Some reflections on looking outside your scientific box

Overall it’s been an interesting week participating in the ABS conference here in Bloomington. An opportunity to see talks and posters on subjects I never would otherwise, like bird song, aggression and face coloration in paper wasps, and competition between seasonally sympatric wren species. I went to a talk just because it was on Beldings ground squirrels (they are very cute!).  It was also interesting to go to the handful of talks on parasites and immune function and see how they are presented at a behavior, as opposed to a disease or epidemiology, meeting. These were interesting, but often with less rigor or complexity than I have come to expect from the studies presented at the disease meetings.

I keep saying this is a very “hard-core behavior” meeting, and I think that still is the best way to describe it. This is where the folk who do focal observations, activity pattern analysis, song pattern analysis, play behavior, and sex role-reversal research present their work. These are things I have not thought about for a long time. There is very little applied or mechanistic work, so less kind of comprehensive or interdisciplinary work looking at the evolutionary mechanisms and patterns in behavior. There are of course talks on those subjects, but they don’t seem to be in the majority. Being a person to dips her scientific quill into the ecology, eco-immunology, and behavior wells, which seems to be the case of a lot of disease ecologists, it’s a bit strange to step back to see work that only work in one of these fields. This research is very interesting and worth-while but I don’t think it would be as satisfying for me. Maybe it is more fun to get to see talks on cool things animals do instead of studying it all the time, I need ecology and interconnectedness for my real work.

So one of the themes of this week has been thinking about how other biologists do their science. I went to a genomics lab meeting on Monday, one of the students who rotated in my lab is doing some work on genome sequences from lonestar ticks and presented her work. She has been looking at genetic sequences from this tick species, comparing it to other available sequenced genomes and trying to find matches for possible genes. When Mandy was showing some candidate gene matches and talked about how they could be related to the biology of the tick, mainly blood-feeding, one thing the PI (principle investigator) said during the meeting was, “Great, we can really emphasize the biology when we present these findings.” Because so much of genomic research is descriptive and mechanistic at a very basic, functional level (Mel can scold me if I am making too much of a generalization here), I guess its not always the case that the researcher brings their story back to the biology or natural history of the study species. You rarely have to remind someone to “emphasize the biology” in a community ecology study, for instance.

During the poster session last night, another IU grad student friend had similar sentiments about the meeting not being very mechanism heavy, and she said you didn’t hear the term “evolution” in the presentations at this meeting. This isn’t an issue of people not “believing” in evolution, more that the evolutionary biology (and sometimes the ecology) of the behaviors they study isn’t always the first priority for their research. This is not the case at more integrative behavior meetings that she is used to going to. It also made us think about the personality of the IU biology department, which is quite interdisciplinary, and in the animal behavior section in particular very strong in terms of evolutionary mechanisms. It was also clear that the people studying disease and parasites in animals do not come to these meetings, or the growing interest in parasites that seems to be everywhere I look hadn’t made it to this community. I had maybe 5 people come to my poster last night, and most of those people were friends or professors who already know about what I do. This is a change from the EEID meeting in Santa Barbara where I was talking to people about my poster for 3 hours. I also got very few questions on my methods or details of the work that I was hammered with at EEID. The behavioral ecology poster next to mine, which was very interesting, had a crowd around it the whole session.

I’m glad everyone is interested in different things. If we all liked the same kind of research it would be pretty boring. We need experts and people that integrate different things, this is what helps us get real understanding. The big thing is that I think scientists from different fields need to be ok talking to each other, thinking about how they can work together and what connections there are between our work. This is where science can be really exciting and innovative.  

Thursday - ABS meeting

Plenary speaker this morning, theme was immune function and animal behavior. Talk was a bit too general for me, which was shared by a fellow eco-immunology student. I guess thats necessary for a talk of this kind, but was hoping to get more out of it than I did. Some interesting examples of direct trade-offs between stress and response to bacterial infection in crickets, though.

High competition in females comes with the term "role reversed species". Funny to hear that in relation to animals. Of course, any female can tell you that females are very competitive, just in a different way.

Female topi deer have intense competition for males in leks. Highly preferred males "become physically exhausted" and "sperm depleted" because all the females have synchronized estrus, lasting for about a day. Quite intense!

Talk from Caroline Drea on masculinized female spotted hyenas. I did a report on this phenomenon for my physiological ecology class. Google this, its pretty crazy.

Apparent this also happens in lemurs. Lots of pictures of lemurs "junk" (the actual term used in the talk).

Presenting at the second poster session of the meeting. It was very crowded, but I ended up getting a spot on the outside row, very nice. Only about 5 people came to my poster, 4 of them were my friends or professors. Very different from the response I have gotten at the last meetings, talked for 3 hours about the same poster at EEID. Oh well, I enjoyed talking to the few people that came by.
Pretty tired now, was at the meeting for 12 hours today. One more talk tomorrow and I'm done.

Some mobile blogging from the ABS meeting

Sign language interpreter at a talk on vocalizations in chickadees. We were wondering how many of the scientific terms actually have their own signs. I bet there are more than we think, but I bet there are a lot of things that challenge them.

Great hypothesis testing from tropical birds. It has taken 10 years to collect enough data to test a series of hypotheses on why a tropical species of wren sing duets. Have to get used to seeing small sample sizes and non-parametric stats for these behavior talks!

Dustin rockin' out the junco short-range songs. These are a group of bird songs that are not studied very often and their role is not very well understood. They sound really crazy, like robot noises. His talk ended with a great animation to a recording made of a male "dive-bombing" a female.

So frustrating when the AV set up detract from the quality of a talk. Can barely hear a word from this speaker, microphone pointing the wrong direction. Slides full of too small images. I think this must actually be an advertisement for a behavioral data collection program.

Second talk about invasive species, didn't really think I would see many of those here.

Saw a poster that was on aggressive behaviors in kittens. This means she got to watch kittens while doing science! Maybe she needs an assistant...

Also saw a poster from the group at Miami University-Ohio that probably has data I helped collect from Bayles Rd when I was a field assistant for them in 2007 :)

What comes now?

Field work is over! Now what? There is something after the field season? Indeed there is, and this part of the research process usually lasts much longer than collecting all our samples. Needless to say, with weather being in the mid-high 90s for the last week and this kind of weather on the horizon, I don’t mind the change of scenery that includes air conditioning! I got a couple requests to talk about this part of the process, what do we do after we have the data and samples from the field season?, so I will do my best to discuss the main part of my work in the lab. To keep things lively and interesting I may also integrate discussions of papers or science news that relate to my research or are otherwise of interest. Also, keep the requests coming for things you would like to see me write about.

I think one of the misconceptions that undergrads have about what its like being an ecologist is that we spend all our time running around in the woods. Unfortunately, that is not the case. When I helped teach an undergrad ecology course, in response to a beginning of the semester survey question on experience with Excel, we had a response along the lines of, he wanted to be an ecologist so learning programs like Excel wasn’t really important. The professor and I thought this was quite funny. When I told this to one of my other grad student friends she said, “If all you did was run around in the woods you would just be a vagabond. You need Excel to go from vagabond to ecologist!” I think that’s a great observation (that you Ms. Mel Toups) because I guess that is a difference between being someone who just likes hiking around outside and someone who is a scientist, and that hiking around in the woods has a larger purpose, involving collecting data, manipulating things in the field, and bringing all that information back into the lab for analysis. So, in my goal to not completely be a vagabond, Excel and other computer related things have become a larger part of my daily life.

The first thing I do when I get a new batch of data is do some exploratory graphing and statistics. This is basically to get an idea of what the data look like, which shows me what the general patterns are and helps me make informed decisions on what the appropriate statistics tests are for this data set.

For example, one of the things I am interested in is what the distribution of ticks on hosts is. In other words, are ticks distributed evenly across all the rodents I caught or are some more parasitized than others? In the 2009 field season, this is what the tick distribution looked like:

The x-axis (horizontal) is the number of ticks per host, the y-axis (vertical) is the number of hosts in each category. This graph shows that there were the most hosts in the zero tick category, most hosts had no ticks, and that few hosts were found with many ticks on them (there was only one host with 33 ticks).

In 2011, this is what the distribution looked like:

There are the same axes on this graph. But you can see that the distribution looks a little different. There appears to be a peak at 1 or 2 ticks, most hosts had 1 or 2 ticks, but there is still a long tail to the distribution, meaning there were still few ticks that had a lot of ticks. Because most classic statistical tests assume your data are “normal” and look like this:

This means that when I do my analysis I have to make sure to tell the program that my data look different, in this case have a “negative binomial” distribution (http://en.wikipedia.org/wiki/Negative_binomial_distribution). We have a great stats consultant on campus that I and others in my lab have talked to before and I will be meeting with her soon to make sure I understand what the appropriate tests are for this data set. I’ll use these statistical tests to see if there are any kinds of hosts (males or females, reproductive or non-reproductive hosts, hosts in certain habitats) that usually have more or less ticks than others. I’ll then extend this to investigating which hosts have tick-borne bacterial infections, but that’s down the road a bit.

