Teaching phylogenetics

Repost from a blog I wrote here.

As career scientists, I think we have two main roles:

1. To conduct good research
2. To communicate the findings

I consider public science outreach to be a responsibility that falls under "communication". If the general public is not informed about the basic background of science, how can we hope for them to understand and support current research? In an effort to further basic science education, several of us from the Nielsen lab have been volunteering our time and talents to teach at the local high school. My contribution was a lesson on Phylogenetics. If you're very interested in this topic, please see the University of California Museum of Paleontology's website on Phylogenetic Resources.

I put together a simple set of activities to introduce the concept of phylogenetic trees, address how we build the trees, and discuss ways in which they are useful. I tried to make it as hands-on as possible, and was supported by several wonderful colleagues who also volunteered their time to assist with the small group activities.

The lesson started with an explanation of what a phylogenetic tree is, and how it is used to represent the relationship between individuals or species. We also discussed how switching the order of labels might or might not affect the information in the tree.

The students then broke into groups to work on an exercise to see if they could apply the lesson about interpreting phylogenetic trees. We then had a second section where we discussed how phylogenetic trees are made. After some discussion where students suggested using physical features or environment differences to build a tree I passed out a tree and a set of species, and asked the students to estimate the relationships between the species using their knowledge about the morphology of the species. Afterwards I had each group come to the front, show their grouping, and explain the logic behind their decision.

Then I described how many scientists now also use information from DNA sequences to learn about the relationships between species. Each group was given three different "gene" sequence alignments, with one sequence per species (species names were encoded by numbers to prevent biases from the last section), and asked to determine the relationship between the species based off of differences between the DNA sequences.

Afterwards I had another student come up to the front and draw the relationship between species based off the DNA sequences (everyone in the class agreed with the tree), and then I revealed the true species names. We compared the tree built with DNA sequences to the tree estimated from morphological traits and discussed differences/similarities between them.

In the last section of class we discussed the following topics:
- Of the three "gene" sequences, one had many informative sites, and one had only two informative sites (and did not give a highly resolved tree). Why might this be?
- What are the applications of phylogenetic trees? For example, being able to determine the history of infectious viruses, like avian flu.

Please feel free to email me (mwilsonsayres at berkeley.edu) if you'd like a copy of the lesson plan and materials I made for this project.

On the farm

My Grandma and Grandpa Wilson had many professions. They were a nurse and a doctor, respectively, and they also had a farm, where I made many wonderful memories as a child. I remember gardening, and feeding cubes to the cows. My brother Doug and I would climb up into the mulberry tree and come down with cups (and stomachs) full of the sweet purple berries. We cleaned up brush, and played on the hay bails. We sat with grandma on the mower, and loved helping her drive it. There were so many things to do and see and smell and taste.

There is a growing trend, that both adults and children spend less time in nature. Of course there are many reasons for the "Nature Deficit", including urbanization, but when you realize that the average American child spends 4-7 MINUTES outside in unstructured play, and 7 HOURS in front of an electronic screen, something has to change.

I think the benefits of exploring the natural world far outweigh any excuses we try to make. Our daughter goes outside at daycare (when the weather is nice: we provided hats and sunscreen), but I like playing with her outside too, so we go make time to go to the park after daycare. Right now she cares less about the playground equipment, and more about interacting with the dogs at the park (and our little dog gets tons of love from the toddlers there, when we take him).

This last weekend we took her to the Little Farm at Tilden Regional Park. It's a wonderful place where anyone can walk up and interact with the animals (you can feed them lettuce and celery). Claire especially loved the birds (chickens, ducks and geese), but was curious about all the animals. She is biased towards our dog, however, and kept trying to call the animals over with the same hand signs she uses with Chip (our chubby chihuahua). I think this place will move into our rotation of weekend science museum and outdoor excursions.

So much for Science to do.

I love David Bowie and Freddie Mercury. They're deep.

Why induce?

I spent today with some lovely moms and moms-to-be, and read a lot of posts on Facebook, so this seems timely. Some of the women commented how they'd like to be induced early, instead of carrying their next pregnancy to the full 40 weeks.

Currently in America, 37 weeks is considered "full-term", but there is mounting evidence that those extra few weeks may be totally worth it (however uncomfortable they may be)!

I've been reading about development lately (in humans and other species), and am really amazed by how much benefit the mother's body can be to facilitating organ and neural development, even in the last few days before birth. As such, it probably shouldn't have been (but still was) a surprise to learn that the second leading cause of mortality in US-born infants is low birth weight and prematurity (http://www.cdc.gov/Features/dsInfantDeaths/).

I have been thinking a lot about how trends in inducing prior to 40 weeks might be affecting humans. In particular, babies born before 39 weeks have a higher incidence of hearing and vision problems, have more challenges nursing, are more likely to experience lung and breathing problems, and be hospitalized in the first year (http://www.ncbi.nlm.nih.gov/pubmed/22421263). But, I'm not sure how the picture looks if these data are normalized for with other indicators of maternal and fetal health (like nutrition, exercise,  or, chromosomal anomalies).

