Another "Yet another mostly male meeting (YAMMM)" from BGI

Well just saw an announcement for this meeting on Twitter: The First Announcement of The Tenth Annual Meeting of the International Conference on Genomics (ICG

And I hoped beyond hope that they would have a decent representation of women speakers at the meeting.  Why did I hope this?  Well, in the past, BGI run meetings have had incredibly skewed gender ratios of speakers.  See this post for a discussion of their past record: Kudos to the DOE-JGI for organizing a genomics meeting w/ a good gender ratio - no kudos to BGI - yet again

I guess I had hoped that perhaps they would try to change their practices after I and other people criticized them for their past record.  So - I went to the web site for the ICG10 meeting advertised in the Tweet.  Oh well, silly me for hoping.

On the front page they have 14 speakers they are promoting - all of them male.

Screen shot from ICG10 web site

On the announcement page they have a slightly different list where the ratio is 14:1
  • Jef Boeke, NYU Langone University School of Medicine, USA
  • Sydney Brenner, 2002 Nobel Laureate in Physiology or Medicine, Singapore
  • Charles Cantor, Sequenom, Inc., USA
  • Julio Celis, Danish Cancer Society Research Center, Denmark
  • Richard Durbin, Wellcome Trust Sanger Institute, UK
  • Leroy Hood, Institute for Systems Biology, USA
  • Thomas Hudson, Ontario Institute for Cancer Research, Canada
  • Maria Leptin, Chair of EMBO, Germany
  • Maynard Olson, University of Washington, USA
  • Aristides Patrinos, J. Craig Venter Institute, USA
  • Mu-ming Poo, University of California, Berkeley, USA
  • Richard Roberts, New England Biolabs, 1993 Nobel Laureate in Physiology or Medicine, USA
  • Eils Roland, Heidelberg University, Germany
  • Mathias Uhlen, Royal Institute of Technology, Sweden
  • Tilhuan Yilma, University of California, Davis, USA
Regardless, this is a consistent pattern of not having an even remotely balanced ratio of male to female speakers at their meetings.  And please, avoid their meetings until they change this.

Science based decision making in education: sleep and school start times in #DavisCA and beyond

In September of last year I wrote a brief post about science and decision making in schools: Nice letter to the editor in the Davis Enterprise taking on school district's anti-science tone.  I include it below since it is very relevant to this post.

----------------------------------
I assume many people heard about the recently released report from the American Academy of Pediatrics where they recommended high school classes start later in the morning than most do right now.  See for example: Let Them Sleep: AAP Recommends Delaying Start Times of Middle and High Schools to Combat Teen Sleep Deprivation.  And this report was covered in all sorts of newsy and bloggy places.   See for example, Amy Graff's article in SFGate and Deborah Netburn in the LA Times.  Overall, the argument presented by the AAP makes sense and seems supported by scientific fundings.  And they go through a lot of scientific reasons for their recommendations.

Alas, Winfred Roberson, superintendant of the Davis, CA schools (also known as the DJUSD) told the Davis Enterprise that the schools here would not be making any changes in response to this report:

“While DJUSD won’t be modifying start times, our role as an educational institution can be to find ways to support our students by giving them the tools that will help them to think through, make adjustments and prioritize their competing forces that may be cutting into the recommended sleep time,” Roberson said. “These are life skills we are helping to build that will help students to function even after graduation.”
And I had missed out on this quote, thankfully, but became aware of it when my wife showed me this letter by Steve Carlip in the Davis Enterprise today:  Don’t ignore the science Davis Enterprise.   I quote from it below:
The superintendent’s response, as reported in Tuesday’s Enterprise, was to simply ignore the science. Instead, he said, the schools will help student “build life skills” to “prioritize their competing forces that may be cutting into the recommended sleep time.” 
Really? The high school is going to teach students to control their circadian rhythms? It’s going to give them the “life skills” to regulate the timing of their bodies’ secretion of melatonin? It will educate them to overcome biological sleep-wake phase delay by sheer force of will?
He completely nailed it here.  I hope Winfred Roberson and the Davis School district rethink their attitude towards scientific studies.
-----------------------------------

Today I found out that the Davis School Board may actually be listening to the science.  For the next school board meeting which is February 5 there is an agenda item on this topic c. Update on the Formation of a DJUSD Sleep Study Committee. The description of the agenda item is as follows:
In August 2014, the American Academy of Pediatrics released a scientific sleep study report that recommended an 8:30 am start time for schools, which would allow secondary students more time to sleep.  The report generated community discussions and concerns since Davis secondary schools start before 8:30 am.
In response, the superintendent initiated the formation of a Sleep Study Committee (made up of students, teachers, counselors, parent/community members and administrators) to examine the benefits and logistical challenges of an earlier school start.    
This update is a report of the formation of the Sleep Study Committee and their charge.  For reiteration, at this time, staff is not offering recommendations about a modified start time.  Staff will wait to review the work of the Sleep Study Committee before offering formal recommendations to the Board. 
So I started digging around for more on the topic and found some things worth reading  But the most interesting thing I found was that there has been a discussion about this exact issue in the county where I grew up: Montgomery County Maryland.  Some of the articles about this area listed below:

It seems to me that Davis, CA really needs to consider this as a possibility.  It could help students in many ways and seems to be a relatively easy (though not free of course) way to improve the lives and learning of students in our town.  I am thrilled that the Board is bringing the topic up again.  Any examples out there of places that have shifted start times based on the AAP recommendation would be great (and what happened ...). 

