Monday, October 21, 2013

Keeping busy

Scientists do lots of things! Here's a little bit about what I've been up to lately:

The Nielsen lab had our second annual retreat. At this meeting we all gave short "chalk talks" about current research we're working on, discussing challenges how to collaborate.

Sept 26: Nielsen lab retreat at Bodega Marine Laboratory 

On Saturday October 5, 2013 Berkeley hosted the Bay Area Population Genomics meeting (it was my turn to organize it this time around). The tweets from the conference are Storified here, and photos are on Flickr.

Oct 5: Introducing Keynote Speaker, Hideki Innan at BAPG IX

The very next day we drove down to San Jose, joined by my dad, where the adults completed the San Jose Rock & Roll Half-Marathon (a first for all three of us!)

Oct 6: Preparing for the San Jose Rock & Roll Half-marathon
The daycare that Little Bear attends was closed for Columbus Indigenous People's Day, so we took the opportunity for a family visit to the Oakland Zoo.

Oct 14: Oakland Zoo
Last week I had my annual eye exam (I actually did better than last year, likely because we're all sleeping better), and got a lot of science done. I finalized revisions and resubmitted my manuscript on human Y diversity, finished peer-reviewing a manuscript, finalized most of my job applications, and met with my current research students to form plans for wrapping up projects by the end of the semester. We also took a family trip to a park down the street after work/daycare.

Oct 16: Playground time. The similarity between their smiles is striking here.
Oh, and on Friday we had a field trip instead of lab meeting; we toured the Museum of Vertebrate Zoology, guided by Jim Patton (more pictures here).

Oct 18: I got to feel platypus fur!!!!
Last weekend we ran some more. I ran 10K (6.2 miles) in the Berkeley 510 race starting at Golden Gate Fields, while Scott completed 8 miles (!!) around town afterwards.

Oct 19: Berkeley 510 10K race
This week is turning out to be another busy one. Today I accepted an invitation to review another manuscript, and attended a session with a panel discussion about the academic job process. Tonight I was very flattered to accept an invitation to attend the "Scholar's Dinner" hosted by an undergraduate student researching with me, Michelle Senar, and her sorority. I had a wonderful time talking with the students about science, life, and future plans.
Oct 21: Scientists before dinner
Tomorrow I give my "finishing talk" for the Miller Institute (am I really in my third year already?!), then need to pack and enjoy the afternoon with my family before getting on a plane to fly to Boston for the annual meeting of the American Society of Human Genetics, where I'll be tweeting (@mwilsonsayres; #ASHG2013).

At the conference I am co-moderating a session on Wednesday:

Wednesday, October 232:00 PM–4:15 PMConcurrent Platform (abstract-driven) Session A (10-18)
SESSION 10 – Which Comes First: The Sequence or the Biology?Hall B2, Level 0 (Lower Level), Convention Center
Moderators:Maja Bucan, Univ. of Pennsylvania
Melissa Wilson Sayres, Univ. of California, Berkeley
I will be presenting a poster on Friday. I've uploaded it to FigShare, and it already has over 200 views, which I'm pretty sure is more than the number of people who will stop by and see it on Friday (though I'm not counting that out yet).

Then, catching a flight back to California.


Tuesday, October 15, 2013

What makes a mammal?

Cross-posted at PandasThumb.

I saw a tweet wondering about what makes an animal a mammal:

So, I thought I'd go through a few of the common ideas about shared physical features of mammals.

What makes a mammal? 
Is it giving live birth? Or having hair/fur? What about feeding their babies milk?

Well, kind of (I'll tell you at the end what really does). First, let's go through these three:

Live birth.
Not all mammals give live birth. Monotreme mammals including the echidna:

Short-beaked echidna. Photo by Fir0002/Flagstaffotos
and platypus:

Swiming Platypus. Photo by Peter Scheunis

don't give birth to live young; They lay eggs.

Okay, so not all mammals give birth to live young.

What about having hair/fur. All mammals have hair/fur, right?

Well, I suppose technically baby dolphins have whiskers, but you wouldn't know it from the adults.

