Low fat sweet biscuits

Last Friday our regular snack-getter was out of town, so for lab meeting, I brought in some homemade banana-chocolate chip biscuits, inspired by the Happy Herbivore:




Low fat sweet biscuits
1 c. wheat flour
1 tsp. baking powder
1 Tbs. sugar
1/2 mashed banana
1/3 c. milk
1 tsp. vanilla
1/2 c. chocolate chips

Combine dry ingredients, cut in banana, like you would for regular biscuits. Add milk, vanilla, and chocolate chips, stirring until just combined (don't overstir). Bake at 400F for 10min.

I made a similar version with blueberries and cinnamon instead of the chocolate chips. I liked them both equally well.

Website design!

I am volunteering as the webmaster for the Graduate Women in Science, and am very proud to announce that as of this morning the new website is active! Check it out:

www.gwis.org

Of course it is, like all things on the internet, a work in progress. Soon I'll be soliciting information from the local chapters for updates and suggestions for content, so continue to check back in, especially for the updates to the resources pages.

Scientists as role models

Chris Gunter has a thought-provoking piece in Genome Biology: "Science: It's a Role Model Thing".

The message I took home is that Scientists need to be unafraid to be themselves. We get really excited about dorky things. We have hobbies. We are obsessive about the topic we chose to study. We are skeptical, critical, and demanding. We laugh. We are imperfect. We learn from our mistakes (hopefully).

One of the reasons I continue to blog about a wide array of topics, is because I want to remind myself, and my readers that Scientists are not somehow super-human and out of touch (I guess you all can correct me on that). We might have strong convictions, and we might have an adjusted sense of normal,  but we have friends, and families, and are curious about more than our tiny corner of research (well, most of us are anyway). I am a Scientist because I love what I do. Science a part of of me. Maybe it is a part I can't turn off, but there are many other parts that make up the whole of who I am.

To be a good role model, we should not hide our personalities, or our interests. We don't need to avoid any mention of being a person outside of lab. We mustn't portray ourselves as robots.

In the immortal words of Dr. Seuss:

"And so... I think that there are some things I do not wish to be. And that is why I think that I just wish to be like ME." 

- Dr. Seuss
I Wish That I Had Duck Feet

Birthday Ham

We tend to eat very little meat. I had a few vegan months, but mostly it's vegetarian. That doesn't mean we don't still very much enjoy the taste of meat. On occasion, to appease the meat gods because I know my husband misses it, we also incorporate a little local meat and fish.

Well, for my birthday this year, my dad sent me a ham! My brothers, also born in the same month, also each received a ham.


But now the question is, what do to with all the ham?

Well, the first day, of course, I made a crock pot full of hambone and bean soup (with carrots, celery and garlic). It was delicious, so we made a second. We're full-up on our ham and beans quota, so needed something new.

This weekend we made pancakes with pan-fried ham on the side.

Tonight I made butternut squash soup (simply boiled and pureed butternut squash with a little vegetable broth... it is delicious on its own), with diced, browned bits of ham. Super-easy, quick and delicious!


The Little Bear enjoyed the ham and beans, as well as pancakes and ham, but wasn't a fan of the butternut squash soup. To each their own. We still have a lot of ham left, so any suggestions are welcome!

One of the most uninteresting parts of being a scientist

Reformatting manuscripts for a new journal is, in my opinion, one of the most tedious parts of being a scientist. I won't say that it is a total waste of time, but it comes close.

I do understand that each journal has a unique format, structure and feel. Each journal wants to make its format consistent for its readers. And, each journal has a slightly (or vastly) different audience that its format caters to.

But, sweet, mother of pearl, it can be frustrating for authors to update, change, add, and repackage information for a new journal. This one allows sub-headings, another does not. This one allows you to merge "Results" with "Discussion", another does not. Some journals and articles have specific word limits, others let you include as much content as you like (although some charge by the page). There are varying limits on the number of tables and figures. Even different pricing for color within figures.

I am very lucky to live in the digital age, where technology exists to easily cut, paste, add, and subtract content. My dad tells me a story where, for his Master's Thesis he literally cut out, then taped in new content, because otherwise he would have had to retype the entire tome.

And citations, whew! I am so glad for the software to assist with updating these. There are so many different formats for citing in the text (only the first author's last name, or up to three authors' last names, or numbered by the first time the citation is present, or some other variant). The bibliographies can be equally involved regarding the small, but important, differences between journals.

Given all of the changes, and the amount of time, that go into choosing to submit to a journal with a different format (which means that, unfortunately, the manuscript has already been rejected from one journal), there are some good things. A new format does require the author to consider their analysis and results from a new structural perspective, considering how to tell the story in a new way. Hopefully the process will also give authors the chance to catch any minor writing errors, and think of new, clearer ways to explain observations.

But, I'm not entirely convinced that those benefits outweigh the time spent trying to wrangle a manuscript into the appropriate format. 

One of the many things I will never understand

When you live with someone you learn all sorts of things. It can be exciting, and eye-opening. You learn their likes and dislikes, and then there are some things you just learn to live with.

Last night I came out from putting the Little Bear to sleep. Scott was watching a documentary on wrestlers (the acting kind). Our conversation:

Me: "What are you watching?"

Scott: "A documentary on wrestling."

Me: "Who's that guy?"

Scott: "Bret Hart."

Me: "Who's he?"

Scott (Totally strait-faced): "The best there is. The best there was. The best there ever will be."

Me: "Right... I think I'll go get ready for bed."

Decreasing morbitity due to vaccinations

The effect of mass vaccinations is astounding. Thanks to the CDC, and Leon Farrant, here is a wonderful infographic about the huge positive effect of vaccination on decreasing morbidity due to several infectious diseases:

As with any medical decision, it is best to discuss with your doctor and see if you are healthy enough, and not allergic to any of the components, before getting vaccinated.

Barring such conflicts, I will not risk my own health, or the health of those I care about, when the benefits of vaccination far outweigh the risks of not vaccinating.

Things I never expected to say...

There are so many things I never expected to say, and then I had a baby. Now she is two years old. Here are a few of the things I've said in the past week:

"You may not saw the dog's head off." (With a toy plastic handsaw)

"Do not punch/hit/kick that baby. We need to be nice to babies." (With pretty much any human baby we see this week. Dolls are okay, but every time she sees a real baby, 8-16mo, she yells, 'I don't like babies!', and lashes out at it for some imaginary offense.)

"Why are you licking the chair?"

"Sure, I'll help you put big girl underwear on your shark." (No, it is not easy.)

"Your dinosaur is afraid of monsters??"

And this one makes me realize we don't say it nearly enough, or else she wouldn't have this association (or maybe it is that I make sure to always say it when we part):
"I love you doesn't mean good-bye."

- Posted using BlogPress from my iPhone

life lessons

I'm hoping to use this when the Bear gets older:

Pitching yourself

Several people in the lab are applying for jobs right now, so the recent article by Roberta Kwok about elevator talks in Nature seems particularly relevant:

http://www.nature.com/naturejobs/science/articles/10.1038/nj7435-137a?WT.mc_id=TWT_NatureJobs

Nancy Baron is quoted in the article, where she "suggests thinking about four key topics":
1. the problem
2. why it matters
3. potential solutions
4. the benefits of fixing it.

I wanted to highlight how important I think these short interactions are, not just for explaining science to a lay audience, but for interacting with peers and collaborators. So much of the doctoral work is focused on precision, on figuring out the nitty gritty details, that when we finish, we sometimes forget how long it took to learn and become comfortable with all of the terminology and background. Another aspect of graduate school, and perhaps to a greater extent the postdoc, and applying for jobs, is to emphasize the areas we are experts in. As such, it is difficult to sometimes admit that we don't know it all. Coupled together, these can result in two very intelligent people speaking to one another, but not fully understanding each other. 

While it may seem like an oversimplification (instead of just a simplification), and go against our very nature to provide details, the ability to concisely give an accessible overview of our science can only improve our interactions. Anyone who wants to know more can easily ask.

Protector.

Today the Little Bear (just recently 2 years old) walked up to me and patted my arm.

Little Bear: "Mommy's scared monsters." Pat, pat.
Me: "What?"
Little Bear: "Mommy's scared monsters."
Me: "Oh, I'm scared of monsters?"
Little Bear: Nodding, more patting. "It's okay. I protect you."

Melt. my. heart.

I guess after that, though, I should have seen tonight coming. She was very tired, but kept waking herself up telling me she was afraid of monsters. First, I told her I would protect her, and turn the star lights (like a night light) on. Then I told her that monsters were like Grover (from the book, "The Monster at the End of This Book"). Then, she asked for her daddy. He told her that Little Brown Dog eats monsters, and that seemed to work, because she is sleeping peacefully now.

Little Brown Dog for the win.

Nuts!

We receive a package of pecans (yum!!) from my grandma every year. Usually I make pies and cookies, but this year thought I would try something new.

The first thing I made was a set of savory nuts. I tossed the pecans with a tablespoon of olive oil, and then tabasco sauce, soy sauce, and cumin, to taste. Then, I toasted them at 450F for ~10 minutes (well, I should have. I let them go 15 minutes, and it was nearly too long... some nuts ended up with a slight burnt popcorn taste.)



I also made something slightly sweet, where the pecans are tossed with an egg white that has been beaten to white peaks, a quarter cup of sugar, and a tablespoon of cinnamon. I was requested to use more sugar the next time, but the consistency was perfect.

Teaching moment

I was very excited to get to teach one lesson for my advisor's course this week. The course is co-taught, and although it was the other professor's time to teach, both were out of town, so my advisor asked myself and one other postdoc to step up for the week.

I had a blast! The course is methods in Statistical Genomics, mainly for statistics and mathematics student. The students were alert (for a 9:30am class at Berkeley, I was especially impressed), and engaged. They asked questions, and really seemed interested in what I was talking about. My main goals for the class were to get them thinking about what kinds of data are available (to apply their statistics to), to help familiarize themselves with where and how to access the data, and to get them thinking about the diversity of the questions they can ask.

Below is my outline for the class, and some references I handed out to the students. I took about an hour to go through the first three points, and my fellow postdoc spent the remaining half hour on the fourth point.

Introduction to Bioinformatics: Finding Data

1.              What kind of data is there:  Overview of the Genome

1.              Central Dogma

1.              DNA --transcribed--> RNA --translated--> Protein

1.              DNA is a double helix (forward/reverse), four nucleotides
(Adenine, Guanine, Cytosine, and Thymine)

2.              Ribosomes transcribe the DNA to form single strands of RNA
(Adenine, Guanine, Cytosine, and Uracil)

3.              RNA is translated into protein

1.              read in triplets

2.              64 permutations of three nucleotides, but only 20 amino acids, plus three stop codons

3.              starting with the start codon, Methionine, and ending in one of the three stop codons, TAG, TGA, TAA

2.              Coding regions

1.              Affected by selection

2.              Genes

1.              5’, 3’ UTR, exons, introns

2.              multiple isoforms (major and minor, mostly similar exons)

3.              Transcripts

1.              miRNA, snoRNA, lcRNA

3.              Repetitive

1.              Transposable elements (SINEs, LINEs)

2.              Simple tandem repeats (microsatellites, mini-satellites)

3.              Copy number variants

4.              Neutral regions

1.              Noncoding

2.              Far or near genes?

3.              CpG sites – mutation rate is 15-30x’s higher than non-CpG sites

1.              Cytosine deaminated into a Uracil à becomes a Thymine upon repair

2.              What kind of data do you want?

1.              Across species: Comparative Genomics

1.              Multiple alignments – mammals, vertebrates, worms, flies,

2.              What kinds of questions?

1.              How has evolved across species

2.              Has gene family (opsins, olfactory, brain-related) expanded in certain lineages?

3.              Which genes are highly conserved across species? (Difficult to ask the opposite, because highly diverged genes will align poorly)

4.              What is the genome structure across viruses (influenza, HIV)

5.              Gene content evolution (e.g. yeast – bread/beer or bacteria – gut microbiome)

2.              Within species: Population Genetics

1.              Data for multiple individuals

2.              Human

1.              Complete Genomics (fewer individuals, higher coverage)

2.              1000 Genomes (more individuals, lower coverage)

3.              HapMap, dbSNP

3.              Non-Human

1.              dbSNP

2.              Flybase, WormBase

4.              What kinds of questions?

1.              Demographic history – out of Africa, human dispersal around the world, mating patterns

2.              Identify genes subject to natural selection (high altitude adaptation or lactose digestion in humans, response to climate change)

3.              Effects of artificial selection (rice domestication, changes in dog genome due to selective breeding)

4.              Evolution of mimicry (poisonous versus nonpoisonous species – butterflies and frogs)

3.              How to get the data?

1.              UCSC Genome Browser - Example downloading gene coding positions on chrX

2.              Galaxy – Example of interface, extracting multiple alignments for all genes on chrX

4.              R example for parsing and analyizing files

1.              Background of the 1000 genomes project, explain vcf

2.              R code to extract .vcf

3.              PCA with subset of 1000genomes

4.       Clustering (UPGMA, Neighbor-Joining)

References

----------------------------------------------------
Get Data
----------------------------------------------------

1. UCSC Genome Browser: www.genome.ucsc.edu   

2. Ensembl: www.ensembl.org

3. NCBI: www.ncbi.nlm.nih.gov

a. Nucleotide                b. Gene              c. dbGap                     
d. dbVar                       e. dbSNP            f. PubMed

4. Wormbase: www.wormbase.org

5. Flybase: www.flybase.org

6. CompleteGenomics: www.completegenomics.com

7. HapMap: www.hapmap.org

8. 1000 Genomes Project: www.1000genomes.org

----------------------------------------------------
Tools

----------------------------------------------------

9. Galaxy: https://main.g2.bx.psu.edu

10. DAVID Functional Annotation: https://david.abcc.ncifcrf.gov

11. BioPerl: www.bioperl.org

12. GitHub: https://github.com

13. Introduction to Unix: http://www.doc.ic.ac.uk/~wjk/UnixIntro/

14. vi cheatsheet: http://www.lagmoster.org/docs/vi2.html

15. ExPASy Bioinformatics Resource Portal: http://www.expasy.org/tools

In case you got the wrong idea

I realized from my last post, you might make the assumption that just because I love my family time on the weekends that I don't do work on the weekends. You would be incorrect.

Generally we have family time from the time I get to daycare, until bedtime for the Bear. We try to take turns putting her to bed, then maybe a little cleaning up (if it isn't my turn to put her to bed), then working for a few hours, then bedtime for the adults.

Why so much work after work? My first inclination is to say, if you are asking that, you're probably not an academic. But, then I realize that many, many people are able to leave their work responsibilities at work, and so I'll try to figure out a better answer.

Well, yes, part of it is pressure to produce. I know that, given my schedule and priorities, I simply do not have the same number of hours to devote to work during the daytime as many of my peers. So, I make up for part of this by working in the evenings (even Friday and Saturday!) But, pressure to produce wouldn't be enough to keep me going. I wouldn't be doing this. I wouldn't be doing science, if it didn't drive me to keep questioning at all hours. I wouldn't be able to stay up late doing work, night after night, if I weren't doing something I truly thought was worth the effort. And I do. I think that the work I do is important, and worth getting right. I think that I owe my collaborators and my peers my time devoted to each project. Sometimes I'm working because I can't wait to see what I've found. Sometimes I'm working because I just like what I'm doing, and making progress can be very motivating. Sometimes, I'm working because I know there is a bug, and if I just take five more minutes, I'm sure I'll figure out where it is. Sometimes I'm working because I know a collaborator is waiting on me before they can proceed. And, sometimes, I'm working because I feel the pressure of keeping up with my childfree peers.

What I wanted to emphasize in my previous post is that, I'm not afraid of hard work, or long hours. What I dislike is the continuous time away from family. So, if you see me at a conference, you'd better believe I'm making the most of that time.

Now, back to work. Tonight I am mapping heterozygous human genotypes to every gene, then merging these with expression values from RNAseq studies, for a collaborator, and, running some test regressions for a project with my new undergrad, because it's fun, and I can't wait to see what we find.

Scientist mom, freak out moment

I usually don't feel much conflict or internal struggles being a scientist and a mom. But, just now, I felt my heart drop to my feet, and my chest tighten, and I felt on the verge of tears. Why?

Because I completed the registration to spend three full days away from my family for a conference I was invited to participate in.

I am so very passionate about the topic of the conference, "Reporting Across the Culture Wars: Engaging Media on Evolution". And, I am thrilled at the invitation to participate. But a very powerful part of me aches at the realization that participating in this life means I will have to spend three days without waking up to my sweet little Bear's smiling face. I will miss three days of her dancing, of her singing, of watching her learn and grow, of reading, and exploring, and, and... everything.


I do understand why so many conferences and workshops plan their events on the weekends, but I don't think it is the way it should be.


As a scientist, I love my work. I love research, and interacting with students and peers. I can't get enough science. But, as a parent, my weekends are precious. They are the time when I get the whole day to spend with my partner, and with my child. If a child weren't in the picture, I would still want time to spend with my family and friends. But, with a child, the weekends disappear faster than ever.


I know there will be many more times over the coming years where both I and my partner will have to spend days away from one another, for science. I expect it. And, I think it may get easier. I just hope that conference organizers will start to recognize what a terrible imposition it is to the quality of life of participants to be expected to give up the precious little time we usually have reserved for our families.

Gene survival and death on the human Y chromosome

The last manuscript from my thesis research was accepted for publication in December, but I've been too distracted to blog about it. It is available through Open Access (thanks, in part, to the Miller Institute for allowing me to use my research funds to pay for the OA fee).

Mol Biol Evol. 2012 Dec 17. [Epub ahead of print]

Gene Survival and Death on the Human Y Chromosome.

Wilson Sayres MA, Makova KD.

Source
Statistics Department and Integrative Biology Department, University of California-Berkeley.

Abstract

Y chromosomes have long been dismissed as "graveyards of genes," but there is still much to be learned from the genetic relics of genes that were once functional on the human Y. We identified human X-linked genes whose gametologs have been pseudogenized or completely lost from the Y chromosome and inferred which evolutionary forces may be acting to retain genes on the Y. Although gene loss appears to be largely correlated with the suppression of recombination, we observe that X-linked genes with functional Y homologs evolve under stronger purifying selection and are expressed at higher levels than X-linked genes with nonfunctional Y homologs. Additionally, we support and expand upon the hypothesis that X inactivation is primarily driven by gene loss on the Y. Using linear discriminant analysis, we show that X-inactivation status can successfully classify 90% of X-linked genes into those with functional or nonfunctional Y homologs.

Undergrads are awesome!

The end of last semester seemed very rushed, and I didn't have a chance to have a "semester end" meeting with the two undergrads I was working with.

With the grant deadline, and peer-reviewing, and trying to make progress on work for other collaborations, I hadn't yet made it a priority to get back in touch, when, *ding*, *ding*. Two new emails in my inbox. Both of the undergraduate students I worked with last semester emailed to see if they could work with me again this semester. I am so very excited to get to work with students who are ambitious, motivated, and very bright!

Of course, I have to have realistic expectations for what can be accomplished during the semester, when they are both taking courses full-time, but slow and steady progress is being made.

One project will be included as part of a larger collaboration. There is still a little extra analysis to do, but I'm starting off the semester by having this student write up the summary of the results and the methods, because I think it is good practice, and also a good reminder of what all we have done since last summer. This student has made tremendous contributions (including many hours of tedious cataloging and parsing), and so I am negotiating authorship for this student on the paper with my collaborators.

The other project has made less progress, but is still very interesting. The student will be leaving at the end of the semester (graduating and going on to different things), and so this semester we are going to focus on writing up the results and at least submitting to an undergraduate journal. If the student is able to get more analysis done this semester also, I think the project will be substantial enough to submit to a peer-reviewed journal. We'll see how it goes.

In our backyard.

On Friday the Bear and I were walking our regular route home from daycare and I saw six police cars and a CSI van about a block from our home, around 5:30. As we got closer a seventh police car showed up.

And, today I found out why: http://police.berkeley.edu/crimealerts/2013/13-020113-4.html

I'm not sure what to think about it.

I understand that I've been pretty fortunate to live in fairly safe places, and that there is a lot of violence in the world that I'm lucky enough not to have experienced (or likely ever will). And so, I don't want to over-react at this stabbing, a block from my home.

But, I am also concerned about the little Bear's safety, and want to do everything in my power to protect her from senseless violence. I guess, I can only do my best to not put us in dangerous situations, while still giving her many opportunities to experience life for herself.

Jury duty

I am on a wait list to get called in for jury duty this afternoon, so working from home. I'm trying to get some writing done, and having a little bit of writer's block.

The jury duty was not as much of a surprise, except that it is almost exactly a year from the last time I was called. I am curious how Alameda country decides who gets put into the yearly rotation, and who never gets called. I haven't done a good job of keeping track of my calls to jury duty, but I think this is number eight.

Last year I sat through three days of jury selection for a civil case regarding asbestos, and then the case was settled out of court. Let's see if this year will be as exciting.