Saturday, March 26, 2016

Blast from the not so distant past - special issue of JMBE on Scientific Ethics

So _ picked up my new issue of Microbe in the mail today and I saw something in it that seemed very intriguing.



A whole section of JMBE - the Journal of Microbiology and Biology Education dedicated to Scientific Ethics.  Sounded intriguing.  So I looked it up.  Took a bit to find it but there it was from December 2014 - Volume 15 number 2
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I don't know about the specific articles but the whole collection seems definitely worth a look and of potentially many uses.

So I have listed the individual papers below.  Kudos to ASM and JMBE for putting this together.  Now off to read some of the papers.


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Friday, March 18, 2016

The #UCDavis Chancellor's Board Positions and the Need for a More Public, Open and Early Disclosure System

So, I assume by now many people out there have heard about the controversy going on at UC Davis over the board positions taken by the UC Davis Chancellor Linda Katehi.  If you have not - here is a brief summary.
  • In late February, Chancellor Katehi accepted a board position at the for profit educational company Devry but then steeped down after complaints.  See for example this story by Diana Lambert in the SacBee for details.  Note - she has admitted that her accepting of this position prior to getting approval from the UC President was a violation of UC policy.
  • Chancellor Katehi received $420,000 in compensation for serving on the board of John Wiley and Son's from 2012-2014.  See this SacBee story by Diana Lambert and Dale Kasler for more detail.  In relation to this report, Chancellor Katehi has apologized and has said she will donate "all the stock proceeds" she made from Wiley to a Scholarship fund for UC Davis students.
  • Chancellor Katehi served on the International Advisory Board of King Abdulaziz University in Saudi Arabia for a year.  This is the same University that has been strongly critiqued for its practice of paying highly cited scholars to become adjunct faculty in order to boost its ratings. It has been reported that she did not attend any of the board meetings in person and did not receive any compensation for this.  See this and this for more detail.  
There have been many responses to these revelations including:
The situation does not appear to be letting up.  I note - in the description above I have tried to be as objective as possible in describing the situation.  And I have been thinking a lot about what I think should happen now.  Do I think the Chancellor should resign?  Should she be fired?  Do we need more faculty to come out in support of her?  What is the best path forward for UC Davis?  I certainly have thoughts on these questions and related topics.  And I assume many people who know me know that I am not exactly shy about expressing my thoughts in public.

But ... there is one major thing that gives me pause here.  And it relates to the comment above about trying "tried to be as objective as possible" here.  The reason this gives me pause here is because one of the key issues at play relates to "Conflicts of Interest" - both real and perceived - in the Chancellor's board positions.  Many critics have argued that each of these board positions comes with major conflicts of interest in the Chancellor's job as the head of a major public university.  The Chancellor's supporters have argued that these board positions at worst involved the appearance of a possible conflict and not any real conflict.

Why I am digging into this conflict of interest topic?  Because I think one key way to help people assess whether there are any real or possible conflicts of interest in one's activities is to fully disclose as much as possible about one's activities.  And I think the UC in general and the Chancellor of UC Davis could do a much much much better job in terms of disclosures.  And I have a proposal for that.

But before we get into that I think it is necessary for me to make some disclosures.  Here are some:
  • I am a Professor at UC Davis
  • I have worked on a few projects with the UC Davis Chancellor Linda Katehi directly and indirectly and I have always had positive interactions with her).
  • I have worked on the UC Davis ADVANCE Project ( to increase the participation and advancement of women in academic science and engineering careers) for which Chancellor Katehi is the lead. 
  • I don't always agree with actions taken by Chancellor Katehi but I do believe she is truly committed to improving UC Davis
  • I have worked for many years on "open access" to scholarly literature (and a little bit to textbooks) and have occasionally been at odds with the John Wiley and Son's company.
  • I was involved in an exposé of what I believe to be unethical behavior of King Abdulaziz University a few years ago in their attempts to buy rankings by trying to have scholars change their institutional affiliations on publications and in citation databases.  See for example this and this and this.  I note - I was threatened by one of the people from KAU who I helped expose.  I am NOT A FAN of KAU.
  • I spent almost two months writing about the pepper spray incident and follow up in 2011 in an effort to help save the image of UC Davis, which I love.  See some of my posts about this here.  The whole incident and the aftermath was very traumatic for the University and many individuals associated with the University, including myself.  There were calls for Chancellor Katehi to resign then.  And there were statements of support by deans and faculty.  I refused to sign either.  I thought she and the UC Davis admins made many mistakes and did not by any means deserve endorsements.  But I also thought it was unclear if their mistakes were enough for them to be pushed out. 
  • Other disclosures of mine are here: https://phylogenomics.wordpress.com/about/disclosures
I have listed these disclosures because I am not sure I can be objective about this story.  And I want everyone reading this to have this information so that you can make your own decision as to whether you think my possible conflicts of interest might cloud my judgement in various ways.  I tried to be objective in outlining what I think the current state of the situation is above, but I understand that not everyone may agree.  And if people think my view of the situation is too biased, well, they probably will not care too much about what I think we should do now.  And I am OK with that.  What I want most is for people to know now just what my positions are, but what might have affected what my positions are.