NMMP dolphin with locator
By U.S. Navy photo by Photographer's Mate 1st Class Brien Aho. [Public domain], via Wikimedia Commons
Pangolins, with their armor-like plates, actually have a little bit of fur on their underside (although it'd be hard to tell):

Tree Pangolin
By Valerius Tygart (Own work) [CC-BY-SA-3.0 or GFDL]
And naked mole rats technically aren't completely naked, they also have whiskers (but they are mostly naked):
Naked Mole Rat Eating
By Ltshears - Trisha M Shears [Public domain], via Wikimedia Commons
So, we'll give hair a maybe. Mammals do have hair, but there are several cases where one might mistake a mammal for not having hair.

Do all mammals feed their babies milk?

Milk Bar - - 474410
By Trish Steel [CC-BY-SA-2.0], via Wikimedia Commons
First, the snarky answer - No. Male mammals generally do not make milk (although they could).

By User:Ltshears, edited by User:julielangford [Public domain]

Second, more serious answer - Yes. I don't know of any species of mammal that nourishes their offspring with anything other than milk. To learn more about mammals, lactation, and milk, check out the blog "Mammals Suck (... Milk)" by Dr. Hinde.

Breast feeding
Breastfeeding. By honey-bee [CC-BY-2.0]

Actually, what makes a mammal is more than just whether they give live birth (because not all do), and have hair, and lactate. And doing each of these things does not necessarily mean the animal should be classified as a mammal. (Note: Although it gives live birth, a tiger shark is not a mammal, it is a shark; sharks are a kind of fish.)

So, what does make a mammal?

Shared evolutionary history
Mammals are a group of species related by their evolutionary history. The picture below is a phylogenetic tree showing the evolutionary relationship between many different species.

CT Amemiya et al. Nature 496, 311-316 (2013) doi:10.1038/nature12027

All mammals share a common ancestral population.

Modified from: CT Amemiya et al. Nature 496, 311-316 (2013) doi:10.1038/nature12027

The classification of "Mammals" was made based of shared physical and anatomical characteristics. But, underlying those, is a shared evolutionary history.

We do make sub-divisions within that larger grouping of mammals. For example, the egg-laying mammals, platypus and echidna are called "Proto-theria", while all other mammals are called "Therians". There are many other sub-classifications, but they are all still part of the broader group of mammals.

There are also larger groupings. For example, on the picture above you can see all the species highlighted in pink are called Tetrapods. These are all descended from a common ancestral population of tetrapods that are generally four-limbed vertebrates.

Although their physical characteristics may change, all species that descended from the common ancestral mammal population will all be mammals.

So, how do you tell what a mammal is? 
Well, the broad rules of thumbs still apply. If you are a Naturalist, roaming through some uncharted region, and you happen across an animal you've never seen, you can start with some of the general physical characteristics (e.g., is it warm-blooded? does it have fur?). But, now you can also take a look at it's DNA as another line of evidence.

You can collect and sequence a sample of DNA from hair, or blood, or a toenail, or even from scat (aka poop), then compare the sequences you find with sequences that are already available to learn more about the creature you sampled. You can build a tree (like the one above) based on the similarity between the sequences. The relationship between the sequences for any one region or gene may not reflect the broader species tree, but it will give you an idea of where your species fits. And, the more DNA sequence you analyze, the better your resolution will be come (although it sometimes happens that biology is just messy).

"Mammals" is the term we use to describe the group of species that generally share a defined set of characteristics (warm blooded, lactating, give live birth, have fur/hair), AND share an evolutionarily recent (300ish million years ago) common ancestral population.

Monday, October 14, 2013

Cars and motorcycles and...

Little Bear and I were doing art and spilled some paint on the floor. She helped me clean up, then I told her that we'd go into the living room to let the floor dry so that we don't slip (our apartment has laminate floors that are slicker than snot when wet).

We were just out of the door way when she turned and rushed back in to her toy box. Hurriedly she picked out toys and said,
"I just need this car, and this motorcycle, and this... (looking around) shark."
She grabbed all three toys, clutched them to her chest, then ran out to the living room.

We proceeded to play cars and sharks while the floor dried.

Saturday, October 12, 2013

Repost: Tell Someone “No”, Get Called a “Whore” – #StandingwithDNLee

A curious story, with an awesome response.


Cross-Posting from PandasThumb
Earlier this year I was invited to contribute to PandasThumb, and have been cross-posting for awhile. It is a great group of bloggers, scientists, and the comments sections are often very engaging (go check it out!). A few months ago PandasThumb was approached by a Blog Editor named Ofek about contributing content to a blog at biology-online (note, don't waste your time checking it out, please). None of us had heard of biology-online, and we were skeptical that there were no other contributors, but Ofek assured us they were restarting after a hiatus, and were looking forward to getting a variety of contributors. After some internal discussion some of us agreed to post there. Despite some administrative annoyances (not being able to cross-post immediately), it didn't feel like it would be much of a burden, and might gain PandasThumb increased traffic.

Biologist and Hip Hop Maven @DNLee5
I met Dr. DNLee (go follow her on twitter @DNLee5, right now) at a conference about communicating science, specifically evolution, between scientists and the media. From that short time I concluded that she is smart, funny, and direct, but also patient, and not prone to exaggeration. Since then, I routinely read her blog, and have chatted with her about research. She's good people.

How not to respond.
Ofek also contacted DNLee about contributing to biology-online. After she declined, he called her a whore. Below is the story, and response in her words. DNLee's response is awesome, and full of encouragement. It was originally posted at Scientific American, but removed, then posted by Isis the Scientist, and now here, and hopefully everywhere.

Neither I nor PandasThumb will contribute to biology-online.

By DNLee

wachemshe hao hao kwangu mtapoa
I got this wrap cloth from Tanzania. It’s a khanga. It was the first khanga I purchased while I was in Africa for my nearly 3 month stay for field research last year. Everyone giggled when they saw me wear it and then gave a nod to suggest, “Well, okay”. I later learned that it translates to “Give trouble to others, but not me”. I laughed, thinking how appropriate it was. I was never a trouble-starter as a kid and I’m no fan of drama, but I always took this 21st century ghetto proverb most seriously:
Don’t start none. Won’t be none.
For those not familiar with inner city anthropology – it is simply a variation of the Golden Rule. Be nice and respectful to me and I will do the same. Everyone doesn’t live by the Golden Rule it seems. (Click to embiggen.)
The Blog editor of Biology-Online dot org asked me if I would like to blog for them. I asked the conditions. He explained. I said no. He then called me out of my name.
My initial reaction was not civil, I can assure you. I’m far from rah-rah, but the inner South Memphis in me was spoiling for a fight after this unprovoked insult. I felt like Hollywood Cole, pulling my A-line T-shirt off over my head, walking wide leg from corner to corner yelling, “Aww hell nawl!” In my gut I felt so passionately:”Ofek, don’t let me catch you on these streets, homie!”
This is my official response:
It wasn’t just that he called me a whore – he juxtaposed it against my professional being: Are you urban scientist or an urban whore? Completely dismissing me as a scientist, a science communicator (whom he sought for my particular expertise), and someone who could offer something meaningful to his brand.What? Now, I’m so immoral and wrong to inquire about compensation? Plus, it was obvious me that I was supposed to be honored by the request..
After all, Dr. Important Person does it for free so what’s my problem? Listen, I ain’t him and he ain’t me. Folks have reasons – finances, time, energy, aligned missions, whatever – for doing or not doing things. Seriously, all anger aside…this rationalization of working for free and you’ll get exposure is wrong-headed.This is work. I am a professional. Professionals get paid. End of story. Even if I decide to do it pro bono (because I support your mission or I know you, whatevs) – it is still worth something. I’m simply choosing to waive that fee. But the fact istold ol’ boy No; and he got all up in his feelings. So, go sit on a soft internet cushion, Ofek, ’cause you are obviously all butt-hurt over my rejection. And take heed of the advice on my khanga.

You don’t want none of this
Thanks to everyone who helped me focus my righteous anger on these less-celebrated equines. I appreciate your support, words of encouragement, and offers to ride down on his *$$.

Tuesday, October 8, 2013

Postdoc Parent: Pants optional

The phone rang at 7:13am. It was Oxford journals calling to get my information so I could pay the fee on my most recently accepted paper. As soon as I answered the phone and found my credit card, Little Bear started fussing, and calling for me. I apologized to the person on the phone as I ran to pick up the Little Bear. She calmed down as soon as I had her, then I proceeded to give my information for payment.

Near the end of my phone call, I was still holding Little Bear. She looked down and shouted, "Mommy, you don't have any pants on!"

The person on the other end certainly heard it, but simply thanked me for providing my information, and wished me a good day. I'd like to thank that person for not calling me out on my morning pantslessness, unlike a certain 2-year-old I know. 