So that’s one of the things that I’ve been up to after being back in the lab. I’ll talk about the lab work and tests I’ll be doing in the next post.

Last Day (insert Logan’s Run reference here)

The field season is done! We had a really successful summer, but I am very glad to be finished. My field assistant Alisha and I were trapping for about 2 months, and collected a ton of data.

Let’s do some numbers:

7 weeks, 21 mornings (up at 5:30am, to the site by 7:00am back again to bait at 4:00pm)

2 sites, 4 sampling periods (groups of 3 trap-nights) at each site

48 unique individuals caught, 42 mice, 6 voles

96 total captures

76 blood samples

637 ticks collected from animals

2,680 ticks collected by dragging

1,518 miles put on our car

Unknown numbers of gnat, chigger, mosquito and tick bites

No cases of tick-borne disease

1 great field assistant, who said she had fun doing work that is probably not common for pre-med undergrads (being a farm girl was good preparation, I think!)

1 very patient and understanding husband, who did get two tick bites from what I brought into the house

What comes next is the ID-ing and processing of all the field samples. If all goes well, this will be all the data I need to complete my PhD. There may be a couple weeks of sampling in the fall depending on what the data look like. I will therefore from now on write about what we do after the field work is over, what happens in the lab and in on the computer to make all this information make sense.

This is kind of an exciting and scary time. All kinds of data with the potential to be great, but also with the potential to be too messy, complicated, or not enough to show clear patterns. I am staying optimistic, however. There are a lot of exciting things planned for all these field samples, things can only get more interesting from here, right?

Science on Tour

Sorry for the long break between posts, a lot has been going on that has kept me from writing as promptly as I would like. But I will try to make up for that in the next couple weeks.

So, summer doesn’t only mean field work, it also is when most of the big scientific conferences are held. This sometimes seems silly, holding an ecology meeting in the summer when a lot of the people going have to collect their data during the summer, but on the other hand it is much easy to schedule when there are not classes in session, plus its usually more fun to see a new place in the summer than the winter. At these meetings, scientists from all over the country come to hear talks and see poster presentations on the latest research going on in their field. It is also a time to catch up with friends you haven’t seen for a while, chat with people you have been wanting to talk to, like someone whose papers you have read, and meet new people who you may have never heard of but turn out to do really cool research or generally be a nice person to hang out with. Drinking a lot of coffee and alcohol also goes along with these meetings, a very important component (this is where some of the really great discussions happen!).

I presented my research at 3 regional conferences this spring, and the Ecology and Evolution of Infectious Disease conference at UC - Santa Barbara was the first of my 3 larger-scale summer conferences. I attended my first EEID meeting last year at Cornell University in Ithaca, NY and had a ridiculously fun time. It was the first conference I had ever been to, and meeting so many big-name folks and getting to talk to so many other people interested in the same stuff I am was kind of overwhelming. But as many people who have attended this meeting will could tell you, once you go to this meeting you want to keep going. It’s a relatively small group, about 300 people, made up of founding professors (some of the famous dudes like: Pete Hudson, Andy Dobson, Jamie Lloyd-Smith, Janis Antonovics), other professors from many universities, post-docs, graduate students, and non-academic Phds and other scientists working for government agencies or national groups. This makes for a diverse group of people from the US and around the world with the connecting interest of integrating disease and parasites into the study of ecology and evolution. Besides being a manageable size, it is also a manageable length with 2 days of talks and poster presentations and a hike scheduled for the third day. This gives everyone a chance to talk to each other, all go to the same talks, and not get too worn out with science and frivolity by the end of the meeting.

To not bog this post down with too much text, I think I’ll focus on some pictures for the rest.

The UCSB Lagoon. There were a lot of pelicins, herons, and other water birds hanging out here.

A very California sunset on the first night.

Kevin Lafferty (UCSB) talking about parasites in stream food-webs. He joked about how having the theme of the day's talks be "diversity" is kind of silly when you're already at an ecology and evolution meeting. Diversity is kind of all we deal with.