OK - so that is a way longer introduction than I had imagined in getting to the question of "what should we do now?" 

A reader who thinks I am not completely compromised might ask - what do I think about the situation and what do I think should happen now?  Here are some comments:

  • I personally think that accepting each of these board positions was really not wise.  Yes, the Chancellor may have accepted them with the best of intentions.  And yes, she may not have done anything inappropriate in her time on the two on which she served (Wiley and KAU).  But I think it would not have been that hard to imagine how these board positions might be perceived - especially by UC Davis students.  And that alone I think should have led to turning down these board positions.  She has admitted Devry was a mistake. She has not admitted (as far as I know) that Wiley was a mistake but has hinted that she can see how some people may not like it.  She has not admitted at all that KAU was a mistake as far as I can tell (and has defended it as being in the interest of promoting diversity), but given that it was known in 2011 widely that they were buying ranking in a seemingly unethical manner, this should have raised some red flags.  I do wonder a bit whether my really unpleasant interaction with KAU has made me more judgmental about this board position than maybe I should be (hence why I thought it was important to disclose this above).
  • Despite the above comments, I do not think that the board positions taken by the Chancellor are enough of a problem to call for her firing or resignation.  There are two major reasons for this.  My min reason for this is that I think one has to weigh the board position issue against all she has done as Chancellor and overall I believe she has done many very good things as Chancellor and that she is truly and deeply committed to UC Davis.  I understand that other people do not agree with this.  So I think in a way how people respond to this board position issue may relate largely to how good a job they think she has been doing as Chancellor.
  • I think a key mistake in this whole situation involved a poor job of disclosure.  More on this below.
  • I think another key mistake has been the slow and minimal communication with UC Davis and the public in response to these issues.  I really wish Chancellor Katehi and UC Davis administrators would hold some town halls or the like to discuss these issues and to explain to us why these board positions were taken.
So in summary - I think the Board positions were mistakes but I do not think they rise to the level of calling for the Chancellor to be fired or to resign.  I do think we should use this situation to completely revisit the topic of conflicts of interest, disclosure, and outside activities of the UC Administrators.  There have been calls, for example, to greatly limit if not stop entirely outside activities, especially at for profit entities, by the UC Chancellors and other higher ups.  I am not sure what I think about these calls, but they are definitely worth considering.  However, I think as a first step the UC could tackle one key issue - Disclosure.  

In general I think disclosures of possible conflicts of interest are done really poorly in academia.  So poorly that before this whole issue cropped up at UC Davis I made a proposal that scholars add disclosures to a centralized universal scholarly ID system known as ORCID.  See Improving Ability to Identify Possible Conflicts of Interest of Scholars 1: Adding a Disclosure Field to ORCID.  This would certainly help when on sees a paper by someone (say, Eric Lander) and would allow one to get more information about their possible conflicts of interest (say, billions of dollars in possible royalties for the institute one runs).  I think such a system would be very useful.  But it is not really enough for the issue at hand here.

So in order to at least get the UC started down a better path in terms of conflicts of interest and activities by UC administrators I propose the following simple steps (and I note - this are just some ideas and thoughts, not a well formulated system at this point).

Proposed Public, Open, and Early Disclosure System for UC Administrators.
  • This system should be applied to all top UC Administrators (UC President, Chancellors, Provosts, Deans, and possibly others)
  • Disclosures of outside activities and potential conflicts of interest must be made publicly available in a centralized location. 
    • This would include Form 700s and other declarations.
    • I have been told such forms are available for all UC Admins.  They are certainly not readily available.
    • UC Administrators should be required to update such disclosures quarterly
  • The disclosures need to be referenced and linked readily and widely:
    • The disclosures should be provided at the administrator's profile pages 
    • Disclosures or links to them should accompany all official communications of these administrators (much in the way disclosures should accompany scholarly publications).
  • Administrators should be required to submit proposed outside activities to the public PRIOR to commencing those activities. 
    • There should be a public commenting period regarding these proposals
    • The specific activities and compensations must be included in all proposals
    • The proposals should include a discussion of the putative benefits to the UC for such activities.
    • There should be a more public, more formal review process for determining if the proposed activities are in the best interest of the UC
  • These disclosures should happen whether or not any other regulations about outside activities happen.
I understand this will not solve all the issues associated with outside activities, conflicts of interest, and such.  But I think one big step would be for the UC to adopt a more open, public, early, easy to find, and widely share disclosure system for outside activities of UC Administrators.  And perhaps, just perhaps, requiring such open, public, and early disclosure system would lead some UC Administrators to think more carefully and clearly about what outside activities they choose to do - or propose to do.

