Eisen Lab Blog

Apparently, the National Academy of Sciences thinks only one sex is qualified to talk about alternatives to sex #YAMMM

Just got this email from Francisco Ayala:

January 9-10, 2015 

In the Light of Evolution IX. Clonal Reproduction: Alternatives to Sex 

Organizers: Michel Tibayrenc, John C. Avise and Francisco J. Ayala 

Beckman Center of the National Academies, Irvine, CA 

Evolutionary studies of clonal organisms have advanced considerably in recent years, but are still fledgling. Although recent textbooks on evolution and genetics might give the impression that nonsexual reproduction is an anomaly in the living world, clonality is the rule rather than the exception in many viruses, bacteria, and parasites that undergo preponderant asexual evolution in nature. Clonality is thus of crucial importance in basic biology as well as in studies dealing with transmissible diseases. 

This Colloquium will bring together specialists in various disciplines, including genetics, evolution, statistics, bioinformatics, and medicine. A balance will be sought between the various disciplines, including clonal animals and plants, animal and human cloning, pathogens, and cancer studies.   

Registration is now open http://www.nasonline.org/programs/sackler-colloquia/upcoming-colloquia/ILE_IX_Clonal_Reproduction.html

Registration fee is $150. 

Graduate students and postdoctoral researchers are eligible for discount fee of $100. 

All meals, break and reception refreshments listed on the agenda are included in the registration fee.
For more information, contact sackler@nas.edu.

Could be interesting right?  Alas, then, I clicked on the link.  And I discovered the meeting could also be referred to as “Only one sex talks about alternatives to sex”.  Men are highlighted in yellow. Women highlighted in green. (Note – I am making some guesses as to gender but I think these are reasoably accurate).

Organizers: Michel Tibayrenc, John C. Avise and Francisco J. Ayala 

I. General Considerations  

  • 8:30 AM Overview: The ILE Series. John C. Avise  
  • 8:40 AM Introduction and Chair, John C. Avise  
  • 8:40 AM  Can eukaryotes be considered clonally propagating cell lines with intermittent sex?, Dave Speijer, University of Amsterdam 
  • 9:30 AM Cancer in Parasitic Protozoan Trypanosoma brucei and Toxoplasma gondii, Zhao-Rong Lun, Sun Yat-Sen University 
  • 10:40 AM Mathematical Models of Clonality, Dominik Wodarz, University of California, Irvine 
  • 11:30 AM The Cost of Sex: Why Aren’t We All Clonal?, Claus-Peter Stelzer, University of Innsbruck 

II. Clonality in Multicellular Organisms  1:30 PM Chair, Zhao-Rong Lun

  • 1:30 PM  Genets, Ramets and Unisexual Reproduction in Plants, Spencer C.H. Barrett, University of Toronto
  • 2:20 PM Clonality in Asexual Invertebrate Animals, John M. Logsdon, Jr., University of Iowa
  • 3:30 PM Natural Clonality in Vertebrate Animals, John C. Avise, University of California, Irvine
  • 4:20 PM Artificial Cloning of Domestic Animals, Carol L. Keefer, University of Maryland

Keynote Address 

  • 6:45 PM Introduction, Michel Tibayrenc
  • 6:50 PM Cloning Humans: Biological and Ethical Considerations, Francisco J. Ayala, University of California, Irvine

III. Clonality in the Microbial World  

  • 8:00 AM Chair, Carol L. Keefer  
  • 8:00 AM Clonality and Intracellular Polyploidy in Virus Evolution and Pathogenesis, Esteban Domingo, Universidad Autónoma de Madrid
  • 8:50 AM The Impermanence of Bacterial Clones, Howard Ochman, University of Texas, Austin
  • 10:00 AM Clonal Reproduction in Fungi, John Taylor, University of California, Berkeley
  • 10:50 AM Clonal Reproduction in Parasitic Protozoa, Michel Tibayrenc, IRD, Montpellier, France

IV. Clonality, Cancer, and Evolution

  • 12:50 PM Organismal Fitness, Somatic Evolution, and Cancer, James DeGregori, University of Colorado School of Medicine
  • 1:40 PM Cancer and Pathogens as Clonal Processes, Edwin L. Cooper, University of California, Los Angeles
  • 2:50 PM Stem Cell Competitions: Evolution, and Cancer Progression, Irving Weissman, Stanford University
  • 3:40 PM Clonal Reproduction: An Evolutionary Curse or Blessing?, Marcel E. Dorken, Trent University
  • 4:30 PM Concluding Remarks, Francisco J. Ayala, University of California, Irvine

So – whether you count just speakers, or speakers plus session chairs, the gender ratio is not good.  Really there is only one woman as far as I can tell involved with this meeting.  Sadly this is not the only meeting at the NAS Beckman Center with gender issues.  See this post for example Today’s YAMMM (Yet Another Mostly Male Meeting) Brought to You by CIFAR & NAS.  Does NAS even make any effort in regard to diversity of speakers?

