Tuesday, September 16, 2014

Jumping in!

I've been at Arizona State University for four weeks. It seems like I've been running around non-stop, and so, I need to sit down and write down what I've actually accomplished these first few weeks. 

  • Space. I have access to my office and lab space. Yay!
  • Orientations. Orientations (University), orientations (Department), orientations (New faculty).
  • Teaching. I'm signed up to co-teach Evolution to 300+ students in Spring 2015, and just put in a proposal for developing my very own class for Fall 2015 (more details about that as soon as I hear whether it is approved). I am also going to be giving guest lectures in two undergraduate courses (Evolution and Human Genetics), and maybe in one graduate course (about current research about sex determination).
  • Research. I completed my portion of the analysis and figures for a joint research project that was submitted for review yesterday! 
  • Library. Introduced myself to the librarians, and learned about the resources available there.
  • Equipment. Ordered lab equipment. I still have more to order, but want to research different options a bit more. I also think it will be good to wait to see what kind of expertise I'll recruit to the lab.
  • Grants. Met with my several grant support office personnel, wrote outlines and tentative specific aims, and submitted pre-proposal paperwork for the three grants I plan to submit within this first year. 
  • Postdocs. Interviewed six postdoctoral applicants. And learned a lot about administrative background/paperwork with different kinds of positions that can be hired, when, and official requirements. Whew!
  • Grads. I don't yet have any graduate students, but I attended the Graduate Student Orientation, and am signed up to attend one of the Brown Bag Lunches to introduce myself to current grad students. I'll also be giving a seminar for one of graduate student colloquiums.
  • Undergrads. Recruited a great group of undergraduates. We've already had our first group lab meeting and individual project meetings, and I'm going to ride this enthusiasm wave for the rest of the semester. I'll write another post soon about the projects we are working on this year. 
I'm happy to receive any unsolicited advice about what you did, wish you would have done, or wish you hadn't done, relating to starting your new faculty position.

Monday, September 15, 2014

Breaking Bio: Sex chromosomes, mathematics, and postdocs

Check out this Breaking Bio podcast about sex chromosomes, mathematics, my research, and postdocs with me!

I had a great time, and feel like I could already do a follow up about some of the topics we discussed. Another day, perhaps. :)

Monday, September 8, 2014

No, the human Y chromosome does not look like a "Y"

A friend brought this news article about the evolution of the rhesus monkey Y chromosome to my attention. The primary work itself is about characterizing the gene content of the rhesus Y chromosome (a laborious, and necessary task). This particular write-up, however, is slightly frustrating for some of the (wrong) assumptions it makes, but most noticable is the image:

The picture of the "X and Y" chromosomes where the X chromosome, presumably, looks like an X, and the Y chromosome looks like a Y. If this were true, we might then assume that chromosome 1 looks like a "1" and chromsome 22 looks like a "22". None of these are true. 

All human chromosomes, even the six acrocentric chromosomes (13, 14, 15, 21, 22, and Y), look kind of like "X's" when they are duplicating, having sister chromatids (see this karyotype, a picture of chromosomes: https://www.mun.ca/biology/scarr/Human_Karyotype.html). And none of the chromosomes look like X's when they are not in the duplication process (see this image from the J. Craig Venter Institute: http://www.jcvi.org/cms/fileadmin/site/research/projects/huref/figure2a.jpg).

Monday, August 18, 2014

Transitioning from postdoc to professor: It begins

Well, today was my first day as an Assistant Professor. I spent the day in orientations, learning about ASU, and swimming through a sea of Human Resources information. Overall, I'd say the day was good. My brain is a little drained tonight, but I wanted to let you all know that things are going well. So, what does that mean? The transition from postdoc to PI is only beginning, but let me give you an update of our academic nomad lifestyle.

