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.

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:

Daughter & I both home sick - she is bored - so we reviewed this https://t.co/T0F15Bv8MH & today she is learning Python via @Codecademy

— Jonathan Eisen (@phylogenomics) October 17, 2016

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.

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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.
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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:

• Washington Post 1/23/15: Montgomery parents plead for later high school start times
• Sentinel 1/27/15: Parents voice overwhelming support for delaying high school start times
• Bethesda Magazine: Parents, Medical Professionals Push for Later School Start Times in Montgomery County ...

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:

Heay @DavisVanguard - have you ever written about the "start school later" issue / topic? (e.g., see http://t.co/pAGnhUUUeP)
— Jonathan Eisen (@phylogenomics) February 2, 2015

@phylogenomics weird.. Anyway, I was on later start time task force in Albany CA. V. successful move to 815 start time for HS.

— Matt MacManes (@PeroMHC) February 3, 2015

@phylogenomics reduced tardiness, better performance in 1st period. Teachers and parents love it - though was initially a tough sell.

— Matt MacManes (@PeroMHC) February 3, 2015

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

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).

My brothers dream come true: baseball meets bioinformatics

James Fraser & Michael Eisen: Baseball Meets Biology

 

Wanted - OpenAccess figures on introductory molecular and cellular biology topics

Quick post here.  I am looking for OpenAccess figures on introductory topics in molecular and cellular biology like DNA, RNA, proteins, transcription, translation, etc.  I want these for multiple purposes including teaching, blog posts, etc.  Anyone out there know of a database of such things?

UPDATE
Some suggestions from Twitter

• NCBI bookshelf (from jewmanchue)

When Universities Grow in the Wrong Places

A bit of a rambling post here but here goes anyway ...

Well, normally I have avoided digging in to UC Davis too much here on my blog.  Mostly because it does not really fit with the themes of evolution, open access, microbiology, genomics, etc.  Plus, overall, I really really like Davis and UC Davis.  The town is very pleasant - simple - but very nice.  I lived on my bike in the Washington DC area, taking my life into my own hands, and now living in bike town USA is great.  In fact, I even have a blog about life in Davis.  And UC Davis is overall a great place to be for me, especially with its strengths in evolution and ecology, population biology, and various aspects of microbiology.

But alas, now all is perfect here in blissville. And one thing that drives me crazy is the mind numbing complexity of the bureaucracy.  I note, I moved to Davis from The Institute for Genomic Research (TIGR), a small non profit research institute that helped lead the genomics revolution.  And mostly I have suffered annoyances of the crazy giant complex system here in silence (except for with a few colleagues here and there).  However, I have been planning to start to discuss some of these issues in public more.  And just as I was thinking about this, it seems that others are also discussing some issues with the need to reform some UC Davis admin activities.

You see, last year we got a new Chancellor (the name they use here for the head of the University).  The new Chancellor is Linda Katehi.  I have met her a few times and overall I am very impressed.  Perhaps the thing that impresses me most is that in times of somewhat bad financial struggles she has decided to take on the bloat in the administrative side of things as one of her first activities.  And it seems this is not all talk.  For example our great local newspaper, the Davis Enterprise has been running a series of articles, most by Cory Golden, on some reports and announcements from UC Davis suggesting that Katehi really will be trying to change things around here.  Alas, the Davis Enterprise is not available for free on the web for all to read.  If you want to get some really insightful stories about UC and UC Davis, you should subscribe.  It is not much and if you have any connection to Davis it is worth the money.

Fortunately for me, and perhaps for you, the Davis Enterprise has agreed to let me post extensive quotes from their articles especially as they relate to UC Davis.  I will delay a bit in posting to try and respect their need for subscribers (unlike with scientific publications, which should all be open and freely available, I do not feel that way about private enterprises like newspapers).  Anyway - I am posting below two stories by Cory Golden of relevance to the UC Davis attempts to change the way things are done here.  One is about reorganization of some administrative functions.  And one is about an outside evaluating group that just wrote a report on some of the challenges for research at UC Davis.  A third is about a campus "vision" statement put out by Katehi.

The main gist is, that UC Davis has enormous potential that is being impeded by some bureaucratic complexities and inefficiencies.  Some good quotes include:

Those included “overstaffing, ineffective personnel and playing 'lawyer games' to be sure that no risks threaten the organization.”

“Over many decades Davis has developed a culture that permeates its institutions and people, one that can best be described as risk-averse, modest and insular.”

And Katehi seems like she is going to try and fix many of them.  No - the plans are not exactly what I would do.  But more on that later.  The direction things are moving is very appealing to me.  I was not inspired by the previous leadership of UC Davis.  I am much more hopeful now and am awaiting these changes very impatiently.

Anyway - thanks to the Davis Enterprise for allowing me to post here.  And please consider subscribing to the paper.  That way you will get stories as they come out ...

Looking to open access (preferably w/ CC licenses) review papers covering introduction to phylogenetic trees and methods

I am teaching a class this spring and as part of the class am having one lecture on "Phylogenetic trees and methods." I would like to link to (and be able to mix and match material from) some review paper on this topic. So I am searching for something that is Open Access and preferably with a broad Creative Commons license. Anyone know of anything good?

And the real mission of #scio10 is fulfilled: kids play with educational freebies

Barcoding, taxonomy and citizen CSI

I just love the continued coverage of the story of the students from Trinity School in New York (a high school) who do investigative DNA barcoding projects. (There is a good new story about this on the LA Times blogs at:Think that sheep's mik cheese comes from a sheep? DNA doesn't lie | Booster Shots | Los Angeles Times)

In the most recent example, two students, Brenda Tan and Matt Cost, did some home barcoding in collaboration with people from the AMNH and Rockefeller University.

Among their findings:

• "an invasive species of insect in a box of grapefruit from Texas"
• "what could be a new species or subspecies of New York cockroach"
• multiple mislabelled food products including (quoted from the press release, I note)
• An expensive specialty “sheep’s milk” cheese made in fact from cow’s milk;
• “Venison” dog treats made of beef;
• “Sturgeon caviar” that was really Mississippi paddlefish;
• A delicacy called “dried shark,” which proved to be freshwater Nile perch from Africa;
• A label of “frozen yellow catfish” on walking catfish, an invasive species;
• “Dried olidus” (smelt) that proved to be Japanese anchovy, an unrelated fish;
• “Caribbean red snapper” that turned out to be Malabar blood snapper, a fish from Southeast Asia.

And what I find most interesting, is this built upon work of other students from Trinity Kate Stoeckle and Louisa Strauss who had done a restaurant based barcoding study last year. 

This type of work is cool in so many ways.  It gets students into science.  It is an applied us of taxonomy (though I note, barcoding is not without controversy in the taxonomy community). It is a useful form of citizen science -- and may eventually provide a way to keep dishonest sellers on their toes ... Kudos to all involved in this 

More on this story can be found at

• Teens turn into DNA detectives
• With DNA Testing, Students Learn What's What in Their Neighborhood
• Doing their 'pest'
• New York High Schoolers May Have Discovered New Cockroach Species

Adopt a GEBA genome program for education - from the DOE/JGI

The DOE Joint Genome Institute’s Education Program is providing opportunities for colleges and universities across the country to “adopt” bacterial genomes, such as those sequenced as part of the "Genomic Encyclopedia of Bacteria and Archaea" (GEBA project), for analysis. This “Adopt a GEBA Genome” Education Program makes available a selection of recently sequenced genomes for use in undergraduate courses. The organisms ideally provide a unifying thread for concepts across the life sciences curriculum. For example, students can analyze the six open reading frames for a given fragment of DNA, compare the results of various gene calling algorithms, assign function by sequence homology, and use gene ortholog neighborhoods for comparative genomics and annotate biochemical pathways, while learning the underlying biological concepts in a variety of science courses.

For more information, and to apply for the November 2, 2009 deadline, see:
http://www.jgi.doe.gov/education/genomeannotation.html

For more on the GEBA project, which I am coordinating, see a video of a talk I gave about it at the JGI User meeting. Slides from that talk are on slideshare here.

Data fro the GEBA project is available at a dedicated IMG site here.

A much much much older talk, from when we just started the project is here:

New DOE Graduate Fellowships in Science, Math, Engineering

Secretary Chu Announces up to $12.5 Million in Recovery Act Funding for New Graduate Fellowships in Science, Mathematics and Engineering

New Funding Highlights the Administration’s Commitment to Empowering Students to Choose Careers in Science

Washington, DC – U.S. Energy Secretary Steven Chu announced today that up to $12.5 million in funding from the American Recovery and Reinvestment Act will be awarded in early 2010 to support at least 80 graduate fellowships to U.S. students pursuing advanced degrees in science, mathematics, and engineering through the newly created Department of Energy Office of Science Graduate Fellowship program. The goal of the fellowship program is to encourage outstanding students to pursue graduate degrees in physics, chemistry, biology, mathematics, engineering, and environmental and computer sciences – fields that will prepare students for careers that can make significant contributions in discovery driven science and science for national needs in energy and the environment.

“Training the next generation of U.S. scientists and engineers is critical to our future energy security and economic competitiveness,” said Secretary Chu. “This Fellowship is part of the Administration’s effort to encourage students to direct their talents towards careers in science and our nation’s next technology revolution.”

To be eligible for the Fellowship, applicants must be U.S. citizens and currently a first or second year graduate student enrolled at a U.S. academic institution, or an undergraduate senior who will be enrolled as a first year graduate student by the fall of 2010. Applicants must be pursuing graduate study and research in the physical, biological, engineering and computational sciences. Interested students can apply online at: http://www.scied.science.doe.gov/SCGF.html

Each fellowship award will be $50,500 per year for three years to provide support for tuition, living expenses, research materials and travel to research conferences. Fellowships will be awarded on the basis of peer review. Applicants may begin submitting applications on September 30, 2009. Completed applications are due November 30, 2009.

Seeking information on undergraduate programs/majors in genomics and/or genome biology?

I am looking around to find examples of undergraduate programs/majors in genomics or genome biology.  I got a couple of potential examples from a post I made on friendfeed but am looking for more.  What I am looking for is not just courses in genomics but majors/programs in genomics ... do they exist and if so, where and what do they look like.  Any information would be helpful.  Here is what I have found so far:

From Google:

• MSU RO: Academic Programs: Genomics and Molecular Genetics
  
• PLoS Biology - The Undergraduate Genomics Research Initiative
  
• Meeting Report: Incorporating Genomics Research into Undergraduate ...
  
• MCB Undergraduate Program - Genetics, Genomics & Development
• Genomics/Bioinformatics :: New Option/Minor Proposal :: Curriculum ...
  
• Incorporating Genomics into Undergraduate Curricula at Wheaton College
  
• Phage Genomics Research Initiative - Division of Biological ...
  
• 123 Genomics - Bioinformatics and Genomics Courses
  

From friendfeed:

• Jason Stajich pointed to Duke's page from their IGSP program
  
• Iddo Friedberg suggested I look at George Mason  - still trying to figure out what is there ...

Anything else?

Excellent Free Science Education Videos from HHMI

I just got in the mail some of the free science education DVDs I ordered from the Howard Hughes Medical Institute. The first one I have looked at is quite good (it is on evolution, of course). I recommend people browse the HHMI catalog here. These could be useful for students as well as for actual courses.

And of course, the best part, they are free.

Another education use of Open Access publications

I was reminded of another important use of Open Access publications last week when I gave a talk at Chico State University. Chico St. is one of the California State Universities (I guess it's formal name is California State University, Chico). The people in the Biology Department there invited me to give a talk (I think this was because of the press coverage of my PLoS Biology paper on the symbionts of the glassy winged sharpshooter - a pest of great concern throughout California since it transmits Pierce's Disease in grapes).

I had a great visit and a nice drive to and from Chico. I met with lots of faculty doing interesting stuff. And after my talk we went to a local pub with some faculty and students. I had opened up my talk discussing the benefits of Open Access publication and how it was just as important as databases like Genbank (In fact, I think it is a good idea to discuss the importance of OA in scientific presentations in general - spreading the word). And much of our conversation at the pub centered on Open Access.

The most interesting thing I found out was that for one of the journal club/discussion courses that they have there, they only use papers from OA journals like PLoS journals. There were two major reasons for this. (1) As a woefully underfunded university (note - read this Arnold), they do not have funds for their libraries to subscribe to a diversity of journals and (2) using OA publications means they can post all the publications or links to them on a web site for students and do not have to make them closed access / password protected to prevent illicit sharing of non Open publications.

So - another benefit of Open Access publishing. Easing access even o major universities in the US, and making it easier to use research papers as part of course readers and course web sites.