being accepted online from September 4, 2014 until November 12, 2014 on the following topics:

      – Surveillance Tools, Diagnostics and an Artificial Diet to Support New Approaches to Vector Control.
      – New Approaches for Addressing Outdoor/Residual Malaria Transmission
      – New Ways to Reduce Pneumonia Fatalities through Timely, Effective Treatment of Children
      – Enable Universal Acceptance of Mobile Money Payments to Create an Economic Ecosystem that Will Help Lift the Poorest Out of Poverty
      – Explore New Ways to Measure Brain Development and Gestational Age
      – New Ways of Working Together: Integrating Community-Based Interventions

      Initial grants will be US $100,000 each, and projects showing promise will have the opportunity to receive additional funding of up to US $1 million. Full descriptions of the new topics and application instructions are available at: www.grandchallenges.org/explorations.

      We look forward to receiving innovative ideas from around the world and from all disciplines. If you have a great idea, please apply. If you know someone who may have a great idea, please forward this message.

      Please also note our Global Health Innovation Group on LinkedIn. Developed in collaboration with Grand Challenges Canada, this group offers a platform to connect and communicate with innovators from around the world. Anyone with a LinkedIn account can join and make use of this forum.

      Thank you for your commitment to solving the world’s greatest health and development challenges.

      The Grand Challenges Team

      Single cell genomics at #UCDavis …

      z

      UCDMCroadshow2014-BGImod.pdf