Storify of Discussions About Shameless Behavior by #AAAS Relating to #Ebola Papers

Does #AAAS care about #Ebola anymore? Nope. And probably never did. #ClosedAccess

In October I wrote a blog post criticizing AAAS (and ASM) for trying to give themselves a pat on the back for making a few papers about Ebola freely available: The Tree of Life: No #AAAS and ASM you do not deserve good PR for freeing up a few papers on Ebola.  The whole thing was a publicity stunt.  And AAAS in particular tried to play up how they were doing this for the benefit of humanity.

So today I decided to check back and look into whether AAAS was making new papers on Ebola freely available. So I searched for the word Ebola in the title or Abstract 

The most recent seemed interesting:

Surely AAAS must still care enough about Ebola to make new papers freely available right? Nope. $20 to rent for a day

How about #2:
Seems useful and worth reading if one works on Ebola.  Free right?  Nope: $20/day

How about #3:

Seems peripherally relevant to Ebola but I would not mind if more Ebola workers read this.  Free right?  Nope.  Guess how much? $20/day
And so on.  A few in the first 10 were, at least for now freely available.  But overall it seems, AAAS and Science have decided Ebola is no longer important.  So much for helping the world.

Removing my name from the author list of #closedaccess "Unified Microbiome Initiative" paper in Science

YAMMA – Yet Another Mostly Male Award – AAAS Public Engagement Award

So – I saw an post on Twitter about the AAAS Public Enagement with Science Award

And I went to check it out since, well, I wondered – how could I win that.  And so I thought – I should look at how I compare to previous winners.  And in one way I compare really well. I am male.

Below is a list of past winners (via AAAS). In yellow I highlight those that appear to be male and green those that appear to be female. I note I base my assignment on appearance and names and descriptions of the people including the descriptions from AAAS. I realize that determining someone’s gender is not always straightforward and that there are people who do not fit into this binary gender division and I apologize for any mistakes made.

  • 2014 James Kakalios 
  • 2013 Steven Strogatz
  • 2012 Richard B. Alley
  • 2011 Nalini Nadkarni
  • 2010 J. John Cohen
  • 2009 May R. Berenbaum
  • 2008 Kenneth R. Miller
  • 2007 Neil deGrasse Tyson
  • 2006 S. James Gates, Jr.
  • 2005 Jane Lubchenco
  • 2004 Eric S. Lander
  • 2003 John Allen Paulos
  • 2002 Bassam Shakhashiri
  • 2001 Ian N. Stewart
  • 2000 Vaclav Smil
  • 1999 Lawrence Krauss
  • 1998 Christopher Wills
  • 1997 Barry T. Peterson
  • 1996 Alan J. Friedman
  • 1995 Carl Sagan
  • 1994 Edward O. Wilson
  • 1993 Science Theatre
  • 1992 Farouk El-Baz
  • 1991 Stephen H. Schneider
  • 1990 William L. Rathje
  • 1989 Robert D. Ballard
  • 1988 Anthony M. Fauci
  • 1987 Philip Morrison

The totals are 24 men and 3 women (and one group).  Or, for those assigned to a gender, 89 % men and 11 % women.  Could this all be about merit?  I don’t think so.  I think there are many examples of areas in which AAAS has problems with gender bias.  For example, consider the recent letter (of which I am a cosigner) regarding AAAS’ reinforcement of “damaging stereotypes“.

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.

No #AAAS and ASM you do not deserve good PR for freeing up a few papers on Ebola

Saw a PR from AAAS about how they were freeing up all of ~ 20 papers on Ebola

In light of what has become the largest Ebola outbreak on record, Science and Science Translational Medicine have compiled over a decade’s worth of their published news and research. Researchers and the general public can now view this special collection for free.

OK. More access is good. But alas, they did not even free up all papers in #AAAS journals with Ebola in the Title or Abstract.

And then I started thinking. What about HIV? TB? Malaria? And as I started Tweeting about this, I saw that ASM also was hopping on the “free Ebola” bandwagon (actually I do not know who did it first).

And so I got angry and started Tweeting away. The Storify below sums up most of the details.

//[View the story “#AAAS and ASM free up Ebola papers show they don’t care about HIV, malaria, TB, etc.” on Storify]
UPDATE 9 AM 8/21

Great.  And now the Lancet has joined the bandwagon.

They write
“The current outbreak of Ebola in west Africa constitutes the largest and most complex to date. Declared a public health emergency of international concern by WHO, the outbreak of a disease with no known treatment or vaccination is proving difficult to contain given the already fragile and under resourced health systems in the affected areas.
The Lancet wishes to assist health workers and researchers working under difficult and dangerous conditions to bring this outbreak to a close. This Ebola hub contains all related resources from The Lancet family of journals offered with free access to support their vital work.”
Since they do not make papers available on TB, malaria, AIDS, cancer, etc does this mean people working on those are not doing vital work?
UPDATE 2: 8/21 5:45 PM
Wiley also trying to get some PR for making papers available.

UPDATE 3: 9/3
Oh look.  ACS cares about Ebola too.  They are making 18 papers available for free.  How generous. Oh and only until February 2015.  After then, they don’t care about Ebola.  Oh and before then, they apparently don’t care about any other affliction affecting the world.  Ebola is the only thing important enough to make freely available.

UPDATE 10/17

As the Ebola situation worsens, journals and publishers are still trying to get props for making certain papers freely available.  For example, AAAS continues to do this – (see this news story here which ends with a statement about a collection of free ebola papers).  Alas they are being sadly selective in what papers they make available.

Here are some that are not available

What a joke.  If #AAAS really cared about infectious diseases and human health and making papers available, they would stop being one of the most anti-open access publishers out there.

If you want consistently #openaccess papers about Ebola, go to #openAccess journals or do a search in Pubmed Central with a “limit” for Open Access papers:

AAAS – Blocking Access to the Scientific Literature Even When They Say It Is "Free"

Today, I wanted to show someone a PDF of a paper of mine that I co-authored in 1999.  The paper was, I think, kind of cool.  It reported the sequencing and analysis of the genome of Deinococcus radiodurans, an incredibly radiation resistant bacterium.  Alas, I did not have a copy on me, and the only electornic device I had with me was my phone.  The person I wanted to show the paper to had their computer, a device with a strange little red trackball and running some sort of Windows operating system, so I looked at it and panicked and said “Maybe you should drive” (as in, maybe they should be the one controlling the computer).

So this person, who shall remain anonymous mostly because of the ancientness of their computer, did the kind of obvious thing, and opened a web browser (don’t even ask which one) and typed in “Pubmed.Com”.  OK – that would work.  I might have preferred going to Google Scholar, but I use Pubmed about as frequently.  And though I do not have a Windows machine or the weird web broswser they used, I have recreated what happened next.

A nice Pubmed window.  And I said, type in “Deinococcus Eisen.” and seven papers showed up.

And so I said “Scroll Down” and “Near the Bottom” and there was the paper “White et al” from 1999.   I was happy to see it said “Free Article” since I could not remember if AAAS had made this article available or not. So I said “Click on that one”.

And we looked around for a minute and at the same time we both realized, there in the upper right corner was a link to Science “Full text”.  And I thought – cool – the text is available just at Science not at Pubmed.  And my colleague clicked on this.

And here is where is got annoying.  A new page comes up from this link:

So – the paper is not actually readily available, one has to register in order to see it.  What a pain.  And my colleague just stopped there and said “I do not want to do this right now” and I said “Understood”.  And we stopped and I never showed him the paper (we could have tried other routes but we both had other things to do).  When I got home this evening I decided to look in more detail at the registration and clicked on the link:

Hmm.  So to register it seems I have to sign up for emails from AAAS and all sorts of other crap.  And I have two choices for email neither of which is “I do not want any FU#*(#@ email from AAAS”.  Great.  So I filled out some parts and scrolled to the bottom to see the Privacy Policy option.    And so I clicked on the link.  And the section on Uses of This Information is pretty annoying:

The information collected may be used by AAAS for the purpose of operating and improving the Science Website, fostering a positive user experience, and delivering the products and services that we offer. We may also use the information we gather to inform you of other products or services available from the Science Website or to contact you about your opinion of current products and services or potential new products and services that may be offered. 

