Wednesday, February 22, 2012

I'm just sayin'...

No one, in a democracy, has the right to not be offended. If so our society would implode. Doing one thing offends someone, but not doing it offends someone else. We aren't a collection of unstoppable forces and the immovable objects, we are people, with feelings, and the ability to get over ourselves.

There are limitations on what one can say, without the expectation of legal repercussions. One cannot lie about someone, in spoken word or written, without potential repercussions. Nor can one spout hate speech (communication that carries no meaning other than the expression of hatred for some group especially in circumstances in which the communication is likely to provoke violence) at one's whim.

But, barring slander and hate speech, we are lucky enough to have the right, the freedom, to say whatever we like to whomever we like, regardless of whether it might offend that person. It's one of the things that makes living in America great. I don't have to worry whether my offhanded sarcastic comment will get me thrown in jail. Now, such comments might prevent my promotion, make my coworkers less inclined to go out of their way to help me, or otherwise make my life more difficult, but that's another can of worms.

Monday, February 13, 2012

This is research


After Rori's post, I'm inspired to put together a video (or more) on my past and current projects, but I felt compelled to write a little about what goes into the research, instead of just the results.

Quick, when I say I'm doing research what is the first thing you think of? Probably something like this:

"Sarah Sawah, photographed by Michael Wakely (Almanac - April 14, 2009, Vol 55, No 29)"

Standing up in a lab, probably messing around with some kind of chemicals, or measuring wee beasties.

Yes, some people do those things, but there is so much more to the world of research. I research using a computer, and yes, it can be very exciting. Sure, if you wandered into our lab space you'd find yourself surrounded by cubicles and people tap, tap, tapping away on their keyboards, but the research we do is so much more than typing.

Let's start with what my research looks like. Now, if you're like I was in undergrad (terrified of computer programming), you might want to brace yourself. On a typical day, I probably write several small codes, something like this:

#!/usr/bin/perl -w
use strict;#-------------------------------------------------------------
# What: This program will remove NR_* gene annotations
my $usage = " [RefSeq chr input]\n";
die $usage unless @ARGV == 1;

open (GENES, "<$ARGV[0]") or die "Cannot open $ARGV[0]:$!\n";
my @genes = ; # Define array

my @filename = split(/\./, $ARGV[0]);
my $file = $filename[0];
my $outfile = "$file"."_no_NR.txt";

open(OUT, ">$outfile");
print OUT "$genes[0]";

foreach my $genes (@genes){
if ($genes =~ m/NM_[0-9]/){
print OUT "$genes";

Still with me? Good. : )

After overcoming my fear of computer programming, I've discovered how accessible, and useful, and yes, fun, writing programs can be (if you're rolling your eyes at that one, I understand, but would argue that writing your first successful program may bring out the inner techie in you too!).

I write codes to analyze DNA sequences, but the real research for me comes, not in writing the actual code writing (although some scientists do study codes, and are very good at it), but in deciding what questions to ask, and how to write the code to test our hypotheses.

For example, I am broadly interested in how sex chromosomes evolve. In mammals, males have an X and a Y chromosome while females have two copies of the X, and several hundred thousand years ago, the X and Y used to be identical. Today, however, the X is still very large (~1100 genes) while the Y is small and degraded (fewer than 100 genes). To study the differences between them, I use codes to align the remaining X and Y sequences, I use codes to look for differences between the sequences (like an A to a T change, or an insertion in one of the sequences), and I use codes to estimate how quickly those sequences are changing.

Studying billions of base pairs of DNA is simply not feasible to do by hand. Further, using computer programs can (if they are properly debugged!) eliminate many forms of accidental human errors. And really, how cools is it that this morning it took me 3 minutes and 27 seconds to read in and analyze ten thousand genes. Ten thousand! In less than four minutes! Really, that's amazing.

Yes, we need biologists who work in the lab, who collect samples, who study beasties big and small, but there is a whole contingent of biologists who follow the same scientific method, who spend hours pouring over data, who discover new and exciting results, and who happen to conduct their research at a desk.

Cool things other people are doing.

Tiny tarsiers - one of my favorite non-human primates - are often thought to be quiet and adorable. Well, they're still adorable, but it turns out that they aren't so quiet - they actually have ultrasonic screams!

And for something completely different, here is a thought-provoking discussion of some of the drawbacks of BMI. Yes, BMI is useful as a general indicator, but I didn't realize that another measure - belly circumference, is likely even better at predicting obesity-related disease susceptibility. Cool.

Sunday, February 12, 2012

Applying for postdocs

Repost from:

I've received a few emails asking me for advice on applying to a postdoctoral research position, so I thought I'd blog about it. I suppose that there are several aspects of applying to any job that are relevant to all applications (e.g., being prompt, thoughtful, researching the employer), but there are some differences that I think warrant a post on applying for postdocs.

Finding a postdoc position usually begins one of three ways.

You (the potential postdoc) may:
1. Send an email to someone you would like to work with, without knowing about availability in the lab.
2. Respond to an advertisement for a postdoc position.
3. Work out an arrangement with your current advisor, or someone you know well at your current institution.

Case 3 is very specific, so I won't address it here. Cases 1 and 2 are actually very similar, and include the same elements. The main difference is that in the first case you will need to be more direct in describing a research plan you have in mind, whereas for the second case, you will need to focus more space on describing which skills you have to bring to the advertised project. That said, both types of emails should include both elements. Below is a set of guidelines for how to format an inquiry email (think Cover Letter) to your potential postdoc employer.

1. Be clear and concise in your initial email.
Your potential employer is busy. It probably wouldn't be exaggerating to say she receives 50-100 emails a day. If your email is poorly constructed, difficult to read, or excessively long, it may not receive the thoughtful once-over reading you are hoping for. Not a good start. So keep it clean (use one, easy to read, font), organized (separate into meaningful paragraphs/sections), and concise (don't repeat yourself or go into descriptive detail).

2. Begin by introducing yourself, briefly describing your research training and lab pedigree. 
Make sure to list your current and previous advisors (if these people are willing to serve as references for you), and briefly list the research areas you have focused on, including your undergraduate and graduate degrees. Specifically highlight the skills you have that align with, but also those that would complement the current goals of the lab you are applying to. You want to show that you will be an asset to your PI and your new lab mates.

3. Propose a feasible research project that fits within the scope of the lab.
Whether working within case 1 or case 2, you will want to describe what you will bring to the project, and also what you hope to learn from the lab environment. Remember, this is training. You should show initiative in bettering yourself. If you are sending a cold email (not responding to an advertisement), make sure the project(s) you propose are feasible within the timescale you plan to be in the lab. If you are responding to an advertisement, it is not unreasonable to suggest another avenue that you could take the research, if time/budget allows. This shows initiative, and forward-thinking.

4. Describe your intentions for applying for independent postdoctoral funding (or state that you already have independent funding secured).
If you weren't already thinking of applying for your own funding, you should be. Receiving postdoctoral funding can only help your future career, and make you more marketable to potential postdoc advisors. Such initiative may help you secure a position in a lab where funding is currently lacking, and give you experience for future funding applications. Further, writing the application will help you formulate your ideas and research goals for your postdoctoral experience, and if it doesn't get funded, can serve as a basis for your future research plans. I know, it takes time, there's so much paperwork, the chances of getting funded are low. Just do it. You'll be better for it.

5. Attach a copy of your (triple-proof-read) CV.
Not only is it important to have an easily readable CV, but it is also important to list the sections in order of importance (which is relative to the position you are applying to). For post postdoctoral positions, this likely means publications and research experience first. Additionally, for postdoctoral applications, do include manuscripts that are in preparation. Your potential advisor will understand that you are finishing up previous work, and it will only be to your advantage to showcase what you have done and that you plan to publish them. Other sections of your CV, including presentations, peer-review service, and outreach may have different orders depending on the priorities of the lab. It is also important to have someone else proof-read your CV. Sure, you'll be forgiven if you left off a period, or forgot an extra tab, but these small mistakes can add up, especially if your CV still has room to grow. So take the extra few days to proof-read it, set it aside, ask a friend for help, and proof-read it again.

6. Some people choose to attach a recent paper that exemplifies the overlap or complement of the applicants research with the lab's goals.
I hesitate to bold this suggestion, because it is more of a personal choice. If you do attach a paper, make sure it is just one paper (maybe, MAYBE two). You don't want to overwhelm your potential employer with too many attachments. They won't be read. This option should probably only be used if you have a very relevant manuscript that is in near-final form, but not yet published. Perhaps, as an alternative, you can offer to share any of your manuscripts (in preparation, published or in review).

Of course, every lab is different, so these rules may go out the window in your particular case. These are just some guidelines I think would help when preparing materials to apply for your postdoc position. I'd be very happy to hear additional thoughts and suggestions!

Monday, February 6, 2012

Daily goings on by the Bay

Have you ever wondered what it would be like to live with me? Oh, no? Well, no worry, you're about to learn anyway. 

Last weekend I was lazy and instead of making something from scratch, we baked some sweet potato tots and vegan "chicken" bites (which are, surprisingly, incredibly delicious!). Not to be completely boring, I decided to take some liberties with my condiments to make a honey-mustard flower. You can see the honey-petals drooping a bit. But this also showcases a quick of mine. I love honey and mustard. Mixed together (honey-mustard), they are okay, but side-by-side they are unbeatable, in my realm of condiments. I love having the vinegar-bite of the honey, and then being able to sweeten it with the honey, or the other way around. 

I'm kind of the same way with tomato sauce and cream sauces. They're both delicious, but I can't stomach a creamy-tomato sauce. Oh, alright, you're right. If I went to someone's house, I'd totally eat the creamy-tomato sauce that they served me, but it is one of my least-favorite foods.

To make up for my lack of fresh vegetables and fruit, I went a little overboard at Berkeley Bowl (our local grocery store, with an amazing produce selection). Starting in the lower left-hand corner and moving clock-wise, I prepared a pomegranate, broccoli, celery, kale, apples, honeydew, golden beet, butternut squash, and mango. We ate some raw, and I juiced a lot in my Birthday Juicer.

I've been getting so busy in lab that I've been skipping lunch, so I'm going to start taking some juice to have as a backup plan. Don't worry, I make sure to eat a healthy breakfast (usually oatmeal with bran, flax seed and some kind of fruit), and try my best to make a healthy homemade dinner at night. Plus, part of the deal of my fellowship is a lunch/speaker every Tuesday. Guess I don't have to worry about lunch tomorrow!

Oh, and lastly, in the normal routine of my life, is Brown Chihuahua. He is often doing things that surprise me. I would venture that he is, the friendliest, quietest, smartest (but obstinate) Chihuahua in the history of ever. He was house-trained when we brought him home from the shelter, and has been a constant fixture in our lives ever since, even being the only attendant in our wedding! Well, apparently Brown Chihuahua learned that Baby Girl leaves tasty snacks morsels in the stroller after our walks because when I went to look for him yesterday I found him here:

Blue and White connections

This afternoon, I hurried home after a seminar to let Brown Chihuahua out, and head up to daycare. I was wearing nice-ish clothes (hey, I'm making an effort!), so decided to change into tennis shoes, yoga pants and my Penn State sweatshirt.

On our walk home from daycare (me pushing Baby Girl in the stroller, with Brown Chihuahua in tow), we were stopped by a guy who had just parked his car. He was nicely dressed, and paused to tell me that he was a Penn Stater also. I've been told this will happen all over the world, so I'll try to keep you updated on my random happenings with other Penn State Alumni.

Well, said guy was very polite and friendly, so we chatted a bit about when we graduated, our degrees and so on. Then we parted ways. 

Nothing special, aside from the act of simply taking the time to chat with a stranger. I miss that. 

Here in Berkeley I've been constantly warned to curb my natural desire to say "hello" to strangers, because there are so many that are unsuspectingly imbalanced. I've already been shouted at, cursed at, routinely accosted for money, and had a woman follow Baby Girl and I several blocks as she repeatedly tried to get a closer look into the stroller. Downtown Berkeley has a lot of culture, stores, restaurants, and is close to campus, but it is not somewhere I want to settle down. I get discouraged and lonely sometimes. But today was a nice reminder that it's okay to be friendly to strangers.

Maybe I'll wear my Penn State sweatshirt more often. 


This morning we slept in twenty minutes because we could. Claire is getting a cold, so she woke herself up snorting on snot every two hours last night. So, when she woke up this morning and didn't mind snuggling a little longer, we obliged. Then, we were rushing to get everything together and get out the door for work. I decided to compromise while getting ready because I wanted to start a transfer of files from my home computer to work, but I also kind of wanted to put some make up on. I decided to start the file transfer, then put on a dab of mascara (this little action helps me feel like I'm not a total zombie when I go into work after a sleepless night). As I was dabbing the mascara, I was struck, because I noticed the whites of my eyes and was transported, in my memory, almost a decade ago.

I was working as a Nurse Assistant (which I still miss some days). One of the benefits of being at a small hospital was that I could help with nearly everything, and got to learn a lot, and meet all sorts of people. I have many memories of working there. I worked nights and weekends for three years during college. It's been so long ago, that I don't think I'll be violating any privacy policies by sharing this with you.

Each shift I would come in, get report, along with the real nurses, and then proceed to go to each of my patients' rooms, checking their blood pressure, temperature, changing linens and assisting with anything else they might need. I walked to one room and saw a tall, slender woman with close-cropped brown hair in a hospital gown, standing over the sink, looking at her eyes in the mirror. Her skin was slightly yellow, but when she turned to look at me, I realized she must have been examining the whites of her eyes. Because they weren't white. They were orange.

She had liver failure. I know (or remember) surprisingly little about this woman. I don't know how long she lived. I don't know anything about her family. But this first image always stuck with me because it spoke volumes to me of how short and unexpected life is. She was attractive, engaging, and dying before my eyes.

I only saw her one other time, but couldn't shake that first image. Our bodies are so frustratingly human. We are susceptible to infections, cancers, and accidents. I'd like to say I made some life-changing decision after seeing this woman, or even after working in the hospital, but it wasn't nearly so dramatic (I definitely made more than my share of mistakes after that experience). I find that she, and other people who have marked me throughout my life, often come back in small doses when I least expect it. Like this morning, reminding me how lucky I am to be rushing out of the house, to love my family, to get frustrated when my dog wants me to pet him instead of doing work, and to be afraid when my daughter has a spectacular fall (ending up with a bright purple bruise, but no lasting damage.

Thank you.

Saturday, February 4, 2012

I really like programming

For someone who avoided computer programming classes, it's funny that I work on a computer. Every. Single. Day. I am a bioinformatician. I study biology using computer programs. I write codes to analyze large data files. And I love it!

I don't know why it was so intimidating to me. I'd like to say it doesn't matter, but I think it does. I think there is a general bias in the US to think math (and computer science) are hard, and therefore unenjoyable. I think it's changing, with respect to computer science, so I hope it starts to change for math, but the only way to promote that is to show how much fun they really are.

Fun. Right.

Okay, I know you're skeptical, but hear me out. Programming and Math share the basic properties that they are based on logic, and therefore, doing either, is like playing a game. It really is fun trying to figure out the answer.

Right now I'm trying to figure out the best (i.e. most time and memory efficient) way to write a new program. What I have is a file with several coding gene sequences in it, and what I need is to know exactly where in the genome each DNA base pair of those sequences maps to (e.g. position 3112026 on chromosome 1). The challenge is that the sequences I have are pieces (exons) that are merged together (whereas in the genome, they will be separated by spaces that are called introns), and right now I don't know where the boundaries between the pieces lie. And, I have ten thousand of these genes. And, the genome is a big search space. So, I need to figure a way to do this quickly, and efficiently, with an algorithm. But, I also need to be careful that I only map unique matches (because there are duplicated genes in the genome, which add another layer of complexity). Exciting!!


Well, perhaps you can at least trust that it is something I, who avoided programming like the plague, have come to enjoy. I like tweaking my codes to make them run faster. I am amazed that, with a little thought, and a few lines of code, I can analyze hundreds of thousands of base pairs of DNA in minutes (or seconds even), something that really isn't feasible by hand. It's so cool!

Friday, February 3, 2012

I hope Michelle Bachmann gets voted out of office. Yesterday.

A recent article discusses the disgusting lows the people in one town have sunk to regarding their attitudes about LGBTQ individuals, and children. I wish their ideas were just because they are uneducated, because we can all learn new things (I do it every day, and hope to the rest of my life). I think anyone is smart enough to know that all people, but especially kids, deserve to be treated with patience, and love, and support.

Unfortunately, in many circles there is a systematic indoctrination to hate, to classify "us versus them", and for people in Bachmann's circle, LGBTQ happen to be a "them". I think her inability to tolerate people who are different from her (e.g. gays, immigrants, other religions), is a failure of our society to accept such hateful views. She can only exhibit so much hatred because those around her affirm those ideas. And, we only hear about her because enough people accepted her bigotry and decided to vote for her. It reflects poorly on tolerant people of every persuasion that she holds a public office.

Friends of mine have claimed that Michelle Bachmann is not a "true Christian", because of her actions. I'm always wary when people talk about "real Christians", or being "true to the faith" because I am confident that, in her mind, Michelle Bachmann is the realest kind of Christian there is. I agree that it is easier to feel justified in hateful behavior when one believes it is divinely supported. Often, my friends that speak of being "true Christians" are the best kind of people, believing in equality, patience, tolerance, and kindness for the sake of doing good. I am happy to say the same beliefs are shared of my atheist, Jewish and Muslim friends. (But maybe it's just that I try to befriend people who will help me be better, regardless of their religious affiliation.)

I am optimistic that many people do their best to do good things (whether they are religious or not), but there will always be people doing bad things (whether they are religious or not). I think religion, versus secular beliefs, has the pitfall that it can more easily be corrupted by people who want to use it to further their own dispicable agendas. Unfortunately, it seems that this is just as easy today as it was 200, 500, 1000 years ago.