Eisen Lab Blog

Today at #UCDavis: Megan Dennis on Autism Genetics: a brief history and the current state

“Autism Genetics: a brief history and the current state”

Speaker: Megan Dennis

UC Davis

Monday, March 7, 2016

4:00-5:00 PM

1022 Life Sciences

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.

//storify.com/phylogenomics/conferences-on-weekends-good-or-bad-idea/embed?border=false&template=slideshow//storify.com/phylogenomics/conferences-on-weekends-good-or-bad-idea.js?border=false&template=slideshow[View the story “Conferences on Weekends? Good or Bad Idea?” on Storify]

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.

//platform.twitter.com/widgets.js

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Worth a look: The Fix Ins’t In (regarding SciHub)

Another interesting post relating to open access in Inside Higher Ed:  The Fix Isn’t In | Library Babel Fish

It is by Barbara Fister and discusses some of her thoughts, as a librarian, on Sci-Hub.

Thanks again to Art Shapiro for pointing me to this.

I am still not sure how I feel about SciHub.  I like that people can get access to more literature.  But I would prefer that that happened by legal means and I think I agree with Fister that this is “not the fix for the mess we’re in.”

Anyway – the post is worth a look.

Worth a look: Open Access Reinterpreted

A post of possible interest at Inside Higher Ed.  By Ernesto Priego: Open Access Reinterpreted | University of Venus

Thanks to Art Shapiro for sending this to me.

Lots of interesting points and also an interesting response from Bjorn Brembs.  Definitely worth a look.

 

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. 

——–
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.

——–

UCR African American Disparities Cluster Hire

Got this in email:

Dear Colleague:

We are writing to ask for your assistance in facilitating our efforts to get the word out about the University of California, Riverside’s (UCR) major new Cluster Hire initiative, which seeks to add three hundred (300) tenured and tenure-track positions in thirty-three (33) cross-disciplinary areas (clusters) as selected through a peer-reviewed competition. Specifically, our cluster hire committee is tasked with overseeing the cluster hire of five positions focused on African American Disparities at the Assistant, Associate and Full professor levels (please see enclosed job announcement).

Successful candidates will become core faculty in the newly established research initiative on African American Disparities. We seek applicants with a strong track record of cross-disciplinary, multi-disciplinary and interdisciplinary research, publications and funding (or funding potential) in African American Disparities for positions in one or more of the following areas: Psychology, Sociology, Political Science, Economics, Public Policy, Business, History, Education, Anthropology, Biological and Medical Sciences.

Review of completed applications will begin on March 31, 2016 and continue until all positions are filled, with the first series of appointments scheduled to begin on July 1, 2016. Questions about the cluster hire positions should be directed to the Chair, African American Disparities Search Committee, Professor Carolyn B. Murray at carolyn.murray.

Your attention and consideration in this matter are greatly appreciated.

Best Regards,

Carolyn B. Murray,

Professor of Psychology

Chair, African American Disparities

Cluster Hire Committee

AA Disparities Colleague Letter 3_1_16.doc

AA Disparities Cluster Job Announcement Update03_01_16.pdf

2016 #UCDavis CTSC T32 Post-doctoral Training Program

UC Davis Clinical and Translational Science Center

T32 Post-doctoral Clinical Research Training Program
Call for Applications

Deadline to submit: Friday, April 1, 2016 at 5:00 pm

All applications and supporting documents must be submitted electronically in a single PDF file to:

Connie Koog at cdkoog

The CTSC is pleased to announce a call for Post-doctoral applicants to receive research funding from the National Institutes of Health (NIH) sponsored T32 Post-doctoral Clinical Research Training Program (CTSC-T32). The CTSC-T32 program is part of a fully integrated approach by the UC Davis CTSC to advance research education and training for multidisciplinary, clinical and translational investigators working to improve human health. The overall goal of the T32 program is to provide post-doctoral scholars with skills required to develop a career in multidisciplinary clinical and translational research relevant to human health. The CTSC-T32 training program is expected to strongly advantage scholars in preparing for successful careers in translational research.