UPDATE 10/25/14 – Some responses from Twitter

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For more on this topic see my other posts on “Diversity in STEM“

UPDATE 2: 10/26 – New NAS Sackler meeting after this one – better but barely in gender ratio

The next Sackler meeting after this one is on “Drawing Causal Inference from Big Data”.  Here are the speakers they list with the same colors as used above.

  • Edoardo Airoldi, Harvard University
  • Susan Athey, Stanford University 
  • Leon Bottou, Microsoft Corporation 
  • Danah Boyd, Microsoft Corporation
  • Peter Buhlmann, ETH Zurich 
  • Susan Dumais, Microsoft Corporation
  • Dean Eckles, Facebook 
  • James Fowler, University of California, San Diego  
  • Michael Hawrylycz, Allen Institute 
  • David Heckerman, Microsoft Corporation 
  • Jennifer Hill, New York University 
  • Guido Imbens, Stanford University
  • Michael Jordan, University of California, Berkeley 
  • Steven Levitt, The University of Chicago 
  • David Madigan, Columbia University
  • Thomas Richardson, University of Washington 
  • Bernhard Schölkopf, Max Planck Institute 
  • Jasjeet Sekhon, University of California, Berkeley 
  • Cosma Shalizi, Carnegie Mellon University  
  • Richard Shiffrin, Indiana University 
  • John Stamatoyannopoulos, University of Washington 
  • Hal Varian, Google, Inc. 
  • Bin Yu, University of California, Berkeley 

That is a ratio of 18:5 or 21% women.  Not sure what the gender balance is for people working on “big data” but still, given the Sackler’s recent issues with gender ratio in fields with an almost 50:50 ratio of men:women I am not willing to give them the benefit of the doubt here.  And I note – the link they provide for Susan Athey goes to the web site of Richard Shiffrin.  So I am just going to assume that the name on the list is correct not the link to Shiffrin.

UPDATE 3: 10/26 – Made a Storify to track discussion of this.

UPDATE 4: 10/26 — and another recent Sackler meeting

Epigenetic changes in the developing brain: Effects on behavior

This meeting was held March 28-29, 2014 at the National Academy of Sciences in Washington, D.C. and organized by Donald W. Pfaff (The Rockefeller University) and Eric Barrington Keverne (King’s College, Cambridge).

  • Introduction and welcome, Donald Pfaff and Barry Keverne
  • Session I. DNA methylation (Chair, Tom Insel)
    • Mechanisms that establish and maintain genomic methylation patterns in mammalian tissues, Tim Bestor, Columbia University
    • Signaling networks that regulate synapse development and dysfunction, Michael Greenberg, Harvard University
    • Impact of early life experiences on DNA methylation: Implications for brain development and behaviour, Frances Champagne, Columbia University
  • Session II. Histone modifications (Chair, Barry Keverne)
    • A histone methylation network regulates epigenetic inheritance, Yang Shi, Harvard University
    • Global Epigenomic Reconfiguration during Mammalian Brain Development, Joseph Ecker, Salk Institute for Biological Studies
    • H3.3 nucleosomal dynamics regulate synaptic development and plasticity in postreplicative neurons, Ian Maze & David Allis, The Rockefeller University
    • Steroid hormone actions on histone tail modifications in the brain, Donald Pfaff, The Rockefeller University
  • 14th Annual Sackler Public Lecture
    • Introduction – Diane Griffin, Vice President, National Academy of Sciences
    • Deconstructing circuits for motor behavior, Thomas Jessell, Columbia University
  • Session III. Genomic imprinting (Chair, Rusty Gage)
    • Genomic imprinting,action and interaction of two genomes in mother, Barry Keverne, Cambridge University
    • Epigenetic regulation of imprinted gene loci, Marisa Bartolomei, University of Pennsylvania Medical School
    • Monoallelic gene expression, Andrew Chess, Mount Sinai Hospital
  • Session IV. Non-coding RNA’s (Chair, Don Pfaff)
    • Linking RNA to Nuclear Architecture, John L. Rinn, Broad Institute of Harvard and MIT
    • Human retrotransposons (“jumping genes”) in health and disease, Haig Kazazian, Johns Hopkins University
  • Session V. CNS applications (Chair, Tim Bestor)
    • Mobile Element Activity in Evolution and Disease, Fred Gage, Salk Institute
    • The Epigenetic Language of the Circadian Clock, Poalo Sassone-Corsi, University of California, Irvine
    • Epigenomics of Major Psychiatric Disease, Art Petronis, University of Toronto
    • Imprinting mechanisms underlying Prader Willi and Angelman syndromes, James Resnick, University of Florida
  • Closing remarks: Brain Exceptionalism, Tom Insel, Director, National Institute of Mental Health, NIH