Wednesday, October 2, 2013

Applications welcome (postdoc, bioinformatician & PhD): studying sex chromosome evolution

Several postdoc, bioinformatician and PhD positions are available in a collaborative project on the evolution of sex chromosomes in plants and animals. The project is a funded by a Sinergia grant from the Swiss National Science Foundation and brings together the labs of Mark Kirkpatrick (Austin, Texas), Nicolas Perrin, and John Pannell (Lausanne, Switzerland). We are studying the evolutionary genomics in plant and animal systems that have largely recombining sex chromosomes. In contrast to model systems such as mammals and flies, these sex chromosomes are highly dynamic parts of the genome. Our project will address questions such as: how does recombination evolve, what drives the rapid turnover in genetic sex determining systems, and what role does sex-antagonistic selection play in genome evolution?

We are looking for researchers with strong backgrounds in evolutionary genetics and/or bioinformatics. The project will involve tight collaboration between theory and modeling (conducted principally in the Kirkpatrick lab in Austin) and testing of the models using amphibian (Perrin lab in Lausanne) and plant models (Pannell lab in Lausanne). The collaboration will involve travel between labs, and the empirical work in Lausanne will be conducted by researchers working side-by-side in groups interested broadly in the evolution of sexual systems, sex allocation, sexual dimorphism and sex chromosomes. The theoretical component will involve both modeling and statistical analyses. The empirical components will involve field work, crosses, the building of genetic linkage maps, and the analysis of molecular and genomic variation produced by NextGen sequencing of multiple genomes and transcriptomes.

The project is funded for three years. We hope to start empirical work by January, 2014. Informal enquiries about empirical parts of the project can be directed to Nicolas Perrin ( and John Pannell (, and about modeling and statistical aspects to Mark Kirkpatrick ( Applications can be sent by email to one of the principal investigators and should include a detailed motivation letter, a curriculum vitae, and the names and addresses of two referees.
 Full consideration will be given to applications received by the 31st October.

Tuesday, October 1, 2013

FigShare: Increasing the impact of scientific posters

Scientists meet up periodically to share their findings, usually at one or more annual meetings. We share results usually in oral presentations or in the form of a poster that we put up and stand near, in case anyone wants to engage in discussion.

I went to the annual meeting of the Society for Molecular Biology and Evolution (SMBE) this past summer. While at SMBE 2013 I saw several oral presentations, and perused through the posters, when I wasn't presenting my own. I had a conversation with a PI who said something to the effect of, "I won't attend a conference unless I am giving a talk."

Okay, well, I suppose once one has obtained the level of status where talk invitations are constantly rolling in the door, I can understand being choosy about the presentation style for a conference. But, presumably, this PI will still have students and postdocs who will want to attend the conference, share their science, and get feedback on current projects. And most of those people will likely not have the prestige of giving a talk. So, how else to scientists share their results?


Too many posters.
But, a drawback of giving a posters is that, despite the larger potential audience, it often seems like few people care as much about learning from posters as they do from talks. Part of this may be the assumption that all the "best" research was chosen for an oral presentation. C'mon, though, we're all in science. We know how arbitrary the talk selections can be. Another part, however, is that it is simply overwhelming to walk into a conference venue with 2000+ posters lined up. A lot of things might happen:
  1. You simply don't have time to make it to all the posters you want to view.
  2. Even if you have the time to stop by every poster you want to look at, the presenter might be busy with other people, or away talking to other people.
  3. The titles you read through might not have captured the essence of the poster, resulting in overlooking a poster you might have really been interested in.
All those posters "disappear".
After the conference, what happens to the posters? Sometimes they are brought back to labs and placed in the hallways. Sometimes they are abandoned at the conference site. And sometimes they're just resigned to join a roll of "previous posters", where eventually the paper will be recycled.

But, there's another option now.

Sharing posters on FigShare
I decided that from now on I will also post pdf files of my posters on FigShare. Now, if you can't make it to my poster, or didn't attend the conference, or didn't even know you were interested in it, you can check out my posters! I think it would be wonderful if conferences started encouraging participants to upload versions of their posters to FigShare, and then compiling them for conference participants to skim prior to attending the meeting.

Another great feature of FigShare is that you can link to relevant material (and update when it becomes available). So for each of these, I linked either to the published version of the paper, or to the arXiv submission. 

Below are links to three recent posters (including an upcoming presentation):