See some responses on Twitter:



Best post doc position ever: w/ Jessica Green, myself, Jay Stachowicz, Jenna Lang

copied from U. Oregon web site

Postdoctoral Research Scholar
Institute of Ecology and Evolution

Posting: 14431
Location: Eugene
Closes: Open Until Filled

Revised Posting
Postdoctoral Position in Microbial Ecology and Evolution
Jessica Green at the University of Oregon (http://pages.uoregon.edu/green/) is currently seeking a postdoctoral researcher to collaborate on the Seagrass Microbiome Project (http://seagrassmicrobiome.org).  

Applicants should have a Ph.D. in a biological, computational, mathematical, or statistical field and strong writing skills.  The ideal candidate will have experience developing and applying models to understand the ecology, evolution, and/or function of complex systems.  Experience in the analysis of environmental sequence data is highly desirable, but not required. 
  
The successful candidate will have the opportunity to creatively and independently tackle one or more of the science questions outlined in the Seagrass Microbiome Project grant proposal (http://seagrassmicrobiome.org/2014-grant-proposal/), funded by the Gordon and Betty Moore Foundation.  

The successful candidate will interact regularly with team members Jonathan Eisen (http://phylogenomics.wordpress.com), Jay Stachowicz http://www-eve.ucdavis.edu/stachowicz/stachowicz.shtml, and Jenna Lang (http://jennomics.com/) at the University of California, Davis through weekly tele-conferencing and also through regular visits to the UC Davis campus. 

At the University of Oregon, the candidate will benefit from ongoing microbiome research programs including the Microbial Ecology and Theory of Animals Center for Systems Biology (http://meta.uoregon.edu/) and the Biology and Built Environment Center (http://biobe.uoregon.edu/).

The position is available for 1 year with the possibility for renewal depending on performance.  The start date is flexible.  Please email questions regarding the position to Jessica Green (jlgreen@uoregon.edu).

To apply
A complete application will consist of the following materials:
(1) a brief cover letter explaining your background and career interests
(2) CV (including publications)
(3) names and contact information for three references 
Submit materials to ie2jobs@uoregon.edu.  Subject: Posting 14431

To ensure consideration, please submit applications by March 10, 2015, but the position will remain open until filled. Women and minorities encouraged to apply.  We invite applications from qualified candidates who share our commitment to diversity. The University of Oregon is an equal opportunity, affirmative action institution committed to cultural diversity and compliance with the ADA. The University encourages all qualified individuals to apply, and does not discriminate on the basis of any protected status, including veteran and disability status.

Quick post - wanted - input on best practices for sample processing & storage for microbiome studies

Over at microBEnet I have a post that may be of interest to many readers: Best practices for sample processing and storage prior to microbiome DNA analysis freeze? buffer? process? | microBEnet: the microbiology of the Built Environment network.  Basically I am hoping to get a discussion going about the ins and outs of sample processing and storage for microbiome studies.  We have been having lots of discussions in my lab and with collaborators about this and thought it would be better to just get everyone involved.




Storify, wrap up of talk by Shirley Tilghman, ex president of #Princeton, at #UCDavis

Shirley Tilghman, ex president of Princeton, gave a talk at UC Davis yesterday as part of the Chencellor's Colloquium. I live Tweeted the talk and made a Storify of some of the Tweets and responses. Here it is

Gender and tenure diversity and Github teams (from #UCDavis)


Thanks to the UC Davis College of Engineering Twitter Feed for pointing me to this


The paper behind this is available as a preprint here.

Abstract:
Software development is usually a collaborative venture. Open Source Software (OSS) projects are no exception; in- deed, by design, the OSS approach can accommodate teams that are more open, geographically distributed, and dynamic than commercial teams. This, we find, leads to OSS teams that are quite diverse. Team diversity, predominantly in of- fline groups, is known to correlate with team output, mostly with positive effects. How about in OSS? 
Using GITHUB, the largest publicly available collection of OSS projects, we studied how gender and tenure diversity relate to team productivity and turnover. Using regression modeling of GITHUB data and the results of a survey, we show that both gender and tenure diversity are positive and significant predictors of productivity, together explaining a sizable fraction of the data variability. These results can inform decision making on all levels, leading to better out- comes in recruiting and performance.
Really, really fascinating.

Trials and tribulations with the "UC Care" medical plan & w/ UCSF, UC Davis health systems

The University of California healthcare options are, well, less than ideal right now, in my opinion.  Here is a little story about my recent experiences.

September 2014.

Forced to switch to the UC Care health plan because UC cancelled the health plan that allowed me to be a part of the Sutter Medical Group. Sutter has always been awesome. Wonderful care. Wonderful people. Rapid scheduling of appointments. And I was very sad to be forced to switch. I kept my primary care physician at Sutter but realized I would have to switch for many other things.

I was not pleased to be pushed into the UC Care plan because my experience with the UC Davis Medical Group has been beyond disappointed in the past.  For example see this: U. C. Davis Medical Group - their time is MUCH more important than yours.  Admittedly, I had not been to people in the UC Davis group in a while, so -- maybe things had changed.

Plus I was pleased to note that the UC Care said I should choose their plan if "You want direct access to all providers without a referral."  Why yes, that sounded good.  Hah hah hah.  Silly me.

September 2014.

Of course.  Just as I switched medical groups I had a serious health issue in need of attention.  Called UC Davis Nuerology  to make an appointment with the specialist recommended by a colleague.  They told me I needed a referral. I told them I had UC Care health plan which says I do not need a referral. They said that it did not matter what plan I had, I needed a referral. So I asked my doctor for a referral.

