Fly Hunt: Chapel Hill

Corbin Jones, at UNC was ridiculously generous with his scarce free time while I was in town. He took me and Shelah on a hike through the forest near his house. It was a very cool place. We walked a couple of miles (maybe?) on this loop through the forest, setting out bait along the way. Early the next morning, Corbin and I went back through to collect the traps. Unfortunately, it had rained quite hard the night before, so most of the traps were flooded and useless. Fortunately, it had rained quite hard the night before, so I was witness to a lovely thunderstorm. For those who don’t know, the San Francisco Bay Area does not have thunderstorms. I see a streak of lightning about once a year here, and I’m not sure that I’ve ever heard thunder. I took a video of the storm with my camera. I love how the thunder goes on forever. I turned out all of the lights, opened my doors, and enjoyed the storm with my hookah.

http://video.google.com/googleplayer.swf?docId=3869308407971584944&hl=en

Anyway, Corbin and I collected the traps and we also found a ton of drosophila feeding on some mushrooms. I’m posting a bunch of pictures of them here, so that someone will tell me what kind of mushrooms these are. The little black insect on the underside are some kind of wasp, but the red-eyed buggers on top are my Drosophila.

I also couldn’t get over the poison ivy in this forest. I grew up around poison ivy, but I’ve never seen anything like this. Apparently, it grows like a giant, red, hairy vine all over these trees. Dead vines were everywhere!

I also saw a lot of really cool insects here, as well as a lizard with a blue tail and a copperhead snake! (I know that’s not an insect there on the right, by the way.)

There were two insects that were really bizarre. One of them is this black freaky thing on the ground (below left) and one was this cryptic little bug that I saw getting attacked by a spider when I was trying to take a close-up picture of the hairy poison ivy. The spider kept running at him and he kept waving his front legs around in the air at the spider. His legs looked like medieval weapons, like maces. Anybody know what these are?


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NESCent – play

I’m pretty sure that I would not be welcome back at the Eisen lab if I wasn’t the instigator of at least one social gathering during this ten-day compu-phylo-info-mindo-bendo-juggernaut. So, I asked Bill to announce on Friday that I was hosting a party that evening at my apartment. BYOB, I’ll bring the hookah!! Here are some pictures from the party. If any NESCent folks are reading this and want more pictures, I’ll post them all on Bill’s NESCent web page soon, or I’ll send you a link to an online photo album.
I had a hard time deciding whether or not I should admit that I can’t remember everyone’s name. Well, I can’t. Sorry! I’m guessing in some cases, so someone please correct me if I get it wrong.

Here, left to right, we have Colleen, Derrick, Karen, Kathleen, and Omar.

Santiago is showing Shelah the cheating way to blow smoke rings with the hookah. Then, he shows off..

Rutger regales Bill with tales of European history.

Taika and Joseph marvel at how intelligent the Americans are.

Jason and I smokin’ hookah with Lauren.


Taika and Libby.

I hosted a second party. It wasn’t as well-attended, but by this time we were all more comfortable with each other, so it was fun. Some of us were more comfortable than others…


Rutger tried to fulfill Libby’s Peter Murphy fantasy.

NESCent – work

I’m back in the Bay Area now. Exhausted, but safe and sound. The phyloinformatics course at NESCent was great. Dave Maddison was our instructor for the first two days. He gave us a nice overview of Mesquite‘s capabilities. At first, I was pretty excited – thinking that I was going to be writing new modules for Mesquite to do all sorts of cool things – but I know now that I probably won’t. Mesquite modules are written in Java, and I don’t know Java, and based on what I heard from the folks in the Java tract of this course, it’s not straightforward to write these modules even if you do know Java. But, Mesquite is pretty powerful as it is, so I’m glad to know more about it, and creating macros in Mesquite is very easy, and it can be run from the command line (although I wish we’d spent more time on this) so I will definitely keep it in mind for future analyses. Also, we used Eclipse to run Mesquite, so I was introduced to that as well.

For the next two days, Sergei Pond and Spencer Muse introduced us to HYPHY. We learned how to partition a multiple sequence alignment, define substitution models, perform relative rate tests, and simulate trees for bootstrapping. Sergei introduced us to the HYPHY batch programming language at the end of the first day. The second day, I took off. I really needed a day off at this point, and since we were in class from 9am-9pm every day for ten days, I had to just pick a day, and this was it. So, I missed out on the nuts and bolts of the HYPHY batch language, but I feel comfortable enough with HYPHY now to use it when I need it.

Then, the class split into two tracts, Java and Perl. The Java folks went off to do whatever it is that Java people do 😉 and Jason Stajich and Rutger Vos spent the next four days with us installing BioPerl on our laptops.

Just kidding! It didn’t take four days to do the installation. But, it was a headache. I’ve spent days trying to get BioPerl running on my computer in the past, so I must admit to the sweet, sweet schadenfreude I felt watching the experts struggle with it. Finally, though, I can use BioPerl modules in my perl scripts – yay! Jason walked us through many of the features in BioPerl. Rutger introduced us to Bio::Phylo, which is a powerful tool for analyzing/manipulating phylogenetic trees. Invaluable, all of it.

For the final two days of the course, Hilmar Lapp and Bill Piel, the course organizers, taught us how to use PostgreSQL and how to use the DBI module to interface with databases in our perl scripts.

There’s no way that in ten days I could walk away from this course a fully-functional bioinformatician, but I really do feel more empowered to become one. And, my future efforts to write the kinds of analysis pipelines that I’ve struggled with in the past are going to be much more efficient.

Fly Hunt: New Harmony to Durham

Here’s my route:

I needed to get to Durham by 4pm (or thereabouts) to check in to my apartment, so I didn’t really have time to dilly-dally, but I couldn’t resist the sign for the Maker’s Mark National Historic Landmark. There was no indication as to how far away it was, so I assumed it was just “right there” somewhere, but I was wrong, and when I found myself following this guy at 15 miles per hour, I knew I should have turned around. But, I felt committed. I drove past a distillery – I think it was Jim Beam – so I felt like I was headed in the right direction. As I drove past, I got this big whiff of a yeasty, syrupy smell that was great. I’d love to live next to a distillery. It occurred to me that there must be Drosophila there, so I turned my car around and drove up to the gate. I think I must have been at a back service entrance or something, but regardless it was locked down like a penitentiary. I strolled along the length of the fence, considering whether or not I should climb over it. I didn’t. I also didn’t see any flies. It was VERY hot.

Right about now, I decided that I should stop to dissect the flies that I had with me in the car, so I started looking for a place. I found an elementary school that had a table near the playground and set up there. I put my hand into the little cooler where I keep the live flies, and it was hotter in there than out, and all of the flies were dead. I tried to dissect a few, but their innards just turned to mush. So, I put them in alcohol and tossed them in the big cooler. Bummer.

I got to the Louie B. Nunn Cumberland Parkway without spotting Maker’s Mark. I did smell another distillery somewhere along the way, and it had been a while since I’d seen a sign for it, so I figured I missed it. And, my little detour had turned into a major digression. I needed to get back on the interstate.

I stopped in Glasgow to call the housing people at Duke to see what the procedure was for a late check-in. (There was some indication from the info that I’d been sent that this was an option.) They told me that if I didn’t get there by 4pm, then I’d have to get a hotel. I asked about the late check-in option, and I was told that I could contact the “on call” person if I was a few minutes after 4pm, not a few hours. So, although I’m annoyed, at least now I don’t feel like I’m in such a rush to get there, since I have to sleep somewhere else tonight anyway.

I drove through part of Daniel Boone National Forest, where I would have camped if I’d made it that far, and I was glad I didn’t make it! Even in the hot middle of the day, I was swarmed by biting insects the instant I stepped out of my car. I’m sure it was miserable at night. And, it was still super hot. I didn’t take any pictures through here. It was pretty, but I think I was a little road weary at this point, and I just wanted to be moving forward. Also, it was just lots of trees, so unless I was looking to get artsy, there wasn’t much to photograph.

I connected with I-75 at Corbin and headed south. I should mention here, that my boyfriend was so kind as to surprise me by fixing the air conditioner in my car. So, it’s struggled, but it’s kept me reasonably comfortable throughout this trip. My car makes this screechy sound if I have the air conditioner on while I’m going slow. The sound gets louder when I accelerate. I’ve been dealing with this by not having the air conditioner on while driving slow. After I left Corbin, I turned on the AC once I got up to speed and heard the screechy belt sound. It didn’t seem to want to go away. I left it on for a couple of minutes and it stopped, but my alternator light came on. To make a long story short, my car broke down. This belt broke. This belt runs my AC compressor and my water pump. (This I discovered while driving and reading my User’s Manual.) As soon as I read “water pump” I looked at my temperature gauge and it was red-hot! So I pulled over.

I was roughly halfway between Williamsburg, Kentucky and Jellico, Tennessee. With no cell phone signal. I opened my hood and grabbed the broken belt. I figured I would let the engine cool down, drive a mile, let the engine cool down, rinse and repeat, until I got to a service station. Have I mentioned yet that it was hot? I did not want to go for a walk, and it was going to take a long time for the engine to cool down, so I slumped over the steering wheel. I thought that if I believed that there was a god out there who might send an angel to rescue me, then it was time to start praying. But, I don’t (sorry mom) so I decided to issue a non-verbal appeal to the kindness of strangers. Fortunately, the spirit of kind strangers sent me an angel. In the form of a picture-perfect hillbilly. And, I mean HILL BILLY. Like this. Except without the shirt, and without so many pearly whites. He was probably 45 years old.

He approached me cautiously. I didn’t see him coming because my head was down. He startled me. I showed him the broken belt. He offered to drive me to find a new belt for my car. He explained that he and his son-in-law were taking his mother back to her house (she’d been over for a barbecue.) Since he had his mom and son-in-law in the car (and I didn’t have any other options) I figured I’d be OK. Have you seen the Texas Chain Saw Massacre? If so, I felt like I might have just gotten into the car with that family (and two little dogs.) I couldn’t understand anything they said because of their thick accents and missing teeth. And, mom (he called her mommy, which I thought was weird) kept asking me questions. I just smiled and nodded.

He took his mommy home, constantly reassuring me that he was not going to drive me into the middle of the forest and kill me. (I would have been much less concerned about this if he’d stopped mentioning it!) When I returned here (mommy’s house) to take a picture, note the “no trespassing” sign, the neighbor came running out of his house at me. He didn’t have a shotgun in hand, but I’m sure he yelled for Bubba to get it.

After dropping mommy off, we went to the house/auto repair shop of a friend of his down the street. This old man dug through what appeared to be an old auto parts shop right next to his house. He didn’t find the right belt for me, so we went down the road to a larger shop, and found it. He charged me $11. Then, my new friend drove me back to my car, and spent about 30 minutes putting the new belt on. I left $20 in the back seat of his car because he refused to take any money from me. After repeatedly declining to go back to his house for barbecue and spend the night if I wanted to (no funny stuff, he says), I was on my way again! Ironically, I’d just had all of the belts in my car replaced less than a year ago – the one that broke looked brand new!

Gene’s house/auto parts. (The house is behind the tree on the left.)

I decided after all that, that I would stop to eat some comfort food. I went to Cracker Barrel and had chicken and dumplings, green beans, and corn bread. They don’t serve beer there or I would have had one for sure. My car started fine when I left.

It took a long time to get through the mountains. I stopped at a hotel near Asheville. I got to sleep at 3:30am. I was supposed to be in class at 9am and I was 3 hours away. So, I slept for 2 hours then drove to Durham. I had to pull over for a 20 minute nap, and that made me exactly 20 minutes late for class. Not too bad.

Fly Hunt: Iowa City to New Harmony

Here’s my route:


I left Iowa City, headed east on I-80. It was an extremely boring drive. I realized that it’s not so much the pretty landscape that you miss when you’re on the interstate (and I know it can be pretty as well,) but you miss the opportunity to see what life is like in that part of the country. For the most part, no one who lives there eats at the Subway at the truck stop, right? Also, it keeps me awake to pay attention to the ever-changing speed limit on rural roads. So, after stopping to eat the best Mexican food in Galesburg, I veered off course and back-tracked a little. I decided that I would follow the Mississippi River south through Illinois. I didn’t know such a thing existed, but I was headed for the Great River Road!

It really was great. For the most part, I didn’t have enough time to stop to see the historical sites, but there’s a big sign on the side of the road that describes all of the towns you’re about to travel through and what was interesting about them. So, even though I couldn’t stop, it was cool knowing the history of the region. One place I had to stop, though was Nauvoo. I had never heard of Nauvoo, but when I entered downtown, it was obvious that SOMETHING was going on. Granted, it was the 4th of July weekend, but there were a ton of people walking up and down the street. I pulled into a park that had public bathrooms and noticed that about half of the cars were from Utah and thought, “that’s odd.” Then, as I continued driving, I saw a sign for the Joseph Smith National Historic Site. Holy sh*%t, I thought, I’ve just stumbled onto Mormontown! So, I drove over to the little district where they’ve renovated all of the historic sites.

I went to Joseph Smith’s grave site, drove past the courthouse jail in which he was assassinated, drove past the house where he lived. Of course, I wanted to take pictures of all of these sites, but as soon as I stepped out of my car, I felt like the daughter of Satan, come to ooh and aah over the cute little Mormon town. I kept saying to myself, “OK, act Mormon, try to look like a Mormon, like you belong here.” I kept thinking some old-timer was going to come running out of his house shouting, “Heathen!” and then all of the apparently pleasant families milling about would turn, glare at me, and then charge. I don’t know much about Mormonism, but I did keep reminding myself that Mormons are probably not the lynch-mob types. (That was before I read about Joseph Smith’s assassination, by the way.) So, I tried to make eye-contact and smile wide. I guess my strategy worked – most people smiled back.

I thought, well, they don’t “look” like Mormons anyway, so I probably don’t look like a non-Mormon. That’s when I saw the Mormon family picnic. It was about 96 degrees and very humid. I couldn’t believe these guys were in slacks and ties! I was thinking, “hey, you’re in Mormontown, loosen your ties, take off your pants.” (I know it’s hard to see, but I felt like it was really obvious that I found them curious, so I didn’t take to much time with the photo.)

Anyway, the Mississippi River right here is stunning. Having spent four years at the University of New Orleans, my prior experience of the river was less than appealing. There, it is wide, muddy, smelly, with industrial shores. Here, it was lush and vibrant and stunning. I’ll put more pictures on the map. Nauvoo is a very cute little town, with several fancy-schmancy B&Bs, a beautiful park, a winery (no Drosophila, though) and a lot of interesting history.

The stretch from Nauvoo to Warsaw was one of the absolute best drives ever (outside of Northern California, I have to add.) It was amazing. I don’t have many pictures from here because I had to concentrate on driving (two lane, winding road.) But, really, if you have the chance, you should go there. The only bad part for campers like me is that it was really buggy and humid. I would not have been comfortable camping there, although there were lots of camping options.

Along the ensuing stretch of the Great River Road, there were a surprising number of wineries and I spent countless hours making my way towards them only to find no Drosophila there. It was close to sunset, and I’d learned (from Bryant) that these flies are active in the evening as well as in the morning, so I thought I might have some luck. However, the grapes are still growing on the vine, and these places often don’t have tasting rooms, so there’s not a lot of wine in the garbage. Lesson learned. In the past, I’ve been fortunate enough to visit wineries (for collecting, of course) just after harvest, when they’re crushing grapes and the fruit flies are going nuts all day long.

So, I realized that I was not going to make it to Kentucky to camp, so I decided to head east for as long as could before stopping. First, I stopped at Pere Marquette State Park. I really needed to dissect the flies that Bryant and I had caught the night before if I wanted to have consistency between samples. I tried to do this in my car, in the parking lot, but it was too cramped, so even though I wasn’t planning to camp, I pitched my tent. I briefly thought that I might just do it at a picnic table, but then I had these visions of all sorts of insects catapulting themselves into the LED light on my dissection scope!

I got to the St. Louis area at around 11pm. I accidentally crossed this bridge into West Alton. I got gas, then pulled away from the gas pumps to escape the insects while I looked over my map to figure out where I was. While I was sitting in my parked car, a guy walked towards me, one hand out, and appeared to be asking me if I wanted something. I must have given him a look of abject horror, because he threw up his hands, shook his head no, shrugged his shoulders, and walked away. Two minutes later, a truck pulled up next to me in my darkened area of the parking lot, and that guy walked up to the truck, the driver got out, they chatted for a second, and something exchanged hands. I decided to leave in the middle of their transaction. I remembered these scenes from movies in which the undercover detective guys are buying drugs on street corners, and I always think, MAN, that’s a crazy-bad part of town! I think I must have been in one of those and didn’t even know it. It was just a weird experience for some reason I can’t entirely put my finger on.

I arrived at Harmonie State Park at about 2:30am. I was surprised to find two women hanging out on the road just in front of the information booth. So, I stopped and asked the nearest one if the worked there (yes) and told her that I just wanted to pitch my tent and sleep for a couple of hours before I hit the road again. She said, “sure, you can do that, it’ll cost you $37.” What?!?!? $37? I raised my eyebrows, and she asked if that was more than I was looking to pay (yes) and then told me that I could camp in town, in New Harmony, at Murphy Park. Now, I’ve
never seen anything like this. It’s small park in a tiny town with a playground and some picnic tables and a little road looping through it, and you can camp there. There were two other trailers there, no tents. I pitched my tent, put out some fly bait (this is mashed bananas mixed with active yeast, by the way.) I slept for about 3 hours and then hit the road again. (No flies at my bait in the morning, even though it was quite warm.) I must add, that it’s only because it was so early and I had so far to go that I didn’t stop to check out the labyrinth. What a strange town. Of course, now that I’m searching online for a picture of this labyrinth, it makes more sense that this town would have a labyrinth.

OK, it’s 6am, I’m starving, and I hit the road. I still have the flies that Bryant collected in his backyard yesterday morning, and if I’d known what was in store for me, I certainly would have dissected them then. But, it was so miserable doing that in the tent, that I decided that, during the daylight, I could stop at a rest stop, ignore the stares, and do the dissections at a proper table of some sorts.

More later…

Fly Hunt: Fort Collins to Iowa City

I’ve started adding pictures to my map, but it’s kind of wonky because the sidebar shows the place markers in the order in which I placed them on the map rather than the order in which I travelled through them. That makes sense, but there’s no way for me to change the order. I don’t like that, so I’ll probably recreate the map when I’m finished. Just FYI.

Anyway. I made it to Durham. It was far from an uneventful journey, and I’ve found myself telling the same stories over and over again (to different people, I hope) and that’s the sort of activity I’d rather save for my senile years. So, I’m going to post a summary here.

Justin and I had a great time getting to Fort Collins, and we’ve got lots of pictures (on the map now) to prove it, so I won’t say much about that. Or, maybe I’ll come back to it.

Here’s my route:

After leaving Fort Collins – and my travel companion 😦 – behind, I stopped at Carhenge on my way to Lincoln. It’s a replica of Stonehenge that’s made of cars painted gray.

There were other car sculptures there. My favorite was the Spawning Salmon.

I had low expectations in terms of the aesthetic appeal of my drive through Nebraska, but I decided to take Route 2 through the sand hills, which were really beautiful. I took some pictures, but it was hard to capture (especially while driving,) so check out this website to learn more about the region. The hills were very green and there were a lot of little ponds between them. For about 4 hours of driving, I was almost always passing or being passed by these really long trains carrying tons and tons of coal. I was impressed by the fact that all of these remote rural towns I passed through had very nice homes and all of the yards were immaculately clean, not like in the rural south, if you know what I mean.

I didn’t collect any flies until I got to Lincoln. When I got there, on the evening of July 5th, all of the campsites were reserved, so I found one that was still vacant at 2am, pitched my tent, and hoped for the best. I put out some bait near my campsite. In the morning, I collected a handful of flies and then headed to the largest winery in Nebraska, James Arthur Vineyards. I hit pay dirt in the dumpster there and collected about a hundred flies. I took all of the flies to Larry Harshman’s lab at the University of Nebraska, but he wasn’t able to help me sort them out, and I would have been there all day trying to key them out, so I left them all together in their vials of sterile food (really just 2% agar with food coloring.) The idea is that they drink the colored water that’s in the agar and evacuate their guts of whatever food they’d been eating in the dumpster. That way, I’m hoping to enrich for the microbes that are persistent residents in the gut. Also, the food coloring makes their entire guts turn (in this case) green, and that makes them easier to dissect.

Larry did walk me over to the museum on campus to see the mammoths. Wow. I had no idea that there were so many different types of mammoths. There were the really big elephant-sized ones, and some as small as a large pig. And, the really big ones don’t look like elephants at all. They look more like giant greyhounds. Really. Look at the long legs on that monster! And, it’s ribcage looks like a cheetah’s. And, I didn’t pull out a tape measure or anything, but it’s head+tusks looked longer than the rest of it’s entire body!

I got to Bryant McAllister’s lab at the University of Iowa at about 7pm. He sorted all of the flies for me and I put all of the species into separate vials. Bryant had put some bait out at a site near the Iowa River, so we left the lab at around 8:30pm to go collect flies. He took me to a sandbar willow forest on the floodplains of the Iowa River. I wish I’d brought my camera, but we were in a hurry to get there before the sun went down, so I forgot it. Here’s someone else’s picture of sandbar willows so you get an idea of what it was like. After traveling down a series of dirt roads, we could hear the roar (ok, it was a hum, but it was a loud hum!) of the mosquitoes as soon as we got out of the car. For the first time in my life, I donned hip waders and we went mucking through the swamp to where he’d put the traps. We (and by that I mean he) caught a lot of lies there. Back to town, go get a burger and a couple of beers, sort the flies at the lab, and then to sleep. In the morning, Bryant collected a bunch of lies in his back yard. Then we went to the lab, where we sorted the new flies, and I dissected the flies I’d caught in Nebraska. I hit the road at about 1pm.

Many heartfelt thanks to Larry and Bryant.

More later…