We may use your contact information in order to send you e-mail, postal mail, or other communications regarding updates at the Science Website, such as Job Alerts, newsletters, new opportunities, and additional listings which may be of interest to you. We may also use it to send you information about third-party products and services that match your interests and preferences, if you opt in for this communication. We do not release any of your contact information to third parties unless we have your permission. The nature and frequency of these messages will vary depending upon the information we have about you. In addition, at the time of registration for certain services, such as Science Careers Job Alerts, or free partial access to any of the Science websites, you have the option to elect to receive additional communications, information, newsletters, and promotions relating to topics that may be of special interest to you. 

We may share information, such as your IP address, with third parties as might be required for technical purposes, such as facilitating user discovery and access via web search engines.

Well they say they will not share information unless I opt in, but the only way to get access to this paper is to opt in.  Great.   And it gets more explicit under the email policies section:

Users of free online services provided by AAAS±such as free partial access to Science, Science Signaling, or Science Translational Medicine, access to ScienceNOW or SAGE KE, e-mail alerting services or Science Careers services±are agreeing that AAAS may contact them by e-mail in exchange for these free services. Users can also opt in for third-party informational e-mails. Users who do not wish to receive e-mail may cancel their online services by following the unsubscribe instructions at the bottom of any e-mail message from AAAS.

So, actually, there is no opt in policy for those wanting free access to papers.  If you want access, you agree to be contacted.  So – I used a email address I have never used for anything else (so I can track who AAAS sells my name to) and sucked it up and registered.  And I checked the box for agreeing to the Privacy Policy even though I felt icky doing it.  Seemed like I should consult with a lawyer before doing that given how long it was.  Certainly not easy access.  And for the form I had to fill out I tried to not fill out anything under “Discipline” but the site would not let me.  I tried to not fill out anything under Lab Products but the site would not let me either.  And so I filled something out and then amazingly, when I submitted the form, I got sent another page where I had to keep filling out information.

And even though I was not subscribing to the journal I had to agree to some subscription policy.  So I clikced on that and got to another policy.  This including a Copyright warning:

Copyright Notice
Although there is no charge for the use of some portions of the materials contained on the Science websites (“Websites”), all the materials are protected under copyright and other laws of the United States, and, under international conventions, similar laws abroad. Please respect the copyrights and related rights of the authors and publishers of the Websites.

And then many many limitations on use

Limitations on Use by (and to) Registered Users
The contents of the Websites as available through the Free Service, may only be accessed, viewed or otherwise used by a Registered User. A Registered User is permitted to view, browse and/or download for temporary copying purposes only the contents of the Websites, provided these uses are for noncommercial personal purposes, and further provided that the Registered User maintains all copyright and any other notices, on all copies. Registered Users are not, however, permitted to store in electronic or any other form, any significant portion of the Websites. Except as provided by law or by this Agreement, the contents of the Websites may not be further reproduced, distributed, transmitted, modified, adapted, performed, displayed (including adaptations/displays such as by “framing”), published or sold in whole or in part, without the prior written permission from AAAS. 

Any use which is commercial and/or non-personal is strictly prohibited, and may subject the Registered User making such uses to immediate revocation of access to this Free Service, as well as any other applicable civil or criminal penalties. Similarly, sharing a Registered User password with a non-Registered User or otherwise making this Free Service available to third parties is strictly prohibited, and may subject the Registered User participating in such activities to immediate revocation of access to this Free Service; and, the Registered User and any third party, to any other applicable civil or criminal penalties. 

In the case of an authorized site license, a Registered User shall cause any employee, agent or other third party which the Registered User allows to use the Free Service materials to abide by all of the terms and conditions of this Agreement. In all other cases, only the Registered User is permitted to access the Free Service materials.

Well, this is getting pretty complicated and there was a lot of other stuff there.   But I checked the box.  I felt even ickier with this one and thought I really should consult a lawyer.  But I did not.  And I submitted this form.