October 2, 2014.

Meanwhile I wrote to one of the people in the UC Davis Neurology Department where I wanted an appointment to ask how I should make an appointment and told him that I had been referred to him by a UC Davis MD (trying to pull some sort of nepotism here). He connected me to his assistant and I sent her the info she asked for.

October 13, 2014. 

I had not heard back from his assistant so I wrote to her again.
I am writing to see if you got this information I sent Oct 3 and if there is any more information you need from me. Thanks
I again did not hear back.

October 19, 2014.

I received a letter in the mail from UC Davis "reminding" me I had an appointment in Neurology scheduled for December 17, 2014.

Now, I guess it was nice to have an appointment.  But I note - they never called me to ask when would be good for an appointment. They never contacted me at all. And this was clearly less than ideal - an appointment in two months.

So I called them to ask - how did this get scheduled? They said they must have scheduled it with me. I told them, no, nobody even contacted me. I then asked - is there anything sooner? Nope. I then asked - what if I cannot make that date and time (I was scheduled to be away). They then said that would cause a significant delay in the appointment. What the $*@#$8? This is not the first time I have had trouble scheduling appointments with UC Davis physicians but this was absurd. I then asked - is there anything I need to do in advance? They said nope. So I waited. Two plus months. For an appointment for which I needed a referral even though I had signed up for UC Care.  Oh - and - I guess just to prove they had no clue what they were doing - they spelled ny name wrong (Johnathan).

December 17, 2014.  

I had my appointment with the neurology specialist.  He was very nice.  Seemed pretty knowledgeable.  He had some disconcerting misconceptions about me and I tried to correct them but he did not seems to be paying attention.  He did not do any of the more complex tests I had seen in the literature that were standard in the literature I had seen for my condition.  He did not even order any such tests.  He concluded the visit with a possible diagnosis and then said he needed to order a series of blood tests to test some alternative possibilities.  They decided I did not need a follow up appointment and that we would wait to see what the blood tests showed before deciding what to do next.  I told them I was not fasting and asked if that mattered and they said no (one of the reasons I ask in advance about blood tests is that freuqently they need me to be fasting and it is easier to do that early in the AM ... but nevermind that ... they said it was not needed).

December 22, 2014

I signed up for Mychart.ucdavis (based on the recommendation from the printout I got when I left the doctor's office)-- an online system to communicate with the UC Davis Medical Group.

December 23, 2014

I got an email saying there were test results in Mychart.

January 2, 2015.  

I still had not heard anything from the doctor's office.  I wrote to him via the MyChart system asking if he had any update based on the test results.  I called too.  No response.

January 6, 2015.

I finally got a message from my doctor.  It had my name wrong, again, in a different way (John).  The message was short, had one useful thing in it and then said he "You need to check in with your PCP-- I have instructed our staff to contact your outside PCP and transmit labs to him and to contact you."  So much for seeing a specialist directly and communicating with them.  Oh, and he ended the message with "Good we checked labs and caught this now before your travels."  What the $&#?  I had no travel plans.  This had nothing to do with travel.  He spelled ny name wrong.  They had me listed as having type II diabetes, when I have type I.  And they wanted me to communicate with my primary care physician instead of him.  Such excellent care.  Oh, and he made a comment about my vitamin B levels being too high when I had told him I was taking a specific prescribed vitamin therapy and that I had taken some that AM (this would likely screw up the blood test - I think to know if vitamin levels are off one has to NOT have recently taken vitamin pills).  Jesus Christ what a sham.  In fact, when I told him I was taking this vitamin prescription, he said something to the effect of "random vitamins don't usually help" and I said "it is not random it is actually prescribed and there are clinical trials showing it has some benefits" but he had never heard of it nor did he seem to care.

January 7, 2015. 

I decided, I needed to see another specialist.  So I went back to a recommendation from another colleague for someone to see at UCSF.  So I checked out the protocol for making an appointment at UCSF and I filled out an online form to request such an appointment.  In the request system it asked for the preferred method of contact for me, and I said email.

January 8, 2015 

A day or so later,  I received an email from their system which said I had an encrypted message regarding my appointment request.  I had to create a new log in to a new system in order to read the message about my appointment request.  The message started with the following:
This email is to acknowledge receipt of your online appointment request for a new patient appointment. We have been unsuccessful in reaching you by phone. Before an appointment can be approved for scheduling we will need the following required documents to start the review process:

·         Referral along with reason or diagnosis
·         Pertinent clinical notes or records
·         Pertinent test results
·         Front and back copy of insurance card and authorization if required by insurance
·         Patient demographic information
What?  Why did they ask for my preferred means of contact if they were then going to call?  Oh well, at least this got through.  I called to ask some questions and only got a machine so I left a message.

Janaury 12, 2015

Appointment with my primary care physician.  He told me they had not received any information from the UC Davis specialist.  But he agreed that it might be good to see a specialist who gave a shit (my words, not his).  So he said they would make a referral to UCSF for me.  I gave them the printout with the information requested from UCSF.  

Janaury 17, 2015. 

Got an email saying my doctor had sent over the referral information to UCSF.  Called UCSF on MLK day and alas they were not open.  But I left another message asking what I had to do to make an appointment.

January 19, 2015.  

My wife took down a message and gave it to me saying UCSF had called about making an appointment.

January 22, 2015.