Update 3/23: some other links of relevance
Been attempting to get for 700s for the Chancellor (as an exercise, not to dig into them in any detail). Writing about it in a seagate post.

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Monday, March 14, 2016

Janelle Ayres talk at #UCDavis on host-microbe-microbiome interactions

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Wednesday, March 09, 2016

Time for #DegreeMadness - where we rank people's statements by what degrees they have not by science

UPDATE 1/1/2018 Replacing the Storify with Wakelet since Storify is going away. I transferred my Storify collection to Wakelet using their import tool. Testing the embed a few different ways.
wakelet Powered by Wakelet

wakeletPowered by Wakelet

wakelet Powered by Wakelet

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Sunday, March 06, 2016

Conferences on Weekends? Good or Bad Idea? Summary of responses to query ..

Lots of fascinating and very useful response to a question I asked yesterday about conferences on weekends.  When I wrote the post I had a personal point of view - that conferences on weekends were bad.  But I knew I had heard many others argue that it was better for some people to have them on weekends and I thought it might be good to hear what people thought.

So I made a Storify of the responses so far.



I also got some good responses on Facebook.

Some of the themes so far are discussed below:

Many factors come into play including
  • Job type
  • Financial status
  • Having children and the children's ages
  • Having partners 
  • Partner's work commitments
  • Distance from meeting
  • Duration of meeting
  • Quality of the conference
Weekends can be BAD for some people if
  • They try to save weekends for family or general life (as in, not work) activities
  • They have children and children are young, seems like many find it harder or less desirable to go away on weekends
  • They get assistance with childcare during the week (e.g., daycare) but not on weekend so then partners have harder time alone on weekend
  • They are in a long-distance relationship weekends may be only chance to see partner
Weekends can be GOOD for some people if
  • They just cannot get away at all during the week 
    • maybe due to clinical commitments 
    • maybe due to heavy teaching loads
  • When they leave their partner(s) take care of family commitments and if partners work during the week, they may be better able to deal with weekends without a partner
  • Even if partners do not work, taking care of family alone during week may be harder than on weekends
Suggestions for how to deal with the challenges of conferences
  • Move the location around so that people are affected differently each time (e.g., travel time can add to the challenges for meetings so if you move the meeting travel time will not always affect people from the same places in the same way)
  • Move the weekend/weekday aspect of the meeting 
  • Make meetings as family friendly as possible (this seems to be true if on weekend or not)
  • Make meetings short
  • Conference participation needs to be optional 
  • Have meeting stat bridge weekdays and weekends and allow registration just for one part
  • Live stream conferences so people can participate remotely
  • Record and post videos 
  • Live Tweet and use other social media to allow people to participate remotely
More comments and thoughts would be welcome and thanks so much to the comments so far.

UPDATE 1:
I will repost the request during the week so that I sample thoughts from people who are not answering questions on weekends.  Doh. Thanks to Fiona Brinkman for pointing this sampling bias out to me.




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Saturday, March 05, 2016

Case Study - what to do when there are disagreements about whether a paper has problems

In light of the ongoing PLOSOne #Creationgate controversy (e.g. see this write up here), I thought I would share a story I have been working on about a case where there are disagreements about whether a paper has problems or not.

So I got this email the other day. It was from an author of a paper who I know who was upset about a paper that was published a while back for which I was the editor. This person wrote to me and the authors of the new paper somewhat angrily critiquing them for some aspects of their paper that related to this person's work. The authors responded to the critique and, well, did not agree with the points of the letter writer. The letter writer wrote again to all of us and again somewhat angrily critiqued the authors.

Then the letter writer wrote just to me asking what I thought should be done - detailing further what they viewed as mistakes of the paper.  The letter writer was quite clear, clearly upset, and had some good points. And the letter writer wanted advice about what should be done here.  I thought about this for some time and wrote and rewrote an email to the letter writer.  The challenge with this case was that this really seemed to be more of a disagreement than a case where an Editor could say "This is right and this is wrong."  So this is what I wrote

Letter Writer

 I appreciate your comments and your intent here.  I think the best course of action is for you to publish more public, formal or informal, comments about the paper.  I am not sure I would support any type of attempt to require the authors to officially revise their paper.  The paper was reviewed by multiple reviewers and the published version is the final outcome of the review process.  I believe the process was fair, rigorous and thorough.  That does not mean of course that it was perfect (note - I am not making any statement here about whether I think your comments and concerns are valid or not).  But as far as I can tell, even if your claims and comments were 100% valid and correct, I probably would still not recommend undertaking any action that would require modifications of the paper by the authors.  I therefore would recommend that you pursue other options including 

 (1) submitting comments about this on the journal web site 
(2) submitting comments at Pubmed Commons or other such sites 
(3) submitting a formal response via the journal 

 If you wish to pursue further the possibility of requesting a modification of the paper by the authors, I am happy to forward this on to the higher ups at the journal and they can tell you how to do this. But as I note, I am not sure this would be the right thing to do here.

 Jonathan Eisen

I don't know if I did the right thing here but I just felt that this was a case where people could just disagree about what was correct.  Any suggestions for how to handle such cases or other examples would be welcome. 
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Friday, March 04, 2016

Would you try to vaginally "seed" your baby's microbiome after a C-section

Well, sadly I just accidentally deleted a whole post about this and cannot find it. So this is going to be way shorter than I would have liked.

I found this opinion piece to be very interesting and a really good case study for discussing the microbiome: Opinion: A Mother’s Microbes | The Scientist Magazine

About the piece
  • Authors: Jack Gilbert and Rob Knight
  • Topic: VMS. Vaginal Microbiome Seeding. Attempting to "seed" the microbiome of an infant born by C-section by collecting microbes from the mother's vagina and applying them to the baby. 
  • Subtopic: A response to a BMJ editorial that seems to have said they do not at this time recommend VMS (I say seems to have said because the people at BMJ decided this was something to put behind a paywall). 
Why do I find it interesting?  Because I think the authors do a good job of showing how hard it is to make some decisions when the evidence is inconclusive.

Quibbles? Sure.  I like much of the approach of Gilbert and Knight but still find parts unconvincing and incomplete.  Some specifics are below:

The paragraph on the conditions associated with C-sections does not in my mind, go into enough detail on how such associations can be spurious and that those conditions could have no causal connection to C-sections.  Instead they simply say we do not know if these associations are due to lack of exposure to the vaginal microbiome of the mother.  That just is not sufficient in my mind.  For example, they mention the association between autism and C-sections.  However, they do not mention that some recent studies suggest that there may not be a causal association (e.g., see this). I think it is imperative when discussing such associations that one also mentions how such associations may have no causal relationship. 

It is unclear what the part near the end is that appears to be a quote from Rob Knight.  Not sure if this is a online formatting issue or what.  But in that section Knight writes "I seeded my newborn child with the vaginal microbes the baby would have received naturally had everything gone according to plan."  I have some quibbles with this as it seems possible that just doing an attempted seeding would not necessarily get the microbes that would have been received naturally

Finally, I have some more major quibbles with the last section.  On the one hand it it is good that they do discuss a risk that could come from VMS (exposure of the baby to pathogens from the mother).  However I think it would have been good in this discussion to also discuss other possible risks.  For example, it seems plausible that exposure to non pathogens from the mother could in fact do some harm (e.g., if one exposure the baby to the wrong non pathogenic organisms perhaps things could go wrong in terms of colonization).  In addition, it seems also plausible that by doing the sending, some parents and medical caregivers and others might be less vigilant at watching the infant for health issues assuming that the seeding made them healthy.  And I am sure there are others.  

It would in fact be good to lay out the possible risks somewhere in more detail.  Why?  Because I think Gilbert and Knight are actually spot on with their final recommendation:
But based on the evidence to date that your child’s microbiome at birth is important and modifiable, we think that parents should make up their own minds how much evidence is enough given the evolutionarily sound logic and clear health advantages of vaginal birth over C-section. 
And I am not just per se talking in the hypothetical.  If I could go back in time to when my daughter was born by a last minute C-section, I think I would have wanted to have done VMS.  And if I could go back in time to when our second child was born by a planned C-section, I definitely would have wanted to have been more aware of this issue and I think we would have seriously considered it.  I probably would have looked in more detail at the possible risks if I had the time but regardless, from what I know now, I think VMS is definitely worth considering in cases of C-sections if the mother's vaginal microbiome does not contain any known dangerous pathogens and if other risks can be considered and balanced.  




Bonus: BMJ did make available an audio commentary about their Editorial. See below:
Made a Storify of some of the discussion around the topic


Some other questions of interest and or papers to look at

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Monday, February 29, 2016

Nina Jablonski talk at #UCDavis on Evolution of Skin Pigmentation

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Saturday, February 27, 2016

3/9 at #UCDavis: Workshop: Authorship and the Promises of Digital Dissemination




AUTHORSHIP AND THE PROMISES OF DIGITAL DISSEMINATION

Wednesday, March 9, 4:00- 5:45 pm

UC Davis School of Law, King Hall, Rm 2100A

A cross-disciplinary panel discussion on authorship in the digital age, with a focus on the specific goals and needs of academic authors. Authors who write to be read care about how their works are published and what that means for reader access. While traditional options and copyright arrangements still predominate in many fields, there are ever-increasing ways to share works of authorship. What works best to get textual and visual works out there and under what circumstances? Join us for this panel discussion with Authors Alliance, where we will explore the opportunities and challenges authors face in maximizing the reach of their work, both in and outside of academia.

Participants:
Mario Biagioli (Law, STS)
Stephanie Boluk (English)
Jonathan Eisen (Biology)
Alexandra Lippman (STS)
Rick Prelinger (UCSC and director of the Prelinger Archive)
Kim Stanley Robinson (Mars Trilogy)
Pam Samuelson (Authors Alliance)
MacKenzie Smith (Library)
Madhavi Sunder (Law)

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Thursday, February 11, 2016

Simple solution: Template text for "National Interest" aspect of NSF Grants

To be filled in for any NSF grant.

-----------------------------------------------------------

In order to meet the requirements of the benevolent, wise, and all knowing HR 3293, it is hereby declared in this written declaration that this National Science Foundation grant has been determined to

1) Be eminently worthy of Federal Funding

AND

2) Is without a doubt in the national interest, as indicated by having the incredibly high probability of achieving: [Insert here one or more of the following]

(A) Increased economic competitiveness in the United States;
(B) Advancement of the health and welfare of the American public;
(C) Development of an American STEM workforce that is globally competitive;
(D) Increased public scientific literacy and public engagement with science and technology in the United States;
(E) Increased partnerships between academia and industry in the United States;
(F) Support for the national defense of the United States; or
(G) Promotion of the progress of science for the United States.

Sincerely,

Your humble National Science Foundation Program officer


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Saturday, February 06, 2016

A very strange & annoying Google Scholar / Biomed Central "glitch" #GamingMetrics

So I discovered a few days ago I had dozens of new publications in 2015.  Cool right?  Here is a screengrab:



And here is another


Until I realized, well, those were published years ago.  WTF are they doing being listed as 2015?  Clearly some glitch. And then I saw a few Tweets that pointed me to figuring out what was going on.

.





So I responded


And some discussion followed





Fascinating. But I knew my papers were not published as preprints. And that they were published years before Google Scholar was not listing them as being published.

So - what happened? I think I now. These papers were all published in one journal - Standards in Genomic Sciences. The journal used to be published semi-independently by the Genomics Standards Consortium. Then they were transferred to / bout.
ht by / merged with Biomed Central and even the web address was forwarded to BMC where they host the archive of articles from before the transfer.  Then there is a new site with articles from after the transfer.

So when I click on the articles from the Google Scholar site I get to a strange thing.  The articles published before the transfer are also listed on the new site http://standardsingenomics.biomedcentral.com/.

For example - the Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T) is shown here with a 2015 publication date:



Although note the Copyright 2010 little bit.  Which is interesting since this paper was in fact published in 2010.  And you can find it on the other site http://standardsingenomics.org with a 2010 publication data here.



And also in Pubmed and Pubmed Central.





So - even though Biomed Central says the new papers will be in the new site and the old papers will be ket in a separate site that is not what is happening.



For some reasons some of the older papers are now being listed in the new site with a new publication date.  And I assume because Google Scholar scrapes from the journal sites, it found the "new" papers and has now added them to it's clustering collection and has fed them into my publication list.  And despite trying I am not sure how to fix this.

I tried to "unmerge" the new publications to see if somehow the old publications showed up.  But they did not.  So .. am not sure what to do here other than to send this to BMC and Google Scholar, which I will do.  Ahh - the perils of automated systems ...

I note -  this does seem to have possibly temporarily increased my total number of citations since it seems like some of these papers are now being considered twice by Google Scholar but not sure about that.  More digging.




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