The move from Berkeley to Tempe.
We had to pack up all of our things in May and move them to a temporary storage facility because our landlord wouldn't let us extend our lease two months. We searched and searched for a sublet for the summer, and a day before we had to move out, providence smiled, and we found a little studio apartment (yes, a studio for two adults, one 3yo, and a chihuahua mix). There were four things that made this sublet amazing: 1) it was less than a block to daycare (I cannot emphasize how wonderful that was); 2) It was about half of what we were paying in rent at our previous apartment; 3) It was one of the few places where the start & end of the sublet matched perfectly with when we needed it, and 4) It had a small fenced-in garden area for LittleBear to play in. So, all things considered, it was perfect for us.

Thanks for help!
That said, moving all of our stuff to temporary storage was less-than-ideal. Many, many, many, thanks to my lab mates who came out to help us load the truck (carrying down a flight of stairs inside and half a flight of stairs outside). Seriously, they rocked it. The movers came at the end of July to pick up our stuff from storage and loaded a truck to bring it to Tempe.

The move.
We split up the move into two days. The first day we drove from Berkeley to Irvine, CA. Then we stayed with some good friends there for a few days (not long enough!), doing a little work, playing some games, relaxing a bit, and even went to Disneyland! Then, we packed up again, and headed out to Tempe. The drives, both times, were marked with a little bit of worry, because LittleBear gets car sick, but with various techniques, we avoided any disasters.

Purple car. 
Then, about 20 minutes from our new rental, we were rear-ended. Luckily most of the damage was to the car, and no one was seriously injured. A little shaken up, but all okay. I can't say the same for the purple pontiac, which was deemed "totaled" by the insurance company. It turns out that because the car was titled and registered in California, we'd have to drive it back to CA (in its unsafe condition) to get it re-tested, if we wanted to keep it, or the insurance company would give us more than we were expecting to take the car off of our hands. So, it is time to say goodbye to the purple car. Now, however, we need to also figure out which car, and how much to spend, to get a new (to us) car.

Getting set up in lab.
Getting things set up is taking a little longer than I expected, even to just get started, but everyone has been super nice, and helpful whenever I ask questions. So, I'm hoping once I get through orientations, and trainings, I'll be able to get up and going pretty soon.

Orientations and trainings.
So far I've taken a few trainings, and gone to a day of orientations. I'm happy about them. I want to know how not to freak out if I'm in front of a class and there's a fire. I want to be prepared to deal quickly and professionally with incidents of harassment (sexual or otherwise). I want to know who to contact and what to do to keep my lab members, my peers, and my students safe and healthy. So, no, I'm not upset about the time spent in the trainings. I think they are a valuable use of my time. The only thing I wish was that I had more time!

Is it glamorous? No. But, it has been fun to meet so many new people, and start brainstorming new projects and grant applications (check back in on me about this one at the end of the Fall). I'll have an update for you at the end of the week, especially if I learn anything really cool in the rest of my trainings.

Monday, July 28, 2014

The value of saying, "I was wrong."

In April I got to meet Margot Adler. We sat together on a panel about gender identity.

She died today.

When we sat down on the panel, she mentioned that she wasn't sure what she was going to talk about, or why she had been chosen to participate on this particular panel. I wasn't quite sure what she was going to talk about either. She started by talking about how righteously angry she got when talking with a group of college girls who stated their preferred pronouns. When she was first learning about transgendered individuals and the efforts towards equality for transgendered people, she recalls how she thought it was naive of these students to think that their struggle was difficult. She recalled how she had been in the thick of fighting for racial equality, and that the struggles today were nothing compared to the hatred and violence that occurred in the 60's and 70's.

And then she paused.

When she began again, she talked about her process of learning about transgendered people and their experiences. She talked about the hate, violence, abuse, and discrimination they are subjected to. She talked about the rejection, and the staggeringly high rates of suicide and attempted suicide.

Margot Adler talked about how she was wrong to be indignant. About how she had changed her mind.

In that gesture, she opened the door for everyone in the audience, for everyone who ever listens to this panel, to change their mind about transgender people (something that many people need to re-evaluate). It was such a refreshing thing to be reminded of the value of saying, "I was wrong." Thank you, Margot.

