Monday, September 23, 2013

Miller Symposium Summary

One of the most unique aspects of being a Miller Fellow is that each year we get to plan a Symposium weekend featuring eight of the most rockin' scientists across all disciplines of science.

The structure of the conference is different than any other conference I have ever attended. Specifically:

Speakers are invited from ALL scientific disciplines. 
Let me tell you, it is extremely challenging, as a planning committee, to agree on what will be interesting to an audience that includes Mathematicians, Earth and Planetary Scientists, Physicists Chemists, and Biologists.

For example, see our speaker line up from last year:

2013 Miller Symposium Speakers

From left to right, starting on the top, our speakers from the 2013 Miller Symposium were:
Pamela Ronald, Professor in the Department of Plant Pathology and the Genome Center, University of California,  Davis
"Plant Genetics and the Future of Food"
Edward Burger, Francis Christopher Oakley Third Century Professor of Mathematics, Williams College / President Elect, Southwestern University
"Thinking Through the Natural Numbers: A Rational and Irrational Look at 1, 2, 3, 4, ..."
Scott Ransom, Astronomer, National Radio Astronomy Observatory & The University of Virginia
"Millisecond Pulsars: Nature's Gifts that Keep on Giving"
Kevin Laland, Professor of Biology, University of St. Andrews, UK
"Cause and Effect in Biology Revisited"
Seth Putterman, Professor of Physics, University of  California, Los Angeles
"Spontaneous Energy Focusing Phenomena"
George Whitesides, Woodford L. and Ann A. Flowers University Professor, Harvard University
"'Simplicity' as a Component of Invention"
John Dabiri, Professor of Aeronautics & Bioengineering, California Institute of Technology
"So Swimming Animals Mix the Ocean?"
Julie Theriot, Professor in the Departments of Biochemistry, Microbiology and Immunology, Stanford  University
"New Directions in Cell Motility: Dynamics and Mechanics of Cell Turning and Pathfinding"
The requirements for inviting speakers are demanding.
The planning committee aims to invite speakers who are:
1. Leaders in their respective fields.
2. Able to give an engaging, accessible lecture to an educated, but very broad audience.
3. Willing to participate and interact with other participants throughout the weekend.

But, oh, so worth it!
I have learned so much from interacting with the speakers, science journalists, and from my peers about awesome science, as well as how to communicate science. Which reminds me, there really should be a concerted effort to figure out how to incorporate quick sketches and hand gestures into public science communication.

Describing my research to Dr. Pam Ronald!
The Miller is unique.
The secluded setting, schedule, and small number of participants make it easy to interact with everyone attending. But, there are two things that really set the Miller Symposium apart from other conferences. The first is how wildly different our fields are from one another. Because everyone knows this, there are many fewer assumptions about background knowledge, and people take the time to really explain the root of the problems they are working on. The second aspect, and perhaps the best, is the general attitude that everyone participating is genuinely interested in hearing about the new and exciting science that others are doing (not just hearing themselves talk). We want to share what we are doing, but we also want to learn from each other.

Awesomeness ensues.

 2013 Miller Symposium participants

Tuesday, September 17, 2013


Beaker was going to be my lab mascot:

But then Little Bear found him, and fell in love with the new "baby":

He, apparently, is smitten as well:

Tuesday, September 10, 2013

Postdoctoral Position in Statistical Genomics at Penn State

I did my graduate work in the Makova lab. The Makova lab is a wonderfully supportive, diverse, and collaborative place to work. Penn State is an excellent academic environment, and State College is a beautiful town. Currently the Makova lab is looking to hire a postdoc to work on an awesome genomics project. Please see the announcement below:
Are you interested in genomics and do you have skills in Bioinformatics, Computational Biology and Statistics? The Makova lab ( in the Department of Biology at The Pennsylvania State University is looking to hire a postdoctoral researcher for an NSF-funded project examining regional variation in mutation rates (see our recent publication in PNAS: Kuruppumullage Don, Ananda, Chiaromonte, Makova 2013).  
With new sequencing technologies, multiple human genomes and their detailed annotations (e.g., ENCODE) are suddenly accessible to us. This gives us a terrific opportunity to explore previously inaccessible evolutionary processes (e.g., mutation) and other biological associations (location of genes in certain mutation states, as identified by HMMs). Such knowledge is vital in a clinical setting where disease mutations need to be evaluated. Our resources and links with medical researchers at Hershey Medical School and computational biologists from the Galaxy team put us in a great position to address these questions.  
Candidates should have experience in bioinformatics, working knowledge of statistics and should have a broad understanding of molecular biology and genetics. Familiarity with next-generation sequencing data analysis is desirable. A PhD is required.  
You will be joining an established dynamic group. We are part of the Center for Medical Genomics ( and of the Center for Comparative Genomics and Bioinformatics ( Penn State is a vibrant scientific community with particular strengths in genomics, bioinformatics and molecular evolution. Our location, in State College, Pennsylvania, is known for excellent schools and numerous opportunities for outdoor activities.  
The starting date is flexible, with an earlier date preferred. This position is funded for one year from date of hire, with good possibility of refunding. Interested applicants should send a pdf with a CV, a statement of research interests, and contact information for three referees to Kateryna Makova at, indicating postdoc in the subject line. Employment will require successful completion of background check(s) in accordance with University policies. Penn State is committed to affirmative action, equal opportunity, and the diversity of its workforce. 
Full disclosure: I just had an amazing visit to Penn State, talking awesome science with faculty, students and staff, and presenting for the Center for Medical Genomics. Yes, I am completely biased.

Some Makova Lab members and me, September 2013.

Monday, September 9, 2013

Trends in Evolution

I recently submitted my article on "Trends in Evolution" to Macmillan Reference USA for an upcoming three-volume set on Modern Science.

I want to thank everyone who commented on the proposed figures here and here, and on facebook and twitter. The publisher has the option to publish some, all or none of the images I suggested, so I'll wait to tell you what I submitted until I learn their decision. Many thanks also to the people who read through the drafts and gave input: Scott Sayres, Linette Wilson, George Wilson, my friend Laura DePriest (thank you for the most extensive comments!) Also, thank you to Norman Johnson for bringing this opportunity to my attention!! As many times as I have been told that I should focus my time and energy on writing primary research manuscripts, I really enjoy communicating science, and talking with the public. Moreover, I genuinely feel that, as a scientist, I have a responsibility to communicate science.

I was allotted 1500 words to give an overview of Evolution, including its original objectives and participants, and a narrative of investigation, describing how it was carried out, and details on challenges, and discussing the future of the field. Another topic, "Natural Selection" was allotted 2500 words (wow!). In any case, here is the list of what the main sections ended up being (apologies to all of the awesome evolutionary science that was not included):
  • Trends in Evolution
  • The origin of evolutionary thought
  • DNA mutates, populations evolve
  • Evolution is more than “survival of the fittest”
  • Ancient genomes
  • Bacteria and viruses
  • Personalized genomics
  • Where is evolution going? 
I'll give you one guess which was my favorite section to write. If you need a hint, see here, here, or here.

Currently the article is out for peer-review right now. If accepted, I will have the "non-exclusive" right to republish limited excerpts of the work, with permission, in a non-competitive publication. I think this blog is pretty non-competitive, so I'll be seeking permission to share it (or parts of it) here!

Thursday, September 5, 2013

Job applications: Priorities.

And so it begins. Job season.

This recent comic from Jorge Cham, where the joke is about your postdoc really being a time for applying for jobs, seemed fitting right now as I am working on my applications. Well, partly.

For most tenure track academic jobs in science you need to have a cover letter, CV, research statement, and a teaching statement. Various schools may have different requirements for the content of each of these, and may request additional materials, but these form the base of your application package.

