About jennomics

I am a Postdoc in Jonathan Eisen's Lab at UC Davis. jennomics@gmail.com


I recently learned about this new NIH initiative to crack down on “brain-doping” in academic researchers. The idea is that if scientists use brain-enhancing (I prefer mental-capacity-enhancing, or mental-creativity-enhancing, or MCE) drugs, it is analogous to athletes using physical performance-enhancing drugs like steroids. So, in the competition for funding, the MCE drug users would be at an unfair advantage.

While I honestly do not know anyone who takes MCE drugs, I must admit that if I did, I would be asking for the hook-up! I believe that the NIH should actually be obligated to prioritize funding for scientists who are willing to risk the (mild!) side effects of MCE drugs in order to produce top-notch scientific results. If I were running a big funding agency, I might well REQUIRE all of the PIs/post-docs/grad students whose salaries were being paid with my grant money to sign a contract outlining their commitment to taking MCE drugs on a regular basis for the duration of the grant. Although some evidence suggests that MCE drugs cause a drastic reduction in the length of a young academician’s career, post-docs and grad students are cheap labor and easily replaced. Really, if you can get one year of high productivity out of a grad student or post-doc via the use of MCE drugs, then you are going to be way ahead of the curve.

I think that the true tragedy of this emerging anti-MCE drug policy is that the researchers who are both law-abiding AND the most enthusiastic about and committed to the advancement of science will be forced to rely solely on the archaic (but legal) substances that we currently associate with increased mental performance: primarily coffee, but also beer and/or wine. The diuretic effects of both caffeine and alcohol serve to frequently distract many young scientists from the task at hand, arguing further for the benefit of using “next-generation” brain-doping substances.

What’s the downside, really? We quickly come up with a cure for cancer? Someone figures out how to grow corn on Mars to power our cars? I say, give me the drugs!

Tucson Drosophila Workshop

My plane stopped in San Diego on the way to Tucson.
I was looking for the wildfires the whole way down there. Here are a couple that I could see as we were descending into San Diego.

I guess I’d have to report that I found my “conference camping” to be quite a success. The weather was great (with one caveat: I had to borrow a sleeping bag and an additional blanket from some locals – thank you!!) It was about 30-45 minutes from campus instead of the 15 minutes I’d anticipated, but who would have thought that Tucson would have some of the worst traffic I’ve encountered in years! Despite the travel time, I really enjoyed returning to the campground to unwind after a long day of staring into a microscope and/or talking with a bunch of super-smart people doing very cool research. The starry night sky was a lovely alternative to a hotel room ceiling, and once I had enough layers, my tent offered a restful night’s sleep with a pretty morning view of the sun peeking over the mountains. I have to admit that I might have felt differently if there had been an active (i.e., late) social nightlife (like, at the hotel bar) with this crowd, but there was not, so I don’t think I missed out on anything because I was far away.

I got to the campground after dark, so I tried to pick a spot that looked appropriately spooky since I would be camping while most of my friends were at Halloween parties.

The view in the morning.

The view in the morning from my sleeping bag.

The general format of the workshop was that someone who is an expert on a particular group of Drosophila would give a brief presentation about the phylogeny and ecology of that group, and then we would each receive a handful of vials, labeled A -M (or whatever) containing different species of that group, and a key. Then, we just figure out which vial has which species and we have plenty of time and help to do it. That was the bulk of it.

We also learned how to observe fly assortative mating behavior and how to squash chromosomes. I have to admit that I was utterly amazed after pulling salivary glands out of a larva, soaking them in a stain, squishing them under a coverslip, and then looking under a microscope to see the polytene chromosomes. I’d always had the impression that only some very skilled microscopy-type folks were able to produce images of chromosomes that were definitively informative. BUT, with plenty of patient instruction and minimal effort, in less than an hour I was able, on my first try, to visualize a chomosomal inversion. (What?!?!? That’s STILL blowing my mind.)

Teri graciously hosted dinner at her house our first night there. This is the view of the moon from her driveway. She has a beautiful house. I wish I’d taken more pictures, but it was dark and I was socializing.

I really loved this sink, though, so I had to take a picture.

We went on a tour of the stock center. This is one of the rooms, full of vials of flies – I don’t remember which group of flies these are. While broadly (and this comes from a microbiologist, remember,) Drosophila all like the same environmental conditions, if you want to keep happy strains in a stock center, you have to have rooms with different temperatures, humidities, etc.

We also took a field trip to collect desert Drosophila. First stop: a giant fallen saguaro cactus. Of course, you must have a machete if you want to collect the desert fruit flies, and we had several, so we caught many.

I tried to find more Drosophila on other cacti (there were many species nearby) but I couldn’t find any. Most of the other dead/decaying ones were very dry. Only the saguaro was appropriately funkified.

Next stop: somewhere in town, near Sergio’s house, I think. We got to see how Sergio traps flies. Choosing the best fly-trapping technique is dependent on all sorts of things, so there’s no one right way to do it, but this method sure did work very well here. That 2-liter bottle is wrapped with some adhesive paper to cover a hole so that the flies cannot escape. If you look closely, you can see many many flies inside the bottle.

We also collected at a few similar traps, containing different sorts of bait at Stacy’s house. My favorite catch there, though, was this praying mantis. I used to see a lot of these as a child in North Carolina, but don’t think I’ve seen one since, so this was particularly nice. Thanks to Aneil for posing with the beastie for me.

There was this sculpture at the entrance to the building where the workshop was held that was such a joy to view each morning (and I say that with a Martha Stewart accent, for those who know.) Truly, it was a joyous celebration of science and scientists. (OK, I’m done now.)
Here’s a chunk of it that has our friend, Drosophila (we’ll assume melanogaster), a DNA double helix, a cactus, a mushroom, cross-section of some plant tissue, and there’s an enzyme-substrate complex over there to the right.

My favorite part (I think) is these two lab-coat guys pulling apart the dividing cells. (But, I took pictures of each part of the sculpture if you want to check out a different one, just let me know.)

On our last evening, after dinner at the Sonoran Desert Museum, Patrick O’Grady gave a nice tribute to Bill Heed. I have to say, as a tribute of my own, that during my “Fly Hunt,” I heard Bill Heed’s name many times. I honestly hadn’t heard of him before, but all of the people who spoke of him were people who I admire and each of them spoke of him with tremendous respect. He was planning to participate as an instructor in this workshop, but died just a month or so before. It’s strange that I should feel such a sense of loss for someone I never met, but nevertheless, I feel like I just missed the opportunity to meet a great naturalist, a great scientist, and a great mentor.

Conference Camping

I’m going to a Drosophila species identification workshop in Tucson next week. I love Tucson. Mostly, I love the surrounding saguaro forests. So, I decided that instead of staying in a hotel, I’ll just camp. I’ll pack light, rent a car, and drive to the campground with my gear. The weather should be perfect: low 80s during the day, mid 50s at night. There’s a campground with showers about 15 minutes away from the workshop, which starts at 9am every day. When I’m camping, I get up with the sun, so I’ll have plenty of time to get there in the morning. Then, in the evening, what do you do in your hotel room, anyway? Watch TV? I’d rather read in a tent. Maybe smoke hookah by the campfire. Wake up with the birds, hike over to the remains of a prehistoric village… So, am I crazy? I’m thinking that if this works out, why not always camp when I go to conferences? It’s cheaper AND it’s doing something that I enjoy. Any thoughts?

Ernst Haeckel

I’m in the process of decorating my new room. I have always been a nomad, and I understate when I admit to moving every year since the day I left home (for college) at age 17. So, decorating is really not something I’ve ever done. (Well, not since that flouncy pink canopy bed I loved so much as a pre-teen.) Typically, as I move in to a new place, I’m already thinking about where I will live next. So, I don’t bother to settle in. However, I think I might actually be settling in to my new place, and I’m starting to think about decorating. I am inspired by a friend (a fan of Albertus Seba,) who will remain nameless because he would be mortified if I posted his name in my blog. What sort of space am I inspired to create? I want a space in which Charles Darwin would feel at home – surrounded by images of the beauty and diversity of nature.

A couple of years ago, I started collecting old chromolithographs, I suppose with the idea of displaying them at some point. They are beautiful and created by a laborious process in painstaking detail, usually by artistically talented biologists. I only have a couple of them. One is from an old German book and is a bunch of crazy looking mushrooms. The other is from a 19th century elementary school astronomy textbook (I bought that one just after Pluto was demoted.) I also have a nice Audubon print. Now that I’m in decorator mode, I decided to collect more, and I (re)discovered Ernst Haeckel.

I was introduced to him in grad school, in a “Theory of Phylogenetics” seminar. He’s the “ontogeny recapitulates phylogeny” guy. I saw his controversial embryo drawings. He also drew this “Tree of Life” that’s STILL what most folks who do not believe in evolution think we’re talking about. His thinking was cutting edge, but he’s best remembered for not quite getting it right and it turns out that he wasn’t entirely honest in the process. But, I digress. There are books dedicated to this topic, and I recommend reading them. What I didn’t know is that he was an artist. He published this book, Artforms of Nature (in German,) that is chock-full of some AMAZING lithographs.

I’m writing about this now because I recently bid a (relatively) large amount of money on ebay for a couple of original Haeckel lithographs. I didn’t win the auctions, and I’m glad because I just found this website that has high-resolution scans of pretty much the whole book. Sure, it’s not as good as having the originals, and I would still love to collect the originals. But, for the purposes of decorating, this resource is great! Print, frame, hang. (Good thing I have access to a large printer!)

OK, so it’s easy to appreciate the beauty of the hummingbird, but what really gets me excited is the prints of the under-appreciated forms of life. Like protists and sea slugs.

Real time, Just in Time

I finally finished posting about my big trip. I hope that I can stay a bit more current now. Today was technically my first day of school. It was mostly an orientation-type meeting. Nevertheless, I was so excited about my first day of school that I woke up an hour early and could NOT go back to sleep. (Unheard of!) I had a great day. I think the highlight of it was when I was having a conversation with a friend/collaborator and some question came up about how the BLAST alignment algorithm works, and I said, “Oh, well, I’ll just run downstairs and ask Ian Korf!” Davis is awesome.

Anyway, here’s a random video I just came across that I took with my camera while I was sorting flies with Spencer Johnston. Indecisive little bugger, isn’t he? (Not Spencer, the inchworm!)


Fly Hunt: Last Leg

We left Vegas, and drove straight home. I was mildly hungover and totally exhausted. Nothing noteworthy happened (I slept a lot, while Saint Justin drove the whole way.) I’ll just post some pictures here.

North of Vegas:


Leaving Nevada:

Cool rocks:
Somewhere in here we enter California:
Welcome home!

Fire damage:

Sailboat on Mono Lake:

California’s happy cows:

Going up (looking back down) the Sonora Pass (my car was maxing out at 20mph here!)

Beautiful river:

Sunset. Trip’s over!

Fly Hunt: College Station to Las Vegas (Part Two)

Day two: I woke up at about 8:30 am, feeling reasonably refreshed. I figured I’d have breakfast in Roswell, but I didn’t get there until lunch time. At some point, I saw female (or was it male??) fruit-fly genitalia in the cloud formations and realized that I was D.O.N.E. with flies. I had to keep my cooler stocked with ice, but other than that – no more. So, now I was just trying to getting to Vegas in time for a drink. Ha! I know – it’s always time for a drink in Vegas (as I later discovered while drinking a Pina Colada for breakfast,) but I’ll say no more about that, as what happens in Vegas…

Roswell was just as cheesy as I’d remembered it, with alien heads for streetlights and “Aliens Welcome” lettered on the Arby’s sign, and “out of this world” omelets. I’d always passed through at night before, and I like it less in the morning light. I tried to check my email at the Civic Center, but I couldn’t connect to their wireless network. I left without eating breakfast. Actually, I’d stopped in Tatum for coffee and ice (for the cooler,) so my appetite was duly suppressed. I thought Tatum was a pretty neat, quintessential New Mexican town. There was obviously a metalwork artist in residence, as every street had a cool metalwork street sign, with a coyote or cactus or something on it. I really liked those signs, AND there were a ton of motorcyclists cruising around. I apparently, as a convertible driver, was welcome into their ranks. “I’ve got a convertible, too!” says one of the silver ponytail guys gathered at the gas station. And, I often got the little hand wave off to the side and down a bit that is typically reserved for their own kin. Maybe it was just the camaraderie of being out on those lonely roads together. I mean, I guess you don’t really find yourself in Tatum if you’re not on a proper road trip.

Leaving Roswell, I entered the part of New Mexico that I love the best. Crazy cactus forests and gorgeous vistas of the mountains in the distance. I drove through Lincoln, “the home of Billy the Kidd” and that was not only beautiful country (by now I was in the foothills of those distant mountains,) but it had this great western frontier feel to it. I think it’s a very well-preserved historic town. You really feel like you stepped back in time a bit. Plenty of signs to let you know what you’re seeing, but no gas stations to sell you trinkets. I stopped in Capitan for some New Mexican food, which I had been craving all day. I ate at El Paisano, a friendly family-run restaurant, with a somewhat upscale decor and the prices to go with it. It wasn’t outrageous, but I think my lunch (with water) was over $10. I got a sampler-type lunch with a couple of enchiladas and a taco and maybe something else. The sauces were great and definitely took care of my craving. It was very good, but not outstanding, and I would probably try a different restaurant the next time I roll through. When I left, I stopped next door at Calamity Jane’s for a cup of coffee, and I have to say that it was the best cup of coffee I had on this trip (and I drank plenty.)

I stopped at the Valley of Fires Recreation Area to take some pictures. I will definitely come back here to camp sometime – I bet I’d be the only camper there, and the terrain is other-worldly. I love how you can see that the rock was once all melty and now it’s dotted with a variety of cacti and some shrub that smelled really nice. The rest of the way to Socorro was very pretty. Once I got there, I had to make a decision about whether I was going to hit the interstate or continue on these smaller roads. Since I’d been going 70 mph pretty much the whole way (and that’s about as fast as I want to go,) I figured I’d stay off the interstate. And, if I went west on 60, then I could check out the Very Large Array, you know, from the movie Contact with Jodie Foster?

As I approached the Very Large Array, it started sprinkling. I could see that there were storms ahead of me in the distance, and the lightning in the clouds made for a fabulous light show. It seemed an appropriate background for the search for extraterrestrial life. I was impressed with how large the radio antennas were and amazed at how vast an expanse of land they cover. I didn’t see them all clustered together like they were in the movie, but maybe I was just in the wrong area.

Then, I entered the storms. I have never driven through the desert in the rain before, and it was spectacular! I think this might be the most memorable part of the trip for me. Unfortunately, I couldn’t take many pictures because I didn’t want to get my camera wet and also, I was a bit frightened, so my adrenaline was pumping and my hands were clenched on the steering wheel. All of a sudden, the parched desert turned into a giant river. The washes that I’ve never seen wet were full and flowing over the road. I was hydroplaning every few hundred feet and I couldn’t see the white lines in the road, my visibility was so limited. Thunder and lightning. What a thrill! I was alone on this long, lonely stretch of road for about an hour and a half, going about 50 mph. And, while a little scary, it was really beautiful. All of the big cracks in the desert ground turned into miniature canyons with miniature rivers carving through them. Little waterfalls everywhere. It was really cool. A side of the desert I’d never seen.

I finally made my way to I-40 (yawn) and to Vegas. I stopped briefly at some big store near the Petrified Forest and stretched my legs and looked at rocks. Later, I could see the lights of Vegas reflected in the clouds from about 100 miles away. I noticed the light emanating from the top of the Luxor at about 50 miles away. The Hoover Dam was under construction or something, so that was really slow-going. I would have enjoyed the opportunity to slow down and enjoy the view, but it was almost 3am and I had been on the road for about 16 hours. Ugh. Here’s the view from the hotel window at the Excaliber.

Fly Hunt: College Station to Las Vegas (Part One)

This was a pretty long, but relatively uneventful leg that I made in two days.

Day One: I stopped in West for Kolaches. Then, I took hwy 6 across West Texas. I’ve traveled due west from the DFW area many times, but I’m not sure I ever took this route. Maybe I always feared it would be too slow and I just wanted to get out of the state already, but I’m glad I took it this time. The speed limit was usually 65 or 70, not too much small town slow down, and it was actually quite pretty. I kept forgetting that I was in West Texas. I passed through a lot of quaint little towns (frequently encouraging me to drink Dr. Pepper on a regular basis,) and beautiful, green, ever so slightly rolling hills and farm country. I stopped on the side of the road many times to kick the rotting prickly pear cactus, hoping that flies would come swarming out. (Not one.) This majestic Brahman bull/cow/whatever watched me and laughed (I know s/he was laughing!!) Anyway, beautiful creature, really. When you drive by, you have to do a double-take because it feel like you just drove past some very large, silver exotic animal.

I tried to make it to Roswell. I’ve been there before, but I thought it might be a different sort of experience to camp there. But, I got out of College Station a bit later than I’d planned, and once again, I’d taken the scenic route, so I didn’t really get close to Roswell before I had to stop. I stayed at a very cheap, but comfortable and clean motel. I think this photo of the towels in the bathroom sorta captures the spirit of the place. Obviously, they wash these towels frequently, and they care enough to fold them as best they can, however, they can’t afford to get new ones when they fall apart. Or, maybe it’s just not wort it. I paid $27 cash for the room, including a $5 key deposit that I got back the next morning. I slept on top of the bedding, wrapped in my own sheet. Those who know me well know that these are extreme measures for me.

I discovered that the flies that Spencer and I collected were all dead. I’m not sure if they didn’t wake up from the CO2 or if it got too hot (but, I was very careful about regulating the temperature – by now I’d learned my lesson!) I still tried to dissect some of them because I knew I had a mushroom feeder that was really different from the other mushroom feeders I’d found, but it was pointless. They all went into the ethanol, whole.

It was after 3am, and I was completely exhausted, but I decided to put the hookah together. I had a nice smoke and watched Blind Date or something – telling myself that I could sleep as long as I wanted in the morning and I’d just get to Vegas when I got to Vegas.

Fly Hunt: Mansfield to College Station

I hung out in Mansfield with my folks for a couple of days. While I was dissecting the flies that I’d caught in Fayetteville, I realized that the light on my scope was getting dim and I’d left the charger at the JGI. Fortunately, I was able to have someone (thanks, Jen!) overnight it to me. But, for a wile there, mom and I were joking that I’d have to do the dissections with her reading glasses (which I tried to do.) Actually, I realized that for some of the flies, I could do the dissections without any magnification at all. I’m such a pro now. (Plus these were a pretty large species, plus their guts are dark purple.)

Jen Lin, this picture’s for you!

A little culinary diversion here. While I was home, we went to Joe T Garcia’s, probably my favorite restaurant in the world. That’s right, move over Michael Mina, Joe T is in la casa. I’m having to stop myself from writing a full restaurant review, but let me just say that if you are in the Ft. Worth area AND you have at least 4 people in your party AND you have a couple of hours to kill, then go there. You will probably have to stand in line outside of the restaurant to get in, almost no matter what time you go, but the experience it is worth the wait. AND, while you’re waiting, walk up to the patio bar and order a pitcher of margaritas and some plastic cups to bring back out to the line with you.

With a happy belly and no hangover (watch out for those margs!) I left my parents’ house the next afternoon and headed south for College Station, stopping in West for some sausage and Kolaches! Yum. I stopped at the Village Bakery on my way there and at the Czech Stop on my way back, and let me tell you, there was no contest in my mind. The Village Bakery was definitely the winner. I’m still kicking myself for straying. I used to go to West every year to hear Brave Combo play at West Fest. I highly recommend this experience to anyone in the area (Holly, are you out there?)

So, I got to College Station and it was raining pretty hard. Spencer took me out to Lick Creek Park to put out some traps. It was wet and muddy. Spencer is a “true gentleman” as he would say of someone he admires, and I had a great time listening to him. I was most fascinated by this insect called Strepsiptera which are very strange and mysterious. The males and females look nothing alike, and you’re almost guaranteed to never see them together. That’s a male on the left and a female on the right, both adults. (Sorry, I can’t remember from where I swiped these images, and I can’t seem to find them again!) The females live their entire lives inside a host insect. They decrease the nutrient intake of the host and cause them to be sterile, but if I remember correctly, they actually extend the lifespan of the host! The female hangs out with the tips of her body projected through the exoskeleton of the host and waits for a male to come along and fertilize her. The males, after emerging from their host insects (literally, on the fly!) have about 5 hours to fly around and find a female to inseminate. Crazy! It’s also interesting how the Strepsipterans hijack their host’s own tissue to create a barrier so that they aren’t recognized as a foreign object. And, there’s more. If you’re as intrigued as I was, which you’re probably not, google them. There’s lots more great stuff. Or, I think that Carl Zimmer might talk about them in his book. I haven’t even read it yet and I have no problem calling it a must-read! It’s at the top of my “reading for nerdy pleasure” list.

So, the next morning, Spencer and I went to the traps. A couple of them were flooded, but a couple of them yielded a pretty good haul. And, we found some more mushroom-feeders. So exiting! I also saw a larva wiggling around in some sap flowing out of a tree. A slime flux, I think it’s called. Collecting with Spencer was so much fun! I’m pretty sure he would have stayed out there poking around in the forest with me all day, but I had to get on the road again, so we went back to the lab to sort flies. This was my best species identification learning experience. By now, I had a little more confidence, thanks to what I’d learned from others along the way, and Spencer had plenty of time to sit with me and help. He had the Patterson and Stone book handy, so we could look in the scope and then flip through it, back and forth. When we were finished sorting the flies, he showed me how he uses the flow cell sorter to estimate genome sizes in flies (and other things, I guess,) but I didn’t have time to stick around for the whole demo.

Oh, I almost forgot! We went to the George Bush Presidential Library and Museum. It was pretty cool. This sculpture has pieces of the Berlin Wall in in, and these horses are supposed to represent freedom or something. I’m no arteest, and while I remember the wall coming down, I think I’m too young (and socially ignorant) to really appreciate what the wall stood for. But the horses were beautiful, and it was cool to see chunks of the wall.

Fly Hunt: Fayetteville to Mansfield

I was prepared to fall in love again with Arkansas as I drove south along hwy 71. I drove from New Orleans to Fayetteville years ago, and found that I loved the Ozarks. Also, I found Fayetteville to be a lovely town full of hippies and jam bands.

This trip was something else. Here was my first hint that I ain’t in college-town nomore. Yep, squirrel puppies. Do you think they’re breeders? Did they forget to spay their squirrel bitch?

Then, I drove past a revival tent. And, it wasn’t like a “Come to the REVIVAL this Saturday night!!” You know, the kind that draws people from 6 counties like a State Fair, so the five year old can stare wide-eyed at her grandma getting tapped on the head and falling, convulsing to the ground, to the soundtrack of a ridiculously talented gospel choir, while at a nearby table Josie sells her wood-carved squirrel puppy nativity scene, next to the enthusiastic purveyor of fossils that somehow prove that the age of the Earth is less that 10,000 years old. No, not like that. It was more like a used car lot. “Come on down to the tent, folks, every Thursday, we got ‘yer best deals on salvation right here. Holy Ghost early bird special from 6-7pm, but you’ll want to stick around for the miraculous miracle hour beginning at 9pm. Our head to toe salvation package comes with a first through tenth commandment, six-day warranty.” Thank goodness it was not a Thursday, or I would have been SO tempted to stick around. As it was I was hungry, and I stopped at this little restaurant called “Grandpa’s catfish” or something like that. Maybe it was “Jack’s” Anyway, I figured that I needed to eat some local catfish, and grandpa’s recipe was probably great. It was a quaint little converted house. What I really loved about the experience was when I ordered the catfish dinner and the waitress (probably Jack’s great-granddaughter) asked me if I wanted “salad or service with that.” I said, what’s “service?” She said, “pinto beans, cole slaw, hush puppies, dressing (tartar sauce,) and green chiles.” Are you kidding me? Who wants SALAD??? Maybe I should have asked her what “salad” was. Anyway, the catfish was overcooked and flavorless and the cornmeal coating was kinda chewy. The service was awesome. There are very few restaurants to which I would return solely based on the service, but this is one for sure!

OK, so I was feeling like the Arkansans were sorta strange, very religious, and somewhat charming, but then I saw this. I had a very strong, very negative reaction to this sign. Click on it and look at it up close. I found it to be vile and disturbing and asinine and somehow insulting. I felt insulted for Jesus. It made me want to leave Arkansas immediately. I spent a lot of time wondering, who ARE these people? Who, after waking up from his Budweiser-induced hangover, still thought that his idea was good enough to make into a giant (10ftX10ft) roadside sign? Who approved it? Who was the artist? Maybe I just don’t get it. I wondered if it would have been funny if it were educated yet stoned Berkeley hippies making up cheesy slogans about the Buddha. I don’t know. I didn’t want to know. I just wanted to get to Texas, the land of the erudite Coors Light drinkers!