So – if you just count all the speaking / session chair slots that comes to 24 slots to men and 3 to women for a wonderful 11% female percentage.  Even if you count just speakers (and not session chairs) the #s don’t look good.  Looking pretty bad NAS Sackler meetings.

UPDATE 5: Copying in my analysis of gender ratio at the most recent Sackler meeting on Symbioses becoming permanent: The origins and evolutionary trajectories of organelles which I refer to above but only via a link out to my post.  Here is the speaker analysis:

  • Organizers: W. Ford Doolittle, Patrick Keeling, and John McCutcheon
  • Distinctive Voices Public Lecture presented by Michael Gray, CIFAR Advisor, Dalhousie University
  • Session 1: Genomes (evolutionary rates, oddities, and reduction)
    • Introduction and welcome remarks – W. Ford Doolittle, CIFAR Advisor & Patrick Keeling, CIFAR Program Director and Senior Fellow
    • John McCutcheon, CIFAR Associate Fellow, University of Montana
    • John Archibald, CIFAR Senior Fellow, Dalhousie University, Nuclear organelles 
    • Andrew Roger, CIFAR Senior Fellow, Dalhousie University, Organelle reduction 
    • Siv Andersson, Uppsala University, Alphaproteobacterial genome evolution 
    • David Smith, University of Western Ontario, Roots of genomic architecture variation 
    • Daniel Sloan, Colorado State University, Cytonuclear co-evolution under extreme mitochondrial mutation rates
    • John Allen, University College London, Why keep genomes?
  • Session 2: Integration/Control (trafficking, signaling, transporters)
    • Debash Bhattacharya, Rutgers University, Transporters in organellogenesis 
    • Nancy Moran, University of Texas, Austin, Insect endosymbionts 
    • Geoff McFadden, University of Melbourne, Diversity of protein trafficking
    • Chris Howe, Cambridge University, Why integrate?
    • Steve Perlman, CIFAR Fellow, University of Victoria, Maternal transmission, sex ratio distortion, and mitochondria 
    • William Martin, Düsseldorf University, Endosymbiont and organelle, what’s the difference? 
    • Moriya Okhuma, Riken University, Metabolic integration across endosymbiotic communities
  • Session 3: Theories and Models
    • Eors Szathmary, Loránd University, A fresh look at cooperation in some major transitions, especially the origin of eukaryotes
    • Marc Ereshefsky, University of Calgary, Evolutionary individuality
    • Peter Godfrey-Smith, City University of New York, Individuality and the egalitarian transitions 
    • Maureen O’Malley, University of Sydney, Philosophical Reflections on Endosymbiosis: Implications for Evolutionary Theory
    • Toby Kiers, University Amsterdam, Bacterial cooperativity
  • Closing remarks J. McCutcheon

That is a ratio of 19:4 for speakers slots for men vs. women.  Sensing a pattern anyone?

UPDATE 6: I feel much better now looking at the meeting before the developing brain meeting.  It is so much better (not). 

In the Light of Evolution VIII: Darwinian Thinking in the Social Sciences. January 10-11, 2014 at the Arnold and Mabel Beckman Center in Irvine, CA. 