I called UCSF Neurology.  It took a long long long time to get through to a person.  When I finally did, I said I was calling to set up an appointment.  The person was immediately somewhat rude.  I gave my name and DOB and the person said I had no referral and my record there was empty.  I said I had been called by UCSF and they had left a message saying I should call about an appointment.  Now, mind you, I am not sure why UCSF had called me - it could have been about setting up an appointment or it could have been just to return my call.  But regardless, I told the receptionist that my doctor's office had told me they had contacted UCSF and that I should call.  The person repeated that they had no record of anything in my file - no calls to me - nothing.   This sounded so weird that I said "Is this definitely the file for Eisen - E-I-S-E-N." and the person snapped back "I do not make spelling mistakes" or something like that.  Nice.  Eventually, the person transfered me to someone else who actually offered to help and to call my doctor's office.  They then said they could call me back after this.  I asked what number they had and the number they said was not one I recognized.  Weird.  But I gave them the correct number and then hung up.

After I hung up I started to get pissed off.  What was the deal here? I signed up for this UC Care health insurance beause I was supposed to be able to make appointments with specialists without referrals.  And I am a UC Professor - with an appointment in a medical school.  I probably get treated better than the random person.  What a scam.  And then I remembered how badly UC Davis Medical Group treated my wife many years before.  And how good the treatment we received from Sutter has been.  So I posted something to Twitter.

And finally I got contacted by someone who actually seemed to care.
Not sure where things are going to go - but at least one person associated with a UC Medical Group is trying to help ...

UPDATE January 29, 2015

Still no call back from UCSF Neurology despite their promises that they would call my doctor and then call me back as soon as possible.  Unbelievable.

UPDATE January 29, 2015 #2

Wrote an email directly to the Doctor I wanted an appointment with.

UPDATE January 29, 2015 #3

Tried to contact the appointment desk.  Was on hold for 30 minutes before I had to hang up.

UPDATE January 30, 2015

Got through to the appointment desk.  OMG how ridiculous.  They said they needed to transfer me to another department (memory and dementia) because that was where I had the referral (I had asked for an appointment in neurology, I have some peripheral neuropathy).  They said the doctor at UCSF had reviewed my chart and that is where they determined I needed an appointment.  And that I would need to contact my doctor about this.

What the F#*$*#?  Completely insane.

UPDATE February 2, 2015

Lesson of the day.  UCSF doctors and personnel, other than the receptionist I interacted with on the phone, really really really do care about getting things right.  After I posted again about this issue to Twitter and sent an email to my brother who forwarded it to people at UCSF, many people stepped up to try to help.  All of them have been incredibly gracious and concerned and helpful.

And at the same time I decided to get a copy of the referral from my primary care physician just in case there was a mistake from their end.

And, well, there it was.  The referral was to see a neurologist for diabetic related neuropathy issues.  Looked good.  Then I looked at page 2.  And there was a comment about my having a history of dementia and that they could not do an MRI due to my pacemaker.  Well.  WTF?  What chaos.

Certainly this explains why UCSF thought I should see the dementia clinic.  It does not explain why UCSF neurology would never return my calls and was rude on the phone, but, well, it does make me feel like a schmuck for the mistake my doctor's office made.

UPDATE February 2, 2015 1:45 PM

Finally - a call from UCSF.  Yay. And they are going to contact my docs office and confirm that I do not have dementia.  And then, maybe then, I will get an appointment.

UPDATE February 2, 2015 5:45 PM

Well, I got a call from the UCSF Neurology appointment desk.  The person said they were calling because I had apparently contacted another doctor who contacted them (were they pissed off about this? sounded like it).  And they told me the first appointment was April 19.  Wow.  That is, like, not soon.  Lovely.  I took it.  But am going to see if there is a way to move it up.

UPDATE April 19, 2015

So - I finally had my appointment with a Neurologist at UCSF.  I had to get up so so early for my 9 AM appointment at UCSF Parnassus campus.  I was planning to take the train at 5:45 AM and then somehow wind my way to the UCSF campus.  And my alarm was somehow silenced.  I woked up at 5:30.  And I literally threw stuff in my bag and changed and jumped in my car.  But there was just no way to make it.  And so I decided to suck it up and drive into SF.  Traffic was bad already that early.  And I was pretty wiped when I got to UCSF.  And I was prepared for the worst.

But OMG.  What a difference.  I was treated so incredibly well by everyone there.  The information desk people on the 1st floor were helpful.  The lab people where I went for blood tests afterwards were pleasant and helpful.  The staff in the Neurology Department were friendly and respectful and helpful.  And my doctor.  Wow.  She was just so great.  Yes I do have some neuropathy.  And yes indeed it does completely suck.  And yes it still freaks me out and stresses me out.  But now I finally feel like I am getting excellent medical care.  And that is uplifting, even though my health is imperfect.  Such a contrast compared to the awful experience at the UC Davis Neurology

UPDATE April 21, 2015

Got a call from a UCSF Neurologist to discuss my blood test results.  My doctor was not available so an alternative doctor called me.  And she was phenomenal too.  Spent quite a while on the phone discussing things.  Came up with a plan.  All based on actual science.

UPDATE April 22, 2015

Got my medical report in the mail from UCSF.  Incredibly detailed report about my appointment, recommendations for me, and more.  Another wonderful feature.  I have STILL not gotten any such thing from UC Davis.