And finally I had it.  It took about an hour.  This may seem minor to many out there but it seems inappropriate to me.  This paper represented hundreds of thousands if not millions of dollars of work funded by the Department of Energy and was published in 1999.  The goal of the work was to share knowledge.  And this is a major roadblock to sharing that knowledge.  Plus, all the restrictions on use and reuse mean that anyone wanting to share the knowledge with others also is restricted.  The agreements imply that I should not use anything from the paper in a talk or a class or in any way.  There is no mention of Fair Use or any other hint that it would be OK to share the material for educational or scholarly purposes. And who knows what crap I am going to get sent to the email address I used for this registration.

So – why are there all these restrictions?  I presume, to make AAAS money in some way.  Is that a bad thing?  Well, in principle I am all for publishers making money.  I subscribe to many newspapers.  I subscribe to many magazines.  I buy lots and lots of books.  I pay for music and movies and other works.  I don’t download anything illegally.  So why not just accept that people should pay for scientific papers?  Well, because this paper, and 1000s and 1000s of others are different than all the other works I list above.  Owen White and I (with some help from some others) wrote this paper.  AAAS and Science did little except handle the peer review and do some copy editing.  They just simply do not deserve the rights they are claiming to this article and to all the others.  And as a society supposedly for the “advancement of science” it seemed to me that they should make it easier to access the old literature. They could certainly make all papers published more than 12 months ago freely and openly available and deposit them in Pubmed Central.  It would be incredible beneficial to science and to scientists.  But they do not.  Is this in the interest of the “advancement of science”?   Unquestionably no.  But I guess they have decided it is in the interest of the “advancement of Science” where the journal and money for the society is the goal and the advancement of science is lost in the ether.

In the end, I deeply regret having ever published in Science.  15 years after publishing this paper I would definitely say it would have been better to have published in another journal – one that makes papers more openly and freely available.  I cannot change the past.  But I will not support AAAS or its activities in the present or the future unless they change policies and practices.

Some related posts:

UPDATE 1. 8/18 – 5 PM. Been Storifying some of the discussion

AAAS and SnapChat collaborate to develop SnapScience to publish scientific papers transiently

Just got this in an email and thought it should be shared.

Washington, DC. August 15, 2014.

Kent Anderson, the newly appointed Publisher of AAAS (see has announced his first action as Publisher – a partnership between AAAS and Snapchat (

Anderson said “Although I will not officially assume the role of Science publisher until 3 November, this was too important a task to not carry out immediately. AAAS has always been looking for new ways to reduce the public availability of scientific publications. AAAS approached Snapchat a few months ago and in secret developed a new App “SnapScience” which allows the transient publication of scientific articles. Article longevity can be set to 1 minute, 5 minutes or 15 minutes.”

Anderson followed this with “This kind of thing I had always hoped to do in my role as president of the Society for Scholarly Publishing but the technology was just not available. Snapchat has developed the perfect platform for the future of AAAS and scholarly publishing in general with its ability to allow readers a glimpse of a scientific article but not allow them to keep it or reread it or redisplay it.”

AAAS CEO Phil Lesher said “We have had serious issues recently with the public demanding access to articles in Science and other AAAS published journals. And in addition, we have published a slew of papers that have needed to be retracted shortly after publication. This solves both issues. First, all papers will only be transiently available, so their there is no need for retractions. Second, even scientists will only have short term access to papers so the public cannot possibly demand access for themselves.”

Anderson also said “We think SnapScience is the perfect way for me to step into my new role as Publisher of the Science family of journals. It is cutting edge. It is exactly the type of thing that publishers have been looking for. And it will be fun.”

AAAS hopes to roll out updates to SnapScience that will allow researchers to also publish data and protocols only transiently as well.

Why I don’t like to pre-submit slides for talks – lessons from #AAASMoBE meeting

So – I gave a talk at a meeting on Thursday.  The meeting was called “Microbiomes of the Built Environment” and it was sponsored by the Alfred P. Sloan Foundation and run by AAAS.

The meeting organizers, as is often the case, wanted me to submit my slides a few days in advance, in theory to make sure they were loaded into their system and that all worked OK.  Well, as usual, I did not do this.  I like to make my talks fresh – just before the meeting so that I can incorporate new ideas into them and so that they do not have that canned feeling that a lot of talks do.