My CV is updated, and I recently finished my research and teaching statements, and am now working on my cover letter. Yay! It is a lot of work, but will be worth it (or at least that's what I need to tell myself). I might even share them here, if there's any interest in seeing/reading them. Let me know!

These statements are valuable because there are so many applicants, and each of us needs to distinguish ourselves, and show the search committee what we'll be bringing to the table. But, they are only the beginning of the story. After submitting all of your materials, if you are lucky enough to get a job interview, you prepare one, or two, presentations to show your past research, and perhaps your future research plans. You also get to spend one to three days meeting with lots of awesome scientists at the University where you are interviewing. Yes, you get to. When else will you have such a tremendous opportunity to sit down and have 30-60 minutes of undivided attention of such a diverse group of researchers?

Then, you wait. And hope.

You still have a life.
But, you'll notice I said "partly" above. And that recent comic only partly describes my current state because I really don't see applying to jobs as my full-time job. I still have research to do, revisions to submit, papers and grants to write, students to mentor, and, a life to live! Yes, I am definitely spending a lot of time preparing my materials, and I won't be as productive in lab because of it, but job applications are not my only goal. Yes, I am really hoping I get a job this year (please, please, please), but I understand that it is intensely competitive, and there is a chance (however much I don't want to admit it) that I won't be a fit at the Universities that have openings this year. Sure, it would stink to be rejected, again, and again, and again. Yeah, it will stink a lot. But, I'm a scientist; it's part of the gig. I feel like, if I'm able to make some modicum of progress on my projects during this time, then regardless of the job outcome, the process would only be a failure if I let it distract me so much that I drop the ball completely on all my other responsibilities. It will be a failure if I stop enjoying this:

Riding the steam trains at Tilden Park
Family playtime at Children's Fairyland in Oakland
after a run around Lake Merritt 

Just goofing off, because we can.


Monday, September 2, 2013

Calculus and Coding... nom, nom, nom.

I have two secrets to confess:

1. I love Calculus. 
I always have. It just seemed to clean, and intuitive. I don't mean to say that it came easy to me, but learning it was not burdensome. And once I understood, I was hooked. Calculus is what made me want to be a math major.

2. I avoided computer programming like the plague throughout high school and college. 
Funny, right, because that is the basis for everything I do now. But, the first program I wrote was as a grad student. I don't know why I avoided it so long. I loved math. But, in my mind programming seemed so wildly different from math that it was intimidating, I really didn't see why I needed it, and nobody I knew was into it. And then, like Calculus, I learned how wonderful coding is, and haven't looked back.

I wish I would have learned programming earlier. Part of my hesitation was fear that it would be too hard, but part of it was that no one ever mentioned it. But maybe I could have gotten over my fear, if I knew others who were doing it. I wasn't encouraged to investigate it, and no one I hung out with coded. Or, if they did, we didn't talk about it. Luckily there are programs to help get young people introduced to technology. For example:

Math is not Computer Science.
I recently realized that my experience is a bit strange because a lot of people equate math with coding. I can tell you, from personal experience, that they are quite different, but both wonderful. In my mind, learning to code is like learning to speak a new language, while math is deciphering the syntax of an ancient language. Mathematics is a way to understand the world, while coding is a way to interact. Mathematics and coding work very well together, but are not dependent upon one another.

But, Mathematics and Comp Sci do have some similarities.
Women are underrepresented in both mathematics and computer science. Terri Oda put together this amazing presentation describing how biology explains the low numbers of women in computer science:

How does biology explain the low numbers of women in computer science? Hint: it doesn't. from Terri Oda

Please also read this excellent interview of Terri Oda by Ciara Byrne here. Perhaps the best quotation is:
"Women in computing tend to have to waste an awful lot of time answering questions related to being a woman in computing. Case in point: My male colleagues are doing science while I'm taking time to answer this email. "