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الاثنين، 9 فبراير 2015

Another "Yet another mostly male meeting (YAMMM)" from BGI

Well just saw an announcement for this meeting on Twitter: The First Announcement of The Tenth Annual Meeting of the International Conference on Genomics (ICG

And I hoped beyond hope that they would have a decent representation of women speakers at the meeting.  Why did I hope this?  Well, in the past, BGI run meetings have had incredibly skewed gender ratios of speakers.  See this post for a discussion of their past record: Kudos to the DOE-JGI for organizing a genomics meeting w/ a good gender ratio - no kudos to BGI - yet again

I guess I had hoped that perhaps they would try to change their practices after I and other people criticized them for their past record.  So - I went to the web site for the ICG10 meeting advertised in the Tweet.  Oh well, silly me for hoping.

On the front page they have 14 speakers they are promoting - all of them male.

Screen shot from ICG10 web site

On the announcement page they have a slightly different list where the ratio is 14:1
  • Jef Boeke, NYU Langone University School of Medicine, USA
  • Sydney Brenner, 2002 Nobel Laureate in Physiology or Medicine, Singapore
  • Charles Cantor, Sequenom, Inc., USA
  • Julio Celis, Danish Cancer Society Research Center, Denmark
  • Richard Durbin, Wellcome Trust Sanger Institute, UK
  • Leroy Hood, Institute for Systems Biology, USA
  • Thomas Hudson, Ontario Institute for Cancer Research, Canada
  • Maria Leptin, Chair of EMBO, Germany
  • Maynard Olson, University of Washington, USA
  • Aristides Patrinos, J. Craig Venter Institute, USA
  • Mu-ming Poo, University of California, Berkeley, USA
  • Richard Roberts, New England Biolabs, 1993 Nobel Laureate in Physiology or Medicine, USA
  • Eils Roland, Heidelberg University, Germany
  • Mathias Uhlen, Royal Institute of Technology, Sweden
  • Tilhuan Yilma, University of California, Davis, USA
Regardless, this is a consistent pattern of not having an even remotely balanced ratio of male to female speakers at their meetings.  And please, avoid their meetings until they change this.

الاثنين، 2 فبراير 2015

Science based decision making in education: sleep and school start times in #DavisCA and beyond

In September of last year I wrote a brief post about science and decision making in schools: Nice letter to the editor in the Davis Enterprise taking on school district's anti-science tone.  I include it below since it is very relevant to this post.

----------------------------------
I assume many people heard about the recently released report from the American Academy of Pediatrics where they recommended high school classes start later in the morning than most do right now.  See for example: Let Them Sleep: AAP Recommends Delaying Start Times of Middle and High Schools to Combat Teen Sleep Deprivation.  And this report was covered in all sorts of newsy and bloggy places.   See for example, Amy Graff's article in SFGate and Deborah Netburn in the LA Times.  Overall, the argument presented by the AAP makes sense and seems supported by scientific fundings.  And they go through a lot of scientific reasons for their recommendations.

Alas, Winfred Roberson, superintendant of the Davis, CA schools (also known as the DJUSD) told the Davis Enterprise that the schools here would not be making any changes in response to this report:

“While DJUSD won’t be modifying start times, our role as an educational institution can be to find ways to support our students by giving them the tools that will help them to think through, make adjustments and prioritize their competing forces that may be cutting into the recommended sleep time,” Roberson said. “These are life skills we are helping to build that will help students to function even after graduation.”
And I had missed out on this quote, thankfully, but became aware of it when my wife showed me this letter by Steve Carlip in the Davis Enterprise today:  Don’t ignore the science Davis Enterprise.   I quote from it below:
The superintendent’s response, as reported in Tuesday’s Enterprise, was to simply ignore the science. Instead, he said, the schools will help student “build life skills” to “prioritize their competing forces that may be cutting into the recommended sleep time.” 
Really? The high school is going to teach students to control their circadian rhythms? It’s going to give them the “life skills” to regulate the timing of their bodies’ secretion of melatonin? It will educate them to overcome biological sleep-wake phase delay by sheer force of will?
He completely nailed it here.  I hope Winfred Roberson and the Davis School district rethink their attitude towards scientific studies.
-----------------------------------

Today I found out that the Davis School Board may actually be listening to the science.  For the next school board meeting which is February 5 there is an agenda item on this topic c. Update on the Formation of a DJUSD Sleep Study Committee. The description of the agenda item is as follows:
In August 2014, the American Academy of Pediatrics released a scientific sleep study report that recommended an 8:30 am start time for schools, which would allow secondary students more time to sleep.  The report generated community discussions and concerns since Davis secondary schools start before 8:30 am.
In response, the superintendent initiated the formation of a Sleep Study Committee (made up of students, teachers, counselors, parent/community members and administrators) to examine the benefits and logistical challenges of an earlier school start.    
This update is a report of the formation of the Sleep Study Committee and their charge.  For reiteration, at this time, staff is not offering recommendations about a modified start time.  Staff will wait to review the work of the Sleep Study Committee before offering formal recommendations to the Board. 
So I started digging around for more on the topic and found some things worth reading  But the most interesting thing I found was that there has been a discussion about this exact issue in the county where I grew up: Montgomery County Maryland.  Some of the articles about this area listed below:

It seems to me that Davis, CA really needs to consider this as a possibility.  It could help students in many ways and seems to be a relatively easy (though not free of course) way to improve the lives and learning of students in our town.  I am thrilled that the Board is bringing the topic up again.  Any examples out there of places that have shifted start times based on the AAP recommendation would be great (and what happened ...). 