Suggestions for best (and worst) lab meeting practices.

A wonderful twitter discussion about suggestions for running lab meetings, with a little about general lab management at the end.

In general, broad suggestions are: 
* Keep lab meetings to an hour.
* Moderate (keep focused on the topic of the week, whatever it may be).
* Snacks are generally a good thing, but not necessary.
* Joint lab meetings are great for new PIs and for outside perspective.
* Be flexible

Particular suggestions:
* Each lab member presents a figure.
* Avoid after 4pm.
* PI should also present.
* PI should share about grants/admin (on occasion).
* No bad-mouthing during lab meeting. Just, don't. 
* Invite grad students or postdocs from other labs to present.
* Lab safety training.
* Code reviews!
* Read/discuss draft manuscripts/grants.
* Schedule for start/end of day or noon-time.

Other than lab meeting advice:
* Create a lab culture that is conducive to asking questions and interactions.
* Lab retreats/potlucks/picnics can be good for building lab connections.

Links mentioned for further discussion/reading:

Tuesday, July 22, 2014

Just think a happy thought...

There are a lot of people chiming in on this article in Science encouraging postdocs to "think happy thoughts": Happy Thoughts May Help Postdocs Handle Stress by Rachel Bernstein.

The hashtag to follow on twitter is, #postdochappythoughts. Really, go check it out.

Certainly there is something to be said for trying to be optimistic, and realistic about the challenges in academia. It is useful to realize that we may, regardless of status, often feel like impostors. But that doesn't mean that there aren't real problems with the academic machine that need to be addressed. There just so many things that you can't "happy thought" your way out of in academia, during graduate school, postdoctoral work, or even as a PI.

Just a few:

I'm at a transition point now. I am finishing my postdoc, and will be starting a tenure track position this Fall (yes, I realize how very lucky I am to be in this position). As I'm preparing for my position as a PI, I'm working to recruit postdoctoral researchers to work with me. I've already talked about making expectations and responsibilities clear for all parties involved in my lab, starting with a clear set of expectations on my web site.

But, there's another aspect that that I am surprised to have run into. Talking with several PIs about recruiting postdocs, I have received this advice (paraphrased):
"Don't offer to pay your postdocs too much. I'd suggest going with the bare minimum. You want to make sure you save money for other projects and other people."



I think this is exactly what @27andaphd is talking about here:
So, what do I think about it?

As a PI, I either have enough funding to pay a fair salary to my lab members, or I don't have enough funding to hire them.

This includes paying for health, dental, and vision insurance. It also includes budgeting money for moving expenses. Why would I want to hire someone, who I view as both a trainee and a colleague, and not care about their well-being?

That brings up a bigger question, though, "What is a fair salary?" Partly what constitutes a fair salary is dependent on location. I think a good rule of thumb, and what I plan to do, is to, at a minimum, follow the NIH salary guidelines. In an area like Berkeley, however, the NIH salary guidelines would still be too low.

No, happy thoughts cannot make postdoc life better. PI's and administrations who give a damn about quality of life will make postdoc life better.

Tuesday, July 8, 2014

Pretty. Already.

"I want Matt* to think I'm pretty."

I was temporarily stunned into silence when I heard those words from my daughter.

Because she's three years old.


So it begins
What?! Already? Is this how it begins? So soon? Why does she care whether he thinks she is pretty? Most importantly: How have I contributed to this? And, what can I do to combat it?

The first answer is "No", this is not how it begins. It begins so much earlier. It begins when she was born. I begins with how we talk to our kids. This video shows pretty clearly some of the common pitfalls in the way we talk to girls.

Have I contributed to this? 
Probably. I tell her she's beautiful. I also tell her she is wonderful, funny, smart.

How can I combat it? 
I can be more aware of the language I use, and how I respond to her behavior.

Ever since she was born, we try to make sure she has an assortment of toys to play with, not just stereotypical girl toys. We also encourage her to take things apart, and encourage her to try again when she wants to give up (girls tend to give up faster than boys and doubt their abilities more).

