Archive | July, 2015

TBT: Soft sheep, hard sheep

23 Jul

10 years ago, Joachim Hermisson and I published a paper in which we coined the term “soft sweep.”

Later, when I defended my PhD and left Joachim’s group, the group gave me a doctor’s hat decorated with a soft sheep and a hard sheep. The two species of sheep probably speciated sympatrically.

I don’t have the hat anymore, but I kept the sheep and I thought I’d share a picture of them today.

soft sheep hard sheep

Soft sheep, hard sheep

Four books I enjoyed reading before and after the birth of our baby

12 Jul

I love reading non-fiction books. Here are the books I most enjoyed reading before and after the birth of our baby

Month -2:  Ina May on natural child birth

This book helped me be confident that I could deliver a baby naturally.

I am not a hard core natural child birth proponent, but I was worried that giving birth in an American hospital would give me very high chances of a C-section even if that wasn’t medically necessary. A good friend sent me a wonderful book by midwife Ina May about natural childbirth. I mainly read the part of the book that consists of birth stories written by new mothers. It was inspiring and interesting, and it made me much more confident that I could deliver a baby. It also convinced me that biking and walking was good for me throughout my pregnancy.

Link to amazon

Month 0-3: The happy baby book

This book made taking care of our newborn less scary and less tiring.

The happy baby book (a gift from my cousin and her partner who are both psychologists) was extremely useful and really helped us to know how to soothe our baby. If you are too busy or tired to read, here is a synopsis: a baby likes to be in a swaddle (even if they may resist being swaddled), a baby likes to be held on their side or stomach, a baby likes sound (white noise, shushing), a baby likes to suck on something (finger, nipple, pacifier), and a baby likes little movements. Do all of those and likely the baby will calm down quickly. It definitely worked for our baby!

Link to amazon

Month 2-5: Working and pumping

This book brought support and advice when I went back to work and needed to pump milk.

When I went back to work, I was still breastfeeding my baby. This meant that I needed to pump breast milk at home and at work. We initially rented a pump from the hospital and then bought one (tip: call your insurance first, they usually pay if you buy through them).

Pumping milk is no fun, but a book I found in a second hand bookstore gave me a lot of information and motivation to keep doing it. The book is the story of a group of women who worked at IBM and who shared a room where they could go to pump during work hours. The women kept a notebook in this room, so that they could write to each other during their pumping sessions. They simply shared stories, frustrations, questions they had and helped each other with advice and support. Later, two of them wrote a book based on the notebook. The women in the book were so real and it almost gave me the feeling that I had friends who were going through the same thing as I was. I always kept the book with the pump and enjoyed reading a few pages during each pumping session.

Link to amazon

Month 6: Baby sign language book

This book convinced us to start learning sign language.

Intuitively, it makes a lot of sense to me that signing with babies is a good idea, but nothing is more convincing to a researcher like me than a randomized trial!

I enjoyed reading a book by Linda Acredolo and Susan Goodwyn, two researchers who pioneered baby sign language. Acredolo and Goodwyn did a randomized controlled trial to find out whether baby sign language had an effect on children’s development. They found that the kids who were taught to sign learned to speak earlier and used more complex sentences (Goodwyn et al 2000). Also they had a higher IQ at age 8 (12 pts difference, going from the 53rd to the 75th percentile, link). I don’t work in the field of child development, but my impression is that a 12 point gain (or 22 percentile points) in IQ is huge. As far as I know, the study has never been replicated, so maybe the real gain is not as big.

However, more important for my daily life is that I love learning sign language & signing with our baby! I have always been intrigued by sign language but I didn’t think I would ever learn a sign language. Now, our baby, who is 12 months old, can sign dog, daddy, flower, monkey, penguin, light, bird and car.

If you are curious, here is a nice video with a baby signing:

Link to amazon

7 reasons why ShareLaTeX works really well to write in LaTeX collaboratively

12 Jul

Screen Shot 2015-07-12 at 3.44.51 PM

A few months ago I published a manuscript on the BioRxiv and then PNAS with 5 coauthors. Four of us used ShareLaTeX to collaboratively write the paper. It worked really well. Here are eight reasons why I like ShareLaTeX:

1. No need to think about a LaTeX editor or any packages on your computer. All work is done online. Great for LaTeX newbies.

2. ShareLaTeX has all the benefits of LaTeX. It is LaTeX, just online. You’ll get the beautiful LaTeX lay-out, and it’s perfect for mathematical equations.

3. No worries about whether you are working on the latest version of the file, you always are, because all work is done on the ShareLaTeX servers. Great for collaborations across timezones.

4. It’s very easy to see what edits your colleagues made. Much more elegant than “track changes” in Word. You can reverse the changes.

5. No need to worry about who else is editing the file, you can work on the same file at the same time!

6. If you need to talk while you’re working on your manuscript, the chat option works too!

7. When you’re done, or need to send a version of the manuscript to someone else, it’s easy to download the entire project (including bib files and figures) to your computer or just the PDF, which is usually enough.

On my wishlist: ShareMathematica

The people from ShareLaTeX now also have an R and Python editor online DataJoy. I haven’t tried it yet, but it could be very useful!

In addition, I hope that the the men and women at ShareLaTeX will think about creating ShareMathematica. For the Mathematica files we used in our project, we ran into version problems occasionally, so that Alison had to send us emails saying: “Please, make sure you use version 8 of the Mathematica file in the DropBox folder!!!” I hope that next time we collaborate, we don’t need to worry about that anymore.

Finally, I wish there was a button that would send our manuscript directly to the ArXiv or the BioRxiv, when we are ready to do so (and remove all the comments before doing so).

Anyways, kudos to the ShareLaTeX team. You made my life a little easier!

(I have no connections to ShareLaTeX, except that I’m a customer)