  • Organized by Brian Skyrms, John C. Avise and Francisco J. Ayala
  • I.  Evolution of Social Norms
    • Bargaining and Fairness, Kenneth Binmore, University College London
    • Cooperation, Natalia Komarova, University of California, Irvine
    • Friendship and Natural Selection, James H. Fowler, University of California, San Diego
    • Reputation and Punishment, Michihiro Kandori, University of Tokyo
  • II. Social Dynamics
    • The Replicator Equation and Other Game Dynamics, Ross Cressman, Wilfrid Laurier University
    • Payoff-Based Learning Dynamics, Alvin Roth, Harvard University
    • Strategic Learning Dynamics, David K. Levine, Washington University
    • Cultural Evolution, Marcus W. Feldman, Stanford University
  • Keynote Address:  Public Goods: Competition, Cooperation, and Spite, Simon A. Levin, Princeton University
  • III. Special Sciences
    • Evolutionary Demography, Kenneth W. Wachter, University of California, Berkeley
    • Folklore of the Elite and Biological Evolution, Barry O’Neill, University of California, Los Angeles
    • Economics, Ted Bergstrom, University of California, Santa Barbara
    • Psychology, Dale Purves, Duke-National University of Singapore Graduate Medical School
  • IV. Applications
    • Evolutionary Implementation in Mechanism Design, Éva Tardos, Cornell University
    • Some Dynamics of Signaling, Brian Skyrms, University of California, Irvine
    • The Rate of Innovation Diffusion in Social Networks, H. Peyton Young, Oxford University
    • Homophily, Culture, and Coordinating Behaviors, Matthew O. Jackson, Stanford University

That is 15:2 males to females in speaking slots and also three main organizers. 

Update 7: A trend in meetings coorganized by John Avise and Francisco Ayala

I note the meeting above in Update 6 is the second recent meeting coorganized by John Avise and Francisco Ayala with a highly skewed gender ratio.  So I decided to go back and look at other meetings they coorganized.  For example here is the next most recent one.

In the Light of Evolution VII: The Human Mental Machinery

Organized by Camilo J. Cela-Conde, Raúl Gutiérrez Lombardo, John C. Avise and Francisco J. Ayala

This meeting was held January 10-12, 2013 at the Arnold and Mabel Beckman Center in Irvine, CA.

  •  I. Theory of Mind 
    • Theory of Mind: Darwin’s legacy, John Searle, University of California, Berkeley
    • Human mind and brain – pathological evidence, Robert E. Clark, University of California, San Diego 
    • Theory of Mind in Other Primates, Robert M. Seyfarth, University of Pennsylvania
  • II. Cognition
    • Evolution of Working Memory, Peter Carruthers, University of Maryland
    • The evolution of episodic memory, Norbert Fortin, University of California, Irvine
    • Natural Basis of Cognition, Terrence J. Sejnowski, Salk Institute for Biological Studies
    • Human and Animal Consciousness, Michael T. Alkire, University of California, Irvine
    • Co-Evolution: Culture, mind and brain, Chet C. Sherwood, George Washington University 
  • Keynote Address 
    • Unusual and Exceptional Capacities of the Human Mind, James L. McGaugh, University of California, Irvine     
  • III. Evolving Piece by Piece: Levels of Modularity in Neurobiology
    • Neuronal Networks of the Moral Judgment, Patricia Churchland, University of California, San Diego
    • Pathological Altruism, Barbara A. Oakley, Oakland University
    • Theory of Justice in Non-Human Primates, Sarah F. Brosnan, Georgia State University
    • Evolutionary Dynamics of Altruism, Martin Nowak, Harvard University
    • Human and Animal Neuroeconomics, Michael Platt, Duke University 
  • IV. Aesthetics 
    • Music and the Brain, Robert Zatorre, Montreal Neurological Institute 
    • Aesthetic and Ethnic Emotions, Oshin Vartanian, University of Toronto, Scarborough
    • Aesthetic Perception: Mind and Brain , Camilo J. Cela-Conde, University of the Baleares Islands, Spain

That is a ratio of 14:3 for speakers of men: women. //platform.twitter.com/widgets.js

UPDATE 8: The next most recent meeting coorganized by Avise and Ayala

In the Light of Evolution VI: Brain and Behavior
January 19-21, 2012
Arnold and Mabel Beckman Center
Organized by Georg F. Striedter, John C. Avise and Francisco J. Ayala