For now it seems like, without other medical indications, there isn't a strong medical case for inducing pregnancy prior to 40 weeks.

This from the girl who was born 3 1/2 weeks early, so take it with a grain of salt.

Misogyny just isn't funny.

I realize I'm lucky to be a woman in science now, given the past overt discrimination, which is why the misogynistic comment from visiting speaker during our morning meeting caught me so off guard. Even in jest, it wasn't funny.

There were four of us (my postdoc advisor, a fellow postdoc, invited speaker, and me), and in introducing my fellow postdoc (FP), my advisor told a story about how FP had really saved the day on a specific project because it was time-sensitive, and the grad student working on it went on maternity leave, then the first postdoc working on it went on maternity leave, then the second postdoc working on it went on family leave for his sick father. The invited speaker responded with, "Well, that's why we shouldn't hire women."

That is the attitude that makes me seriously reconsider academia.

I should mention however, that my advisor was quick to respond that he's actually very happy to have so many women in his lab, and that they feel comfortable taking maternity leave, because its hard enough to be a woman in science. (win) And, my fellow postdoc spoke up to say that he is expecting a baby in September. (win)

Those are the attitudes that make me realize I can make it in academia.

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Update: I'll be writing a longer version for the GWIS E-news. It won't be very different, but I'll post it here when it's done.

Women in Science

When I found out I was pregnant, during the last year of my thesis work, I was thrilled, and nervous, and terrified. After waiting till the traditional 12 week mark, I was excited to tell my fellow Graduate Women in Science (GWIS) members about our impending arrival. We had an informal meeting planned in the basement of Irving's (a local coffee/bagel shop), and I figured the end of the meeting would be the perfect time to tell everyone. As it happened, we had a great meeting, and as we all packed up and started walking back to campus, someone brought up babies. Perfect! 

But then it turned into a discussion about how none of them could imagine having a baby during grad school: the time-commitment, the stress, the inability to focus completely on research and extracurricular activities. I mean really, our careers are the most important thing right now, and having a baby would put us on the wrong track. In addition to any pregnancy-related ailments, we have to take off time for the delivery/recovery, then we can't routinely work 10-12 hour days because we have a tiny person to look after. How can we compete? And, we wouldn't want to risk the possibility that we might want to take time extra off to spend with our babies while they're little, further pausing our research. That's career suicide. 

Oh...

So, I didn't say anything. I didn't have the courage to speak up because I didn't have any answers. And then I didn't really find another opportunity to say it. Not in the - "yay, I'm having a baby" sense, anyway. I was very lucky, and my fellow GWISers threw me a fantastic (and very surprise!) baby shower with delicious food and games. But, we never really talked about how having a baby changes, or doesn't change, things. And I feel like we all missed out because of it. 

I defended when my baby girl was 5 months old (she was in the back with my husband and family). Now I'm a postdoc. Yes, I do miss out on a lot of the social interactions. I miss out on going to the bar, or partying late in San Francisco. And, I feel like I am not able to make as much progress as quickly as I'd like. But I am making progress. I have several projects started, and moving in the right direction. The final paper from my thesis work is submitted (fingers-crossed and waiting to hear back!), and had I had a paper published last month. Will it be enough to find the career of my dreams, or will choosing to have children hold me back? Since I only have this one life, this one sample, I guess I'll never know. 

So, for now, I'm enjoying motherhood, and research. I love all my babies!

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The frustrating case for women in STEM, taken from: http://genomebiology.com/2012/13/3/148

The 'scissors' pattern of gender distribution within career stages in biological sciences at German universities. The figure shows the percentage of male and female university students through graduation, PhDs awarded, scientific staff (includes post-doctoral fellows, some junior group leaders, and research scientists with university or PhD degrees), Habilitation (awarded for research accomplishments following the PhD as well as teaching experience, which is often a pre-requisite for university professorships in Germany), and professors[1]. A similar pattern has been found in other countries, for example, Australia [2]. For further information on gender equality in science in the EU, see [3]. Biology Genome Biology 2012 13:148   doi:10.1186/gb-2012-13-3-148

The 'scissors' pattern of gender distribution within career stages in biological sciences at German universities. The figure shows the percentage of male and female university students through graduation, PhDs awarded, scientific staff (includes post-doctoral fellows, some junior group leaders, and research scientists with university or PhD degrees), Habilitation (awarded for research accomplishments following the PhD as well as teaching experience, which is often a pre-requisite for university professorships in Germany), and professors[1]. A similar pattern has been found in other countries, for example, Australia [2]. For further information on gender equality in science in the EU, see [3].

Biology Genome Biology 2012 13:148   doi:10.1186/gb-2012-13-3-148