Friday, September 26, 2014

Fall 2014: Projects and people

Projects and people in the Wilson Sayres lab in Fall 2014. At the end of Spring 2015 we will check back in with all of our accomplishments, what we learned, and where we'll be heading.

Projects are listed alphabetically. Project members are listed first in ascending order of reported year in school, then alphabetically by last name. 
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All the projects
Principal Investigator: Dr. Melissa Wilson Sayres



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Comparative Fertility 
Investigating the evolution of genes involved in fertility.

Undergraduate: Brittany Hammis (freshman)

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Lepidoptera life history and simulations
Investigating variations in genome evolution and life history, and investigating the effects of demographic history on estimates of mutation rates.



Undergraduate: Christopher Negrich (freshman)
Undergraduate: Samantha Daly (sophomore)

Undergraduate: Ashley Amidan  (junior)
Undergraduate: Melinda Jenner  (senior)




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Mammary tissue evolution - Joint with Cartwright Lab
Investigating the evolution of pre-pregnancy mammary tissue development in humans.

Undergraduate: Caroline Erickson (sophomore) – Joint with Cartwright Lab
Undergraduate: Jaclyn Williams  (junior)


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Proteome Evolution
Investigating positive selection in tissue-specific proteomes.

Undergraduate: David Barclay (junior)
Undergraduate: William Martelly (junior)


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Pseudoautosomal region diversity
Investigating diversity in the pseudoautosomal region of the sex chromosomes.

Undergraduate: Danny Cotter (freshman)
Undergraduate: Sarah Brotman (sophomore)


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Squamate sex determination
Investigating sex determination mechanisms and sex chromosome evolution in squamates.

Undergraduate: Shawn Rupp (junior)
Undergraduate: Hien Vu (junior)


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Turner syndrome
Investigating parent-of-origin effects for the single X chromosome in people with Turner syndrome.

Undergraduate: Jada Wang (freshman)
Undergraduate: Marshall Styers (freshman)
Undergraduate: Kara Schaffer (junior)






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X-Y recombination
Investigating the timing of X-Y recombination suppression.

Undergraduate: Alix Marinello (freshman)
Undergraduate: Reena Ygot (senior)


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Tuesday, September 23, 2014

Advice from tenured professors for pre-tenure faculty

I recently attended a workshop put on by the College of Liberal Arts and Sciences at Arizona State University where six tenured professors gave advice for pre-tenure faculty. Here are my notes from the workshop:

There is no free lunch.
When you've arrived on campus and someone invites you out to lunch, keep your antenna up as to why  they invited you out.

  • Don't commit to anything at lunch, give yourself time to consider it.
  • Stay out of departmental politics.
  • Avoid the perception that you've joined a faction (e.g., routinely going to lunch with a prominent member of a faction).
  • Seek advice from people within your department (they are familiar with your specific department, but may give you biased advice about specific situations).
  • Also seek advice from ppl outside your University (they aren't familiar with your specific department, but they can give unbiased advice about general situations).
  • Your job is to get your work done. You can always use your work as an excuse to avoid politics. 

Find balance.
  • Don't shut yourself down at your desk.
  • Learn to say "no" constructively (e.g., I cannot commit to X, but I could do Y; or, I'm interested, but already committed to Z.).

Be a good colleague/academic citizen.
  • Serve on student committees.
  • Serve on committee for department fellowships.
  • Important to be visible. You want your colleagues to know you and be invested in thou.
  • When it comes to collaborations, seek out people in your unit first before other units on campus (pre-tenure).
  • Scholarly presence in research *AND* physical presence.
  • Look past your own CV
  • At faculty meetings, if you have an opinion, share it; it is the best way for colleagues to get to know you.

Research and Teaching first, but Service is still important.
  • Service to the department *AND* service to the profession.
  • National service >> Local service.
  • Service to the profession makes you visible (e.g., editorial boards, Symposium moderator/organizer)
  • ~10 external reviewers requested for tenure packet. If no one in the field knows you, they won't even agree to review your packet.
  • If a position is 40% research, 40% teaching, 20% service, that service component corresponds to one 8hr day (in a 40hr work week).

Mentoring you receive.
  • You will never have a mentor like your PhD mentor again (someone so invested in your future success).
  • You don't have a cohort of grad students or postdocs, but you are not alone.
  • Build your support network. 
  • Seek a multiplicity of mentors, in your field, different levels in the pipeline.

Mentoring you give.
  • You are a visible role model
  • Portray a sane work-life balance for your students and lab members (even if you're still working on it).
  • You may not feel like a professor, but people will treat you like one. Act like it. 

Think beyond tenure.
  • If all of your activities are done for the sole purpose of working towards tenure, you're going to be sorely disappointed after you get it. 
  • Don't put all your eggs in one basket AND Don't spread yourself too thin.
  • Do some research every day, no matter how small.
  • Tenure criteria an the bylaws are the minimum requirements, and are open to interpretation.
  • Do not meet the tenure criteria, exceed it.
  • Tenure extensions: Tenure clock extensions are granted (at Arizona State University) for a variety of reasons, not just having a child (parental leave, elderly care, medical condition, lab equipment delay… talk with your chair if you have concerns). If your request for tenure extension is approved, it is sealed in an envelope, and no one on your tenure committee will know the reason, only that it was approved, and the extension can not be used against you. 

Questions to ask yourself, and honestly reflect on your answers.
  • What do you want out of faculty life?
  • What is it worth to you? 
  • When is the cost too high?

Take-home:For the first time, you call all the shots. You are on your own, but you are fully capable of doing it.



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. 

Accomplishments:
  • 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!

Glamorous? 
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."
Yikes.

Just.

Wow.

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.

Three.

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