  • Session I. Brains in History: Descent with Modification
    • Chair, John C. Avise, University of California, Irvine
    • Evolution of Brain Development, Georg Striedter, University of California, Irvine
    • Evolution of Neuronal Cell Types, Nipam H. Patel, University of California, Berkeley
    • Homology and Homoplasy of Behavior and Neural Circuits, Paul S. Katz, Georgia State University
    • Evolution of Cognitive Traits, Lucia F. Jacobs, University of California, Berkeley
  • Session II. Brains in Ecology: Adapatation by Natural Selection
    • Chair, Georg Striedter, University of California, Irvine
    • Adaptation of Neuron-typical Molecules and Processes, Harold H. Zakon, University of Texas, Austin
    • Evolution of Specialized Sensory Systems, Kenneth C. Catania, Vanderbilt University
    • Evolution of Specialized Motor Systems, Andrew H. Bass, Cornell University
    • Evolving Neural Mechanisms of Social Diversity and Cognition, James L. Goodson, Indiana University
  • Keynote Address
    • Introduction, Francisco J. Ayala, University of California, Irvine
    • Evolution of Centralized Nervous Systems, R. Glenn Northcutt, Scripps Institution of Oceanography
  • Session III. Evolving Piece by Piece: Levels of Modularity in Neurobiology
    • Chair, Lucia F. Jacobs, University of California, Irvine
    • Molecular Models in Neurobiology, Kenneth S. Kosik, University of California, Santa Barbara
    • Devolpmental Modules in Nervous Systems, Leah A. Krubitzer, University of California, Davis
    • Neuroanatomical and Physiological Modules, Jon H. Kaas, Vanderbilt University
    • Modularity of Cognitive Processes, Jessica F. Cantlon, University of Rochester
  • Session IV. Human Evolution: Brains and Behavior
    • Chair, Francisco J. Ayala, University of California, Irvine
    • Molecular Aspects of Human Brain Evolution, Todd M. Preuss, Emory University School of Medicine
    • Evolution of Primate Brain Morphology, Suzana Herculano-Houzel, Universidade Federal do Rio de Janeiro
    • Evolution of Primate Brain Functions, Lizabeth M. Romanski, University of Rochester
    • The Evolution of Human Cognition, Clark Barrett, University of California, Los Angeles
  • Concluding Remarks
    • Francisco J. Ayala, University of California, Irvine
That isa ratio of 17:6 if one includes all slots (chairs, speakers, etc) or 14:5 if you just include speaking slots. 

UPDATE 9: This is NOT just about speaking at meetings.

I note – many of the Sackler meetings turn into special collections in PNAS and thus the limited representation of women speakers (which is a problem) is made worse by then directly affecting publishing in PNAS.

UPDATE 10: 10/27/14. Going back to another Avise/Ayala meeting from 2001

In the Light of Evolution V: Cooperation

Organized by Joan E. Strassmann, David C. Queller, John C. Avise, and Francisco J. Ayala
January 7-8, 2011

(Note Joan Strassmann is one of my favorite scientists and people on the planet – great to see her in a role as coorganizer here)

  • Session I. Foundations of Cooperation
    • John C. Avise, University of California, Irvine, Chair
    • Insect Societies: pinnacles of cooperation – Peter Nonacs, University of California, Los Angeles
    • Families in vertebrates – Dustin R. Rubenstein, Columbia University
    • The major evolutionary transitions In bacterial symbiosis – Joel L. Sachs, University of California, Riverside
    • Kin, kith, and kind: the varieties of social experience – David C. Queller, Rice University
  • Session II. Genetic Basis of Cooperation and Conflict
    • David Queller, Chair
    • Altruism and cheating in a social microbe, Dicytostelium discoideum – Joan E. Strassmann, Rice University
    • A prokaryotic model system –Greg Velicer, Indiana University
    • The evolution of restraint in simple communities – Ben Kerr, University of Washington
    • Selfish genetic elements – Jack H. Werren, University of Rochester
  • Banquet Lecture
    • Francisco J. Ayala, University of California, Irvine, Introduction
    • Evolution of insect society: eat, drink and be scary – Gene E. Robinson, University of Illinois at Urbana-Champaign
  • Session III. Hamiltonian Medicine
    • Joan E. Strassmann, Chair
    • Genomic imprinting, helpers at the nest, and age at menarche David Haig, Harvard University 
    • Pathology from evolutionary conflict – Steven A. Frank, University of California, Irvine 
    • The sociobiology of drug resistance and pathogen virulence – Andrew Read, Pennsylvania State University
    • Microbial sociality: implications for disease – Kevin Foster, Harvard University
  • Session IV. Are Humans Different?
    • Francisco J. Ayala, Chair
    • Cooperation and conflict in traditional cultures – Beverly I. Strassmann, University of Michigan 
    • The cultural niche – Robert Boyd, University of California, Los Angeles
    • Social Bonds to Social Preferences; the foundations for human moral sentiments  – Joan Silk, University of California, Los Angeles
    • What does primate cooperation tell us? – Dorothy Cheney, University of Pennsylvania
  • Concluding Remarks
    • John C. Avise, University of California, Irvine

So – for speaking and chairing slots – that comes to a ratio of 17:5 male to female.  Even with Joan Strassmann being involved as a coorganizer (and she is truly wonderful in a million ways) this meeting still has the NAS and Avise/Ayala pattern of very few female speakers or session chairs, even in fields where ther are many candidates.  Yuck.

I think I would make one recommendation out of this to begin with – John Avise and Francisco Ayala should not be allowed to run any NAS meetings again.  And NAS needs to have and use policies on educating meeting organizers about gender bias and requiring some type of efforts to have reasonable representations of diversity among speakers and chairs.

UPDATE 11: Meetings from 1990s I went to while in graduate school

Just scanned in notes from some of these NAS Beckman Center meetings that I attended while in graduate school at Stanford.  I added them to my collection of “Retroblogging Meetings and Seminars: Posting Scans of Notes“.  The meetings then had even worse gender ratios of speakers.

1994: Tempo and Mode in Evolution.  See scans here. All speakers except one were male.
1997: Genetics and the Origin of Species. See scans here.

——–
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.

——–

Faculty position in Population Genomics and Computational Biology at CSU Monterey Bay

JOB ANNOUNCEMENT:

Assistant Professor, Population Genetics and Computational Biology

The Biology program within the Division of Science and Environmental Policy at California State University, Monterey Bay seeks a population geneticist with strong computational biology skills to fill a tenure track assistant professor position. The applicant should be a dedicated teacher capable of successfully involving undergraduates in research. The successful candidate will work with other faculty to develop undergraduate curricula, professional outreach programs, and extramural research or programmatic funding. Additional information on the Division and the Biology program can be found at sep.csumb.edu, the university and its vision at about.csumb.edu/vision-statement, and our exceptional undergraduate research program at uroc.csumb.edu.

Continue reading “Faculty position in Population Genomics and Computational Biology at CSU Monterey Bay”

Advice needed from a future reviewer…

I found myself writing this email to some collaborators, but halfway through realized that it’d be nice to get EVERYBODY’s input. Probably, one of you is going to review my next paper, so how awesome would it be for you to just tell me what you think now, and make both of our lives easier later.

To test whether taxa vary significantly across groups of samples, we first need to filter the OTU table to get rid of OTUs that are not present in most of the samples and/or that do not vary across samples. This must happen for statistical reasons.

As far as I know, there are two ways to do this. One, is to remove OTUs that occur in fewer than 25% of the samples (25% is suggested by the QIIME folks). The other is to calculate the variance of the OTUs across samples and remove the OTUs that have a variance less than 0.00001 (0.00001 is an arbitrary number thrown out there by the phyloseq developer.)

A third option would be to apply both criteria.

My inclination would be to go with the third option, but mostly because I want to limit as much as possible the number of hypothesis tests that we do in order to avoid draconian p-value corrections.

I’m not a big fan of arbitrary thresholds, but they are so frequently required that I’ve made my peace with them. However, if someone can suggest a non-arbitrary threshold, that’d be great.

But mostly, I want to make sure that everyone agrees now on the method that we use so that I only have to do this once. Thoughts?

A year ago, I came up with a great acronym for our project – ICIS – what do I do now?

About a year ago, when we starting meeting and discussing our new project on the future of scholarly communications, we decided it would be important to have a title and if possible a brief acronym. Now – I love coming up with such project names and acronyms and think I have done a good job with such tasks in the past.  Somehow I wanted to find a cool acronym for a project on scholarly communication, and publishing, and openness, and social media and more.  And I just could not come up with anything great.  

And this was starting to get semi urgent since we had a meeting coming up and needed to make a web site and needed names and titles and such.  So the group of us involved in the project (myself, Mackenzie Smith and Mario Biagioli) started sending around ideas to each other. Among the ideas first proposed:

  • IFHA Innovating Academic Publishing Project
  • The UC Davis IFHA project on Innovating Academic Publishing” with a project acronym of IAP

But I did not like this so I started doodling:

Screenshot 2014-10-23 14.36.48

Screenshot 2014-10-23 14.35.45

So I compiled some ideas and sent around a list

  • ISP: Innovating Scholarly Publishing
  • iSP: Innovating Scholarly Publishing
  • i2SP: Innovations in Scholarly Publishing  (with the 2 being a superscript)
  • i2AP: Innovations in Academic Publishing  (with the 2 being a superscript)
  • i2SP2: Innovations in Scholarly Publishing Project  (with the 2 being a superscript)
  • i2AP2: Innovations in Academic Publishing Project  (with the 2 being a superscript)
  • IN-A-PUB: Innovating Academic Publishing
  • SP2.0: Scholarly Publishing 2.0

Other ideas circulated (some mine, some others)

  • LIAP: Lab for Innovating Scholarly Communication, pronounced LEAP?
  • Innovating Academic Communication – IACOM
  • Innovating Academic Publishing – IAPUB
  • Innovating Scholarly Publishing – ISPUB
  • Innovating Scholarly Communication – ISCOM or INSCOM
  • COMMIS: communications innovation in scholarship

And then I came up with one I loved and sent around a suggestion:

“ok here is my favorite so far – innovating communication in scholarship – ICIS (pronounced isis —)”

Other ideas circulated:

  • pubs 2.0
  • innopubs
  • scholar 2.0

But I said I still liked ICIS best and, well, it won.  Yay.  We had a project name.   And we used it for our meetings and our website: icis.ucdavis.edu.  I was so proud of this name.  It sounded nice.  It conjured up images of ISIS the Goddess.  And every time we discussed the project I could remember the struggle to come up with a name and how happy I was when it came to me.

And then the ICIS name got, well, polluted.  Or, at least, the sound of the name got polluted by the group known variously as the Islamic State of Iraq and the Levant (aka ISIL), Islamic State of Iraq and Syria (aka ISIS).  And though I would hope it would be clear that our ICIS project is not connected in any way to ISIL/ISIS.  But yet, when I mention the project name to people, I invariable get some comment.  And Alison Fish, the first post doc working on the project just told me that she also gets some murmuring when she mentions the name during talks.

So we are in the midst of our annual retreat for the project now.  We have six people working on the project – myself, Mario Biagioli, Mackenzie Smith, Allison Fish, Alessandro Delfanti, and Alexandra Lippman.  And we all liek the ICIS name but are not sure what to do now?  So – in the interest of openness and communication I proposed to everyone (and they at least seemed to agree) that it might be good to ask the broader community for input here.

So – any suggestions?  What do you recommend we do?  Should we change the name?  Change how we say it?  Should we stick to our name and pronunciation?  And ideas, thoughts, or suggestions would be welcome.

Curating a Storify About this

//storify.com/phylogenomics/should-we-rename-our-icis-project/embed?template=slideshow//storify.com/phylogenomics/should-we-rename-our-icis-project.js?template=slideshow
[View the story “Should we rename our ICIS project?” on Storify]

Microbiology Book for Kids: It’s Catching by Jennifer Gardy and Josh Holinaty

A few days ago I wrote about how I wanted to share some information about what I have found to be good childrens’ science books (based on reading books to my kids).  Well, here is another one: It’s Catching: The Infectious World of Germs and Microbes by Jennifer Gardy and Josh Holinaty.

I first became aware of Jennifer Gardy’s talents in making catchy microbe-themed kids material when she released the Youtube video “The A-Z of Epidemiology: germs from Anthrax to Zoonoses. A disturbing bedtime book for kids.” which is simply awesome. (Note – great animation by Tom Scott):

I watched this video many many many times with my kids – always resulting in painful laughter and entertainment.

I should note that I am collaborating with Jennifer on at least one project (The Kitten Microbiome) and think she is a brilliant scientist and science communicator.  But once I saw her “It’s Catching” I realized she really could have a full career as a children’s science book and video maker.  It’s Catching is both entertaining (like the video) but also educational with information on the history of microbiology and how microbes are studied.  Definitely a good one if you are looking for fun and funny science and/or microbiology themed books for kids.

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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.

——–

Talk at #UCDavis: Standardizing Species: Listening to, representing, and universalizing bird sounds in the 20th Century

Talk: Standardizing Species: Listening to, representing, and universalizing bird sounds in the 20th Century

hui_10-21-14.pdf

Microbe-themed art of the month: Seung-Hwan Oh portraits w/ mold

OK this is pretty cool (from a microbe-art-science point of view): An Artist Who Paints Portraits With Mold | WIRED.  Seung-Hwan Oh “had to set up a micro-fungus farm in his studio” and he puts film in a warm wet environment (note to self – there could be a new human microbiome aspect of this project depending on what warm wet environment is chosen) and sometimes seeds the system with some mold.  And then he lets nature do its work.