My talk was to be 15 minutes long and was to focus on my Sloan Foundation funded project “microBEnet: the microbiology of the built environment network” (see for information about the project). I figured, I would work on the talk on the plane – five plus hours to edit a talk I had given relatively recently on the topic of this project.  And all would be good.  Plus, United had told me there would be WiFi on the plane so if I needed any new material I should be able to get it from the web right?  Well, the flight took off on time – 8 AM on Wednesday morning.  And I opened my laptop once allowed and paid the $15+ dollars for the WiFi and got to work.  Then, about 10 minutes later, the WiFi died and despite heroic efforts by the flight attendants, it never came back. And I plugged away at my slides doing some edits of the following presentation.

I had given this talk for the Annual Sloan Foundation meeting in May of 2013. I had other talks about but they were focused on specific aspects and this was my most recent talk on the whole project. And, well, I started doing some minor edits on it, but, well, the slides felt too filled with boring text. And it did not seem to me to capture what I wanted to talk about. So I did the one thing that always helps me in such cases. I shut my computer and got our a notebook and started writing out and drawing out what I really wanted to talk about. And I finally started to have something I liked.

I liked this because what we are trying to do with microBEnet is to create an actual network and this was a visual way of representing our network. So then I got a bit more detailed

This was better. We were trying to help people in the field and help others who might be interested get connected, stay connected, and get rapid, easy access to information and tools. For example, we have been curating a reference collection for the field. And this reference collection has a lot of inputs and a lot of potential uses. In my previous talk I just listed some of this and had a screenshot of the web site. But it would be better to show this no?

Now this was feeling even better. I had a visual framework for the talk. Now I could fill in the details of what I wanted to cover in each of the parts of the network diagram.

So now I had some idea as to what I might want to say on these topics. No slides yet, but some idea as to what I might want to cover. And then, still not back on the computer I thought it would be good to write out an outline / the flow of the talk again. So I did.

Still felt good.

Now all I needed was a title ..

And then finally I felt I could go back to the computer. And so I started working on converting this all into slides.

For the remaining 2 hours of the flight I tried but it was slow going. I wanted to make as much as possible be visual and I needed all sorts of new slides and material from the web (no web connection still) and more. We landed. I took a Taxi to the hotel. I worked on my talk a bit from my room. I emailed various people asking for certain images and slides. And then I had to go to the speaker’s dinner. And I got back to my room at about 9:30. And then I worked on my talk until about 3. And finally I was close to being done. Got a very brief few hours of sleep. Got up. Went to the meeting. Did a couple of minor modifications of my slides in the back of the room. Posted my slides to Slideshare. And then gave my talk.

Here are the final slides

Not perfect. But much more visual. Much more networky. Much better at showing what we actually do and try to do on my project.  And much fresher to me so it was certainly not a canned talk.  Not a polished talk .. but not a canned one.

For more about the meeting, including videos of talks (including mine) see the Storify I made.

Better late than never – video interview of me from #AAAS2012 – Evolvability, the Built Environment and Open Science

Well, better late than never. An interview of me by Stan Malloy at the AAAS Meeting from February 2012 has been posted at MWV Episode 72 – Jonathan Eisen – Evolvability, the Built Environment and Open Science.  From their site

On this episode, Jonathan talks about “evolvability,” the probability that organisms can invent new functions. To do this, he has been using genome data in conjunction with experimental information to try and understand the mechanisms by which new functions have originated. 

Another area of interest for Eisen is the “built environment.” We live and work in buildings or structures which are non-natural environments, new to microbes. These “new” environments represent a controlled system in which to study the rules by which microbial communities form. 

Jonathan is interested in these environments as basic science vehicle and he shares the importance of studying the built environment for science and human health.
Finally Jonathan explains his interest in “open science,” the ways in which science is shared. At it’s core, Eisen wants to leverage cheaper technologies to accelerate the progress of science in a positive way. 

This episode was recorded at the American Association for the Advancement of Science Meeting in Vancouver, British Columbia on February 18, 2012.

 See the interview via Youtube below: