Improving Ability to Identify Possible Conflicts of Interest of Scholars 1: Adding a Disclosure Field to ORCID

Real and perceived conflicts of interest are a critically important topic in scholarly activities that I believe has not received enough attention from the scientific community.  Right now, disclosures of possible conflicts of interest are handled incredibly very unevenly and poorly by academia and industry and government.  Even when people do the right thing and make detailed disclosures, such information is hard to find and ephemeral.  There are many things that the community could do to improve the ability to find such information.

One simple step that I believe could be useful would be to link disclosures to universal scholar ID systems.  Although there are multiple UID systems for scholars, right now the UID of choice appears to be ORCID. ORCID currently allows scholars to compile information about their education, employment, funding and scholarly works.

I therefore propose that ORCID add a new category: DISCLOSURES.  What would be included here? Well, I don’t know exactly but would include things like board membership, stock in companies, funding not listed elsewhere, any other significant relationship with a group, and more.  Sure this could get messy.  But I think we need to do more to make it easier to share and find information that could be a actual or potential conflict of interest.
Something like this:
If anyone knows of other tools for doing this I would love to hear about them.

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 

NIH Announces Revised Genome Data Release Policies

Just got notified of this by the UC Davis Med. School grants administration: NOT-OD-14-124: NIH Genomic Data Sharing Policy.  Lots of interesting things in here including a summary of the comments that they received on the draft policy.

I have copied some of the more interesting and relevant bits below:

  • Sharing research data supports the NIH mission and is essential to facilitate the translation of research results into knowledge, products, and procedures that improve human health.  NIH has longstanding policies to make a broad range of research data, in addition to genomic data, publicly available in a timely manner from the research activities that it funds. 
  • The public comments have been posted on the NIH GDS website.
  • The statement of scope remains intentionally general enough to accommodate the evolving nature of genomic technologies and the broad range of research that generates genomic data.
  • Several comments were submitted by representatives or members of tribal organizations about data access.  Tribal groups expressed concerns about the ability of DACs to represent tribal preferences in the review of requests for tribal data.
  • The GDS Policy expects that basic sequence and certain related data made available through NIH-designated data repositories and all conclusions derived from them will be freely available.  It discourages patenting of “upstream” discoveries, which are considered pre-competitive, while it encourages the patenting of “downstream” applications appropriate for intellectual property.  
  • NIH expects investigators and their institutions to provide basic plans for following this Policy in the “Genomic Data Sharing Plan” located in the Resource Sharing Plan section of funding applications and proposals.  Any resources that may be needed to support a proposed genomic data sharing plan (e.g., preparation of data for submission) should be included in the project’s budget. 
  • Large-scale non-human genomic data, including data from microbes, microbiomes, and model organisms, as well as relevant associated data (e.g., phenotype and exposure data), are to be shared in a timely manner. 

It may have been a flawed #OpenAccess "Sting" but WE ROCKED IT so submit to our journal …

I suppose I knew this was coming … but did not expect it so soon … see the email I received below.  Focus in particular on the part highlighted in yellow …. 

Dear Colleague, 

British Biotechnology Journal (BBJ) is an OPEN peer-reviewed, OPEN access, INTERNATIONAL journal, inspired from the great OPEN Access Movement. We offer both Online publication as well as Reprints (Hard copy) options. Article Processing Charge is only 50 US$ as per present offer. This journal is at present publishing Volume 4 (i.e. Fourth year of operation). 

2. Transparent and High standard Peer review:
In order to maintain highest level of transparency and high standard of review, this journal presently follows highly respected and toughest Advanced OPEN peer-review system(Example Link1, Link2, Link3, Link4, Link5, Link6, Link7, Link8, Link9, Link10,Link11, etc). We hope that you will appreciate this Advanced OPEN peer-review system, which is expected to give doubtless scholarly benefit and impact to the authors in long run. Additionally we strongly encourage and promote “Post-publication Peer review” by ourcomment section. 

As per a recent report (Link) of Science journal (present Impact factor 31), one of our journal passed a stringent test of quality of Peer review by rejecting a fake article (Link1,Link2, Link3). We applaud the dedication and hard-work of our peer reviewers and editors to maintain the high standard of our journals. It was reported that only few journals (20), out of total 304 journals tested, rejected the fake article after substantial peer review. We are happy that our journal was among these few successful journals along with industry leaders like PLoS One, Hindawi, etc. We believe that the result of this experiment also proved the efficacy of our Advanced OPEN peer review and ‘post publication’ peer review system. Though the report is debated, as it did not include subscription journals, we normally support any effort to improve the quality and transparency of peer review. 

3. Proposed Time Schedule:
Submission to first editorial decision with review comments: 3 weeks
Submission to publication: 6 weeks
State-of-the-art ‘running issue’ concept gives authors the benefit of ‘Zero Waiting Time’ for the officially accepted manuscripts to be published.
4. Abstracting/indexing:
Many respected abstracting/indexing services covered our journals.

  • (United Nation’s Database)

  • (United Nation’s FAO database)

  • OARE
  • (United Nations Environment Programme (UNEP), Yale University, etc.)

5. Authors’ profile:
Considering high peer review standard, quality control, etc. our journals have been chosen by academicians of many famous universities, institutes, etc. A glimpse of authors’ profileis provided here

6. Testimonials:
Appreciation of our esteemed satisfied authors is the greatest inspiration behind the hard-work of our editorial team. Some of the testimonials are available here

7. Article Processing Charge (or Publication Charge):
Article Processing Charge (or Publication Charge): Manuscript submitted within 1st July, 13 — 30th September, 2013 will be eligible for 90% discount on normal Article Processing Charge (APC) of 500 USD. (i.e. Effective APC: 50 USD). For more information visit here

7.1. Reprints (Hard copy):
Reprints (Hard copy) are also available at extra cost. For detailed information please see here (Reprint information link). 

8. Sample papers:

  1. Antibacterial and Antiviral Activities of Essential Oils of Northern…..
  2. African Cassava: Biotechnology and Molecular Breeding to the Rescue
  3. Growth Inhibition of Some Phytopathogenic Bacteria by Cell-Free Extracts fromEnterococcus sp
  4. Primary Somatic Embryos from Axillary Meristems and Immature Leaf Lobes of Selected ..
  5. Effects of Initiating Antihypertensive Therapy with Amlodipine or Hydrochlorothiazide on Creatinine Clearance in Hypertensive Nigerians with Type 2 Diabetes Mellitus
  6. Preparation of Protein Extraction from Flower Buds of Solanum lycopersicum for Two-Dimensional Gel Electrophoresis
  7. Diversity of Bacterial Community in Fermentation of African Oil Bean Seeds (Pentaciethra macrophylla Benth) by comparison of 16S rRNA Gene Fragments
  8. The Application Development of Plant-Based Environmental Protection Plasticizer
  9. Genetic Variability, Heritability and Genetic Advance in Pearl Millet (Penisetum glaucum [L.] R. Br.) Genotypes

9. Highly qualified Editors:

  • Prof. Y. Dai,
  • Associate Director of Research, Revivicor Inc. Blacksburg, USA

  • Prof. Viroj Wiwanitkit, Department of Laboratory Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
  • Dr. Jean-Marc Sabatier, Université de la Méditerranée-Ambrilia Biopharma inc., France
  • Dr. Robert L. Brown, Food and Feed Safety Research Unit, USDA-ARS-SRRC, New Orleans, USA
  • Dr. Giuseppe Novelli, Università di Roma Tor Vergata, Rome, Italy
  • Dr. Juan Pedro Navarro – Aviñó, Technical University of Valencia, Spain
  • Dr. Nikolaos Labrou, Department of Agr. Biotechnology, Agricultural University of Athens, Greece.

10. Manuscript submission 

Option 1:
Online submission (recommended): Subcentral (
Option 2:
Email attachment to the editorial office at

General Guideline for Authors:
To download MS word SDI paper template click here
To download SDI Manuscript Submission form click here
To download Latex paper template click here

with regards,
Ms. Samapika Mondal
British Biotechnology Journal : An OPEN peer reviewed journal; E-mail:
Reg. Office:
UK: SCIENCEDOMAIN international, Third Floor, 207 Regent Street, London, W1B 3HH,UK,Registered in England and Wales, Company Registration Number: 7794635, Fax: +44 20-3031-1429
USA: SCIENCEDOMAIN international, One Commerce Centre, 1201, Orange St. # 600, Wilmington, New Castle, Delaware, USA, Corporate File Number: 5049777, Fax: +1 302-397-2050
India: SCIENCEDOMAIN international, U GF, DLF City Phase-III, Gurgaon, 122001, Delhi NCR, Corp. Firm Registration Number: 255 (2010-11), Fax: +91 11-66173993

Institutional repository success story: Master’s on "War Eagles" contributes to amazing ring recovery story

Image from NPR.

So I just heard this amazing story on NPR. “Journey Of The Ring: Lost In WWII, Now Back With POW’s Son.”  In summary – a US Military member David Cox was taken as a POW in World War II in Germany.  While a captive he ended up trading a treasured ring for some chocolate. He returned home and made a replica of the ring but always felt bad about having had to trade the ring for food.  He passed away a few years ago.  Three or so weeks ago, two Americans – Mark and Mindy Turner – were invited to a dinner at the house of Martin and Regina Kiss and it turns out the Kiss’s had the ring.  But they did not know who the original owner was.  So the Turners did some searching based on the inscription on the ring and the figured out who the original owner was and it has now been returned to David Cox’s son.

So – how on earth is this a story connected to institutional archives.  Well, it turns out that the Turners figured out who the original owner of the ring was because their Google searches based on the ring’s inscriptions took them within a few minutes to this Master’s Thesis posted in 2006 at the NC State Digital Repository: War Eagles: A Bird’s Eye View of 305th Bomb Group and the Eighth Air Force from the experiences of David C. Cox and Joseph B. Boyle – NCSU Digital Repository.  The thesis was written by Norwood McDowell, who happens to be the younger Cox’s son in law.  And his thesis was about the elder Cox and had a brief discussion of the ring.

Kudos to all involved, including NC State and Norwood McDowell for making his Masters thesis available.

Postdoc position in innovating scholarly communication at #UCDavis w/ me, Mario Biagioli & Mackenzie Smith


Postdoc Position in Innovating Scholarly Communication

A new UC Davis initiative on “Innovating the Communication of Scholarship” is hiring a 3-year postdoctoral fellow, starting September 1, 2013. This is a cross-disciplinary project to study the future of academic publishing, involving faculty from the Center for Science and Innovation Studies, the Library, the Genome Center, and the School of Law (with additional collaborators in Computer Science, English, Philosophy, and the Graduate School of Management). Research topics include open access models, peer review, new forms of quality metrics, data publication, use of social media, and new forms of misconduct.
The successful candidate will conduct research, collaborate on or lead organization of conferences, workshops, pedagogical activities, and grant writing. A Ph.D. is required in a relevant field such as Science and Technology Studies, Library and Information Sciences, Communication, Law, Science, or English. Other disciplines will be considered depending on the specific focus of the candidate?s research and other experience. Qualified applicants will have experience working successfully in teams and managing multi-year projects. He or she will possess excellent written and oral communication and administrative skills.
Salary is based on experience and qualifications according to UC Davis guidelines.
To apply: E-mail a PDF file containing your CV, short description of your research experience relevant to this position, and contact details for three references to Mario BiagioliMacKenzie SmithJonathan Eisen.

I am highly skeptical of the CHORUS system proposed by scientific publishers as an end run around PubMed Central

Just read this news story … Scientific Publishers Offer Solution to White House’s Public Access Mandate – ScienceInsider

It reports on an effort by various scientific publishers to create something they call “CHORUS” which stands for “Clearinghouse for the Open Research of the United States.” They claim this will be used to meet the guidelines issued by the White House OSTP for making papers for which the work was supported by federal grants available for free within 12 months of being published.

This appears to be an attempt to kill databases like Pubmed Central which is where such freely available publications now are archived.  I am very skeptical of the claims made by publishers that papers that are supposed to be freely available will in fact be made freely available on their own websites.  Why you may ask am I skeptical of this?  I suggest you read my prior posts on how Nature Publishing Group continuously failed to fulfill their promises to make genome papers freely available on their website.

See for example:

We need to make sure such papers are freely available permanently and the only way to do this is via making them available outside of the publishers own sites.  Pubmed Central seems to be a good solution for this.  I would be happy to hear other possible solutions – but leaving “free” papers under the control of the publishers is a bad idea.

UPDATE 6/27/2013

Saw this Tweet

// Seemed potentially really interesting. Read the story and got pointed to a new Nature paper on the ancient horse genome. I guess not so surprisingly, despite the fact that they report a new genome sequence, it is not openly available. We really cannot trust Nature on this can we? They could say “Well, this is a draft genome, and we did not mean to apply our policy to draft genomes.” Well, that would be weird since, well, they have applied this to draft genomes before. And then I decided to search for other examples … and in about ten minutes I found a few. See



Quick post – Nature Publishing Group buys into #OpenAccess publisher Frontiers

In case you have not hear – Nature Publishing Group continues to play around with open publishing and other open science initiatives (when they switch some of their big journals to fully OpenAccess I will stop referring to it as playing around …).  The latest is that Nature has bought into the Frontiers publishing group which publishes a series of Open Access journals.  For more on this see:

Hat tip to many people who have sent this info to me.  Not 100% sure what to make of it, but it is interesting …

A day to think, to pause, to ponder

Today is not an easy day for me.

I pause today to think about a person in my life.  A person who was dedicated to science and discovery and improving the human condition.  A person who was idealistic and sensitive and also had some mental health issues.  A person who was pushed over the edge by an overly aggressive, misguided investigation.  A person who became lost in some sort of downward spiral triggered by this investigation.  A person who then took their own life and in one moment created a catastrophic ripple in the world around them.

This person was not Aaron Swartz, though I am thinking of him today too. The person I refer to was my father.  On this day, February 7, 1987, my father Howard J. Eisen took his own life.  I was a freshman in college then.  Enjoying life on my own at Harvard.  Exploring the world of new friends, academic pursuits, and the usual college antics.  And then it all exploded.  The details are a bit of a blur and most are not really important for what I write about here.  But suffice it to say I was devastated.

I flew home to Maryland with my brother and slowly the details emerged.  My father was a researcher at the NIH.  A paper was being prepared for publication by a post doc who worked for a colleague / boss of my father and who my father also worked with.  My father was apparently asked to look at the paper and some “discrepancies” were noted and my father helped launch an investigation into the work.  The NIH panel that was brought in to investigate the work of this post doc was very aggressive – very unpleasant – and even though no accusations of wrong doing were made against my father – the style and tone of the investigation pushed him over the edge.  And he could not dig himself out.  Some people knew he was having trouble with the whole incident but others (e.g., myself) were not in the loop at all.  I knew nothing.  Perhaps people thought I had enough going on as a freshman in college or perhaps it just never came up.  But all I knew was discovered after finding out my father had died, by taking his own life, on February 7, 1987.

Losing my father at the age of 18 was devastating.  Still is.  The fact that he killed himself made it even worse of course.  There were even news stories for a while about it – in the Washington Post, and New York Times, and the Associated Press and Nature and such.  Some of the stories helped in a way because they did not accuse my father of any wrong doing.  For example the Washington Post reported

“Dr. Howard J. Eisen, a respected scientist at the National Institutes of Health, committed suicide at his Bethesda home last week while under pressure from an investigation he helped initiate of alleged scientific fraud by a coworker. 

The suicide has shocked the NIH community and outraged some scientists there, who think that the stress of the investigation triggered Eisen’s death. They view it as a case of the system making a responsible scientist suffer even though he acted aggressively to uncover possible dishonesty in his laboratory. Eisen’s friends and family acknowledged that his personality-he was intensely idealistic and unusually sensitive-made him vulnerable.”

And the Nature article, by Joe Palca, reported “NIH made no allegations against Eisen.” Did these make me feel better?  I suppose.  But of course, not really.  Suicide is brutal for those left behind (and I am sure for those who commit it).  I have never recovered.  But I note – the life and death of my father, and the story of the investigation, have shaped my life.  It is why, when I went to graduate school, my #1 criterion for choosing a PhD advisor was that they were a good, kind person.  After struggling with some of the people I worked with I found such a person in Phil Hanawalt and, really, never wanted to leave his lab.  I see so many examples of scientists and MDs and administrators abusing their positions of power and finding someone who does not do any such things can sometimes be a challenge.

The story behind my father’s death is also why, a few years ago, when I realized my father’s publications were not freely and openly available that I got so angry.  My father had, in a way, died over his research.  And for it to not be available pained me to no end.  When David Dobbs wrote a story about my quest to Free my Father’s publications I felt some peace that I had done something in his name.  And when I finally made them all available a week later, I was truly happy.

The story behind my father’s death is also why, when people have pointed out to me that I have been a bit over the top in critiquing others, that I back off.  And I have tried to get others on the web and in my arena to be much more careful about avoiding personal attacks (e.g, see here).

I also note that the story behind my father’s death is why the death of Aaron Swartz hit home so hard to me.  I knew Aaron a tiny bit (having met a SciFoo many years ago) but not in any deep way.  I read the stories about his JStor download and even wrote about it a little bit.  But I was not aware of the demented, aggressive prosecution of him and when I read about his death I was devastated.  The story reminded me a great deal of my father.  I wrote about Swartz and about the follow up PDFTribute movement (here and here) but it felt a bit awkward since I did not know quite how to discuss my own personal feelings about this story.  So I said nothing.  But now, in tribute to my father, I am trying to not ignore the facts around his death.  They are a part of his life and a part of why I am the way I am.  So I write this post.  And I call for others out there to remember – life is fragile.  Be careful with your words and your actions.  No – one cannot blame everyone – or anyone really – for complex things like suicide.  But we can all do a little bit to improve how we treat others.  And on this day, when I am 44, the same age as my father was when he died, that is what I think about.

My father, Howard J. Eisen

UPDATE 2/8: See my brother’s nearly simultaneously written post about this topic (which we did not discuss – typical – here).

Storification of responses