While in So-Cal we figured we needed to get some real Mexican food. This is one grilled veggie taco. Yes, there are tortillas and some beans under that luscious pile of veggies. So good!

Dusk over the UCSB campus, mountains in the background.

California ground squirrel. I was so excited when I first saw one of these guys running around on campus. They are super cute, interesting coloration, have big burrows on the sides of hills. We didn't know what they were for a couple days until someone found out what they were. And as a bonus, found out they do carry plague, so you don't want to catch any of their fleas!

Beach walk as the hike scheduled into the conference. This is the usual weather for mornings in Santa Barbara (cloudy, chilly)

Two kinds of barnacles on a big rock. Barnacles are classic ecology systems used for studying community ecology. Having your study organisms be latched onto rocks make them pretty easy to study.

A big red snail and some anemones in a tidal pool. I had never seen a tide pool before, so this was really neat.

After the beach hike me and another student (former IU undergrad, now at Penn State) went to downtown Santa Barbara, which is about a 30 minute bus ride from the campus. Very sunny, beautiful beach, mountains adjacent, could see why people like living and visiting here.

 UCSB was a cool place to visit. Met a lot of great people and talked about a lot of cool science. Made me excited to get back to finishing the field season and work on the manuscript of some of last summer's work. Ellen Ketterson, one of the professors in our department, told me that when meetings make you feel like that, excited about your work and what is going to come out of it, you know you're doing the right thing. Wise words.

Pests

Sorry about being a little late on this post. We pulled a double week (7 days in a row in the field) so I didn’t have much time for anything else. But one of the animals we caught looked like this, so it was worth the work!

Nymphal ticks covering this little guy (actually girl), juvenile mouse

All work with living organisms, in the lab, greenhouse, or field, has issues with pests, things that interfere with your work, which you then have to use some problem solving skills to work around. This could mean making sure everything is sterilized when making media or spraying for white flies in the greenhouse. In our case, we have pests of our animal traps and us.

The biggest pests to the animals trapping is raccoons. Baby raccoons can be cute and all, but when they mess with your research enough they definitely lose their cuteness. Raccoons like our traps because we bait them with peanut-butter flavored Bamba. (Everyone loves Bamba!) The reach into the traps to get the Bamba out, and in the process trip it closed so the animals we want aren’t able to get in. Once they trip it closed, they sometimes try to get in again, biting the edges of the trap, throwing them around, or biting and ripping the shields on top of the trap. 

We found the shields like this after our first night at one of the field sites. Almost all the traps had been tampered with by raccoons, and I was really worried about the prospects there. Luckily they seemed to lose interest after we weren’t there for a week, and the amount of damage from raccoons has gone down significantly. One of our solutions was to make trap-sized “staples” out of wire (actually old flags) that are used to attach the trap to the ground. This works reasonably well, but some really determined critters are able to rip out the staple and move the trap. That is basically the only thing we have figured out to do to try and thwart them. It seems like raccoons being attracted to the Bamba is just something we’re going to have to deal with, but luckily it hasn’t been bad enough.

Shields that were ripped beyond use by racoons

Trap bitten up around the edges.

The main pest of people (me and my field assistant, Alisha) are biting gnats/midges. The very wet spring has caused an unseasonably large outbreak of these awful little bugs (http://tinyurl.com/6brehwj) that caused us no end of grief. Bug spray has no effect on them and they go right for your eyes, ears, nose, neck and mouth, all the places that your really don’t want bug bites. Alisha and I both had our eyes and lips swell up a few times. My first day out, I wore a short-sleeved shirt, like I normally do, but I had never had these kinds of bugs to deal with. My neck and arms got so bit up that my lab-mates were asking what happened to me. Later, one said that when she was complaining about her bug bites she stopped to say, “I shouldn’t complain, mine aren’t as bad as Evie’s!” Needless to say, I have been wearing a long-sleeved shirt ever since.

Our first solution was to tie a bandana around our ears and neck to at least block some from getting those areas. But this meant they still got to your face and neck. 

See if you can spot the gnats all over Alisha's bandana.

We looked all over Bloomington for mosquito head nets, but everyone else in town must have been having the same problems because everywhere was sold out. Eventually I just ordered a couple off Amazon.com (thank you, Amazon Student – free two-day shipping!). 

Our lives are much better now. Some still make their way in or try to bite around your neck where the net comes down, but it is so much easier to work without a cloud of mean, biting gnats trying to bite you everywhere. Plus, we look like hard-core field ecologists with this get-up!