We also want to help her to be independent and responsible. We try to give her the freedom to make decisions about her life (within reason, I mean, she is three). That said, there are a lot of ways a three-year-old can be involved. She helps chose books we'll read, and the activities we'll do. She also helps with chores around the house and cleaning up her own messes.

She also helps choose her clothes. It would be an understatement to say my daughter loves pink and frilly dresses. As her parents, we let her wear what she wants, making a mental note that we would do the same with any child (although we do try to sneak some other colors and styles in). We also try to encourage her to get dirty, to explore, to investigate, and to question. The dresses will wash. And what's wrong with a few stains anyway? The experiences are worth so much more.

So, what did I respond with? I told her that it doesn't matter what anyone else thinks of her. She is pretty and she should wear whatever she likes to wear, because she likes it.

And then we went and played in the dirt.

Mud is exponentially more fun than dirt.

*Names changed

Friday, June 20, 2014

New academic lab thoughts, recruiting, goals

I am starting my lab in the School of Life Sciences (housed in the Biodesign Institute) at Arizona State University and recruiting all levels: undergraduates, graduate students, postdocs, and a programmer/computational lab manager.

I am thinking through how I want my lab to run, and what kind of advisor I want to be. I think having a clear list of expectations and responsibilities will help. So, I'll start it here, put a copy on my lab website, and update as needed. Please share your thoughts and comments, especially what has worked for you (as an undergraduate, grad student, postdoc, or advisor).

The ad for postdocs is here. Appointments for postdocs are one year, and renewable for up to three years. I'm looking for postdocs who will be excellent colleagues and mentors to the other members of the lab.

My responsibilities to my postdocs:
  • Assist with identifying and writing postdoctoral fellowships
  • Develop project ideas, including independent projects that can be taken with the postdoc
  • Interpret results
  • Proof-read manuscripts
  • Discuss future career goals (e.g., do you want to teach, go into academia, continue in research?), and plan ways to facilitate these goals
  • Support travel to at least one meeting per year
  • Meet regularly to discuss progress & pitfalls
Expectations of my postdocs:
  • Participate in weekly lab meetings
  • Prepare for our regular progress/pitfalls meetings and a follow up email of progress and goals 
  • Maintain a set of lab notes, including directories of data, annotated codes & versions, detailed methods. These need to sufficient to reproduce results without additional instructions.
  • Attend departmental seminars
  • Participate in general lab responsibilities (servers, maintain common areas, taking turns hosting visitors)
  • Be available in the lab/office for a minimum pre-arranged set of hours to facilitate interactions
  • Optional, but preferred: Mentor at least one undergraduate student

Graduate Students
I missed the graduate student recruitment, but I can still bring in a graduate student this year, working together with the department, if there is mutual interest. I am also happy to discuss plans with juniors and seniors in college, who are interested in graduate school.

My responsibilities to my graduate students: 
  • Assist with identifying and writing graduate student fellowships (before and during PhD)
  • Develop project ideas
  • Interpret results
  • Proof-read and contribute to writing of manuscripts
  • Discuss future career goals (e.g., do you want to teach, go into academia, continue in research?), and plan ways to facilitate these goals
  • Support travel to at least one meeting per year
  • Meet weekly to discuss progress and pitfalls

Expectations of my graduate students:
  • Participate in weekly lab meetings
  • Prepare for our regular progress/pitfalls meetings and a follow up email of progress and goals 
  • Maintain a set of lab notes, including directories of data, annotated codes & versions, detailed methods. These need to sufficient to reproduce results without additional instructions.
  • Write and submit a pre-doctoral fellowship proposal
  • Proof-read manuscripts from other lab members
  • Regularly attend departmental seminars
  • Present a poster or talk of research progress at conference at least once a year.
  • Participate in general lab responsibilities (servers, maintain common areas, taking turns hosting visitors)
  • Be available in the lab/office for a minimum pre-arranged set of hours to facilitate interactions
  • Optional, but preferred: Mentor at least one undergraduate student


I really enjoy working with undergraduate research students (see my past students here). There are many projects in bioinformatics and computational biology for undergraduate students. If you are an undergraduate interested in working in my lab, please read through the kinds of research we do, and the following expectations and responsibilities, then email me 1) your resume, and 2) one page or less describing your research interests and course background.