See more about his Impermanence works here. (Really – check out the works – they are wild).

At that site the work is described in the following way:

The visual result of the symbiosis between film matter and organic matter is the conceptual origin of this body of work. The process involves the cultivation of emulsion consuming microbes on a visual environment created through portraits and a physical environment composed of developed film immersed in water. As the microbes consume light-sensitive chemical over the course of months or years, the silver halides destabilize, obfuscating the legibility of foreground, background, and scale. This creates an aesthetic of entangled creation and destruction that inevitably is ephemeral, and results in complete disintegration of the film so that it can only be delicately digitized before it is consumed.

Also see his Tumbl page where one can find many other images like this one:

Hat tip to Kate Scow for posting about this on Facebook.

——–
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.

——–

At #UCDavis: the UC #OpenAccess Policy & what it means for you (10/22, 1:30-3 pm)

The UC Open Access Policy and what it means for you (10/22 from 1:30-3pm)

A Discussion with Catherine Mitchell and Dr. Robert Powell on the UC OA policy
Date & Time: Wednesday, October 22, 2014 from 1:30-3:00pm
Location: Shields Library, Nelle Branch Room, 2nd floor (at the far end of the main reading room)

The UC Open Access Policy (http://osc.universityofcalifornia.edu/open-access-policy/ or http://uc-oa.info) was passed by the UC Academic Senate on July 24, 2013, and is going into effect for all UC campuses, including UC Davis, on November 1, 2014. The policy grants UC faculty the right to make their articles freely available to the public by depositing a pre-publication copy in an open access repository. What does this policy mean for faculty at UC Davis?

Come to this talk by Catherine Mitchell of the California Digital Library (CDL), who will describe the tools and services that CDL is developing to support the policy, and Dr. Robert Powell of Chemical Engineering, who will give background on the policy and its passage through the UC Senate. Afterwards a Q&A panel will be held with the speakers, UC Davis librarians and open access researchers to answer questions and discuss the implications of the policy and open access.

This talk is being held during Open Access Week 2014, an annual international event to raise awareness about open access issues.

Kids’ Microbiology Book Review: Germ Stories

I was going through some kids’ books today and found quite a few that I thought were wonderful and thought – well – I should post about some of them.  So that is what I am going to do.

The first I want to write about is Germ Stories by Arthur Kornberg with Illustrations by Adam Alaniz and Photos by Roberto Kolter.

 

I used to read it to my daughter all the time (she is two years older than my son) and then sometimes, when she was older, she would read it to my son.  A few things I like about this book:

  1. It is not all about pathogens – there are sections on yeast, penicillin, gut microbes and Myxococcus (although it is miswritten as Myxobacterium). 
  2. Everything is done as poetry / songs.  Some are cheesy, but my kids liked them.
  3. Each section on a different microbes has a little poem/song, a drawing, and a picture or two as well as a few mini facts (or I guess, micro facts). 
  4. The material is a bit scary / gross at times but not too over the top.
Anyway – I definitely recommend it if you want a microbiology book that will be good for reading to and reading by kids.

I added this book to a collection I am making via Amazon on “Microbiology Books for Kids“.  I will write about some of the other ones at another time.

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UPDATE – Wanted other suggestions for good kids’ microbiology themed books …

——–
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.

——–

UC #OpenAccess policy comments wanted from Academic Senate members by 1/7/15

The University invites comments on the proposed draft Presidential Policy on Open Access, which is based on the Academic Senate Open Access Policy for all Academic Senate members adopted on July 24, 2013.

The proposed new policy extends open access rights and responsibilities to all non-Senate members of the UC community who are authors of scholarly articles, including faculty, other academic personnel, students, administrators, and staff. The policy allows non-Senate authors of scholarly articles to maintain legal control over their research articles while making their work freely available to the public. In addition, the proposed policy outlines procedures for implementing the policy for all UC authors, both Senate and non-Senate. Although the policy assumes all authors will make their scholarly articles available to the public, there is a procedure, which authors must undertake proactively, to opt out of the open access process.

The proposal is located on the UCOP Academic Personnel and Programs website, “Policies under review,” under the “Systemwide Review” tab at http://www.ucop.edu/academic-personnel-programs/academic-personnel-policy/policies-under-review/index.html. If you prefer these documents as attachments, please let me know.