Congrats to newly minted “Dr” – Katie Dahlhausen

Congratulations to Katie Dahlhausen (actually, I should write this as “Dr. Katie Dahlhausen”) for finishing her PhD in the Biophysics Graduate Group here at UC Davis.  Her thesis was  entitled “Koala Poop Smells Good: How I Know This and Ways to Increase the Impact of Research Through Education & Outreach”.

Here are some pics / Tweets from her exit seminar and PhD bell ringing ceremony.












Thanks to all for "Suggestions for 11 year old daughter who wants to learn to code"

I am so thankful to the whole community out there who gave answers to my request for suggestions for my 11 year old daughter who wants to learn to code.

//[View the story “Suggestions for 11 year old daughter who wants to learn to code” on Storify]

Today we were both home sick and when she said she was bored she then asked if we could try some of the examples people suggested.  And we ended up playing around with Python at Codeacademy and she spent hours on it.  So much fun. See below:


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:


Simple microbiome quiz and then mapping function from PGED

Just did this: Map-Ed Genetics: Pin Yourself on Our World Map! (the microbiome one – there are two right now – the other is personal genomics – and others coming).  Best part is browsing the map of other participants afterwards.

Ooh – cool – got to get this "Illustrated Children’s Book Introduces Invisible World Of #Microbes"

Just saw this news story: Illustrated Children’s Book Introduces Invisible World Of Microbes.  This looks like a potentially good addition to the list of books that could be called “Microbiology for Kids.”  I have made a collection at Amazon of examples in this area.  Any other suggestions for microbiology books for kids? //

12 hours of me: Slideshows w/ audio from "BIS2C: Biodiversity & the Tree of Life" at #UCDavis

Well, it has taken a few months of processing but I have finally gotten my lectures from the introductory biology course I teach uploaded in some way to share.  The course is “BIS2C: Biodiversity and the Tree of Life” and it is the third quarter of a three quarter introductory biology series at UC Davis.  Each year some 2300 or so students take this series which means that we at UC Davis have to offer each of the courses (BIS2A, BIS2B, and BIS2C) each quarter.   Every fall I co-teach BIS2C.  Alas we do not have a lecture hall big enough for 700 students, so we do the course in two sections.  The way we teach it each of the faculty double up and teach their part of the course to each section.  The course also has a weekly lab.  It is a machine of sorts.

This fall I taught 13 lectures for the course.  I covered basically phylogenetic methods, the big picture of the tree of life, and microbial diversity.  I used the Apple presentation program Keynote for slides for my lectures and I used the “Record Slideshow” option to record audio in synch with the slides.  After a bit of pain, I managed to convert these recordings into video and then posted them to Youtube.  And today I am sharing them with you.  There are imperfections of course.  But I thought some might find them useful.  Plus I have made a YouTube playlist for all the lectures if you want to just sit down and enjoy 12 hours or so of me.  Now if only Youtube would allow me to change the thumbnail image for each lecture …  Plus I note – next year I will be doing much more interactive learning in class so this may be the last record of some of these lectures …

Lecture 1: Introduction to Course and the Tree of Life

Lecture 2: Trees, Taxa and Groups

Lecture 3: Characters

Lecture 4: Phylogenetic Inference

Lecture 5: Phylogenetic Inference

Lecture 6: The Tree of Life

Lecture 7: The Three Domains

Lecture 8: Three Domains and Microbial Diversity

Lecture 9: Microbial Diversity

Lecture 10: Endosymbioses and Lateral Gene Transfer

Lecture 11: Endosymbioses and Lateral Gene Transfer

Lecture 12: Extremophiles

Lecture 13: Human Associated Microbes

w/o a doubt the best aspect of #AAASmtg – giving my kids science schwag #GoScience

Woohoo – my kids are doing their 1st chemistry experiment (well 1st formal one)


Wow – Sacramento Zoo Education Team incredibly impressive

Went to the Sacramento Zoo yesterday with my brother, our wives, and our kids.  We met up there at 2:15 PM because my brother’s 2 year old daughter is obsessed with orangutans and there was a educational talk scheduled for 2:15.

The talk was impressive and when it was over and the Zoo “Animal Ambassador” team started heading to the anteaters, well, we followed them.  And then, when that was over, we followed them to the clearing near the reptile house where they did an outdoor show with their Harris Hawk Saguaro.

The woman leading the show was one of the best public-science-education speakers I have ever seen.  Really.  She had a perfect temperament, explained complex topics, showed incredible respect to children asking bizarre questions, and showed a deep respect for the hawk that really blew me away (they realized that their activities with the hawk had been too repetitive and that it was getting bored so they were trying many new things to diversify it’s life, for example).  We lingered and lingered soaking up everything she was doing.  I wish I could remember her name to give her extra props but I will figure it out.

Here are some pics — most by me, some by my brother

Blast from the past: 1997 Walter J. Gores Teaching Awards at Stanford w/ Condoleezza Rice

Just got this digitized. One of my proudest moments. In 1997 I received the Walter J. Gores Award for excellence in teaching for my work on the “SME Core” at Stanford. The SME Core was a new way to teach Science, Math and Engineering for non science majors.


The SME Core was an initiative coordinated in part by then Stanford Provost Condoleezza Rice.  I worked with her office on and off for 3 years to help get the SME Core program up and running.  (I note – whatever you think of her now – at the time I really really liked her – she was great to interact with, brilliant, and I think inspired in pushing this SME program).

For more on the SME Core see

It seems the SME Core may have gone away after I left Stanford.  But I think it was a great program – full year integrated courses that covered science, math and engineering on a specific topic.  I ended up helping design a course on Heart Disease (and was head TA).  And the faculty in the course changed my life – in particular interactions with David Botstein, Rick Myers and David Cox who were three of the four instructors – that is what got me into genomics.  But also – working on designing the course – and helping run it for two years – was an amazing experience.  By tracking / interacting with undergrads for a full year I got to know students at a level not possible in single quarter courses.  I will try to write more about the SME Core at some point but I was very proud to have received Stanford’s biggest teaching award – the Walter J. Gores Award for my work on the program.  So I am posting the video of the presentation because – well – I like it …