See some responses on Twitter:



Best post doc position ever: w/ Jessica Green, myself, Jay Stachowicz, Jenna Lang

copied from U. Oregon web site

Postdoctoral Research Scholar
Institute of Ecology and Evolution

Posting: 14431
Location: Eugene
Closes: Open Until Filled

Revised Posting
Postdoctoral Position in Microbial Ecology and Evolution
Jessica Green at the University of Oregon (http://pages.uoregon.edu/green/) is currently seeking a postdoctoral researcher to collaborate on the Seagrass Microbiome Project (http://seagrassmicrobiome.org).  

Applicants should have a Ph.D. in a biological, computational, mathematical, or statistical field and strong writing skills.  The ideal candidate will have experience developing and applying models to understand the ecology, evolution, and/or function of complex systems.  Experience in the analysis of environmental sequence data is highly desirable, but not required. 
  
The successful candidate will have the opportunity to creatively and independently tackle one or more of the science questions outlined in the Seagrass Microbiome Project grant proposal (http://seagrassmicrobiome.org/2014-grant-proposal/), funded by the Gordon and Betty Moore Foundation.  

The successful candidate will interact regularly with team members Jonathan Eisen (http://phylogenomics.wordpress.com), Jay Stachowicz http://www-eve.ucdavis.edu/stachowicz/stachowicz.shtml, and Jenna Lang (http://jennomics.com/) at the University of California, Davis through weekly tele-conferencing and also through regular visits to the UC Davis campus. 

At the University of Oregon, the candidate will benefit from ongoing microbiome research programs including the Microbial Ecology and Theory of Animals Center for Systems Biology (http://meta.uoregon.edu/) and the Biology and Built Environment Center (http://biobe.uoregon.edu/).

The position is available for 1 year with the possibility for renewal depending on performance.  The start date is flexible.  Please email questions regarding the position to Jessica Green (jlgreen@uoregon.edu).

To apply
A complete application will consist of the following materials:
(1) a brief cover letter explaining your background and career interests
(2) CV (including publications)
(3) names and contact information for three references 
Submit materials to ie2jobs@uoregon.edu.  Subject: Posting 14431

To ensure consideration, please submit applications by March 10, 2015, but the position will remain open until filled. Women and minorities encouraged to apply.  We invite applications from qualified candidates who share our commitment to diversity. The University of Oregon is an equal opportunity, affirmative action institution committed to cultural diversity and compliance with the ADA. The University encourages all qualified individuals to apply, and does not discriminate on the basis of any protected status, including veteran and disability status.

السبت، 31 يناير 2015

Quick post - wanted - input on best practices for sample processing & storage for microbiome studies

Over at microBEnet I have a post that may be of interest to many readers: Best practices for sample processing and storage prior to microbiome DNA analysis freeze? buffer? process? | microBEnet: the microbiology of the Built Environment network.  Basically I am hoping to get a discussion going about the ins and outs of sample processing and storage for microbiome studies.  We have been having lots of discussions in my lab and with collaborators about this and thought it would be better to just get everyone involved.




الأربعاء، 28 يناير 2015

Storify, wrap up of talk by Shirley Tilghman, ex president of #Princeton, at #UCDavis

Shirley Tilghman, ex president of Princeton, gave a talk at UC Davis yesterday as part of the Chencellor's Colloquium. I live Tweeted the talk and made a Storify of some of the Tweets and responses. Here it is

الجمعة، 23 يناير 2015

Gender and tenure diversity and Github teams (from #UCDavis)


Thanks to the UC Davis College of Engineering Twitter Feed for pointing me to this


The paper behind this is available as a preprint here.

Abstract:
Software development is usually a collaborative venture. Open Source Software (OSS) projects are no exception; in- deed, by design, the OSS approach can accommodate teams that are more open, geographically distributed, and dynamic than commercial teams. This, we find, leads to OSS teams that are quite diverse. Team diversity, predominantly in of- fline groups, is known to correlate with team output, mostly with positive effects. How about in OSS? 
Using GITHUB, the largest publicly available collection of OSS projects, we studied how gender and tenure diversity relate to team productivity and turnover. Using regression modeling of GITHUB data and the results of a survey, we show that both gender and tenure diversity are positive and significant predictors of productivity, together explaining a sizable fraction of the data variability. These results can inform decision making on all levels, leading to better out- comes in recruiting and performance.
Really, really fascinating.

الخميس، 22 يناير 2015

Trials and tribulations with the "UC Care" medical plan & w/ UCSF, UC Davis health systems

The University of California healthcare options are, well, less than ideal right now, in my opinion.  Here is a little story about my recent experiences.

September 2014.

Forced to switch to the UC Care health plan because UC cancelled the health plan that allowed me to be a part of the Sutter Medical Group. Sutter has always been awesome. Wonderful care. Wonderful people. Rapid scheduling of appointments. And I was very sad to be forced to switch. I kept my primary care physician at Sutter but realized I would have to switch for many other things.

I was not pleased to be pushed into the UC Care plan because my experience with the UC Davis Medical Group has been beyond disappointed in the past.  For example see this: U. C. Davis Medical Group - their time is MUCH more important than yours.  Admittedly, I had not been to people in the UC Davis group in a while, so -- maybe things had changed.

Plus I was pleased to note that the UC Care said I should choose their plan if "You want direct access to all providers without a referral."  Why yes, that sounded good.  Hah hah hah.  Silly me.

September 2014.

Of course.  Just as I switched medical groups I had a serious health issue in need of attention.  Called UC Davis Nuerology  to make an appointment with the specialist recommended by a colleague.  They told me I needed a referral. I told them I had UC Care health plan which says I do not need a referral. They said that it did not matter what plan I had, I needed a referral. So I asked my doctor for a referral.

October 2, 2014.

Meanwhile I wrote to one of the people in the UC Davis Neurology Department where I wanted an appointment to ask how I should make an appointment and told him that I had been referred to him by a UC Davis MD (trying to pull some sort of nepotism here). He connected me to his assistant and I sent her the info she asked for.

October 13, 2014. 

I had not heard back from his assistant so I wrote to her again.
I am writing to see if you got this information I sent Oct 3 and if there is any more information you need from me. Thanks
I again did not hear back.

October 19, 2014.

I received a letter in the mail from UC Davis "reminding" me I had an appointment in Neurology scheduled for December 17, 2014.

Now, I guess it was nice to have an appointment.  But I note - they never called me to ask when would be good for an appointment. They never contacted me at all. And this was clearly less than ideal - an appointment in two months.

So I called them to ask - how did this get scheduled? They said they must have scheduled it with me. I told them, no, nobody even contacted me. I then asked - is there anything sooner? Nope. I then asked - what if I cannot make that date and time (I was scheduled to be away). They then said that would cause a significant delay in the appointment. What the $*@#$8? This is not the first time I have had trouble scheduling appointments with UC Davis physicians but this was absurd. I then asked - is there anything I need to do in advance? They said nope. So I waited. Two plus months. For an appointment for which I needed a referral even though I had signed up for UC Care.  Oh - and - I guess just to prove they had no clue what they were doing - they spelled ny name wrong (Johnathan).

December 17, 2014.  

I had my appointment with the neurology specialist.  He was very nice.  Seemed pretty knowledgeable.  He had some disconcerting misconceptions about me and I tried to correct them but he did not seems to be paying attention.  He did not do any of the more complex tests I had seen in the literature that were standard in the literature I had seen for my condition.  He did not even order any such tests.  He concluded the visit with a possible diagnosis and then said he needed to order a series of blood tests to test some alternative possibilities.  They decided I did not need a follow up appointment and that we would wait to see what the blood tests showed before deciding what to do next.  I told them I was not fasting and asked if that mattered and they said no (one of the reasons I ask in advance about blood tests is that freuqently they need me to be fasting and it is easier to do that early in the AM ... but nevermind that ... they said it was not needed).

December 22, 2014

I signed up for Mychart.ucdavis (based on the recommendation from the printout I got when I left the doctor's office)-- an online system to communicate with the UC Davis Medical Group.

December 23, 2014

I got an email saying there were test results in Mychart.

January 2, 2015.  

I still had not heard anything from the doctor's office.  I wrote to him via the MyChart system asking if he had any update based on the test results.  I called too.  No response.

January 6, 2015.

I finally got a message from my doctor.  It had my name wrong, again, in a different way (John).  The message was short, had one useful thing in it and then said he "You need to check in with your PCP-- I have instructed our staff to contact your outside PCP and transmit labs to him and to contact you."  So much for seeing a specialist directly and communicating with them.  Oh, and he ended the message with "Good we checked labs and caught this now before your travels."  What the $&#?  I had no travel plans.  This had nothing to do with travel.  He spelled ny name wrong.  They had me listed as having type II diabetes, when I have type I.  And they wanted me to communicate with my primary care physician instead of him.  Such excellent care.  Oh, and he made a comment about my vitamin B levels being too high when I had told him I was taking a specific prescribed vitamin therapy and that I had taken some that AM (this would likely screw up the blood test - I think to know if vitamin levels are off one has to NOT have recently taken vitamin pills).  Jesus Christ what a sham.  In fact, when I told him I was taking this vitamin prescription, he said something to the effect of "random vitamins don't usually help" and I said "it is not random it is actually prescribed and there are clinical trials showing it has some benefits" but he had never heard of it nor did he seem to care.

January 7, 2015. 

I decided, I needed to see another specialist.  So I went back to a recommendation from another colleague for someone to see at UCSF.  So I checked out the protocol for making an appointment at UCSF and I filled out an online form to request such an appointment.  In the request system it asked for the preferred method of contact for me, and I said email.

January 8, 2015 

A day or so later,  I received an email from their system which said I had an encrypted message regarding my appointment request.  I had to create a new log in to a new system in order to read the message about my appointment request.  The message started with the following:
This email is to acknowledge receipt of your online appointment request for a new patient appointment. We have been unsuccessful in reaching you by phone. Before an appointment can be approved for scheduling we will need the following required documents to start the review process:

·         Referral along with reason or diagnosis
·         Pertinent clinical notes or records
·         Pertinent test results
·         Front and back copy of insurance card and authorization if required by insurance
·         Patient demographic information
What?  Why did they ask for my preferred means of contact if they were then going to call?  Oh well, at least this got through.  I called to ask some questions and only got a machine so I left a message.

Janaury 12, 2015

Appointment with my primary care physician.  He told me they had not received any information from the UC Davis specialist.  But he agreed that it might be good to see a specialist who gave a shit (my words, not his).  So he said they would make a referral to UCSF for me.  I gave them the printout with the information requested from UCSF.  

Janaury 17, 2015. 

Got an email saying my doctor had sent over the referral information to UCSF.  Called UCSF on MLK day and alas they were not open.  But I left another message asking what I had to do to make an appointment.

