Thursday, January 31, 2013

An unsuccessful Symposium proposal

I think it is much easier to share successes than failures. But, I also think there is as much, if not more, we can learn from our failures than our successes. In this particular case, I don't think there was much more we could have done. A colleague and I wrote a proposal for a Symposium, and ours was not chosen, likely because it didn't pique the interest of enough of the organizing committtee membrs. But, I still think it is an exciting proposal, and so wanted to share it here. It was limited to be quite short, so perhaps what I can learn from this experience is that I need to develop the skills to better convey excitement for a topic in a very limited space.

Moving background selection to the foreground

According to the neutral theory of evolution most mutations are expected to be neutral, nearly neutral, or deleterious. It is the class of nearly neutral and deleterious mutations that may, in fact, predominantly drive the evolution and structure of the genome. The removal of deleterious mutations by purifying selection can affect genetic variation at linked neutral sites by a process called background selection. There is renewed interested in understanding background selection across diverse organisms, and comparing diversity between the sex chromosomes and the autosomes to distinguish its effects from other evolutionary forces, such as demography and positive selection. Recent advances include new theoretical approaches to more comprehensively model the complexity of background selection in a coalescent framework. These models are especially powerful when combined with recent developments resulting in dramatically increased sample sizes, improved identification of rare variants, and the ability to estimate fine-scale recombination rates using next-generation sequencing technology.

Thursday, January 24, 2013


It has been a pretty crazy couple of weeks (I was up till 5am getting some new results for a collaborator's grant), and i sometimes need to remind myself that I actually do quite a bit of living outside of work.

This weekend we went out for a belated birthday dinner to a Japanese place, Kirala, that i've been wanting to try. The food and service were excellent. The Bear ate a bowl of tofu, a bowl of miso soup, and three pieces of unagi sushi. I was so proud!!

During the weekend we dogsat for our very lovely neighbors. The two big dogs are such a change from our little brown chihuahua, but everyone got along well.

We also found a glider on sale at Target. We all love it!
The Bear tried to snuggle both of her doggies in the chair. One was much more cooperative than the other.

She was actually very good at "helping" put together the chair and the dresser we got (also a great deal).

Tonight the Bear and I decided to do some creative reusing of the old boxes, with the help of some paints.

After they're all decorated, we will build a fort. A fabulous fort.
- Posted using BlogPress from my iPhone

Saturday, January 19, 2013

No guilt cookie dough (great for kids!)

I had a genius idea last week. The Bear and I were making cookies, and she wanted to eat the cookie dough. And really, who doesn't love cookie dough? Terrorists, that's who. So, basically, I had to figure out a way to let her eat cookie dough, or the terrorists win.

With national security in mind, I did some quick thinking and came up with this awesomely delicious, super-easy, and even healthy, cookie dough recipe that she could help me make (she just turned two), and I would feel good for letting her eat it.

No Guilt Cookie Dough
1/2 smashed banana
1/4 cup whole wheat flour
1/4 cup oats
1/4 tsp vanilla (optional)
1 Tbs flax seed + 1-2Tbs water (optional)

Directions: Mix everything together (seriously, it's so easy). For the kids, it is fun to have them help measure and dump into an over-sized bowl.

Basically the banana, and flour form the sweet base (plus oats, if you like oatmeal cookie mix). Depending on the size of your banana you might need a little more or less flour/oats to get the desired consistency. The flax seed does help with the consistency (without having to add eggs), but isn't necessary, and the vanilla just makes it seem more like cookie doug instead of mashed bananas. Everything else is to taste. We didn't have any add-ins, but you could easily spice it up with something fun.

Add-in ideas: cinnamon, nutmeg, raisins, shredded coconut, chocolate chips, mini M&Ms, nutella, chopped nuts, fruit bits, orange peel, splash of lemon juice... just go wild!

Thursday, January 17, 2013

The names have not been changed.

I know it isn't funny to anyone but me, but I wanted to share my sleep-deprived humor. I've been staying up way too late many nights in a row, and so last night fell asleep when I took the Bear to bed. We also had a friend come over last night, about the same time. 

The names have not been changed in this story, because, it wouldn't make sense if I did.

