Apologizing in advance

Baby girl and I will be taking our first flight by ourselves. We depart at 5:50am, and are heading to Nebraska to visit family, and to meet with some professors at University of Nebraska - Lincoln.

I have a single backpack packed for us, with a smaller "goody" bag inside that I can take out. The smaller bag has snacks, toys and flip books for baby girl.

I'm apologizing in advance, in the case that baby girl decides to share her ear-piercing scream with the plane cabin. We have been very lucky so far. We've flown to Arizona, Arkansas, Pennsylvania and Ireland, and all have gone very well, but there is always a first time for a tantrum.

I should be getting some sleep, but instead I'm working on revisions for a manuscript, and responding to a collaborator. And then a shower. Then double-check that I have everything packed. And then a nap before getting up and heading to the airport.

Exciting!

Similarities

Complaint about homeschooling: Socialization

One of the critiques that homeschoolers hear, and voice their frustrations over, is that their children, by virtue of being home-schooled are not being "socialized."

I agree that this is a general, and unfair criticism, assuming that homeschooling parents aren't the small minority who actually do prohibit their children from interacting with others. But in general children who are home-schooled are give the opportunities to interact with other children at the park, during sports lessons, for music or arts classes.

I do wonder whether home-schooled children are less likely to experience conflict with peers. Not bullying. Bullying is definitely a good thing, but being teased by friends can help introduce us to other perspectives, question our own, and hearing other's opinions can help us learn to accept, respond to, or ignore criticism. I think it is healthy to learn how to deal with embarrassment from peers. Being embarrassed intentionally by a parent is bullying. Being embarrassed unintentionally by a friend is a learning experience. Also, I think learning how it feels when you have offended a friend is quite valuable.

I can't remember the specifics, but I remember, in middle school, getting into a fight with my best friend over something I had said, flippantly. I remember thinking it would be just something in passing, but it really hurt her feelings, and we didn't talk for several days afterwards. I felt awful, and really came to understand why my comment was so hurtful to her.

Beyond this, however, organized school gave me the opportunity to routinely interact with people, in unstructured times (waiting before/after school, recess, and lunch), and learn how my world view wasn't the only one. There isn't the same amount of unstructured time to do that at sports practice, music lessons, or art lessons.

In general, think that there is a difference between spending an hour with children who are not your siblings, and spending a day with many child who are not your siblings. And I see a benefit in this. But, perhaps a very active parent can ensure their child will have several such opportunities, so this isn't, necessarily, a difference between home-schooled and organized-schooled children.

Complaint about organized schooling: Exploration and free thought

The people I know who are considering homeschooling are educated women. I have no doubts that they would find ways to ensure their children learned the appropriate materials, but, in my opinion, there are no benefits of homeschooling that cannot be achieved by an involved parent of an organized schooled child.

What especially gets me is the implication that children who attend organized school, do not get to experience the "wonders" of exploring the environment, or going on grand adventures. Phooey.

Heck, two days ago I was talking to a friend who worked it out so that both he and his wife had sabbatical at the same time, and they took their two kids to spend 2 months in France. They switched off their time, between research and homeschooling for those two months.  What an experience! And then, when they returned to the US, they enrolled their kids in school again.

Maybe we can't all afford to do this, but neither can homeschoolers. However, we all can take our children on mini-adventures, either for an afternoon, a day, or a couple weeks, as time allows. Being in school doesn't prevent this. Having a disengaged parent does.

School year

It is the time of year when many children start their school year. There are many parts of our education system that I think could be improved (to be discussed later), but, with parental support, I think that organized school does work well.

Several friends posted comments today disparaging organized school and advocating homeschooling.

One in particular posted a quotation:

"We ask children to do for most of a day what few adults are ale to do for even an hour. How many of us, attending, say, a lecture that doesn't interest us, can keep our minds from wandering? Hardly any." - John Holt

I think this is misleading (intentionally or not). School is not one long lecture. In fact, many schools are quite interactive, especially at younger ages. Reading, Math, Art, Music, Science. Constant stimulation, and switching subjects. There may be other, valid, arguments for homeschooling, but trying to justify it by claiming organized schooling is equivalent to sitting through one, giant, boring, lecture is dishonest.

I fully agree that a 9-3, every day, same schedule is not ideal for fostering creativity and critical thought, but not all schools follow this model. My elementary school was fantastic. We went on at least a field trip a month - I remember seeing Charlotte's web, a musical about pigs, and the Dallas Symphony Orchestra. We also visited the science museum regularly (where you could be INSIDE a bubble!). We had hands-on science classes. I remember dissecting a cow's eye and a pig's heart. We didn't memorize spelling lists, we learned how to incorporate new words into our vocabulary.

I attended four schools, and unfortunately not all of my school experiences were like the one described above. But they could have been. They should have been.

And beyond that, my parents were active in my schooling, constantly supplementing my "formal" education.

That isn't to say that homeschooling is necessarily inferior. Specifically, here is a list outlining many frustrations of homeschooling parents. I agree with the writer that nearly all of these are also invalid arguments. However, just like not all teachers are excellent, not all parents are qualified to homeschool. But, I think (hope) the exceptions to qualified educators, organized or home, are the minority.

Here are some useful resources for those considering homeschooling.

http://www.secularhomeschool.com/content/

http://www.atheistview.com/secular_homeschool.htm

Scientist mom

Great day in the lab. Saw a clear talk about recent research, made progress on two projects, met with an undergrad who will be researching with me this year, and talked through a new project idea.

After work met up with a visiting Mathematician and friend. Picked up baby girl from daycare. Worried that she isn't acting herself. Take dog on a walk.

Go to dinner. Pizza is good, but baby is content just to sit with me. Back home with baby girl - she is fussy and cuddly. Listen to a good math conversation: group theory.

Baby vomits all over the rug.

Clean up baby. Rock her. Say good-night to friend. Get baby to drink some pedialyte and put her to bed.

Clean rug. Brush teeth. Respond to emails. Set alarm for 8am meeting with collaborators in the Netherlands. Read titles of recently published research. Blog. Bed.

- Posted using BlogPress from my iPhone

Puppy love

There has been a ton of buzz about a tumblr feed that took off: dogshaming. The site went viral and was inundated with submissions. Then there were many people who lamented that it is the dogs, and not the owners who are being shamed for their dog's actions.

Okay, sure, owners are partly to blame for their dog's behavior (I especially dislike the dogshaming in reference to being aggressive or biting), but many of the photos refer to dogs who have messed in the house, or gotten into the trash, or are doing other dog-like things. Sure, we dog owners don't like it when our furry family members do something along these lines, but we all love our dogs in spite of these behaviors.

For example, I could submit several dogshamings of our cuddly brown chihuahua rescue:

1. I gladly lick anything the baby shares with me, in between her bites.

2. If my humans don't take the trash out, I'll find all their buried treasures (seriously, why do they throw this stuff away?).

3. I whine pathetically at the playground so all the parents/kids think I'm neglected, and will come pet me.

Although I sometimes get upset with things he does, he is a part of our family, and is an awesome dog. He rarely barks, protects our house, is a great snuggler, a good jogging partner (for me), and waits for everyone to go to bed before he turns in for the night. Most of all, he is our daughter's best friend:

I agree, we can, as dog parents, probably spend more time training our animals, and shouldn't blame them for their bad behavior. But, dogshaming is just an outlet for the frustrations that come with any relationship.

I don't know any of the submitters, but all of the photos posted feature dogs that look well-fed, groomed, and in good health. There are many, many ways to be a bad pet parent (just ask the 3-4 million shelter animals that are euthanized every year). I don't think dogshaming is one of them.

Accessible Research: Boar sperm transplant

In researching for my K99 grant application, I came across this paper, and couldn't pass up the chance to write about it:

Transplantation of Normal Boar Testicular Cells Resulted in Complete Focal Spermatogenesis in a Boar Affected by the Immotile Short-tail Sperm Defect

DOI: 10.1111/j.1439-0531.2006.00651.x

M Mikkola, A Sironen, C Kopp, J Taponen, A Sukuru, J Vilkki, T Katila, and M Anderson

Reproduction in Domestic Animals, Volume 41, Issue 2, pp124-138, 2006

It is a very strait-forward paper, which makes my job easy. Take home message:

Sperm stem cell transplants. One pig produces poorly-functioning sperm (think infertility) and the other produces healthy, happy sperm. Take healthy sperm stem cells, implant them very carefully into the testes of an individual who produces poorly-functioning sperm, and the new stem cells can take hold, and start producing healthy sperm. Amazing. We should be very, very, cautiously optimistic, because the researchers only conducted two trials. That said, this treatment worked in these specific domesticated boars, which means, because of evolutionary similarities, this method has a chance of working to address sperm-related infertility in humans as well.

An interesting implication, though, is that the healthy, and more abundant, sperm cells are genetically those of the donor. So, any children sired are more likely to come for the donor sperm, and thus would be more similar, genetically, to the donor than the treated individual, who co-produced the offspring. There could be some very interesting cases of parental origin and responsibility if this treatment ever makes it to humans. 

- - - - - - - 

Also, I know you're just dying to know what my K99 is about. I'll let you know, once I have all the details hashed out. 

10 steps for writing a K99/R00 grant application

How to write a grant:

1. Write;

2. Rewrite; 

3. Rewrite;

4. Rewrite;

5. Rewrite;

6. Rewrite;

7. Rewrite;

8. Rewrite;

9. Submit; and, 

10. Wait.

I am on step #4, and have a little over a month to go before my submission deadline. I'm working on the NIH Pathway to Independence award. This is composed of a K99 portion, which provides one to two years of funding for postdoctoral training, and a R00 portion, which provides three years of funding as a new investigator, contingent upon re-approval.

As I am still in the process, I don't have any spectacular advice, but, as usual, Google delivered. Here are some useful resources for preparing a K99/R00:

http://k99advice.blogspot.com/2011/03/general-advice.html

http://scientopia.org/blogs/chemicalbilology/category/k99r00/

 Good luck everyone!

Accessible Research: Hummingbirds!

One of my favorite parts of being in Berkeley is listening for, and trying to catch a glimpse of hummingbirds. The ones near our apartment have a beautiful twitter/tweet that is very distinct, but finding where it is coming from can sometimes be challenging.

I recently had the fortune to come upon a hummingbird catching a snack:

Hummingbird eating (middle of the picture). Berkeley, CA. Aug 2012.

This second picture is so neat to me, because it was taken at just the right time so you can see the wings in motion.

Hummingbird in flight (middle of the picture). Berkeley, CA. Aug 2012.

I've been studying genome sequences, and I thought, surely, by now, there must be a hummingbird genome sequence. Well, there may be one in the works, but the closest I could find was a paper from 2009, and so I figured I could sum it up here for you all

There are many reasons why it would be useful to be able to study hummingbird genomes including their amazing evolutionary adaptations for hover flight, and, it's just awesome that they are just so very small, and have super teeny-tiny eggs, for a bird:

Elephant bird, ostrich, and hummingbird eggs by Frans Lanting.

So, here is your brain tidbit for tonight:

The smallest avian genomes are found in hummingbirds

1. T. Ryan Gregory, 
2. Chandler B. Andrews, 
3. Jimmy A. McGuire and
4. Christopher C. Witt

doi:10.1098/rspb.2009.1004

Hummingbird hover flight is thought to take up a lot of energy. Cells that are smaller tend to be more efficient at exchanging gas. And, smaller cells are correlated with smaller genome sizes. So, it was thought that hummingbirds should have smaller cells, and also smaller genomes relative to other birds.

One can measure the size of a genome using... okay, I try to avoid technical jargon here, but I just have to tell you. The name of the technique is: Feulgen image analysis densitometry. Whoa! Please read the link if you want more details, but the quick and dirty is that this method uses a dye to color the nucleus (where the DNA resides) of the cells of the species you are interested in, and then compares the size and density to the size and density of the nucleus of a species with a known genome size. For example, say you come to me with 100 silver coins, and want to know much silver is in each coin, but didn't have the money/time/experience/ability to analyze each coin and figure out exactly how much silver is in it. I could take a silver coin from my pocket, one that I know how much silver is in it, and use that as a standard for comparison. For each of your coins, I can estimate approximately how much silver is in it, by determining how much larger or smaller that coin is relative to my coin. (Note, the coin example doesn't take into account density, but hey, if it were a perfect analogy, it wouldn't be an analogy.)

The researchers measured the genome sizes of 37 (THIRTY-SEVEN!) hummingbird species, and observed that the size of hummingbird genomes is, indeed, reduced relative to chicken. They also conclude that this reduction happened in the common ancestor of all hummingbirds, which might indicate that the common ancestor also had high metabolic function, and perhaps was also small. Cool. They also found that four tropical hummingbirds did not have smaller genome sizes, and think that this might be due to the particular environments they live in.

So, it seems that constantly spending a lot of energy might lead to having smaller cells and, consequently, smaller genomes. It will be great to have a hummingbird genome someday to figure out which parts of the genome are different (and which might have been lost) relative to other, larger birds.

And, because it's just fun, I want to end by sharing that the authors mention, hummingbirds have the largest relative heart and lung volumes of any vertebrates, not just birds (Suarez et al. 1991; Suarez 1992). Awesome!

Bill Nye on Evolution

I have always thought that Bill Nye's love of Science is infectious. He inspired me growing up, and he is still a wonderful role model. Now, however, instead of seeing him just as a Scientist, I get to see him as an activist, working towards better public Science policies.

Thanks.

What am I doing here?

Or, more precisely, what is the purpose of this blog.

I woke up in a start last night, from a nightmare. Everything was going fine. I had applied to all of these great jobs and went on the interviews. I thought things were going well... and then all the Universities rejected me because they'd gone to my blog and decided they didn't want someone who was so open about their thoughts/personal life.

Then I was wondering: Is it really smart to have a non-anonymous blog? Am I sharing too much? Does anyone really care about the mundane family/food/life stuff I post about? Would you all rather see just Science-posts? What if some psychopath starts stalking me because of the blog? Am I opening my daughter up to child predators? Is it really going to harm my academic career to post openly about my life? What about all the times I change my mind on topics - will I be called a hypocrite because my past blog posts forever (hypothetically) retain my past thoughts? Should I poll people to see what they think about the blog content? Am I worrying needlessly?

Okay, hold on. Maybe I'm channeling some of the Science Friday podcast I listened to yesterday about Anxiety (a book club discussion about Monkey Mind: A Memoir of Anxietyby Daniel Smith).

After a couple more hours of sleep, I woke up with clearer thoughts.

1. I like not being anonymous. I'm a real person. I'm happy to discuss more about anything I write. I don't claim to be an expert in life, I'm just sharing my experience of it.

2. I like sharing (some) about my personal life. In my career as a scientist, I don't want to be defined by my personal life, or my family. They don't determine whether the research I'm doing is good or valid. However, I think it is useful for everyone to see scientists as people. We have lives, and interests, and hobbies, and opinions. We struggle with decisions and work to find a balance between what satisfies us intellectually and what satisfies us emotionally (and sometimes they are the same thing!).

3. I like writing about science. I love it, in fact. Someday I may write for a science-specific arena, but this isn't it.  I will write about science, experiences as a scientist, and science outreach, but these things are only a component of who I am, and so they will only be a component of this blog.

4. I will change my mind - it's what people do.

5. The likelihood of many of my fears becoming a reality are quite small, and likely not going to result from sharing information on my blog. Probably. Right?

6. Will potential employers reject me because of the blog? Maybe. I may never know if this, right here, will be why I don't get a job. But, I think #1 and #2 are important enough that an institution who values their employees as a whole individual will appreciate the value in sharing the human side of scientists. Am I giving them too much credit?

And... cue my panic and retraction next Fall when I fail to get a single interview.

Planning ahead for November

Wondering what to do in November?

The weather is going to start getting cold and dreary in most of the country, but it will be beautiful here in the Bay Area. Better than the weather, the American Society of Human Genetics (ASHG) is holding its annual meeting November 6-10 in San Francisco.  And, because you are all early birds, I'm sure you'll be thrilled to come to hear me talk about diversity on the human sex chromosomes (and watch me lay down the time-keeping law as a co-moderator):

Session Number and Title: 50, Population Genetics Genome-Wide

Session Date: Friday, November 09, 2012

Session Time: 8:00 AM - 10:15 AM

Location: Moscone Center, Room 134, Lower Level North

Moderators: Melissa Wilson Sayres and Sarah Tishkoff

Looking forward to seeing you there!

Note: the early registration deadline is Tuesday September 4th.

-------

Wherever it is allowed, I'll be tweeting. And, barring any restrictions from the conference organizers (which supersede my approval), I preemptively give you all permission to tweet my talk.

How to market science?

What is the best way to market science to girls?

A friend shared this video with me awhile ago, and I've been sitting on it. Trying to decide what I think of the whole mess.

1,011,929 views; 1,276 likes, 8,576 dislikes (7:08pm PST, Aug 20, 2012) = 12.95% positive

Many people have shared their concerns about the stereotypes, particularly perpetuating expectations that women must be thin and beautiful. A member of the advisory panel for the project discusses her shock at the  representation of "sexy girl science on the one hand and real guy science on the other". The website itself features a tube of lipstick in the title, but also  features profiles of women in science, and highlights various STEM careers.

I also saw many people link to other videos that were, in their opinions, more appropriately geared towards actually recruiting women to the sciences, like this one:

54,376 views; 852 likes, 18 dislikes (7:08pm PST, Aug 20, 2012)  = 97.93% positive

I personally prefer the second video, because it is witty, funny, and more representative of what I actually do in the lab. But, even though the second video has a hugely positive rating (almost 98% positive responses) and the first is poorly received (~13% positive), I can't help but notice that the first one has 20 times more views. So, even though youTube viewers don't like it, it is getting wild exposure. Maybe it's like a train wreck, you can't help but look.

But really, I've waited to chime in because I wanted to think of how I perceived the options for a career in STEM growing up, and what could have, or did, encourage me to pursue a career in science, and what didn't. Okay, okay, I graduated 10 years ago, so I'm pretty much a dinosaur to today's middle school and high school students, but many of my experiences have stuck with me.

Given that this is my blog, the experiences I'm going to share are uniquely mine. I'm sure many girls had different experiences and different circumstances, but here are mine.

Some background: I love math. I've always loved math. I didn't realize this was a problem until high school, when people started telling me how hard it is for women in Mathematics. Oh, really? But, I really like my classes, and my math teachers were awesome (or maybe I was just on the same nerdy vibe). Uh, okay. But, I still went to class, participated in the Math Club, and attended Math Day at the University of Nebraska-Lincoln (UNL).

I loved Math Day! I loved getting to do math for the sake of doing math, and competing with my peers, and spending time with other math geeks. Sure, there tended to be more guys than girls there, but I remember just being super-inspired by all the smart people. It was a rush to try to solve things faster than everyone else.

Lesson 1: Large scale Math days and competitions = A good way to increase interest in math.

After high school, I decided to pursue a Math major in college. The Mathematics department at Creighton was (and I'm sure still is) a fantastic place. The professors were supportive but challenging. The classes were small and I got to know all of my classmates. I love how pure math is. Things flow logically, and there isn't the same level of ambiguity as in other STEM fields. Of my major courses, all of the upper-division courses were taught by men. They inspired me and encouraged me, more than the one female math professor I had (who I think really didn't like me much). Sure, it would have been nice to have a female professor, and I definitely think there are barriers to women in academia that go beyond basic gender discrimination that should be addressed, but that isn't the issue now. I'm just thinking about, would it have mattered to have female math professors? Perhaps in a department that wasn't as inclusive or just plain awesome as the one I was lucky enough to find myself in. But, as it was it was so much more important to me to have patient, genius, math geeks - people who really got into the theorems, and weren't afraid to made mistakes, and get chalk all over their pants, and pushed me to learn alongside them instead of letting me memorize equations. 

Lesson 2: Geekdom and a general lack of jackassness in professors = A good way to increase interest in science and math. 

With the encouragement of my advisor and friend, I applied for a summer Research Experience for Undergraduates (REU) at UNL in Mathematical Biology. I know, applied math (I can feel the collective cringe of the pure mathematicians now). But wait... someone will pay me... to do research... for the whole summer?!?! This was the best summer job ever! Who knew, you could get up, eat breakfast, go to work, and spend all day thinking about and working on super-awesome questions? A little nerd speak for you: We built a stochastic model for tumor growth up until the point of metastasis, incorporating different kinds of treatments. I also got to learn about the other groups, including some fundamentals of game theory and population dynamics, and discrete and continuous calculus. I learned how to learn. I learned how to play bridge. And, I learned that I wanted to do research for the rest of my life.

Lesson 3: Exposure to research experiences = A good way to increase interest in STEM. 

From here, I applied to grad school, decided to pursue a PhD in Bioinformatics & Genomics at Penn State, and am now I am a postdoctoral fellow at UC Berkeley. I'll go into those later, because by this point, I was already hooked.

When I was growing up, I didn't need someone to tell me that it's okay to be pretty in Science. I didn't need a person who identifies as female to show me that it is okay for me to like Math, and want to do Science. I needed creativity, and competition, and wonder, and to be allowed to explore the full awesomeness of doing research. And reinforcement.

I really think the question should be, "What is the best way to market Science?". Emphasizing that it has to be "for girls" not only excludes boys, but it can, in my experience, make girls wonder (or made me wonder), what is it about me that I need someone to market specifically to me? And what about trans people? This doesn't in any way mean we shouldn't include diversity in our marketing (in gender, in ethnicity, skin pigmentation, physical abilities, etc). But, as a girl looking at science, I just wanted to see the Science, to be a scientist. I didn't want to be reminded that I was a "girl scientist".

Now, the whole issue of being a female in science, the difficulty of finding a support network through grad school and beyond, and the loneliness of actually being a female researcher is a whole different issue. But by this point, I'm stuck. I've been sucked into the world of research, and I don't want to get out. It seems like there are some pretty strait forward and attainable ways to get girls into science - and wowzers, they seem like they'd work for everyone!

It's keeping them that's the problem.

Almond cookies

I love to cook and to bake. For me it is stress-reliever in two ways. First, the simple act of making something, and being creative is enjoyable to me. Second, I can gain some peace-of-mind by having a better idea about what is in the food I'm putting in my body and giving to my family. The things I try are not elaborate or time-consuming, because I simply don't have time for it. I hope by posting them here I can give some ideas to people who want to try to incorporate new, healthy dishes into their diets, without much additional work.

However, this recipe is a great example of how vegan food is not necessarily healthy food. Cookies!

I tweaked a recipe from 1,000 Vegan Recipes (1,000 Recipes)for peanut butter cookies (really a great recipe book!), but used almond butter instead. They have a rich almond flavor, are slightly sweet, but a little dry, so I'd recommend eating them with a cup of tea or coffee. As you'll see below, the dryness is likely due to my substitutions.

Almond Butter Cookies

3/4 cup creamy almond butter

1/2 cup Earth Balance margarine

1/2 cup sugar

6 tablespoons water (originally calls for three, but the ingredients didn't stick together... the final product might have been less dry if I'd used more fat instead of water)

1 teaspoon vanilla

2 1/2 cups wheat flour (also probably contributed to the dryness, as the recipe calls for regular flour)

1 tablespoon baking powder

1/8 teaspoon salt (Called for 1/4 teaspoon, but I don't like salty cookies)

Combine dry ingredients first, then add wet ingredients and mix until smooth. Chill at least an hour in the fridge. Roll dough on a floured surface and cut out shapes (or make traditional balls and compress with criss-cross fork marks), and bake at 350 F for approximately 10 minutes.

These cookies were not baby-approved, but they were husband approved (although, I think he likes anything in cookie form).

Repost: Racism, Sexism and the Science Pipeline

Sikivu_Hutchinson has a wonderful piece about diversity in Science. The whole thing is worth reading(http://freethoughtblogs.com/blackskeptics/2012/08/15/beyond-starship-enterprise-racism-sexism-the-science-pipeline/), but here is an excerpt I thought was particularly striking:

In 2008, African Americans who’d received Science and Engineering doctorates were only 4% of the faculty at U.S. colleges and universities.  At Cal Tech, one of the leading science and technology institutions in the country, African Americans are less than 1% of the faculty.  They are 4% of the faculty at MIT.  In her report “Barriers for Black Scientists” chemistry professor Donna Nelson found that, “Blacks represented 8.8 percent of chemistry B.S. recipients in 2004 and 1.3 percent of all chemistry professors at the FY2005 “top 50” chemistry departments. The ratio 8.8 percent to 1.3 percent—versus a corresponding ratio of 37.7 percent to 77.5 percent for white males—indicates that black chemistry majors do not enjoy the supply of same-race faculty role models and mentors that majority chemistry majors do.” 

Conservatives who disdain “liberal multiculturalism” in higher education dismiss such concerns about diversity in hiring as handwringing.  According to this view there is only one standard academia should use; objective and unbiased, untainted by affirmative action.  Yet white students are beneficiaries of cradle to grave affirmative action.  White students grow up seeing the dominant image of rational, trailblazing scientific discovery (from films like Dr. Strangelove to 2001: A Space Odyssey to Close Encounters to The Right Stuff, etc.) as spearheaded by courageous rugged individualist white males.  They are socialized to believe in a template of “purely” meritocratic success and individual achievement. Meritocracy becomes gospel and lucre.  They can take it to the bank and use it to repel the less qualified savages. Racial or gender others who make it into science’s inner sanctum are either interlopers scrounging for handouts or shining exceptions bootstrapping up from the inner city wilds.  At the insular level of college Physics and Engineering white male dominance is perpetuated by “boy’s club” peer groups, networks, faculty and administrative support systems that facilitate access for the racial majority.  

Thoughts about eggs

I've really been incorporating a lot of vegan dishes into our diets, because it is delicious, and a challenge, and can be healthier. I don't shun meat, or dairy, but think that limiting them (from standpoint of the average American diet), is a very good idea.

That said, eggs are one of the few protein sources that my daughter will eat regularly (she doesn't care for the consistency of meats, scoffs at most cheeses, doesn't care for tempeh, and will occasionally eat tofu). So, I make eggs.

The status of eggs seems to be so controversial, but nutritionally it really comes down to this (environmentally and ethically is a different subject): eggs are high in proteins and some good nutrients, but they are also high in cholesterol. Recent research shows that regular consumption of egg yolks is associated with increased plaque formation in the arteries (a risk factor for heart disease). Still, when part of a diet that is routinely low in fat and cholesterol, many argue that eggs can be a nutritious addition.

So, what are we to do? Or, more precisely, what will I do? Well, like with most things, I'll take eggs in moderation, as part of a predominantly plant-based diet. I will, on occasion, make my vegan biscuits, plain low-sodium gravy with an egg cooked without oil, and not stress about it.

Vegan biscuits:

1 cup whole wheat flour

2 Tablespoons shorting (or 1/2 banana)

1 Tablespoon baking powder

1/2 cup milk

Mix flour and baking powder. Cut in shortening or banana in small pieces. Add milk and stir just until combined (the best biscuits are stirred the least). Shape into two large biscuits, or four small biscuits. Bake at 450 F for approximately 10 minutes.

And it will be delicious.

Repost: Procreation as a Moral Failing

A friend pointed me over to Academic Jungle, where she also discussed procreation and academia, but went into more specific responses to some of the arguments against having children. Enjoy: http://academic-jungle.blogspot.com/2012/08/procreation-as-moral-failing.html

Breeder

A friend is headed to grad school soon, and is upset because his family is hassling him about his choice to not have kids now, or possibly ever.

However, his response to it really struck a nerve:

Dear Breeders: It's nice that you've found contentment in having children, starting a family, and working to support those things. But if one more of you fucking people starts poo-pooing on my plans for the next 10 years or so because they don't include starting a family, I'm going to punch you in the face. My plans are bigger and more important than children and I don't appreciate constantly being told that I'm stupid for not having them soon.

So, with kindest regards: please go fuck yourselves.

Ouch. I get where you're coming from. Probably more so being female (y'know, because we're expected to have a ticking clock), having experienced lots of overt and subversive pressure to have kids. I found grad school to be overwhelmingly anti-child (well, anti-two-working-parent, and not very child-friendly). For awhile I was ambivalent about having a child, and still think my life would be fulfilled if I had chosen not to have a child (granted, now that I have one, there would be a gaping festering wound if I lost her, but that's more about losing someone you love than an assessment of my hypothetical life with or without offspring). In my opinion, having a baby isn't easy. It isn't awe-inspiring by its virtue, nor is having a child necessarily better than not having had a child. I definitely don't think it is for everyone, and no one should be forced or coerced into parenthood.

I guess the "breeder" comment as a collective statement towards parents stings a little because it is really so much harder than I expected to be a mother in Science, precisely because of the "breeder" mentality that persists among STEM fields. The day I was planning to tell my grad school friends I was pregnant, I didn't because they randomly started discussing how insane it would be to have a child in grad school, it would pretty much tank any career prospects, and what kind of person would do that, right? And just last week a bunch of colleagues (all child-free) made disparaging remarks about a pregnant visiting scientist, because they consider having children incompatible with being successful. This woman has been awarded millions in grants and funding, published extensively, worked at the top Institutions in the country... what more does she have to do?

You will definitely be among like-minded people in grad school, but please keep in mind that those of us who have become parents aren't all jackasses like your uncle. Well, maybe I'm a little of a jackass, but I fully and gladly support everyone's personal choices regarding becoming a parent.

It really is so strange/different to find myself in a world (scientific research) where the basic assumption is that we won't have children, but will instead focus all of our energy on figuring things out, and, hopefully, making the world a better place. Having children is so looked down upon (again, not to belabor the point, but especially for women), that mothers in science are stereotyped as being lazy, not committed, and not competitive. It has given me a totally different perspective, from when I lived in the world where kids were the norm/expectation.

I think over-population is a problem. I think we are in an environmental crisis, and popping out babies isn't going to fix either.

Having a baby won't fix self-esteem (might even lower it), it won't increase overall happiness, statistically (no matter how much one justifies the "immeasurable" joy of parenthood, we parents miss happy hour, free-time, and sleeping in, which are quite measurable), and it won't give you a leg-up in your career (well, actually male scientists with kids are, on average, more successful than those without - weird - women without kids fall in the middle, and women with kids bring up the rear). What an argument for parenthood, right?

By all means focus on your goals and plans. I do that too.

I didn't choose to have a child because I wanted someone to love me, or because I thought she might let me live on. I hope that she finds something she loves and makes her name, and I will make my own. I plan on being a badass Scientist in my own right, and am doing my best to make headway in that direction. I nearly peed my pants when I was at my conference this summer and a grad student came up to me and told me she had nearly memorized one of my papers and used it as the reference for her current project - seriously? Yeah, I did that. A baby didn't do that for me.

But I do have a baby. And just because I have a baby, I shouldn't have to quietly put up with constant degradation, pigeon-holeing, and assumptions, on top of the huge inconvenience having a child makes to attending conferences, networking outside of business hours, and somehow squeezing 10-14 hours of research into a day. Because Science was built by people who didn't have children, or had spouses who stayed at home to do all the child-rearing.

And what's more, I get it from both sides. I'm not a committed scientist because I have a child, and what kind of mother am I to send my child to daycare all day? The "letting other people raise your child" people really get on my nerves. No, I'm not letting other people raise my child. I do a damned good job of raising her myself. I stay up with her when she's sick. I get up early when she can't sleep. I make her breakfast and dance with her in the morning. I pick her up from daycare and play with her at the park before coming home and making dinner. I clean her, and I clean up after her. I take her to museums, and show her the transit of Venus. I read with her, and show her how to brush her teeth. I am currently trying to figure out if she just has a gastrointestinal infection, or an allergy. I worry that I'm not feeding her diverse enough foods, and I wonder if she knows that I love her. No. Someone else is not raising my child. Someone else is caring for her, for a few hours a day, while I get to do something I really love, and think is truly valuable, working more efficiently than I have ever before in my life.

What's more: she is awesome. This growing, learning, thriving, curious, hilarious, inspiring, lovely, unconditional person is incredible. I see things differently with her. I pause more. I enjoy more. I learn so much. Textures and shapes and colors are all so alive around me. I've learned to truly listen. I laugh. A lot. I love. I love completely. I get to explore. I get to be creative in ways that I wouldn't on my own. I get to see through her eyes. I am reminded about how wonderful, and how fleeting, life is.

There is no one reason why I chose to have a child. And no one reason why I chose to be a scientist. For me, there's no going back, on either.

I guess I am a breeder. It just hurts, no, it really sucks, to know that even with a PhD, with all I've accomplished, many of my colleagues see me as only that.

Branching out - recipe suggestions welcome!

Last week I made homemade saag paneer using this recipe minus the serrano chile pepper. It was good, but not quite what I was looking for, so if you have any suggestions for a great spicy, spinach-based recipe, please send them my way!

It was mostly baby-approved. She didn't really like the onion pieces.

Time to jump into the ArXiv?

As part of the Miller Institute here at Berkeley, I've had the wonderful opportunity to meet weekly with scientists from across disciplines (including chemistry, physics, astronomy, biology, and mathematics). One topic that comes up a lot at our discussions is how to address the challenges, while maintaining the benefits, of peer-review.

In science we design experiments, test hypotheses, draw conclusions, write up manuscripts interpreting the results, and then submit our research findings for peer-review. This process takes different forms in different disciplines. In Biology, generally, peer-review takes the form of submitting a manuscript to a journal, the editors take a cursory read through the research and decide if it fits the scope of the journal. If it does, the editors seek out experts in the field of study and request that these researchers read the article and write a summary of their professional opinions of the strengths and weaknesses of the article, specifically assessing whether the methods and analyses are sound, and should be published, or whether more/different work should be done. These reviewers are, typically, anonymous, meaning that the authors will not know who has submitted suggestions regarding the submitted research. Often it takes a couple rounds of comments from the reviewers/editors, revisions and resubmissions, and then - yay! - the paper is published. The time from submission to publication can take as little as a few weeks, or upwards of 12 months.

In my opinion, the purpose of peer review is to strengthen Scientific research, specifically identifying and addressing concerns about methodology and interpretations that might lead to faulty conclusions. Peer-review can also catch cases of academic dishonesty (including plagiarism, and falsifying data). It isn't always perfect (see examples of falsifying caught after publication, here, here, here, and here), but generally peer-review seems to be a good tool for facilitating the self-correcting nature of Science.

A benefit often touted of anonymous peer-review is that reviewers (especially new scientists) need not worry about being retaliated against if they bring up concerns regarding a manuscript. A major concern about the traditional peer-review, is that the time between submission and publication can drag out the sharing of research-findings, and hinder scientific advances.

It wasn't until I spoke with scientists from other fields, specifically astrophysics and astronomy, that I learned about a completely different way to achieve peer-review, using a pre-print server called the arXiv (arxiv.org).

I haven't used the arXiv, but my understanding of it, as explained by my colleagues, is that researchers upload their draft manuscripts to the arXiv as soon as the paper is in a complete or near-complete form (for example, at the same time as I would submit a manuscript for peer-review to a journal). Others might even submit abstracts or preliminary data, to stake a claim on a particular research topic. The arXiv is then published daily, completely open-access, so anyone can immediately review the most-recent research, add their own comments to the site, and the authors can upload revised versions, as they choose to address comments from the community. While some authors choose to also submit to peer-reviewed journals, it is not required of authors in all fields; submitting to the arXiv is sufficient (for academic success) in some disciplines.

In addition to getting scientific research out immediately, another benefit of the arXiv are that the reviewers are not anonymous, so discussions can ensue about particular concerns. However, because there is no filter as to what can be uploaded to the arXiv, it is entirely possible for manuscripts with no scientific merit to get wide-distribution and, perhaps to those not familiar with the format of the arXiv, the facade of scientific approval.

The debate in Biology, and especially Computational/Theoretical/Quantitative Biology going on now is whether the benefits of the arXiv outweigh any drawbacks. Most importantly, how beneficial is it to get research to the community as quickly as possible?

There is one other drawback to the arXiv that makes me, as a potential submitter, very nervous: being scooped.

A paper is "scooped" if someone else publishes the same (or very similar) concept before you get a chance to publish yours. But, wait, if it is on the arXiv, isn't that documentation that I had the idea first? Well, yes, but... the arXiv isn't commonly used in Biology yet, so it isn't clear how important or how much priority will be given to authors who publish there before "traditional" peer review. This is especially concerning if the novelty of the paper is the idea (which is easy to reproduce with the same or different data) versus a method (which is more difficult to replicate). Maybe this isn't a valid concern, because anonymous reviewers could, one might argue, just as easily "scoop" ideas from a manuscript they have reviewed. Furthermore, perhaps posting ideas/research early might facilitate more collaborations instead of competitions between research groups.

All said, I think that submitting to pre-print servers can be a very valuable tool for facilitating scientific discourse and advances. Will I start submitting there? We will have to wait and see.

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

See also discussions here:  http://gcbias.org/2012/07/22/arxiving-our-papers/.

And, from the above post, a link to finding which journals allow what kind of archiving: http://www.sherpa.ac.uk/romeo/

Small steps

I am very excited to report that I have submitted my first paper from my postdoc. It is in the editor's (and hopefully soon reviewers') hands. I will definitely blog more about it soon, especially because I will be preparing a talk on the same subject for the ASHG (American Society of Human Genetics) meeting this coming November.

In my continual efforts to find balance, I made us a colorful dinner of pan-seared Pacific Salmon, roasted butternut squash, and steamed zucchini.

The little one ate the zucchini, didn't care too much for this dinner. She was too busy climbing things and waiting to show her daddy her very first pony tail:




And yes, I'm blogging this from my phone as I wait for cupcake pajamas to fall asleep... she was too hyper for her regular bedtime tonight.

- Posted using BlogPress from my iPhone

Summer Research Students

Also posted here.

This summer I had the opportunity to serve as a research mentor for undergraduate students, and I jumped on it. I put together project summaries, interviewed students, and ultimately choose two students. We set up schedules and discussed project outlines at the beginning of the summer. This morning, both students presented their summaries at our group's lab meeting. I am so proud of both of them! 

I learned so much from working with both of them; time management, how to work with different personalities, and the importance of preparing for meetings and setting deadlines, among other things. Although I thanked them in person during lab meeting, I would again like to acknowledge their enthusiasm for science, their research accomplishments, and their dedication to research throughout the summer. I have now mentored three undergraduate students (the first was at Penn State), and can say that all of the experiences have both enriched me, and eliminated any reservations I  had about mentoring students. Likely these students have just lulled me into a false sense of security regarding future mentoring experiences. Below is a brief introduction to each student, a summary of their project, and description of their accomplishments.

Project 1:

Kevin Luo just finished his first year at UC Berkeley in the Molecular and Cell Biology (MCB) program. He has yet to determine his primary emphasis, but enjoys research and is currently planning to pursue it in the future. Kevin's summer research focus was studying the evolution of mammalian X and Y chromosomes:

Evolution of the X and Y chromosome

The mammalian sex chromosomes, X and Y, are unique in the human genome because they used to be identical (they evolved from a homologous pair of autosomes). Today, after a series of recombination suppression events (forming evolutionary strata) the sex chromosomes are extremely different, with the large X chromosome found in both males and females, containing over 1000 genes, while the Y chromosome is restricted to males, and contains fewer than 100 genes. This project focused on the evolution of X- and Y-linked genes in a variety of species to learn about strata formation on mammalian sex chromosomes. Kevin learned how to data mine, align divergent sequences, build phylogenetic trees, and analyze results.

Project goals:

1.    Literature review of X and Y chromosomes

a.     Four evolutionary strata on the human X chromosome (Lahn and Page, 1999)

b.     The DNA sequence of the human X chromosome (Ross et al., 2005)

c.      The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes (Skaletsky et al., 2003)

2.    Identify homologous X- and Y-linked sequence

a.     Introduction to NCBI

b.     Data mining in the UCSC genome browser

3.    Align X and Y sequences

a.     Intro to alignment algorithms (e.g., BLAST, Clustalw, PRANK)

b.     Assessing open reading frames

4.    Build phylogenetic trees

a.     Introduction to phylip, and tree-building algorithms

b.     Write code to run replicate analyses

5.    Prepare presentation to share results

a.     Prepare powerpoint

b.     Share research and results at lab meeting

Project 2:

Paulina Tsai just finished her third year at UC Berkeley in the MCB program. She is a Physiology major with a Cal Teach and Global Poverty and Practice minor. Paulina's summer research focus was studying gene duplication in nematode worms and flies:

Gene duplication in nematode worms and flies

Phosphotase genes have been shown to be involved in male meiosis. The evolutionary history of phosphotase gene has not been well-analyzed, due to a lack of genomic data for multiple species. We are curious whether this expansion was specific to certain nematode worm or fruit fly lineages, or whether the expansion was more ancestral. This project utilized comparative genomics analysis of recently sequenced nematode and insect genomes to address these questions. Paulina learned how to build phylogenetic trees, conduct sequence similarity searches across a diverse array of species, and analyze results.

Project goals:

1.    Literature review of PP1 gene evolution

a.     PP1 phosphatases regulate multiple stages of sperm development and motility in Caenorhabditis elegans (Wu et al., 2011)

b.     Sperm chromatin: Fertile grounds for proteomic discovery of clinical tools (Wu and Chu, 2008)

2.    Comparative Genomics

a.     Introduction to UCSC genome browser, flybase and wormbase

b.     Working with multiple alignments

3.    Address concerns with genomic data

a.     Eliminate in silico duplicate sequences

b.     Consider frame-shift and other ORF-disrupting mutations

4.  Alignments/Phylogenetics

a.     Compare alignment algorithms for highly-diverged sequences

b.     Build/compare phylogenetic trees using different methods

5.    Prepare presentation to share results

a.     Prepare powerpoint

b.     Share research and results at lab meeting