January 19, 2015.  

My wife took down a message and gave it to me saying UCSF had called about making an appointment.

January 22, 2015.

I called UCSF Neurology.  It took a long long long time to get through to a person.  When I finally did, I said I was calling to set up an appointment.  The person was immediately somewhat rude.  I gave my name and DOB and the person said I had no referral and my record there was empty.  I said I had been called by UCSF and they had left a message saying I should call about an appointment.  Now, mind you, I am not sure why UCSF had called me - it could have been about setting up an appointment or it could have been just to return my call.  But regardless, I told the receptionist that my doctor's office had told me they had contacted UCSF and that I should call.  The person repeated that they had no record of anything in my file - no calls to me - nothing.   This sounded so weird that I said "Is this definitely the file for Eisen - E-I-S-E-N." and the person snapped back "I do not make spelling mistakes" or something like that.  Nice.  Eventually, the person transfered me to someone else who actually offered to help and to call my doctor's office.  They then said they could call me back after this.  I asked what number they had and the number they said was not one I recognized.  Weird.  But I gave them the correct number and then hung up.

After I hung up I started to get pissed off.  What was the deal here? I signed up for this UC Care health insurance beause I was supposed to be able to make appointments with specialists without referrals.  And I am a UC Professor - with an appointment in a medical school.  I probably get treated better than the random person.  What a scam.  And then I remembered how badly UC Davis Medical Group treated my wife many years before.  And how good the treatment we received from Sutter has been.  So I posted something to Twitter.

And finally I got contacted by someone who actually seemed to care.
Not sure where things are going to go - but at least one person associated with a UC Medical Group is trying to help ...

UPDATE January 29, 2015

Still no call back from UCSF Neurology despite their promises that they would call my doctor and then call me back as soon as possible.  Unbelievable.

UPDATE January 29, 2015 #2

Wrote an email directly to the Doctor I wanted an appointment with.

UPDATE January 29, 2015 #3

Tried to contact the appointment desk.  Was on hold for 30 minutes before I had to hang up.

UPDATE January 30, 2015

Got through to the appointment desk.  OMG how ridiculous.  They said they needed to transfer me to another department (memory and dementia) because that was where I had the referral (I had asked for an appointment in neurology, I have some peripheral neuropathy).  They said the doctor at UCSF had reviewed my chart and that is where they determined I needed an appointment.  And that I would need to contact my doctor about this.

What the F#*$*#?  Completely insane.

UPDATE February 2, 2015

Lesson of the day.  UCSF doctors and personnel, other than the receptionist I interacted with on the phone, really really really do care about getting things right.  After I posted again about this issue to Twitter and sent an email to my brother who forwarded it to people at UCSF, many people stepped up to try to help.  All of them have been incredibly gracious and concerned and helpful.

And at the same time I decided to get a copy of the referral from my primary care physician just in case there was a mistake from their end.

And, well, there it was.  The referral was to see a neurologist for diabetic related neuropathy issues.  Looked good.  Then I looked at page 2.  And there was a comment about my having a history of dementia and that they could not do an MRI due to my pacemaker.  Well.  WTF?  What chaos.

Certainly this explains why UCSF thought I should see the dementia clinic.  It does not explain why UCSF neurology would never return my calls and was rude on the phone, but, well, it does make me feel like a schmuck for the mistake my doctor's office made.

UPDATE February 2, 2015 1:45 PM

Finally - a call from UCSF.  Yay. And they are going to contact my docs office and confirm that I do not have dementia.  And then, maybe then, I will get an appointment.

UPDATE February 2, 2015 5:45 PM

Well, I got a call from the UCSF Neurology appointment desk.  The person said they were calling because I had apparently contacted another doctor who contacted them (were they pissed off about this? sounded like it).  And they told me the first appointment was April 19.  Wow.  That is, like, not soon.  Lovely.  I took it.  But am going to see if there is a way to move it up.

UPDATE April 19, 2015

So - I finally had my appointment with a Neurologist at UCSF.  I had to get up so so early for my 9 AM appointment at UCSF Parnassus campus.  I was planning to take the train at 5:45 AM and then somehow wind my way to the UCSF campus.  And my alarm was somehow silenced.  I woked up at 5:30.  And I literally threw stuff in my bag and changed and jumped in my car.  But there was just no way to make it.  And so I decided to suck it up and drive into SF.  Traffic was bad already that early.  And I was pretty wiped when I got to UCSF.  And I was prepared for the worst.

But OMG.  What a difference.  I was treated so incredibly well by everyone there.  The information desk people on the 1st floor were helpful.  The lab people where I went for blood tests afterwards were pleasant and helpful.  The staff in the Neurology Department were friendly and respectful and helpful.  And my doctor.  Wow.  She was just so great.  Yes I do have some neuropathy.  And yes indeed it does completely suck.  And yes it still freaks me out and stresses me out.  But now I finally feel like I am getting excellent medical care.  And that is uplifting, even though my health is imperfect.  Such a contrast compared to the awful experience at the UC Davis Neurology

UPDATE April 21, 2015

Got a call from a UCSF Neurologist to discuss my blood test results.  My doctor was not available so an alternative doctor called me.  And she was phenomenal too.  Spent quite a while on the phone discussing things.  Came up with a plan.  All based on actual science.

UPDATE April 22, 2015

Got my medical report in the mail from UCSF.  Incredibly detailed report about my appointment, recommendations for me, and more.  Another wonderful feature.  I have STILL not gotten any such thing from UC Davis.