So, our friend J.J. came over, so he and Scott could work on some electronics. I woke up around midnight, a little disoriented, after a very vivid dream, where I was certain that J.J. told us his parents were coming over the next day. There are several reasons why I should have realized this wasn't true. But, for argument's sake, just accept that the likelihood of this happening is near zero. In any case, I wasn't coherent enough to deduce that J.J.'s parent's coming over wasn't logical, but I had a sliver of doubt, and was starting to worry about all the cleaning I would need to do before they came, so had to ask:

Me: "Are J.J.'s parent's coming over tomorrow?"
Scott: Laughter. Then, to his credit, "No, J.J.'s parents are not coming over. Maybe you should go back to bed."
Me: Confused look. "Oh, okay, I didn't think that made sense."
Scott: "Also, J dropped off a key to their apartment, so we can dogsit this weekend."
Me: Wondering why he said J instead of J.J., but let it slide. "Oh? Where is he going?"
Scott: "He's headed to Lake Tahoe this weekend. I told J it wouldn't be a problem."
Me: Wondering if this is some new friend nickname. "Why are you calling him J? His name is J.J.."
Scott: "What? I thought it was J."
Me: "Nope, J.J."
Scott: "I thought our neighbor's name was Jay."
Me: "What?"
Scott: "Jay, our neighbor."
Me: "I'm confused."
Scott: "Our. neighbor. Jay. dropped. off. the. key. to. his. apartment. He asked if we would watch their dogs."
Me: "Ohh....but, I thought you were talking about J.J., and it was weird that you were calling him Jay, and I would have known if you had said dog-zuh, because J.J. only has one dog, but Jay and Jen have two dogs." (deep breath)
Scott: "Maybe you should go to bed."
Me: "I think I will."

I think, given the extenuating circumstances, it was completely reasonable to be confused about the names (not the parents coming over... that was completely unreasonable). 

Wednesday, January 16, 2013

I love being a Scientist

This morning I was invited to review a paper on testis evolution.

Best. Birthday present. Ever.

I, of course, said yes. In addition to being super-interesting, I really love the process of peer review. I am still wondering how important the one-way anonymous aspect really is. And, I would really prefer if the reviewers comments were available alongside the paper, if it is accepted. There are some journals that do this, but it is far from common practice. In addition to giving some context, making reviewer comments available could also help get discussion going, on a website.

But, for now, I'll just be happy to participate in the process. Woot!!

Sunday, January 13, 2013

Geek outs

I really just don't have the time for in depth posts, at least for the next several weeks, but I thought of a great idea, I'm going to post my "geek outs". That is, moments where I'm reveling in my geekdom.

Moment: I realized that I'm sitting in my living room, working on my laptop, and controlling processes on machines in five different locations, like a boss. Only super-spies do that. And ninja-scientist-moms.


I am still in the wonderful situation of having too many projects that I find interesting, and too little time. I guess that means it is about time for me to apply for faculty positions and recruit some students to help me! Well, that will have to wait until the fall.

Presently I am stalling patiently waiting on a very large file to transfer, after testing some new code. I'm really excited because this is for a project I've been putting off for several weeks, and it feels nice to be making progress on it again. 

No exciting pictures this time, but I thought I'd give an update.

My super-exciting Y diversity paper was rejected again. The major criticisms were that it was difficult to read given the very short format of the journal, and that it just wasn't interesting. A collaborator was quite upset at the rejection, but, I haven't really been bothered by it. They didn't have major complaints about the science, and, whenever I find time to reformat for a journal with a longer format, I'm confident it will get published. I think eternal optimism is a character flaw that suits me well as a scientist. 

I've been learning a lot about RNAseq, pregnancy and Rheumatoid Arthritis, as well as managing large files. I have run into a "segmentation fault" problem (running out of computer memory) with one of the programs I'm using that I haven't been able to solve. It is immensely frustrating because it only occurs with certain runs, and, since I've automated the code submission, there isn't any human errors in the syntax that could cause it. After many failed efforts I think I may have to break down and email the authors of the paper about the code. Let's hope they are responsive.

The Bear is keeping us very busy. We had to switch daycares at the New Year. Our old daycare closed for personal reasons (although they might reopen sometime in February), and after searching and interviewing, we found a new one that isn't as convenient, location-wise, but that we really like. The first couple days the Bear wasn't very happy going, but on Friday, she went in, and came home without any tears! A bonus of this place is that they are a husband and wife couple from Chile and speak fluent Spanish and English with the kids. It has been a great motivator for me to brush up, and improve my Spanish.

At the library today I picked up several Spanish music CDs to play, and kids books in Spanish to read to the Bear. I'm a little embarrassed at how much I have forgotten, but am excited to learn alongside the Bear.


Wednesday, January 9, 2013

Too busy to blog

I've been wrapped up in life (read research and family) the last several weeks, and won't have much time (ever?) until after an upcoming grant deadline in early Feb, but thought I'd check in with you all.

Over the past several weeks we celebrated two years of being parents:

We had fun playing with the Bear's new toolset, which she quickly informed us, was actually for making "coffee":

We celebrated Christmas with family in Pennsylvania and two different Hanukah celebrations in Berkeley:

The Bear got to play with her cousins and play in the snow:

I feel like I'm constantly running. There isn't ever a time where I'm not wearing both my "scientist" and "mommy" hats, and I've been neglecting many others. Luckily, I have a good role model for how to balance it all: