rebeccmeister: (cricket)
Yesterday was warm, so it seemed like there were more crickets out and about during our evening surveys.

I was going to run circadian crickets last night, but in the evening B came into the house with a worried look on his face. When we went out to the table on the porch, the deli cups that had held the crickets for the experiment had been knocked over, and a lid was missing. Out of the four crickets I'd set aside, the long-winged one was the only one that was totally gone.

Later in the evening, when I went out to put out crickets from the day's haul, I startled a rat, who raced off the table into a big, open grating at the edge of the porch.

We are now keeping the pint cups underneath a larger bin, with a rock on top, and I'm now being more careful to seal the lids closed.

Other wildlife: lots of very large wolf spiders (abdomen the size of a dollar coin), a handful of tiny mice (one of which was spotted eating a cricket), lots of toads and tree frogs, rattlesnakes, and an alligator lizard.

It looks like the Whittier wildfire is drawing to a close, to judge by the decrease in smoke and bright spots that we can see at night.
rebeccmeister: (cricket)
4 reasons why it's easier to run the circadian experiment here than in the lab at Berkeley:

1. Kitchen's right here, so I don't have to prepare 3-5 meals in advance and cart them in with me.
2. Bed's right here, so I can sleep in a real bed without an added commute.
3. We are collecting the crickets in the evening and then running the experiment the following day. While we hold them, we're giving them water, but no food. So I don't have to arrange to take away food several hours before the experiment. This means I won't have to get up early to take away food on any days where I run the noon timepoint.
4. Our schedules are consistently night-shifted, so sleep is much more consistent.

Main reason why it's harder: Very, very few long-winged crickets with pink flight muscle so far. But L pointed out that it's still worthwhile to run the oodles of short-winged crickets to get at least some sense as to metabolism in lab vs. field. And while we're getting some exercise, it's in smoke-filled air (Whittier fire), and it isn't rowing. Also, it's unsurprisingly hard to find any quiet space whatsoever to gather my thoughts.

Cool things observed during last night's circadian trial (9 pm timepoint): one female with a spermatophore, two short-winged females with underdeveloped ovaries, which means they're on the younger side, which is good. The 5x Granny Lamp works decently well for field dissections, which is great.

Yesterday during the day: hiked 11 miles, north up the main road to Gate 2 along Figueroa Mountain Road, then back down along Lisque Valley road, pausing to listen for daytime crickets every so often. Figueroa Mountain Road gave us better views of the Whittier Fire, which grew a lot bigger yesterday. It appears to be a favorite among local cyclists (argh should have brought my bike for multiple reasons). The others learned about how stupid it is to hike in the middle of the day in the summer in a climate like this (I knew but participated anyway because I'm stupid and was curious about the terrain). Lots of spots along Lisque Valley Road looked like decent cricket habitat, but we didn't hear anything. It appears that even the most desperate of males stop chirping during the middle of the day, from around 11 am to 3 pm, perhaps due to the heat. We confirmed this by listening near the fields where we've been doing our nighttime surveys towards the end of the day. Still, I feel like we learned a lot, and it also looks like our trip could add a lot of info to Open StreetMaps.

Speaking of which - at the last minute we got a GPS at REI, right as we were heading out of town. Based on [personal profile] scrottie's recommendation, we got a Garmin etrex 20x hiking GPS. (also, I've used his GPS before, so I had some familiarity with how to operate it). I am SO GLAD we got it. Totally worthwhile, and now I'm tempted to keep it instead of passing it over to the lab and getting a reimbursement for it.

Double nighttime surveys last night. Nighttime temperatures have been on the low side, compared to what I remember from last year. Yesterday I finally had the presence of mind to put an iButton outside near the crickets we're holding, so we'll have more information about daytime and nighttime temperatures in the shade, at least. We have been able to collect around 80 crickets within an hour, among 4 people. We saw much less activity during our second survey, from 11 pm - midnight, but part of that may have to do with the fact that we still had all the crickets from the earlier survey in captivity. We're having reasonably good luck with mark-recapture within our two survey plots so far - "classroom" and "garden." They're maybe 1/8 of a mile apart, and there isn't any evidence of movement across that scale yet. Collections are female-biased, because the females are running around, looking for males, while the males establish territories at the openings to burrows, to amplify their songs. When we get too close, they will abruptly stop chirping and dive into their holes.

As we add more people to the team, we'll keep adding to our survey areas, which will hopefully help with getting more crickets for my experiments, too. We're also keeping all of the last-instar crickets we collect, so we can wait until they emerge as adults and see what ratio of long-winged to short-winged crickets we get. That should tell us more about why we're getting an extreme short-winged bias again (same pattern as last year) - whether it's because the long-winged crickets are off flying somewhere where we aren't catching them, or whether there just aren't all that many long-winged crickets out there under the current conditions.

Other interesting wildlife: one rattlesnake (of course B pestered it more so he could get video of it rattling), a couple of big frogs, a tree frog, a mouse (eating a cricket!!), lots of large spiders (maybe tarantulas, but not all that hairy??), lots of black widows, lots of darkling beetles. We hear coyotes a lot at night.

Pitfall traps have been highly unsuccessful so far (1 male out of 5 traps). I think they're going to require a bunch of tweaking.

A lot of the long-winged males I've checked for flight muscle status also have a whole bunch of parasites glommed on to their armpits.

Today we'll take it easier than yesterday, probably with another trip into town for groceries and such.
rebeccmeister: (cricket)
My brain is complete mush today.

But I needed to squeeze in a Skype meeting this morning with my long-distance undergrad, who has been determinedly plugging away at learning the basics with R. We have two main tasks left with the current stage of data analysis, which we basically need to translate from English into syntax. The first is figuring out how to read in a bunch of files from a bunch of directories. This should be straightforward.

The second task is one I'd been scratching my head over. When recording cricket activity, I set up the timelapse video to record 4 crickets at a time. Our tracking software assigns individual numbers to individuals, but for various reasons individual crickets wind up having between 1 and 10 different numbers assigned to them. So, how to separate out data for each individual cricket? I'd been thinking of coming up with a method to subset the track files by the assigned ID numbers. This would require figuring out how to import a ragged data file, then figuring out a kind of complicated reference scheme.

But then today C pointed out that because the crickets are spatially separated from each other, it would probably be a whole lot simpler to just subset based on each cricket's xy coordinates. We don't expect cricket 1 to ever show up in the area occupied by cricket 2, unless something went seriously wrong with the setup (nothing did).

Foreheadslap to self. Good job, undergraduate! You rock.

This startup is a VERY good idea. I need to pay a visit.

Hookey

Jun. 30th, 2017 12:40 pm
rebeccmeister: (cricket)
We are back in California. Theoretically, I could have gone to work today. But I am still so angry about how much of my life got flushed down the toilet when those samples were destroyed. That was a lot of nights sleeping at the lab, empty evenings where I couldn't get more work done and couldn't go home. Mornings where I was too tired or out of it or jet-lagged to go rowing.

I feel like I had more time last year to help [personal profile] sytharin with the garden. It's hard to garden long-distance. It's hard to get exercise in the lab.

I have had to put other projects on the back burner while working on the circadian experiment because it is too hard to jump around and keep that many projects in the forefront of my mind.

So I stayed home today. Went rowing. Am getting caught up on the interwebs. And I'll probably run off on some errands in a bit. Work will still be there when I get back on Monday, and July is going to be hellishly busy.
rebeccmeister: (Acromyrmex)
I'm inclined to agree with the notion that you should celebrate a paper's submission. I got the message this morning that the Manuscript of Doom IV's estimated length is 10 pages, which is the longest length permitted for them to actually look at the thing and decide what to do next.

I mean, they may just bounce it back without review. But on the other hand, it's in. I also think it's the strongest work I've ever submitted to that particular silly journal, so I'm more optimistic about it than I have been about prior submissions. In all of the previous cases, my doubts were clearly vindicated by the reviewers' feedback, but I don't know what they'll wind up deciding to target this time around. With the leafcutter research, there's often a roulette element depending on which aspects of the system the reviewers are experts on (fungal physiology, plant-insect interactions, leafcutter coevolutionary biology, nutrition).

Then there's this other mountain of work in front of me that I should get back to. Lots of data analysis, but I'm also eager to make progress on the cricket lifespan/reproduction manuscript.

-

I was hoping I had enough crickets last week to finish out hemolymph assays in one go. I am so optimistic sometimes. Out of 28 long-winged crickets, only 10 had pink flight muscle, so my sample sizes are inadequate for two timepoints (11 am and 8 pm). Thankfully, I had enough pink-muscled crickets for the 11 pm timepoint, so I don't have to repeat that one.

As of last night I'm up to 4 LW-pink for 8 pm (yargh, wish I had more). Momentarily I'll find out for another 11 am set. I'm not especially optimistic, because I think long-winged females of this species (California) may indeed histolyze their flight muscle earlier in adulthood than the Florida species.

I have more crickets set up for tomorrow, if I need them, and for Monday as well. Back to the grind.
rebeccmeister: (Acromyrmex)
I suspect I'll always feel that moment of anxiety immediately after clicking the "submit" button when submitting a manuscript for publication.

I think the last time I tried submitting to this particular journal, the submission quickly bounced back because it was estimated to be too long for publication. We have tried to get this one sufficiently under length, but of course I have my doubts. And if it's a desk-reject it will also bounce back quickly.

Best to move on to other projects in the meantime.
rebeccmeister: (Default)
Yesterday, I encountered a series of headlines:

To life growth, Janey Yellen says make it easier for women to work.

Then, The meaning of life in a world without work. [Note: when I later tried to relocate this article, I discovered that it's a popular subject to speculate on; the speculations actually date back to an era when people also speculated on further shortening of the workday]

But then, you know, The gig economy celebrates working yourself to death.

Also, I really cannot imagine robots completely replacing human beings across all forms of work. Certain lines of industry are going to persist, and they aren't especially glamorous because they require, well, work. And then, how can the people engaged in that work - labor, really - be expected to support this mysterious class of people who don't work?

This is already going on, of course.

I still don't know what to do with Janey Yellen's assertions.

Also, here's an interesting blurb about the history of employer-provided health insurance, in case you hadn't seen it and were interested.
rebeccmeister: (Acromyrmex)
Last Friday, I sent my PhD advisor a finalized draft of the current Manuscript of Doom*, where we have one remaining issue to address before it's ready for submission: it's too long. This is not a horrible problem, but it does require time and thought. She is a whiz-genius at shortening, so I asked for help.

Communication about the timing of tasks like this can be tricky to orchestrate by long distance, though, so when I hadn't heard a peep from her by Tuesday, I did some additional work to prune the reference list and sent over the revised version as a nudge. She replied to say, "Oh, I'd started working on this already, but I'll fold my changes into your version." And I haven't heard anything since then, so once again I have no idea what kind of timecourse I'm looking at. I do know better than to poke the sleeping bear too many times in a row on short notice, though.

All right, fine, I can work on one of a half-dozen other projects in the meantime, right?

...except task-switching isn't always so simple. The next item on the list was data analysis for the circadian project, and then again, I hit a sticking point where I needed to meet with my postdoc supervisor and confer before moving forward.

In the meantime, I'm helping an undergrad knock out her honors thesis at record speed, helping a grad student turn around a grant report, and gearing up for more circadian-type fun times next week. Oh, and working on a couple more manuscript reviews.

The challenge, for me, is that all these things leave me with weird, awkward time gaps. I want to do productive things with the time gaps, but sometimes I fail because they aren't long enough for me to pick up other projects, remember where I left off, and make headway.

Oh well. At least I'm not bored or underemployed?


* Manuscript of Doom = whatever current project feels like it's taking FOREVER to complete. This one's from my last dissertation chapter in 2011, for instance. I think it had a more clever name, like Manuscript of Doom IV: The Thunderdome, but I don't remember anymore.
rebeccmeister: (cricket)
I'm trying to work on a bunch of concentration-heavy computer tasks these days, blasting through a couple of manuscript reviews, working on manuscript-writing, and analyzing the data from the circadian experiment.

The lab is NOT the ideal place for these projects, but on Mondays, Tuesdays, and Thursdays, I have undergrads working on various things, so I can't leave. They're pretty independent, but have occasional questions.

White noise is inadequate.

I get one of these, if I could:
http://www.pierreemmanuelvandeputte.com/work/2012/corkhelmet.php

Instead, for now, I'm ruining my hearing with this.
https://youtu.be/qUZfGc_Y6LY
rebeccmeister: (cricket)
[As posted to other social media]:

As you undoubtedly know by now, one of my favorite George Pocock quotations is: "No one will ask you how long it took to build; they will only ask who built it."

Nonetheless, at the end of a long day of data quality-control and analysis I find it satisfying to tally up some numbers.

So far, this circadian experiment has involved gearing up to run time points 45 times, across a 5-month period. I've poked and dissected 393 crickets, and we'll wind up using data from 211 of them. In some respects this is a far cry from the 6 different radiotracer experiments from 2015 (averaged ~250 crickets/experiment), but of course there are some major qualitative differences between experiment types. Overall I would say the radiotracer experiments were less grueling.

And regardless, that's a lot of crickets to have poked. Thank you, crickets.

-

Also, I suspect I'm not quite finished with it all. I'll take my current analyses and will run with them for now because I'm giving a conference presentation in one and a half weeks, but I am thinking that I'll have more confidence in these results if I boost all my sample sizes to closer to 9 crickets per morph per tracer per timepoint (so 9 crickets x 2 morphs x 3 tracers x 5 timepoints = 270 total). The good news is that if I decide to proceed, I at least have my cricket-rearing protocol in good shape, so completion should be straightforward. In addition, I'm feeling fairly confident about my method for characterizing lipid oxidation.

It has been quite a ride.
rebeccmeister: (cricket)
Here is a grid of sample sizes for the circadian experiment:

Sample sizes.jpg

We haven't been able to decide which is worse, the 1 am timepoint or the 9 am timepoint. I'm leaning towards the 9 am timepoint. You'd think 9 am doesn't sound all that bad, right? But we have to make sure the crickets are in a postingestive state, so someone has to take away their food 4 hours before the timepoint. And the 9 am timepoint actually starts at 8 am, so that means getting to campus by 4 am.

Even morning people have limits, and my limit is having to wake up before 4 am.

Also, when the timepoint starts at 8 am, that means we have to prepare certain things right before the experiment itself starts, so the work actually begins closer to 7 am.

To top things off, the person who has been helping on this project, through thick and thin, lost track of things and slept in this morning. As a result, I learned that I *can* run the whole experiment by myself. That said, I really, really, really hope I never, ever have to do that again.

Those glucose samples are crossed out because of a snafu with our respirometry setup. I have to manually set the range for our high-precision carbon dioxide detector, but early on I set the range too low and so our measurements of the amount of carbon dioxide exhaled are underestimates. We might be able to get that info from our collaborator who measures the C-13 sample enrichment, but I'm not certain of that yet.

Also, my Halloween costume is made of polyester, and polyester smells awful, especially when one is sweating from all the extra anxiety and running around.
rebeccmeister: (cricket)
We're back on deck with the circadian experiment.

One of the most challenging aspects, for me, is when I have these long evenings that I can't really put to effective use. I tried to work on some statistical analyses last night, but I really needed to look stuff up in Zar, which was at home. So I just ate too many biscotti instead.

I have this other massive stats book at work called Applied Linear Statistical Models (which I will call NKNW after its authors), but it's ever-so-slightly more mathematical and less pragmatic than Biostatistical Analysis (aka Zar). So when I need to look up something like how to calculate statistical power, NKNW doesn't actually help.

Nor does the internet, because as we all know the internet isn't a vetted source, and you'll find about 12 different sources with 12 different styles of calculations. In addition, for a lot of stats stuff it's helpful to learn a consistent set of variables and calculations because there's a hell of a lot of sloppy work out there and it's easy to get stuck in a swamp of incomprehension because someone defines things in a slightly different fashion. And that's how "Data Science" got invented.

Today, however, I have Zar again, so maybe I can fwump myself over this hurdle and on to the next thing (job applications again).
rebeccmeister: (Acromyrmex)
Step 1: Find ads. Note deadlines. Organize spreadsheet and decide whether or not to apply.

Step 2: Work on individual applications. For each application, look up info about the department so as to re-tailor materials to specifics of job ad description and department interests.

Step 3: Start individual online application process for individual application. Discover, partway through, that some totally random piece of information is needed. Hunt down the random information.

Step 4: Submit application. Send copies of materials in highly-organized format to reference letter writers, thanking them profusely yet again for writing reference letters for you.

Step 5: Wait several months without hearing anything.

The academic job hiring cycle is annual: ads come out in the summer and early fall up through around January for positions that generally start the following fall. Good luck getting other employment options to line up with that timeline!

-

Meanwhile, in the garden. [livejournal.com profile] sytharin has been out of town on vacation, so it has been up to [livejournal.com profile] scrottie and me to harvest and cook as much as we can. Here was last week's harvest:

Weekly garden harvest

That's a plant pot full of the Black Prince tomatoes. A-plus, would grow again. That bucket got turned mostly into ketchup.

The cucumbers are more challenging to use up. I finally took some time yesterday to turn a bunch of the pickling cucumbers into refrigerator pickles:

Cucumber problem (halfway) solved

Today I picked a two-thirds plant pot of tomatoes and used them plus that giant cucumber (size of my foot!) to make another batch of cucumber pico de gallo. So, only three medium-large slicing cucumbers left to deal with for now.

Tomato production is starting to wind down, for the Black Princes, at least. There are a couple other varieties in the backyard that look like they're just starting to pick up, but the plants aren't as crazily overgrown as the Black Prince plants, so the net haul won't be as large. Oh - [livejournal.com profile] scrottie picked about a gallon of cherry tomatoes, too. I think we're doing all right with tomatoes for the year.
rebeccmeister: (Acromyrmex)
Fun and rewarding stuff:

I'm attending two conferences in Florida at the end of the month. The main one is the International Congress of Entomology, held every four years. The previous Congress was held in South Korea, and I was lucky to get to attend it thanks to the grant that funded my work in Texas and Nebraska.

Orlando is a slightly less exciting destination. On the flipside, I'll give a talk about some of the cricket work from Nebraska, on amino acid metabolism in the context of nutrition and the cricket life history trade-off between flight and reproduction. Yesterday I finally had a few minutes to revisit the book Protein Turnover, which is mammal-focused but has a great chapter covering amino acid metabolism. I'm looking forward to making progress on the Nebraska work.

The second conference is a day-long satellite meeting of the North American Section of the International Union for the Study of Social Insects (IUSSI-NAS).

Things could get weird at the IUSSI-NAS meeting. There's a researcher from another group who did some fairly slapdash but high-profile studies on nutrition in a primitive fungus-growing species, who will be giving a talk about his findings. Another grad student from my PhD lab and I (=academic siblings) are both going to present on our work with desert leafcutter ants, in which we've come to a different set of conclusions via different means. We're going to keep the emphasis on high-quality science and insights that can apply to systems beyond fungus-growing ants. I also hope to have the associated manuscript finally off my desk by around the time the meeting rolls around. It still needs a couple more days of hiding in the library and intense concentration.

Other than that, there's not a whole lot going on (as [livejournal.com profile] scrottie would say, I'm being boring). Rowing has been helpful for taking my mind off of academic concerns, but the academic matters are pressing and are still keeping me busy at the moment. I always hold on to some optimism that things will settle down in a month or so, but I don't know how realistic that optimism is. I may just need to be even more proactive about managing my time and priorities to ensure I leave time and space for life outside of academic work.

Next week

Sep. 9th, 2016 07:16 pm
rebeccmeister: (cricket)
Next week, I am TAKING A BREAK from running the circadian experiment.

OY.

Instead: Job applications, leafcutter manuscript, poster for conference, talk for conference, project planning and update meetings.

Maybe sleep, too.

More rowing.
rebeccmeister: (cricket)
1. K overheard me saying: "Stop jumping on my hand! You have no head" (said to a freshly decapitated cricket)

2. Last night a feisty cricket managed to jump straight out of its box at my face and onto my glasses. If you've ever worked with crickets, you're already acquainted with the Scrambling-After-the-Escaped-Cricket Dance. But the glasses took things to a whole new level. However, I still won.
rebeccmeister: (cricket)
I totally didn't make it to the boathouse this morning. I'm pretty sure that I needed those extra 2.5 hours of sleep on C's office floor instead. Especially given how physically painful it felt to get up again at 7 am (more painful than the 3:30 wake-up to ride over to the lab).

Our current stable isotope tracer for characterizing lipid metabolism is not ideal. Apparently L started out trying palmitic acid in the beginning. That's the same lipid tracer as I used in Nebraska, though I used a radiotracer, not a stable isotope tracer. He was never able to obtain a reproducible signal with palmitic acid, so eventually they triangulated on oleic acid instead, injecting a bolus of pure oleic acid with a single C-13 label on the carbon that's easiest to label. A quick check of my notes about my palmitic acid experiences confirm why L never got any signal - only around 1% of the injected radiolabeled palmitate ever got oxidized over a 3-hour time period.

There are a couple of problems with the 1-13C oleic acid. The biggest one is that the amount of oleic acid we're injecting is equivalent to the total amount of lipid present in the entire cricket hemolymph pool. Hardly a tracer, unless there's incredibly high hemolymph lipid turnover. Along with that, as I'm doing the injections, I've observed a couple of crickets that have apparently bled heavily sometime during the 60-minute incubation period, and I'm not entirely sure about what's going on there. I haven't seen nearly as much bleeding during the injections themselves as compared to the glucose injections, but it still seems like there's something strange going on.

Uniformly-labeled C-13 oleic acid should generate a stronger signal, but it's also expensive. I would also need to think about the best injection vehicle for to dilute out this nonpolar compound.

We shall see what the preliminary samples reveal. They have just reached our collaborator today.
rebeccmeister: (bikegirl)
Please hold off until at least Thursday or maybe Friday or the weekend. I am too busy and overwhelmed to deal with you until then.

Thanks,
rebeccmeister
rebeccmeister: (cricket)
Intellectually, I have come a long ways in the past year and a half. It's a relief to be able to look back and see that as I revise my research statement. I'm incredibly grateful to both TZ and CMW for their roles in getting me to this point.

On the other hand, I need to get two manuscripts submitted this fall: the leafcutter one, and the next cricket one. I also need to get 1-2 more cricket manuscripts ready to go shortly thereafter.

Oh, there are also the ongoing feeding and oxidation experiments.

Almost every day, though, I'm aware of how fortunate I am to be able to do this kind of good work.

Status

Jul. 25th, 2016 05:16 pm
rebeccmeister: (bikegirl)
Sleep deprivation is catching up with me, hard.

Friday night/Saturday morning: Up until 3 am to complete our last glucose circadian trial (samples will be shipped off this week for gas analysis). Then up again at 9 am to finish packing and get into the lab, pack more, and head out to Sedgwick.

We reached the field station just before 6 pm on Saturday. Traffic wasn't horrible but we hit a couple of slowdowns somewhere south of San Jose (Gilroy), so we followed the Goog's suggestion to hop off Highway 101 and onto Highway 25, past Pinnacles National Park, which made for some nice sight-seeing en route.

There was an organic grocery store on the highway about a five minutes' drive from the reserve, so we picked up supplies for a simple supper. By the time that wrapped up, it was starting to get dark. As we walked from the dining area towards our tents, I encountered the first female crickets. It was time to start cricket-hunting.

I believe we were up until somewhere around midnight that first night. Apparently, the crickets were much more abundant this year than last, seeing as we were able to collect close to 100 crickets in only two hours between the six of us (five adults, one five-year-old). So we were able to quickly accomplish our first aim of collecting enough crickets to replenish the lab stocks. With that task out of the way, we were then able to focus on a second goal of assaying cricket hemolymph and body composition for crickets in the field.

I managed to sleep in until around 7:45 am on Sunday. We spent the morning regrouping and generating plans for Sunday night, then drove out to Pismo Beach to dip our toes in the ocean in the afternoon.

For night #2, we conducted two activity surveys, one between 9-10 pm, another between 4-5 am. So I slept from around 11 until 4, then from 5-6. At least we learned that we'll never have to get up at 4 am again because the crickets were no longer active at that hour.

At 6, we got up, packed and cleaned up, and hit the road by 7:30 so we could get back to campus by 12:30 and one of the undergrads could make it to her course.

Now I am unpacking and repacking to head to the Midwest tomorrow morning for vacation, so to speak.

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