Post-doctoral scholars pursuing health related research at UC Davis are eligible to apply. Scholars will be selected based on a competitive application process in which student academic qualifications, career goals, and the quality of the training environment will be important considerations for funding.

Applicants must work with a UC Davis faculty mentor and develop a proposed research plan in consultation with that mentor to be submitted with the application. Award recipients are required to make a two year (July 1, 2016 – June 30, 2018) commitment to all components of the training program; which includes the proposed research, didactic instruction and exposure to clinical care. Scholars may earn a master’s in clinical research, if they choose, during the training.

Awardees will receive a stipend, funds for research and travel expenses. For those pursuing the MAS in Clinical Research, full tuition will be covered. Please be advised that the research budget must be administered under the current NIH directive with respect to clinical trial research and can only be used to offset research costs that do not directly support clinical trials. For example, T32 funds may not be used to pay subjects or purchase medications. In addition, all funds must be managed by UC Davis, and not by off-site entities. As always, direct billing for services is permitted. All budgetary items should be reviewed and approved prior to initiating studies.

PLEASE NOTE: All funding is contingent upon final NIH Notice of Award for the CTSC grant.

Eligibility Criteria:

· Current UC Davis postdoctoral scholar or eligible for recruitment to UC Davis

· U.S. citizen, noncitizen nationals, or have legal admission into the U. S. as a permanent citizen at the time of application

· Strong academic credentials and good communication skills

· Ability to commit to all requirements of the training program, including an observer in selected clinical rotations

· Proposed research project must be relevant to human health

· Interest in developing a career in multidisciplinary, translational biomedical research

· Identification of a faculty mentor and strong mentor support

Application Instructions:

Applications with supporting documents, which include: a copy of your CV, two letters of recommendation, one must be from your proposed faculty mentor and that mentor’s biosketch in a single PDF file; submitted by email to Connie Koog at: cdkoog. No paper applications will be accepted.

Applications will be reviewed by a CTSC committee chaired by program directors Dr. Nicholas Kenyon and Dr. Julie Schweitzer.

For questions, please contact Connie 916-703-9132 or cdkoog@ucdavis.edu.

2016 T32 Postdoc Call_Final.pdf

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

//storify.com/phylogenomics/vaginal-microbiome-seeding-would-you-do-it-what-do/embed?border=false&template=slideshow//storify.com/phylogenomics/vaginal-microbiome-seeding-would-you-do-it-what-do.js?border=false&template=slideshow[View the story “Vaginal Microbiome Seeding – would you do it? what do you think about it?” on Storify]

Some other questions of interest and or papers to look at

——–
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.

——–

Careers in Data Science seminar by Insight Data Science on 3/10

Forwarding this:

Dear Colleagues,

Davis Postdoc Entrepreneurship and Career group (DPEC) will host a seminar, “Careers in Data Science”, by Dr. Amrine and Dr. Soofi, two program directors of the Insight Data Science Fellows Program.

Insight Data Science is an intensive, seven-week postdoctoral training fellowship that bridges the gap between academia and a career in data science. The application deadlines of Data Science and Data Engineering fellowships are on March 21 and March 28, 2016 respectively.

This talk is intended for anyone who is interested in data science; all backgrounds are welcome!

When: Thurs, 10th March 2016, 12:00 pm – 1:30 pm (networking event to follow)
Where: Auditorium 1005, Genome and Biomedical Sciences Facility (GBSF)
Speakers: Katie Amrine, PhD and Wafa Soofi, PhD

We encourage you to mtnyunt.

Thanks.

With Best Regards,
Tun Nyunt (PhD)

Davis Postdoc Entrepreneurship and Career group (DPEC),

UC Davis

Insight Data Science Seminar_March2016.pdf

At #UCDavis 3/9: “Authorship and the Promises of Digital Dissemination,”

20160309_ucdavis_poster_smallA 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.

20160309_UCDavis_poster_small.pdf