My responsibilities to my undergraduate students: 
  • Preparing a structured project
  • Analyzing and interpreting results
  • Proof-read and contribute substantially to writing results
  • Discuss future career goals (e.g., do you want to teach, go into academia, continue in research?), and plan ways to facilitate these goals
  • Meet weekly to discuss progress and pitfalls

Expectations of my undergraduate students:
  • Participate in weekly lab meetings
  • Prepare for our regular progress/pitfalls meetings and a follow up email of progress and goals 
  • Maintain a set of lab notes, including directories of data, annotated codes & versions, detailed methods. These need to sufficient to reproduce results without additional instructions.
  • Present a short talk or poster of research results to the lab once a year.
  • Be available in the lab/office for a minimum pre-arranged set of hours to facilitate interactions

Tuesday, April 29, 2014

Some postdoctoral fellowships in Biology

When I was looking I had a heck of a time finding a summary of postdoctoral fellowships to apply for, so thought my compilation might assist others. This list is by no means comprehensive, but it’s a start. I’m happy to update this post with other suggestions (and links and descriptions). I especially tried to include whether the fellowships are available to international students or not. I’ve ordered them by approximate submission date, but as submission dates change every year, please don’t rely on these. Similarly, the links were active at the time of this posting. If they aren’t working, you can probably find the fellowship with a simple google search.

Lists Compiled by other people:

UC Berkeley: Postdoctoral Fellowships in the Biological Sciences
Life Sciences Research Foundation Fellowship 
- Due ~October
- LSRF awards fellowships across the spectrum of the life sciences: biochemistry; cell, developmental, molecular, plant, structural, organismic population and evolutionary biology; endocrinology; immunology; microbiology; neurobiology; physiology; virology.- Similar structure as NSF postdoc- Only one LSRF fellow allowed in a lab at any given time- U.S. citizens are eligible to work in any geographic location while holding an LSRF fellowship. Non-U.S. citizens must work in a U.S. laboratory to be eligible for an LSRF fellowship. 
NSF postdoctoral fellowship 
- Due ~October 
- The focus this year is, “Intersections of Biology and Mathematical and Physical Sciences“.- applicants must be U.S. citizens (or nationals) or permanent residents of the United States (i.e., have a “green card”) at deadline. 
NIH postdoctoral fellowship (using form SF424) 
- Due ~December 
- Applicants must be citizens or non-citizen nationals of the United States, or have been lawfully admitted to the United States for permanent residence.
L’Oreal Fellowships for Women in Science 
- Due ~December 
- Has both US and International options 
Graduate Women in Science Grants/Fellowships 
- Due ~January 
- All women scientists that are conducting research in the natural sciences regardless of nationality are eligible for application for any of the SDE/GWIS Fellowships.
Branco Weiss fellowship 
- Due ~March 
Helen Hay Whitney Foundation Fellowship 
- Due ~July 
- Fellowships may be awarded to US citizens planning to work in laboratories either in the US, Canada, or abroad and also to foreign citizens for research in laboratories in the US only.
EMBO Fellowships 
- Due 15th August and 15th February 
- The EMBO Long-Term Fellowships are awarded for a period of up to two years and support post-doctoral research visits to laboratories throughout Europe and the world. International exchange is a key feature in the application process. All fellowships must involve movement between countries and one of those countries must be an EMBC Member State. 
Human Frontier Science Program 
- Due August 
- Long-Term Fellowships (LTF) are reserved for applicants with a Ph.D. in a biological discipline to embark on a new project in a different field of the life sciences. Preference is given to applicants who propose an original study in biology that marks a departure from their previous Ph.D. or postdoctoral work so as to learn new methods or change study system.